A De Novo Nucleoside Synthesis and Late-Stage

Heterobenzylic Fluorination Strategy

by

Michael Weiwei Meanwell

M.Sc., University of Victoria, 2015

B.Sc. (Hons.), University of British Columbia, 2014

Thesis Submitted in Partial Fulfillment of the

Requirements for the Degree of

Doctor of Philosophy

in the

Department of Chemistry

Faculty of Science

© Michael W. Meanwell 2020

SIMON FRASER UNIVERSITY

Summer 2020

Copyright in this work rests with the author. Please ensure that any reproduction or re-use is done in accordance with the relevant national copyright legislation.

ii

Approval

Name: Michael Weiwei Meanwell

Degree: Doctor of Philosophy

Title: A De Novo Nucleoside Synthesis and Late-Stage Heterobenzylic Fluorination Strategy

Examining Committee: Chair: Krzysztof Starosta Associate Professor

Robert Britton Senior Supervisor Professor

Roger Linington Supervisor Associate Professor

Robert Young Supervisor Professor

Peter Wilson Internal Examiner Associate Professor

Christopher Vanderwal External Examiner Professor Department of Chemistry University of California, Irvine

Date Defended/Approved: July 30, 2020

iii

Abstract

Nucleoside analogues constitute almost half of today’s major anticancer and antiviral

therapeutics. Despite this, synthetic routes to these valuable molecules have typically

relied on carbohydrate starting materials, which can significantly impair efforts in medicinal

chemistry. Moreover, nucleoside scaffolds with increased complexity (e.g., C2’ or C4’

substitution) often require lengthy syntheses (up to 18 steps). Toward a goal of

streamlining nucleoside synthesis, we have developed a one-pot proline-catalyzed α-

fluorination/aldol reaction that generates enantiomerically enriched fluorohydrins that can

serve as versatile building blocks for the construction of nucleoside analogues. Most

importantly, this process enables access to variously functionalized nucleoside analogues

in only 3 steps from commercial starting materials. The development of this process and

practical application in rapidly accessing C2’- and C4’- modified nucleoside analogues,

locked nucleic acids (LNAs), and iminonucleosides should inspire future efforts in drug

design. Similar challenges also obstruct the synthesis of carbohydrate analogues (CAs),

another important class of molecules to drug discovery efforts. To streamline CA

synthesis, we developed several new proline-catalyzed α-functionalization/aldol reactions

for constructing stereochemically rich and densely functionalized aldol adducts. In only 2

steps, these aldol adducts were then readily converted into a structurally diverse collection

of CAs including iminosugars, annulated furanoses, bicyclic nucleosides, and fluorinated

carbacycles.

Incorporation of a fluorine atom can have several profound effects on a drug’s

physiochemical properties – including metabolic stability, membrane permeability, and

potency. However, the introduction of fluorine into the heterobenzylic position of drug

molecules has remained an unsolved synthetic challenge. Towards this goal, we describe

the first unified platform for the late-stage mono- and difluorination and

trifluoromethylthiolation at heterobenzylic positions. This technology should become a

dynamic tool for drug-lead diversification.

Keywords: proline catalysis, nucleoside analogues, carbohydrate analogues, diversity-

oriented synthesis, late-stage fluorination

iv

Dedication

To my mom for everything that she does for her family

v

Acknowledgements

I am immensely grateful to my supervisor Prof. Rob Britton for the amazing opportunities

and valuable lessons he has given me. I am thankful for his endless patience and positivity

that is constant even in the most challenging of times. His passion and enthusiasm for

chemistry is truly an inspiration and is something I try to emulate everyday.

I am thankful to committee members Prof. Roger Linington and Prof. Robert Young for

their helpful suggestions and kind encouragement over the course of my studies. I want

to thank Prof. Peter Wilson for serving as my internal examiner but also for always showing

a keen interest in my research progress. I am thankful to Prof. Christopher Vanderwal for

taking the time out of his busy schedule to serve as my external examiner.

Some key aspects of this work would not have been possible without the support and help

of Dr. Steven M. Silverman at Merck Process. Thank you for all your efforts and

contributions.

I am thankful to Dr. Rainer E. Martin at Hoffman-La Roche for his support and efforts on

numerous projects.

Thank you to all members of the Britton group both past and present for insightful

discussions and for helping create such a wonderful place to work. To those that I had an

opportunity to collaborate with, it was truly a pleasure to have worked with you. I am

especially grateful to Dr. Matthew Nodwell for mentoring me and helping me through some

of the lows in life. A special thanks goes out to Dr. Milan Bergeron-Brlek, who mentored

me as an undergraduate student, for showing me the ropes in the lab.

I would not be here without the constant love and support of my friends and family. I am

very thankful to my Uncle Nicholas Meanwell for all the advice and help he has given me.

I want to thank my brother, Jason Wang, for believing in me even when I didn’t – you will

always be my best friend, teammate, and opponent. I am grateful to my partner, Nastaran

Yousefi, for her everlasting love and understanding, and for helping me see that there is

more to life than chemistry. I am thankful to my loving parents, Neil Meanwell and Sherrie

Wang, for giving me every opportunity in life to succeed and teaching me there is no

replacement for a strong work ethic.

vi

Table of Contents

Approval .......................................................................................................................... ii

Abstract .......................................................................................................................... iii

Dedication ...................................................................................................................... iv

Acknowledgements ......................................................................................................... v

Table of Contents ........................................................................................................... vi

List of Tables ................................................................................................................. viii

List of Figures................................................................................................................. ix

List of Schemes .............................................................................................................. xi

List of Acronyms ............................................................................................................ xiii

Chapter 1. Introduction .............................................................................................. 1

1.1. Fluorine in medicinal chemistry .............................................................................. 1

1.1.1. Conformational influence ............................................................................... 2

1.1.2. Metabolic stability .......................................................................................... 4

1.1.3. Potency ......................................................................................................... 5

1.1.4. Membrane permeability ................................................................................. 6

1.2. Fluorine as a synthetic handle ............................................................................... 7

1.2.1. Defluorination of C(sp3-F) bonds .................................................................... 7

1.2.2. C(sp2)-F nucleophilic substitution ................................................................. 10

1.2.3. Hydrodefluorination ..................................................................................... 12

1.3. Thesis overview ................................................................................................... 13

Chapter 2. Development of an α-fluorination/aldol reaction and an annulative fluoride displacement for de novo nucleoside analogue synthesis .............. 16

2.1. Nucleoside analogues in drug discovery .............................................................. 17

2.2. Current challenges in NA synthesis ..................................................................... 18

2.3. Proposal for de novo NA synthesis ...................................................................... 20

2.4. Development of an α-fluorination/aldol reaction and an annulative fluoride displacement ................................................................................................................. 21

2.5. Synthesis of C2’-modified nucleoside analogues ................................................. 25

2.6. Experimental ....................................................................................................... 26

General considerations .............................................................................................. 26

Chapter 3. A short de novo synthesis of C4’ nucleosides and locked nucleoside analogues ........................................................................................................... 81

3.1. C4’-modified NAs in drug discovery ..................................................................... 81

3.1.1. Synthetic challenges .................................................................................... 82

3.2. Rapid synthesis of C4’-modified NAs ................................................................... 84

3.2.1. Locked nucleic acids.................................................................................... 87

3.3. Experimental ....................................................................................................... 89

General considerations .............................................................................................. 89

vii

Chapter 4. A platform for diversity-oriented synthesis of carbohydrate analogues 108

4.1. Introduction to carbohydrate analogues ............................................................. 108

4.2. Development of α-functionalization/aldol reactions ............................................ 112

4.3. Rapid synthesis of CAs...................................................................................... 118

4.4. Experimental ..................................................................................................... 121

General Procedures ................................................................................................. 122

Chapter 5. A convenient late-stage flourination of pyridylic C-H bonds ............ 162

5.1. Synthesis of heterobenzylic fluorides ................................................................. 162

5.1.1. Deoxyfluorination ....................................................................................... 163

5.1.2. Halide-exchange reaction .......................................................................... 165

5.1.3. Electrophilic fluorination of heterobenzylic anions ...................................... 166

5.1.4. Late-stage C-H bond fluorination ............................................................... 167

5.1.5. Monofluoromethylation of C(sp2)-H bonds ................................................. 170

5.2. Late-stage fluorination of pyridylic C-H bonds .................................................... 170

5.3. Conclusion......................................................................................................... 177

5.4. Experimental ..................................................................................................... 177

General considerations ............................................................................................ 177

Chapter 6. Direct heterobenzylic monofluorination, difluorination and trifluoromethylthiolation with dibenzenesulfonamide derivatives ............... 188

6.1. Direct functionalization of heterobenzylic C-H bonds ......................................... 188

6.1.1. 18F-fluorination ........................................................................................... 195

6.2. Conclusion......................................................................................................... 195

6.3. Experimental ..................................................................................................... 196

General Considerations ........................................................................................... 196

Chapter 7. Future Work .......................................................................................... 218

7.1. Synthesis of NA and CA Screening-Libraries ..................................................... 218

7.2. Incorporating NAs into Antisense Oligonucleotides ............................................ 219

References ................................................................................................................. 220

Appendix A. Liquid-Chromatography Chromatograms .................................... 242

viii

List of Tables

Table 1.1. Fluorine’s effect on potency and selectivity ..................................................... 5

Table 1.2. Caco-2-permeability of Xa factor inhibitors ..................................................... 6

Table 4.1. α-functionalization/aldol reactions between pentanal and dioxanone (75) ... 113

Table 4.2. Optimization of α-chlorination/aldol with isovaleraldehyde (204) and thiopyranone 206.aketone and aldehyde added at the same time. ........ 114

Table 5.1 Fluorination of 4-alkylpyridines using NFSI. ................................................. 171

Table 6.1 Mono- and difluorination of 4-ethylpyridine (354) and alkyl quinolines 355 and 356 ....................................................................................................... 189

ix

List of Figures

Figure 1.1. Examples of fluorine-containing molecules in medicinal chemistry. ............... 1

Figure 1.2. The effect of fluorine’s on conformation ......................................................... 2

Figure 1.3. Structural conformations of 17 and 18 ........................................................... 3

Figure 1.4. Stragetic use of fluroine to block unproductive metabolsim ........................... 4

Figure 1.5. A) Metabolic precursors of fluoroacetic acid (21). B) Mediating the metabolic profile of KSP inhibitors ............................................................................ 5

Figure 2.1 Nucleoside analogues in drug discovery ...................................................... 17

Figure 2.2. Current challenges in nucleoside synthesis ................................................. 18

Figure 2.3. A ribose-last approach to NAs inspired by the prebiotic synthesis of deoxyribonucleosides. B. proline-catalyzed α-chlorination/aldol ............. 20

Figure 2.4. Optimization of αFAR and AFD ................................................................... 21

Figure 2.5. Mechanism of cyclization of 107a and 107b ................................................ 22

Figure 2.6. Scope of nucleoside and NA synthesis. ....................................................... 24

Figure 2.7. C3’/C5’ protected nucleosides (R = C(CH3)2) and β-L-nucleosides. ............. 25

Figure 2.8. C2’-modified nucleoside analogues (R = C(CH3)2) ....................................... 26

Figure 3.1. C4’ analogues in medicinal chemistry .......................................................... 81

Figure 3.2. Synthesis of C4’-modified analogues (R = C(CH3)2) .................................... 86

Figure 3.3. Common locked nucleic acid analogues ...................................................... 87

Figure 3.4. Short syntheses of LNAs ............................................................................. 88

Figure 4.1 Carbohydrate analogues in drug discovery ................................................. 108

Figure 4.2. Development of α-functionalization/aldol reactions for drug discovery ....... 111

Figure 4.3. Ketone scope of α-chlorination/aldol reaction ............................................ 115

Figure 4.4. Scope of α-functionalization/aldol reactions. .............................................. 117

Figure 4.5. Scope of α-functionalization/aldol reactions ............................................... 118

Figure 4.6. Platform for rapid diversity-oriented synthesis (253 = 5-(methanesulfonyl)-1-phenyl-1H-tetrazole) ............................................................................. 118

Figure 4.7. Rapid synthesis of CAs.aα:β = 2.5:2.bα:β = 3:1. ......................................... 120

Figure 4.8. Conversion of fluorohydrins 221, 226, and 230 into biologically relevant molecules ............................................................................................. 121

Figure 5.1. Primary sites of metabolism in omeprazole (277) and pioglitazone (279) and the effects of heterocycles and fluorine on physicochemical properties in omarigliptin (278) and gefitinib (280). ................................................... 163

Figure 5.2 Common deoxyfluorination reagents .......................................................... 164

Figure 5.3. Common electrophilic fluorinating N-F reagents ........................................ 166

Figure 5.4 Selective pyridylic fluorination of C-H Bonds .............................................. 174

Figure 6.1. Heterobenzylic fluorides in discovery ......................................................... 188

Figure 6.2. Mono- and difluorination of pyridines, quinolines, pyrimidines, isoquinolines, quinazolines, and purines. .................................................................... 191

x

Figure 6.3. Trifluoromethylthiolation and chlorination of purines and quinazolines ....... 193

Figure 7.1. C2’/C4’-modified NAs for incorporation into oligonucleotides ..................... 219

xi

List of Schemes

Scheme 1.1. Deflourative functionalization. A) Glycosylation of glycosyl fluorides. B) Friedel-Crafts reaction of aliphatic tertiary fluorides .................................. 7

Scheme 1.2. Stereospecific fluoride displacement .......................................................... 9

Scheme 1.3. A) Nucleophilic aromatic substitution for macrocyclization. B. Process scale intramolecular nucleophilic heteroaromatic substitution .......................... 10

Scheme 1.4. Reactivity pathways of gem-difluoroalkenes ............................................. 11

Scheme 1.5. Hydrodefluorination strategies .................................................................. 12

Scheme 1.6. The development of an α-fluorination/aldol reaction (αFAR) and an annulative fluoride displacement (AFD) for nucleoside analogue synthesis ............................................................................................................... 13

Scheme 1.7. Development of new α-functionalization/aldol reactions for carbohydrate analogue synthesis ................................................................................ 14

Scheme 1.8. The direct monofluorination, difluorination, and trifluoromethylthiolation of heterobenzylic C-H bonds ...................................................................... 14

Scheme 2.1. MacMillan’s de novo synthesis of C2’-modified NAs ................................. 19

Scheme 2.2. A 3-step synthesis of NAs......................................................................... 20

Scheme 2.3. Application to the synthesis of MK-3682 penultimate (130) (R = C(CH3)2).26

Scheme 3.1. Common building blocks for the construction of C4’-modified NAs ........... 82

Scheme 3.2. Merck’s syntheses of MK-8591 ................................................................. 83

Scheme 3.3. Synthesis of C4’-allyl C2’-deoxy NA (R = C(CH3)2) ................................... 87

Scheme 4.1. Diversity-oriented synthesis approaches to CAs ..................................... 109

Scheme 4.2. One-pot synthesis of chlorohydrins and DKR of α-chloroaldehydes through proline-catalyzed aldol reactions .......................................................... 112

Scheme 5.1. Deoxyfluorination of quinine led to inversion (282), retention (283), and rearrangement (284) products .............................................................. 164

Scheme 5.2. Late-stage enzymatic oxidation enabled deoxyfluorination ..................... 165

Scheme 5.3 Halide-exchange reaction with silver fluoride ........................................... 165

Scheme 5.4 Halide-exchange reaction for the synthesis of 18F radiotracer (290) ......... 166

Scheme 5.5. Heterobenzylic fluorination of camptothecin ........................................... 167

Scheme 5.6. Manganese-catalyzed C-H fluorination for the generation of 18F radiotracers .......................................................................................... 168

Scheme 5.7. Transition metal-free radical C-H fluorination .......................................... 168

Scheme 5.8. Palladium-catalyzed diastereoselective C-H fluorination ......................... 169

Scheme 5.9 Sanford’s palladium-catalyzed C-H fluorination methods ......................... 169

Scheme 5.10. Fluorination with Selectfluor .................................................................. 170

Scheme 5.11. Fluorination of 4-(cyclopropylmethyl)pyridine (311) and a mechanistic proposal for the formation of 308 and decomposition products of NFSI 172

Scheme 5.12 Direct fluorination of the potent aldosterone synthase inhibitors 333 and 335 ....................................................................................................... 175

xii

Scheme 5.13 Site-selective late-stage fluorination of pyridylic, benzylic, or aliphatic C-H bonds, contrasted with classical α-fluorination ...................................... 176

Scheme 6.1 Late-stage mono- and difluorination, trifluoromethylthiolation of heterocycles ............................................................................................................. 194

Scheme 6.2. 18F-fluorination of heterocycle 407 .......................................................... 195

Scheme 7.1. Synthesis of C2’/C4’-modified NA and ProTide libraries ......................... 218

xiii

List of Acronyms

[α]D specific rotation at the sodium D line (589 nm)

oC Degrees Celsius

Ac acetyl

AcOH acetic acid

AFD annulative fluoride displacement

AIBN azobisisobutyronitrile

BAIB (Diacetoxyiodo)benzene

Bn benzyl

BuLi butyllithium

tBuOK potassium tert-butoxide

CAs carbohydrate analogues

CSA camphor-10-sulfonic acid

D dextrorotatory

DCE 1,2-dichloroethane

DIPEA N,N-diisopropylethylamine

DMF N,N-dimethylforamide

DMSO dimethylsulfoxide

4-DPN-IPN 2,4,5,6-tetrakis(diphenylamino)isophthalonitrile

D-pro D-pro

dr diastereomic ratio

E+ electrophile

EC50 half maximal effective concentration

ee enantiomeric excess

e.g. Exempli grata

Equiv. equivalents

Et ethyl

Et2O diethyl ether

EtOAc ethyl acetate

αFAR α-fluorination-aldol reaction

FDA Food and Drug Administration

18F-DOPA [18F]fluorodeoxyphenylalanine

[18F]FDG 2-deoxy-[18F]fluoroglucose

GABA Gamma Aminobutyric Acid

HAT hydrogen atom transfer

HBTU Hexafluorophosphate Benzotriazole Tetramethyl Uronium

xiv

Het heterocycle

HFIP 1,1,1,3,3,3-Hexafluoro-2-propanol

HMBC heteronuclear multiple bond correlation

HPLC high-performance liquid chromatography

HSQC heteronuclear single quantum coherence

4-HTP 4-hydroxythiophenol

Hz Hertz

i isopropyl

IC50 half maximal inhibitory concentration

i.e. Id est

K2CO3 potassium carbonate

KHMDS potassium bis(trimethylsilyl)amide

KSP kinesin spindle protein

L levorotary

LDA lithium diisopropyl amine

LEDS light-emitting diode

LG leaving group

LNAs locked nucleic acids

L-pro L-proline

M molar

MDG multidrug resistance protein 1 (MDR) ratio

Me methyl

MeCN acetonitrile

MeNO2 nitromethane

MeOH methanol

mmol millimole

mol mole

NaDT sodium decatungstate

NAs nucleoside analogues

n normal (alkyl chain prefix)

NBS N-bromosuccinimide

NCS N-chlorosuccinimide

NFSI N-fluorobenzenesulfonimide

NMP N-methyl-2-pyrrolidine

NMR nuclear magnetic resonance

nOe nuclear Overhauser effect

Nu nucleophile

xv

Pe membrane permeability

PET Positron Emission Tomography

P-gp P-glycoprotein

pKa −logKa

pH −log[H+]

Ph phenyl

PhthNSCF3 N-trifluoromethylthiophthalimide

PMP 1,2,2,6,6-pentamethylpiperidine

PNB p-nitrobenzoate

ppm parts-per-million

PRMT5 Protein arginine methyltransferase 5

rt room temperature

SET single electron transfer

SNAr nucleophilic aromatic substitution

t tertiary

TBS tert-butyldimethylsilyl

TCDI 1,1’-thiocarbonyldiimidazole

TEMPO (2,2,6,6-tetramethylpiperidine-1-yl)oxidanyl

TFA trifluoroacetic acid

THF tetrahydrofuran

TIPS triisopropylsilyl

TMP 2,2,6,6-tetramethylpiperidine

TS transition structure

δ chemical shift (in ppm) from tetramethylsilane

1

Chapter 1. Introduction

1.1. Fluorine in medicinal chemistry

The strategic use of fluorine and fluorine-containing motifs has profoundly impacted drug

design and development.1,2 Remarkably, since the first fluorinated drug (fludrocortisone (1),

Figure 1.1) was released to the market in 1955, over 270 fluorine-containing drugs have been

approved by the U.S. Food and Drug Administration (FDA) and now constitute roughly a third of

all major pharmaceuticals.3 Continued efforts in this vibrant area of chemical research have led

to a greater understanding of the effects of fluorine incorporation and its application in drug design.

Fluorine is often introduced into a drug candidate to enhance its pharmacokinetic and

pharmacodynamic properties such as potency, membrane permeability, lipophilicity,

bioavailability, and metabolic stability. 3–6 However, the influence of fluorination on these

properties can be difficult to predict. In recent years, innovations in chemical synthesis7,8 have

enabled access to novel fluorinated motifs,5,9 thus providing new opportunities to probe the effect

of fluorination on drug properties. Due to its low positron emission energy (0.64 MeV) and

favourable half-life (t1/2 = 109.8 min), novel 18F radiotracers in PET (positron emission

tomography) imaging as disease diagnostics are also highly valuable.10–13 Most notably, 2-deoxy-

[18F]fluoroglucose ([18F]FDG, 2)14 and 18F-DOPA (3)15 are clinical radiotracers used in diagnosing

and monitoring disease progression in cancer and Parkinson’s disease, respectively. Considering

the utility of fluorine in pharmaceuticals and clinical radiotracers, it is expected that the number of

fluorine-containing pharmaceuticals and radiotracers will continue to grow.

Figure 1.1. Examples of fluorine-containing molecules in medicinal chemistry.

2

1.1.1. Conformational influence

Figure 1.2. The effect of fluorine’s on conformation

Fluorine can uniquely affect molecular conformations.1,4,6,16,17 The predominant conformer

is influenced by energic contributions from dipole-dipole interactions, charge-dipole interactions,

and hyperconjugation. Due to the highly polarized nature of C-F bonds, the associated low lying

σ*C-F antibonding orbital can readily accept donating electron density from vicinal C-H bonds. This

form of hyperconjugation is known as the gauche effect and significantly influences molecular

conformations of 1,2-difluoroalkanes to favour the gauche conformer. 4,16,17 For instance, in 1, 2–

difluoroethane the gauche conformer (4a) is the lowest energy conformation in contrast to the

anti-conformer (4b) which is expected to have the least steric hindrance (Figure 1.2A). In the

gauche conformer, the σ*C-F orbital is aligned antiparallel with a vicinal σC-H bonding orbital so that

the σC-H orbital can donate electron density into the vacant σ*C-F orbital. Notably, the gauche effect

is more pronounced in systems featuring F-C-C-O or F-C-C-N (see 6 - 8). Comparatively,

electrostatic interactions (i.e. charge-dipole, dipole-dipole) offer a greater degree of stabilization

than hyperconjugation. In cases where the adjacent substituent bears a positive charge (e.g. 9 –

11), charge-dipole interactions with the partially negative fluorine atoms results in these molecules

adopting the gauche conformer. Likewise, dipole-dipole interactions within the same molecule

can also provide stabilization towards a particular conformation. For example, in α-

fluoroacetamide (12) the fluorine and the carbonyl oxygen are oriented antiperiplanar to minimize

the net dipole of the molecule, thus providing an overall stabilization of 7.5 kcal/mol. A weak

3

hydrogen bonding interaction between the amide N-H and fluorine may also contribute to this

stabilization.

Figure 1.3. Structural conformations of 17 and 18

In drug design, introduction of a fluorine atom is a common tool used for changing

molecular conformations to tune basicity and target-binding affinity. Towards studying

conformation-activity relationships, O’Hagan first synthesized and then evaluated the binding

properties of 3F-GABA enantiomers (17 and 18) against GABAA receptor and GABA

aminotransferase. 18 While both enantiomers were considerably less potent than the natural

substrate GABA, 17 and 18 themselves exhibited similar binding affinities toward GABAA

receptor, however, GABA aminotransferase metabolized 18 10-fold faster compared to 17.

O’Hagan rationalized these observations based on the conformational preferences of each

enantiomer which are summarized in Figure 1.3. As discussed previously, the gauche conformers

(17a/17b and 18b/18c) were assigned as the more stable conformations. Furthermore,

conformers 18a and 17c are disfavoured owing to the antiperiplanar alignment of NH3+ and

fluorine which increases each conformers’ net dipole. The equipotency of the two analogues

towards GABAA receptor suggests that the antiperiplanar alignment of the NH3+ and COO- in 17b

and 18b, both energetically favourable conformations, is important to receptor recognition.

Interestingly, the metabolism of 18 by GABA aminotransferase produced 10-fold more hydrogen

fluoride compared to 17. For elimination of fluoride to occur, fluoride must be positioned

antiperiplanar to a β-hydrogen. Taken together, this points towards conformation 18c possessing

4

the preferred binding orientation of NH3+ and COO- which is an energetically disfavoured

conformation in 17.

1.1.2. Metabolic stability

Many classes of metabolic enzymes, such as cytochrome P450 (CYP) enzymes,

hydrolases, and peroxidases, are involved in drug metabolism.19 The resulting drug metabolites

can provide crucial insight into metabolic pathways and help guide drug design efforts. The short

C(sp3) -F bond (1.40 Å) is the strongest bond (110 kcal/mol) in organic chemistry and, due to

fluorine’s small Van der Waals radius (1.47 Å), it is an effective isostere for a hydrogen atom or a

hydroxyl group. In drug development, strategic fluorine incorporation can be used to block

unproductive metabolism. As a notable example, the aryl fluorides in Ezetimibe (20), a drug used

to reduce cholesterol absorption in patients with hypercholesterolaemia, prevents CYP mediated

aromatic C-H oxidation and O-demethylation that was previously observed in the initial lead

compound 19.20 Ultimately, fluorine replacement, in addition to stereoselective benzylic oxidation

and demethylation, led to a 50-fold increase in activity and an improved pharmacological profile.

Figure 1.4. Stragetic use of fluroine to block unproductive metabolsim

Toxic fluorine-containing metabolites, such as fluoroacetic acid (21), are a recognized

problem when working with fluorinated drugs. Fluoroacetic acid, which can also be generated

from several metabolic precursors (Figure 1.5, 22-27), is lethal to humans at levels ranging from

2 – 10 mg/kg and has encountered toxicological issues during drug discovery campaigns.3 For

instance, to develop an effective treatment for taxane-refractory solid tumors, Merck investigated

piperidine-based kinesin spindle protein (KSP) inhibitors with a specific focus of reducing P-

glycoprotein (P-gp) efflux by tuning the pKa of the piperidine nitrogen to a range of 6.5 to 8.0.21 P-

gp efflux is measured as the ratio of the IC50 evaluated in a cell-line overexpressing P-gp over the

5

IC50 in the parental cell-line that does not express P-gp and is denoted as the multidrug resistance

protein 1 (MDR) ratio.21

Figure 1.5. A) Metabolic precursors of fluoroacetic acid (21). B) Mediating the metabolic profile of KSP inhibitors

As shown in Figure 1.5, the N-2-fluoroethyl analogue 28 had an MDR ratio of 4.5, well

below the predetermined maximum threshold of 10, and an optimal pKa value (7.6). However, in

rats 28 was found to be severely toxic as it undergoes N-dealkylation presumably leading to

fluoroacetic acid via a metabolic precursor 22. Interestingly, fluorine incorporation into the

piperidine ring produced the desired reduction in basicity for compound 30 (MK-0731) while also

avoiding the production of fluoroacetic acid as a primary metabolite.

1.1.3. Potency

compound R R1 17β-HSD1 IC50 (nM)

17β-HSD2 IC50 (nM)

selectivity factor

31 H H 69 1950 28 32 F H 8 940 118 33 F F 56 312 6

Table 1.1. Fluorine’s effect on potency and selectivity

6

The tactical introduction of fluorine into drug candidates is widely used to enhance potency

and target affinity.1,4,6 As mentioned previously, one of the more common strategies is the

substitution of a hydrogen atom for a fluorine atom.9 The effectiveness of this approach largely

depends on the drug-target interactions that are being optimized. For example, Hartmann

explored aryl fluoride substitutions of 31 for the selective inhibition of 17β-hydroxysteroid

dehydrogenase 1 (17β-HSD1), an important target for treating osteoporosis.22,23 32 demonstrated

improved potency and selectivity over 17β-hydroxysteroid dehydrogenase 1 (17β-HSD2), which

catalyzes the reverse reaction (i.e. oxidation of estradiol). Accordingly, it was postulated fluorine

increases the acidity of the phenol moiety allowing for increased hydrogen bonding with Glu282

and His221 in the active site of 17β-HSD1, a key interaction that mimics the enzyme’s natural

substrate (estrogen). Addition of a second fluorine atom reduced potency and selectivity, thus

suggesting the phenol proton has an optimal pKa for this interaction.

1.1.4. Membrane permeability

compd R R1 Caco-2-permeability compd R2 Caco-2-permeability

34 H CH3 1.20 ± 0.09 x 10-6 cm/s 38 H 0.8 x 10-6 cm/s 35 F CH3 3.14 ± 0.10 x 10-6 cm/s 39 F 7.4 x 10-6 cm/s 36 H CF3 3.38 ± 0.08 x 10-6 cm/s 40 CN < 0.1 x 10-6 cm/s 37 F CF3 4.86 ± 0.33 x 10-6 cm/s

Table 1.2. Caco-2-permeability of Xa factor inhibitors

A drug candidate’s cellular membrane permeability (Pe) can significantly affect its

pharmacological and toxicological profiles.4 In regard to passive diffusion across cellular

membranes, Pe decreases with molecular size and increases with lipophilicity. Fluorine

incorporation has been used to increase a molecule’s lipophilicity and, consequently, improve a

molecule’s membrane permeability via passive diffusion by affecting lipophilicity, intramolecular

hydrogen bonding interactions, and amine basicity. As an illustrative example, compounds 34-40

7

were investigated for their Xa factor inhibition for the development of anticoagulant drugs.24,25

Substituting fluorine in for the hydrogen ortho to the anilide N-H resulted in improved membrane

permeability as measured by the Caco-2 permeability assay for 35, 37, and 39 compared to their

hydrogen analogues. Presumably, the ortho anilide N-H is a hydrogen bond donor that interacts

with the ortho fluoride to increase membrane permeability. In contrast, replacement of the

hydrogen with a nitrile instead significantly reduces permeability in 40 as no intramolecular

hydrogen bonding is achievable.

1.2. Fluorine as a synthetic handle

Over the past two decades, C-F bond forming reactions have been explored extensively

to facilitate the growing utility of fluorinated molecules in pharmaceuticals,26 disease

diagnostics,10,11,13 agrochemicals,27 and material science.28 This has also resulted in the

investigation into the unique reactivity of C-F bonds (i.e. C-F bond activation) themselves and the

use of fluorinated molecules as versatile building blocks in chemical synthesis.29,30 To date, C-F

bond activation has been used for glycosylation,31–41 Friedel-Crafts,42–49 nucleophilic

substitution,50–56 dehydrofluorination, 57–60 transition metal cross-coupling,61–64 and halide-

exchange reactions.65,66

1.2.1. Defluorination of C(sp3-F) bonds

Scheme 1.1. Deflourative functionalization. A) Glycosylation of glycosyl fluorides. B) Friedel-Crafts reaction of aliphatic tertiary fluorides

8

Fluoride abstraction with a Lewis acid is a common way to exploit C-F bond reactivity in

defluorinative functionalization reactions. For instance, Lewis acids catalyze the glycosylation of

glycosyl fluorides.32 This has led to the emergence of glycosyl fluorides as an attractive alternative

to traditional glycosyl donors (i.e. glycosyl halides,68 pentenyl glycosides,67

trichloroacetimidates68) in carbohydrate synthesis. The additional strength of the C-F bond affords

glycosyl fluorides improved stability over other glycosyl halides and trichloroacetimidates while

also remaining reactive under mild glycosylation conditions. As depicted in Scheme 1.1A,

Montgomery reported fluoride abstraction with tris(pentafluorophenyl)borane to catalyze the

stereospecific glycosylation of over 35 mono- and disaccharides with a variety of silyl ethers.36

Mechanistically, anchimeric assistance facilitates fluoride abstraction, via oxacarbenium

intermediate 42, and ultimately enables the stereospecific delivery from the silyl ether. Activation

of pyranosyl and furanosyl fluorides with other Lewis acids are well-documented. The use of

C(sp3)-F bond defluorination in Friedel-Crafts alkylations have also been independently reported

by Stephan,45–47 Moran,48 Paquin,44 and Kemnitz.49 Notably, Moran has demonstrated the use of

aliphatic tertiary fluorides in Friedel-Crafts reactions (Scheme 1.1B).48 Here, the

tris(pentafluorophenyl)borane catalyst abstracts fluoride to generate the carbocation species for

reaction with electron-rich (hetero)arenes. While fluorine is generally considered a poor hydrogen-

acceptor, Paquin showed the carbocation species could also be generated from benzylic fluorides

by hydrogen-bonding with HFIP (a strong hydrogen-bond donor) in the synthesis of 1,1-diaryl

methanes.44

9

Scheme 1.2. Stereospecific fluoride displacement

Rare examples of nucleophilic substitutions of aliphatic fluorides under basic or neutral

conditions exist.50–53 Hu reported the intramolecular fluoride displacement of benzylic fluorides

with tertiary and secondary alkoxides for the synthesis of annulated dihydrofurans (Scheme 1.2A)

In this one-pot-two-step sequence, treatment of 47 with n-butyllithium afforded the organolithium

species which then reacts with benzaldehyde to form the alkoxide in situ. Investigations into the

mechanism of cyclization revealed that the loss of fluoride occurred via an SN2 process. From

their work towards bicyclic morpholine and piperidine cores, researchers at Pfizer Inc. explored

nucleophilic fluoride displacement for the construction of the second ring.51 As depicted in

Scheme 1.2B, exposing 51 to KHMDS was unsuccessful due to geometric constraints; however,

under the same reaction conditions, they were able to cyclize compound 52 to compound 54 in

excellent yield. The PNB protecting group allowed epimerization of the α-fluoromethine, thus

enabling backside attack from the tethered alkoxide.

10

1.2.2. C(sp2)-F nucleophilic substitution

Scheme 1.3. A) Nucleophilic aromatic substitution for macrocyclization. B. Process scale intramolecular nucleophilic heteroaromatic substitution

Contrary to reactivity trends observed in nucleophilic substitution reactions of aliphatic

fluorides, aryl fluorides are the most reactive among the aryl halides towards nucleophilic aromatic

substitution (SNAr).29 It is believed SNAr is a step-wise process that proceeds through a transient

reaction intermediate known as the Meisenheimer complex (57), though there is recent evidence

supporting a concerted pathway.69 In SNAr reactions, the rate-determining step (RDS) is the

addition of the nucleophile to the aryl halide. This process kinetically favours aryl fluorides over

other aryl halides due to fluorine being comparatively small and strongly electron-withdrawing.

The preferential reactivity of aryl fluorides is demonstrated in the reaction between 1-bromo-3-

chloro-5-fluorobenzene and cyanoacetate which exclusively displaces fluoride to afford a single

regioisomer (> 30:1).56,70 SNAr reactions have proven to be a highly useful tool for the construction

of macrocycles, as well as for heterocycle synthesis and functionalization in drug discovery. As

shown in Scheme 1.2, reacting 55 with potassium carbonate led to a productive macrocyclization

and afforded the 14-membered ring macrocycle 56 for the synthesis of cycloisodityrocine

derivatives.71 Amgen Inc reported a scalable route to their dual FLT3/CDK4 inhibitor AMG 925

11

(60) for the treatment of acute myeloid leukemia in which the 3-fluoro-pyridyl moiety is a synthetic

handle for base-promoted intramolecular SNAr cyclization to afford the tricyclic intermediate 59.54

Scheme 1.4. Reactivity pathways of gem-difluoroalkenes

The C(sp2)-F bond of fluoroalkenes can undergo nucleophilic substitution through a similar

addition-elimination pathway observed in SNAr reactions. For instance, upon base or acid

treatment gem-difluoroalkenes 61 engage in intramolecular nucleophilic substitutions to generate

a variety of cyclic scaffolds including cyclopentenes, dihydrofurans, dihydropyrroles, and

dihydrothiophenes.55 The double bond of gem-difluoroalkenes is highly polarized as the 13C NMR

indicates an electron deficient difluoromethylene carbon (~ 155 ppm) and an electron rich

methylene carbon (~ 90 ppm).55 Notably, these characteristics engender gem-difluoroalkenes

with two additional modes of reactivity. Rather than eliminating fluoride to regenerate the double

bond, the intermediate carbanion 65 can react with electrophiles to afford 1, 2-addition products.

Alternatively, in the case where the γ-carbon is substituted with a leaving group, an SN2’ process

can lead to difluoromethyl alkene products 66.

12

1.2.3. Hydrodefluorination

Scheme 1.5. Hydrodefluorination strategies

Recently reported protocols for the selective hydrodefluorination of trifluoromethyl

aromatics have provided direct access to the corresponding difluoromethyl products, a valuable

motif in modern drug design. 57–60 While several transition metal cross-coupling and C-H

functionalization reactions have been well-established for introducing difluoromethyl groups into

aromatics and heteroaromatics, 72–88 converting a trifluoromethyl group directly into the

difluoromethyl analogue is a powerful tool for a medicinal chemist. Admittedly, over

hydrodefluorination to the corresponding monofluoromethyl and methyl derivatives is a common

concern in developing these methodologies.57–60 Olah reported the selective hydrodefluorination

of 1,3-bis(trifluoromethyl)arenes using magnesium powder under acidic conditions.58 As

highlighted in Scheme 1.5A, these conditions converted Netupitant (67) into its difluoromethyl

analogue 68 without producing any of the monofluoromethyl side-product. Conversely,

13

subsequent work by Jui58 and Gouverneur59 relied on photoredox approaches to generate a

radical anion intermediate 70. Following loss of fluoride, the resulting difluoromethyl radical 71 is

then trapped via hydrogen atom transfer (HAT) to afford the desired difluoromethyl analogue.

1.3. Thesis overview

In this thesis, the discoveries of 1) novel proline-catalyzed α-functionalization/aldol

reactions for short syntheses of nucleoside and carbohydrate analogues and 2) the late-stage

functionalization of heterobenzylic C-H bonds are presented.

Scheme 1.6. The development of an α-fluorination/aldol reaction (αFAR) and an annulative fluoride displacement (AFD) for nucleoside analogue synthesis

Chapter 2 reports a “ribose-last” approach for the 3-step de novo synthesis of nucleoside

analogues (NAs). NAs are the leading class of antiviral drugs and make up a significant portion

of anticancer therapeutics. Our strategy involves the development of a proline-catalyzed α-

fluorination/aldol reaction (αFAR) to access enantioenriched fluorohydrin intermediates 77 and

unprecedented annulative fluoride displacement (AFD) reaction for cyclization to a protected

nucleoside core 78. The utility of this unique process is highlighted in the synthesis of several C2’-

modified NAs.

Chapter 3 discusses the short syntheses of C4’-modified NAs via 1,2-additions of Grignard

reagents to the aforementioned fluorohydrin intermediates 77 and subsequent AFD. To date,

current syntheses have relied on semisynthetic approaches that are lengthy (~10 steps),

protracted, and not amenable to rapid diversification. Furthermore, we also present short

syntheses of locked nucleic acids (LNAs), a class of conformationally rigid NAs that are

incorporated into oligonucleotides to increase stability and potency of antisense therapeutics.

Ultimately, this process creates opportunities for preparing diversity libraries and will support

future efforts in drug discovery.

14

Scheme 1.7. Development of new α-functionalization/aldol reactions for carbohydrate analogue synthesis

Chapter 4 presents the development of novel asymmetric α-functionalization/aldol reactions for

the synthesis of carbohydrate analogues (CAs). Current syntheses of CAs have relied on

semisynthetic approaches that have limited rapid access to structurally diverse CAs. In contrast,

our strategy readily constructs several unique CA scaffolds from 81, a versatile building block that

can be generated using only proline-catalysis and cheap achiral building blocks in a single step.

This 3-step synthesis enabled access to iminosugars, annulated furanoses, bicyclic nucleosides,

and fluorinated carbacycles.

Scheme 1.8. The direct monofluorination, difluorination, and trifluoromethylthiolation of heterobenzylic C-H bonds

Chapter 5 reports the late-stage monofluorination of pyridylic C-H bonds with N-

fluorobenzenesulfonimide (NFSI). There have been significant advances in the fluorination of

benzylic C-H bonds but these methods have not translated to the fluorination of heterobenzylic

C-H bonds. This strategy is the first method reported for the selective C-H fluorination of 2- and

4-alkyl pyridines, and proceeds via a transient N-sulfonated pyridinium intermediate. Most

importantly, the reaction is tolerant to a wide range of different functional groups present in drug

discovery and we demonstrate its utility for site-selective drug lead fluorination. Considering

nearly 60% of all FDA approved drugs contain at least one heterocycle, this reaction should

become a useful tool for the modulation of drug leads’ physicochemical properties.

15

Chapter 6 reports the improved versatility of the work presented in Chapter 5 and both the C-H

monofluorination and difluorination of pyridines, pyrimidines, quinolines, purines, isoquinolines,

and quinazolines are presented. While advances in the addition of fluoroalkyl radicals to

heterocycles have been made, direct C(sp3)–H heterobenzylic fluorination is comparatively

unexplored. Here we demonstrate both mono- and difluorination of a range of alkyl heterocycles

using a convenient process that relies on transient sulfonylation by the electrophilic fluorinating

agent N-fluorobenzenesulfonimide. We also report heterobenzylic trifluoromethylthiolation and

18F-fluorination, providing a suite of reactions for late-stage C(sp3)–H functionalization of drug

leads and radiotracer discovery.

16

Chapter 2. Development of an α-fluorination/aldol reaction and an annulative fluoride displacement for de novo nucleoside analogue synthesis

The results presented in this chapter have been reported in part, see:

Meanwell, M.; Silverman, S. M.; Lehmann, J.; Adluri, B.; Wang, Y.; Cohen, R.; Campeau, L.-C.;

Britton, R. 2020, Science. Accepted.

Several colleagues contributed to this work. Dr. Steven M. Silverman optimized the route to

compounds 121 and 122. Dr. Johannes Lehmann developed the route to 130. Dr.

Bharanishashank Adluri optimized the AFD reaction for 106 and 108. Dr. Yang Wang obtained

analytical data for compounds 113, 114, and 118. Dr. Ryan Cohen developed the J-based

configurational analysis for the determination of relative configuration.

17

2.1. Nucleoside analogues in drug discovery

Figure 2.1 Nucleoside analogues in drug discovery

As fundamental biomolecules, nucleosides play key roles in diverse cellular processes

ranging from cell signalling to metabolism.89 Not surprisingly, synthetic nucleoside analogues

(NAs), designed to mimic their natural counterparts, are widely exploited in medicinal chemistry90–

95 and used as tool compounds in chemical biology. In fact, NAs have been in use for over half a

century for the treatment of cancer90,92 and represent the largest class of small molecule antivirals

(e.g., 86 – 91, Figure 2.1). 94,95 Mechanistically, NAs operate as toxic antimetabolites that interfere

with nucleic acid synthesis.95 Alternatively, following in vivo phosphorylation, the resulting

nucleotide analogues can inhibit enzymes crucial to cancer cell growth or viral replication (e.g.,

DNA/RNA polymerases, ribonucleotide reductases or nucleoside phosphorylases).90,95 Recently,

NAs have also demonstrated promise as epigenetic modulators, and both decitabine and

azacitidine inhibit DNA methyltransferase and have been approved for cancer therapy.95

The continued discovery and development of anticancer and antiviral NAs builds on

several decades of medicinal chemistry knowledge. 92,96,97 For example, in the early 1980’s it was

found that fluorination at C2' improves metabolic stability (i.e., decreases hydrolysis) and can

influence furanose conformation and enzyme binding (PSI-620698: 86, Figure 2.1).4,94,96 Likewise,

18

replacement of a proton at C2' with a methyl group alters the conformation, and thus C2'-methyl

NAs operate as nonobligate chain terminators.97,99 Modifications at C3' generally interrupt

extension of a growing nucleic acid chain, while C4' functionalization (e.g., methyl, azido, alkynyl)

can beneficially influence furanose conformation or attenuate reactivity of the C3' and C5' alcohols

toward chain extension (MK-8591: 89). 97,100 Modified nucleobases have also been studied to

improve potency, pharmacokinetic and pharmacodynamic properties. For example, NAs

possessing 5-membered ring nucleobases such as ribavirin (90)101 mimic structurally related

intermediates in de novo purine nucleotide biosynthesis and can modulate the activity of enzymes

in this pathway.102 In recent years there has also been increased interest in unnaturally configured

NAs.103,104*For example, the -L-NA Lamivudine (3TC)91 has found widespread use in the

treatment of HIV-1/AIDS and several -D-thymidine analogues have demonstrated promise as

antimalarials. 91

2.2. Current challenges in NA synthesis

Figure 2.2. Current challenges in nucleoside synthesis

Despite decades of NA research, the synthesis of NAs still presents many challenges.105 Firstly,

NAs are often synthesized from naturally occurring carbohydrates, which limits patterns of

substitution and furanose stereochemistry. Secondly, the addition of nucleobases to activated

ribose derivatives (i.e., the Vorbrüggen reaction) often fails or proceeds with poor

diastereoselectivity when NAs are functionalized at C2' or C4'. 106,107 Thirdly, modifications at C2'

often require multistep protecting group manipulations of the C3' and C5' alcohol functions. While

such processes can be accomplished with siloxanes for discovery purposes,108 they are cost

prohibitive on production scale. Lastly, modular and efficient strategies for producing C4' modified

* By convention, -D-NAs are naturally configured (e.g., 86 – 91), while L- denotes the NA is epimeric at

C4' and - or - indicates a trans- or cis-relationship, respectively, between the nucleobase and the C4'-CH2OH group.

19

NAs do not exist, which continues to challenge medicinal and process research chemists. In fact,

a recent summit of key opinion leaders highlighted the synthesis of noncanonical nucleosides as

an “emerging area of high potential impact”.109 While efforts to develop de novo NA syntheses

have aimed to address these challenges, the resulting processes are often lengthy and target-

specific, as highlighted by the 16-step process required to produce the C4'-modified NA MK-8591

(89).107 As a notable example of de novo NA synthesis, MacMillan reported the synthesis of C2'-

modified NAs, including the core of sofosbuvir (86), using a sequence that involved a Mukaiyama

aldol coupling between a ketene acetal (93) and an α-oxyaldehyde (94).110

Scheme 2.1. MacMillan’s de novo synthesis of C2’-modified NAs

Here we disclose a straightforward process for NA synthesis that involves a one-pot,

proline-catalyzed -fluorination-aldol reaction of heteroaryl-substituted acetaldehydes 76

followed by reduction or organometallic addition and annulative fluoride displacement (AFD). This

concise (2-3 step) process addresses several major and longstanding challenges in NA synthesis

by enabling direct access to C3'/C5' protected NAs 78 (and hence C2' modified NAs), providing

flexibility in nucleobase substitution, and offering a direct route to C4' modified NAs. We expect

this strategy will become a powerful tool that enables and inspires drug design.

20

Scheme 2.2. A 3-step synthesis of NAs

2.3. Proposal for de novo NA synthesis

Figure 2.3. A ribose-last approach to NAs inspired by the prebiotic synthesis of deoxyribonucleosides. B. proline-catalyzed α-chlorination/aldol

In a proposed prebiotic synthesis of DNA(25),111 couplings between nucleobase-type

enamines (e.g., 96, Figure 2.3) and glyceraldehyde form a nucleobase iminium ion (e.g., 98) prior

to the furanose in a “ribose-last” approach. We identified a complementary approach that also

involves the terminal cyclization of a nucleobase-iminium ion. Our experiences with ribose

synthesis from chlorohydrins suggested that N/Cl hemiaminals are too unstable to serve as

precursors to related nucleobase iminium ions (Figure 2.3B). Control of both the relative and

absolute stereochemistry may be possible through an organocatalytic aldol reaction of a

dihydroxyacetone derivative (e.g., 97) 112 and the -fluoroaldehyde 100. This approach to NAs

would require i) harnessing the reactivity of notoriously unstable -fluoroaldehydes113,114 coupled

21

with the additional challenge of a nucleobase connected at the same position (e.g., 100), and ii)

the development of an annulative fluoride displacement (AFD) reaction to form the ribose ring in

the last step.

2.4. Development of an α-fluorination/aldol reaction and an annulative fluoride displacement

Figure 2.4. Optimization of αFAR and AFD

To explore this conceptually new approach to NAs, we investigated the -fluorination113 of

-pyrazolyl aldehyde 104 (Figure 2.4) and eventually found that a combination of L-proline and

N-fluorobenzenesulfonimide (NFSI) in DMF115 provided an α-fluorohydrate (not shown) as the

sole product. While we were unable to dehydrate this material, it was eventually found that the

direct addition of dioxanone 75 in MeCN to the reaction mixture afforded the fluorohydrins 105a

and 105b in good yield and enantioselectivity (Figure 2.4, entry 2). As indicated, the fluorohydrins

105a and 105b were formed as a ~1.4:1 mixture of epimers at the pseudo anomeric carbon

(indicated with *) that do not interconvert under the reaction or isolation/purification conditions.

This result suggests that a relatively slow epimerization of -pyrazolyl--fluoroaldehydes

precludes a dynamic kinetic resolution,116 or that the transition structure for the proline catalyzed

aldol reaction between dioxanone 75 and (R)- or (S)--pyrazolyl--fluoroaldehydes are

energetically similar. Notwithstanding, we anticipated that the AFD would proceed via the

formation of a transient azacarbenium cation117 (i.e., an SN1 process), rendering the fluoromethine

configuration inconsequential. To investigate this novel cyclization strategy (i.e., AFD), reduction

of the fluorohydrins 105a and 105b provided a mixture of 1,3-syn diols that was then treated with

one of several Lewis acids in an attempt to promote displacement of the fluoride by the distal

22

alcohol function. After considerable experimentation, an AFD reaction using fluorophilic

Sc(OTf)3118 was realized that afforded the NA 106 in 38% yield as a single -anomer (entry 4).

Additionally, we found that treatment of a mixture of the diols 105a and 105b with base (NaOH)

resulted in the formation of a mixture of - and -anomeric NAs that varied in composition

depending on reaction time and equivalents of base (entries 5 and 6). Using a large excess of

NaOH (10 equiv, entry 6), the -anomer 106 was formed as the exclusive product in excellent

yield (76%).

Figure 2.5. Mechanism of cyclization of 107a and 107b

To further examine the mechanism of cyclization, the intermediate diols 107a and 107b

were separated by flash column chromatography and their relative stereochemistry assigned by

J-based configurational analysis and/or X-ray analysis of derivatives (see experimental section

for full details). Subjecting the purified syn-fluorohydrin 107a to the AFD reaction (NaOH, CH3CN,

Panel C) promoted a clean cyclization to the -anomer 106 via an SN2 process, in contrast to our

expectations. Similarly, the anti-fluorohydrin 107b cyclized to afford the -anomer 108, again via

stereochemical inversion. Fortuitously, under these same reaction conditions the -anomer 108

epimerizes to afford the naturally configured -anomer 106, and thus both fluorohydrin aldol

products 105 can be transformed together into a single naturally configured -D-NA via this

straightforward reaction sequence. It is notable that the enantiomeric purity of the NA 106 (e.r. =

95:5, Figure 2.4 entry 6) represents an average of the enantiomeric purities of the epimeric

fluorohydrin FAR products 105.

23

In order to assess the general utility of this uniquely concise NA synthesis, we prepared a

collection of acetaldehyde derivatives through the straightforward alkylation of several

heterocycles with bromoacetaldehyde diethyl acetal (109) (Figure 2.6). Using either Selectfluor

or NFSI as the electrophilic fluorinating agent (F+), the resulting aldehydes 110 then underwent

proline-catalyzed αFAR with dioxanone 75 to provide a collection of fluorohydrin aldol products

111 functionalized with one of the heterocycles uracil, thymine, triazole, deazadenine, pyrazole,

phthalimide, adenine or 2,6-dichloropyrimidine. These fluorohydrins were generally produced in

good to excellent yield and enantiomeric purity. In the case of the adenine containing fluorohydrin,

the enantiomeric purity was lowered by competing (non-proline) catalysis in the αFAR. Each of

the αFAR products was isolated as a mixture of epimers at the fluoromethine center that

subsequently underwent a 1,3-syn selective carbonyl reduction and AFD promoted by either base

(NaOH, Panel B) or a Lewis acid (Panel C) as indicated. We were pleased to find that several

heterocycles were compatible with this process and that uracil, thymine or adenine-substituted

acetaldehydes could be exploited in short (4 step total) de novo syntheses of the endogenous

ribonucleosides uridine (113), 5-methyluridine (114) and adenosine (A: 120). In general, the

optimal Lewis acids for promoting AFD reactions were InCl3 or Sc(OTf)3, while pyrazole- and

uracil-derived fluorohydrins cyclized using NaOH. With the exception of trifluoromethyluracil 118

and deazaadenines 121 and 122, the NAs were produced as an approximate average of the

enantiomeric purities of the individual fluorohydrin epimers 111. Thus, the majority of NAs

examined in this study undergo epimerization following AFD, providing a straightforward means

to convert the mixture of epimeric aldol products into a single, naturally configured -D-nucleoside

analogue. For the triazole 117, trifluoromethyl uracil 118 and deazaadenines 121 and 122, αFAR

products (e.g., 111) were reduced, separated and treated individually with Sc(OTf)3 or InCl3. As

indicated in Figure 2.6C, for trifluoromethyl uracil, only the anti-fluorohydrin underwent AFD to

form 118, which did not epimerize under the reaction conditions.

24

Figure 2.6. Scope of nucleoside and NA synthesis.

In the case of the deazaadenine, both the syn-fluorohydrin and anti-fluorohydrin

underwent AFD to provide the - and α-anomers 121 and 122, respectively, confirming that these

25

reactions proceed via direct fluoride displacement. To evaluate the practical utility of these

processes, several of the αFARs were demonstrated on >10 g scale (e.g., 113, 114, 118, 119

and 121 (Figure 2.6)) and proceeded without complication, though we noted a small improvement

in diastereoselectivity when reactions were executed on larger scale. We also found that the C-

linked NA 116 could be prepared using this sequence of reactions starting from a

dichloropyrimidine, further extending the utility of this strategy to an additional and important class

of NAs.119 Here, however, the major product of the αFAR cyclizes to an α-D-nucleoside

analogue103 and undergoes a second cyclization event under the reaction conditions to form the

tricycle 116. In addition to naturally configured NAs, this strategy can be easily adapted for the

synthesis of enantiomeric (L-configured) nucleosides and NAs (Figure 2.7) by simply using D-

proline in the αFAR. Thus, L-uridine (ent-113) and the L-configured NA ent-117 were accessed in

this straightforward manner. While crude reaction mixtures were generally treated with aqueous

acid to remove the acetonide protecting group and enable isolation of the targeted NA, eliminating

this step allowed us to isolate C3'/C5'-protected NAs directly (e.g., 123 and 124, Figure 2.7).

Figure 2.7. C3’/C5’ protected nucleosides (R = C(CH3)2) and β-L-nucleosides.

2.5. Synthesis of C2’-modified nucleoside analogues

This modification provides a solution to the challenge of selective C3'/C5' protection that

is required for producing C2'-modified NAs. To demonstrate that these acetonide-protected NAs

can be further derivatized using standard protocols, several C2'-modified NAs were prepared,

including C2'-deoxy (125), C2'-oxo (126), C2'-3º alcohol (127) and C2'-epi (128) (Figure 2.8).

26

Figure 2.8. C2’-modified nucleoside analogues (R = C(CH3)2)

Considering the potential for this process to impact the large-scale production of NAs, we

examined the synthesis of the D-uridine derivative 123 starting with 900 g of uracil. Without

additional optimization, we were able to generate ~380 g of the respective aldol adduct, which

was readily converted into the protected uridine 123 in excellent yield by base-promoted AFD.

Oxidation of the C2'-OH function followed by deprotection and addition of MeMgBr in THF gave

the tertiary alcohol 130 (Scheme 2.3). This later compound is a previously-reported intermediate

in the large-scale production of MK-3682 (Uprifosbuvir: 131),120 an HCV NS5B RNA polymerase

inhibitor developed for the treatment of HCV.

Scheme 2.3. Application to the synthesis of MK-3682 penultimate (130) (R = C(CH3)2).

2.6. Experimental

General considerations

L- and D-proline (99% purity) were purchased from Alfa Aesar. All reactions described were

performed at ambient temperature and atmosphere unless otherwise specified. Column

chromatography was carried out with 230-400 mesh silica gel (E. Merck, Silica Gel 60).

Concentration and removal of trace solvents was done via a Buchi rotary evaporator using

acetone-dry-ice condenser and a Welch vacuum pump.

27

Nuclear magnetic resonance (NMR) spectra were recorded using deuterochloroform (CDCl3),

deuteromethanol (CD3OD), deuteroacetone ((CD3)2CO), deuteroacetonitrile (CD3CN) or

deuterodimethyl sulfoxide (DMSO-d6) as the solvent. Signal positions (δ) are given in parts per

million from tetramethylsilane (δ 0) and were measured relative to the signal of the solvent (1H

NMR: CDCl3: δ 7.26; CD3OD: δ 3.31; (CD3)2CO: δ 2.05; CD3CN: δ 1.96; DMSO-d6: δ 2.50; 13C

NMR: CDCl3: δ 77.16; CD3OD: δ 49.00; (CD3)2CO: δ 29.84; CD3CN: δ 1.32; DMSO-d6: 39.5).

Coupling constants (J values) are given in Hertz (Hz) and are reported to the nearest 0.1 Hz. 1H

NMR spectral data are tabulated in the order: multiplicity (s, singlet; d, doublet; t, triplet; q, quartet;

sept, septet; m, multiplet; br broad), coupling constants, number of protons. NMR spectra were

recorded on a Bruker Avance 600 equipped with a QNP or TCI cryoprobe (600 MHz), Bruker 400

(400 MHz) or Bruker 500 (500 MHz). Diastereomeric ratios (dr) are based on analysis of crude

1H-NMR. Assignments of 1H are based on analysis of 1H-1H-COSY and nOe spectra. Assignments

of 13C are based on analysis of HSQC spectra.

High performance liquid chromatography (HPLC) analysis was performed on an Agilent 1100

HPLC, equipped with a variable wavelength UV-Vis detector.

High-resolution mass spectra were performed on an Agilent 6210 TOF LC/MS, Bruker MaXis

Impact TOF LC/MS, or Bruker micrOTOF-II LC mass spectrometer.

Infrared (IR) spectra were recorded neat on a Perkin Elmer Spectrum Two FTIR spectrometer.

Only selected, characteristic absorption data are provided for each compound.

Optical rotation was measured on a Perkin-Elmer Polarimeter 341 at 589 nm.

General Procedure A (one-pot organocatalytic α-fluorination/aldol reaction)

A sample of aldehyde (1.5 equiv.) was added to a stirred suspension of NFSI (1.5 equiv.),

L-proline (1.5 equiv.), and NaHCO3 (1.5 equiv.) in DMF (0.75 M) at 4 °C. When complete

conversion to the α-fluoroaldehyde was observed by 1H-NMR spectroscopic analysis, 2,2-

dimethyl-1,3-dioxan-5-one (75) (1.0 equiv.) in CH2Cl2 or THF or MeCN (1.25*DMF vol.) was then

added and the resulting mixture was allowed to warm to room temperature. After a further 36-72

hours, or when complete consumption of 75 was observed by 1H NMR spectroscopic analysis of

small reaction aliquots, the mixture was diluted with CH2Cl2 and the organic layer was washed

once with saturated sodium bicarbonate solution and once with water. The organic layer was then

28

dried over MgSO4, concentrated under reduced pressure and the crude product was purified by

flash chromatography as indicated.

General Procedure B (syn-reduction)

To a stirred solution of syn- and anti-fluorohydrins (1.0 equiv) in MeCN (0.10 M) at -15˚C was

added tetramethylammoniumtriacetoxyborohydride (5.0 equiv) and acetic acid (10 equiv). The

resulting mixture was stirred 16 hours or until complete consumption of starting material (as

determined by TLC analysis). The reaction mixture was then diluted with a saturated solution of

Rochelle salt and washed three times with CH2Cl2. The organic layer was separated, dried over

MgSO4, concentrated under reduced pressure, and the crude product was purified by flash

chromatography.

General Procedure C (base promoted cyclization)

To a stirred solution of syn-diols, syn- and anti-fluorohydrins (1.0 equiv.) in MeCN (0.10 M) was

added 2 M NaOH (1.5 - 10 equiv.) and the reaction mixture was stirred for 3 hours or until no

starting material remained (as determined by TLC analysis). The reaction mixture was diluted with

CH2Cl2 and washed with saturated ammonium chloride solution. The organic layer was separated,

dried over MgSO4, filtered, and concentrated under reduced pressure. The crude product was

purified by flash chromatography.

General Procedure D (Lewis acid promoted cyclization)

To a stirred solution of syn-diols, syn- and anti-fluorohydrin (1.0 equiv.) in MeCN (0.10 M) was

added Sc(OTf)3 or InCl3 (0.10 – 2.5 equiv.) and the reaction mixture was stirred for 6 hours or until

complete consumption of starting material (as determined by TLC analysis). The reaction mixture

was diluted with CH2Cl2 and was washed with saturated sodium bicarbonate solution. The organic

layer was separated, dried over MgSO4, filtered, and concentrated under reduced pressure. The

crude product was purified by flash chromatography.

Preparation and characterization of all compounds

Preparation of S1, aldehyde SM1, aldol adduct A1, diol adducts 107a/107b, and nucleoside

analogues 106, 108, and 124

29

A solution of pyrazole (1.00 g, 14.7 mmol, 1.0 equiv.), bromoacetaldehyde diethyl acetal (2.67

mL, 17.6 mmol, 1.2 equiv.) and K2CO3 (4.06 g, 29.4 mmol, 2.0 equiv.) was stirred in DMF (74 mL)

for 36 hours at 90 °C. The reaction mixture was then filtered and washed with 40 mL of CH2Cl2

and concentrated under reduced pressure. Purification of crude S1 by flash chromatography

(pentane:ethyl acetate – 7:3) afforded S1 (2.43 g, 90 % yield) as a colorless oil. A solution of S1

(0.100g, 0.543, 1.0 equiv.) was heated to 90˚C in 0.5 M HCl (0.54 mL) for 5 hrs. Upon complete

conversion to SM1, the reaction mixture was concentrated under reduced pressure and the

resulting product SM1 was used in the next reaction without purification.

Data for S1: IR (neat): = 2977, 2904, 1516, 1396, 1129, 1063, 751, 621

cm-1; 1H NMR (400 MHz, CDCl3): δ 7.51 (d, J = 1.8 Hz, 1H), 7.46 (d, J = 2.3

Hz, 1H), 6.24 (dd, J = 2.3, 1.8 Hz, 1H), 4.77 (t, J = 5.5 Hz, 2H), 4.22 (d, J =

5.5 Hz, 2H), 3.70 (m, 2H), 3.41 (m, 2H), 1.16 (t, J = 7.1 Hz, 6H); 13C NMR

(125 MHz, CDCl3): δ 139.7, 130.6, 105.6, 101.7, 63.8, 55.2, 15.3

HRMS (EI+) calcd for [C9H17N2O2]+ 185.1285; found 185.1284

α-fluorination/aldol

Following General Procedure A, a solution of SM1 (0.543 mmol), NFSI (0.170 g, 0.543 mmol), L-

proline (0.063 g, 0.543 mmol) and NaHCO3 (0.045 g, 0.543 mmol) was stirred for 12 hours at 4°C

in DMF (0.72 mL). 75 (0.043 mL, 0.362 mmol) in MeCN (0.90 mL) was then added and the

reaction mixture was stirred for 60 hrs at room temperature. Purification of the crude fluorohydrin

A1 by flash chromatography (pentane:Et2O – 25:75) afforded a mixture of syn- and anti-

fluorohydrins A1 (0.060 g, 64 % yield, dr 1.4:1) as a light yellow oil.

Data for syn- and anti-fluorohydrins A1: IR (neat): = 2989, 1749, 1446,

1376, 1091, 1042, 764 cm-1; 1H NMR (600 MHz, CDCl3): δ 7.88, 7.78,

7.63, 6.45, 6.44, 6.39, 6.37, 4.89, 4.50, 4.36, 4.34, 4.31, 4.26, 4.07, 4.04,

1.50, 1.45, 1.45, 1.34; 13C NMR (150 MHz, CDCl3): δ 209.0, 207.4,

141.7, 141.4, 131.5, 131.1, 107.7, 107.5, 101.8, 101.4, 95.0, 94.6, 74.3,

72.4, 71.0, 70.2, 67.0, 66.9, 24.0, 23.7, 23.7, 23.4; 19F NMR (470 MHz, CDCl3): δ -144.9, -154.1

HRMS (EI+) calcd for [C11H16FN2O4]+ 259.1089; found 259.1093

30

Syn-reduction of syn-and anti-fluorohydrins A1

Following General Procedure B, Me4NHB(OAc)3 (0.968 g, 3.68 mmol) and AcOH (0.442 mL, 7.36

mmol) were added to a stirred solution of A1 (0.190 g, 0.736 mmol) at -15 °C in MeCN (7.36 mL)

and the reaction mixture was stirred for 18 hrs. Purification of the crude diols 107a and 107b by

flash chromatography (pentane:ethyl acetate – 1:1) afforded a mixture of 107a and 107b (0.151g,

79% yield, d.r. (syn/anti) = 1:1.2) as a colourless oil.

Data for syn-diol, syn-fluorohydrin 107a: []D20 = +83.2 (c 0.37 in MeCN);

IR (neat): = 3001, 1442, 1375, 1039, 918, 749 cm-1;1H NMR (600 MHz,

CDCl3): δ 7.68 (d, J = 2.4 Hz, 1H), 7.64 (d, J = 1.5 Hz, 1H), 6.38 (dd, J =

2.4, 1.5 Hz, 1H), 6.18 (d, J = 51.2 Hz, 1H), 4.27 (dd, J = 22.4, 8.8 Hz, 1H),

3.95 (dd, J = 11.1, 5.6 Hz, 1H), 3.93 (dd, J = 9.5, 8.0 Hz, 1H), 3.80 (m, 1H), 3.70 (dd, J = 11.2,

11.0 Hz, 1H), 1.52 (s, 3H), 1.39(s, 3H); 13C NMR (150 MHz, CDCl3): δ 141.5, 132.0, 107.2, 99.0,

91.9 (d, J = 211.0 Hz), 72.3 (d, J = 21.8 Hz), 70.6, 67.1, 63.8, 28.7, 19.4; 19F NMR (470 MHz,

CD3CN): δ -150.3

HRMS (EI+) calcd for [C11H18FN2O4]+ 261.1245; found 261.1255

Data for syn-diol, anti-fluorohydrin 107b: []D20 = -10.8 (c 0.91 in MeCN); IR

(neat): = 3646, 3001, 1443, 1375, 1039, 918 cm-1; 1H NMR (600 MHz,

CDCl3): δ 7.70 (d, J = 0.9 Hz, 1H), 7.65 (d, J = 2.5 Hz, 1H), 6.40 (dd, J =

2.5, 0.9 Hz, 1H), 6.29 (dd, J = 48.4, 2.9 Hz, 1H), 4.41 (ddd, J = 8.0, 4.0, 2.9

Hz, 1H), 3.87 (m, 2H), 3.52 (dd, J = 11.3, 2.7 Hz, 1H), 3.17 (dd, J = 8.8, 8.8 Hz, 1H), 1.34 (s, 3H),

1.16 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 142.1, 132.0, 106.9, 98.9, 93.1 (d, J = 207.9 Hz), 76.2

(d, J = 24.7 Hz), 72.2 (d, J = 5.3 Hz), 67.3 (d, J = 4.6 Hz), 63.8, 28.5, 19.3; 19F NMR (470 MHz,

CD3CN): δ -145.9

HRMS (EI+) calcd for [C11H18FN2O4]+ 261.1245 found 261.1262

Cyclization of diols 107a and 107b

Following General Procedure C, a mixture of 107a and 107b (0.025 g, 0.096 mmol, d.r. (syn/anti)

= 1:1) and 2 M NaOH (0.48 mL, 0.962 mmol) was stirred in MeCN (0.96 mL) at 50˚C for 5 hrs.

Purification of the crude 124 by flash chromatography (pentane:ethyl acetate – 65:35) afforded

nucleoside analogue 124 (0.018 g, 76 % yield) as a white solid.

31

Data for nucleoside analogue 124: []D20 = -58.9 (c 2.0 in MeCN); IR (neat):

= 3339, 2926, 1647, 1450, 1397, 1092, 1045, 759 cm-1;1H NMR (400 MHz,

CD3CN): δ 7.70 (d, J = 2.4 Hz, 1H), 7.56 (d, J = 1.6 Hz, 1H), 6.30 (dd, J = 1.6,

2.4 Hz, 1H), 5.70 (s, 1H), 4.47 (d, J = 4.6 Hz, 1H), 4.12 (dd, J = 4.6, 9.6 Hz,

1H), 4.11 (dd, J = 4.6, 9.6 Hz, 1H), 3.91 (dd, J = 9.6, 10.3, 1H), 3.83 (dd, J =

4.6, 9.6 Hz, 1H), 3.72 (br s, 1H), 1.54 (s, 3H), 1.43 (s, 3H); 13C NMR (100 MHz, CD3CN): δ 141.7,

130.1, 106.7, 101.7, 96.1, 74.7, 74.4, 71.8, 65.9, 29.3, 20.1

HRMS (EI+) calcd for [C11H17N2O4]+ 241.1183; found 241.1197

Deprotection of nucleoside analogue 124

124 (0.021g, 0.088 mmol) was dissolved in MeOD (1.0 mL) and two drops of 1 M HCl was added

and the solution was left for 12 hrs at room temperature. Subsequently, the reaction mixture was

concentrated under reduced pressure to afford 106 as a white solid (0.018 g, 100%).

Data for nucleoside analogue 106: []D20 = +70.4 (c 0.48 in MeOH); IR (neat):

= 3325, 2944, 2832, 1449, 1022, 631 cm-1;1H NMR (600 MHz, CD3CN): δ

7.74 (d, J = 2.3 Hz, 1H), 7.58 (d, J = 1.0 Hz, 1H), 6.30 (dd, J = 2.3, 1.0 Hz, 1H),

5.70 (d, J = 4.3 Hz, 1H), 4.51 (m, 1H), 4.33 (m, 1H), 4.08 (br s, 1H), 3.74 (dd, J

= 12.3, 2.8 Hz, 1H), 3.67 (d, J = 5.7 Hz, 1H), 3.59 (dd, J = 12.3, 2.5 Hz, 1H), 3.52 (d, J = 4.3 Hz,

1H); 13C NMR (150 MHz, CD3CN): δ 141.2, 131.1, 106.4, 94.7, 87.2, 76.6, 72.3, 63.4.

HRMS (EI+) calcd for [C8H13N2O4]+ 201.0870; found 201.0870

Cyclization of diol 107b

A solution of 107b (0.043 g, 0.165 mmol) and 2 M NaOH (0.21 mL, 0.443 mmol, 2.5 equiv.) was

stirred for 4 hrs in MeCN (1.65 mL) at 50˚C. Purification of the crude 108 by flash chromatography

(pentane:ethyl acetate – 65:35) afforded nucleoside analogue 108 (0.026 g, 76 % yield) as a white

solid

Data for nucleoside analogue 108: []D20 = +72.2 (c 0.98 in MeCN); IR

(neat): = 3366, 2992, 1306, 1383, 1200, 1076, 754 cm-1,1H NMR (600

MHz, CD3CN): δ 7.76 (d, J = 2.3 Hz, 1H), 7.56 (d, J = 1.2 Hz, 1H), 6.35 (d,

J = 2.3 Hz, 1H), 5.38 (d, J = 0.9 Hz, 1H), 4.12 (dd, J = 0.9, 2.1 Hz, 1H), 3.94

(d, J = 2.1, 9.7 Hz, 1H), 3.81 (dd, J = 5.0, 10.6 Hz, 1H), 3.59 (m, 2H), 3.37 (m), 1.45 (s, 3H), 1.33

32

(s, 3H); 13C NMR (150 MHz, CDCl3): δ 142.1, 131.0, 108.2, 99.9, 71.8, 65.4, 65.2, 64.7, 59.0,

29.1, 19.9

HRMS (EI+) calcd for [C11H17N2O4]+ 241.1183; found 241.1176

Determination of relative stereochemistry for diol 107a

Diol 107a was converted into the bis-p-nitro-benzoyl ester and recrystallized in ethanol. This

allowed for the relative stereochemistry to be assigned using single X-ray crystallography (see X-

ray structures).

Determination of relative stereochemistry for nucleoside analogue 106

Analysis of 2D NOESY of nucleoside analogue 106 supported the indicated

stereochemistry

Determination of relative sterchemistry for nucleoside analogue 108

Analysis of 2D NOESY of nucleoside analogue 108 supported the

indicated stereochemistry

33

Figure S2.1. Cyclization of diols 107a and 107b. Following General Procedure C, diols 107a and

107b were cyclized separately to the same product (106). The α-anomer resulting from an SN2

cyclization from 107b epimerizes following cyclization to the thermodynamically more stable β-

anomer 17 under the reaction conditions. Moreover, taking a 2:1 mixture of products (108:106)

and following General Procedure C affords only the β-anomer 106. Note also the e.r. of 106 (95:5)

represents the average e.r. of 107a (93:7) and 107b (98:2). Such emperizations have been

reported for nucleosides.121

Determination of enantiomeric excess of diol 107a

Following General Procedures A and B, using a 1:1 mixture of L-: D-proline, a racemic sample of

diol 107a was prepared. The enantiomeric diols were separated by chiral HPLC using a Lux® 3µm

Amylose-1 column; flow rate 0.40 mL/min; eluent: hexanes-iPrOH 90:10; detection at 210 nm;

retention time = 6.66 min for (+)-107a; 8.10 min for (-)-107a (see chromatograms).The

enantiomeric ratio of the optically enriched (+)-107a diol was determined using the same method

(93:7 e.r.).

Determination of enantiomeric excess of diol 107b

Following General Procedures A and B, using a 1:1 mixture of L-: D-proline, a racemic sample of

diol 107b was prepared. The enantiomeric diols were separated by chiral HPLC using a Lux® 3µm

Amylose-1 column; flow rate 0.40 mL/min; eluent: hexanes-iPrOH 90:10; detection at 210 nm;

retention time = 6.13 min for (-)-107b; 11.72 min for (+)-107b (see chromatograms).The

34

enantiomeric ratio of the optically enriched (-)-107b diol was determined using the same method

(98:2 e.r.).

Determination of enantiomeric excess of nucleoside analogue 124

Following General Procedures A, B, and C, using a 1:1 mixture of L-: D-proline, a racemic sample

of nucleoside 124 was prepared. The enantiomeric nucleosides were separated by chiral HPLC

using a Lux® 3µm-i-Cellulose-5 column; flow rate 0.10 mL/min; eluent: hexanes-iPrOH 90:10;

detection at 254 nm; retention time = 8.91 min for (-)-124; 13.32 min for (+)-124 (see

chromatograms).The enantiomeric ratio of the optically enriched (-)-124 was determined using

the same method (95:5 e.r.).

Preparation of aldol adduct A2, diol adducts D2, and nucleoside analogues 113, 123, and ent-

113

α-fluorination/aldol

The corresponding starting aldehyde/hydrate SM3 was prepared following literature

procedures.122 Following General Procedure A, a solution of aldehyde (1.32 mmol), NFSI (0.416

g, 1.32 mmol), L-proline (0.152 g, 1.32 mmol) and NaHCO3 (0.111 g, 1.32 mmol) was stirred for

12 hours at 4°C in DMF (1.76 mL). 75 (0.105 mL, 0.880 mmol) in THF (2.64 mL) was then added

and the reaction mixture was stirred for 96 hrs at 4˚C. Purification of the crude fluorohydrin A2 by

flash chromatography (pentane:ethyl acetate – 1:1) afforded an inseparable mixture of syn- and

anti- fluorohydrins A2 (0.159 g, 60 % yield, d.r. 1.2:1) as an off-white solid.

Data for syn- and anti-fluorohydrins A2: IR (neat): = 3432, 2992, 2900,

1692, 1381, 1079 cm-1; 1H NMR (600 MHz, CDCl3): δ 8.87, 8.79, 7.74,

7.68, 6.68, 6.67, 5.80, 5.77, 4.53, 4.40, 4.34, 4.33, 4.30, 4.13, 4.11, 4.06,

3.70, 3.48, 1.52, 1.46, 1.44, 1.44; 13C NMR (150 MHz, CDCl3): δ 211.3,

208.7, 162.8, 162.6, 150.3, 149.8, 141.7, 141.1, 103.2, 102.6, 102.1, 101.9, 90.7, 90.3, 73.3, 71.4,

70.7, 70.5, 66.6, 66.5, 23.7, 23.6, 23.6, 23.3; 19F NMR (470 MHz, CDCl3): δ –162.0, –178.6

HRMS (EI+) calcd for [C12H16FN2O6]+ 303.0987; found 303.0982

35

Syn-reduction of syn-and anti-fluorohydrins A2

Following General Procedure B, Me4NHB(OAc)3 (0.174g, 0.660 mmol) and AcOH (0.076 mL,

1.32 mmol) were added to a stirred solution of A2 (0.040g, 0.130 mmol) at -15 °C in MeCN (1.32

mL) and the reaction mixture was stirred for 24 hrs. Purification of the crude diols D2a and D2b

by flash chromatography (pentane:ethyl acetate – 1:3) afforded diols D2a and D2b (0.020 g, 50

%, d.r. (syn/anti) = 1.2:1) as white solids.

Data for syn-diol, syn-fluorohydrin D2a: 1H NMR (600 MHz, MeOD): δ 7.76

(d, J = 8.0, 1H), 6.46 (dd, J = 44.4, 4.8 Hz, 1H), 5.73 (d, J = 8.0 Hz, 1H),

4.03 (ddd, J = 18.3, 7.0, 5.0 Hz, 1H), 3.82 (dd, J = 11.4, 5.1 Hz, 1H), 3.71

(m, 2H), 3.60 (dd, J = 11.4, 8.1 Hz, 1H), 1.42 (s, 3H), 1.28 (s, 3H); 13C NMR

(150 MHz, MeOD): δ 165.8, 151.7, 143.1 (d, J = 2.6 Hz), 102.9, 100.1, 94.3 (d, J = 208.4 Hz),

74.6 (d, J = 24.6 Hz), 73.7 (d, J = 4.5 Hz), 67.3, 65.3, 28.3, 19.7.

HRMS (EI+) calcd for [C12H18FN2O6]+ 305.1143; found 305.1142

Data for syn-diol, anti-fluorohydrin D2b: 1H NMR (600 MHz, MeOD): δ 7.90

(d, J = 8.1 Hz, 1H), 6.71 (dd, J = 44.2, 6.1 Hz, 1H), 5.74 (d, J = 8.1 Hz, 1H),

4.32 (m, 1H), 3.81 (m, 3H), 3.60 (m, 1H), 1.43 (s, 3H), 1.32 (s, 3H); 13C

NMR (150 MHz, MeOD): δ 165.8, 152.2, 143.0, 103.2 100.2, 92.6 (d, J =

204.4), 75.9 (d, J = 2.8 Hz), 71.5 (d, J = 29.1 Hz), 65.7, 64.5 (d, J = 2.2 Hz), 28.6, 19.4.

HRMS (EI+) calcd for [C12H18FN2O6]+ 305.1143; found 305.1123

Cyclization of diols D2a and D2b

Following General Procedure C, a solution of D2 (0.022 g, 0.072 mmol, d.r. syn/anti = 1.2:1) and

2 M NaOH (0.36 mL, 0.72 mmol) was stirred for 24 hours in MeCN (0.72 mL). Purification of the

crude 123 by flash chromatography (CH2Cl2:MeOH – 92.5:7.5) afforded nucleoside analogue 123

(0.019 g, 95% yield) as a white solid.

Data for nucleoside analogue 123: []D20 = +48.1 (c 0.90 in MeOH); IR (neat):

= 2912, 1436, 1407, 1042, 952, 697 cm-1; 1H NMR (600 MHz, (CD3)2CO): δ

7.71 (d, J = 8.0 Hz, 1H), 5.81 (s, 1H), 5.61 (d, J = 8.0 Hz, 1H), 4.45 (d, J = 4.6

Hz, 1H), 4.20 (dd, J = 9.8, 4.7 Hz, 1H), 4.12 (dd, J = 10.0, 10.0 Hz, 1H), 3.90

(dd, J = 10.0, 4.8 Hz, 1H), 3.86 (ddd, J = 10.0, 10.0, 4.7 Hz, 1H), 1.56 (s, 3H),

36

1.42 (s, 3H); 13C NMR (150 MHz, (CD3)2CO): δ 164.2, 151.8, 142.4, 103.4, 102.3, 94.5, 75.3,

74.6, 72.5, 66.1, 33.1, 22.8

HRMS (EI+) calcd for [C12H17N2O6]+ 285.1081; found 285.1085

Deprotection of nucleoside analogue 123

123 (0.019g, 0.068 mmol) was dissolved in MeOD (0.68 mL) and two drops of 1 M HCl was added

and the solution was left for 12 hrs at room temperature. Subsequently, the reaction mixture was

concentrated under reduced pressure to afford nucleoside 113 as a white solid (0.017 g, 100%).

The spectral data matched previous reports.123

Data for nucleoside 113: [α]D20 = -23 (c = 0.1, MeOH); IR (neat): ν = 3347,

2927, 2857, 1679, 1464, 1381, 1260, 1202, 1104, 1053, 806 cm–1; 1H NMR

(600 MHz, MeOD): δ 8.03 (d, J = 8.1 Hz, 1H), 5.91 (d, J = 4.7 Hz, 1H), 5.70

(d, J = 8.1 Hz, 1H), 4.18 (dd, J = 4.9, 4.9 Hz, 1H), 4.15 (dd, J = 4.9, 4.9 Hz,

1H), 4.00-4.01 (m, 1H), 3.84 (dd, J = 12.2, 2.6 Hz, 1H), 3.74 (dd, J = 12.2, 3.1

Hz, 1H); 13C NMR (150 MHz, MeOD): 166.2, 152.5, 142.7, 102.6, 90.6, 86.4, 75.7, 71.3, 62.3

HRMS (EI+) calcd for [C9H13N2O6]+ 245.0768; found 245.0770

Determination of relative stereochemistry for diol D2a and D2b

Based on J-based configurational analysis of compounds D5a/D5b,

D8a/D8b and XRD analysis of compounds 107a, D7b, D9a a clear trend

was established between the stereochemistry at the fluoromethine center

and the chemical shift of the fluoromethine proton (*). In every case, the

syn-fluorohydrin diol has a lower chemical shift than the diastereomeric anti-fluorohydrin diol.

Here, D2a has a chemical shift of 6.46 ppm while D2b has a chemical shift of 6.71 ppm for the

flouromethine proton. D2a was assigned as the syn-fluorohydrin diol and D2b the anti-fluorohydrin

diol.

37

Determination of relative stereochemistry for nucleoside 123

Analysis of 2D NOESY of nucleoside 123 revealed the indicated

stereochemistry. Furthermore, the 1H NMR and 13C NMR of nucleoside

113 matched reported data.123

Figure S2.2. Cyclization of diols D2a and D2b. Following General Procedure C, diols D2a and

D2b were cyclized separately to the same product (123). The α-anomer resulting from an SN2

cyclization from D2b epimerizes following cyclization to the thermodynamically more stable β-

anomer 123. Such emperizations have been reported for nucleosides.121

Determination of enantiomeric excess of nucleoside ent-113

Following General Procedures A, B, and C, using a 1:1 mixture of L-: D-proline, a racemic sample

of nucleoside ent-123 was prepared. The enantiomeric nucleosides were separated by chiral

HPLC using a Lux® 3µm Amylose-1 column; flow rate 0.25 mL/min; eluent: hexanes-iPrOH 85:15;

detection at 254 nm; retention time = 19.99 min for (-)-123; 23.30 min for (+)-123 (see

chromatograms).The enantiomeric ratio of the optically enriched ent-123 was determined using

the same method (95:5 e.r.).

38

Preparation of aldol adducts A3, diol adducts D3, and nucleoside analogues NA3 and 114

α-fluorination/aldol

The corresponding starting aldehyde/hydrate SM3 was prepared following literature

procedures.124 Following General Procedure A, a solution of SM3 (0.40 mmol), NFSI (0.126 g,

0.40 mmol), L-proline (0.046 g, 0.40 mmol) and NaHCO3 (0.034 g, 0.40 mmol) was stirred for 14

hours at 4°C in DMF (0.53 mL). Dioxanone 75 (0.032 mL, 0.27 mmol) in CH2Cl2 (0.67 mL) was

then added and the reaction mixture was stirred for 96 hrs at 4°C. Purification of the crude

fluorohydrin A3 by flash chromatography (pentane:ethyl acetate – 3:7) afforded fluorohydrin A3

(0.072 g, 84 % yield, d.r. 1.3:1 ) † as an off-white solid.

Data for syn- and anti-fluorohydrins A3: IR (neat): = 2995, 1696, 1451,

1376, 1087, 1049 cm-1; 1H NMR (600 MHz, CDCl3): δ 8.65, 8.60, 8.52,

7.57, 7.46, 7.41, 7.23, 6.67, 6.66, 6.64, 6.52, 4.59, 4.54, 4.52, 4.40, 4.39,

4.36, 4.35, 4.35, 4.33, 4.33, 4.32, 4.32, 4.12, 4.11, 4.07, 4.06, 3.67, 3.37,

1.97, 1.95, 1.95, 1.94, 1.52, 1.51, 1.51, 1.49, 1.47, 1.46, 1.45, 1.44; 13C NMR (150 MHz, CDCl3):

δ 211.4 208.5, 207.9, 206.4, 163.4, 163.2, 163.2, 163.1, 150.8, 150.5, 149.9, 149.9, 137.2, 136.2,

135.7, 134.6, 112.6, 112.0, 111.9, 111.0, 102.1, 102.1, 101.8, 101.7, 91.9, 90.8, 90.7, 90.1, 73.7,

73.0, 71.5, 70.8, 70.6, 70.5, 68.2, 68.0, 67.1, 66.8, 66.6, 66.5, 24.0, 23.9, 23.7, 23.7, 23.7, 23.6,

23.6, 23.4, 12.7, 12.7, 12.7, 12.7; 19F NMR (470 MHz, CDCl3): δ –159.9, –161.6, –169.6, –177.8

HRMS (EI+) calcd for [C13H18FN2O6]+ 317.1143; found 317.1142

Syn-reduction of syn-fluorohydrin and anti-fluorohydrins A3

Following General Procedure B, Me4NHB(OAc)3 (0.416 g, 1.58 mmol) and AcOH (0.181 mL, 3.16

mmol) were added to a stirred solution of A3 (0.100 g, 0.316 mmol) at -15 °C in MeCN (2.10 mL)

and the reaction mixture was stirred for 18 hrs. Purification of the crude diol D3a by flash

chromatography (pentane:ethyl acetate – 3:7) afforded diols D3a and D3b (0.063 g, 63 % yield,

d.r. (syn:anti) = 1.3:1) as a white solid.

† Mixture of 2 diastereomers and their corresponding tautomers (1:1.1:0.65:0.28). Varying the pH of the solution changes the ratio of these products. Following reduction, only 2 products (d.r. (syn/anti) = 1.3:1) are present in the crude.

39

Data for syn-diol, syn-fluorohydrin D3a: []D20 = -11.8 (c 1.0 in MeOH); IR

(neat): = 3363, 2924, 2858, 1674, 1380, 1209, 1075 cm-1; 1H NMR (600

MHz, CD3CN): δ 7.42 (d, J = 0.90 Hz, 1H), 6.36 (dd, J = 44.9, 5.1 Hz, 1H),

4.04 (ddd, J = 18.1, 6.6, 5.1 Hz, 1H), 3.79 (dd, J = 11.3, 4.5 Hz, 1H), 3.67

(m, 2H), 3.55 (m, 1H), 1.83 (d, J = 0.90 Hz, 3H), 1.39 (s, 3H), 1.24 (s, 3H); 13C NMR (150 MHz,

CD3CN): δ 164.7, 151.5, 137.9, 111.7, 99.9, 94.0 (d, J = 205.9 Hz), 74.8 (d, J = 25.1 Hz), 73.0 (d,

J = 4.3 Hz), 67.1, 65.0, 28.8, 19.9, 12.7; 19F NMR (470 MHz, CD3CN): δ –169.1

1H NMR in MeOD for syn-diol, syn-fluorohydrin D3a for relative stereochemical assignment:1H

NMR (600 MHz, MeOD): δ 7.58 (s, 1H), 6.43 (dd, J = 4.1 Hz, 1H), 4.06 (m, 1H), 3.81 (m 1H), 3.71

(m, 2H), 3.59 (m, 1H), 1.89 (s, 3H), 1.41 (s, 3H), 1.26 (s, 3H).

HRMS (EI+) calcd for [C13H20FN2O6]+ 319.1300; found 319.1329

Data for syn-diol, anti-fluorohydrin D3b: []D20 = +26.2 (c 0.45 in CH3CN);

IR (neat): = 3360, 2922, 2855, 1670, 1380, 1207, 1078 cm-1; 1H NMR

(600 MHz, MeOD): 7.72 (d, J = 1.1 Hz, 1H), 6.71 (dd, J = 44.3, 6.8 Hz, 1H),

4.32 (m, 1H), 3.82 (m, 3H), 3.60 (m, 1H), 1.90 (d, J =1.1 Hz, 3H), 1.44 (s,

3H), 1.32 (s, 3H); 13C NMR (150 MHz, MeOD): δ 166.1, 152.5, 138.3,

112.0, 100.2, 92.6 (d, J = 204.7 Hz), 75.9, 71.3 (d, J = 29.9 Hz), 65.7, 64.4 (d, J = 2.1 Hz), 28.6,

19.5, 12.4. 19F NMR (470 MHz, CD3CN): δ –160.3

HRMS (EI+) calcd for [C13H20FN2O6]+ 319.1300; found 319.1320

Cyclization of diols D3a and D3b

Following General Procedure C, a solution of D3a and D3b (0.100 g, 0.314 mmol, d.r. syn/anti =

1.5:1) and 2 M NaOH (0.236 mL, 0.472 mmol) was stirred for 10 hours in MeCN (3.14 mL).

Purification of the crude nucleoside NA3 by flash chromatography (ethyl acetate) afforded

nucleoside NA3 (0.089 g, 95 % yield) as a white solid.

40

Data for nucleoside NA3: []D20 = +39.4 (c 1.1 in MeCN); IR (neat): ν = 3405,

2993, 1687, 1267, 1138, 845, 734 cm–1; 1H NMR (600 MHz, CD3CN): δ 9.04

(br s, 1H), 7.19 (d, J = 1.1 Hz, 1H), 5.67 (s, 1H), 4.22 (dd, J = 4.8, 3.1 Hz,

1H), 4.15 (dd, J = 9.1, 3.5 Hz, 1H), 4.02 (dd, J =10.1, 9.8 Hz, 1H), 3.70 (m,

2H), 3.55 (m, 1H), 1.85 (d, J = 1.1 Hz, 3H), 1.53 (s, 3H), 1.41 (s, 3H); 13C

NMR (150 MHz, CD3CN): δ 164.9, 151.6, 137.5, 111.8, 102.3, 93.8, 74.7,

74.1, 72.1, 65.6, 29.6, 20.5, 12.7

HRMS (EI+) calcd for [C13H19N2O6]+ 299.1238; found: 299.1277

Deprotection of nucleoside analogue NA3

NA3 (0.010g, 0.034 mmol) was dissolved in MeOD (0.34 mL) and two drops of 1 M HCl was

added and the solution was left for 12 hrs at room temperature. Subsequently, the reaction mixture

was concentrated under reduced pressure to afford 114 as a white solid (8.7 mg, 100%). The

spectral data matched previous reports.125

Data for nucleoside analogue 114: []D20 = -33.0 (c = 0.1 in MeOH); IR (neat):

ν = 3346, 2928, 2867, 1688, 1466, 1378, 1262, 1200, 1104, 1050, 803 cm–1;

1H NMR (600 MHz, MeOD): δ 7.86 (d, J = 1.1 Hz, 1H), 5.91 (d, J = 4.6 Hz,

1H), 4.15-4.18 (m, 2H), 3.98-4.00 (m, 1H), 3.86 (dd, J = 12.2, 2.7 Hz, 1H),

3.75 (dd, J = 12.2, 3.0 Hz, 1H), 1.88 (d, J = 0.9 Hz, 3H); 13C NMR (150 MHz,

MeOD): δ 166.4, 152.7, 138.4, 111.5, 90.3, 86.3, 75.5, 71.3, 62.3, 12.4.

HRMS (EI+) calcd for [C10H15N2O6]+ 259.0925; found: 259.0923

Determination of relative stereochemistry for diol D3a and D3b

Based on J-based configurational analysis of compounds D5a/D5b,

D8a/D8b and XRD analysis of compounds 107a, D7b, D9a a clear trend

was established between the stereochemistry at the fluoromethine center

and the chemical shift of the fluoromethine proton (*). In every case, the

syn-fluorohydrin diol has a lower chemical shift than the diastereomeric anti-fluorohydrin

diol.Here, D3a has a chemical shift of 6.43 ppm while D3b has a chemical shift of 6.69 ppm for

the fluoromethine proton. D3a was assigned as the syn-fluorohydrin diol and D3b the anti-

fluorohydrin diol.

41

Determination of absolute stereochemistry

Comparison of []D20 values of nucleoside 114 with literature values confirmed absolute

stereochemistry.126

Figure S2.3. Cyclization of diols D3a and D3b. Following General Procedure C, diols D3a and

D3b were cyclized separately to the same product, NA3. The α-anomer resulting from an SN2

cyclization from D3b epimerizes following cyclization to the thermodynamically more stable β-

anomer NA3. Such emperizations have been reported for nucleosides.121

Determination of enantiomeric excess of nucleoside NA3

Following General Procedures A, B, and C, using a 1:1 mixture of L-: D-proline, a racemic sample

of nucleoside NA3 was prepared. The enantiomeric nucleosides were separated by chiral HPLC

using a Lux® 3µm Amylose-1 column; flow rate 0.25 mL/min; eluent: hexanes-iPrOH 85:15;

detection at 254 nm; retention time = 5.18 min for (+)-NA3; 12.61 min for (-)-NA3 (see

chromatograms).The enantiomeric ratio of the optically enriched (+)-NA3 was determined using

the same method (91:9 e.r.).

Preparation of aldol adduct A4, diol adducts D4a/D4b, and nucleoside analogue 116

α-fluorination/aldol and syn-reduction of syn-and anti-fluorohydrins

Following General Procedure A, a solution of 2-(4,6-dichloropyrimidin-5-yl)acetaldehyde (0.250

g, 1.31 mmol, 1 equiv.), NFSI (0.413 g, 1.31 mmol, 1 equiv.), L-proline (0.151 g, 1.31 mmol, 1

42

equiv.) and NaHCO3 (0.110 g, 1.31 mmol, 1 equiv.) was stirred for 1 hr at 4°C in DMF (1.19 mL).

Dioxanone 75 (0.521 mL, 4.36 mmol, 3.33 equiv.) was added and the reaction mixture was stirred

for 24 hrs at 4°C. Purification of the crude fluorohydrin A4 by flash chromatography (pentane:ethyl

acetate – 3:7) afforded fluorohydrin A4 (0.301 g, 68 % yield) as an orange oil. Following General

Procedure B, Me4NHB(OAc)3 (2.16 g, 8.21 mmol) and AcOH (0.905 mL, 16.4 mmol) were added

to a stirred solution of A4 (0.555 g, 1.64 mmol) at -15 °C in MeCN (16.4 mL) and the reaction

mixture was stirred for 24 hrs. Purification of the crude diol D4a by flash chromatography

(pentane:ethyl acetate – 4:1) afforded diol D4a (0.295 g, 53 % yield) as an off-white solid.

Data for syn-diol D4a: []D20 = +26.6 (c 5.0 in MeCN); IR (neat): = 3000,

1442, 1375, 1039, 918, cm-1; 1H NMR (600 MHz, CDCl3): δ 8.73 (s, 1H),

6.05 (dd, J = 46.0, 7.9 Hz, 1H), 4.64 (m, 1H), 3.89 (dd, J = 11.5, 5.7 Hz,

1H), 3.80 (m, 1H), 3.73 (dd, J = 9.1, 8.5 Hz, 1H), 3.61 (dd, J = 11.5, 9.5 Hz,

1H), 1.29 (s, 3H), 0.94 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 161.5, 157.4, 127.8, 98.3, 91.1 (d,

J =179.4 Hz), 75.5 (d, J = 21.3 Hz), 71.7 (d, J = 5.5 Hz), 66.6, 63.3, 28.2, 18.7; 19F NMR (470

MHz, CDCl3): δ –193.0

HRMS (EI+) calcd for [C12H16Cl2FN2O4]+ 341.0466; found 341.0425

Cyclization of diol D4a

Following General Procedure C, a solution of D4a (0.014 g, 0.044 mmol, 1 equiv.) and 2 M NaOH

(0.11 mL, 0.22 mmol, 5 equiv.) was stirred for 15 minutes in MeCN (0.30 mL). Purification of the

crude nucleoside 116 by flash chromatography (ethyl acetate:pentane – 50:50) afforded

nucleoside 116 (6.4 mg, 51% yield) as a white solid.

Data for nucleoside analogue 116: []D20 = +51.2 (c 0.34 in CH2Cl2); IR

(neat): = 3363, 2927, 1602, 1598, 1571, 1408, 968 cm-1; 1H NMR (600

MHz, CD3CN): δ 8.66 (s, 1H), 4.19 (dd, J = 10.1, 4.9 Hz, 1H), 3.91 (dd, J

= 10.2, 10.1 Hz, 1H), 3.86 (dd, J = 10.1, 4.7 Hz, 1H), 3.30 (ddd, J = 10.2,

10.1, 4.8 Hz, 1H), 1.56 (s, 3H), 1.51 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 176.6, 160.8, 158.7,

114.6, 101.7, 82.2, 79.1, 75.6, 69.0, 64.7, 28.9, 19.5.

HRMS (EI+) calcd for [C12H14ClN2O4]+ 285.0637; found 285.0644

43

Determination of the relative stereochemistry for nucleoside 116

Analysis of 2D NOESY of nucleoside 116 revealed the indicated

stereochemistry.

Determination of enantiomeric excess of diol D4a

Following General Procedures A and B, using a 1:1 mixture of L-: D-proline, a racemic sample of

diol D4a was prepared. The enantiomeric diols were separated by chiral HPLC using a Lux® 3µm

Amylose-1 column; flow rate 0.25 mL/min; eluent: hexanes-iPrOH 90:10; detection at 254 nm;

retention time = 11.81 min for (-)-D4a; 12.68 min for (+)-D4a (see chromatograms).The

enantiomeric ratio of the optically enriched (+)- D4a diol was determined using the same method

(95:5 e.r.).

Preparation of S5, hydrate SM5, aldol adduct A5, diol adducts D5a and D5b, and nucleoside

analogue 117

A solution of 1,2,3-triazole (1.00 mL, 17.2 mmol, 1.0 equiv.), bromoacetaldehyde diethyl acetal

(3.10 mL, 20.7 mmol, 1.2 equiv.) and K2CO3 (4.75 g, 34.4 mmol, 2.0 equiv.) was stirred for 24

hours at 90 °C in DMF (86 mL). The reaction mixture was then filtered and washed with 40 mL of

CH2Cl2 and concentrated under reduced pressure. Purification of crude S5 by flash

chromatography (pentane:ethyl acetate – 7:3) afforded S5 (2.90 g, 91% yield) as a colorless oil.

A solution of S5 (0.100 g, 0.54 mmol, 1.0 equiv.) was heated to 90˚C in 0.5 M HCl (0.54 mL) for

5 hours. Upon complete conversion to SM5, the reaction mixture was concentrated under reduced

pressure and the resulting product SM5 was used in the reaction without purification.

Data for S5: 1H NMR (400 MHz, CDCl3): δ 7.68 (d, J = 0.90 Hz, 1H), 7.66

(d, J = 0.90 Hz, 1H), 4.76 (t, J = 5.3 Hz, 1H), 4.48 (d, J = 5.3 Hz, 2H), 3.73

(m, 2H), 3.47 (m, 2H), 1.17 (m, 6H); 13C NMR (125 MHz, CDCl3): δ 133.8,

124.9, 101.1, 64.0, 52.9, 15.3.

HRMS (EI+) calcd for [C8H16N3O2]+ 186.1237; found 186.1233

α-fluorination/aldol

44

Following General Procedure A, a solution of S5 (0.54 mmol), Selectfluor (0.192 g, 0.54 mmol),

L-proline (0.063 g, 0.54 mmol) and NaHCO3 (0.045 g, 0.54 mmol) was stirred for 12 hours at 4°C

in DMF (0.72 mL). Dioxanone 75 (0.043 mL, 0.36 mmol) in MeCN (0.43 mL) was then added and

the reaction mixture was stirred for 72 hrs at room temperature. Purification of the crude

fluorohydrin A5 by flash chromatography (Et2O) afforded fluorohydrin A5 (0.061 g, 65 % yield,

d.r. 1:1) as a light yellow oil.

Data for syn- and anti-fluorohydrins A5: IR (neat): = 3138, 2990, 1749,

1455, 1379, 1224, 1070, 799 cm-1; 1H NMR (600 MHz, CDCl3): δ 8.24

(1H), 8.12 (1H), 7.79 (1H), 7.77 (1H), 6.89 (1H), 6.86 (1H), 4.74 (1H), 4.49

(1H), 4.33 (2H), 4.26 (1H), 4.14 (1H), 4.06 (1H), 3.89 (1H), 1.55 (3H), 1.48

(3H), 1.44 (3H), 1.31 (3H); 13C NMR (150 MHz, CDCl3): δ 210.8, 209.4, 134.5, 134.5, 124.4,

124.4, 102.1, 102.0, 94.5, 93.5, 72.1, 71.3, 70.8, 70.1, 66.5, 66.5, 23.8, 23.5, 23.4, 23.4; 19F NMR

(470 MHz, CDCl3): δ -154.6, -163.8.

HRMS (EI+) calcd for [C10H15FN3O4]+ 260.1041; found 260.1044

Syn-reduction of syn-and anti-fluorohydrins A5

Following General Procedure B, Me4NHB(OAc)3 (0.391 g, 1.49 mmol) and AcOH (0.170 mL, 2.98

mmol) were added to a stirred solution of A5 (0.077 g, 0.30 mmol) at -15 °C in MeCN (3.00 mL)

and the reaction mixture was stirred for 24 hrs. Purification of the crude diols D5a and D5b by

flash chromatography (CH2Cl2:MeOH – 96:4) afforded diols D5a and D5b (0.072 g, 94 % yield,

d.r. (syn/anti) = 1.2:1) as white solids.

Data for syn-diol, syn-fluorohydrin D5a: []D20 = +52.4 (c 0.51 in MeCN);

IR (neat): = 3432, 2997, 2253, 1444, 1375, 1071, 1039 cm-1;1H NMR

(600 MHz, CD3CN): δ 8.17 (d, J = 1.0 Hz, 1H), 7.78 (d, J = 1.0 Hz, 1H),

6.69 (dd, J = 48.1, 4.7 Hz, 1H), 4.36 (ddd, J = 18.4, 5.0, 5.0 Hz, 1H), 3.79

(dd, J = 11.4, 5.0 Hz, 1H), 3.63 (m, 2H), 3.54 (m, 2H), 1.39 (s, 3H), 1.31 (s, 3H); 13C NMR (150

MHz, CD3CN): δ 135.2, 126.2, 100.0, 95.9 (d, J = 206.7 Hz), 74.7 (d, J = 22.7 Hz), 73.1 (d, J =

4.4 Hz), 66.0, 65.2, 28.8, 19.9; 19F NMR (470 MHz, CDCl3): δ -156.0

HRMS (EI+) calcd for [C10H17FN3O4]+ 262.1198; found 262.1209

45

Data for syn-diol, anti-fluorohydrin D5b: []D20 = +40.0 (c 0.37 in MeCN);

IR (neat): = 3000, 1442, 1375, 1039, 918, 740 cm-1;1H NMR (600 MHz,

CD3CN): δ 8.22 (d, J = 1.0 Hz, 1H), 7.79 (d, J = 1.0 Hz, 1H), 6.78 (dd, J =

46.4, 6.0 Hz, 1H), 4.53 (ddd, J = 10.4, 6.0, 4.7 Hz, 1H), 4.09 (br s, 1H),

3.83 (m, 2H), 3.57 (m, 2H), 3.41 (br s, 1H), 1.35 (s, 3H), 1.34 (s, 3H); 13C NMR (150 MHz, CD3CN):

δ 135.3, 125.7, 100.0, 96.5 (d, J = 204.3 Hz), 74.2 (d, J = 2.3 Hz), 72.9 (d, J = 27.2 Hz), 65.4,

65.3 (d, J = 2.0 Hz), 28.9, 19.8; 19F NMR (470 MHz, CDCl3): δ -151.2

HRMS (EI+) calcd for [C10H17FN3O4]+ 262.1198; found 262.1206

Cyclization of diol D5a

Following General Procedure C, a solution of D5a and D5b (0.025 g, 0.096 mmol, 1.0 equiv, d.r.

(syn/anti) = 1.2:1) and Sc(OTf)3 (0.118 g, 0.239 mmol, 2.5 equiv.) was stirred in dry MeCN (1.00

mL). After 12 hours, pyridine (0.50 mL) and acetic anhydride (0.25 mL) were added and the

reaction mixture was left to stir for 3 hrs. Purification of the crude 117 by flash chromatography

(pentane:ethyl acetate – 1:3) afforded nucleoside analogue 117 (0.015 g, 47 % yield) as a clear

colorless oil.

Data for nucleoside analogue 117: []D20 = +1.3 (c 0.60 in CH2Cl2); IR (neat):

= 2926, 1747, 1373, 1227, 1064 cm-1; 1H NMR (600 MHz, CDCl3): δ 7.76 (s,

1H), 7.26 (s, 1H), 6.19 (d, J = 3.7 Hz. 1H), 5.85 (dd, J = 5.0, 3.8 Hz, 1H), 5.63

(dd, J = 5.3, 5.0 Hz, 1H), 4.49 (ddd, J = 5.3, 4.3, 3.0 Hz, 1H), 4.41 (dd, J =

12.4, 3.0 Hz, 1H), 4.22 (dd, J = 12.4, 4.3 Hz, 1H), 2.13 (s, 3H), 2.13 (s, 3H), 2.06 (s, 3H); 13C NMR

(150 MHz, CDCl3): δ 170.5, 169.6, 169.5, 134.3, 122.9, 90.0, 81.0, 74.5, 70.8, 62.9, 20.8, 20.6,

20.6;

HRMS (EI+) calcd for [C13H18N3O7]+ = 328.3005; found 328.3000

Determination of relative stereochemistry for diol D5a

The relative stereochemistry of diol D5a was determined by J-based

configurational analysis. See J-based configurational analysis

section for details.

46

Determination of relative stereochemistry for diol D5b

The relative stereochemistry of diol D5b was determined by J-based

configurational analysis. See J-based configurational analysis section

for details.

Determination of relative stereochemistry for nucleoside 117

Analysis of 2D NOESY of nucleoside 117a supported the indicated

stereochemistry.

Figure S2.5. Cyclization of diol 5a. Following General Procedure D, diol D5a was cyclized

separately to 117 while diol D5b did not cyclize. This suggests the product generated from the

diol mixture comes only from the D5a diol via an SN2 cyclization.

Determination of enantiomeric excess of diol D5a

Following General Procedures A and B, using a 1:1 mixture of L-: D- proline, a racemic sample

of diol D5a was prepared. The enantiomeric diols were separated by chiral HPLC using a Lux®

3µm i-Cellulose-5 column; flow rate 0.20 mL/min; eluent: hexanes-iPrOH 90:10; detection at 210

47

nm; retention time = 4.69 min for (+)-D5a; 5.80 min for (-)-D5a (see chromatograms).The

enantiomeric ratio of the optically enriched (+)-D5a diol was determined using the same method

(93:7 e.r.).

Determination of enantiomeric excess of diol D5b

Following General Procedures A and B, using a 1:1 mixture of L-: D- proline, a racemic sample

of diol D5b was prepared. The enantiomeric diols were separated by chiral HPLC using a Lux®

3µm i-Cellulose-5 column; flow rate 0.20 mL/min; eluent: hexanes-iPrOH 90:10; detection at 210

nm; retention time = 3.94 min for (-)-D5b; 4.95 min for (+)-D5b (see chromatograms).The

enantiomeric ratio of the optically enriched (+)-D5b diol was determined using the same method

(96:4 e.r.).

Determination of enantiomeric excess of diols ent-D5a

Following General Procedures A and B, using a 1:1 mixture of L-: D- proline, a racemic sample

of diol ent-D5a was prepared. The enantiomeric diols were separated by chiral HPLC using a

Lux® 3µm i-Cellulose-5 column; flow rate 0.20 mL/min; eluent: hexanes-iPrOH 90:10; detection

at 210 nm; retention time = 4.69 min for (+)-D5a; 5.80 min for (-)-D5a (see chromatograms).The

enantiomeric ratio of the optically enriched ent-D5a diol was determined using the same method

(95:5 e.r.).

Determination of enantiomeric excess of diols ent-D5b

Following General Procedures A and B, using a 1:1 mixture of L-: D- proline, a racemic sample

of diol ent-D5b was prepared. The enantiomeric diols were separated by chiral HPLC using a

Lux® 3µm i-Cellulose-5 column; flow rate 0.20 mL/min; eluent: hexanes-iPrOH 90:10; detection

at 210 nm; retention time = 3.94 min for (-)-D5b; 4.95 min for (+)-D5b (see chromatograms).The

enantiomeric ratio of the optically enriched ent-D5b diol was determined using the same method

(95:5 e.r.).

48

Preparation of S6, hydrate SM6, aldol adduct A6, diol adducts D6a and D6b, and nucleoside

analogue 118

A solution of trifluoromethyluracil (1.00 g, 5.52 mmol, 1.0 equiv.), bromoacetaldehyde diethyl

acetal (1.66 mL, 11.1 mmol, 2.0 equiv.) and K2CO3 (1.53 g, 11.1 mmol, 2.0 equiv.) was stirred for

24 hours at 90 °C in DMF (27.6 mL). The reaction mixture was then filtered and washed with 40

mL of CH2Cl2 and concentrated under reduced pressure. Purification of crude S6 by flash

chromatography (pentane:ethyl acetate – 7:3) afforded S6 (0.605 g, 37% yield) as a colorless oil.

A solution of S7 (0.100 g, 0.340 mmol, 1.0 equiv.) was heated to 90˚C in 0.5 M HCl (0.34 mL) for

5 hours. Upon complete conversion to aldehyde/hydrate SM6, the reaction mixture was

concentrated under reduced pressure and the resulting aldehyde/hydrate SM6 was used in the

reaction without purification.

Data for S6: IR (neat): = 3430, 2988, 2800, 1109, 1025cm-1; 1H NMR

(600 MHz, CDCl3): δ 8.56 (br s, 1H), 7.82 (s, 1H), 4.61 (t, J = 5.0 Hz),

3.88 (d, J =5.0 Hz), 3.78 (m, 2H), 3.54 (m, 2H), 1.21 (m, 6H); 13C NMR

(150 MHz, CDCl3): δ 158.6, 150.0, 147.0 (q, J = 5.8 Hz), 121.9 (q, J =

270.5 Hz), 104.7 (q, J =33.5 Hz), 100.0, 64.6, 51.0, 15.3

HRMS (EI+) calcd for [C11H16F3N2O4]+ 297.1057; found 297.1056

α-fluorination/aldol

Following General Procedure A, a solution of SM6 (0.340 mmol), NFSI (0.107 g, 0.340 mmol), L-

proline (0.039 g, 0.340 mmol) and NaHCO3 (0.029 g, 0.340 mmol) was stirred for 12 hours at 4°C

in DMF (0.45 mL). Dioxanone 75 (0.027 mL, 0.227 mmol) in CH2Cl2 (0.57 mL) was then added

and the reaction mixture was stirred for 96 hrs at 4°C. Purification of the crude fluorohydrin A6 by

flash chromatography (pentane:ethyl acetate – 65:35 ) afforded fluorohydrin A6 (0.050 g, 60 %

yield) as a light yellow oil.

Data for syn- and anti- fluorohydrins A6: IR (neat): = 2991, 1699, 1450,

1087, 1049 cm-1; 1H NMR (600 MHz, CD3CN): δ 9.53, 9.52, 8.15, 8.11,

6.58, 6.46, 4.62, 4.56, 4.55, 4.43, 4.31, 4.29, 3.98, 3.98, 1.43, 1.40, 1.40,

1.38; 13C NMR (150 MHz, CD3CN): δ 208.4, ,207.9, 159.6, 159.5, 150.6,

150.1, 144.0, 144.0, 123.6, 123.5, 106.6, 106.0, 102.4, 102.3, 95.3, 92.4,

49

76.3, 76.1, 69.9, 69.1, 67.9, 67.8, 24.5, 24.4, 24.2, 23.9; 19F NMR (470 MHz, CD3CN): δ –64.1, –

64.1, –161.4, –169.1

HRMS (EI+) calcd for [C13H14F4N2NaO6]+ 393.0680; found 393.0682

Syn-reduction of syn-and anti-fluorohydrins A6

Following General Procedure B, Me4NHB(OAc)3 (0.355 g, 1.35 mmol) and AcOH (0.155 mL, 2.79

mmol) were added to a stirred solution of A6 (0.100 g, 0.27 mmol, 1 equiv.) at -15 °C in MeCN

(1.80 mL) and the reaction mixture was stirred for 24 hrs. Purification of the crude diols D6a and

D6b by flash chromatography (pentane:ethyl acetate – 4:1) afforded diols D6a (0.040 g, 40%

yield) and D6b (0.019 g, 19% yield) as white solids.

Data for syn-diol, syn-fluorohydrin D6a: []D20 = +18.4 (c 0.50 in CH2Cl2);

IR (neat): = 3426, 2996, 1702, 1463, 1379, 1070 cm-1; 1H NMR (600

MHz, CD3CN): δ 9.42 (br s, 1H), 8.10 (s, 1H), 6.33 (dd, J = 45.1, 5.6 Hz,

1H), 4.28 (dd, J = 14.8, 5.6 Hz, 1H), 3.79 (dd, J = 11.1 5.5 Hz, 1H), 3.70

(m, 2H), 3.60 (dd, J = 9.5, 2.7 Hz, 1H), 3.55 (dd, J = 10.4, 9.5 Hz, 1H), 1.35

(s, 3H), 1.30 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 159.5, 150.1, 144.2 (q, J = 6.3 Hz), 123.5

(q, J = 266.4 Hz), 106.3 (q, J = 32.9 Hz), 99.9, 96.3 (d, J = 210.9 Hz), 73.9 (d, J = 3.8 Hz), 70.5

(d, J = 24.5 Hz), 65.4, 63.0, 29.1, 19.8; 19F NMR (470 MHz, CD3CN): δ –64.1, –168.0.

HRMS (EI+) calcd for [C13H17F4N2NaO6]+ 395.0837; found 395.0836

Data for syn-diol, anti-fluorohydrin D6b: []D20 = -37.2 (c 1.1 in CH2Cl2); IR

(neat): = 3424, 1703, 1466, 1379, 1281, 1138, 1042 cm-1; 1H NMR (600

MHz, CD3CN): δ 8.26 (s, 1H), 6.67 (dd, J = 43.0, 4.9 Hz, 1H), 4.34 (m, 1H),

3.78 (dd, J = 11.2, 5.1 Hz, 1H), 3.72 (m, 2H), 3.54 (dd, J = 11.2, 8.3 Hz,

1H), 1.39 (s, 3H), 1.26 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 159.5,

150.6, 144.2, 123.6 (q, J = 272.9 Hz), 105.9 (q, J = 32.5 Hz), 100.0, 92.5 (d, J = 206.1 Hz), 74.2

(d, J = 4.4 Hz), 72.3 (d, J = 27.7 Hz), 65.4, 64.8, 29.0, 19.7;19F NMR (470 MHz, CD3CN): δ –64.1,

–161.7.

HRMS (EI+) calcd for [[C13H17F4N2NaO6]+ 395.0837; found 395.0838

Cyclization of diols D6a and D6b

50

Following General Procedure D, a solution of D6a and D6b (0.045 g, 0.121 mmol, d.r. (syn/anti)

= 1:2) and Sc(OTf)3 (8.9 mg, 0.018 mmol, 0.15 equiv.) was stirred for 24 hours in dry MeCN (1.21

mL). Purification of the crude 118 by flash chromatography (pentane:ethyl acetate – 3:7) afforded

nucleoside 118 (0.013 g, 45 % yield (from anti-fluorohydrin D6b)) as a colorless oil.

Data for nucleoside analogue 118: []D20 = -16.7 (c 0.49 in CH2Cl2); IR

(neat): = 3405, 2924, 2854, 1702, 1465, 1276 cm-1; 1H NMR (600

MHz, CD3CN): δ 9.33 (br s, 1H), 7.97 (q, J =1.2 Hz, 1H), 6.18 (d, J =

4.1 Hz, 1H), 4.86 (m, 2H), 4.42 (dd, J = 3.6, 2.4 Hz, 1H), 3.67 (m, 2H),

3.21 (dd, J =5.6, 4.4 Hz, 1H), 1.36 (s, 3H), 1.30 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 159.4,

149.9, 143.6 (q, J =6.0 Hz), 123.6 (q, J =269.7 Hz), 113.6, 103.4 (q, J =33.2 Hz), 87.7, 84.7, 82.8,

80.2, 64.0, 25.7, 24.0; 19F NMR (470 MHz, CD3CN): δ –63.8

HRMS (EI+) calcd for [C13H16F3N2O6]+ 353.0955; found 353.0971

Determination of relative stereochemistry for nucleoside 118

Analysis of 2D NOESY of nucleoside 118 supported the indicated

stereochemistry.

Determination of relative stereochemistry for diols D6a and D6b

Based on J-based configurational analysis of compounds D5a/D5b,

D8a/D8b and XRD analysis of compounds 107a, D7b, D9a a clear trend

was established between the stereochemistry at the fluoromethine center

and the chemical shift of the fluoromethine proton (*). In every case, the

syn-fluorohydrin diol has a lower chemical shift than the diastereomeric anti-fluorohydrin diol.

Here, D6a has a chemical shift of 6.33 ppm while D6b has a chemical shift of 6.67 ppm for the

fluoromethine proton. D6a was assigned as the syn-fluorohydrin diol and D6b the anti-fluorohydrin

diol.

51

Figure S2.6. Cyclization of diol D6b. Following General Procedure D, diol D6b was cyclized

separately to 118 while diol D6a did not cyclize. This suggests the product from generated from

the diol mixture comes only from the D6b diol via an SN2 cyclization.

Determination of enantiomeric excess of nucleoside 118

Following General Procedures A, B, and C using a 1:1 mixture of L-:D- proline, a racemic sample

of nucleoside 118 was prepared. The enantiomeric nucleosides were separated by chiral HPLC

using a a Lux® 3µm Amylose-1 column; flow rate 0.25 mL/min; eluent: hexanes-iPrOH 90:10;

detection at 254 nm; retention time = 9.10 min for (+)-118; 13.14 min for (-)-118 (see

chromatograms).The enantiomeric ratio of the optically enriched (-)-118 nucleoside was

determined using the same method (94:6 e.r.).

Preparation of S7, hydrate SM7, aldol adduct A7, diol adducts D7a and D7b, and nucleoside

analogue 119

α-fluorination/aldol and syn-reduction of syn-and anti-fluorohydrins A7

Following General Procedure A, a solution of phthalimidoacetaldehyde (0.100 g, 0.529 mmol, 1.5

equiv.), NFSI (0.167 g, 0.529 mmol, 1.5 equiv.), L-proline (0.061 g, 0.529 mmol, 1.5 equiv.) and

2,6-lutidine (0.061 mL, 0.529 mmol, 1.5 equiv.) was stirred for 12 hours at 4°C in DMF (0.71 mL).

Dioxanone 75 (0.042 mL, 0.353 mmol, 1 equiv.) in CH2Cl2 (0.88 mL) was then added and the

reaction mixture was stirred for 48 hrs at room temperature. Purification of the crude fluorohydrin

52

A7 by flash chromatography (pentane:ethyl acetate – 1:1) afforded fluorohydrin A7 (0.069 g, 58

% yield, d.r. 2.2:1) as a yellow oil. Following General Procedure B, Me4NHB(OAc)3 (0.776 g, 2.95

mmol) and AcOH (0.337 mL, 5.90 mmol) were added to a stirred solution of A7 (0.200 g, 0.59

mmol) at -15 °C in MeCN (5.90 mL) and the reaction mixture was stirred for 24 hrs. Purification

of the crude diols D7a and D7b by flash chromatography (pentane:ethyl acetate – 3:7) afforded

diols D7a and D7b (0.094 g, 47 % yield, d.r. (syn/anti) = 1.5:1) as white solids.

Data for syn-diol, syn-fluorohydrin D7a: []D20 = -11.4 (c 2.0 in CH2Cl2); IR

(neat): = 3442, 2992, 1785, 1724, 1377, 1074, 721 cm-1; 1H NMR (600

MHz, CD3CN): δ 7.93 (m, 2H), 7.89 (m, 2H), 6.07 (dd, J = 48.6, 7.9 Hz,

1H), 4.76 (m, 1H), 4.43 (m, 1H), 3.73 (m, 2H), 3.58 (dd, J = 8.8, 6.0 Hz,

1H), 3.47 (m, 1H), 3.41 (m, 1H), 1.21 (s, 3H), 0.92 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 167.8

(d, J = 1.5 Hz), 136.0, 132.5, 124.6, 99.1, 91.1 (d, J = 202.0 Hz), 73.3 (d, J = 6.6 Hz), 71.8 (d, J

= 25.3 Hz), 65.1, 64.5, 28.1, 19.3; 19F NMR (470 MHz, CD3CN): δ –157.8

HRMS (EI+) calcd for [C16H19FNO6]+ 340.1191; found 340.1190

Data for syn-diol, anti-fluorohydrin D7b: []D20 = -1.0 (c 2.3 in CH2Cl2); IR

(neat): = 3442, 2992, 1784, 1725, 1375, 1070, 723 cm-1; 1H NMR (600

MHz, CD3CN): δ 7.94 (m, 2H), 7.89 (m, 2H), 6.34 (dd, J = 46.0, 9.2 Hz,

1H), 4.80 (m, 1H), 3.92 (ddd, J = 9.5, 1.8, 1.4 Hz, 1H), 3.84 (m, 2H), 3.73

(m, 1H), 3.60 (dd, J = 10.8, 8.7 Hz, 1H), 3.30 (m, 1H), 1.47 (s, 3H), 1.35 (s, 3H); 13C NMR (150

MHz, CD3CN): δ 168.1 (d, J = 1.6 Hz), 136.0, 132.3, 124.6, 99.4, 89.5 (d, J = 202.4 Hz), 75.1,

68.7 (d, J = 31.7 Hz), 65.3, 63.1 (d, J = 3.1 Hz), 28.6, 19.5; 19F NMR (470 MHz, CDCl3): δ –159.8

HRMS (EI+) calcd for [C16H19FNO6]+ 340.1191; found 340.1172

Cyclization of diols D7a and D7b

Following General Procedure C, a solution of D7a and D7b (0.033 g, 0.097 mmol, 1.0 equiv., d.r.

(syn/anti) = 2:1) and Sc(OTf)3 (0.120 g, 0.243 mmol, 2.5 equiv.) was stirred for 6 hours in MeCN

(0.65 mL). 0.25 mL of pyridine and 0.25 mL of acetic anhydride were added and the reaction

mixture was allowed to stir for a further 1.5 hrs. Purification of the crude 119 by flash

chromatography (pentane:ethyl acetate – 7:3) afforded nucleoside analogue 119 (0.027 g, 69 %

yield) as a colourless oil.

53

Data for nucleoside analogue 119: []D20 = -9.0 (c 1.96 in CH2Cl2); IR (neat):

= 2922, 1781, 1744, 1721, 1374, 1222, 1047, 720 cm-1; 1H NMR (500 MHz,

CDCl3): δ 7.88 (m, 2H), 7.77 (m, 2H), 5.94 (dd, J = 6.0, 4.1 Hz, 1H), 5.87 (d,

J = 4.1 Hz, 1H), 5.65 (dd, J = 6.1, 6.0 Hz, 1H), 4.49 (dd, J = 12.1, 3.4 Hz,

1H), 4.29 (ddd, J = 9.5, 5.9, 3.4 Hz, 1H), 4.21 (dd, J = 12.1, 5.9, 1H), 2.12

(s, 3H), 2.11 (s, 3H), 2.09 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 170.9, 169.8, 169.7, 166.9,

134.8, 131.7, 124.0, 82.8, 79.2, 72.0, 70.6, 63.2, 20.9, 20.7, 20.7

HRMS (EI+) calcd for [C19H19NO9 + NH4]+ 423.1398; found 423.1378

Determination of relative stereochemistry for diol D7b

Recyrstallization in ethanol allowed for the relative stereochemistry to

be assigned using single X-ray crystallography (see X-ray structures).

Determination of the relative stereochemistry for nucleoside 119

Analysis of 2D NOESY of nucleoside 119 supported the indicated

stereochemistry.

54

Figure S2.7. Cyclization of diols D7a and D7b. Following General Procedure D, diol D7a was

cyclized separately to 119 while diol D7b cyclized to a mixture of 119 and its corresponding α-

anomer. The diol mixture comes from both diols via an SN2 cyclization and some epimerization of

the α-anomer. Such emperizations have been reported for nucleosides.121

Determination of enantiomeric excess of diol ent-D7a

Following General Procedures A and B, using a 1:1 mixture of L-:D- proline, a racemic sample of

diol D7a was prepared. The enantiomeric nucleosides were separated by chiral HPLC using a a

Lux® 3µm Amylose-1 column; flow rate 0.25 mL/min; eluent: hexanes-iPrOH 90:10; detection at

254 nm; retention time = 9.10 min for (-)-D7a; 13.14 min for (+)-D7a (see chromatograms).The

enantiomeric ratio of the optically enriched (+)-D7a diol was determined using the same method

(95:5 e.r.).

Preparation of SM8, aldol adduct A8, diol adducts D8a/D8b, and nucleoside analogues 121/122

A solution of deazadenine (0.500 g, 1.79 mmol, 1.0 equiv.), bromoacetaldehyde diethyl acetal

(0.323 mL, 2.15 mmol, 1.25 equiv.) and K2CO3 (0.491 g, 3.58 mmol, 2.0 equiv.) was stirred for 24

hours at 90 °C in DMF (9.00 mL). The reaction mixture was then filtered and washed with 10 mL

of CH2Cl2 and concentrated under reduced pressure. Purification of crude S8 by flash

chromatography (pentane:ethyl acetate – 7:3) afforded S8 (0.375 g, 53 % yield) as a white solid.

A solution of S8 (17.0 g, 43.0 mmol, 1.0 equiv.) was heated to 70˚C in 2.0 M HCl (129 mL, 258

mmol, 6.0 equiv.) for 1 hours. The reaction mixture was then cooled to room temperature and

allowed to stir for a further 2 hrs. The reaction mixture was stored overnight at -20 °C and the

55

formed precipitate was then filtered and washed with 1:1 dioxane:water (10 mL x 2). The filtrate

SM8 was dried under reduced pressure and the resulting product SM8 (7.88 g, 54 % yield) was

used in the reaction without purification.

Data for S8: 1H NMR (600 MHz, CDCl3): δ 8.61 (s, 1H), 7.50 (s, 1H), 4.67

(t, J = 5.1 Hz, 1H), 4.35 (d, J = 5.1 Hz, 2H), 3.73 (m, 2H), 3.48 (m, 2H),

1.16 (m, 6H); 13C NMR (150 MHz, CDCl3): δ 152.7, 151.1, 150.8, 136.3,

116.9, 100.7, 63.9, 50.6, 47.7, 15.3

HRMS (EI+) calcd for [C12H16ClIN3O2]+ 395.9970; found 395.9973

α-fluorination/aldol

Following General Procedure A, a solution of SM8 (2.00 g, 5.86 mmol, 1 equiv.), NFSI (1.85 g,

5.86 mmol, 1.0 equiv.), L-proline (0.674 g, 5.86 mmol, 1.0 equiv.) and NaHCO3 (0.984 g, 11.71

mmol, 2.0 equiv.) was stirred for 18 hours at 20°C in DMF (10 mL). Dioxanone 75 (0.762 g, 5.86

mmol, 1.0 equiv.) was then added and the reaction mixture was stirred for 36 hrs at room

temperature. Purification of the crude A8 by flash chromatography (25-75% ethyl acetate in

pentane) afforded syn- and anti-fluorohydrins A8 (1.58 g, 57 % yield, d.r. 1.2:1) as a light yellow

solid.

Data for syn-and anti-fluorohydrins A8: IR (neat): = 3145, 2988, 1747,

1575, 1539, 1444, 1205, 1084, 949, 734 cm-1; 1H NMR (600 MHz, dmso-

d6): δ 8.76, 8.74, 8.39, 8.24, 6.89, 6.85, 6.37, 6.12, 4.98, 4.76, 4.61, 4.32,

4.30, 4.05, 3.95, 3.93, 1.40, 1.34, 1.33, 1.31; 13C NMR (150 MHz, dmso-

d6): δ 206.3, 206.1, 151.6, 151.5, 151.3, 151.2, 151.0, 134.5, 134.1, 116.8,

116.7, 100.4, 100.1, 91.4, 09.4, 76.1, 74.7, 68.7, 68.0, 66.6, 66.4, 55.3, 55.1, 24.6, 24.1, 22.9,

22.7; 19F NMR (470 MHz, dmso-d6): δ –146.0, –152.6

HRMS (EI+) calcd for [C14H15ClFIN3O4]+ 469.9774; found 469.9779

syn-reduction of syn-and anti-fluorohydrins A8

Following General Procedure B, NaHB(OAc)3 (0.316 g, 1.49 mmol, 5 equiv.) and AcOH (0.171

mL, 2.98 mmol, 10 equiv.) were added to a stirred solution of A8 (0.140 g, 0.298 mmol, 1 equiv.)

at 0 °C in MeCN (2.8 mL). The reaction mixture was then stirred at room temperature for 2hrs.

56

Purification of the crude diols D8a and D8b by flash chromatography (pentane:ethyl acetate –

70:30) afforded diols D8a and D8b (0.141 g, 77 % yield, d.r. (syn/anti) = 1.5:1) as a white solid.

Data for syn-diol, syn-fluorohydrin D8a: []D20 = -19.6 (c 2.0 in CH2Cl2); IR

(neat): = 3335, 2989, 2890, 1577, 1540, 1445, 1206, 1076, 951 cm-1;1H

NMR (600 MHz, dmso-d6): δ 8.73 (s, 1H), 8.27 (s, 1H), 6.73 (dd, J = 49.4,

7.0 Hz, 1H), 6.08 (br s, 1H), 4.84 (d, J = 4.1 Hz, 1H), 4.59 (m, 1H), 3.59

(m, 1H), 3.44 (m, 1H), 3.42 (m, 1H), 3.33 (m, 1H), 1.16 (s, 3H), 1.13 (s,

3H); 13C NMR (150 MHz, dmso-d6): δ 151.4, 151.2, 151.1, 134.5, 116.7, 97.8, 92.0 (d, J = 203.3),

73.2 (d, J =5.7 Hz), 71.0 (d, J = 24.2 Hz), 63.8, 62.5, 54.9, 28.0, 19.1; 19F NMR (470 MHz, dmso-

d6): δ –147.1

HRMS (EI+) calcd for [C14H15ClFIN3O4]+ 471.9931; found 471.9940

Data for syn-diol, anti-fluorohydrin D8b: []D20 = -11.6 (c 0.38 in CH2Cl2);

IR (neat): = 3363, 2931, 2890, 1579, 1540, 1444, 1212, 1067, 951 cm-

1; 1H NMR (600 MHz, dmso-d6): δ 8.73 (s, 1H), 8.34 (s, 1H), 6.97 (dd, J

= 46.9, 7.9 Hz, 1H), 5.74 (d, J = 5.7 Hz, 1H), 5.22 (d, J = 5.7 Hz, 1H), 4.61

(m, 1H), 3.84 (m, 1H), 3.72 (m, 1H), 3.52 (dd, J = 11.7, 8.7 Hz, 1H), 1.35 (s, 3H), 1.20 (s, 3H); 13C

NMR (150 MHz, dmso-d6): δ 151.5, 151.4, 151.2, 134.1, 116.6, 97.9, 90.9 (d, J = 203.5 Hz), 74.3,

69.1 (d, J =30.3 Hz), 64.2, 61.4, 54.8, 28.4, 19.0; 19F NMR (470 MHz, , dmso-d6): δ –146.3

HRMS (EI+) calcd for [C14H15ClFIN3O4]+ 471.9931; found 471.9940

Cyclization of diol D8a

Following General Procedure D, a solution of D9a (0.050 g, 0.106 mmol, 1.0 equiv.) and InCl3

(2.3 mg, 0.011 mmol, 0.10 equiv.) was stirred for 16 hrs in dry MeCN (1.00 mL). Purification of

the crude nucleoside 121 by flash chromatography (20-80% ethyl acetate in pentanes) afforded

nucleoside 121 (0.029 g, 61 % yield) as a white solid.

Data for nucleoside analogue 121: []D20 = -23.9 (c 0.46 in CH2Cl2); IR

(neat): = 3339, 3113, 2935, 1576, 1539, 1445, 1207, 1108, 951 cm-1;

1H NMR (600 MHz, dmso-d6): δ 8.69 (s, 1H), 8.23 (s, 1H), 6.34 (d, J = 3.1

Hz, 1H), 5.19 (dd, J = 6.3, 3.1 Hz, 1H), 5.14 (br s, 1H), 4.94 (dd, J = 6.3,

2.9 Hz, 1H), 4.20 (m, 1H), 3.56 (m, 2H), 1.54 (s, 3H), 1.31 (s, 3H); 13C

57

NMR (150 MHz, dmso-d6): δ 151.2, 150.8, 150.4, 133.9, 116.7, 113.2, 89.4, 86.3, 83.9, 80.9,

61.4, 53.7, 27.0, 25.1.

HRMS (EI+) calcd for [C14H16ClIN3O4]+ 451.9869; found 451.9875

Cyclization of diol D8b

Following General Procedure D, a solution of D8b (0.050 g, 0.106 mmol, 1.0 equiv.) and InCl3

(2.3 mg, 0.011 mmol, 0.10 equiv.) was stirred for 16 hrs in dry MeCN (1.00 mL). Purification of

the crude nucleoside 122 by flash chromatography (20-80% ethyl acetate in pentanes) afforded

nucleoside 122 (0.034 g, 70 % yield) as a white solid.

Data for nucleoside analogue 122: []D20 = -47.8 (c 0.51 in CHCl3); 1H

NMR (600 MHz, dmso-d6): δ 8.66 (s, 1H), 7.81 (s, 1H), 6.73 (d, J = 4.3

Hz, 1H), 5.22 (br s, 1H), 4.91 (m, 2H), 4.41 (dd, J = 3.6, 3.1 Hz, 1H),

3.62 (m, 2H), 1.32 (s, 3H), 1.23 (s, 3H); 13C NMR (150 MHz, dmso-d6):

δ 151.0, 150.7, 149.8, 134.6, 116.3, 112.3, 85.6, 83.1, 81.9, 79.4, 62.5,

51.9, 25.2, 23.9.

HRMS (EI+) calcd for [C14H16ClIN3O4]+ 451.9869; found 451.9888

Determination of relative stereochemistry for diol D8a

The relative stereochemistry of diol D8a was determined by J-based

configurational analysis. See J-based configurational analysis section

for details.

Determination of relative stereochemistry for diol D8b

The relative stereochemistry of diol D8b was determined by J-based

configurational analysis. See J-based configurational analysis section

for details

58

Determination of relative stereochemistry for nucleoside 121

Analysis of 2D NOESY of nucleoside 121 supported the indicated

stereochemistry.

Determination of relative stereochemistry for nucleoside 122

Analysis of 2D NOESY of nucleoside 122 supported the indicated

stereochemistry.

59

Figure S2.8. Cylization of diols D8a and D8b. Following General Procedure D, diol D8a was

cyclized separately to 121 while diol D8b cyclized to 122. This supports an SN2 cyclization without

subsequent epimerization.

Determination of enantiomeric excess of diol D8a

Following General Procedures A and B, using a 1:1 mixture of L-:D- proline, a racemic sample of

diol D8a was prepared. The enantiomeric diols were separated by chiral HPLC using an IB

column; eluent: 90:10 (MeCN:water) to 10:90 (MeCN:water); detection at 230 nm; retention time

= 12.23 min for (+)-D8a; 13.39 min for (-)-D8a (see chromatograms).The enantiomeric ratio of the

optically enriched ent-D8a diol was determined using the same method (90:10 e.r.).

Determination of enantiomeric excess of diol D8b

Following General Procedures A and B, using a 1:1 mixture of L-:D- proline, a racemic sample of

diol D8b was prepared. The enantiomeric diols were separated by chiral HPLC using a IG column;

eluent: 90:10 (MeCN:water) to 10:90 (MeCN:water); detection at 230 nm; retention time = 12.35

min for (-)-D8b; 12.56 min for (+)-D8b (see chromatograms).The enantiomeric ratio of the optically

enriched ent-D8b diol was determined using the same method (93:7 e.r.).

60

Preparation of SM9, aldehyde S9, aldol adduct A9, diol adducts D9a/D9b, and nucleoside

analogues SI9/NA9

A solution of iodouracil (2.50 g, 10.5 mmol, 1.0 equiv.), bromoacetaldehyde diethyl acetal (1.91

mL, 12.7 mmol, 1.2 equiv.) and K2CO3 (2.92 g, 21.1 mmol, 2.0 equiv.) was stirred for 16 hours at

90 °C in DMF (70 mL). The reaction mixture was filtered, and the filtrate was diluted with 200 mL

of ethyl acetate. The organic layer was washed 3 times with water, separated, dried over MgSO4,

filtered, and concentrated under reduced pressure. Purification of crude S9 by flash

chromatography (pentane:ethyl acetate – 75:25) afforded S9 (0.301 g, 8% yield) as a white solid.

A solution of S9 (0.142 g, 0.401 mmol, 1.0 equiv.) was heated to 90˚C in 0.5 M HCl (0.40 mL) for

5 hours. Upon complete conversion to aldehyde/hydrate SM9, the reaction mixture was

concentrated under reduced pressure and the resulting aldehyde/hydrate SM9 was used in the

reaction without purification.

Data for S9: IR (neat): = 2975, 1686, 1439, 1121, 1059, 1021 cm-1; 1H

NMR (600 MHz, CDCl3): δ 8.56 (br s, 1H), 7.82 (s, 1H), 4.61 (t, J = 5.0

Hz), 3.88 (d, J =5.0 Hz), 3.78 (m, 2H), 3.54 (m, 2H), 1.21 (m, 6H); 13C

NMR (150 MHz, CDCl3): δ 158.6, 150.0, 147.0 (q, J = 5.8 Hz), 121.9 (q,

J = 270.5 Hz), 104.7 (q, J =33.5 Hz), 100.0, 64.6, 51.0, 15.3

HRMS (EI+) calcd for [C10H16IN2O4]+ 355.0149; found 355.0145

α-fluorination/aldol and syn-reduction of syn- and anti-fluorohydrins A9

Following General Procedure A, a solution of S9 (0.401 mmol), NFSI (0.126 g, 0.401 mmol), L-

proline (0.046 g, 0.401 mmol) and NaHCO3 (0.034 g, 0.401 mmol) was stirred for 12 hours at 4°C

in DMF (0.53 mL). Dioxanone 75 (0.053 mL, 0.270 mmol) in CH2Cl2 (0.67 mL) was then added

and the reaction mixture was stirred for 72 hrs at 4°C. Purification of the crude fluorohydrin A9 by

flash chromatography (pentane-ethyl acetate – 1:1) afforded fluorohydrin A9. as a yellow oil.

Following General Procedure B, Me4NHB(OAc)3 (0.066 g, 0.251 mmol) and AcOH (0.0.30 mL,

0.502 mmol) were added to a stirred solution of A9 (0.021 g, 0.049 mmol) at -15 °C in MeCN

(0.49 mL) and the reaction mixture was stirred for 24 hrs. The crude diols D9a and D9b were

used directly for the cyclization owing to challenges with stability and purification.

61

Cyclization of diols D9a and D9b

Following General Procedure C, a solution of D9a and D9b (16.2 mg, 0.038 mmol, 1 equiv.) and

2 M NaOH (0.038 mL, 0.38 mmol, 10 equiv.) was stirred for 18 hours in MeCN (1.51 mL).

Purification of the crude nucleoside SI9 by flash chromatography (CH2Cl2:MeOH – 90:10) afforded

nucleoside SI9 as a white solid. SI9 (10.3 mg, 0.025 mmol) was dissolved in MeOD (0.25 mL)

and two drops of 1 M HCl was added and the solution was left for 12 hrs at room temperature.

Subsequently, the reaction mixture was concentrated under reduced pressure to afford NA9 as a

white solid. The spectral data matched previous reports.122

Data for nucleoside analogue SI9: 1H NMR (600 MHz, MeOD): δ 7.99 (s,

1H), 5.58 (s, 1H), 4.35 (d, J = 4.5 Hz, 1H), ,4.19 (dd, J =10.0, 4.6 Hz, 1H),

4.08 (dd, J =10.0, 9.7 Hz, 1H), 3.83 (m, 2H), 1.57 (s, 3H), 1.45 (s, 3H); 13C

NMR (150 MHz, MeOD): δ 162.8, 151.7, 147.2, 102.5, 95.7, 74.5, 73.8, 72.5,

68.9, 65.8, 29.3, 20.0

Data for nucleoside NA9: [α]D20 = -41 (c = 0.1, MeOH); IR (neat): ν = 3353,

2929, 1679, 1447, 1262, 1101, 1023, 799 cm–1; 1H NMR (600 MHz, MeOD):

δ 8.61 (s, 1H), 5.86 (d, J = 3.6 Hz, 1H), 4.16-4.17 (m, 2H), 4.02-4.03 (m, 1H),

3.89 (dd, J = 12.2, 2.6 Hz, 1H), 3.76 (dd, J = 12.1, 2.5 Hz, 1H); 13C NMR (150

MHz, MeOD): δ 162.8, 152.2, 147.3, 90.9, 86.3, 76.1, 70.9, 68.3, 61.7.

HRMS (EI+) calcd for [C9H12IN2O6]+ 370.9735; found: 370.9739

Determination of relative stereochemistry for diols D9a

Recyrstallization in ethanol allowed for the relative stereochemistry to be

assigned using single X-ray crystallography (see X-ray structures).

62

Preparation of nucleoside analogue 125

To a solution of nucleoside analogue 125 (0.100 g, 0.352 mmol, 1 equiv.) in THF (3.52 mL) was

added 1, 1’- thiocarbonyldiimidazole (0.125 g, 0.704 mmol, 2 equiv.). The reaction mixture was

stirred for 24 hrs. Subsequently, CH2Cl2 (10 mL) was added to the reaction mixture and washed

with water 3 times. The organic layer was dried over MgSO4, filtered, and concentrated under

reduced pressure to yield crude S125. Purification of crude S125 by flash chromatography (ethyl

acetate) afforded S125 (0.129 g, 96%).

Data for nucleoside analogue S125: []D20 = +25.8 (c 1.2 in MeCN); IR

(neat): = 3000, 1701, 1443, 1375, 1039, 918, 749 cm-1; 1H NMR (600

MHz, CD3CN): δ 9.34 (br s, 1H), 8.38 (s, 1H), 7.73 (s, 1H), 7.43 (d, J = 7.4

Hz, 1H), 7.04 (s, 1H), 6.08 (d, J = 5.2 Hz, 1H), 5.88 (d, J = 5.2 Hz, 1H),

5.69 (d, J = 7.4 Hz, 1H), 4.22 (m, 2H), 4.06 (dd, J = 10.4 Hz, 1H), 3.83

(ddd, J = 10.4, 10.3, 5.0 Hz, 1H), 1.55 (s, 3H), 1.39 (s, 3H); 13C NMR (150

MHz, CD3CN): δ 184.8, 164.1, 151.3, 143.3, 138.4, 132.3, 119.8, 103.8,

102.9, 92.4, 82.7, 73.5, 72.8, 65.5, 29.5, 20.4.

HRMS (EI+) calcd for [C16H19N4O6S]+ 395.1020; found 395.1010

To a solution of nucleoside S125 (0.020 g, 0.045 mmol, 1 equiv.) in dry toluene (3.0 mL) under

nitrogen was added tributyltin hydride (0.024 mL, 0.090 mmol, 2 equiv.) and AIBN (1.8 mgs, 0.011

mmol, 0.25 equiv.). The resulting reaction mixture was purged with nitrogen for 30 minutes.

Subsequently, the reaction mixture was stirred for 16 hrs at 90 °C. The reaction mixture was

diluted with CH2Cl2 (10 mL). The organic layer was washed with water, separated, dried over

MgSO4, filtered, and concentrated under reduced pressure to yield crude 125. Purification of

crude 125 by flash chromatography (ethyl acetate) afforded nucleoside 125 (6.8 mg, 57%) as a

colorless oil.

Data for nucleoside analogue 125: []D20 = +7.8 (c 0.32 in MeOH); 1H NMR

(600 MHz, CD3CN): δ 8.94 (br s, 1H), 7.50 (d, J = 8.2 Hz, 1H), 6.14 (dd, J =

8.7, 2.1 Hz, 1H), 5.63 (d, J = 8.2 Hz, 1H), 4.10 (dd, J = 10.0, 4.6 Hz, 1H),

4.00 (dd, J = 10.3, 10.0 Hz, 1H), 3.94 (m, 1H), 3.35 (ddd, J = 10.3, 10.0, 4.6

Hz, 1H), 2.27 (m, 1H), 2.17 (m, 1H), 1.52 (s, 3H), 1.37 (s, 3H); 13C NMR

(150 MHz, CD3CN): δ 164.1, 151.6, 142.6, 103.3, 102.2, 84.4, 76.3, 72.7,

65.6, 36.4, 29.8, 20.5.

63

HRMS (EI+) calcd for [C12H17N2O5]+ 269.1132; found 269.1111

Preparation of nucleoside analogue 126

To a solution of nucleoside analogue 106 (0.020 g, 0.083 mmol, 1.0 equiv.) in dry CH2Cl2 (0.83

mL) was added TEMPO (1.3 mg, 0.008 mmol, 0.10 equiv.) and (diacetoxyiodo)benzene (0.067

g, 0.208 mmol, 2.5 equiv.). Following 18 hrs or complete consumption of 106 as monitored by 1H

NMR spectroscopy, the reaction mixture was cooled to room temperature and diluted with CH2Cl2.

The organic layer was then washed with saturated sodium bicarbonate solution, dried over

MgSO4, filtered, and concentrated under reduced pressure to yield crude 126. Purification of the

crude nucleoside 126 by flash chromatography (pentane:ethyl acetate – 1:1) afforded nucleoside

126 (0.019 g, 92 % yield) as a white solid.

Data for nucleoside analogue 126: []D20 = -115.6 (c 1.0 in MeCN); IR (neat):

= 3001, 2989, 1694, 1374, 1305, 1088 cm-1; 1H NMR (600 MHz, CD3CN):

δ 7.80 (d, J = 2.4 Hz, 1H), 7.62 (d, J = 1.5 Hz, 1H), 6.36 (dd, J = 2.4, 1.5 Hz,

1H), 5.78 (s, 1H), 4.69 (d, J = 11.1 Hz, 1H), 4.22 (d, J = 10.0, 5.0 Hz, 1H),

4.13 (dd, J = 10.6, 10.6 1H), 3.87 (ddd, J = 11.1, 10.0, 5.0 Hz, 1H), 1.56 (s,

3H), 1.45 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 201.5, 143.3, 133.2, 108.1, 103.5, 86.5, 76.8,

69.4, 66.1, 29.3, 20.0.

HRMS (EI+) calcd for [C11H14N2O4+H3O]+ 257.1132; found 257.1130

Determination of relative stereochemistry for nucleoside 126

Analysis of 2D NOESY of nucleoside 126 supported the indicated

stereochemistry

Preparation of nucleoside analogue 127

To a stirred solution of nucleoside 126 (0.020 g, 0.084 mmol, 1.0 equiv.) in dry THF (0.84 mL)

was added methylmagnesium bromide (0.126 mL, 0.378 mmol, 4.5 equiv.) at -78°C and the

resulting reaction mixture was stirred for 3.5 hrs. The reaction mixture was quenched at -78°C

with 0.50 mL of an ammonium chloride:methanol solution (1:1 – saturated ammonium chloride

64

solution:methanol) and warmed to room temperature. The resulting mixture was diluted with 3 mL

of CH2Cl2 and washed twice with water. The organic layer was dried over MgSO4, filtered, and

concentrated under reduced pressure to give crude 127. Purification of crude 127 by flash

chromatography (ethyl acetate:pentane – 30:70) afforded nucleoside analogue 127 (19.1 mg,

90%) as a white solid.

Data for nucleoside analogue 127: []D20 = -117.7 (c 0.57 in CH2Cl2); IR (neat):

= 3425, 2992, 1398, 1384, 1088, 851cm-1; 1H NMR (600 MHz, CD3CN): δ

7.73 (d, J = 2.3 Hz, 1H), 7.60 (d, J =1.3 Hz, 1H), 6.33 (dd, J = 2.3, 1.3 Hz, 1H),

5.60 (s, 1H), 4.13 (d, J = 10.0 Hz, 1H), 4.06 (dd, J = 9.8, 4.7 Hz, 1H), 3.93 (dd,

J = 10.1, 9.8 Hz, 1H), 3.54 (s, 1H), 3.48 (ddd, J =10.1, 10.0, 4.7 Hz, 1H), 1.53

(s, 3H), 1.41 (s, 3H), 1.36 (s, 3H); 13C NMR (150 MHz, CD3CN): 142.1, 132.5, 107.2, 102.2, 95.1,

80.5, 78.4, 71.6, 66.2, 29.7, 20.6, 20.4.

HRMS (EI+) calcd for [C12H19N2O4]+ 255.1339; found 255.1333

Determination of relative stereochemistry for nucleoside 127

Analysis of 2D NOESY of nucleoside 127 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 128

To a solution of nucleoside analogue 123 (0.025g, 0.088 mmol, 1 equiv.) in CH2Cl2 (0.45 mL) at

0˚C was added dropwise diethylaminosulfur trifluoride (0.058 mL, 0.44 mmol, 5 equiv.). The

reaction mixture was warmed to room temperature and allowed to stir for 1 hr. Subsequently,

ethyl acetate (10 mL) was added and the organic layer was washed 3 times with saturated sodium

bicarbonate solution. The organic layer was then separated, dried, filtered, and concentrated

under reduced pressure. Purification of the crude S128 by flash chromatography (CH2Cl2:MeOH

95:5) afforded 2’,2’-anhydrouridine S128 (0.012 g, 51 % yield) as a white solid. 2’,2’-

anhydrouridine S128 (0.011 g, 0.039 mmol, 1 equiv.) was dissolved in a 1 M HCl:MeOH solution

(0.20mL:0.20mL). The reaction mixture was heated to 50˚C for 24hrs and then concentrated

65

under reduced pressure to yield nucleoside 128 (9.5 mg, 100% yield). The spectral data matched

previous reports.126

Data for nucleoside analogue 128: 1H NMR (600 MHz, dmso-d6): δ 11.28 (d,

J = 2.1 Hz, 1H), 7.62 (d, J = 8.1 Hz, 1H) 5.98 (d, J = 4.5 Hz, 1H), 5.56 (dd, J

= 8.1, 2.1 Hz, 1H), 3.99 (dd, J = 4.4, 3.2 Hz, 1H), 3.89 (dd, J = 3.6, 3.2 Hz,

1H), 3.73 (ddd, J = 5.6, 4.6, 3.6 Hz, 1H), 3.60 (dd, J = 11.6, 4.6 Hz, 1H), 3.56

(dd, J = 11.6, 5.6 Hz, 1H); 13C NMR (150 MHz, dmso-d6): δ 163.4, 150.5,

142.3, 100.0, 85.1, 84.7, 75.5, 75.1, 60.7

HRMS (EI+) calcd for [C9H13N2O6]+ 245.0768; found 245.0777

Preparation of nucleoside analogue 130

To a solution of nucleoside 123 (0.285 g, 1.0 mmol, 1.0 equiv.) in dry dioxane (20 mL) was added

(diacetoxyiodo)benzene (0.805 g, 2.5 mmol, 2.5 equiv.) and TEMPO (0.031 g, 0.20 mmol, 0.2

equiv.). The reaction mixture was stirred for 24 hrs at room temperature until complete

consumption of starting material was detected by TLC analysis. The reaction mixture was

concentrated to 2 mL and purified with flash chromatography (CH2Cl2:Et2O – 75:25) to afford

ketone 129 (0.265 g, 0.94 mmol, 94 % yield) as a white solid. Ketone 129 (0.053 g, 0.19 mmol,

1.0 equiv.) was dissolved in methanol (0.94 mL) and 3 drops of AcCl were added. The solution

was stirred for 12 hrs at room temperature until complete consumption of starting material was

detected by TLC analysis. The reaction mixture was concentrated under reduced pressure to a

white solid S130. The spectral data matched previous reports.127 The crude product was

subsequently dissolved in tetrahydrofuran (4.0 mL) and the resulting solution was cooled to -78°C

and methyl magnesium bromide (3.0 M in THF, 0.38 mL, 1.13 mmol, 6.0 equiv.) was added. The

resulting brown suspension was stirred at -78 °C for 3 hrs. The reaction mixture was quenched at

-78 °C with a solution of methanol:TFA (10:1) and then concentrated under reduced pressure.

The crude product 130 was purified by flash chromatography (CH2Cl2:MeOH – 85:15) to yield

nucleoside analogue (0.024 g, 49 % yield) as a white solid. The spectral data matched previous

reports.128

66

Data for nucleoside analogue 130: 1H NMR (600 MHz, MeOD): δ 7.86 (d, J

= 8.1 Hz, 1H), 5.96 (s, 1H), 5.64 (d, J = 8.1 Hz, 1H), 3.85 (m, 4H), 1.29 (s,

3H).

HRMS (EI+) calcd for [C10H15N2O6]+ 259.0925; found 259.0915

Examples of large-scale preparation of αFAR products

The following scaleup work was carried out by a CRO (WuXi AppTec). No additional optimization

of the reaction conditions was done for large scale synthesis and in most cases only select

chromatographed fractions were included in the final mass.

Large-scale preparation of A2

Three reactions were ran in parallel. To a large reactor was charged DMF (2.1 L) and

uracil (300.0 g, 2.68 mol, 1.0 equiv.) at 15-25°C. Then, the reactor was individually charged with

DBU (807 mL, 5.35 mol, 2.0 equiv.) and 2-bromo-1,1-diethoxy-ethane (483 mL, 3.21 mol, 1.2

equiv.). The reaction mixture was heated to 90°C-100oC for 16 hrs. The reaction mixture cooled

to 25oC and the three batches were combined and concentrated to dryness to give a residue. To

the residue was water (2.5 L) and the pH of the resulting mixture was adjusted with 1M HCl to 6-

7 and extracted with EtOAc (2.0 L x 8). The combined organic layer was dried with Na2SO4, filtered

and the filtrate was concentrated to dryness under reduced pressure to give a residue. The crude

residue was triturated with MBTE (3 L) at 20oC for 60 minutes. The crude residue was purified by

silica gel chromatography (petroleum ether: EtOAc: CH2Cl2 = 10: 2: 1). The alkylated uracil

product (738 g, 3.23 mol, 40.3% yield) was isolated as a white solid.

To a large reactor was charged HCl (1 M, 2.89 L, 1.0 equiv.) and the alkylated thymine

product (660 g, 2.89 mol, 1.0 equiv.) at 15-25°C. The reaction mixture was heated to 90~100°C

and stirred for 3 hours. Following complete consumption of starting material, the reaction mixture

was cooled to 0oC and stirred for 30 minutes. The resulting suspension was filtered, dried, and

67

the crude product was used in the next step without further purification. The aldehyde/hydrate

(425 g, 2.76 mol, 95.4%) was obtained as an off-white solid.

To a large reactor was charged with DMF (2800 mL) and aldehyde (400 g, 2.60 mol, 1.0

eq) and the resulting mixture was cooled to 4°C. Then, the reactor was individually charged with

NFSI (818 g, 2.60 mol, 1.0 equiv.), NaHCO3 (218 g, 2.60 mol, 1.0 equiv.) and L-proline (299 g,

2.60 mol, 1.0 equiv.). The reaction mixture was stirred at 4°C for 18 hrs. HPLC (ET24077-13-

P1A) showed starting material (RT = 0.34) was consumed completely. To the reaction mixture

was added dropwise a solution of dioxanone (226 g, 1.74 mol, 0.67 eq) in CH2Cl2 (1.3 L) at 4°C.

The reaction mixture was stirred at 15~25°C for 18 hrs. HPLC (ET24077-13-P1A) showed starting

material (RT = 1.72 min) showed the α-fluorohydrate was completely consumed. 14.0 L H2O was

added into the reaction mixture and extracted with EtOAc (3.0 L x 8). The organic phase was

dried with Na2SO4, then filtered, and the filtrate was concentrated to dryness under reduced

pressure to give a residue. The residue was purified by flash silica gel chromatography (Eluent of

0~50% ethyl acetate/petroleum ether gradient) to afford A2 as a yellow oil (380 g, 72% yield, d.r.

1:1).

Large-scale preparation of A3

To a large reactor was charged DMF (1.7 L) and thymine (85.0 g, 0.674 mol, 1.0 equiv.) at 15-

25°C. Then, the reactor was individually charged with DBU (203 mL, 1.35 mol, 2.0 equiv.) and 2-

bromo-1,1-diethoxy-ethane (122 mL, 0.809 mol, 1.2 equiv.). The reaction mixture was heated to

90°C for 14.5 hrs. The reaction mixture was concentrated to dryness to give a residue. To the

residue was added EtOAc (1.7 L) and water (1.7 L), the organic layer was separated, the aqueous

layer was extracted with EtOAc (1.7 L x 2). The combined organic layer was washed with brine

(500 mL), dried with Na2SO4, filtered and the filtrate was concentrated to dryness under reduced

pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®;

5000 g SepaFlash® Silica Flash Column, Eluent of 30~60% Ethyl acetate/Petroleum ether

68

gradient @ 800mL/min). The alkylated thymine product (80.0 g, 301 mmol, 22.37% yield, 91.3%

purity) was obtained as an off white solid.

To a large reactor was charged HCl (1 M, 330 mL, 1.0 equiv.) and the alkylated thymine product

(80.0 g, 0.330 mol, 1.0 equiv.) at 15-25°C. The reaction mixture was heated to 90~100°C and

stirred for 15 hours. HPLC (ET17680-15-P1A) indicated starting material (RT = 2.77) was

consumed completely. The mixture was concentrated to dryness and the crude product was used

into the next step without further purification. aldehyde and hydrate (63.0 g mixture) was obtained

as an off white solid.

To a large reactor was charged with DMF (190 mL) and aldehyde (0.131 mol, 1.0 eq) and the

resulting mixture was cooled to 4°C. Then, the reactor was individually charged with NFSI (41.3

g, 0.131 mol, 1.0 equiv.), NaHCO3 (11.0 g, 0.131 mol, 1.0 equiv.) and L-proline (15.1 g, 0.131mol,

1.0 equiv.). The reaction mixture was stirred at 4°C for 18.5 hrs. HPLC (ET17918-3-P1A) showed

starting material (RT = 1.99) was consumed completely. 1. To the reaction mixture was added

dropwise a solution of dioxanone (11.4 g, 0.088 mol, 0.67 eq) in CH2Cl2 (200 mL) at 4°C. The

reaction mixture was stirred at 15~25°C for 20.5 hrs. 570 mL CH2Cl2 was added into the mixture,

and the organic phase was washed with water (190 mL x 3). The organic phase was dried with

Na2SO4, then filtered, and the filtrate was concentrated to dryness under reduced pressure to give

a residue. The residue was purified by flash silica gel chromatography (ISCO®; 330 g

SepaFlash® Silica Flash Column, Eluent of 0~100% ethyl acetate/petroleum ether gradient @

200 mL/min) to afford A3 as a yellow oil (21.0 g, 76% yield, d.r. 3:1 (syn:anti)).

Large-scale preparation of A5

This reaction was executed without further optimization. Crude A5 was purified by column

chromatography to afford 16.5 g of A5 (impure fractions were discarded).

69

Large-scale preparation of A6

The reaction was executed without further optimization. The reaction was stopped after only 16

hrs. Crude A6 was purified by prep-HPLC to afford 36.6 g of A6 (impure fractions were discarded).

Large-scale preparation of A8

The reaction was executed without further optimization. Crude A8 was purified by prep-HPLC to

afford 47 g of A8 (impure fractions were discarded).

70

J-based configurational analysis (JBCA)

The fluorine stereoconfigurations of the following compounds were assigned using NMR J-based

configuration analysis, and then the assignments were verified using density functional theory

calculations. The other stereocenters were known based on synthesis.

NMR Spectroscopy

NMR samples were prepared by dissolving several mg in 0.75 mL of DMSO-d6. These solutions

were then transferred to 5-mm NMR tubes. Proton chemical shifts were referenced to residual

DMSO-d5 at 2.50 ppm, and carbon chemical shifts were referenced to DMSO-d6 at 39.52 ppm.

NMR spectra were acquired on either a 600 MHz Bruker AVANCE III HD spectrometer equipped

with a 5-mm triple resonance (HCN) helium cryoprobe or a 500 MHz Bruker AVANCE III HD

spectrometer equipped with a 5-mm inverse Prodigy probe. Data were processed using Mnova,

version 12.0.4. 1H, 13C, COSY, HSQC, and HMBC data were acquired for all compounds to

assign the proton and carbon chemical shifts. Either NOESY or ROESY spectra were acquired

using a 200 ms mixing time to aid in the stereochemical determinations.

DFT calculations

Density functional theory (DFT) calculations of NMR parameters, chemical shifts (, ppm) and

coupling constants (J, Hz), were performed in order to verify the peak assignments and relative

stereoconfiguration. Initially, an ensemble of conformers was generated using a mixed

torsional/low-mode sampling search with the OPLS3e force field, as implemented in

Macromodel.129 The set of conformers less than 5 kcal/mol were then further subjected to DFT

geometry optimizations and frequency determinations (to verify potential energy minima) using

the B3LYP/6-31G(d) model chemistry in Gaussian ’16.130 Isotropic magnetic shielding values, ,

were then calculated starting from the optimized geometries using either WP04/cc-pVDZ or

B97X-D/6-31G(d,p) gauge-including atomic orbital (GIAO) methods for proton and carbon,

71

respectively, with implicit solvent corrections from the polarized continuum model (PCM). Linear

scaling factors [ = intercept – / -slope] were applied to convert the values to chemical shifts,

, in ppm. The scaling factors were previously determined from a large test set of known

structures, curated by Rablen et.al.131 and Lodewyk et.al.132 (1H: intercept = 31.8465, slope = -

0.9976; 13C: intercept = 198.1218, slope = -0.9816). Coupling constants were calculated using

the B3LYP/6-31G(d) model chemistry. Gibbs free energies were calculated using M06-2X/6-

31+G(d,p) with SMD solvation model, and both chemical shifts and coupling constants were

weighted according to the Boltzmann energy distribution.

72

Analysis of syn-diol, syn-fluorohydrin D8a and syn-diol, anti-fluorohydrin D8b

Figure S2.10. DFT calculated conformation of D8b

Figure S2.11. DFT calculated conformation of D8a

73

Table S2.5. Experimental and DFT-calculated coupling constants for compounds D8a and D8b

Table S2.6. Analysis of experimental and DFT-calculated 1H NMR chemical shifts for

compounds D8a and D8b

Analysis of Coupling Constants

Expt Expt DFT DFT

Coupling Atoms Sample 1 Sample 2 R-isomer S-isomer

1J_FC (24,12) 203.4 204.7 -274.5 -285.3

2J_FC (24,13) 29.9 24.5 31.7 23.9

3J_FC (24,14) < 1 5.8 -0.1 4.4

3J_HC (27,2) 3.0 3.7 6.8 6.2

3J_HC (27,8) 5.2 5.2 4.6 4.8

2J_HC (27,13) 2.3 2.4 -3.1 -2.9

3J_HC (27,14) 1.7 1.4 1.8 0.4

2J_FH (27,24) 46.8 49.5 48.6 52.4

3J_HF (28,24) < 1 14.9 1.8 12.6

3J_HH (28,27) 8.0 7.0 9.6 7.8

4J_HF (29,24) 2.0 < 1 3.5 -1.6

3J_HH (29,28) 2.0 3.7 2.5 3.1

Analysis of 1H Chemical Shifts DFT DFT

Expt Expt S R Expt. Diff DFT Diff

atom C# ID Sample 1 Sample 2 ppm ppm ppm ppm

H 4 25 8.75 8.74 8.88 8.90 0.01 -0.02

H 8 26 8.37 8.28 7.51 7.42 0.09 0.09

H 12 27 6.97 6.73 6.49 6.70 0.24 -0.21

H 13 28 4.61 4.60 5.48 5.63 0.01 -0.15

H 14 29 3.85 3.41 3.38 4.19 0.44 -0.81

H 16 31 3.78 3.45 3.98 4.22 0.33 -0.24

H 17 32 3.54 3.33 3.33 3.74 0.21 -0.41

H 17 33 3.73 3.59 3.82 3.79 0.14 0.03

H 21 34,36,35 1.38 1.14 1.20 1.35 0.24 -0.15

H 22 37,39,38 1.23 1.17 1.38 1.49 0.06 -0.11

74

Table S2.7. Analysis of experimental and DFT-calculated 13C NMR chemical shifts for

compounds D8a and D8b

Analysis of 13C Chemical Shifts DFT DFT

Expt Expt S R Expt. Diff DFT Diff

atom C# ID Sample 1 Sample 2 ppm ppm ppm ppm

C 1 1 117.1 116.7 120.5 121.1 0.36 -0.60

C 2 2 152.0 151.1 153.0 152.5 0.90 0.54

C 4 4 151.7 151.2 154.3 153.7 0.45 0.52

C 8 8 134.6 134.4 135.5 135.8 0.18 -0.26

C 12 12 91.3 92.0 99.8 100.6 -0.71 -0.85

C 13 13 69.5 70.9 76.2 74.5 -1.36 1.76

C 14 14 74.7 73.2 77.2 76.2 1.48 0.99

C 16 16 61.8 62.4 64.6 64.8 -0.56 -0.21

C 17 17 64.7 63.9 66.2 66.8 0.80 -0.51

C 19 19 98.4 97.8 102.9 102.8 0.53 0.06

C 21 21 19.5 19.0 21.0 20.8 0.43 0.13

C 22 22 28.9 28.0 30.8 31.3 0.90 -0.50

75

Figure S2.12. Summary of J-based configurational analysis for compounds D8a and D8b

76

Analysis of syn-diol, syn-fluorohydrin D5a and syn-diol, anti-fluorohydrin D5b

Table S2.8. Experimental and DFT-calculated coupling constants for compounds D5a and D5b

Table S2.9. Analysis of experimental and DFT-calculated 1H and 13C NMR chemical shifts for

compounds D5a and D5b

Coupling Constant Analysis

Isomer: 1 2 R S

Coupling Expt Expt DFT DFT3J H10,F 15.4 3.7 0.0 11.4

3J H10,H5 2.7 1.7 -0.2 2.73J H10,H12 7.5 8.6 9.2 8.5

2J H12,F 49.8 47.3 50.0 55.72J F,C10 23.4 28.3 29.4 22.63J F,C5 6.2 < 1 0.1 5.04J F,C6 < 1 2.4 0.3 -0.4

Chemical Shift Analysis

Isomer: 1 2 R S

chemical shifts Expt Expt DFT DFT D-Expt D-DFT

H1' 3.33 3.54 3.75 3.37 -0.21 0.382

H1'' 3.60 3.74 3.83 3.71 -0.14 0.116

H5 3.23 3.83 4.23 3.50 -0.6 0.737

H6 3.43 3.80 4.13 3.83 -0.37 0.303

H8 1.24 1.30 1.36 1.34 -0.06 0.019

H9 1.22 1.41 1.48 1.29 -0.19 0.193

H10 4.48 4.53 5.17 4.96 -0.05 0.207

H12 6.63 6.71 6.75 6.72 -0.08 0.03

H17 7.87 7.86 8.00 7.95 0.01 0.048

H18 8.45 8.56 8.02 7.98 -0.11 0.045

C1 64.0 64.2 67.2 66.6 -0.23 0.51

C3 97.9 98.0 103.1 103.0 -0.14 0.17

C5 73.1 74.0 76.7 76.4 -0.9 0.23

C6 61.4 61.2 65.0 64.7 0.19 0.35

C8 28.2 28.5 31.1 30.9 -0.29 0.14

C9 18.9 19.1 21.1 20.9 -0.11 0.22

C10 71.2 69.4 76.2 76.6 1.7 -0.33

C12 95.0 95.0 99.4 99.4 0 -0.02

C17 133.7 133.8 134.8 134.8 -0.11 -0.06

C18 125.7 124.7 130.7 130.2 1.04 0.53

77

Figure S2.13. Summary of J-based configurational analysis for compounds D5a and D5b

78

Single crystal X-ray diffraction

Suitable crystals were suspended in paratone oil, mounted on a MiTeGen Micro Mount, and

transferred to the X-ray diffractometer, which was set to 150 K using an Oxford Cryosystems

Cryostream. Data was collected at 150 K on a Bruker Smart instrument equipped with an APEX

II CCD area detector fixed at a distance of 5.0 cm from the crystal and a Cu Kα fine focus sealed

tube (λ = 1.54178 Å) operated at 1.5 kW (45 kV, 0.65 mA), filtered with a graphite monochromator.

Data were collected and integrated using the Bruker SAINT software package and were corrected

for absorption effects using the multi-scan technique (SADABS133). The structures were solved

with direct methods (SIR92) and subsequent refinements were performed using SHELXL134 and

ShelXle.135 Hydrogen atoms on carbon atoms were included at geometrically idealized positions

(C–H bond distance 0.95Å) and were not refined. The isotropic thermal parameters of the

hydrogen atoms were fixed at 1.2 times that of the preceding carbon atom. Diagrams were

prepared using Mercury136 and POV-RAY.137 Thermal ellipsoids are shown at the 50% probability

level.

Deposition numbers:

Bis-PNB ester of 107a: 1955427

D7b: 1955420

Figure S2.14. XRD structure of compound D7b

79

Figure S2.15. XRD structure of compound Bis-PNB ester of 107a

The crystal for the diffraction experiment was selected from those provided. The crystal was a

colorless block of dimensions 0.10mm x 0.15 mm x 0.075 mm. All diffraction measurements were

made at approximately at 100 K on a Bruker Apex II diffractometer. The refinement is complete

at an excellent level (R = 2.46%) and the molecular geometry shows no unusual quantities. The

compound has crystallized in the centrosymmetric space group P-1 as an anhydrous racemate

with one molecule in the asymmetric unit.

Figure S2.16. XRD structure of compound D9a

80

Compound Reference Bis-PNB ester of 107a D9a D7b

Chemical Formula C25H23N4O10F C12H16FIN2O6 C16H18O6FN

Formula Mass 558.47 430.1709 339.31

Crystal System

Triclinic

a/Å 16.7932(13) 9.2762(4) 7.9861(18)

b/Å 15.8691(11) 9.6024(4) 8.252(3)

c/Å 19.4773(14) 9.8870(4) 12.936(3)

α/˚ 90 69.8990(10) 79.83(2)

β/˚ 90 64.8030(10) 81.342(19)

γ/˚ 90 87.7980(10) 89.66(2)

Unit cell volume/Å3 5190.6(7) 742.28(5) 829.4(4)

Temperature/K 150(2) 100.15 150(2)

Space group Pbca P-1 P1

Number of formula unit per cell/Z

8 2 2

Radiation type Cu Kα

Cu Kα

Absorption coefficient, μ/mm-1

1.001 17.367 0.951

No. of reflections 4759 18953 4704

Flack parameter - - -0.4 (3)

Rint 0.0309 0.0383 0.0764

Final R1 values (I>2σ(I)) 0.0642 0.0246 0.0693

Final wR(F2) values (I>2σ(I)) 0.1932 0.0632 0.1717

Final R1 values (all data) 0.0711 0.0246 0.0846

Final wR(F2) (all data) 0.2018 0.0632 0.1846

Goodness of fit 1.050 1.116 1.021

Table S2.10. Summary of XRD analysis

81

Chapter 3. A short de novo synthesis of C4’ nucleosides and locked nucleoside analogues

The results presented in this chapter have been reported in part, see:

Meanwell, M.; Silverman, S. M.; Lehmann, J.; Adluri, B.; Wang, Y.; Cohen, R.; Campeau, L.-C.;

Britton, R. 2020, Science. Accepted

Dr. Steven M. Silverman made several contributions to this work. S.M.S. helped develop the

methodology, provided insightful discussions, and synthesized compounds 151-156, 163, and

171-174.

3.1. C4’-modified NAs in drug discovery

Figure 3.1. C4’ analogues in medicinal chemistry

C4’-modified NAs have attracted much attention from drug discovery over the years.

Nucleocidin (132, Figure 3.1), isolated from Streptomyces calvus in 1956, was one of the first C4’-

modified nucleosides reported.138 Its potent antimicrobial properties inspired decades of research

into the effects of different C4’ substituents on the antibiotic, antiviral and chemotherapeutic

properties of NAs. Motivated by the early success of nucleocidin and zidovudine, initial focus on

NAs involved C4’-fluoro- and azido modifications. C4’-methyl and C4’-cyano substitutions have

also been explored and collectively have led to the observation that C4’-substitutions can

profoundly affect nucleoside conformations, thus significantly impacting their binding with target

enzymes and chain termination during replication.96,97 Together, these efforts have informed drug

discovery campaigns. Currently, MK-8591 (also known as islatravir or EFdA), a reverse

transcriptase inhibitor, is in Phase II clinical trials for the treatment of HIV infection.107,139,140 In

82

2011, Balapiravir, a perester prodrug of 4’-azidocytidine (134), advanced to Phase I clinical trials

for the treatment of Dengue fever.141

3.1.1. Synthetic challenges

Scheme 3.1. Common building blocks for the construction of C4’-modified NAs

Synthesis of C4’-modified NAs have largely relied on semisynthetic approaches that are

lengthy and not amenable to rapid library generation to support drug discovery efforts. 135, 138,

and 142 are examples of building blocks used for installing C4’-modifications. 4’,5’-Unsaturated

nucleosides such as 135 have allowed access to C4’-azido and -fluoro substitutions in as few as

7 steps (Scheme 3.1A).142 In contrast, C-C bond formation at C4’ has required more laborious

approaches.143,144 For instance, the C4’-methyl (141) and -ethyl analogues (143) of toyocamycin,

83

an antibiotic, were synthesized in 12 and 13 steps respectively.145 As an additional practical

challenge, separate total synthesis were required to access these two similar analogues (Scheme

3.1C).

Scheme 3.2. Merck’s syntheses of MK-8591

Merck’s recent development of MK-8591 as a HIV treatment has renewed interest in

exploring novel synthetic routes to structurally diverse NAs for both drug discovery and process

scale production.107,139,140 Structurally, MK-8591 presents a unique synthetic challenge as it

contains both C4’- and C2’-modifications. Merck’s first approach featured an enzymatic

desymmetrization of 144 to enable a 16-step enantioselective de novo synthesis of MK-8591.107

Though innovative, this strategy was as long as previously reported semisynthetic routes (12-18

steps).146 Towards a more efficient synthesis, Merck, in collaboration with Codexis, reported a

remarkable biocatalytic cascade for the 3-step synthesis of MK-8591 from racemic 2-

ethynylglycerol in 51% overall yield.139 This short sequence relied on the engineering of five

enzymes, as well as the use of four auxiliary enzymes, to catalyze reactions with non-natural

84

substrates. Here, enzymatic asymmetric oxidization and phosphorylation irreversibly transformed

2-ethynylglycerol (147) into intermediate 148 in excellent yield and enantioselectivity.

Subsequently, in a single pot, three enzymatic reactions (aldol reaction, phosphate transfer, and

glycosylation) reversibly converted 149 into MK-8591 and dihydrogen phosphate. As a

complicating factor, dihydrogen phosphate is a known inhibitor of phosphopentomutase, the

enzyme responsible for phosphate transfer in the aforementioned process. In order to improve

the yield of this one pot process, sucrose phosphorylase (SP) and sucrose were added to the

reaction mixture to convert the generated inorganic phosphate into glucose-1-phosphate, thereby

consuming dihydrogen phosphate and driving the desired reaction to completion. As a critical

aspect, this new enzymatic glycosylation is highly stereoselective and avoids the poor

diastereoselectivity commonly associated with glycosylation of C2’- and C4’-modified furanoses.

In 2020, Merck utilized their enzymatic glycosylation in a stereoselective 9-step route to MK-8591

from 2-deoxyribose.140

3.2. Rapid synthesis of C4’-modified NAs

Having ready access to a range of αFAR products, we anticipated that addition of

organometallic reagents (rather than reduction with hydride) would provide tertiary alcohols

whose subsequent AFD would lead directly to C4'-modified NAs. Toward this goal, we examined

reactions of the deazaadenine-substituted fluorohydrin 150 with a range of organometallic

reagents (e.g., MeMgCl, MeMgBr, Me2Zn, Me3ZnLi, MeLi, Me2Mg, Me3MgLi) in CH2Cl2 or THF at

-78C, 0C or room temperature (Figure 3.2). From this panel of experiments, MeMgX reagents

in CH2Cl2 proved to be most compatible with the densely functionalized fluorohydrin. Executing

the 1,2-addition reaction at -78C proved a necessity, as higher temperatures promoted 1,2-

hydride shift/fluoride displacement as a major degradative pathway. With regards to

stereochemistry, the 1,2-addition reactions generally gave mixtures of tertiary alcohols with a

preference for addition to the re face. 112 Surprisingly, when the reaction was executed in CH2Cl2

and the crude reaction mixture was allowed to warm to room temperature overnight, the

intermediate magnesium alkoxide 151a underwent AFD to provide the C4-modified NA 152

directly. Remarkably, this sequence enables access to enantiomerically enriched C4'-modified

NAs in only 3 steps from simple achiral heterocycles and bromoacetaldehyde diethyl acetal.

Alternatively, quenching the mixture of magnesium alkoxides 151a and 151b with ammonium

chloride followed by a subsequent Lewis acid promoted AFD using InCl3 gave the anomeric -D

NA 153. Thus, in this case, each of the magnesium alkoxides 151a and 151b cyclize selectively

85

using complimentary base- or Lewis acid promoted AFD processes to afford access to -L and

-D configured NAs, both unnaturally configured NAs that are of significant contemporary interest

to medicinal chemists.103,104,147

These results inspired us to examine the reaction of several additional organomagnesium

reagents with fluorohydrin aldol adducts containing triazole, deazaadenine, thymine, pyrazole or

trifluoromethyluracil functions (Figure 3.2). Here, we found the degree of stereoselectivity in 1,2-

addition reactions depended strongly on both the solvent and heterocycle. For example, the

addition of MeMgBr to ketofluorohydrins in THF generally gave mixtures of tertiary alcohols of

different composition to those generated in CH2Cl2. Curiously, the addition of MeMgBr to

ketofluorohydrins substituted with triazole gave predominantly 1,3-syn-diols that underwent AFD

to produce the naturally configured NA β-D-160. Clearly, subtle differences in chelation structures

involving the heterocycle and/or -alkoxide function and organomagnesium reagents play a

significant role in determining the stereochemical outcome of these 1,2-addition reactions and

controlling this aspect of the process will be the subject of future studies. Notwithstanding,

exploiting these straightforward reactions, a collection of deazaadenine-substituted NAs 152 –

156 were readily accessed as both - and -anomers. In general, and as noted above, base

promoted AFD resulted in C3', C5'-protected NAs (e.g., 157 – 159, 161 – 163), while AFD

promoted by Lewis acids resulted in deprotection or protecting group migration (e.g., 153 and

155). As summarized in Figure 3.2, a range of densely functionalized C4'-modified NAs could be

rapidly accessed from the corresponding ketofluorohydrin aldol adducts, including NAs

substituted with methyl, cyclopropyl, aryl and alkynyl groups. From this study, it is clear that much

larger collections of C4'-modified NAs (e.g., focused screening libraries) are now readily available.

It is worth highlighting that each of the C4'-methyl, cyclopropyl, p-methoxyphenyl, p-chlorophenyl,

alkynyl NAs 152 – 163 were prepared in only 3 or 4 steps total, which compares favourably to all

existing syntheses of members of these important classes of NAs.

86

Figure 3.2. Synthesis of C4’-modified analogues (R = C(CH3)2)

87

Scheme 3.3. Synthesis of C4’-allyl C2’-deoxy NA (R = C(CH3)2)

In an effort to demonstrate the advantage of this route for accessing NAs with

modifications at both C2' and C4', we prepared a C4'-modified, C2'-deoxy NA (Scheme 3.3). Here,

C4'-allyl thymine 166 was readily prepared in good yield through addition of allylmagnesium

bromide to the fluorohydrin aldol adduct 164 followed by base-promoted AFD. A Barton-

McCombie deoxygenation then gave the 4'-allyl NA 166 in only 6 steps total from thymine.

3.2.1. Locked nucleic acids

Figure 3.3. Common locked nucleic acid analogues

Locked nucleic acids (LNAs) are rigid nucleoside scaffolds possessing a methylene bridge

between the 2’-oxygen and the 4’-carbon. As depicted in Figure 3.3, structural variations such as

exchanging the oxygen contained within the bridge for a carbon, nitrogen, or sulfur, as well as

modifications to the methylene bridge (e.g. 170) have been reported.148–153 When incorporated

into oligonucleotides, LNAs can enhance oligomer stability and binding affinity towards

complimentary DNA or RNA strands, and thus have shown great promise as DNA-based

diagnostics and antisense therapies. 148

88

Figure 3.4. Short syntheses of LNAs

As a final demonstration of the broader utility of this process for NA synthesis, we aimed

to exploit C4'-functionalization for the preparation of locked nucleic acids (LNAs).148 These

conformationally restricted NAs demonstrate improved stability and their incorporation in

antisense oligonucleotides can lead to significant increases in specificity and potency. However,

much like syntheses of other C4'-modified NAs, the synthesis of LNAs is often protracted.

Towards a unified LNA synthesis, we evaluated the addition of alkynylmagnesium bromide to the

thymine-containing aldol adduct 164 and found the reaction gave two diastereomeric addition

products 171 and 172 in excellent overall yield. Remarkably, the major product was transformed

directly into the unusual LNA 174 by simply reacting with NaOH, which promoted both the AFD

reaction and a subsequent cyclization between the free alcohol function and alkyne in excellent

overall yield (Figure 3.4). It is notable that this 4-step total synthesis compares well with the 23-

step route reported for the analogous uracil LNA 170154 (see Figure 3.2). We were also able to

generate the unusual alkyne-functionalized LNA, a previously unreported scaffold in nucleoside

chemistry, by simply effecting an AFD of the 1,2-addition product 173. From here, formation of

the 2,2'-anhydrothymidine followed by deprotection and treatment with base in warm DMF155 gave

the LNA 175. This unique scaffold is primed for further diversification through standard click or

Sonagashira coupling reactions.

89

3.3. Experimental

General considerations

All reactions described were performed at ambient temperature and atmosphere unless otherwise

specified. Column chromatography was carried out with 230-400 mesh silica gel (E. Merck, Silica

Gel 60). Concentration and removal of trace solvents was done via a Buchi rotary evaporator

using acetone-dry-ice condenser and a Welch vacuum pump.

Nuclear magnetic resonance (NMR) spectra were recorded using deuterochloroform (CDCl3),

deuteromethanol (CD3OD), deuteroacetone ((CD3)2CO), deuteroacetonitrile (CD3CN) or

deuterodimethyl sulfoxide (DMSO-d6) as the solvent. Signal positions (δ) are given in parts per

million from tetramethylsilane (δ 0) and were measured relative to the signal of the solvent (1H

NMR: CDCl3: δ 7.26; CD3OD: δ 3.31; (CD3)2CO: δ 2.05; CD3CN: δ 1.96; DMSO-d6: δ 2.50; 13C

NMR: CDCl3: δ 77.16; CD3OD: δ 49.00; (CD3)2CO: δ 29.84; CD3CN: δ 1.32; DMSO-d6: 39.5).

Coupling constants (J values) are given in Hertz (Hz) and are reported to the nearest 0.1 Hz. 1H

NMR spectral data are tabulated in the order: multiplicity (s, singlet; d, doublet; t, triplet; q, quartet;

sept, septet; m, multiplet; br broad), coupling constants, number of protons. NMR spectra were

recorded on a Bruker Avance 600 equipped with a QNP or TCI cryoprobe (600 MHz), Bruker 400

(400 MHz) or Bruker 500 (500 MHz). Diastereomeric ratios (dr) are based on analysis of crude

1H NMR. Assignments of 1H are based on analysis of 1H-1H-COSY and nOe spectra. Assignments

of 13C are based on analysis of HSQC spectra.

High performance liquid chromatography (HPLC) analysis was performed on an Agilent 1100

HPLC, equipped with a variable wavelength UV-Vis detector.

High-resolution mass spectra were performed on an Agilent 6210 TOF LC/MS, Bruker MaXis

Impact TOF LC/MS, or Bruker micrOTOF-II LC mass spectrometer.

Infrared (IR) spectra were recorded neat on a Perkin Elmer Spectrum Two FTIR spectrometer.

Only selected, characteristic absorption data are provided for each compound.

Optical rotation was measured on a Perkin-Elmer Polarimeter 341 at 589 nm.

General Procedure A (Grignard additions)

90

A stirred solution of fluorohydrin aldol adduct (1 equiv.) in CH2Cl2 (0.025 M) was cooled to -78°C.

Organomagnesium reagent (2.2 – 5 equiv.) was added dropwise and the resulting reaction

mixture was stirred for 5 hrs. The reaction mixture was quenched at -78°C with an ammonium

chloride:methanol solution (1:1 – saturated ammonium chloride solution:methanol) and warmed

to room temperature. The resulting mixture was diluted with CH2Cl2 and washed twice with water.

The organic layer was dried over MgSO4, filtered, and concentrated under reduced pressure to

give crude product. The crude product was either purified by flash chromatography or used

directly for cyclization.

General Procedure B (base promoted cyclization)

To a stirred solution of syn-diols, syn- and anti-fluorohydrins (1.0 equiv.) in MeCN (0.10 M) was

added 2 M NaOH (1.5 - 10 equiv.) and the reaction mixture was stirred for 3 hours or until no

starting material remained (as determined by TLC analysis). The reaction mixture was diluted with

CH2Cl2 and washed with saturated ammonium chloride solution. The organic layer was separated,

dried over MgSO4, filtered, and concentrated under reduced pressure. The crude product was

purified by flash chromatography.

General Procedure C (Lewis acid promoted cyclization)

To a stirred solution of syn-diols, syn- and anti-fluorohydrin (1.0 equiv.) in MeCN (0.10 M) was

added Sc(OTf)3 or InCl3 (0.10 – 2.5 equiv.) and the reaction mixture was stirred for 6 hours or until

complete consumption of starting material (as determined by TLC analysis). The reaction mixture

was diluted with CH2Cl2 and was washed with saturated sodium bicarbonate solution. The organic

layer was separated, dried over MgSO4, filtered, and concentrated under reduced pressure. The

crude product was purified by flash chromatography.

Preparation of nucleoside analogue 152

Methylmagnesium chloride (3.0 M in THF, 1.49 mL, 4.47 mmol, 2.1 equiv.) was added dropwise

to a solution of 150 (syn-/anti-fluorohydrin = 3:1, 1.00 g, 2.13 mmol, 1.0 equiv.) at -78°C in CH2Cl2

(10 mL). The reaction mixture was stirred at this temperature for 2 hrs and then allowed to warm

gradually to room temperature and stirred for 12 hrs. The reaction mixture was quenched with

saturated ammonium chloride solution and diluted with ethyl acetate. The organic layer was

separated, dried over MgSO4, filtered, and concentrated under reduced pressure. Purification of

91

crude product 152 by flash chromatography (0-10% MeOH in CH2Cl2) afforded nucleoside 152

(0.418 g, 42%) as a white solid.

Data for nucleoside analogue 152: []D20 = -13.6 (c 0.28 in CH2Cl2); IR

(neat): = 3443, 2250, 1661, 1053, 1005, 821 cm-1; 1H NMR (600 MHz,

CDCl3): δ 8.64 (s, 1H), 7.55 (s, 1H), 6.28 (d, J = 7.6 Hz, 1H), 4.92 (ddd, J =

9.8, 7.5, 4.4 Hz, 1H), 4.21 (d, J = 4.5 Hz, 1H), 3.83 (d, J = 12.6 Hz, 1H),

3.74 (d, J = 12.6 Hz, 1H), 3.40 (d, J = 9.8 Hz, 1H), 1.53 (s, 3H), 1.49 (s,

3H), 1.42 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 153.2, 151.0, 151.0, 132.6, 118.1, 99.2, 89.9,

79.1, 75.5, 73.9, 66.2, 52.8, 27.4, 23.0, 20.8

HRMS (EI+) calcd for [C15H18ClIN3O4]+ 466.0025; found 466.0054

Determination of relative stereochemistry for nucleoside 152

Analysis of 2D NOESY of nucleoside 152 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 153

Methylmagnesium chloride (3.0 M in THF, 1.56 mL, 4.68 mmol, 2.2 equiv.) was added dropwise

to a solution of 150 (syn-/anti-fluorohydrin = 3:1, 1.00 g, 2.13 mmol, 1.0 equiv.) at -78°C in CH2Cl2

(20.0 mL). The resulting reaction mixture was stirred at -78°C for 5 hrs. The reaction mixture was

quenched with an ammonium chloride:methanol solution (1:1 – saturated ammonium chloride

solution:methanol) and warmed to room temperature. The reaction mixture was diluted with

CH2Cl2 (50 mL) and the organic layer was separated, dried over MgSO4, filtered, and

concentrated under reduced pressure. Purification of crude product 151b by flash

chromatography (pentane:ethyl acetate – 65:35) afforded 151b (0.498 g, 48%) as an off-white

solid.

92

Data for 151b: []D20 = -17.7 (c 1.8 in CH2Cl2); IR (neat): = 3316, 2991,

1206, 1086, 863, 736 cm-1; 1H NMR (600 MHz, dmso-d6): δ 8.76 (s,

1H), 8.28 (s, 1H), 6.92 (dd, J = 45.8, 3.3 Hz, 1H), 6.23 (d, J = 5.0 Hz,

1H), 4.65 (s, 1H), 4.45 (m, 1H), 3.44 (d, J =11.1 Hz, 1H), 3.28 (d, J =

8.0 Hz, 1H), 3.23 (d, J = 11.1, 1H), 1.28 (s, 3H), 1.13 (s, 3H), 0.75 (s,

3H);13C NMR (150 MHz, dmso-d6): δ 151.5, 151.4, 151.2, 134.3, 116.0, 98.3, 90.2 (d, J = 202.7

Hz), 74.1 (d, J = 4.5 Hz), 70.1 (d, J = 25.1 Hz), 70.0, 66.7, 55.2, 28.4, 19.7, 18.1; 19F NMR (470

MHz, dmso-d6): δ –151.1

HRMS (EI+) calcd for [C15H19ClFIN3O4]+ 486.0087; found 486.0080

To a stirred solution of 151b (0.100 g, 0.206 mmol, 1.0 equiv.) in dry MeCN (2.0 mL) was added

InCl3 (0.046 g, 0.206 mmol, 1.0 equiv.). The resulting reaction mixture was heated to 50°C for 2

hrs. 2,2-dimethoxypropane (0.214 mg, 2.06 mmol, 10.0 equiv.) and camphorsulfonic acid (9.6

mg, 0.041 mmol, 0.20 equiv.) were added and the reaction mixture was stirred for a further 1 hr

at 50 °C. The reaction mixture was then concentrated and purified by flash chromatography (0-

10% MeOH in CH2Cl2) to afford nucleoside 153 (0.049 g, 51%) as a white solid.

Data for nucleoside analogue 153: []D20 = +1.4 (c 0.84 in MeOD); 1H

NMR (600 MHz, CDCl3): δ 8.58 (s, 1H), 7.68 (s, 1H), 6.83 (d, J = 4.5

Hz. 1H), 5.01 (dd, J = 6.0, 4.7 Hz, 1H), 4.77 (d, J = 6.0 Hz, 1H), 3.79

(dd, J = 10.9, 5.2 Hz, 1H), 3.74 (dd, J = 10.9, 3.6 Hz, 1H), 2.02 (dd, J

= 5.2, 3.6 Hz, 1H), 1.48 (s, 3H), 1.41 (s, 3H), 1.31 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 152.6,

150.8, 150.3, 134.5, 117.4, 113.2, 85.1, 85.0, 83.0, 81.1, 69.5, 50.8, 25.6, 24.1, 17.4.

HRMS (EI+) calcd for [C15H18ClIN3O4]+ 466.0025; found 466.0000

Determination of relative stereochemistry for nucleoside 153

Analysis of 2D NOESY of nucleoside 153 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 154

93

Ethynylmagnesium chloride (0.5 M in THF, 8.94 mL, 4.47 mmol, 2.1 equiv.) was added dropwise

to a solution of 150 (syn-/anti-fluorohydrin = 3:1, 1.00 g, 2.13 mmol, 1.0 equiv.) at -78°C in CH2Cl2

(10 mL). The reaction mixture was stirred at this temperature for 2 hrs and then allowed to warm

gradually to room temperature and stirred for 12 hrs. The reaction mixture was quenched with

saturated ammonium chloride solution and diluted with ethyl acetate. The organic layer was

separated, dried over MgSO4, filtered, and concentrated under reduced pressure. Purification of

crude product 154 by flash chromatography (0-10% MeOH in CH2Cl2) afforded nucleoside 154

(0.415 g, 41%) as a white solid.

Data for nucleoside analogue 154: []D20 = -29.5 (c 0.58 in MeOH); IR

(neat): = 3291, 2924, 1446, 1201, 1023, 600 cm-1; 1H NMR (600 MHz,

dmso-d6): δ 8.72 (s, 1H), 8.02 (s, 1H), 6.44 (d, J = 8.1 Hz, 1H), 5.05 (dd,

J = 8.1, 3.6 Hz, 1H), 4.44 (d, J = 3.6 Hz, 1H), 4.16 (s, 1H), 4.01 (d, J =

13.2 Hz, 1H), 3.82 (d, J = 13.2 Hz, 1H), 3.44 (br s, 1H), 1.49 (s, 3H), 1.43

(s, 3H);13C NMR (150 MHz, dmso-d6): δ 151.7, 151.4, 151.1, 132.8, 116.6, 97.5, 86.5, 81.1, 80.5,

75.0, 74.1, 72.3, 64.2, 53.0, 28.5, 18.9

HRMS (EI+) calcd for [C16H16ClIN3O4]+ 475.9869; found 475.9849

Determination of relative stereochemistry for nucleoside 154

The relative stereochemistry was assigned based on comparison of the chemical shift of the

anomeric proton with compounds 152 and 156.

Preparation of nucleoside analogue 155

Ethynylmagnesium chloride (0.5 M in THF, 8.94 mL, 4.47 mmol, 2.1 equiv.) was added dropwise

to a solution of 150 (syn-/anti-fluorohydrin = 3:1, 1.00 g, 2.13 mmol, 1.0 equiv.) at -78°C in CH2Cl2

(20 mL). The resulting reaction mixture was stirred at -78°C for 1 hr. The reaction mixture was

quenched with an ammonium chloride:methanol solution (1:1 – saturated ammonium chloride

solution:methanol) and warmed to room temperature. The reaction mixture was diluted with

CH2Cl2 (50 mL) and the organic layer was separated, dried over MgSO4, filtered, and

concentrated under reduced pressure. Purification of crude product S155 by flash

chromatography (pentane:ethyl acetate – 65:35) afforded S155 (0.720 g, 68%, 1:1 mixture of

diastereomers) as an off-white solid.

94

To a stirred solution of S155 (0.050 g, 0.101 mmol, 1.0 equiv.) in dry MeCN (2.0 mL) was added

InCl3 (0.022 g, 0.101 mmol, 1.0 equiv.). The resulting reaction mixture was heated to 50°C for 2

hrs. 2,2-dimethoxypropane (0.124 mL, 1.01 mmol, 10.0 equiv.) and camphorsulfonic acid (4.7

mg, 0.020 mmol, 0.20 equiv.) were added and the reaction mixture was stirred for a further 1 hr

at 50 °C. The reaction mixture was then concentrated and purified by flash chromatography (0-

10% MeOH in CH2Cl2) to afford nucleoside 155 (0.029 g, 60%) as a white solid.

Data for nucleoside analogue 155: []D20 = +6.3 (c 2.0 in CH2Cl2); 1H

NMR (600 MHz, CDCl3): δ 8.59 (s, 1H), 7.82 (s, 1H), 6.85 (d, J = 4.6

Hz, 1H), 5.03 (dd, J = 6.0, 4.9 Hz, 1H), 4.98 (d, J =6.0 Hz, 1H), 3.97

(dd, J =11.5, 4.4 Hz, 1H), 3.92 (dd, J =11.5, 3.5 Hz, 1H), 2.82 (s, 1H),

2.18 (dd, J = 4.4, 3.5 Hz, 1H), 1.53 (s, 3H), 1.34 (s, 3H); 13C NMR

(150 MHz, CDCl3): δ 152.7, 150.9, 1505., 134.6, 117.4, 114.6, 85.3, 83.0, 82.9, 80.6, 78.2, 77.8,

68.7, 51.4, 25.7, 24.5.

HRMS (EI+) calcd for [C16H16ClIN3O4]+ 475.9869; found 475.9885

Determination of relative stereochemistry for nucleoside 155

Analysis of 2D NOESY of nucleoside 155 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 156

Phenylmagnesium chloride (2.0 M in THF, 2.24 mL, 4.47 mmol, 2.1 equiv.) was added dropwise

to a solution of 150 (syn-/anti-fluorohydrin = 3:1, 1.00 g, 2.13 mmol, 1.0 equiv.) at -78°C in CH2Cl2

(10 mL). The reaction mixture was stirred at this temperature for 2 hrs and then allowed to

gradually warm to room temperature and stirred for 12 hrs. The reaction mixture was quenched

with saturated ammonium chloride solution and diluted with ethyl acetate. The organic layer was

separated, dried over MgSO4, filtered, and concentrated under reduced pressure. Purification of

crude product by flash chromatography (0-10% MeOH in CH2Cl2) afforded nucleoside 156 (0.496

g, 45%) as a white solid.

95

Data for nucleoside analogue 156: []D20 = -23.6 (c 1.7 in CH2Cl2); IR

(neat): = 3309, 2990, 2938, 1575, 1538, 1445, 1200 cm-1; 1H NMR (600

MHz, dmso-d6): δ 8.70 (s, 1H), 7.63 (s, 1H), 7.43 (m, 5H), 6.55 (d, J = 8.3

Hz, 1H), 5.55 (d, J = 6.9 Hz, 1H), 4.77 (d, J = 3.8 Hz, ,1H), 4.67 (ddd, J

=8.3, 6.9, 3.8 Hz, 1H), 3.81 (d, J = 12.9 Hz, 1H), 3.68 (d, J =12.9 Hz, 1H),

1.62 (s, 3H), 1.50 (s, 3H); 13C NMR (150 MHz, dmso-d6): δ 152.0, 151.3, 151.0, 140.4, 133.4,

128.5, 128.0, 125.3, 111.8, 97.4, 86.1, 80.8, 73.9, 72.5, 67.0, 54.3, 28.3, 20.2

HRMS (EI+) calcd for [C20H20ClIN3O4]+ 528.0182; found 528.0206

Determination of relative stereochemistry for nucleoside 156

Analysis of 2D NOESY of nucleoside 156 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 157

Following General Procedure A, cyclopropylmagnesium bromide (1.0 M in 2-methylTHF, 0.79

mL, 0.79 mmol, 5 equiv.) was added to a solution of 164 (0.050 g, 0.158 mmol, 1 equiv.) in CH2Cl2

(6.30 mL) at -78 °C. The reaction mixture was stirred for 5 hrs. Without further purification, crude

S157 was dissolved in MeCN (1.60 mL) and 2 M NaOH (0.193 mL, 0.395 mmol) was added and

the reaction mixture was stirred for 4 hrs at 50 °C. Purification of crude product S157 by flash

chromatography (pentane:ethyl acetate – 30:70) afforded nucleoside 157 (0.021 g, 40 % yield)

as an off-white solid.

Data for nucleoside analogue 157: []D20 = -32.6 (c 0.47 in CH2Cl2); IR

(neat): = 3500, 3251 2997, 2175, 1690, 1088, 888 cm-1; 1H NMR (600

MHz, CDCl3): δ 7.10 (s, 1H), 6.04 (d, J = 7.9 Hz, 1H), 4.25 (dd, J = 7.9,

5.1 Hz. 1H), 4.08 (d, J = 5.1 Hz, 1H), 3.70 (d, J = 11.9 Hz, 1H), 3.63 (d, J

= 11.9 Hz, 1H), 3.15 (br s, 1H), 1.93 (s, 3H), 1.44 (s, 3H), 1.43 (s, 3H),

1.21 (m, 1H), 0.63 (m, 1H), 0.55 (m, 1H), 0.46 (m, 1H), 0.42 (m, 1H); 13C

96

NMR (150 MHz, CDCl3): δ 163.3, 151.0, 134.9, 111.9, 100.1, 87.5, 81.2, 74.0, 72.5, 64.3, 25.9,

25.6, 16.2, 12.9, 1.31, 0.50.

HRMS (EI+) calcd for [C16H22N2O6]+ 339.1551; found 339.1575

Determination of relative stereochemistry for nucleoside 157

Analysis of 2D NOESY of nucleoside 157 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 158

Following General Procedure A, p-tolylmagnesium bromide (1.0 M in THF, 0.712 mL, 0.71 mmol)

was added to a solution of 164 (0.050 g, 0.158 mmol) in CH2Cl2 (6.30 mL) at -78 °C. The reaction

mixture was stirred for 4.5 hrs. Without further purification, crude S158 was dissolved in MeCN

(1.58 mL) and 2 M NaOH (0.198 mL, 0.395 mmol) was added and the reaction mixture was heated

to 50°C for 4 hrs. Purification of crude product 158 by flash chromatography (pentane:ethyl

acetate – 35:65) afforded nucleoside 158 (0.024 g, 39 % yield over two steps) as colorless oil.

Data for nucleoside analogue 158: []D20 = -56.5 (c 0.4 in MeOH); IR

(neat): = 3432, 2939, 1700, 1466, 1378, 1129, 1051 cm-1; 1H NMR (600

MHz, CD3CN): δ 8.96 (br s, 1H), 7.38 (d, J = 8.1 Hz, 2H), 7.26 (d, J = 8.1

Hz, 2H), 6.78 (d, J = 0.90 Hz, 1H), 6.24 (d, J = 8.2 Hz, 1H), 4.76 (d, J =

3.8 Hz, 1H), 4.19 (s, 1H), 3.80 (d, J = 13.2 Hz, 1H), 3.73 (d, J = 13.2 Hz,

1H), 3.48 (br s), 2.35 (s, 3H), 1.68 (d, J = 0.90 Hz, 3H), 1.60 (s, 3H), 1.49

(s, 3H); 13C NMR (150 MHz, CD3CN): δ 164.6, 152.8, 139.6, 138.7, 137.4, 130.6, 126.7, 112.0,

99.2, 88.9, 81.6, 74.9, 74.3, 68.7, 29.0, 21.4, 20.8, 12.8.

HRMS (EI+) calcd for [C20H25N2O6]+ 389.1707; found 389.1707

97

Determination of relative stereochemistry for nucleoside 158

Analysis of 2D NOESY of nucleoside 158 supported the indicated

stereochemistry

Preparation of nucleoside analogue 159

Following General Procedure A, p-methoxyphenylmagnesium bromide (0.5 M in THF, 1.58 mL,

0.79 mmol, 5 equiv.) was added to a solution of 164 (0.050 g, 0.158 mmol, 1 equiv.) in CH2Cl2

(6.30 mL) at -78 °C. The reaction mixture was stirred for 5 hrs. Without further purification, crude

S159 was dissolved in MeCN (1.60 mL) and 2 M NaOH (0.193 mL, 0.395 mmol) was added and

the reaction mixture was stirred for 4 hrs at 50 °C. Purification of crude product 159 by flash

chromatography (pentane:ethyl acetate – 30:70) afforded nucleoside 159 (0.026 g, 41 % yield)

as a white solid.

Data for nucleoside analogue 159: []D20 = -52.8 (c 1.0 in CH2Cl2); IR

(neat): = 3197, 2990, 1693, 1252, 1036, 834 cm-1; 1H NMR (600 MHz,

CDCl3): δ 7.38 (d, J = 8.7 Hz, 2H), 6.96 (d, J = 8.7 Hz, 2H), 6.78 (s, 1H),

6.37 (d, J = 7.9 Hz, 1H), 4.75 (d, J = 4.1 Hz, 1H), 4.16 (m, 1H), 3.87 (d, J

= 13.1 Hz, 1H), 3.84 (s, 3H), 3.79 (d, J = 13.1, 1H), 2.99 (br s, 1H), 1.63

(s, 3H), 1.56 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 163.2, 159.9, 151.1,

135.8, 131.8, 126.5, 114.5, 111.7, 98.7, 88.7, 80.6, 74.8, 73.2, 67.7, 55.6, 28.1, 20.4, 12.7.HRMS

(EI+) calcd for [C20H25N2O7]+ 405.1656; found 405.1650

Determination of relative stereochemistry for nucleoside analogue 159

Analysis of 2D NOESY of nucleoside 159 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 160

98

Methylmagnesium iodide (3.0 M in THF, 0.39 mL, 1.16mmol, 3 equiv.) was added dropwise to a

solution of A5 (0.100 g, 0.388 mmol, 1 equiv.) at -78°C in CH2Cl2. The resulting reaction mixture

was gradually warmed to -10°C and allowed to stir for 2 hours. Following completion of the

reaction as monitored by TLC analysis, the reaction mixture was quenched with saturated

ammonium chloride solution and diluted with CH2Cl2. The organic layer was subsequently washed

twice with water and once with brine. The organic layer was then dried over MgSO4, filtered, and

concentrated under reduced pressure. Purification of crude product S160 by flash

chromatography (pentane:ethyl acetate – 25:75) afforded S160 (0.089 g, 84%) as a light yellow

oil.

Data for S160: 1H NMR (600 MHz, CDCl3): δ 8.16, 8.02, 7.76, 7.76, 6.80,

6.58, 4.62, 4.52, 4.40, 4.31, 4.07, 3.81, 3.59, 3.55, 3.45, 3.25, 3.13, 3.10,

1.52, 1.47, 1.45, 1.40, 1.38, 1.17; 13C NMR (150 MHz, CDCl3): δ 134.2,

134.1, 124.9, 124.3, 99.8, 99.8, 95.6, 93.4, 72.4, 72.4, 71.9, 71.8, 70.2,

70.0, 67.9, 67.8, 28.8, 28.7, 20.0, 19.8, 19.2, 18.5; 19F NMR (470 MHz, CDCl3): δ –157.8, -162.8

HRMS (EI+) calcd for [C11H19FN3O4]+ 276.1354; found 276.1366

To a solution of S160 (0.060 g, 0.218 mmol, 1 equiv.) in dry MeCN (2.18 mL) was added Sc(OTf)3

(0.268 g, 0.545 mmol, 2.5 equiv.). After stirring the reaction mixture for 16 hrs, 0.50 mL of acetic

anhydride and 0.50 mL of pyridine were added to the reaction mixture. The reaction mixture was

stirred for a further 4 hrs and then diluted with CH2Cl2. The organic layer was washed with twice

with 1 M HCl and once with water, dried over sodium sulfate, filtered, and concentrated under

reduced pressure to yield crude 160. Purification of crude product 160 by flash chromatography

(pentane:ethyl acetate – 60:40) afforded 160 (0.024 g, 32 % yield).

Data for nucleoside analogue 160: []D20 = +18.4 (c 1.46 in CH2Cl2); IR (neat):

= 2925, 1744, 1374, 1215, 1049 cm-1; 1H NMR (600 MHz, CDCl3): δ 7.76

(d, J = 0.60 Hz, 1H), 7.75 (d, J = 0.60 Hz, 1H) 6.19 (d, J = 4.7 Hz, 1H), 6.02

(dd, J = 5.4, 4.7 Hz, 1H), 5.67 (d, J = 5.4 Hz, 1H), 4.17 (d, J = 12.0 Hz, 1H),

4.08 (d, J = 12.0 Hz, 1H), 2.15 (s, 3H), 2.09 (s, 3H), 2.03 (s, 3H), 1.37 (s, 3H);

13C NMR (150 MHz, CDCl3): δ 170.3, 169.3, 169.2, 134.4, 122.7, 89.4, 85.6, 75.0, 71.9, 67.9,

20.8, 20.5, 20.5, 19.3.

HRMS (EI+) calcd for [C14H20N3O7]+ 342.1296; found 342.1312

99

Determination of relative stereochemistry for nucleoside analogue 160

Analysis of 2D NOESY of nucleoside 160 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 161

Following General Procedure A, methylmagnesium bromide (3.0 M in THF, 0.258 mL, 0.78 mmol,

4 equiv.) was added to a solution of A1 (0.050 g, 0.194 mmol, 1 equiv.) in CH2Cl2 (3.90 mL) at -

78 °C. The reaction mixture was stirred for 6 hrs. Crude S161 was purified by flash

chromatography (ethyl acetate-pentane – 6:4) to yield S161 (0.026 g, 49 % yield). S161 (0.030 g,

0.109 mmol) was dissolved in MeCN (1.09 mL) and 2 M NaOH (0.545 mL, 1.09 mmol, 10 equiv.)

was added and the reaction mixture was stirred for 5 hrs at 50 °C. Purification of crude nucleoside

analogue 161 by flash chromatography (pentane:ethyl acetate – 25:75) afforded 161 (0.017 g, 61

% yield) as a light yellow oil.

Data for nucleoside analogue 161: []D20 = +11.3 (c 0.38 in CH2Cl2); );

IR (neat): = 3383, 2992, 2922, 1382, 1199, 1090, 908 cm-1 1H NMR

(600 MHz, CDCl3): δ 7.60 (d, J = 2.4 Hz, 1H), 7.59 (d, J = 1.6 Hz, 1H),

6.35 (dd, J = 2.4, 1.6 Hz, 1H), 5.29 (d, J = 1.3 Hz, 1H), 4.12 (dd, J =

3.0, 1.3 Hz, 1H), 3.98 (d, J = 3.0 Hz, 1H), 3.76 (d, J = 11.3 Hz, 1H), 3.52 (d, J = 11.3 Hz, 1H),

1.47 (s, 3H), 1.44 (s, 3H), 1.41 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 141.3, 129.3, 107.4, 99.6,

72.6, 70.3, 67.3, 64.9, 57.0, 28.8, 20.5, 19.0.

HRMS (EI+) calcd for [C12H19N2O4]+ 255.1339; found 255.1320

100

Determination of relative stereochemistry for nucleoside analogue 161

Analysis of 2D NOESY of nucleoside 161 supported the indicated

stereochemistry

Preparation of nucleoside analogue 162

Following General Procedure A, p-methoxyphenylmagnesium bromide (0.5 M in THF, 4.66 mL,

2.33 mmol, 3 equiv.) was added to a solution of A1 (0.200 g, 0.775 mmol, 1 equiv.) in CH2Cl2

(7.75 mL) at -78 °C. The reaction mixture was stirred for 6 hrs. Crude S162 was purified by flash

chromatography (ethyl acetate-pentane – 4:6) to yield S162 (0.157 g, 55 % yield). S162 (0.155 g,

0.423 mmol, 1 equiv.) was dissolved in MeCN (2.82 mL) and 2 M NaOH (0.53 mL, 1.06 mmol,

2.5 equiv.) was added and the reaction mixture was stirred for 5 hrs at 50 °C. Purification of crude

nucleoside analogue 162 by flash chromatography (pentane:ethyl acetate – 40:60) afforded 162

(0.085 g, 58 % yield) as a light orange oil.

Data for nucleoside analogue 162: []D20 = -14.8 (c 1.4 in CH2Cl2); IR

(neat): = 3418, 2991, 1611, 1512, 1250, 1032, 759 cm-1; 1H NMR (600

MHz, CD3CN): δ 7.69 (d, J = 2.7 Hz, 1H), 7.56 (d, J = 1.4 Hz, 1H), 7.39

(d, J = 8.9 Hz, 2H), 6.91 (d, J = 8.9 Hz, 2H), 6.35 (dd, J = 2.7, 1.4 Hz,

1H), 5.99 (d, J = 7.9 Hz, 1H), 4.73 (dd, J = 7.9, 3.7 Hz, 1H), 4.59 (d, J =

3.7 Hz, 1H), 3.92 (d, J = 13.3 Hz, 1H), 3.78 (s, 3H), 3.68 (d, J = 13.3 Hz,

1H), 1.62 (s, 3H), 1.51 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 160.6, 141.5, 133.7, 132.1, 128.4,

114.8, 107.6, 99.1, 93.9, 82.0, 75.9, 75.1, 68.9, 56.3, 29.0, 21.2.

HRMS (EI+) calcd for [C18H23N2O5]+ 347.1601; found 347.1610

101

Determination of relative stereochemistry for nucleoside 162

Analysis of 2D NOESY of nucleoside 162 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 163

p-Chlorophenylmagnesium bromide (1.0 M in diethyl ether, 4.32 mL, 4.32 mmol, 3.2 equiv.) was

added dropwise to a stirred solution of fluorohydrin aldol adduct A6 (0.500 g, 1.35 mmol, 1 equiv.)

in THF (10.0 mL) at 0°C. The resulting reaction mixture was stirred for 14 hrs at room temperature

and for a further 8 hrs at 40°C. The reaction mixture was then diluted with ethyl acetate (100 mL)

and washed once with water (100 mL) and once with brine (50 mL). The organic layer was

separated, dried over MgSO4, filtered, and concentrated under reduced pressure to give crude

163. Purification of crude nucleoside analogue 163 by flash chromatography (pentane:ethyl

acetate – 50:50) afforded 163 (0.289 g, 46%).

Data for nucleoside 163: []D20 = +10.5 (c 0.8 in CH2Cl2); IR (neat):

= 3087, 2996, 1699, 1467, 1283, 1129, 1085 cm-1; 1H NMR (600

MHz, dmso-d6): δ 11.94 (br s, 1H), 8.74 (s, 1H), 7.57 (d, J = 8.7 Hz,

2H), 7.50 (d, J = 8.7 Hz, 2H), 6.13 (d, J = 7.2 Hz, 1H), 5.67 (br s,

1H), 4.66 (d, J =4.3 Hz, 1H), 4.17 (dd, J =6.8, 4.3 Hz, 1H), 3.98 (d,

J =13.4 Hz, 1H), 3.88 (d, J =13.4 Hz, 1H), 1.63 (s, 3H), 1.40 9s, 3H);

13C NMR (150 MHz, CD3CN): δ 159.9, 150.5, 144.3 (q, J = 5.9 Hz), 138.0, 134.9, 129.9, 128.1,

124.1 (q, J = 269.0 Hz), 104.0 (q, J = 32.0), 99.6, 84.7, 81.6, 73.6, 73.6, 67.7, 28.6, 19.9; 19F NMR

(470 MHz, CD3CN): δ –62.9

HRMS (EI+) calcd for [C19H19ClF3N2O6]+ 463.0878; found 463.0875

102

Determination of relative stereochemistry for nucleoside 163

Analysis of 2D NOESY of nucleoside 163 supported the indicated

stereochemistry.

Preparation of nucleoside analogue 165

Following General Procedure A, allylmagnesium bromide (1.0 M in diethyl ether, 1.42 mL, 1.42

mmol, 4.5 equiv.) was added to a solution of 164 (0.100 g, 0.316 mmol, 1 equiv.) in CH2Cl2 (12.6

mL) at -78 °C. The reaction mixture was stirred for 5 hrs. Without further purification, crude S165

was dissolved in MeCN (3.16 mL) and 2 M NaOH (0.395 mL, 0.79 mmol, 2.5 equiv.) was added

and the reaction mixture was stirred for 4 hrs at 50 °C. Purification of crude 165 by flash

chromatography (CH2Cl2:MeOH – 4:96) afforded nucleoside analogue 165 (0.050 g, 47 % yield)

as a dark orange oil.

Data for nucleoside analogue 166: []D20 = -6.0 (c 0.4 in MeOH); IR

(neat): = 3340, 2992, 1670, 1376, 1044 cm-1; 1H NMR (600 MHz,

CD3CN): δ 8.95 (br s, 1H), 7.27 (s, 1H), 6.02 (d, J = 8.3 Hz, 1H), 5.87 (m,

1H), 5.22 (d, J = 17.7 Hz, 1H), 5.20 (d, J = 10.1 Hz, 1H), 4.31 (ddd, J =

9.3, 8.3, 4.9 Hz, 1H), 4.11 (d, J = 4.9 Hz, 1H), 3.68 (d, J = 12.2 Hz, 1H),

3.64 (d, J = 12.2 Hz, 1H), 3.41 (d, J = 9.3 Hz, 1H), 2.50 (dd, J =14.2, 6.7

Hz, 1H), 2.41 (dd, J = 14.2 , 8.1 Hz, 1H), 1.85 (s, 3H), 1.40 (s, 3H), 1.39 (s, 3H); 13C NMR (150

MHz, CD3CN): δ 164.6, 152.3, 136.8, 133.7, 120.4, 112.3, 100.3, 88.4, 81.7, 73.9, 73.3, 65.3,

41.7, 26.9, 22.4, 12.8.

HRMS (EI+) calcd for [C16H22N2O6]+ 339.1551; found 339.1556

103

Determination of relative stereochemistry for nucleoside 165

Analysis of 2D NOESY of nucleoside 165 supported the indicated

stereochemistry

Preparation of nucleoside analogue 166

To a solution of nucleoside 165 (0.022 g, 0.061 mmol, 1 equiv.) in dry THF (0.61 mL) was added

1, 1’- thiocarbonyldiimidazole (0.022 g, 0.122 mmol, 2 equiv.). The reaction mixture was stirred

for 18 hrs. Subsequently, CH2Cl2 (5 mL) was added to the reaction mixture and washed with

water 3 times. The organic layer was dried over MgSO4, filtered, and concentrated under reduced

pressure to yield crude S166. Purification of crude S166 by flash chromatography (pentane:ethyl

acetate – 40:60) afforded S166 (0.018 g, 66% yield). To a solution of nucleoside S166 (0.014 g,

0.031 mmol, 1 equiv.) in dry toluene (4.45 mL) under nitrogen was added tributyltin hydride (8.35

µL, 0.031 mmol, 1 equiv.) and AIBN (5.1 mgs, 0.031 mmol, 1.0 equiv.). The resulting reaction

mixture was purged with nitrogen for 30 minutes. Subsequently, the reaction mixture was stirred

for 16 hrs at 90 °C. Upon competition, CH2Cl2 was added to reaction mixture and the washed with

water. The organic layer was dried over MgSO4, filtered, and concentrated under reduced

pressure to yield crude 166. Purification of crude 166 by flash chromatography (ethyl acetate)

afforded nucleoside analogue 166 (6.0 mg, 61%) as a white solid.

Data for nucleoside analogue 166: []D20 = +13.3 (c 0.46 in CH2Cl2); IR

(neat): = 2924, 1690, 1467, 1375, 1263, 1226, 1053 cm-1; 1H NMR (600

MHz, CDCl3): δ 8.26 (s, 1H), 7.31 (d, J = 1.1 Hz, 1H), 6.38 (dd, J = 9.6, 4.8

Hz, 1H), 5.86 (m, 1H), 5.25-5.27 (m, 2H), 4.22 (d, J = 5.2 Hz, 1H), 3.69 (d,

J = 12.0 Hz, 1H), 3.64 (d, J = 12.0 Hz, 1H), 2.50 (m, 2H), 2.41 (dd, J =

13.5, 4.8 Hz, 1H), 2.00 (dd, J = 13.5, 9.6, 5.2 Hz, 1H), 1.92 (s, 3H), 1.37

(s, 6H); 13C NMR (150 MHz, CDCl3): δ 163.3, 150.0, 135.0, 131.9, 120.2, 111.1, 99.5, 85.8, 84.0,

73.9, 63.9, 40.9, 37.8, 25.6, 22.5, 12.7

HRMS (EI+) calcd for [C16H23N2O5]+ 323.1601; found 323.1580

104

Preparation of fluorohydrins 171 and 172

Following General Procedure A, ethynylmagnesium chloride (0.5 M in THF, 3.5 mL, 1.75 mmol,

3.5 equiv.) was added to a solution of 164 (0.160 g, 0.50 mmol, 1 equiv.) in CH2Cl2 (25.0 mL) at

-78 °C. The reaction mixture was stirred for 4 hrs. The crude products 171 and 172 were purified

by flash chromatography (ethyl acetate:hexane – 70:30) to afford 171 (0.058 g, 38 % yield) and

172 (0.072 g, 42 % yield) as white solids.

Data for fluorohydrin 171: []D20 = -38.0 (c 1.2 in MeOH); IR (neat): = IR

(neat): = 3395, 2994, 1694, 1468, 1381, 1282, 1043 cm-1; 1H NMR (600

MHz, CD3CN): δ 9.29 (br s, 1H), 7.41 (s, 1H), 6.40 (dd, J = 43.4, 4.6 Hz,

1H), 4.54 (m, 1H), 4.27 (m, 1H), 4.22 (m, 1H), 3.82 (d, J = 9.5 Hz, 1H),

3.79 (d, J = 11.5 Hz, 1H), 3.75 (d, J = 11.5 Hz, 1H), 2.81 (s, 1H), 1.85 (s,

3H), 1.41 (s, 3H), 1.28 (s, 3H); 13C NMR (150 MHz, CD3CN): δ 164.8, 151.4, 137.7, 111.5, 100.8,

94.1 (d, J = 206.9 Hz), 84.4, 75.7, 73.6 (d, J = 3.8 Hz), 73.4 (d, J = 24.7 Hz), 69.3, 67.3, 28.8,

19.4, 12.8; 19F NMR (470 MHz, CD3CN): δ –175.5

HRMS (EI+) calcd for [C15H20N2O6]+ 343.1300; found 343.1305

Data for fluorohydrin 172: []D20 = -60.8 (c 0.4 in MeOH); IR (neat): =

3320, 2944, 2832, 1670, 1449, 1022, 638 cm-1; 1H NMR (600 MHz, dmso-

d6): δ 11.47 (br s, 1H), 7.56 (s, 1H), 6.36 (dd, J = 43.7, 4.1 Hz, 1H), 6.21 (d,

J = 5.3 Hz, 1H), 5.37 (br s, 1H), 4.14 (m, 1H), 3.71 (d, J = 8.7 Hz, 1H), 3.68

(br s, 1H), 3.42 (s, 1H), 3.16 (d, J = 5.0 Hz, 1H), 1.78 (s, 3H), 1.33 (s, 3H), 1.21 (s, 3H); 13C NMR

(150 MHz, dmso-d6): δ 163.6, 150.0, 136.7, 109.2, 98.8, 92.7 (d, J = 206.6 Hz), 83.7, 76.2, 72.8

(d, J = 2.8 Hz), 71.2 (d, J = 24.6 Hz), 68.2, 65.7, 27.8, 18.7, 12.1;19F NMR (470 MHz, dmso-d6):

δ –170.5

HRMS (EI+) calcd for [C15H20N2O6]+ 343.1300; found 343.1298

Preparation of nucleoside analogue 174

Following General Procedure B, a solution of 172 (0.100 g, 0.292 mmol, 1.0 equiv.) and NaOH

(29.2 mg, 0.73 mmol, 2.5 equiv.) in MeCN (2.0 mL) was heated to 50 °C for 36 hrs. Purification

of the crude 174 by flash chromatography (0-10% MeOH in dichloromethane) afforded nucleoside

analogue 174 (58.6 mg, 62 % yield) as a white powder.

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Data for nucleoside analogue 174: []D20 = -8.7 (c 0.6 in CH2Cl2); IR (neat):

= 2994, 1748, 1690, 1270, 1043 cm-1; 1H NMR (600 MHz, dmso-d6): δ

11.42 (s, 1H), 7.61 (d, J = 1.3 Hz, 1H), 5.46 (s, 1H), 4.86 (s, 1H), 4.63 (d, J

= 11.2 Hz, 1H), 4.45 (d, J = 2.6 Hz, 1H), 4.37 (d, J = 2.6 Hz, 1H), 4.23 (d, J

= 11.2 Hz, 1H), 3.91 (s, 1H), 1.84 (s, 3H), 1.51 (s, 3H), 1.30 (s, 3H); 13C

NMR (150 MHz, dmso-d6): δ 163.8, 158.8, 150.0, 135.0, 109.3, 100.4, 87.2,

83.0, 78.4, 76.5, 71.9, 58.5, 28.7, 19.5, 12.0

HRMS (EI+) calcd for [C15H19N2O6]+ 323.1238; found 323.1235

Preparation of nucleoside analogue 173

Following General Procedure C, a solution 171 (0.220 g, 0.64 mmol, 1 equiv.) and 2M NaOH

(0.640 mL, 1.28 mmol, 2.0 equiv.) was heated to 50°C and stirred for 24 hours in MeCN (6.4 mL).

Purification of the crude 173 by flash chromatography (MeOH:CH2Cl2 – 3:97) afforded nucleoside

analogue 173 (0.144 mg, 70 % yield) as a white powder.

Data for nucleoside analogue 173: []D20 = +30.8 (c 1.66 in CH2Cl2); 1H

NMR (600 MHz, CD3CN): δ 9.06 (br s, 1H), 7.48 (s, 1H), 6.16 (d, J = 8.2

Hz, 1H), 4.61 (ddd, J = 8.4, 8.2, 3.7 Hz, 1H), 4.41 (d, J = 3.7 Hz, 1H), 4.06

(d, J = 13.3 Hz, 1H), 3.88 (d, J = 13.3 Hz, 1H), 3.64 (d, J = 8.4 Hz, 1H), 3.29

(s, 1H) 1.86 (s, 3H), 1.48 (s, 3H), 1.43 (s, 3H); 13C NMR (150 MHz, CD3CN):

δ 164.7, 152.5, 136.9, 112.7, 99.3, 89.4, 81.2, 80.8, 76.5, 75.5, 73.9, 65.9, 29.1, 19.7, 13.1

HRMS (EI+) calcd for [C15H19N2O6]+ 323.1238; found 323.1245

Determination of relative stereochemistry for nucleoside 173

Analysis of 2D NOESY of nucleoside 173 supported the indicated

stereochemistry

A solution of 173 (0.050 g, 0.155 mmol, 1 equiv.) in dry CH2Cl2 (0.78 mL) was cooled to 0 °C and

diethylaminosulfur trifluoride (0.102 mL, 0.776 mmol, 5 equiv.) was added dropwise over 5

106

minutes. The resulting reaction mixture was slowly warmed to room temperature over 3 hrs.

Following completion of the reaction, as monitored by TLC analysis, the reaction mixture was

diluted with 5 mL of ethyl acetate and washed with 3 mL of H2O (3x). Subsequently, the organic

layer was dried over MgSO4, filtered, and concentrated under reduced pressure. Purification of

the crude product by flash chromatography (ethyl acetate) afforded nucleoside analogue S173

(0.043g, 91%) as a white solid.

Data for nucleoside analogue S173: []D20 = -47.5 (c 1.1 in MeCN); IR

(neat): = 3284, 3002, 1626, 1554, 1497, 1134, 1066, 1030 cm-1; 1H NMR

(600 MHz, CD3CN): δ 7.46 (s, 1H), 6.32 (d, J = 5.3 Hz, 1H), 5.13 (d, J =

5.3 Hz, 1H), 4.74 (s, 1H), 4.10 (d, J = 13.7 Hz, 1H), 4.00 (d, J = 13.7 Hz,

1H), 2.87 (s, 1H), 1.87 (s, 3H), 1.47 (s, 3H), 1.34 (s, 3H); 13C NMR (150

MHz, CD3CN): δ 173.1, 161.5, 132.3, 119.6, 99.7, 91.8, 87.4, 79.8, 79.1, 77.8, 74.6, 64.9, 29.0,

19.3, 14.4

HRMS (EI+) calcd for [C15H17N2O5]+ 305.1132; found 305.1108

To a solution of S173 (0.042 g, 0.138 mmol, 1 equiv.) in wet MeCN (2.76 mL) was added InCl3

(0.122g, 0.553 mmol, 4 equiv.). The resulting reaction mixture was heated to 50 °C and was

stirred for 16 hrs or until the reaction was complete as monitored by TLC. The reaction mixture

was concentrated under reduced pressure and purified by flash chromatography (MeOH:CH2Cl2

– 7.5:92.5) to afford S175 (0.038 g, 96%). To a solution of S175 (0.038 g, 0.133 mmol, 1 equiv.)

in DMF (1.73 mL) was added K2CO3 (0.096g, 0.69 mmol, 5 equiv.). The resulting reaction mixture

was heated to 90 °C and stirred for 7 days or until the reaction was complete as monitored by 1H

NMR spectroscopy. Subsequently, the reaction mixture was filtered, concentrated under reduced

pressure, and the crude product was purified by flash column chromatography (MeOH:CH2Cl2 –

10:90) to afford 175 (0.027g, 71%) as a white solid.

Data for nucleoside analogue 175: []D20 = +16.9 (c 1.0 in MeOH); IR (neat):

= 3261, 2988, 1686, 1272, 1203, 1047, 799 cm-1; 1H NMR (600 MHz, CD3CN):

δ 9.43 (br s, 1H), 7.31 (d, J = 1.1 Hz, 1H), 5.48 (s, 1H), 4.27 (s, 1H), 4.15 (s,

1H), 4.03 (d, J = 8.0 Hz, 1H), 3.93 (d, J = 8.0 Hz, 1H), 3.16 (s, 1H), 1.85 (d, J

= 1.1 Hz, 3H); 13C NMR (150 MHz, CD3CN): δ 165.1, 151.4, 135.6, 111.0, 88.6,

80.9, 80.3, 80.2, 75.8, 75.2, 75.1, 13.0

HRMS (EI+) calcd for [C12H13N2O5]+ 265.0819; found 265.0813

107

10-20g scale preparation of 164

39.0 g of A3 was dissolved in 240 mL of ethyl acetates and repurified by prep-HLPC to give 18.0

g of product. The 18.0 g product was dissolved in 240 mL of CH2Cl2 and concentrated under

reduced pressure to give 17.5 g of 164. The 17.5 g of 164 was freeze-dried to obtain 15.8 g of

164 as a white solid (94.3 % purity).

Data for syn-fluorohydrin 164: []D20 = -89.4 (c 1.1 in MeOH); IR (neat):

= 2993, 1694, 1450, 1369, 1082, 1045 cm-1; 1H NMR (400 MHz,

CDCl3): δ 8.30 (br s, 1H), 7.57 (dd, J = 1.3, 1.2 Hz, 1H), 6.66 (ddd, J =

42.7, 2.3, 1.3 Hz, 1H), 4.40 (dd, J = 8.9, 1.4 Hz, 1H), 4.33 (dd, J = 17.7,

1.4 Hz, 1H), 4.12 (d, J = 17.7 Hz, 1H), 4.10 (ddd, J = 15.4, 3.1, 2.3 Hz,

1H), 3.64 (d, J = 3.0 Hz, 1H), 1.95 (d, J = 1.2 Hz, 3H), 1.52 (s, 3H), 1.46 (s, 3H); 13C NMR (100

MHz, CDCl3): δ 211.2, 163.2, 149.9, 137.1 (d, J = 4.0 Hz), 111.0, 102.1, 90.2 (d, J = 207.8 Hz),

71.6 (d, J = 2.3 Hz), 70.9 (d, J = 23.4 Hz), 66.5, 23.8, 23.4, 12.6; 19F NMR (470 MHz, CDCl3): δ –

177.8

HRMS (EI+) calcd for [C13H18FN2O6]+ 317.2929; found 317.1142

108

Chapter 4. A platform for diversity-oriented synthesis of carbohydrate analogues

Several colleagues contributed to this work. Gaelen Fehr developed the methodology for α-

chlorination/aldol reactions and synthesized compounds 207-212, 231-233, 235, 236, 256, 257,

and 265-269. Dr. Weiwu Ren synthesized compounds 221, 230, 274, and 276. Dr.

Bharanishashank Adluri synthesized compounds 231, 234, and 270-272.

4.1. Introduction to carbohydrate analogues

Figure 4.1 Carbohydrate analogues in drug discovery

Carbohydrates are essential biomolecules that play critical roles in cell signaling and

metabolism.156 Consequently, structural mimics of carbohydrates (carbohydrate analogues

(CAs)), have found widespread use in drug discovery and chemical biology and have had a

profound impact in therapeutic areas such as diabetes,157 virology158 and cancer.159,160 As a

notable example, Oseltamivir (Tamiflu, 176 (Figure 4.1)), a neuraminidase inhibitor, is a WHO

essential medicine for treating influenza and was the frontline drug used during the H1N1

pandemic in 2009.161 Likewise, Miglitol (178) is an antidiabetic drug that functions by inhibiting α-

glucosidases and decreasing the carbohydrate metabolism in patients with type II diabetes.157

From a mechanistic perspective, therapeutic CAs often inhibit enzymes involved in carbohydrate

processing (glycoside hydrolases and transferases), and thus mitigate the effects of dysregulated

metabolism. As selective probe molecules, CAs are often used to gain insight into enzyme

109

function and disease pathology.162 Importantly, carbohydrates and CAs are also core structural

units found in several approved drugs (e.g., doxorubicin, vancomycin) and play a vital role in their

therapeutic efficacy.

Scheme 4.1. Diversity-oriented synthesis approaches to CAs

Unsurprisingly, CAs display a high degree of structural diversity. The canonical endocyclic

oxygen is frequently exchanged for a nitrogen,163 carbon,164 or sulfur,165 and the ring-size varied,

with 5- and 6-membered rings being the most common. While the structural landscape of CAs is

vast, a smaller collection of scaffolds has dominated drug discovery efforts owing to their

predictive properties. For example, iminosugars are CAs in which the endocyclic oxygen is

replaced with a nitrogen that is protonated at physiological pH, mimicking the oxacarbenium ion

transition state traversed during hydrolysis by glycoside hydrolases (GHs).163,166 The

corresponding sulfur analogues or thiosugars possess distinct geometries, conformations, and

electronic properties that can profoundly influence their physiochemical properties (e.g.,

metabolic stability, bioavailability, lipophilicity, potency).165 Carbasugars or cyclitols have shown

promise as transition-state analogues and inhibitors of α-glycosidases.164 While diversity-oriented

synthesis (DOS) approaches are useful for the discovery of new CAs and exploring their

associated chemical space, these methods often rely on the derivatization of naturally occurring

carbohydrates, leading to lengthy synthetic sequences (> 10 steps) that can limit structural

diversity and drug discovery efforts.167 For example, several DOS strategies rely on single step

transformations of stereochemically rich CA cores to generate screening libraries. Wong has

reported a library of potent and selective α-fucosidase inhibitors derived from 1-aminomethyl-

110

fuconojirimycin (182) (Figure 1).168 Here, the advantage of late-stage diversification using a robust

reaction (i.e. amide coupling) is challenged by the 12-step route required to access the key

scaffold 182. DOS approaches that provide access to stereochemically and structurally diverse

scaffolds have also been reported. For example, Marcaurelle demonstrated the use of 2,3-

unsaturated C-glycoside scaffolds to synthesize several new bicyclic carbohydrates in as few as

6 total steps.169 Recently, Loh reported a robust strategy for the diversification of carbohydrates

using hydrogen- and halogen-bond catalyzed strain release glycosylation to produce complex

O,N-glycoside analogues.170 The synthesis of CA building blocks for incorporation into

oligosaccharides has also attracted interest, and new platforms for producing CA-containing

oligosaccharides have been exploited in the generation of tobramycin analogues that target

pathogenic RNA. 171

111

Figure 4.2. Development of α-functionalization/aldol reactions for drug discovery

As an alternative de novo approach, we have described a one-pot process that involves

the proline-catalyzed α-chlorination of aliphatic aldehydes followed by a L-proline-catalyzed aldol

reaction with dioxanone 75 to produce syn-chlorohydrins of general structure 188 in good yield,

diastereoselectivity, and enantioselectivity.172 Chlorohydrin scaffolds produced via this -

chlorination/aldol reaction (CAR) have proven to be versatile building blocks for the construction

of CAs including carbasugars (e.g., 190)173 and iminosugars (e.g., 191).116,174 For example, we

have exploited this process in the discovery of inhibitors of OGlcNAcase174 and -

galactosidases173,175 (i.e. 190 and 191). As detailed in Chapters 2 and 3, we have reported a

complimentary proline-catalyzed α-fluorination/aldol reaction (FAR) that supports the rapid

synthesis of nucleoside analogues (NAs, e.g., 192).176 Critical to this NA synthesis is the stability

of heteroaryl-C-F functions (compared to heteroaryl-C-Cl), which enabled the production and

isolation of fluorohydrin aldol adducts (e.g., 189: R = heteroaryl). A subsequent intramolecular

112

displacement of the fluoride results in stereospecific formation of the carbohydrate core of

nucleosides and NAs. While these unique CARs and FARs provide a convenient means to

construct CAs and NAs, all efforts here have relied on the well-established reactivity of dioxanone

75 as the aldol coupling partner and thus limited our exploration of more unusual carbohydrate

scaffolds. We envisioned new -functionalization/aldol reactions, involving a larger variety of

electrophiles and carbonyl compounds, would support the rapid construction diverse collections

of CAs. Here, we describe the development of these reactions and ultimately demonstrate their

broad utility for synthesizing CAs.

4.2. Development of α-functionalization/aldol reactions

Scheme 4.2. One-pot synthesis of chlorohydrins and DKR of α-chloroaldehydes through proline-catalyzed aldol reactions

Asymmetric enamine catalysis utilizing chiral amines has been widely exploited in the

enantioselective α-functionalization of aldehydes, including α-chloro-,177 α-fluoro,115 α-hydroxy,178

α-amino,179 α-thio,180 and α-trifluoromethyl aldehydes.181 Despite intense efforts, many of these

aldehydes remain underutilized as chiral building blocks owing in part to their instability, volatility,

propensity to epimerize and/or challenges with their purification.115 For these reasons, processes

that avoid isolation of α-functionalized aldehydes but still take advantage of their synthetic

potential as chiral building blocks are highly sought. We previously demonstrated that proline

catalyzes the racemic -chlorination of aldehydes, the interconversion of the resulting racemic -

chloroaldehydes and finally their aldol reactions with dioxanone 75.172 As depicted in Scheme 4.2,

we proposed that electrostatic repulsion between the Cl and O atoms in the transition structure

113

leading to anti-chlorohydrins served as the key diastereodiscriminating interaction in this dynamic

kinetic resolution (DKR). The high levels of enantioselectivity then derive from H-bonding, which

directs the facial approach of the correctly configured -chloroaldehyde to the proline-derived

enamine through a Houk-List-type transition structure TS1.182

entry X+ source solvent syn:anti %ee yield

1 NCS CH2Cl2 6:1 94 72

2 NCS CH2Cl2:DMF 2.2:1 ND ND

3 NFSI CH2Cl2:DMF 15:1 96 61

4 PhthN-SCF3 CH2Cl2:DMSO 6:1 91 52

5 NBS CH2Cl2:DMF 1.5:1 ND 21

6 CbzNNCbz MeNO2 3:1 98 45

Table 4.1. α-functionalization/aldol reactions between pentanal and dioxanone (75)

To explore the broader utility of this strategy, we prepared a series of α-functionalized

pentanal derivatives and evaluated their reactivity in proline-catalyzed aldol reactions with

dioxanone 75. Here, α-functionalization/aldol reactions were performed as two-step-one-pot

sequences (see experimental section for details). Specifically, we examined the L-proline

catalyzed α-functionalization of pentanal using a series of electrophilic reagents (e.g., N-

chlorosuccinimide (NCS), N-fluorobenzenesulfonimide (NFSI), N-trifluoromethylthiophthalimide

(PhthN-SCF3)), and subsequently added dioxanone 75 and examined the production of aldol

adducts 198, 200 – 203. As shown in Table 4.1, this process preferentially affords syn-

fluorohydrin 200, -trifluoromethylthiohydrin 201, -bromohydrin 202, and -aminohydrin 203 in

variable diastereoselectivity and excellent enantioselectivity. Notably, the observed

diastereoselectivity for the formation of the series of halohydrins (198 (d.r. 15:1), 200 (d.r. 2.2:1),

and 202 (d.r. 1.5:1)) correlated well with increasing electronegativity of the halogen atom. Thus,

despite the smaller van der Waals radius for F (F = 1.47 Å; Cl = 1.75 Å; Br = 1.85 Å) and shorter

bond length (C(sp3)-F = 1.40 Å; C(sp3)-Cl = 1.79 Å; C(sp3)-Br = 1.97 Å), the reactions of

enantiomeric α-fluoroaldehydes were more greatly differentiated based on the increased charge

density on F (ENF = 3.98; ENCl = 3.16; ENBr = 2.96). These results are in accord with our original

proposal172 that electrostatic repulsion between the O and X atoms in TS-2 disfavour production

of anti-halohydrins 199. To gauge the effect of solvent polarity, the αCAR was repeated in CH2Cl2

114

(rather than 9:1 CH2Cl2-DMF) and we observed a substantial increase in diastereoselectivity

(2.2:1 to 6:1; see Table 4.1 entries 1 and 2). This observation further supports the role of

electrostatic interactions in the diastereodifferentiating step. As summarized in Table 4.1 (entry

4), the -trifluoromethylthioaldehyde derived from pentanal also underwent a highly diastero- and

enantioslective aldol reaction with dioxanone 75. Considering that both the organocatalyzed -

fluorination115 and -trifluoromethylthiolation183 of aldehydes proceed with almost no

enantioselctivity (ee’s <15%), the high level of stereoselectivity in these processes is attributed to

DKR of the intermediate -fluoro- and -trifluoromethylthioaldehydes. Thus, proline-catalyzed

racemization is more facile than the subsequent aldol reactions (i.e., krac > k(D) or k(L)). In the case

of the α-aza aldehyde generated from the reaction of pentanal and dibenzyl azodicarboxylate

(entry 6), steric hindrance precludes formation of a proline enamine required for racemization.

Furthermore, in a separate experiment the proline-catalyzed aldol reaction between (S)-2-Cbz-

aminopentanal and dioxanone yielded the corresponding anti-aminohydrin as the sole product,

confirming that these α-aminoaldehydes do not racemize under the reaction conditions (krac <

k(L)). Likewise, the L-proline catalyzed aldol of 2-phenylpropanal and dioxanone affords an equal

mixture of syn- and anti- diastereomers (see experimental section).

Table 4.2. Optimization of α-chlorination/aldol with isovaleraldehyde (204) and thiopyranone 206.aketone and aldehyde added at the same time.

Having demonstrated the use of dioxanone (75) in several α-functionalization/aldol

reactions, we were intrigued to expand the scope of compatible ketones. As summarized in Table

4.2, we began by examining the L-proline catalyzed αCAR of tetrahydro-4H-thiopyranone (206)

entry additive temp. (°C) solvent A solvent B 207:208 yield

1a None RT CH2Cl2 None N.D. <5%

2a None RT DMSO None N.D. 0%

3a None 0 CH2Cl2 None N.D. <5%

4 None 0 CH2Cl2 DMSO 10:1 38%

5 H2O 0 CH2Cl2 DMSO 10:1 45%

115

with isovaleraldehyde. Carrying out this reaction using our previously reported one-step-one-pot

procedure in a variety of solvents afforded the desired syn-chlorohydrin, albeit in low yield (See

Table 4.2, entries 1-3). Suspecting that competitive chlorination of thiopyranone 206 was

complicating this process, we adopted a two-step-one-pot sequence. Satisfyingly, when the L-

proline catalyzed α-chlorination of isovaleraldehyde was first carried out in CH2Cl2 at 0 °C and

then followed by direct addition of thiopyranone 206 in DMSO, the desired 207 was produced in

good yield and excellent diastereo-and enantioselectivity (entry 4). Addition of catalytic amounts

of water with the thiopyranone led to modest improvements in yield while catalytic amounts of

TFA had minimal effect (Table 4.2, entry 5). Using this straightforward process, several additional

ketones (O-TBS-hydroxyacetone, cyclohexanone, and tetrahydro-4H-pyran-4-one) were

engaged in αCARs giving syn-chlorohydrins 207 and 209 – 211 in good yield and excellent

diastereo- and enantioselectivity. Unfortunately, simple aliphatic ketones such as acetone,

cyclopentanone, and 3-pentanone, were incompatible (e.g., 212-217).

Figure 4.3. Ketone scope of α-chlorination/aldol reaction

With several new α-functionalization/aldol reactions in hand, we were eager to

demonstrate the broad applicability of this technology to synthesize CA building blocks through

the use of a panel of functionally diverse aldehydes. Towards this goal, we synthesized a

collection of fluorohydrins (218 – 230 and 237 – 242), chlorohydrins (231-234),

trifluoromethylthiohydrins (243-247), and aminohydrins (235 and 236) in excellent enantio- and

diastereoselectivity. As shown in Figure 4.3, the functional group compatibility of the αFAR is

highlighted in the reactions of TIPS-protected 3-hydroxypropanal and Cbz-protected 3-

aminopropanal, which delivered the unusual fluorohydrins 226 and 230 bearing a heteroatom at

116

each position in the carbon chain. Overall, the αFAR was tolerant to alkyl-, alkene-, alkyne-and

(hetero)aryl substituents. Furthermore, simply using D-proline enables access to enantiomeric

syn-fluorohydrins 221 and 226. Gratifyingly, adding 206 and cyclohexanone neat to reaction

mixtures of α-fluoroaldehydes (generated from pentanal, pentenal, and phthalimidoacetaldehyde)

successfully engaged in α-FARs to afford anti-aldol-syn-fluorohydrin products (237 – 242) in good

to excellent yield. We were particularly encouraged by the ability to engage α-fluoro-α-

phthalimidyl-acetaldehyde in productive aldol reactions to afford 241 and 242 and have reported

similar heteroaryl-C-F containing aldol intermediates for NAs synthesis. Considering the SCF3

group is commonly used to increase lipophilicity (Hansch hydrophobicity parameter π = 1.44) and

modulate pKa,184 the utility of this process was further highlighted in the production of syn-

trifluoromethylthiohydrins containing an alkyl (243 and 245), alkene (244), aryl (246), or heteroaryl

(247) in excellent diastereo- and enantioselectivity. To the best of our knowledge, these are the

first examples of an asymmetric reaction involving α-(trifluoromethylthio)aldehyde. Finally, we

explored the compatibility of a small collection of aldehydes in αCARs with OTBS-

hydroxyacetone, which afford chlorohydrins 231-234, and demonstrated that α-amination/aldol

reactions deliver enantiomerically enriched syn-aminohydrins (235 and 236).

117

Figure 4.4. Scope of α-functionalization/aldol reactions.

118

Figure 4.5. Scope of α-functionalization/aldol reactions

4.3. Rapid synthesis of CAs

Figure 4.6. Platform for rapid diversity-oriented synthesis (253 = 5-(methanesulfonyl)-1-phenyl-1H-tetrazole)

To demonstrate the utility of these aldol adducts for rapidly producing diverse scaffolds for

medicinal chemistry, several readily available chlorohydrins, fluorohydrins,

119

trifluoromethylthiohydrins, and aminohydrins were converted into a diverse collection of

iminosugars, bicyclic nucleoside analogues, annulated furanoses, and fluorinated CAs (Figure

4.6). Hydrogenation of syn-aminohydrins allowed access to cyclic hydrazones 256 and 257 in

excellent yield over 2 total steps. This compares favourably with syntheses of azafagomines 254

and 255, a class of α-fucosidase inhibitors, that required 17 step syntheses.185 The recent use of

258 as potent and selective PRMT5 inhibitors for cancer treatment highlights the importance of

bicyclic nucleoside analogues, a relatively unexplored NA scaffold.186 In attempt to develop a

more efficient approach to this class of compounds, we prepared bicyclic NAs 259 and 260 in 3

total steps via a 1,3-syn reduction and indium chloride mediated cyclization from fluorohydrins

259 and 260. Presumably, under cyclization conditions, epimerization occurs to give a mixture of

α- and β- anomers. Given the synthetic challenges currently associated with NA synthesis, this

short sequence should provide new opportunities for medicinal chemistry. We also evaluated the

utility of fluoro- and trifluoromethylthiohydrins as building blocks for the synthesis of fluorinated

carbacycles. As depicted in Figure 4.7, Julia-Kocienski olefination and subsequent RCM of 223,

239, 240 and 244 afforded bicyclic carbacycles 261 – 264 in only 3 total steps. 1,3-syn reduction

with sodium borohydride and subsequent microwave cyclization of syn-chlorohydrins 198, 207,

209, 211, and 233 afforded uniquely annulated tetrahydrofuran (THF) products 265 – 269,

including scaffolds that have not yet been reported 265 and 266. Alternatively, 1,3-syn reductive

amination with benzyl amine followed by reflux in toluene under basic conditions of 231, 232 and

234 gave access to selectively protected 5’-deoxy-iminosugars 270 – 272. 1,3-syn or 1,3-anti

selective reduction of the vicinal fluorohydrin 230 followed by removal of the silyl protecting group

and oxidation of the resultant primary alcohol delivered the epimeric 2-deoxy-2-fluoropyranoses

273 and 274. This short sequence avoids the iterative alcohol protection-deprotection steps

commonly required in fluorosugar synthesis. Hydrogenation of the Cbz-protected amino

fluorohydrin 226 (made using D-proline catalysis) gave directly and in excellent yield a previously

undescribed fluorinated analogue 275 of the drug migalastat (galafold),187 a pharmacological

chaperone used to treat Fabry disease. As an additional target of interest, we also prepared a

fluorinated analogue 276 of D-ribo-phytosphingosine, a precursor to the potent natural killer T cell

stimulator α-galactosylceramide,188 in a straightforward manner through the reductive amination

of the fluorohydrin 221 with benzyl amine, followed by hydrogenolysis.

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Figure 4.7. Rapid synthesis of CAs.aα:β = 2.5:2.bα:β = 3:1.

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Figure 4.8. Conversion of fluorohydrins 221, 226, and 230 into biologically relevant molecules

In summary, we have developed a DOS approach that relies on achiral and readily

accessible starting materials to access an array of highly relevant CA scaffolds for drug discovery.

These processes are enabled by an expanding family of α-functionalization/aldol reactions that,

in a single step, can afford stereochemically rich and densely functionalized aldol adducts in good

yield and excellent diastereo- and enantioselectivity. These versatile building blocks were rapidly

derivatized, through a suite of established procedures, into a variety of CAs in 1-2 steps.

4.4. Experimental

Data for compounds 207-212, 231-236, 256, 257, and 265-269 were reported in the thesis of G.

Fehr.189

L- and D-proline (99% purity) were purchased from Alfa Aesar. All reactions described were

performed at ambient temperature and atmosphere unless otherwise specified. Column

chromatography was carried out with 230-400 mesh silica gel (E. Merck, Silica Gel 60).

Concentration and removal of trace solvents was done via a Buchi rotary evaporator using

acetone-dry-ice condenser and a Welch vacuum pump.

Nuclear magnetic resonance (NMR) spectra were recorded using deuterochloroform (CDCl3),

deuteromethanol (CD3OD) or deuterodimethyl sulfoxide (DMSO-d6) as the solvent. Signal

positions (δ) are given in parts per million from tetramethylsilane (δ 0) and were measured relative

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to the signal of the solvent (1H NMR: CDCl3: δ 7.26; CD3OD: δ 3.31; DMSO-d6: δ 2.50; 13C NMR:

CDCl3: δ 77.16; CD3OD: δ 49.0; DMSO-d6: 39.5). Coupling constants (J values) are given in Hertz

(Hz) and are reported to the nearest 0.1 Hz. 1H NMR spectral data are tabulated in the order:

multiplicity (s, singlet; d, doublet; t, triplet; q, quartet; sept, septet; m, multiplet; br broad), coupling

constants, number of protons. NMR spectra were recorded on a Bruker Avance 600 equipped

with a QNP or TCI cryoprobe (600 MHz), Bruker 400 (400 MHz) or Bruker 500 (500 MHz).

Diastereomeric ratios (dr) are based on analysis of crude 1H-NMR. Assignments of 1H are based

on analysis of 1H-1H-COSY and nOe spectra. Assignments of 13C are based on analysis of HSQC

spectra.

High performance liquid chromatography (HPLC) analysis was performed on an Agilent 1100

HPLC, equipped with a variable wavelength UV-Vis detector and Chiralcel OD-H chiral column

(0.46 cm x 25 cm). Enantiomeric excess (ee) has been determined using corresponding bis-p-

nitrobenzoate of all syn-fluorohydrins except for 228, 238, 241, and 242 which required no

derivatization.

High-resolution mass spectra were performed on an Agilent 6210 TOF LC/MS, Bruker MaXis

Impact TOF LC/MS, or Bruker micrOTOF-II LC mass spectrometer.

Infrared (IR) spectra were recorded neat on a Perkin Elmer Spectrum Two FTIR spectrometer.

Only selected, characteristic absorption data are provided for each compound.

Optical rotation was measured on a Perkin-Elmer Polarimeter 341 at 589 nm.

General Procedures

General Procedure A (α-fluorination/aldol reaction with dioxanone)

A sample of aldehyde (1.5 equiv.) was added to a stirred suspension of NFSI (1.5 equiv.),

L-proline (1.5 equiv.), and NaHCO3 (1.5 equiv.) in DMF (0.75 M) at -10 °C. When complete

conversion to the α-fluoroaldehyde was observed by 1H NMR spectroscopic analysis, 2,2-

Dimethyl-1,3-dioxan-5-one (75) (1.0 equiv.) in CH2Cl2 (0.055 – 0.10 M) was then added and the

resulting mixture was allowed to warm gradually to room temperature. After a total of 72 hrs, or

when complete consumption of the 75 was observed by 1H NMR spectroscopic analysis of small

reaction aliquots, the mixture was diluted with Et2O and the organic layer was washed twice with

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water and once with brine. The organic layer was then dried over MgSO4, concentrated under

reduced pressure and the crude product was purified by flash chromatography as indicated.

General Procedure B (α-fluorination/aldol reaction with cyclohexanone/thiopyranone 206)

A sample of aldehyde (1.0 equiv.) was added to a stirred suspension of NFSI (1.5 equiv.),

L-proline (1.0 equiv.), and NaHCO3 (1.0 equiv.) in DMF (0.75 M) at -10 °C. When complete

conversion to the α-fluoroaldehyde was observed by 1H NMR spectroscopic analysis,

cyclohexanone or thiopyranone 206 (5.0 – 10.0 equiv.) was then added and the resulting mixture

was allowed to warm gradually to room temperature. After a total of 18 hrs, the mixture was diluted

with Et2O and the organic layer was washed twice with water and once with brine. The organic

layer was then dried over MgSO4, concentrated under reduced pressure and the crude product

was purified by flash chromatography as indicated.

General Procedure C (α-trifluoromethylthiolation/aldol reaction)

A sample of aldehyde (2.0 equiv.) was added to a stirred suspension of NFSI (1.5 equiv.),

L-proline (2.0 equiv.), and NaHCO3 (2.0 equiv.) in DMSO (0.75 M) at room temperature. When

complete consumption of aldehyde was observed by 1H NMR spectroscopic analysis, 2,2-

Dimethyl-1,3-dioxan-5-one (75) (1.0 equiv.) in CH2Cl2 (5 x vol. of DMSO) was then added and the

resulting mixture was stirred for a further 48 – 72 hrs. When complete consumption of the 75 was

observed by 1H NMR spectroscopic analysis of small reaction aliquots, the mixture was diluted

with Et2O and the organic layer was washed twice with water and once with brine. The organic

layer was then dried over MgSO4, concentrated under reduced pressure and the crude product

was purified by flash chromatography as indicated.

General Procedure D (olefination/ring-closing metathesis)

To a stirred solution of 5-(methanesulfonyl)-1-phenyl-1H-tetrazole (2 – 2.2 equiv.) in dry THF (0.80

M) at -78oC was added dropwise a 1 M LiHMDS (2 – 2.2 equiv.) and the resulting reaction mixture

was stirred for 30 minutes. A solution of fluorohydrin (or trifluoromethylthiohydrin) (1.0 equiv.) in

dry THF (0.30 – 0.50 M) was then added dropwise and the reaction mixture was allowed to stir

for 5 hrs at -78°C. Following complete consumption of fluorohydrin (or trifluoromethylthiohydrin),

as monitored by TLC analysis, the reaction mixture was quenched with saturated ammonium

chloride solution and diluted with CH2Cl2. The organic layer was washed twice with water,

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separated, dried over MgSO4, filtered, and concentrated under reduced pressure. The crude

alkene was purified by flash chromatography as indicated. A mixture Grubbs II catalyst (0.05

equiv.) and alkene (1.0 equiv.) in dry toluene (0.025 M) was purged with N2 for 45 minutes in a

sealed reaction vessel and subsequently heated to 80 - 90°C for 6 -12 hrs. The reaction mixture

was then diluted with CH2Cl2 and washed twice with water. The organic layer was dried with

MgSO4, filtered, and concentrated under reduced pressure. The crude carbacycle was purified by

flash chromatography as indicated.

General Procedure E (reduction and benzoylation)

To a stirred solution of racemic or optically enriched syn-fluorohydrin (1.0 equiv) in MeOH (0.15

M) was added sodium borohydride (1.5 equiv), and the resulting mixture was stirred at room

temperature for 1 hour or until no starting material remained (as determined by TLC analysis).

The reaction mixture was then diluted with CH2Cl2 and washed with H2O. The organic layer was

removed, dried over MgSO4, concentrated under reduced pressure, and the crude product was

purified by flash chromatography. To a solution of purified diol in CH2Cl2 (0.10 M) was added

triethylamine (6.0 equiv.), either p-nitro benzoyl chloride (3.0 equiv.) or p-bromo benzoyl chloride

(3.0 equiv.), and 4-dimethylaminopyridine (cat.), and left to stir for 1 hour or until no starting

material remained (as determined by TLC analysis). The reaction mixture was diluted with CH2Cl2

and washed with NaHCO3. The organic layer was removed, dried over MgSO4, concentrated

under reduced pressure, and the crude product was purified by flash chromatography.

General Procedure F (hydrogenation)

Through a solution of fluorohydrin (1.0 equiv) and Pd/C (50 % by weight) in MeOH (0.10 M) was

bubbled H2 gas for 1 hr. The reaction vial was then sealed and left over night. The reaction mixture

was then filtered, concentrated under reduced pressure, and the crude product was purified by

flash chromatography.

Preparation and characterization of all compounds

Preparation of aldol adduct 200

Following General Procedure A, a solution of pentanal (0.050 mL, 0.470 mmol), NFSI (0.149 g,

0.470 mmol), L-proline (0.054 g, 0.470 mmol), and NaHCO3 (0.039 g, 0.470 mmol) was stirred for

45 minutes at -10 °C in 0.65 mL of DMF. Dioxanone 75 (0.0380 mL, 0.314 mmol) in CH2Cl2 (5.6

mL) was added and the reaction mixture was left to stir at room temperature for 72 hrs. Purification

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of the crude fluorohydrin 200 by flash chromatography (pentane:EtOAc – 9:1) afforded

fluorohydrin 200 (0.045 g, 61 % yield) as a colourless oil.

Data for syn-fluorohydrin 200: []D20 = -6.2 (c 2.27 in CHCl3); IR (neat):

= 3429, 2990, 1742, 1376, 1225, 1091, 864 cm-1; 1H NMR (600 MHz,

CDCl3): δ 4.69 (dddd, J = 47.3, 9.0, 4.0, 1.6 Hz, 1H), 4.39 (dd, J = 8.5,

1.1 Hz, 1H), 4.30 (dd, J = 17.7, 1.5 Hz, 1H), 4.08 (d, J = 17.5 Hz, 1H),

3.80 (ddd, J = 27.2, 8.5, 1.5 Hz), 3.29 (s, 1H), 1.94 (m, 1H), 1.61 (m,

1H), 1.52 (m, 1H), 1.50 (s, 3H), 1.43 (s, 3H), 1.42 (m, 1H), 0.97 (t, J = 7.0 Hz, 3H); 13C NMR (150

MHz, CDCl3): δ 212.6, 101.8, 91.4 (d, J = 175.3), 71.9 (d, J = 5.1 Hz), 71.4 (d, J = 18.0 Hz), 66.9,

32.6 (d, J = 20.8 Hz), 23.8, 23.8, 18.5 (d, J = 5.4 Hz), 14.3; 19F NMR (470 MHz, CDCl3): δ –202.4

HRMS (EI+) calcd for [C11H20FO4]+ 235.1340; found 235.1354

Determination of the absolute stereochemistry for fluorohydrin 200

Following General Procedure E, the fluorohydrin 200 (0.105 g, 0.449 mmol) was converted into

the corresponding bis-p-bromobenzoate 200-XRD. Recyrstallization in dichloromethane and

ethanol (1:1) allowed for the absolute stereochemistry to be assigned using single X-ray

crystallography (see X-ray structures).

Determination of enantiomeric excess of fluorohydrin 200

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 200 was prepared. Following General Procedure E, optically enriched and racemic

samples of 200 (0.015 g, 0.064 mmol) were converted into the bis-p-nitrobenzoate derivative. The

enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a DIACEL

CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 80:20; detection at 260

nm; retention time = 17.27 min for (-)-200-Bis-PNB; 22.06 min for (+)-200-Bis-PNB (see

chromatograms).The enantiomeric excess of the optically enriched bis-p-nitrobenzoate derivative

was determined using the same method (96% ee).

Preparation of aldol adduct 219

Following General Procedure A, a solution of propanal (0.050 mL, 0.687 mmol), NFSI (0.217 g,

0.687 mmol), L-proline (0.079 g, 0.687 mmol) and NaHCO3 (0.058 g, 0.687 mmol) was stirred for

45 minutes at -10 °C in DMF (0.92 mL). Dioxanone 75 (0.055 mL, 0.458 mmol) in CH2Cl2 (8.3 mL)

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was then added and the reaction mixture was stirred for 48 hrs. Purification of the crude

fluorohydrin 219 by flash chromatography (pentane-EtOAc 4:1) afforded fluorohydrin 219 (0.053

g, 56 % yield) as a yellow oil.

Data for syn-fluorohydrin 219: []D20 = -13.5 (c 3.42 in CHCl3); IR (neat): =

3428, 2990, 1742, 1378, 1225, 1091, 864 cm-1;1H NMR (600 MHz, CDCl3): δ

4.90 (dq, J = 47.0 Hz, 6.5 Hz, 1H), 4.38 (dd, J = 8.5, 1.4 Hz, 1H), 4.30 (dd, J =

17.6, 1.5 Hz, 1H), 4.08 (d, J = 17.6, 1H), 3.75 (ddd, J = 26.1, 2.5, 2.5, 1H), 3.29

(d, J = 2.7), 1.50 (s, 3H), 1.43 (s, 3H), 1.43 (dd, J = 24.0, 6.6 Hz, 3H); 13C NMR (150 MHz, CDCl3):

δ 212.1, 101.6, 88.0 (d, J = 171.0 Hz) , 72.3 (d, J = 17.7 Hz), 72.0 (d, J = 5.1 Hz), 66.8, 23.7, 23.7,

16.4 (d, J = 22.9 Hz); 19F NMR (470 MHz, CDCl3): δ -195.5

HRMS (EI+) calcd for [C9H16FO4]+ 207.1027; found 207.1054

Determination of relative stereochemistry for fluorohydrin 219

Following General Procedure E, the fluorohydrin 219 (0.105 g, 0.449 mmol) was converted into

the corresponding p-nitrobenzoyl diester (219-XRD). Recyrstallization in ethanol allowed for the

relative stereochemistry to be assigned using single X-ray crystallography (see X-ray structures).

Determination of enantiomeric excess of fluorohydrin 219

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 219 was prepared. Following General Procedure E, optically enriched and racemic

samples of 219 (0.040 g, 0.19 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a

DIACEL CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 80:20; detection

at 260 nm; retention time = 28.1 min for (-)-219-Bis-PNB; 37.4 min for (+)-219-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically enriched bis-p-nitrobenzoate derivative

was determined using the same method (95% ee).

Preparation of aldol adduct 220

Following General Procedure A, a solution of 3-methylbutanal (0.050 mL, 0.465 mmol), NFSI

(0.147 g, 0.465 mmol), L-proline (0.053 g, 0.465 mmol), and NaHCO3 (0.039 g, 0.465 mmol) was

stirred for 45 minutes at -10 °C in 0.60 mL of DMF. Dioxanone 75 (0.037 mL, 0.31 mmol) in CH2Cl2

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(5.4 mL) was stirred for 72 hrs. Purification of the crude fluorohydrin 220 by flash chromatography

(pentane-EtOAc 4:1) afforded fluorohydrin 220 (0.049 g, 67 % yield) as a colorless oil.

Data for syn-fluorohydrin 220: []D20 = -117 (c 2.6 in CHCl3); IR (neat): =

3526, 2968, 1740, 1377, 864;1H NMR (600 MHz, CDCl3): δ 4.39 (d, J = 8.7

Hz, 1H), 4.30 (d, J = 17.8 Hz, 1H), 4.21 (dd, J = 46.5, 9.6 Hz, 1H), 4.08 (d, J

= 17.6 Hz, 1H), 3.95 (dd, J = 28.6, 8.8 Hz, 1H), 3.26 (d, J = 2.5 Hz, 1H), 2.26

(m, 1H), 1.50 (s, 3H), 1.43 (s, 3H), 1.07 (d, J = 6.6 Hz, 3H), 0.92 (d, J =6.6

Hz, 3H); 13C NMR (150 MHz, CDCl3): δ 212.8, 101.6, 96.1 (d, J = 178.1 Hz), 71.5 (d, J = 6.2 Hz),

69.2 (d, J = 18.4 Hz), 66.7, 28.1 (d, J = 20.0 Hz), 23.6, 23.6, 19.1 (d, J = 4.8 Hz), 18.1 (d, J = 9.3

Hz); 19F NMR (470 MHz, CDCl3): δ –203.3

HRMS (EI+) calcd for [C11H20FO4]+ 235.1340; found 235.1334

Determination of enantiomeric excess of fluorohydrin 220

Following General Procedure A, using a 1:1 mixture of L-: D-proline, a racemic sample of the

fluorohydrin 220 was prepared. Following General Procedure E, optically enriched and racemic

samples of 220 (0.035 g, 0.15 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric fluorohydrin were separated by chiral HPLC using a DIACEL

CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 93.5:6.5; detection at 260

nm; retention time = 24.94 min for (+)-220-Bis-PNB; 27.31 min for (-)-220-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically pure bis-p-nitrobenzoate derivative

was determined using the same method (95 % ee).

Preparation of aldol adduct 221

Following General Procedure A, a solution of pentadecanal (0.453 g, 2.0 mmol), NFSI (0.731 g,

2.0 mmol), D-proline (0.23 g, 2.0 mmol) and NaHCO3 (0.168 g, 2.0 mmol) was stirred for 3 hrs at

-10 °C in DMF (2.7 mL). Dioxanone 75 (0.287 mL, 1.33 mmol) in CH2Cl2 (24 mL) was stirred for

48 hours. Purification of the crude fluorohydrin by flash chromatography (pentane-EtOAc 30:1)

afforded fluorohydrin 221 (0.239 g, 48% yield) as a clear oil.

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Data for syn-fluorohydrin 221: []D20 = -83.0 (c 1.2 in CHCl3); IR (neat):

= 3530, 2924, 2854, 1740, 1337, 1224, 1090, 865 cm-1; 1H NMR (600

MHz, CDCl3): δ 4.66 (ddd, J = 47.3, 8.9, 4.9 Hz, 1H), 4.38 (dd, J = 8.7,

1.4 Hz, 1H), 4.30 (dd, J = 17.5, 1.4 Hz, 1H), 4.07 (d, J = 17.5 Hz, 1H),

3.79 (dddd, J = 27.1, 8.5, 3.1, 1.7 Hz, 2H), 3.31 (d, J = 3.1 Hz, 1H), 1.92 (m, 1H), 1.25-1.63 (26

H), 0.88 (dd, J =6.6, 6.6 Hz, 3H); 13C NMR (150 MHz, CDCl3): δ 212.3, 101.6, 91.5 (d, J = 174.9

Hz) , 71.7 (d, J = 5.3 Hz), 71.2 (d, J = 18.5 Hz), 66.7, 32.1, 30.4 (d, J = 21.3 Hz), 29.8, 29.8, 29.8,

29.8, 29.6, 29.6, 29.5, 25.4, 25.3, 23.6, 23.6, 22.8, 14.2; 19F NMR (470 MHz, CDCl3): δ –201.9

HRMS (EI+) calcd for [C21H39FNaO4]+ 397.2725; found 397.2755

Determination of relative stereochemistry for fluorohydrin 221

Analysis of 1H-NMR of fluorohydrins 200 and 221 revealed identical signals between 1.60 and

4.70 ppm indicating the two compounds share the same relative stereochemistry.

Determination of enantiomeric excess of fluorohydrin 221

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 221 was prepared. Following General Procedure E, optically enriched and racemic

samples of 221 (0.050 g, 0.13 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric p-nitrobenzoyl esters were separated by chiral HPLC using a

DIACEL CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 80:20; detection

at 260 nm; retention time = 8.76 min for (+)-221-Bis-PNB; 12.06 min for (-)-221-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically enriched bis-p-nitrobenzoate derivative

was determined using the same method (91% ee).

Preparation of aldol adduct 222

Following General Procedure A, a solution of 4-methyl-4-nitropentanal (0.050 mL, 0.379 mmol),

NFSI (0.119 g, 0.379 mmol), L-proline (0.044 g, 0.379 mmol), and NaHCO3 (0.032 g, 0.379 mmol)

was stirred for 120 minutes at -10 °C in 0.50 mL of DMF. Dioxanone 75 (0.030 mL, 0.253 mmol)

in CH2Cl2 (5.5 mL) was stirred for 72 hrs. Purification of the crude fluorohydrin 222 by flash

chromatography (pentane-EtOAc 3:1) afforded fluorohydrin 222 (0.034 g, 46 % yield) as a

colorless oil.

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Data for syn-fluorohydrin 222: []D20 = -71.6 (c 1.9 in CHCl3); IR (neat):

= 3515, 2989, 1741, 1540, 1376, 861, cm-1;1H NMR (500 MHz, CDCl3): δ

4.77 (ddd, J = 48.7, 10.0, 1.0 Hz, 1H), 4.35 (dd, J = 9.0, 1.3 Hz, 1H), 4.30

(dd, J = 17.7, 1.4 Hz, 1H), 4.08 (d, J = 17.7 Hz, 1H), 3.76 (dddd, J = 27.4,

8.9, 2.3, 2.3 Hz, 1H), 3.43 (d, J = 2.3 Hz, 1H), 2.57 (m, 1H), 2.30 (m, 1H), 1.69 (s, 3H), 1.67 (s,

3H), 1.48 (s, 3H), 1.40 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 212.5, 101.8, 87.9 (d, J = 176.9

Hz), 87.1, 72.2 (d, J = 18.6 Hz), 71.2 (d, J = 5.5 Hz) 66.5, 41.3 (d, J = 20.5 Hz), 28.0, 25.4, 23.6,

23.5; 19F NMR (470 MHz, CDCl3): δ –201.4

HRMS (EI+) calcd for [C12H21FNO6]+ 294.1347; found 294.1359

Determination of enantiomeric excess of fluorohydrin 222

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 222 was prepared. Following General Procedure E, optically enriched and racemic

samples of 222 (0.050 g, 0.171 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric fluorohydrin were separated by chiral HPLC using a DIACEL

CHIRALCEL-OD column; flow rate 1.5 mL/min; eluent: hexanes-iPrOH 80:20; detection at 260

nm; retention time = 34.51 min for (-)-222-Bis-PNB; 37.98 min for (+)-222-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically pure bis-p-nitrobenzoate derivative

was determined using the same method (95% ee).

Preparation of aldol adduct 223

Following General Procedure A, a solution of pentenal (0.050 g, 0.60 mmol), NFSI (0.189 g, 0.60

mmol), L-proline (0.069 g, 0.60 mmol) and NaHCO3 (0.055 g, 0.60 mmol) was stirred at -10 °C in

DMF (0.80 mL) for 1 hr. Dioxanone 75 (0.048 mL, 0.40 mmol) in CH2Cl2 (7.2 mL) was stirred for

72 hours. Purification of the crude fluorohydrin 223 by flash chromatography (pentane-EtOAc

85:15) afforded fluorohydrin 223 (0.059 g, 64 % yield) as a light yellow oil.

Data for syn-fluorohydrin 223: []D20 = -115.8 (c 2.46 in CHCl3); IR (neat):

= 3509, 2989, 1740, 1643, 1422, 1377, 1089, 863 cm-1; 1H NMR (600 MHz,

CDCl3): δ 5.83 (m, 1H), 5.20 (d, J = 17.4 Hz, 1H), 5.14 (d, J = 9.9, 1.0 Hz,

1H), 4.73 (dddd, J = 47.0, 7.0, 7.0, 1.3 Hz, 1H), 4.39 (dd, J = 8.9, 1.0 Hz,

1H), 4.30 (dd, J = 17.7, 1.0 Hz), 4.08 (d, J = 17.6), 2.69 (m, 1H), 2.48 (m, 1H) 1.49 (s, 3H), 1.43

(s, 3H);13C NMR (150 MHz, CDCl3): δ 212.4, 133.0 (d, J = 7.6 Hz), 118.5, 101.6, 90.5 (d, J =

130

178.0 Hz), 71.5 (d, J = 5.3 Hz), 70.5 (d, J = 18.2 Hz), 66.6, 34.9 (d, J = 22.2 Hz), 23.6, 23.6; 19F

NMR (470 MHz, CDCl3): δ –201.6

HRMS (EI+) calcd for [C11H18FO4]+ 233.1184; found 233.1202

Determination of relative stereochemistry for fluorohydrin 223

Following General Procedure F, the fluorohydrin 223 (0.105 g, 0.45 mmol) was converted to the

fluorohydrin 200. Comparison of 1H and 19F NMR with fluorohydrin 200 confirmed relative

stereochemistry.

Determination of the absolute stereochemistry for fluorohydrin 223

Following General Procedure F, the fluorohydrin 223 (0.105 g, 0.45 mmol) was converted to the

fluorohydrin 200. Comparison of []D values with fluorohydrin 200 confirmed absolute

stereochemistry

Determination of enantiomeric excess of fluorohydrin 223

Following General Procedure F, the optically enriched sample of 223 (0.105 g, 0.45 mmol) was

converted into fluorohydrin 200. Following General Procedure E, the optically enriched and

racemic samples of fluorohydrin 200 were converted into their corresponding bis-p-nitrobenzoate

derivative. The enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a

DIACEL CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 80:20; detection

at 260 nm; retention time = 17.27 min for (-)-200-Bis-PNB; 22.06 min for (+)-200-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically enriched bis-p-nitrobenzoate derivative

was determined using the same method (93 % ee).

Preparation of aldol adduct 224

Following General Procedure A, a solution of 3-(4-methoxyphenyl)propanal (0.050 mL, 0.317

mmol), NFSI (0.100 g, 0.317mmol), L-proline (0.037 g, 0.317 mmol), and NaHCO3 (0.027 g, 0.317

mmol) was stirred for 90 minutes at -10 °C in 0.43 mL of DMF. Dioxanone 75 (0.025 mL, 0.211

mmol) in CH2Cl2 (3.8 mL) was stirred for 72 hrs. Purification of the crude fluorohydrin 224 by flash

chromatography (pentane-EtOAc 4:1) afforded fluorohydrin 224 (0.034 g, 51 % yield) as a white

solid.

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Data for syn-fluorohydrin 224: []D20 = -233.4 (c 3.0 in CHCl3); 1H

NMR (600 MHz, CDCl3): δ 7.20 (d, J = 8.8 Hz, 2H), 6.86 (d, J =

8.8Hz, 2H) 4.81 (dddd, J = 46.8, 7.3, 7.3 Hz, 0.8 Hz, 1H), 4.40 (d,

J = 8.8 Hz, 1H), 4.26 (d, J = 17.8 Hz, 1H), 4.07 (d, J = 17.8 Hz,

1H), 3.79 (s, 3H), 3.77 (d, J = 24.1, 8.8 Hz, 1H), 3.39 (br s, 1H), 3.15 (m, 1H), 2.99 (m, 1H), 1.46

(s, 3H), 1.39 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 212.7, 158.6, 130.6, 128.9 (d, J = 8.0 Hz),

114.1, 101.7, 91.9 (d, J = 179.2 Hz), 71.4 (d, J = 5.1 Hz), 70.1 (d, J =18.1 Hz), 66.6, 55.4, 35.8

(d, J = 22.4 Hz), 23.6, 23.5; 19F NMR (470 MHz, CDCl3): δ –200.1

HRMS (EI+) calcd for [C16H22FO5]+ 313.1446; found 313.1450

Determination of enantiomeric excess of fluorohydrin 224

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 224 was prepared. Following General Procedure E, optically enriched and racemic

samples of 224 (0.040 g, 0.128 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric fluorohydrin were separated by chiral HPLC using a DIACEL

CHIRALCEL-OD column; flow rate 1.5 mL/min; eluent: hexanes-iPrOH 93.5:6.5; detection at 260

nm; retention time = 74.8 min for (+)-224-Bis-PNB; 110.4 min for (-)-224-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically pure bis-p-nitrobenzoate derivative

was determined using the same method (95% ee).

Preparation of aldol adduct 225

Following General Procedure A, a solution of pentynal (0.050 g, 0.61 mmol), NFSI (0.192 g, 0.61

mmol), L-proline (0.070 g, 0.61 mmol) and NaHCO3 (0.051 g, 0.61 mmol) was stirred for 1.5 hrs

at -10°C in DMF (0.81 mL). Dioxanone 75 (0.049 mL, 0.41 mmol) in CH2Cl2 (7.3 mL) was stirred

for 48 hours. Purification of the crude fluorohydrin by flash chromatography (pentane-EtOAc; 9:1)

afforded fluorohydrin 225 (0.052 g, 55 % yield) as a light yellow oil.

Data for syn-fluorohydrin 225: []D20 = -62.9 (c 3.42 in CHCl3); IR (neat):

= 3512, 3293, 2993, 1743, 1378, 1224, 1033 cm-1; 1H NMR (500 MHz,

CDCl3): δ 4.86 (dddd, J = 46.4, 7.3, 7.3, 1.5 Hz, 1H), 4.38 (dd, J = 8.9, 1.5

Hz, 1H), 4.31 (dd, J = 17.6, 1.6 Hz, 1H), 4.10 (d, J = 17.7 Hz, 1H), 4.00

(ddd, J = 27.9, 9.1, 1.5 Hz, 1H), 2.76 (m, 2H), 2.04 (t, J = 2.8 Hz, 1H), 1.49 (s, 3H), 1.43 (s, 3H);

13C NMR (150 MHz, CDCl3): δ 212.2, 101.7, 89.0 (d, J = 180.0 Hz), 79.0 (d, J = 15.4 Hz), 71.3 (d,

132

J = 5.1 Hz), 70.8, 69.7 (d, J = 17.4 Hz), 66.6, 23.7, 23.6, 20.4 (d, J = 28.9 Hz); 19F NMR (470

MHz, CDCl3): δ –200.1

HRMS (EI+) calcd for [C11H16FO4]+ 231.1027; found 231.1042

Determination of relative stereochemistry for fluorohydrin 225

Following General Procedure F, the fluorohydrin 225 (0.10 g, 0.43 mmol) was converted to the

fluorohydrin 200. Comparison of 1H and 19F NMR with fluorohydrin 200 confirmed relative

stereochemistry.

Determination of the absolute stereochemistry for fluorohydrin 225

Following General Procedure F, the fluorohydrin 225 (0.10 g, 0.43 mmol) was converted to the

fluorohydrin 200. Comparison of []D values with fluorohydrin 200 confirmed absolute

stereochemistry.

Determination of enantiomeric excess of fluorohydrin 225

Following General Procedure F, the optically enriched sample of 225 (0.10 g, 0.43 mmol) was

converted into fluorohydrin 200. Following General Procedure E, the optically enriched and

racemic samples of fluorohydrin 200 were converted into their corresponding bis-p-nitrobenzoate

derivative. The enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a

DIACEL CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 80:20; detection

at 260 nm; retention time = 17.27 min for (-)-225-Bis-PNB; 22.06 min for (+)-225-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically enriched bis-p-nitrobenzoate derivative

was determined using the same method (92% ee).

Preparation of aldol adduct 227

Following General Procedure A, a solution of 3-(5-methylfuran-2-yl)propanal (0.050 mL, 0.376

mmol), NFSI (0.119 g, 0.376 mmol), L-proline (0.029 g, 0.376 mmol), and NaHCO3 (0.032 g, 0.376

mmol) was stirred for 90 minutes at -10 °C in 0.50 mL of DMF. Dioxanone 75 (0.030 mL, 0.251

mmol) in CH2Cl2 (4.5 mL) was stirred for 72 hrs. Purification of the crude fluorohydrin 227 by flash

chromatography (pentane-EtOAc 5:1) afforded fluorohydrin 227 (0.038 g, 53 % yield) as a

colorless oil.

133

Data for syn-fluorohydrin 227: []D20 = 16.4 (c 2.5 in CHCl3); 1H NMR

(600 MHz, CDCl3): δ 6.02 (d, J = 3.1 Hz, 1H), 5.88 (d, J = 3.1 Hz, 1H),

4.95 (ddd, J = 46.8, 6.9, 6.9 Hz, 1H), 4.41 (d, J = 9.0 Hz, 1H), 4.29 (d,

J = 17.6 Hz, 1H), 4.08 (d, J = 17.6 Hz, 1H), 3.82 (dd, J = 27.4, 8.8 Hz,

1H), 3.34 (d, J = 1.5 Hz, 1H), 3.18 (m, 1H), 3.06 (m, 1H), 2.26 (s, 3H),

1.49 (s, 3H), 1.42 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 212.4, 151.4, 149.0 (d, J = 9.5 Hz),

108.3, 106.4, 101.7, 89.4 (d, J = 179.3 Hz) , 71.4 (d, J = 5.1 Hz), 70.4 (d, J = 17.7 Hz), 66.6, 29.5

(d, J = 25.2 Hz), 23.6, 23.6, 13.7; 19F NMR (470 MHz, CDCl3): δ –201.2

HRMS (EI+) calcd for [C14H20FO5]+ 287.1289; found 287.1289

Determination of enantiomeric excess of fluorohydrin 227

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 227 was prepared. Following General Procedure E, optically enriched and racemic

samples of 227 (0.043 g, 0.15 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric fluorohydrin were separated by chiral HPLC using a DIACEL

CHIRALCEL-OD column; flow rate 1.5 mL/min; eluent: hexanes-iPrOH 93.5:6.5; detection at 260

nm; retention time = 30.00 min for (-)-227-Bis-PNB; 40.48 min for (+)-227-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically pure bis-p-nitrobenzoate derivative

was determined using the same method (95% ee).

Preparation of aldol adduct 228

Following General Procedure A, a solution of hydrocinnamaldehyde (0.050 mL, 0.38 mmol), NFSI

(0.120 g, 0.38 mmol), L-proline (0.044 g, 0.38 mmol), and NaHCO3 (0.032 g, 0.38 mmol) was

stirred for 75 minutes at -10 °C in 0.50 mL of DMF. Dioxanone 75 (0.036 mL, 0.30 mmol) in CH2Cl2

(4.5 mL) was stirred for 72 hrs. Purification of the crude fluorohydrin 228 by flash chromatography

(pentane-EtOAc 4:1) afforded fluorohydrin 228 (0.053 g, 62 % yield) as a colorless oil.

Data for syn-fluorohydrin 228: []D20 = -3.1 (c 2.1 in CHCl3); IR (neat):

= 3511, 2923, 1739, 1705, 1650, 1585, 1453, 863, 698 cm-1;1H NMR

(600 MHz, CDCl3): δ 7.30 (m, 5H), 4.87 (dd

d, J = 46.5, 7.0, 7.0 Hz, 1H), 4.42 (dd, J = 9.0, 0.9 Hz, 1H), 4.27 (dd, J = 17.7, 1.0 Hz, 1H), 4.08

(d, J = 17.6 Hz, 1H), 3.79 (dd, J = 27.6, 9.0 Hz, 1H), 3.42 (br s, 1H), 3.24 (m, 1H), 3.05 (m, 1H),

134

1.48 (s, 3H), 1.40 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 212.6, 136.9 (d, J = 8.1 Hz), 129.6,

128.7, 126.8, 101.7, 91.7 (d, J = 177.8 Hz) , 71.4 (d, J = 5.2 Hz), 70.2 (d, J = 18.1 Hz), 66.6, 36.7

(d, J = 22.4 Hz), 23.6, 23.5; 19F NMR (470 MHz, CDCl3): δ –200.1

HRMS (EI+) calcd for [C15H20FO4]+ 283.1340; found 283.1365

Determination of relative stereochemistry for fluorohydrin 228

Reduction with sodium borohydride of the fluorohydrin 228 (0.105 g, 0.37 mmol) in methanol

allowed for conversion to the corresponding syn-diol 228-XRD. Recyrstallization in ethanol (1:1)

allowed for the relative stereochemistry to be assigned using single X-ray crystallography (see X-

ray structures)

Determination of enantiomeric excess of fluorohydrin 228

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 228 was prepared. The enantiomeric fluorohydrin were separated by chiral HPLC

using a DIACEL CHIRALCEL-OD column; flow rate 1.5 mL/min; eluent: hexanes-iPrOH 97:3;

detection at 260 nm; retention time = 12.80 min for (-)-228; 13.64 min for (+)-228 (see

chromatograms). The enantiomeric excess of the optically pure 228 was determined using the

same method (98% ee).

Preparation of aldol adduct 229

Following General Procedure A, a solution of 3-(4-bromophenyl)propanal (0.050 g, 0.236 mmol),

NFSI (0.074 g, 0.236 mmol), L-proline (0.028 g, 0.236 mmol), and NaHCO3 (0.020 g, 0.236 mmol)

was stirred for 120 minutes at -10 °C in 0.30 mL of DMF. Dioxanone 75 (0.022 mL, 0.157 mmol)

in CH2Cl2 (2.8 mL) was stirred for 72 hrs. Purification of the crude fluorohydrin 229 by flash

chromatography (pentane-EtOAc 4:1) afforded fluorohydrin 229 (0.034 g, 61 % yield) as a white

solid.

Data for syn-fluorohydrin 229: []D20 = -76.4 (c 0.8 in CHCl3); IR (neat):

= 3513, 2989, 1740, 1490, 1377, 864cm-1;1H NMR (600 MHz, CDCl3):

δ 7.44 (d, J = 8.2 Hz), 7.16 (d, J = 8.2 Hz), 4.80 (ddd, J = 46.8, 7.2, 7.2,

0.9 Hz, 1H), 4.40 (d, J = 18.9 Hz, 1H), 4.27 (d, J = 17.7 Hz, 1H), 4.08 (d,

J = 17.7 Hz, 1H), 3.75 (dd, J = 27.6, 9.0 Hz, 1H), 3.42 (br s, 1H), 3.18 (m, 1H), 2.97 (m, 1H), 1.46

(s, 3H), 1.39 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 212.6, 136.0 (d, J = 7.2 Hz), 131.8, 131.4,

135

120.8, 101.7, 91.4 (d, J = 179.9 Hz) , 71.3 (d, J = 5.0 Hz), 70.2 (d, J = 17.1 Hz), 66.6, 36.2 (d, J

= 22.4 Hz), 23.6, 23.5; 19F NMR (470 MHz, CDCl3): δ –200.6

HRMS (EI+) calcd for [C15H19BrFO4]+ 361.0445; found 361.0434

Determination of enantiomeric excess of fluorohydrin 229

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 229 was prepared. Following General Procedure E, optically enriched and racemic

samples of 229 (0.037 g, 0.103 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric fluorohydrin were separated by chiral HPLC using a DIACEL

CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 80:20; detection at 260

nm; retention time = 52.3 min for (+)-229-Bis-PNB; 63.5 min for (-)-229-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically pure bis-p-nitrobenzoate derivative

was determined using the same method (95% ee).

Preparation of aldol adduct 230

A solution of 3-OTIPS-propanal (1.152 g, 5.0 mmol, 1.5 equiv.), Selectfluor (1.77 g, 5.0 mmol, 1.5

equiv.), and L-proline (0.576 g, 5.0 mmol, 1.5 equiv.) were dissolved in 50 mL DMF (0.1 M) and

stirred at 4 °C for 3 hrs or until the reaction was complete as determined by TLC analysis. The

reaction mixture was diluted with 500 mL of diethyl ether and washed 3 x H2O (100 mL). The

organic layer was removed, dried over MgSO4, and concentrated under reduced pressure.

Dioxanone 75 (0.434 g, 3.33 mmol, 1.0 equiv.) and L-proline (0.306 g, 2.7 mmol, 0.8 equiv.) were

added to the crude α-fluoroaldehyde in 25 mL of CH2Cl2 (0.2 M). After 48 hours, the reaction

mixture was diluted with CH2Cl2 and washed with H2O. Purification of the crude fluorohydrin 230

by flash chromatography (pentane-EtOAc; 20:1) afforded fluorohydrin 230 (0.692 g, 55 % yield)

as a colorless oil.

Data for syn-fluorohydrin 230: []D20 = -25.6 (c 5.0 in CHCl3); IR (neat): =

3503, 2994, 2867, 1741, 1224, 1094, 883 cm-1; 1H NMR (600 MHz, CDCl3):

δ 4.75 (dddd, J = 47.1, 5.7, 5.7, 1.9 Hz, 1H), 4.41 (dd, J = 8.5, 1.4 Hz, 1H),

4.31 (dd, J = 17.5, 1.4 Hz, 1H), 4.08 (d, J = 17.6 Hz, 1H), 4.05 (ddd, J =

27.4, 9.4, 1.7 Hz, 2H), 4.02 (dd, J = 18.5, 5.5 Hz, 1H), 3.33 (br s, 1H), 1.50 (s, 3H), 1.44 (s, 3H),

136

1.07 (m, 21H); 13C NMR (150 MHz, CDCl3): δ 211.7, 101.6, 91.0 (d, J = 178.1 Hz) , 71.7 (d, J =

5.2 Hz), 69.6 (d, J = 18.2 Hz), 66.8, 62.4 (d, J = 27.4 Hz), 23.7, 23.7, 18.1, 12.1; 19F NMR (470

MHz, CDCl3): δ –209.0

HRMS (EI+) calcd for [C18H36FO5Si]+ 379.2311; found 379.2343

Determination of the absolute stereochemistry for fluorohydrin 230

Following General Procedure E, the fluorohydrin 230 (0.050 g, 0.13 mmol) was converted into the

corresponding bis-p-bromobenzoate derivative 230-XRD. Recyrstallization in dichloromethane

and ethanol (1:1) allowed for the absolute stereochemistry to be assigned using single X-ray

crystallography (see X-ray structures).

Determination of enantiomeric excess of fluorohydrin 230

Following General Procedure A, using a 1:1 mixture of L-:D- proline, a racemic sample of the

fluorohydrin 230 was prepared. Following General Procedure E, optically enriched and racemic

samples of 230 (0.050 g, 0.13 mmol) were converted into the corresponding bis-p-nitrobenzoate

derivative. The enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a

DIACEL CHIRALCEL-OD column; flow rate 1.0 mL/min; eluent: hexanes-iPrOH 80:20; detection

at 260 nm; retention time = 6.26 min for (-)-230-Bis-PNB; 8.33 min for (+)-230-Bis-PNB (see

chromatograms). The enantiomeric excess of the optically enriched bis-p-nitrobenzoate derivative

was determined using the same method (99 % ee).

Preparation of aldol adduct 237

Following General Procedure B, a solution of pentanal (0.050 mL, 0.47 mmol), NFSI (0.148 g,

0.47 mmol), L-proline (0.054 g, 0.47 mmol) and NaHCO3 (0.039 g, 0.47 mmol) was stirred at -10

°C in DMF (0.63 mL) for 75 minutes. Cyclohexanone (0.488 mL, 4.70 mmol) was added and the

reaction mixture was stirred for 18 hours. Purification of crude fluorohydrin 237 by flash

chromatography (pentane:EtOAc – 95:5 → 90:10) afforded fluorohydrin 237 (0.051 g, dr = 10:1,

54% yield) as an off-white solid.

137

Data for syn-fluorohydrin 237: []D20 = -16.4 (c 1.65 in CH2Cl2); IR (neat): =

3498, 2957, 2938, 2863, 1698, 1450, cm-1; 1H NMR (600 MHz, CDCl3): δ 4.55

(ddd, J = 47.8, 8.3, 4.2 Hz, 1H), 3.77 (dddd, J = 29.0, 8.3, 4.2, 2.1 Hz, 1H),

3.55 (d, J = 4.2 Hz, 1H), 2.45 (m, 1H), 2.36 (dddd, J = 13.4, 13.4, 6.2, 1.1

Hz, 1H), 2.23 (m, 1H), 2.12 (m, 1H), 1.85 – 1.97 (2H), 1.55 – 1.78 (3H), 1.36 – 1.55 (3H), 0.96

(dd, J = 7.4, 7.4 Hz, 3H); 13C NMR (150 MHz, CDCl3): δ 215.7, 92.7 (d, J = 174.1 Hz), 72.2 (d, J

= 19.3 Hz), 52.8 (d, J = 3.5 Hz), 42.9, 32.8 (d, J = 21.2), 30.1, 27.8, 24.8; 19F NMR (470 MHz,

CDCl3): δ –199.3

HRMS (EI+) calcd for [C11H20FO2]+ 203.1442; found 203.1421

Determination of enantiomeric excess of fluorohydrin 237

Following General Procedure E, the optically enriched and racemic samples of fluorohydrin 237

were converted into their corresponding p-nitrobenzoyl diesters. The enantiomeric p-nitrobenzoyl

diesters were separated by chiral HPLC using a Lux® 3µm Amylose-1 column; flow rate 0.40

mL/min; eluent: hexanes-iPrOH 90:10; detection at 254 nm; retention times = 8.96 min and 10.37

min (see chromatograms). The enantiomeric excess of the optically enriched p-nitrobenzoyl

diesters was determined using the same method (94 % ee).

Preparation of aldol adduct 238

Following General Procedure B, a solution of pentanal (0.0.50 mL, 0.47 mmol), NFSI (0.148 g,

0.47 mmol), L-proline (0.054 g, 0.47 mmol) and NaHCO3 (0.039 g, 0.47 mmol) was stirred for 75

minutes at -10 °C in DMF (0.63 mL). Thiopyranone 206 (0.546 g, 4.70 mmol) was added and the

reaction mixture was stirred for 24 hours at 4°C. Purification of crude fluorohydrin 238 by flash

chromatography (pentane-Et2O 4:1) afforded syn-fluorohydrin 238 (0.049 g, 47% yield) as a white

solid.

Data for syn-fluorohydrin 238: []D20 = -16.4° (c 1.65 in CH2Cl2); IR (neat):

= 3353, 2952, 1706, 1428, 510 cm-1; 1H NMR (600 MHz, CDCl3): δ 4.58

(ddd, J = 48.0, 8.8, 2.3 Hz, 1H), 3.95 (ddd, J = 26.7, 6.6, 2.3 Hz, 1H), 3.07

(m, 1H), 3.06 (m, 1H), 2.94 – 3.02 (3H), 2.72 – 2.86 (3H), 1.88 (m, 1H), 1.64

(m, 1H), 1.60 (m, 1H), 1.51 (m, 1H), 1.42 (m 1H), 0.97 (dd, J = 7.4, 7.4 Hz, 3H);13C NMR (150

MHz, CDCl3): δ 211.7, 92.8 (d, J = 173.6 Hz), 71.8 (d, J = 20.8 Hz), 55.2 (d, J = 3.1 Hz), 44.7,

138

32.9 (d, J = 20.9 Hz), 32.5 (d, J = 1.2 Hz), 30.9, 18.7 (d, J = 4.9 Hz), 14.0; 19F NMR (470 MHz,

CDCl3): δ –197.6

HRMS (EI+) calcd for [C10H18FO2S]+ 221.1006; found 221.0999

Determination of enantiomeric excess of fluorohydrin 238

Using a 1:1 mixture of L-: D-proline, a racemic sample of fluorohydrin 238 was prepared. The

enantiomeric fluorohydrins were separated by chiral HPLC using a Lux® 3µm Amylose-1 column;

flow rate 0.40 mL/min; eluent: hexanes-iPrOH 90:10; detection at 254 nm; retention time = 7.14

min for (+)-238; 8.89 min for (-)-238 (see chromatograms). The enantiomeric excess of the

optically enriched fluorohydrin 238 was determined using the same method (84% ee).

Preparation of aldol adduct 239

Following General Procedure B, a solution of pentenal (0.050 g, 0.595 mmol), NFSI (0.188 g,

0.595 mmol), L-proline (0.069 g, 0.595 mmol) and NaHCO3 (0.050 g, 0.595 mmol) was stirred for

1.5 hrs at -10°C in DMF (0.79 mL). Cyclohexanone (0.62 mL, 5.95 mmol) was added and the

reaction mixture stirred for 16 hours. Purification of crude fluorohydrin 239 by flash

chromatography (pentane:EtOAc – 95:5 → 90:10) afforded fluorohydrin 239 (0.059 g, 50% yield)

as a white solid.

Data for syn-fluorohydrin 239: []D20 = +22.2 (c 0.60 in CH2Cl2); IR (neat):

= 3513, 2937, 2863, 1698, 1449, 1132 cm-1; 1H NMR (600 MHz, CDCl3):

δ 5.83 (dddd, J = 17.2, 10.3, 7.2, 7.0 Hz, 1H), 5.19 (dd, J = 17.2, 1.5 Hz,

1H), 5.13 (d, J = 10.3 Hz, 1H), 4.57 (ddd, J = 47.7, 8.3, 4.7 Hz, 1H), 3.80

(dddd, J = 29.7, 8.3, 4.1, 2.0 Hz, 1H), 3.58 (d, J = 4.1 Hz, 1H), 2.74 (m, 1H), 2.67 (m, 1H), 2.42 –

2.55 (2H), 2.36 (dddd, J = 13.4, 13.4, 6.1, 1.1 Hz, 1H), 2.22 (m, 1H), 2.12 (m, 1H), 1.93 (m, 1H),

1.73 (ddddd, J = 13.0, 13.0, 13.0, 3.6, 3.6 Hz, 1H), 1.67 (ddddd, J = 13.0, 13.0, 13.0, 3.6, 3.6 Hz,

1H), 1.42 (dddd, J = 12.7, 12.7, 12.7, 3.6, 3.6 Hz, 1H); 13C NMR (150 MHz, CDCl3): δ 215.6, 133.3

(d, J = 7.5 Hz), 118.4, 92.0 (d, J = 177.6 Hz), 71.6 (d, J = 18.8 Hz), 52.7 (d, J = 3.6 Hz), 42.8, 35.4

(d, J = 23.4 Hz), 30.0, 27.8 24.8; 19F NMR (470 MHz, CDCl3): δ –198.7

HRMS (EI+) calcd for [C11H18FO2]+ 201.1285; found 201.1260

Determination of relative stereochemistry for fluorohydrin 239

139

Following General Procedure D, the fluorohydrin 239 was converted to carbacycle 263. NOE

analysis of carbacycle 263 confirmed relative stereochemistry of fluorohydrin 239.

Determination of enantiomeric excess of fluorohydrin 239

Following General Procedure E, optically enriched and racemic samples of fluorohydrin 239 were

converted into their corresponding p-nitrobenzoyl diesters. The enantiomeric p-nitrobenzoyl

diesters were separated by chiral HPLC using a Lux® 3µm i-Cellulose-3 column; flow rate 0.20

mL/min; eluent: hexanes-iPrOH 85:15; detection at 254 nm; retention times = 4.32 min and 6.09

min (see chromatograms). The enantiomeric excess of the optically enriched p-nitrobenzoyl

diester was determined using the same method (96% ee).

Preparation of aldol adduct 240

Following General Procedure B, a solution of pentenal (0.100 mL, 1.02 mmol), NFSI (0.319 g,

1.02 mmol), L-proline (0.118 g, 1.02 mmol) and NaHCO3 (0.086 g, 1.02 mmol) was stirred for 60

minutes at -10 °C in DMF (1.35 mL). Thiopyranone 206 (1.19 g, 10.2 mmol) was then added and

the reaction mixture was stirred for 24 hrs at 4°C. Purification of the crude fluorohydrin 240 by

flash chromatography (pentane:Et2O – 4:1) afforded syn-fluorohydrin 240 (0.069 g, dr = 6:1, 31

% yield) as a waxy white solid.

Data for syn-fluorohydrin 240: []D20 = -11.0 (c 0.30 in CH2Cl2); IR (neat):

= 3455, 2929, 1703, 1428, 1117, 923 cm-1;1H NMR (600 MHz, CDCl3): δ

5.82 (dddd, J = 17.1, 10.3, 7.0, 6.9 Hz, 1H), 5.21 (dd, J = 17.1, 1.4 Hz, 1H),

5.15 (d, J = 10.3, 1H), 4.61 (ddd, J = 47.7, 5.9, 2.0 Hz, 1H), 3.97 (ddd, J =

27.5, 6.4, 2.0 Hz, 1H), 3.09 (m, 1H), 3.05 (m, 1H), 3.04 (m, 1H), 2.99 (m, 1H), 2.97 (m, 1H), 2.81

(m, 2H), 2.76 (m, 1H), 2.64 (m, 1H), 2.51 (m, 1H) ; 13C NMR (150 MHz, CDCl3): δ 211.7, 132.8

(d, J = 7.3 Hz), 118.7, 92.1 (d, J = 176.3 Hz), 71.2 (d, J = 19.3 Hz), 55.1 (d, J = 3.0 Hz), 44.7, 35.4

(d, J = 22.2 Hz), 32.4, 30.8; 19F NMR (470 MHz, CDCl3): δ -197.0

HRMS (EI+) calcd for [C10H16FO2S]+ 219.0850; 219.0833

Determination of relative stereochemistry for fluorohydrin 240

140

Following General Procedure D, the fluorohydrin 240 was converted to carbacycle 264. NOE

analysis of carbacycle 264 confirmed relative stereochemistry of fluorohydrin 240.

Preparation of aldol adduct 241

Following General Procedure B, a solution of phthalimidoacetaldehyde (0.050 g, 0.265 mmol),

NFSI (0.84 g, 0.265 mmol), L-proline (0.031 g, 0.265 mmol) and 2,6-lutidine (0.031 mL, 0.265

mmol) was stirred at 4°C in DMF (0.35 mL) for 16 hrs. cyclohexanone (0.275 mL, 2.65 mmol)

was added and the reaction mixture was stirred for 18 hours. Purification of crude fluorohydrin

241 by flash chromatography (pentane:EtOAc – 60:40) afforded fluorohydrin 241 (0.068 g, d.r. =

5:1, 84% yield) as a white solid.

Data for fluorohydrin 241: 1H NMR (600 MHz, CDCl3): δ 7.92, 7.91, 7.78,

7.78, 6.29, 6.07, 5.37, 4.63, 3.51, 2.93, 2.92, 2.89, 2.80, 2.44, 2.41, 2.30,

2.25, 2.16, 2.01. 1.99, 1.87, 1.78, 1.71; 13C NMR (150 MHz, CDCl3): δ

215.9, 213.5, 167.1, 167.1, 134.9, 134.8, 131.7, 131.6, 124.1, 124.1, 89.9,

88.3, 69.9, 65.5, 51.8, 51.0, 43.3, 42.7, 32.4, 28.3, 27.8, 26.1, 25.4, 24.8; 19F NMR (470 MHz,

CDCl3): δ –156.0, –160.7

HRMS (EI+) calcd for [C16H17FNO4]+ 306.1136; observed 306.1135

Determination of enantiomeric excess of fluorohydrin 241

Using a 1:1 mixture of L-: D-proline, a racemic sample of fluorohydrin 241 was prepared. The

enantiomeric fluorohydrins were separated by chiral HPLC using a Lux® 3µm Amylose-1 column;

flow rate 0.40 mL/min; eluent: hexanes-iPrOH 90:10; detection at 254 nm; retention times = 26.70

min and 28.10 min (see chromatograms). The enantiomeric excess of the optically enriched

fluorohydrin 241 was determined using the same method (92% ee).

Preparation of aldol adduct 242

Following General Procedure B, a solution of phthalimidoacetaldehyde (0.050 g, 0.265 mmol),

NFSI (0.84 g, 0.265 mmol), L-proline (0.031 g, 0.265 mmol) and 2,6-lutidine (0.031 mL, 0.265

mmol) was stirred at 4°C in DMF (0.35 mL) for 15 hrs. Thiopyranone 206 (0.307 g, 2.65 mmol)

was added and the reaction mixture was stirred for 18 hours. Purification of crude fluorohydrin

242 by flash chromatography (pentane:EtOAc – 60:40) afforded fluorohydrin 242 (0.075 g, d.r. =

5:1, 87% yield) as a white solid.

141

Data for fluorohydrin 242: 1H NMR (600 MHz, CDCl3): δ 7.93, 7.92, 7.79,

7.79, 6.26, 6.11, 5.37, 4.78, 3.44, 3.25, 3.24, 3.16, 3.11, 3.09, 3.03, 2.99,

2.98, 2.85, 2.80, 2.79; 13C NMR (150 MHz, CDCl3): δ 212.8, 210.2, 167.1,

167.1, 135.1, 134.9, 131.6, 131.5, 124.3, 124.2, 89.6, 88.3, 70.1, 66.1,

54.6, 53.6, 45.7, 44.9, 34.6, 31.3, 30.7, 30.1; 19F NMR (470 MHz, CDCl3): δ –155.5, –158.5

HRMS (EI+) calcd for [C15H14FNO4S + NH4]+ 341.0966; observed 341.0938

Determination of enantiomeric excess of fluorohydrin 242

Using a 1:1 mixture of L-: D-proline, a racemic sample of fluorohydrin 242 was prepared. The

enantiomeric fluorohydrins were separated by chiral HPLC using a Lux® 3µm Amylose-1 column;

flow rate 0.70 mL/min; eluent: hexanes-iPrOH 80:20; detection at 254 nm; retention times = 15.99

min and 17.07 min (see chromatograms). The enantiomeric excess of the optically enriched

fluorohydrin 242 was determined using the same method (90% ee).

Preparation of aldol adduct 243

Following General Procedure C, a solution of pentanal (0.100 mL, 0.941 mmol), N(SCF3)Phth

(0.232 g, 0.941 mmol), L-proline (0.108 g, 0.941 mmol), and NaHCO3 (0.078 g, 0.941 mmol) was

stirred for 50 minutes at RT in DMSO (1.30 mL). Dioxanone 75 (0.044 mL, 0.270 mmol) in CH2Cl2

(5.6 mL) was stirred for 60 hrs. Purification of crude trifluoromethylthiohydrin 243 by flash

chromatography (pentane:Et2O – 9:1) afforded trifluoromethylthiohydrin 243 (0.082 g, d.r. = 6:1,

55 % yield) as a light yellow oil.

Data for syn- trifluoromethylthiohydrin 243: []D20 = -111.1° (c 3.0 in

CH2Cl2); IR (neat): = 3508, 2961, 1735, 1741, 1377, 1110, 861, 735 cm-

1; 1H NMR (600 MHz, CDCl3): δ 4.42 (dd, J = 9.1, 1.5 Hz, 1H), 4.30 (dd, J

= 17.6, 1.5 Hz, 1H), 4.08 (d, J = 17.6 Hz, 1H), 4.08 (m, 1H), 3.70 (dd, J =

2.2, 1.7 Hz, 1H), 3.46 (m, 1H), 2.00 (m, 1H), 1.87 (m, 1H), 1.48 (s, 3H), 1.42 (s, 3H), 0.95 (dd, J

= 7.4, 7.4 Hz, 3H); 13C NMR (150 MHz, CDCl3): δ 213.5, 131.6 (q, J = 306.6 Hz), 101.7, 72.4,

71.4, 66.5, 47.0, 36.7, 23.8, 23.7, 20.3, 13.8; 19F NMR (470 MHz, CDCl3): δ –39.4

HRMS (EI+) calcd for [C12H19F3O4S + NH4]+ 334.1294; found 334.1303

Determination of relative stereochemistry for trifluoromethylthiohydrin 243

142

Following General Procedure F, trifluoromethylthiohydrin 244 was converted to

trifluoromethylthiohydrin 243. 1H NMR analysis revealed identical signals with 243 synthesized

using General Procedure C.

Determination of enantiomeric excess of fluorohydrin 243

Following General Procedure E, optically enriched and racemic samples of

trifluoromethylthiohydrin 243 were converted into their corresponding p-nitrobenzoyl diesters. The

enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a Lux® 3µm Amylose-

1 column; flow rate 0.50 mL/min; eluent: hexanes-iPrOH 92.5:7.5; detection at 254 nm; retention

time = 6.20 min and 9.35 min (see chromatograms). The enantiomeric excess of the optically

enriched p-nitrobenzoyl diester was determined using the same method (90% ee).

Preparation of aldol adduct 244

Following General Procedure C, a solution of pentenal (0.100 mL, 1.01 mmol), N(SCF3)Phth

(0.250 g, 1.01 mmol), L-proline (0.116 g, 1.01 mmol), and NaHCO3 (0.085 g, 1.01 mmol) was

stirred for 50 minutes at RT in DMSO (1.35 mL). Dioxanone XX (0.061 mL, 0.506 mmol) in CH2Cl2

(6.7 mL) was added and the reaction mixture was stirred for 60 hrs. Purification of the crude

trifluoromethylthiohydrin 244 by flash chromatography (pentane-Et2O 4:1) afforded

trifluoromethylthiohydrin 244 (0.103 g, d.r. = 6:1, 65 % yield) as a light yellow oil.

Data for syn-trifluoromethylthiohydrin 244: []D20 = -100.5° (c 1.28 in

CH2Cl2); IR (neat): = 3650, 3150, 1737, 1377, 1224, 1109 cm-1;1H NMR

(600 MHz, CDCl3): δ 5.79 (m, 1H), 5.18 (d, J = 17.0 Hz, 1H), 5.14 (d, J =

10.3 Hz, 1H), 4.42 (d, J = 9.0 Hz, 1H), 4.29 (d, J = 17.8 Hz, 1H), 4.12 (d, J

= 9.0 Hz, 1H), 4.07 (d, J = 17.8 Hz, 1H), 3.63 (s, 1H), 3.51 (dd, J = 10.1, 4.8 Hz, 1H), 2.78 (ddd,

J = 14.3, 9.9, 7.9 Hz, 1H), 2.68 (ddd, J = 14.3, 6.6, 5.1 Hz, 1H), 1.48 (s, 3H), 1.42 (s, 3H); 13C

NMR (150 MHz, CDCl3): δ 213.3, 134.4, 131.6 (q, J = 303.5 Hz), 118.7, 101.8, 72.3, 70.4, 66.4,

46.3, 38.9, 23.8, 23.6; 19F NMR (470 MHz, CDCl3): δ –39.7

HRMS (EI+) calcd for [C12H17F3O4S + NH4]+ 332.1138; found 332.1110

Determination of relative stereochemistry for trifluoromethylthiohydrin 244

143

Following General Procedure D, the trifluoromethylthiohydrin 244 was converted to carbacycle

262. NOE analysis of carbacycle 262 confirmed relative stereochemistry of

trifluoromethylthiohydrin 244.

Determination of enantiomeric excess of trifluoromethylthiohydrin 244

Following General Procedure F, trifluoromethylthiohydrin 244 was converted to

trifluoromethylthiohydrin 243. Following General Procedure E, optically enriched and racemic

samples of trifluoromethylthiohydrin 243 were converted into their corresponding p-nitrobenzoyl

diesters. The enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a Lux®

3µm Amylose-1 column; flow rate 0.50 mL/min; eluent: hexanes-iPrOH 92.5:7.5; detection at 254

nm; retention time = 6.92 min and 10.52 min (see chromatograms). The enantiomeric excess of

the optically enriched p-nitrobenzoyl diester was determined using the same method (91% ee).

Preparation of aldol adduct 245

Following General Procedure C, a solution of isovaleraldehyde (0.050 mL, 0.456 mmol),

N(SCF3)Phth (0.113 g, 0.456 mmol), L-proline (0.053 g, 0.456 mmol), and NaHCO3 (0.038 g,

0.456 mmol) was stirred for 50 minutes at RT in DMSO (0.61 mL). Dioxanone XX (0.027 mL,

0.228 mmol) in CH2Cl2 (3.04 mL) was added and the reaction mixture was stirred for 60 hrs.

Purification of the crude trifluoromethylthiohydrin 245 by flash chromatography (pentane:Et2O –

88:12) afforded trifluoromethylthiohydrin 245 (0.060 g, d.r. = 10:1, 42 % yield) as a colorless oil.

Data for syn-trifluoromethylthiohydrin 245: []D20 = -106.0° (c 2.15 in CH2Cl2);

IR (neat): = 3508, 2967, 173, 1101, 865 cm-1;1H NMR (600 MHz, CDCl3): δ

4.41 (dd, J = 9.0, 1.3 Hz, 1H), 4.30 (dd, J = 17.6, 1.5 Hz, 1H), 4.19 (d, J = 9.0

Hz, 1H), 4.08 (d, J = 17.6 Hz, 1H), 3.73 (dd, J = 2.3, 1.3 Hz, 1H), 3.35 (d, J =

5.5 Hz, 1H), 2.18 (m, 1H), 1.47 (s, 3H), 1.43 (s, 3H), 1.10 (dd, J = 5.8, 5.7 Hz, 3H); 13C NMR (150

MHz, CDCl3): δ 213.6, 131.6 (q, J = 305.0 Hz), 101.7, 72.2, 70.4, 66.5, 53.5, 33.1, 23.8, 23.7,

20.8, 19; 19F NMR (470 MHz, CDCl3): δ –38.6

HRMS (EI+) calcd for [C12H19F3O4S + NH4]+ 334.1294; found 334.1266

Preparation of aldol adduct 246

Following General Procedure C, a solution of 3-(4-methoxyphenyl)propanal (0.050 mL, 0.317

mmol), PhthN(SCF3) (0.078 g, 0.317 mmol), L-proline (0.037 g, 0.317 mmol), and NaHCO3 (0.027

144

g, 0.317 mmol) was stirred for 50 minutes at RT in DMSO (0.42 mL). Dioxanone 75 (0.019 mL,

0.228 mmol) in CH2Cl2 (2.11 mL) was added and the reaction mixture stirred for 60 hrs.

Purification of crude trifluoromethylthiohydrin 246 by flash chromatography (pentane:Et2O –

80:20) afforded trifluoromethylthiohydrin 246 (0.032 g, d.r. = 10:1, 56 % yield) as a yellow oil.

Data for syn-trifluoromethylthiohydrin 246: []D20 = -61.4° (c 1.6 in

CH2Cl2); IR (neat): = 3518, 1736, 1512, 1108, 863 cm-1;1H NMR (600

MHz, CDCl3): δ 7.15 (d, J = 8.5 Hz, 2H), 6.85 (d, J = 8.5 Hz, 2H), 4.40

(dd, J = 9.1, 1.3 Hz, 1H), 4.20 (dd, J = 17.6, 1.5 Hz, 1H), 4.01 (d, J =

17.6 Hz, 1H), 3.89 (d, J = 9.1 Hz, 1H), 3.80 (s, 3H), 3.58-3.62 (2H), 3.26 (dd, J = 13.7, 11.0 Hz,

1H), 3.21 (dd, J = 13.7, 5.5 Hz, 1H), 1.46 (s, 3H), 1.34 (s, 3H;13C NMR (150 MHz, CDCl3): δ 213.6,

158.6, 131.6 (q, J = 306.0 Hz), 130.5, 130.0, 114.1, 101.7, 72.4, 69.2, 66.4, 55.4, 48.2, 39.2, 23.8,

23.6; 19F NMR (470 MHz, CDCl3): δ –39.7

HRMS (EI+) calcd for [C17H21F3O5S + NH4]+ 412.1400.1340; found 412.1369

Determination of enantiomeric excess of trifluoromethylthiohydrin 246

Using sodium borohydride in methanol, optically enriched and racemic samples of

trifluoromethylthiohydrin 246 were converted into their corresponding diols. The enantiomeric

diols were separated by chiral HPLC using a Lux® 3µm Amylose-1 column; flow rate 0.50 mL/min;

eluent: hexanes-iPrOH 95:5; detection at 254 nm; retention time = 6.01 min and 8.49 min (see

chromatograms). The enantiomeric excess of the optically enriched diol was determined using

the same method (93% ee).

Preparation of aldol adduct 247

Following General Procedure C, a solution of 3-(5-methylfuran-2-yl)propanal (0.050 mL, 0.376

mmol), N(SCF3)Phth (0.093 g, 0.376 mmol), L-proline (0.043 g, 0.376 mmol), and NaHCO3 (0.032

g, 0.376 mmol) was stirred for 50 minutes at RT in DMSO (0.50 mL). Dioxanone 75 (0.023 mL,

0.188 mmol) in CH2Cl2 (2.50 mL) was added and the reaction mixture stirred for 60 hrs.

Purification of crude trifluoromethylthiohydrin 247 by flash chromatography (pentane:Et2O –

85:15) afforded trifluoromethylthiohydrin 247 (0.032 g, d.r. > 10:1, 46 % yield) as a colorless oil.

145

Data for syn-trifluoromethylthiohydrin 247: []D20 = -101.7° (c 1.0 in

CH2Cl2); IR (neat): = 3517, 2995, 1736, 1386, 1113, 737 cm-1;1H NMR

(600 MHz, CDCl3): δ 6.00 (d, J = 2.8 Hz, 1H), 5.86 (d, J = 2.8 Hz, 1H),

4.42 (dd, J = 9.0, 1.3 Hz, 1H), 4.26 (dd, J = 17.6, 1.3 Hz, 1H), 4.05 (d,

J = 17.6 Hz, 1H), 4.03 (d, J = 9.0 Hz, 1H), 3.76 (dd, J = 10.6, 5.1 Hz, 1H), 3.62 (dd, J = 2.3, 1.3

Hz, 1H), 3.31 (dd, J = 15.1, 10.6 Hz, 1H), 3.18 (dd, J = 15.1, 5.1 Hz, 1H), 2.26 (s, 3H), 1.48 (s,

3H), 1.40 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 213.6, 151.6, 149.9, 131.4 (q, J = 306.0 Hz),

108.6, 106.2, 101.7, 72.4, 70.3, 66.4, 45.8, 33.2, 23.8, 23.6, 13; 19F NMR (470 MHz, CDCl3): δ –

39.8

HRMS (EI+) calcd for [C15H19F3O5S + NH4]+ 386.1244; found 386.1227

Determination of enantiomeric excess of trifluoromethylthiohydrin 247

Following General Procedure E, optically enriched and racemic samples of

trifluoromethylthiohydrin 247 were converted into their corresponding p-nitrobenzoyl diesters. The

enantiomeric p-nitrobenzoyl diesters were separated by chiral HPLC using a Lux® 3µm Amylose-

1 column; flow rate 0.50 mL/min; eluent: hexanes-iPrOH 95:5; detection at 254 nm; retention time

= 20.83 min and 22.46 min (see chromatograms). The enantiomeric excess of the optically

enriched p-nitrobenzoyl diester was determined using the same method (93% ee).

Preparation of nucleoside analogue 259

To a stirred solution of fluorohydrins 241 (0.105 g, 0.344 mmol, 1.0 equiv) in MeCN (3.00 mL) at

-15˚C was added tetramethylammoniumtriacetoxyborohydride (0.453 g, 1.72 mmol, 5.0 equiv)

and acetic acid (0.190 mL, 3.44 mmol, 10 equiv). The resulting mixture was stirred 16 hours. The

reaction mixture was then diluted with a saturated solution of Rochelle salt and washed three

times with CH2Cl2. The organic layer was separated, dried over MgSO4, filtered and concentrated

under reduced pressure. The crude product S260 was purified by flash chromatography

(EtOAc:pentane – 70:30) to afford S259 as a white solid (0.076 g, 72%)

To a stirred solution of syn-diol-fluorohydrins S259 (0.076, 0.248 mmol, 1.0 equiv.) in MeCN (2.50

mL) was added InCl3 (0.014 g, 0.062 mmol, 0.25 equiv.) and the reaction mixture was stirred for

24 hours. The reaction mixture was diluted with CH2Cl2 and was washed with saturated sodium

bicarbonate solution. The organic layer was separated, dried over MgSO4, filtered, and

146

concentrated under reduced pressure. The crude product 259 was purified by flash

chromatography (EtOAc:pentane – 25:75) to afford 259 as a colorless oil (42.7 mg, 60%)

Data for nucleoside analogue 259: []D20 = +46.6 (c 0.38 in CH2Cl2); IR

(neat): = 3475, 2935, 1708, 1370, 720 cm-1; 1H NMR (600 MHz, CDCl3):

δ 7.88 (m, 2H), 7.77 (m, 2H), 6.13 (d, J = 5.0 Hz, 1H), 4.40 (ddd, J = 11.8,

5.0, 4.8 Hz, 1H), 4.03 (ddd, J = 10.6, 10.6, 4.1 Hz, 1H), 3.13 (d, J =11.9

Hz, 1H), 2.22 (m, 1H), 1.94 (m, 1H), 1.85 (m, 2H), 1.62 (dddd, J = 11.9, 11.9, 4.6, 3.2 Hz, 1H),

1.51 (m, 1H), 1.23 – 1.40(3H); 13C NMR (150 MHz, CDCl3): δ 169.1, 134.6, 132.1, 123.8, 84.4,

81.1, 75.3, 51.4, 31.7, 25.4, 24.0, 24.0

HRMS (EI+) calcd for C16H18NO4 [M + H+] 288.1230; found 288.1246

Determination of relative stereochemistry for nucleoside 259

Analysis of 2D NOESY of nucleoside 259 supported the indicated

stereochemistry

Preparation of nucleoside analogue 260

To a stirred solution of fluorohydrins 242 (0.097 g, 0.30 mmol, 1.0 equiv) in MeCN (3.00 mL) at -

15˚C was added tetramethylammoniumtriacetoxyborohydride (0.395 g, 1.50 mmol, 5.0 equiv) and

acetic acid (0.172 mL, 1.50 mmol, 10 equiv). The resulting mixture was stirred 16 hours. The

reaction mixture was then diluted with a saturated solution of Rochelle salt and washed three

times with CH2Cl2. The organic layer was separated, dried over MgSO4, filtered and concentrated

under reduced pressure. The crude product S260 was purified by flash chromatography

(EtOAc:pentane – 70:30) to afford S260 as a white solid (0.068 g, 70%)

To a stirred solution of syn-diol-fluorohydrins S260 (0.047, 0.143 mmol, 1.0 equiv.) in MeCN (1.43

mL) was added InCl3 (7.9 mg, 0.036 mmol, 0.25 equiv.) and the reaction mixture was stirred for

24 hours. The reaction mixture was diluted with CH2Cl2 and was washed with saturated sodium

bicarbonate solution. The organic layer was separated, dried over MgSO4, filtered, and

concentrated under reduced pressure. The crude product 260 was purified by flash

chromatography (EtOAc:pentane – 40:60) to afford 260 as a colorless oil (23.7 mg, 73%)

147

Data for nucleoside analogue 260: []D20 = +18.6 (c 2.37 in CH2Cl2); IR

(neat): = 3475, 2923, 1774, 1709, 1373, 719 cm-1; 1H NMR (600 MHz,

CDCl3): δ 7.88 (m, 2H), 7.77 (m, 2H), 6.13 (d, J = 4.9 Hz, 1H), 4.40 (ddd,

J = 11.5, 4.7, 4.7 Hz, 1H), 4.03 (ddd, J = 11.2, 11.2, 3.6 Hz, 1H), 3.35 (d,

J = 11.9 Hz, 1H), 2.98 (dd, J = 13.1 11.9 Hz, 1H), 2.82 (m ,2H), 2.69 (m, 1H), 2.50 (m, 1H), 2.10

(m ,1H), 1.74 (m , 1H); 13C NMR (150 MHz, CDCl3): δ 169.2, 134.8, 131.9, 124.0, 83.0, 80.2, 75.2,

51.3, 33.5, 27.6, 27.4

HRMS (EI+) calcd for C15H19N2O4S [M + NH4+] 323.1060; found 323.1037

Determination of relative stereochemistry for nucleoside 260

Analysis of 2D NOESY of nucleoside 260 supported the indicated

stereochemistry

Preparation of carbocycle 261

Following General Procedure D, to a stirred solution of 5-(methanesulfonyl)-1-phenyl-1H-tetrazole

(0.126 g, 0.560 mmol) in dry THF (0.70 mL) at -78oC was added dropwise a 1 M LiHMDS (0.560

mL, 0.560 mmol) and the resulting reaction mixture was stirred for 30 minutes. A solution of

fluorohydrin 223 (0.052 g, 0.224 mmol) in dry THF (0.45 mL) was then added dropwise and the

reaction mixture was allowed to stir for 5 hrs at -78°C. Purification of crude alkene S261 by flash

chromatography (pentane:EtOAc – 80:20) afforded alkene S261 (0.034 g, 65 % yield) as a

colorless oil. A mixture Grubbs II catalyst (2.9 mg) and alkene S261 (0.034 g, 0.148 mmol) in dry

toluene (5.91 mL) was purged with N2 for 45 minutes in a sealed reaction vessel and subsequently

heated to 80°C for 6 hrs. Purification of crude carbacycle 261 by flash chromatography

(pentane:EtOAc – 75:25) afforded carbacycle 261 (0.019 g, 63 % yield) as a white solid.

Data for carbacycle 261: []D20 = -32.8 (c 0.50 in CH2Cl2); 1H NMR (600 MHz,

CDCl3): δ 5.45 (s, 1H), 4.96 (dd, J = 46.8, 5.6 Hz, 1H), 4.61 (s, 1H), 4.51 (d, J =

13.5 Hz, 1H), 4.13 (m, 1H), 4.10 (d, J = 13.5 Hz, 1H), 2.71 (dd, J = 3.8, 1.5 Hz,

1H), 2.62 (ddd, J = 19.2, 5.6, 2.6 Hz, 1H), 2.31 (dd, J = 21.2, 19.2 Hz, 1H), 1.57

(s, 3H), 1.44 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 128.2, 117.8, 99.4, 88.5 (d, J

= 166.5 Hz), 66.1 (d, J = 2.7 Hz), 65.9 (d, J = 27.7 Hz), 63.7, 29.0, 27.4 (d, J = 22.1), 20.0.

148

HRMS (EI+) calcd for [C10H16FO3]+ 203.1078; found 203.1058

Preparation of carbocycle 262

Following General Procedure D, to a stirred solution of 5-(methanesulfonyl)-1-phenyl-1H-tetrazole

(0.066 g, 0.295 mmol) in dry THF (0.37 mL) at -78oC was added dropwise a 1 M LiHMDS (0.295

mL, 0.295 mmol) and the resulting reaction mixture was stirred for 30 minutes. A solution of

fluorohydrin 244 (0.042 g, 0.134 mmol) in dry THF (0.54 mL) was then added dropwise and the

reaction mixture was allowed to stir for 3 hrs at -78°C. Purification of the crude alkene S262 by

flash chromatography (pentane:Et2O – 80:20) afforded alkene S262 (0.023 g, 56 % yield) as a

colorless oil. A mixture Grubbs II catalyst (2.9 mg) and alkene S262 (0.021 g, 0.067 mmol) in dry

toluene (2.70 mL) was purged with N2 for 30 minutes in a sealed reaction vessel and subsequently

heated to 90°C for 6 hrs. Purification of the crude carbacycle 262 by flash chromatography

(pentane:EtOAc – 80:20) afforded carbacycle 262 (0.013 g, 74 % yield) as a white solid.

Data for carbacycle 262: []D20 = -54.3 (c 0.83 in CH2Cl2); IR (neat): = 3470,

1430, 1111, 879, cm-1;1H NMR (600 MHz, CDCl3): δ 5.52 (m, 1H), 4.62 (m, 1H),

4.48 (dd, J = 13.4, 2.6 Hz, 1H), 4.11 (m, 1H), 4.06 (d, J = 13.4 Hz, 1H), 3.75 (m,

1H), 3.00 (d, J = 18.8 Hz, 1H), 2.94 (d, J = 1.4 Hz, 1H), 2.21 (ddd, J = 18.8, 4.4,

2.1 Hz, 1H), 1.58 (s, 3H), 1.43 (s, 3H); 13C NMR (150 MHz, CDCl3): δ 130.9 (q, J

= 307.7 Hz), 128.8, 119.6, 99.6, 67.6, 65.7, 63.8, 41.5 (q, J = 1.6 Hz), 29.0, 27.4, 20.1; 19F NMR

(470 MHz, CDCl3): δ –39.9

HRMS (EI+) calcd for [C11H16F3O3S]+ 285.0767; found 285.0780

Determination of relative stereochemistry for carbacycle 262

Analysis of 2D NOESY of carbacycle 262 supported the indicated

stereochemistry

Preparation of carbacycle 263

Following General Procedure D, to a stirred solution of 5-(methanesulfonyl)-1-phenyl-1H-tetrazole

(0.134 g, 0.60 mmol) in dry THF (0.75 mL) at -78oC was added dropwise a 1 M LiHMDS (0.60

mL, 0.60 mmol) and the resulting reaction mixture was stirred for 30 minutes. A solution of

149

fluorohydrin 239 (0.060 g, 0.30 mmol) in dry THF (1.20 mL) was then added dropwise and the

reaction mixture was allowed to stir for 5 hrs at -78°C. Purification of the crude alkene S263 by

flash chromatography (pentane:EtOAc – 90:10) afforded alkene S263 (0.031 g, 52 % yield) as a

white solid. A mixture Grubbs II catalyst (5.5 mg, 0.05 equiv.) and alkene S263 (0.026 g, 0.13

mmol) in dry toluene (5.30 mL) was purged with N2 for 30 minutes in a sealed reaction vessel and

subsequently heated to 80°C for 8 hrs. Purification of the crude carbacycle 263 by flash

chromatography (pentane:Et2O – 85:15) afforded carbacycle 263 (15.9 mg, 72 % yield) as a

colorless oil.

Data for carbacycle 263: []D20 = -111.3 (c 0.3 in CH2Cl2); IR (neat): = 3418,

2925, 2853, 1447, 1003 cm-1;1H NMR (600 MHz, CDCl3): δ 5.17 (m, 1H), 4.68

(dddd, J = 52.2, 13.8, 8.2, 5.6 Hz, 1H), 3.99 (m, 1H), 2.50 (m, 1H), 2.44 (m, 1H),

2.26 (m, 1H), 2.23 (m, 1H), 2.09 (d, J = 3.7 Hz), 2.06 (m, 1H), 1.95 (m, 1H), 1.87

(m ,1H), 1.81 (m ,1H), 1.39 (ddd, J = 13.2, 3.8, 3.8 Hz, 1H), 1.24 (ddd, J = 13.0,

3.8, 3.8 Hz, 1H), 1.13 (dd, J = 12.8, 3.7 Hz, 1H); 13C NMR (150 MHz, CDCl3): δ 136.9 (d, J = 1.8

Hz), 113.0 (d, J = 8.8 Hz), 90.6 (d, J = 171.2 Hz) , 71.2 (d, J = 19.2 Hz), 42.4 (d, J = 4.8 Hz), 35.4,

29.8 (d, J = 19.8 Hz), 28.7, 28.3; 19F NMR (470 MHz, CDCl3): δ –191.8

HRMS (EI+) calcd for C10H16FO4 171.1180; found 171.1154

Determination of relative stereochemistry for carbacycle 263

Analysis of 2D NOESY of carbacycle 263 supported the indicated

stereochemistry

Preparation of carbocycle 264

Following General Procedure D, to a stirred solution of 5-(methanesulfonyl)-1-phenyl-1H-tetrazole

(0.099 g, 0.44 mmol) in dry THF (0.55 mL) at -78oC was added dropwise a 1 M LiHMDS (0.440

mL, 0.440 mmol) and the resulting reaction mixture was stirred for 30 minutes. A solution of

fluorohydrin 240 (0.048 g, 0.220 mmol) in dry THF (2.20 mL) was then added dropwise and the

reaction mixture was allowed to stir for 3 hrs at -78°C. Purification of the crude alkene S264 by

flash chromatography (pentane:EtOAc – 85:15) afforded alkene S264 (0.029 g, 61 % yield) as a

150

off-white solid. A mixture Grela catalyst (5.9 mg, 0.10 equiv.) and alkene S264 (0.019 g, 0.088

mmol) in dry toluene (3.52 mL) was purged with N2 for 30 minutes in a sealed reaction vessel and

subsequently heated to 80°C for 8 hrs. Purification of the crude carbacycle 264 by flash

chromatography (pentane:EtOAc – 90:10) afforded carbacycle 264 (0.013 g, 71 % yield) as a

white solid.

Data for carbacycle 264: []D20 = -77.2 (c 0.53 in CH2Cl2); IR (neat): = 3424,

2924, 1426, 1290, 1088, 1057, 1021 cm-1;1H NMR (600 MHz, CDCl3): δ 5.27 (m,

1H), 4.64 (dddd, J = 52.7, 15.5, 9.3, 6.3 Hz, 1H), 4.00 (ddd, J = 16.3, 9.3, 7.1 Hz,

1H), 3.01 (dd, J = 12.9, 2.9 Hz, 1H), 2.85 (m, 1H), 2.63 (m, 2H), 2.55 (m, 1H),

2.53 (m, 1H), 2.43 (dd, J = 12.8, 12.4 Hz, 1H), 2.35 (m, 1H), 2.32 (m, 1H), 2.27

(m, 1H); 13C NMR (150 MHz, CDCl3): δ 138.9, 116.2 (d, J = 10.4 Hz), 90.3 (d, J = 172.2 Hz), 71.5

(d, J = 17.8 Hz), 45.3 (d, J = 5.6 Hz), 31.8, 30.8, 30.3 (d, J = 20.0 Hz); 19F NMR (470 MHz, CDCl3):

δ –191.4

HRMS (EI+) calcd for [C9H14FOS]+ 189.0744; found 189.0757

Determination of relative stereochemistry for carbacycle 264

Analysis of 2D NOESY of carbacycle 264 supported the indicated

stereochemistry

Synthesis of 2-fluoro-2-deoxy- D-altrose acetonide 273

The fluorohydrin 230 (0.150 g, 0.397 mmol, 1 equiv.) in MeCN (0.45 mL, 0.9 M) was added to a

stirred solution of Me4NBH(OAc)3 (0.520 g, 1.98 mmol, 5 equiv.) and AcOH (0.23 mL, 3.97 mmol,

10 equiv.) in MeCN (2.0 mL, 0.2 M) at -25°C and the resulting mixture was stirred for 24 hours.

The reaction mixture was then quenched by addition of a saturated aqueous solution of sodium

tartrate. The aqueous layer was removed and extracted four times with CH2Cl2, and the combined

organic layers were dried over MgSO4 and concentrated under reduced pressure. Purification of

the crude product by flash chromatography (pentane-EtOAc; 75:25) afforded the 1,3 syn-

fluorodiol (0.114 g, 76 %).

151

To a cold solution (0 °C) of the 1,3-syn-fluorodiol (0.060 g, 0.16 mmol) in THF (1.6 mL) was added

a solution of tetrabutylammonium fluoride in THF (1 M, 0.18 mL, 0.18 mmol), and the reaction

mixture was stirred for 30 minutes. The reaction mixture was then diluted with Et2O (2 mL) and

was washed with a solution of saturated aqueous ammonium chloride. The organic layer was

dried over MgSO4 and concentrated under reduced pressure. Purification of the crude product by

flash chromatography (CH2Cl2-MeOH 95:5) afforded the deprotected 1,3-syn-fluorotriol (32 mg,

91% yield). To a cold (0°C) solution of bis-(acetoxy)iodobenzene (35 mg, 0.108 mmol) and the

1,3-syn-fluorotriol (23 mg, 0.103 mmol), in CH2Cl2 (1.1 mL), was added 2,2,6,6-

tetramethylpiperidinyloxy (1 mg, cat.) and the reaction mixture was allowed to gradually warm to

room temperature and stirred for 5 hours and the reaction mixture was concentrated under

reduced pressure. Purification of the crude fluorohydrin 273 (dr 1:1) by flash chromatography

(pentane-EtOAc 5:5) afforded 273 (15 mg, 65% yield) as a clear oil.

Data for 2-fluoro-2-deoxy- L-altrose acetonide (273) []D20 = + 2.5 (c 0.83 in

CHCl3); IR (neat): = 3413, 2918, 1078, 1043 cm-1; 1H-NMR (600 MHz,

CDCl3): 5.12 (2H), 4.68 (2H), 4.38 (1H), 4.27 (2H), 4.16 (1H), 3.91 (7H),

3.27 (1H), 2.68 (1H), 2.30 (1H), 1.49 (12H); 13C-NMR (150 MHz, CDCl3): =

100.4, 100.3, 92.9, 91.8, 89.2, 86.5, 69.0, 68.7, 67.7, 67.6, 64.4, 62.6, 62.3, 59.4, 29.2, 29.1, 19.5,

19.4 19F-NMR (470 MHz, CDCl3): δ -194.9, -216.5 HRMS (ESI) m/z calcd for C9H16FO5 [M + H]+

223.0976, found 223.0965

Synthesis of 2-fluoro-2-deoxy-L-galactose (274)

To a cold (0 °C), stirred solution of fluorohydrin 230 (0.189 g, 0.500 mmol, 1.0 equiv.) in dry THF

(0.1 M) was added a solution of catechol borane in THF (1.1 mL, 1.0 M, 2.2 equiv.). The resulting

mixture was allowed to warm gradually to room temperature and was then stirred for an additional

45 minutes or until complete consumption of starting chlorohydrin was observed by TLC analysis.

The mixture was then diluted with MeOH (to 0.05 M) and a solution of saturated aqueous sodium

tartrate was added. The biphasic mixture was stirred vigorously for 2 hours, after which time the

aqueous layer was removed and extracted three times with Et2O. The combined organic layers

were dried over MgSO4, concentrated under reduced pressure, and the crude product was

purified by flash chromatography (pentane- EtOAc; 2:1) to yield the 1,3-anti-fluorodiol (0.056 g,

82 %)

152

To a cold solution (0 °C) of the 1,3-anti-fluorodiol (0.076 g, 0.20 mmol, 1 equiv.) in THF (2.0 mL)

was added a solution of tetrabutylammonium fluoride in THF (1 M, 0.22 mL, 0.22 mmol, 1.1

equiv.), and the reaction mixture was stirred for 4 hours. The reaction mixture was then diluted

with Et2O (2 mL) and was washed with a solution of saturated aqueous ammonium chloride. The

organic layer was dried over MgSO4 and concentrated under reduced pressure. Purification of

the crude product by flash chromatography (CH2Cl2-MeOH 95:5) afforded the deprotected 1,3-

anti-fluorotriol (41 mg, 91% yield) (See Pre274-XRD for X-ray). To a cold (0°C) solution of bis-

(acetoxy)iodobenzene (12.9 mg, 0.040 mmol) and the 1,3-anti-fluorotriol (9 mg, 0.04 mmol), in

CH2Cl2 (0.40 mL), was added 2,2,6,6-tetramethylpiperidinyloxy (1 mg, cat.) and the reaction

mixture was allowed to gradually warm to room temperature and stirred for 8 hours and the

reaction mixture was concentrated under reduced pressure. Purification of the crude fluorohydrin

(dr 1:0.1.0) by flash chromatography (pentane-EtOAc 5:5) afforded (4.6 mg, 51 % yield) as a clear

oil. The purified product (4.6 mg, 0.020 mmol) was then dissolved in CH2Cl2 (0.20 mL) and and

0.05 mL of TFA was added. The reaction mixture was left to stir for 24 hrs and the solvent was

removed under reduced pressure to give pure 274 (4.3 mg, 100%) as a colorless oil. The data for

274 matched those of previously reported for 2-fluoro-2-deoxy-D-galactose.190

Synthesis of fluorohydrin 226 and 2-fluoro-2-deoxy migalastat (275)

Following General Procedure A, a solution of 3-N-Cbz-aminopropanal (0.10 g, 0.483 mmol), NFSI

(0.152 g, 0.483 mmol), (R)-proline (0.056 g, 0.483 mmol) and NaHCO3 (0.041 g, 0.483 mmol)

was stirred for 3 hours at -10 °C in DMF (0.65 mL). Dioxanone 2 (0.039 mL, 0.322 mmol) in CH2Cl2

(5.8 mL) was stirred for 24 hours. Purification of the crude fluorohydrin 226 by flash

chromatography (pentane-EtOAc 3:1) afforded fluorohydrin 226 (0.056 g, 49 % yield) as a yellow

oil. 1H-NMR spectroscopic analysis of this material indicated that it exists as a complicated 1:1

mixture of fluorohydrin 226:hemiminals (1:1 mixture of diastereomers).

Following General Procedure C, the fluorohydrin 226 (0.051 g, 0.144 mmol) and Pd/C powder

were stirred in MeOH (1.4 mL) with bubbling in H2 gas for 18 hrs. The Pd/C was filtered off, the

solvent was removed under reduced pressure, and the crude product (dr 7:1)was purified with

153

flash chromatography (EtOAc: pentanes; 40:60) to give a white powder (0.024 g, 83 %). The

purified product (0.028 g, 0.139 mmol) was then dissolved in MeOH (1.4 mL) and 0.5 mL of 1 M

HCl was added. The reaction mixture was left to stir for 24 hrs and the solvent was removed under

reduced pressure to give pure 275(0.022 g, 97%).

Data for 2-fluoro-2-deoxy migalastat (275): []D20 = + 10.7 (c 1.88 in MeOH);

IR (neat): = 3307, 2952, 2464, 1406, 1111, 1055 cm-1; 1H NMR (500 MHz,

MeOD): 5.25 (dddd, J = 49.2, 10.8, 9.3, 5.6 Hz, 1H), 4.06 (m, 1H), 3.80 (m,

3H), 3.57 (ddd, J = 12.4, 5.6, 2.3 Hz, 1H), 3.40 (dd, J = 8.1, 5.3 Hz, 1H), 3.08

(m, 1H); 13C NMR (150 MHz, MeOD): 88.5 (J = 175.5 Hz), 73.1 (d, J = 17.7 Hz), 68.9 (d, J =

10.1 Hz), 62.0, 60.4, 45.0 (d, J = 32.6); 19F NMR (470 MHz, MeOD):δ -204.5

HRMS (ESI) m/z calcd for C6H13FNO3+ [M + H]+ 166.0874, found 166.0893

Determination of enantiomeric excess of fluorohydrin 226

Following General Procedure A, using a 1:1 mixture of L: D - proline, a racemic sample of the

fluorohydrin 226 was prepared. Following General Procedure B, the optically enriched and

racemic samples of fluorohydrin 226 (0.055 g, 0.155 mmol) were converted into their

corresponding cyclized products. These were then diacylated with R)-(+)-MTPA-OH (3 equiv.),

DIC (6 equiv.), pyridine (3 equiv.), and 4-dimethylaminopyridine (cat.) in CH2Cl2 (0.10 M). By

analysis of 19F NMR it was determined that the enantiomeric excess was 92 %.

Synthesis of (5R)-5-D-ribo-fluorophytosphingosine (276)

To a stirred solution of the fluorohydrin 221 (0.187 g, 0.50 mmol, 1.0 equiv.) in 5.0 mL of THF (0.1

M) was added to benzylamine (0.137 mL, 1.25 mmol, 2.5 equiv.) and glacial acetic acid (0.030 g,

0.50 mmol, 1.0 equiv.), and the resulting mixture was stirred at 20°C for 2 hours or until complete

conversion into the corresponding imine was accomplished (as determined by 1H-NMR

spectroscopic analysis of small samples removed from the reaction mixture). NaCNBH3 (0.080 g,

1.25 mmol, 2.5 equiv.) was then added and the mixture was stirred for a further 1 hour. The

reaction mixture was then diluted with CH2Cl2 to a concentration of 0.05 M and treated with water.

The layers were separated and the organic layer was washed with brine, dried (MgSO4), and

concentrated under reduced pressure. The crude product was purified by flash chromatography

154

(CH2Cl2-MeOH; 15:1) to afford the reductive amination product (0.206 g, 88 % yield). Pd/C (2 mg)

was added to a stirred solution of purified product (9.3 mg, 0.02 mmol, 1.0 equiv.) in 0.20 mL of

MeOH (0.1 M) under a H2 atmosphere. After 24 hrs the reaction was filtered, concentrated under

reduced pressure, and purified by flash column chromatography (CH2Cl2-MeOH; 20:1) to give the

debenzylated product (7 mg, 93 %). A solution of the debenzylated product (9 mg, 0.024 mmol)

in 0.25 mL MeOH (0.1 M) was added 0.05 mL of 1 M HCl and left for 24 hrs. The reaction mixture

was then concentrated under reduced pressure to afford pure 276 (8.7 mg, 98 %).

Data for (5R)-5-D-ribo-fluorophytosphingosine (276): []D20

= -4.5 (c 0.75 in DMSO-d6); IR (neat): = 3425, 2924, 1025,

1005, 822, 760, 614 cm-1; 1H NMR (600 MHz, DMSO-d6):

= 7.84 (br s), 4.69 (ddd, J = 47.5, 8.6, 4.7 Hz, 1H), 3.80 (dd,

J = 9.8, 2.7 Hz, 1H), 3.75 (dd, J = 11.2, 3.8 Hz, 1H), 3.58

(dd, J = 11.0, 9.4 Hz, 1H), 3.28 (dd, J = 29.6, 9.8 Hz, 1H), 1.77 (m, 1H), 1.56 (m, 1H), 1.26 (m, 26

H), 0.87 (dd, J = 6.8, 6.8 Hz, 3H); 13C NMR (150 MHz, DMSO-d6): = 91.8 (J = 173.1 Hz), 71.1

(d, J = 18.1 Hz), 67.8 (d, J = 5.0 Hz), 56.9, 54.5, 31.3, 30.4 (d, J = 21.4 Hz), 29.0, 29.0, 29.0, 29.0,

28.9, 28.9, 28.7, 24.8, 24.8, 22.1, 13.9; 19F NMR (470 MHz, DMSO-d6):δ -201.0

HRMS (ESI) m/z calcd for C18H39FNO3+ [M + H]+ 336.2908, found 336.2920

155

Figure S4.1. XRD structure of compound 219-XRD

156

Figure S4.2. XRD structure of compound 200-XRD

157

Figure S4.3. XRD structure of compound 228-XRD

158

Figure S4.4. XRD structure of compound 230-XRD

159

Figure S4.5. XRD structure of compound Pre274-XRD

160

Compound Reference 219-XRD 200-XRD 228-XRD 230-XRD Pre274-

XRD

Chemical Formula C23H23N2O10F C25H27O6Br2F C15H21O4F C32H43Br2FO7Si C9H17FO5

FW 506.43 602.28 284.32 746.57 224.22

Crystal System Orthorhombic Orthorhombic Orthorhombic Monoclinic Triclinic

Space group P212121 P212121 P212121 P21 P1

a/Å 7.8910(2) 5.5445(4) 5.60440(10) 12.6483(4) 9.3287(6)

b/Å 11.8417(3) 18.6627(13) 13.0932(3) 11.3201(4) 9.3568(5)

c/Å 24.9605(6) 24.3453(19) 20.2022(4) 13.4868(4) 25.3029(1

5)

α/˚ 90 90 90 90 91.911(2)

β/˚ 90 90 90 115.6810(10) 97.536(2)

γ/˚ 90 90 90 90 90.195(3)

Unit cell volume/Å3 2332.38(10) 2519.1(3) 1482.43(5) 1740.29(10) 2188.2(2)

Z 4 4 4 2 8

Temperature/K 150(2) 150(2) 296(2) 150(2) 150(2)

Radiation type Cu Kα Cu Kα Cu Kα Cu Kα Cu Kα

Absorption

coefficient, μ/mm-1

1.023 4.476 0.83 3.689 1.038

161

All Reflections 16537 16215 9652 25308 60788

Unique Reflections 4273 4631 2610 6336 14635

Flack parameter 0.03(4) 0.002(8) 0.07(5) 0.001(5) 0.04(3)

Rint 0.0337 0.0389 0.0205 0.0305 0.0532

Final R1 values

(I>2σ(I))

0.0281 0.0251 0.0368 0.0351 0.0436

Final wR(F2) values

(I>2σ(I))

0.0735 0.0642 0.1023 0.0916 0.1146

Final R1 values (all

data)

0.0286 0.0258 0.0388 0.0361 0.0437

Final wR(F2) (all data) 0.074 0.0648 0.1048 0.0927 0.1147

Goodness of fit 1.049 1.034 1.085 1.031 1.044

162

Chapter 5. A convenient late-stage flourination of pyridylic C-H bonds

The results presented in this chapter have been reported in part, see:

Meanwell, M.; Nodwell, M.; Martin, R. E.; Britton. R. Angew. Chem. Int. Ed. 2016, 55, 13244-

13248 and Meanwell, M.; Britton, R. Synthesis 2018, 50, 1228-1236.

Dr. Matthew Nodwell synthesized compound 343 and contributed insightful discussions to this

work.

5.1. Synthesis of heterobenzylic fluorides

Nitrogen-containing heteroaromatics are privileged scaffolds in both pharmaceutical and

agrochemical research.191–195 In fact, roughly 60% of FDA approved drugs incorporate a nitrogen-

containing heterocycle, of which pyridines, thiazoles, and imidazoles are among the most

common.191 The prevalence of these heterocycles in approved pharmaceuticals has inspired

significant advances in both their synthesis196,197 and functionalization198 that enable the fine-

tuning of potency and physicochemical properties of drug leads. Thus, through the careful choice

and positioning of substituents, features such as basicity (Figure 5.1; 277199,200), inter- and

intramolecular hydrogen bonding (Figure 5.1; 278201), and π-stacking interactions (Figure 5.1;

278201) can be optimized for ligand-target binding.202 Notably, owing to the small size of fluorine

atoms, the polarized nature of carbon-fluorine bonds and consequent impact on compound

lipophilicity, hydrofluorocarbon substituents (e.g., CF3 and CH2F) can have profound effects on

biological activity.1,4,6,9,203–205 In addition, fluorine is also an isostere for both hydrogen and

hydroxyl groups, and strategic fluorination at metabolically labile sites is a common tactic

employed to mediate enzymatic degradation and adjust pharmacokinetic properties.1,4,6,9,203–205

For example, installation of the aryl fluoride in the anti-cancer drug gefitinib (280) markedly

prevents metabolism at this position, resulting in an increased in vivo half-life (Figure 5.1).206

Owing to their relatively weak C-H bond strength, heterobenzylic C-H bonds are also prone to

metabolism (see 277 and 279207 Figure 5.1). Thus, strategic fluorination at these centers provides

unique opportunities to modulate basicity and metabolism. However, heterobenzylic fluorination,

especially at a late-stage in a synthesis or on structurally complex and functional group-rich drug

leads, remains a significant synthetic challenge.204,205

163

Figure 5.1. Primary sites of metabolism in omeprazole (277) and pioglitazone (279) and the effects of heterocycles and fluorine on physicochemical properties in omarigliptin (278) and gefitinib (280).

Over the past decade several late-stage C-H fluorination strategies have been reported

that enable the direct fluorination of benzylic C(sp3)–H bonds.208–212 These strategies are

particularly useful tools for lead optimization and also present opportunities for the 18F-labelling of

ligands for positron-emission tomography (PET) imaging.213 In contrast, however, there are very

few examples of heterobenzylic fluorination. In fact, rarely have C(sp3)–H fluorination reactions

been demonstrated on molecules that include a heterocycle. While this may relate to fundamental

incompatibilities between electrophilic fluorinating agents and nucleophilic heteroaromatics, there

is a clear need for robust reactions that engender the synthesis of heterobenzylic fluorides.

Previous reviews on late-stage C-H fluorination8,204,205,214 have included examples of

heterobenzylic monofluorination, however, there is no focused review on the topic. Here, we will

provide a survey of methods available for the synthesis of heterobenzylic fluorides, summarize

recent advances in this area and identify limitations that we hope will inspire further investigation.

5.1.1. Deoxyfluorination

The most common strategy to access heterobenzylic fluorides is through

deoxyfluorination.215–226 While these processes are not late-stage transformations and require

prior synthesis of a heterobenzylic alcohol, they have proven to be a valuable resource for

medicinal chemists. Here, reagents such as DAST,217–221 Deoxofluor,216 and Xtalfluor227 (Figure

164

5.2), have enabled transformation of a broad range of heterobenzylic alcohols into the

corresponding heterobenzylic fluorides. Mechanistically, these reagents function by activation of

the hydroxyl group followed by nucleophilic displacement by fluoride.

Figure 5.2 Common deoxyfluorination reagents

Deoxyfluorination at the heterobenzylic position in quinoline-,215 pyrazole-,216,217

pyrimidine-,218,219 thiophene-,220 imidazole-,221 thiazole-,222 pyridine-,223 and purine-containing226

heterocycles, among others224,225 have been described. Though deoxyfluorination is a robust and

widely used transformation, it is fundamentally limited by a reliance on the prior formation of a

heterobenzylic alcohol and can be complicated by the formation of by-products derived from

elimination or isomerization processes.214 In 2009, Gilmour and colleagues reported the

deoxyfluorination of quinine alkaloids using DAST in THF at -20 °C as part of a broader medicinal

chemistry campaign (Scheme 5.1).215 Here, products derived from both stereochemical inversion

282 and retention 283 were produced in low to modest yield. In addition, the ring-expanded

azepane 284 was produced via formation of an aziridinium intermediate.

Scheme 5.1. Deoxyfluorination of quinine led to inversion (282), retention (283), and rearrangement (284) products

A recent and particularly interesting example of this transformation was reported by Huisman and

co-workers, who introduced a heterobenzylic alcohol via the selective late-stage oxidation of 285

with microcytochrome P450 monooxygenase followed by deoxyfluorination, which provided access

to the fluoromethyl imidazole 286 (Scheme 5.2).228

165

Scheme 5.2. Late-stage enzymatic oxidation enabled deoxyfluorination

5.1.2. Halide-exchange reaction

Halide exchange reactions have also proven useful for the synthesis of heterobenzylic

fluorides, and have been described for purines,226 imidazoles,229 pyridines,230 quinolines,231–233

indoles,234 benzofurans,235 thiazoles236 and other heterocycles.237 However, as with

deoxyfluorination, the requirement for prior installation of a heterobenzylic halide limits the utility

of these processes and their suitability as late-stage modifications for lead optimization.

Scheme 5.3 Halide-exchange reaction with silver fluoride

An excellent example of halide exchange was reported as part of an investigation into the

cytostatic activity of 6-(fluoromethyl)purine nucleoside analogues. Here, Hocek and co-workers

converted the protected 6-(iodomethyl)purine nucleoside 287 into its fluoromethyl derivative 288

using silver fluoride in THF (Scheme 5.3).226 Silver fluoride, tetrabutylammonium fluoride (TBAF),

potassium fluoride, cesium fluoride, and hydrogen pyridinium fluoride (Olah reagent) are common

fluoride sources used in halide exchange reactions, and their efficient preparation as 18F isotopes

has provided opportunities for the synthesis of 18F-labelled radiotracers for PET imaging.232,236,237

For example, Sutherland and colleagues have reported a radiotracer for imaging of the

translocator protein. Here, K18F in MeCN under moderate heating rapidly converted 289 into its

18F-fluorinated derivative 290 in 38% radiochemical yield (Scheme 5.4).232

166

Scheme 5.4 Halide-exchange reaction for the synthesis of 18F radiotracer (290)

Recently, Yan and co-workers reported a late-stage iodination of 2-alkyl quinolines with iodine

and triphenylphosphine in the presence of sodium bicarbonate. Coupling this process with a

subsequent halide exchange reaction using silver(II) fluoride provided a means to access 2-

fluoroalkyl quinolines in excellent yield.233

5.1.3. Electrophilic fluorination of heterobenzylic anions

Figure 5.3. Common electrophilic fluorinating N-F reagents

The deprotonation of a heterobenzylic methyl or methylene by strong base, followed by

reaction with an electrophilic fluorinating agent (e.g., Figure 5.3) has also provided access to

heterobenzylic fluorides. Here, however, the substrate scope is often limited to molecules with

little additional functionality or relatively acidic heterobenzylic protons. Thus, to facilitate

deprotonation, the heterobenzylic position is often adjacent to a carbonyl,238 nitro,239 or sulfonate

group.240 Notably, this strategy can also provide access to difluorinated adducts by simply

employing an excess of base and fluorinating reagent.241 While much less common, fluorination

of unfunctionalized alkyl heterocycles have also been reported. For example, in 1991, Anders and

co-workers investigated the deprotonation of 4-alkyl pyridines using LDA followed by reaction with

various electrophiles, including NFSI, a process that delivered the corresponding pyridylic fluoride

in modest yield.242

167

Scheme 5.5. Heterobenzylic fluorination of camptothecin

As a notable additional example, Varchi and co-workers utilized this sequence in their fluorination

of the TES-protected natural product camptothecin (291, Scheme 5.5).243 Here, deprotonatation

with LiHMDS at -78 ˚C in THF, and subsequent addition of NFSI, afforded 292 in excellent yield.

5.1.4. Late-stage C-H bond fluorination

Following Groves and co-workers pioneering report on the fluorination of unactivated C(sp3)-H

bonds in 2012,244 several complimentary C-H fluorination strategies have been developed that

provide access to aliphatic,244,245 allyl,246 or benzylfluorides.208–212 Many of these processes take

advantage of the observation made by Sammis and Paquin that electrophilic fluorinating agents

such as NFSI and Selectfluor are capable of transferring a fluorine atom to an intermediate

carbon-centered radical owing to their low N-F bond dissociation energies (Selectfluor BDENF =

62.2 kcal/mole in H2O; NFSI BDENF = 63.5 kcal/mole in H2O).247 Unfortunately, as pointed out

earlier by Crugeiras,248 these reagents are often incompatible with basic amines. Thus, the

preponderance of reports on C-H fluorination that employ electrophilic fluorinating reagents lack

examples of nitrogen-containing heterocycles. Uniquely, the C(sp3)-H fluorination reaction

described by Groves relies instead on the in situ formation of a Mn(IV) species that is a competent

fluorine transfer agent. It has also been demonstrated that this process is amenable to 18F-

fluorination of benzylic C-H bonds213 including the two heterobenzylic C-H 18F-fluorination

reactions depicted in Scheme 5.6 (i.e., 294 and 295).

168

Scheme 5.6. Manganese-catalyzed C-H fluorination for the generation of 18F radiotracers

In 2015, Yi and co-workers described a transition metal-free radical benzylic fluorination using

potassium persulfate in combination with Selectfluor. It was also demonstrated that 8-

(fluoromethyl)quinoline (297) could be produced in 80% yield using this process (Scheme 5.7).212

The authors proposed that thermal decomposition of persulfate generates a sulfate radical that

abstracts a benzylic hydrogen atom. Subsequent fluorine atom transfer from Selectfluor249

provides the fluorinated adduct. Interestingly, an additional 1.5 equiv. of both potassium persulfate

and Selectfluor led to selective difluorination. The authors also noted a competitive benzylic

oxidation reaction that predominated at lower temperatures.

Scheme 5.7. Transition metal-free radical C-H fluorination

Transition metal catalyzed stereocontrolled fluorinations have also been employed for the

synthesis of enantiopure heterobenzylic fluorides.250–252 The Pd-catalyzed β-C(sp3)-H directed

fluorination reported by Yu and co-workers for the synthesis of enantiopure anti-β-fluoro-α-amino

acids provided 299 in 43 % yield and excellent diastereoselectivity (Scheme 5.8).250 Here, it was

proposed that the active catalyst (PdIILn) is formed in situ from the quinoline ligand coordinating

to Pd(TFA)2. A trans-substituted 5-membered palladacycle derived from C(sp3)-H activation

169

undergoes oxidative addition with Selectfluor to generate a Pd(IV) fluoride intermediate.

Reductive elimination then affords the pyridylic fluoride 299.

Scheme 5.8. Palladium-catalyzed diastereoselective C-H fluorination

In 2006, the palladium-catalyzed directed C-H fluorination of both heterobenzylic and aryl C-H

bonds was reported by Sanford and co-workers and represents the first example of metal-

catalyzed heterobenzylic fluorination (Scheme 5.9).253 Here, following generation of an

intermediate 5-membered palladacycle, oxidation by N-fluoropyridinium triflate to Pd(IV) and a

subsequent reductive elimination generates a new C-F bond. In 2012, Sanford and co-workers

described an important advance by demonstrating that the palladium-catalyzed C-H fluorination

could also be effected using nucleophilic fluoride (Scheme 5.9).254 Here, a hypervalent iodine

source is responsible for oxidation of Pd(II) to Pd(IV), which upon ligand exchange with silver

fluoride and subsequent reductive elimination generates 8-(fluoromethyl)quinolines 303.

Scheme 5.9 Sanford’s palladium-catalyzed C-H fluorination methods

In the same year, Freeze and collegues described the heterobenzylic fluorination of quinazoline

304 with Selectfluor in their synthesis of nicotinamide phosphoribosyltransferase inhibitors

170

(Scheme 5.10; 305).58 Given these mild conditions, this simple reaction may well prove useful for

the the late-stage fluorination of other heterobenzylic C-H bonds.

Scheme 5.10. Fluorination with Selectfluor

5.1.5. Monofluoromethylation of C(sp2)-H bonds

In 2012, Baran and co-workers reported an efficient and complementary synthesis of

heterobenzylic fluorides by demonstrating that these compounds could be accessed through the

direct functionalization of heteroaromatic C(sp2)–H bonds.88 Here, it was shown that a zinc

monofluoromethane sulphinate, in the presence of an oxidant, effected the direct

monofluoromethylation of xanthines, pyridines, quinoxalines , and pyrroles. Notably, in cases

where multiple monofluoromethylation events are possible, single products were observed with

excellent regioselectivity. Mechanistically, it was proposed that the reaction involves a Minisci-like

radical process, whereby a zinc monofluoromethane sulphinate generates a nucleophilic CH2F

radical. Through the use of alternative zinc sulphinate salts it was also shown that heterocycles

could be readily modified by addition of CF3, CF2H, and CH2CF3.

5.2. Late-stage fluorination of pyridylic C-H bonds

In 2014, we reported the direct fluorination of unactivated C-H bonds using the unique

combination of a decatungstate photocatalyst and N-fluorobenzenesulfonimide (NFSI).211,245,255

Considering our prior success in the fluorination of aliphatic,245,255 acyl,245 and benzylic211 C – H

bonds, we endeavoured to expand the reaction scope to include the fluorination of relatively weak

pyridylic C –H bonds (4-picoline BDE (CH3) 87 kcalmol-1 vs. toluene BDE (CH3) 90 kcalmol-1).256

As a significant complicating factor, however, Crugeiras has reported248 that several amine bases

react with NFSI at the sulfonyl group (and not the electrophilic fluorine) and decompose this

reagent.

171

entry conditions (pyridine)

solvent additive (1 equiv.)

t (h) Product (%yield)

1 A (306) MeCN HCl 24 308 (0) 2 A (306) MeCN none 24 308 (0) 3 A (306) MeCN-H2O HCl 24 308 (0) 4 A (307) MeCN-H2O TFA 36 309 (38) 5 A (306) MeCN AlF3 18 308 (26) 6 B (306) MeCN AlF3 18 308 (32) 7 B (306) MeCN none 18 308 (29) 8 C (306) MeCN none 18 308 (79) 9 D (306) MeCN none 15 308 (87)

10 D (306) benzene none 18 308 (81) 11 D (306) EtOAc none 18 308 (90) 12 D (307) MeCN none 18 310 (61)

Table 5.1 Fluorination of 4-alkylpyridines using NFSI.

In an effort to prevent such undesired sulfonyl transfer reactions, we initiated our investigation by

exploring the fluorination of N-oxides and various Brønsted acid salts of 4-ethylpyridine (306) and

4-isobutylpyridine (307) under our standard decatungstate/NFSI reaction conditions.245 As

summarized in Table 5.1 (entries 1–4), while we were unable to effect the fluorination of salts of

4-ethylpyridine, 4-isobutylpyridine·TFA was fluorinated selectively at the branched aliphatic

position (entry 4). While encouraging, this result suggested that protonation disfavours formation

of the intermediate pyridylic radical. The addition of Lewis acids of varying strength was also

explored and we were delighted and surprised to find that pyridylic fluorination of 4-ethylpyridine

occurred only in the presence of AlF3 (entry 5), a relatively weak and largely insoluble Lewis acid.

To assess the individual roles of the various reagents now present, the reaction was repeated

without the decatungstate or photoirradiation, and a similar outcome was observed (entry 6), thus

clearly indicating that the photocatalyst was not a participant. Furthermore, removal of AlF3 also

had no effect on the reaction outcome (entry 7). In fact, simply stirring 4-ethylpyridine with an

excess of NFSI in MeCN led cleanly to 4-(1-fluoroethyl)pyridine (308). Remarkably, only a single

related example of this operationally straightforward process has been reported; in 1996

DesMarteau found257 that 2- and 4-picoline react with the highly reactive fluorinating agent

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(CF3SO2)2NF (fluorine plus detachment (FPD) = 200.5 kcalmol-1 in CH3CN vs. 229.6 kcalmol-1 for

NFSI)258 and base in CH2Cl2 to provide fluoromethyl-picolines, along with lesser amounts of

difluoromethyl and fluoropyridine products. Quite distinctly, in the present reaction, the addition of

base (NaHCO3 or Li2CO3) had little effect on the outcome (entries 8 and 9), and the reaction

proceeds equally well in C6H6 and EtOAc (entries 10 and 11) but gives poorer results in CH2Cl2

and THF. Optimally, simply heating a mixture of 4-ethylpyridine and NFSI in MeCN at 60°C

afforded 4-(1-fluoroethyl)pyridine (308) in excellent yield (87%, entry 9). Gratifyingly, reaction of

4isobutylpyridine (307) under the same conditions afforded the pyridylic fluorination product 310

(entry 12), with selectivity complimentary to that observed in the photocatalytic C-H fluorination of

the same substrate (entry 4).

Scheme 5.11. Fluorination of 4-(cyclopropylmethyl)pyridine (311) and a mechanistic proposal for the formation of 308 and decomposition products of NFSI

Our previous studies211 have shown that benzylic fluorination can involve radical

propagation by NFSI, and we questioned whether radical intermediates are involved in the

present pyridylic fluorination. When the reaction of 4-ethylpyridine with NFSI (Table 5.1, entry 9)

was repeated with addition of the galvinoxyl free-radical trap,259 the yield of 4-(1-

fluoroethyl)pyidine (306) was not affected. Moreover, fluorination of 4-(cyclopropylmethyl)pyridine

(311)260 with NFSI delivered only the pyridylic fluoride 312 in excellent yield (Scheme 5.11). The

absence of rearrangement products 313 or 314 suggests this reaction does not proceed via a

pyridylic radical or cation generated through a SET process.247 Further investigation of the

fluorination of 4-ethylpyridine provided additional insight. For example, when NFSI was replaced

173

with N-fluoropyridinium triflate, an equally reactive fluorinating agent,258 only unreacted starting

materials were recovered, thus suggesting that NFSI plays a critical role. Moreover, the major

byproducts produced in the 4-ethylpyridine fluorination were found to be benzenesulfonamide,

phenylsulfonyl fluoride, dibenzenesulfonimide and, to a lesser extent, products apparently derived

from phenylsulfonyl nitrene261 (Scheme 5.11). Based on these findings and the propensity of

nitrogen nucleophiles to react with NFSI at the sulfur,248 we posit that this pyridylic fluorination

involves a transient reaction between pyridine and NFSI to generate N-sulfonylpyridinium salt 315

and a nitrene.261 Loss of an α-methylene proton from the pyridinium then affords the resonance

stabilized tautomer 316, which can subsequently react with NFSI to provide the fluoroalkylpyridine

308. Phenylsulfonyl fluoride, which is generated in this reaction, may also play a role and serve

as the key sulfonylating reagent. While it is conceivable that this process could be initiated by

transient fluorination of the pyridine nitrogen, when a mixture of pyridine and NFSI was heated in

MeCN-d3, the expected N-fluoropyridinium salt was not detected by 1H or 19F NMR spectroscopy.

A corollary of this mechanistic proposal is that pyridylic fluorination is restricted to 2- and 4-

substituted pyridines, where deprotonation results in a resonance-stabilized carbanion. As

detailed below, 3-substituted pyridines fail to engage in productive reactions with NFSI.

174

Figure 5.4 Selective pyridylic fluorination of C-H Bonds

In order to evaluate the regioselectivity and scope of this reaction, we investigated the

fluorination of a structurally diverse collection of alkylpyridines (Figure 5.4). In general, the direct

C-H fluorination of 2- and 4-alkyl pyridines and annulated pyridines proceeds in good to excellent

yield. Notably, the reaction is highly tolerant to common functional groups, including amides,

esters, ketones, imidazolidinones, tertiary alcohols, and sulfonamides. While conceptually,

fluoroalkyl pyridines could be accessed from the deprotonation of alkyl pyridines using a strong

base, followed by reaction with NFSI, the reaction of 4-ethylpyridine with LDA followed by NFSI

optimally provided the fluoroethyl pyridine 308 in inferior yield (57%). Moreover, the reaction of

175

5,6,7,8-tetrahydroisoquinoline with LDA followed by NFSI delivered none of the fluorinated adduct

324, and these conditions only effected α-fluorination of carbonyl-containing substrates (see the

Supporting Information). Conversely, fluorination of 5,6,7,8-tetrahydroisoquinoline using our

optimized method (Table 5.1, entry 9) provided 324 in good yield and with complete selectivity for

fluorination at C5. Likewise, fluorination of 6,7-dihydro-5H-cyclopenta[b]pyridine262 afforded the

7-fluoro adduct 323 exclusively. This selectivity is consistent with the mechanistic proposal

outlined above and the fact that other 3-alkylpyridines (e.g., 321, 322, and 326) failed to undergo

fluorination. Importantly, this predictive selectivity creates opportunities for site-selective

fluorination in more complex or annulated pyridines263–268 (e.g., 323 – 325, 331, and 332), thus

making this method a potentially powerful tool for the late-stage modification of drug leads.

Substrates containing acid-sensitive functionalities were also well tolerated under the mild

reaction conditions, which enabled access to the tertiary alcohols 327 and 329. Interestingly,

pyridylic fluorination occurs in preference to fluorination at the α-carbon of ketones, amides, and

esters (e.g., 325, 331, and 332), which further highlights the enhanced acidity of the pyridylic

proton following activation (Figure 5.4) and the distinctness of this process from classical

deprotonation/fluorination strategies.

Scheme 5.12 Direct fluorination of the potent aldosterone synthase inhibitors 333 and 335

With an interest in exploring the reliability of this transformation for medicinal chemistry

purposes, the potent (IC50 < 10 nm) aldosterone synthase (CYP11B2) inhibitors 333 and 335 268

were also reacted with NFSI to afford the fluorinated analogues 334 and 336 in good yield and

with complete regioselectivity for the position indicated. It is notable that this simple modification

should have a measurable influence on both the acidity (ΔpKa ≈ 1.4)269 and metabolic stability of

these drug leads.

176

Scheme 5.13 Site-selective late-stage fluorination of pyridylic, benzylic, or aliphatic C-H bonds, contrasted with classical α-fluorination

To demonstrate the utility of this advance within the context of site-selective late-stage C-

H fluorination, we explored the fluorination of esters derived from ibuprofen and leucine (Scheme

5.13). When employing our photocatalytic decatungstate reaction conditions245 with the TFA salts

of 337 and 341, we observed complete selectivity for the expected211,245,255 benzylic or aliphatic

fluorination products 340 and 343, respectively. Conversely, simply heating the esters 337 and

341 with NFSI in MeCN delivered the corresponding pyridylic fluorides 338 and 342 in good yield.

Notably, treatment of 337 with LDA followed by NFSI provided complimentary selectivity and

afforded the α-fluoroester 339 as the exclusive product.

177

5.3. Conclusion

In summary, we have developed a convenient and regioselective fluorination reaction that

enables the late-stage fluorination of pyridylic C-H bonds. This reaction tolerates a wide variety

of functional groups and offers selectivity complementary to decatungstate-catalyzed C-H

fluorination. Importantly, this process provides a means to directly modulate basicity, improve

lipophilicity, and alter the metabolic profile of 2- and 4-alkylpyridines. Considering that pyridines

are prominent scaffolds in small-molecule drugs, this simple reaction may well serve as an

enabling tool in medicinal chemistry. Further optimization aimed at decreasing reaction times

(e.g., in continuous flow) may expand the utility of this process to include radiotracer synthesis

using [18F]NFSI270 (18F t1/2 = 110 min).

5.4. Experimental

General considerations

All reactions were carried out with commercial solvents and reagents that were used as

received. For extended NaDT photochemical reactions, degassing of the solvent was carried out

via several freeze/pump/thaw cycles. Flash chromatography was carried out with Geduran®

Si60 silica gel (Merck). Concentration and removal of trace solvents was done via a Büchi rotary

evaporator using dry ice/acetone condenser, and vacuum applied from an aspirator or Büchi V-

500 pump. All reagents and starting materials were purchased from Sigma Aldrich, Alfa Aesar,

TCI America, and/or Strem, and were used without further purification. All solvents were

purchased from Sigma Aldrich, EMD, Anachemia, Caledon, Fisher, or ACP and used without

further purification, unless otherwise specified.

Nuclear magnetic resonance (NMR) spectra were recorded using chloroform-d (CDCl3),

acetonitrile-d3 (CD3CN), or methanol-d4 (MeOD). Signal positions (δ) are given in parts per million

from tetramethylsilane (δ 0) and were measured relative to the signal of the solvent (1H NMR:

CDCl3: δ 7.26, CD3CN: δ 1.96, MeOD: δ 3.31; 13C NMR: CDCl3: δ 77.16, CD3CN: δ 118.26,

MeOD: δ 49.00). Coupling constants (J values) are given in Hertz (Hz) and are reported to the

nearest 0.1 Hz. 1H NMR spectral data are tabulated in the order: multiplicity (s, singlet; d, doublet;

t, triplet; q, quartet; quint, quintet; m, multiplet), coupling constants, number of protons. NMR

spectra were recorded on a Bruker Avance 600 equipped with a QNP or TCI cryoprobe (600

MHz), Bruker 500 (500 MHz), or Bruker 400 (400 MHz). Assignments of 1H and 13C NMR spectra

178

are based on analysis of 1H-1H COSY, HSQC, and HMBC spectra, where applicable. Methyl

propiolate was added to the crude reaction mixtures and used as an internal standard. Yields

were then calculated following analysis of 1H NMR spectra. phenylsulfonylfluoride,

benzenesulfonamide, and dibenzenesulfonimide were identified by comparison of their spectral

data to that reported previously.

High-resolution mass spectra were performed on an Agilent 6210 TOF LC/MS, Bruker

MaXis Impact TOF LC/MS, or Bruker micrOTOF-II LC mass spectrometer.

Preparative RP –HPLC was performed on an Agilent series 1200 instrument with a

Phenomenex Gemini-NX C18 preparative column (5 um 110 Å 50 x 30 mm, flow rate 15 mL/min).

General Procedure 1: pyridylic fluorination

To a solution of substrate in CH3CN (0.1 M substrate) was added N-fluorobenzenesulfonimide

(NFSI) (3.0 eq) and Li2CO3 (1.1 eq). The resulting reaction mixture was then heated to 60 °C for

18-24 h. The reaction mixture was cooled, diluted with CH2Cl2 and washed with saturated

NaHCO3 solution. The organic layer was dried (MgSO4), concentrated, and the crude reaction

product was purified by column chromatography on silica gel (as indicated).

Preparation of compound 308

Prepared following General Procedure 1: 4-ethylpyridine (50.0 mg, 0.466 mmol), NFSI (0.441 g,

1.40 mmol, 3.0 eq.), Li2CO3 (38.2 mg, 0.517 mmol, 1.1 eq.). Purified by flash chromatography

using ethyl acetate – pentane (50:50) as the eluent. Yield determined by analysis of 1H NMR

spectra of crude reaction product using an internal standard (methyl propiolate): 87 %

1H NMR (400 MHz, CD3CN): δ 8.74 (d, J = 6.6 Hz, 2H), 7.98 (d, J = 6.4 Hz, 2H),

5.99 (dq, J = 47.5, 6.7 Hz, 1H), 1.69 (dd, J = 24.5, 6.9 Hz, 3H); 13C NMR (150

MHz, CD3CN): δ 162.7 (d, J = 20.6 Hz), 142.3, 124.1 (d, J = 9.0 Hz) , 89.8 (d, J

= 171.8 Hz), 22.3 (d, J = 23.0 Hz); 19F NMR (470 MHz, CD3CN): –180.8

HRMS (EI+) calcd for [C7H9NF]+ 126.0714, found 126.0717

Preparation of compound 312

179

Prepared following General Procedure 1: 4-(cyclopropylmethyl)pyridine (30.0 mg, 0.225 mmol),

NFSI (0.213 g, 0.676 mmol, 3.0 eq.), Li2CO3 (18.3 mg, 0.248 mmol, 1.1 eq.). Purified by flash

chromatography using ethyl acetate – pentane (50:50) as the eluent. Yield determined by the

analysis of 1H NMR spectra of crude reaction product using an internal standard (methyl

propiolate): 73 %

1H NMR (500 MHz, CD3CN): δ 8.63 (d, J = 5.6 Hz, 2H), 7.42 (d, J = 5.5 Hz, 2H),

4.89 (dd, J = 47.8, 9.3 Hz, 1H), 1.31 (m, 1H), 0.73 (m, 2H), 0.64 (m, 1H), 0.58

(m, 1H); 13C NMR (150 MHz, CD3CN): δ 150.9, 150.0 (d, J = 23.0 Hz), 121.3 (d,

J = 7.4 Hz), 97.6 (d, J = 171.8 Hz), 17.0 (d, J = 28.2 Hz), 4.07 (d, J = 2.2 Hz),

2.92 (d, J = 9.1 Hz); 19F NMR (470 MHz, CD3CN) –174.2.

HRMS (EI+) calcd for [C9H11FN]+ 152.0870, found 152.0866

Preparation of compound 318

Prepared following General Procedure 1: 4-propylpyridine (28.0 mg, 0.231 mmol), NFSI (0.219 g,

0.693 mmol, 3.0 eq.), Li2CO3 (18.7 mg, 0.254 mmol, 1.1 eq.). Purified by flash chromatography

using ethyl acetate – pentane (50:50) as the eluent. Yield determined analysis of 1H NMR spectra

of crude reaction product using an internal standard (methyl propiolate): 86 %

1H NMR (500 MHz, CDCl3): δ 8.74 (d, J = 6.0 Hz, 2H), 7.73 (d, J = 6.0 Hz, 2H),

5.62 (ddd, J = 47.8, 7.6, 4.4 Hz, 1H), 1.99 (m, 2H), 1.06 (t, J = 7.5 Hz, 3H) 13C

NMR (150 MHz, CDCl3): δ 159.6 (d, J = 22.5 Hz), 140.8, 122.4 (d, J = 9.1 Hz),

91.9 (d, J = 180.3 Hz), 29.3 (d, J = 22.2 Hz), 8.24 19F NMR (470 MHz, CDCl3):

–186.5

HRMS (ESI+) calcd for [C8H11NF]+ 140.0870, found 140.0868

Preparation of compound 323

Prepared following General Procedure 1: 6,7-dihydro-5H-cyclopenta[b]pyridine (25.0 mg, 0.201

mmol), NFSI (0.199 g, 0.603 mmol, 3.0 eq.), Li2CO3 (16.3 mg, 0.221 mmol, 1.1 eq.). Purified by

flash chromatography using ethyl acetate – pentane (40:60) as the eluent. Yield determined by

analysis of 1H NMR spectra of crude reaction product using an internal standard (methyl

propiolate): 52 %

180

1H NMR (500 MHz, CDCl3): δ 8.55 (d, J = 4.8 Hz, 1H), 7.66 (d, J = 7.7 Hz, 1H),

7.26 (dd, J = 7.7, 4.9 Hz, 1H), 5.95 (ddd, J = 56.6, 6.4, 2.5 Hz, 1H), 3.18 (m, 1H),

2.90 (m, 1H), 2.41 (m, 2H) ; 13C NMR (150 MHz, CDCl3): δ 159.2 (d, J = 16.8 Hz),

148.4 (d, J = 2.3 Hz), 137.0 (d, J = 4.3 Hz), 133.2 (d, J = 1.6 Hz) 123.7(d, J = 3.3

Hz), 95.0 (d, J = 176.0 Hz), 30.3 (d, J = 23.3 Hz), 27.4; 19F NMR (470 MHz, CDCl3): –167.6

HRMS (EI+) calcd for [C8H9NF]+ 138.0714, found 138.0719

Preparation of compound 324

Prepared following General Procedure 1: 5,6,7,8-tetrahydroisoquinoline (50.0 mg, 0.375 mmol),

NFSI (0.356 g, 1.13 mmol, 3.0 eq.), Li2CO3 (30.5 mg, 0.413 mmol, 1.1 eq.). Purified by flash

chromatography using ethyl acetate – pentane (30:70) as the eluent. Yield determined by

analysis of 1H NMR spectra of crude reaction product using an internal standard (methyl

propiolate): 68 %

1H NMR (600 MHz, MeOD): δ 8.41 (s, 1H), 8.40 (d, J = 5.3 Hz, 1H), 7.47 (d, J =

5.3 Hz, 1H), 5.64 (ddd, J = 49.7, 5.3, 5.3 Hz, 1H), 2.90 (m, 1H), 2.79 (m, 1H),

2.14 (m, 1H), 2.00 (m, 1H), 1.89 (m, 1H); 13C NMR (150 MHz, MeOD): δ 149.0,

145.6 (d, J = 1.4 Hz), 143.4 (d, J = 18.0 Hz), 133.2 (d, J = 3.3 Hz), 122.7 (d, J =

5.0 Hz), 86.4 (d, J = 170.0 Hz), 28.2 (d, J = 20.0), 24.7, 17.3 (d, J = 5.2 Hz); 19F

NMR (CDCl3): –166.5.0

HRMS (EI+) calcd for [C9H11FN]+ 152.0870, found 152.0871

Preparation of compound 325

Prepared following General Procedure 1: 6,7-dihydroisoquinolin-8(5H)-one (30.0 mg, 0.204

mmol), NFSI (0.193 g, 0.612 mmol, 3.0 eq.), Li2CO3 (16.6 mg, 0.224 mmol, 1.1 eq.). Purified by

flash chromatography using ethyl acetate – pentane (50:50) as the eluent. Yield determined by

analysis of 1H NMR spectra of crude reaction product using an internal standard (methyl

propiolate): 51 %

181

1H NMR (600 MHz, CDCl3): δ 9.21 (s, 1H), 8.85 (d, J = 5.1 Hz, 1H), 7.57 (d, J

= 5.2 Hz, 1H), 5.75 (ddd, J = 48.8, 9.0, 4.2 Hz, 1H), 2.96 (ddd, J = 17.8, 6.9,

4.2 Hz), 1H), 2.67 (ddd, J = 17.5, 11.0, 4.9 Hz, 1H), 2.58 (m, 1H), 2.43 (m, 1H);

13C NMR (150 MHz, CDCl3) δ 195.0 (d, J = 1.7 Hz), 153.6, 149.6 (d, J = 18.9

Hz), 148.8, 126.0 (d, J = 4.3 Hz), 121.4 (d, J = 6.8 Hz), 86.7 (d, J = 178.7 Hz),

34.9 (d, J = 8.7 Hz), 29.1 (d, J = 20.7 Hz); 19F NMR (470 MHz, CDCl3): –178.7

HRMS (EI+) calcd for C9H9FNO+ 166.0663, found 166.0660

Preparation of compound 332

Prepared following General Procedure 1: ethyl 2-(6,7-dihydro-5H-cyclopenta[c]pyridine-6-

carboxamido)-4-methylpentanoate (20.0 mg, 0.0657 mmol), NFSI (0.062 g, 0.20 mmol, 3.0 eq.),

Li2CO3 (5.0 mg, 0.072 mmol, 1.1 eq.). Purified by flash chromatography using ethyl acetate –

pentane (60:40) as eluent. Yield determined by analysis of 1H NMR spectra of crude reaction

product using an internal standard (methyl propiolate): 69 %. Characterization data shown for one

diastereomer.

1H NMR (600 MHz, MeOD): δ 8.58 (s, 1H), 8.53 (d, J = 5.1 Hz, 1H), 7.55 (d,

J = 5.0 Hz, 1H), 6.28 (d, J = 54.4, 5.7 Hz, 1H), 4.52 (t, J = 7.2 Hz, 1H), 4.21

(m, 2H), 3.49 (m, 2H) , 3.18 (m, 1H), 1.79 (m, 1H), 1.70 (m, 2H), 1.31 (t, J

= 7.4 Hz, 3H), 1.04 (d, J = 6.6 Hz, 3H), 1.00 (d, J = 6.6 Hz, 3H); 13C NMR

(150 MHz, MeOD) δ 174.3 (d, J = 2.8), 174.0, 150.4 (d, J = 18.2 Hz), 148.8,

147.3, 139.0 (d, J = 4.4 Hz), 121.2, 98.8 (d, J = 184.3 Hz), 62.4, 53.2 (d, J

= 20.2 Hz), 52.6, 41.3, 33.2 (d, J = 3.3 Hz), 26.1, 23.3, 21.8, 14.5; 19F NMR

(470 MHz, MeOD): –175.0

HRMS (EI+) calcd for [C17H24FN2O3]+ 323.1771, found 323.1778

Preparation of compound 327

Prepared following General Procedure 1: 8-vinyl-5,6,7,8-tetrahydroisoquinolin-8-ol (14.0 mg,

0.0799 mmol), NFSI (0.076 g, 0.24 mmol, 3.0 eq.), Li2CO3 (7.0 mg, 0.088 mmol, 1.1 eq.). Purified

by flash chromatography using ethyl acetate – pentane (80:20) as the eluent. Yield determined

by analysis of 1H NMR spectra of crude reaction product using an internal standard (methyl

propiolate): 58 %. Characterization data shown for one diastereomer.

182

1H NMR (500 MHz, CDCl3): δ 9.00 (s, 1H), 8.57 (d, J = 5.7 Hz, 1H), 7.48 (d, J

= 5.8, 1H), 6.04 (dd, J = 17.3, 10.6 Hz, 1H), 5.59 (ddd, J = 48.5, 8.4, 6.0 Hz,

1H), 5.39 (d, J = 10.6 Hz, 1H), 5.33 (d, J = 17.2 Hz, 1H), 2.47 (m, 1H), 2.31

(m, 2H), 2.08 (m, 1H); 13C NMR (150 MHz, CDCl3) δ 153.1 (d, J = 19.2 Hz),

143.2, 141.1, 141.0 (d, J = 3.5 Hz), 138.9, 124.6 (d, J = 7.2 Hz), 117.1, 86.6

(d, J = 179.4 Hz), 71.4, 33.0 (d, J = 7.6 Hz), 25.2 (d, J = 19.3 Hz); 19F NMR (CDCl3) –175.0

HRMS (ESI+) calcd for [C11H13FNO]+ 194.0976, found 194.1006

Preparation of compound 329

Prepared following General Procedure 1: 8-(1-(phenylsulfonyl)-1H-indol-2-yl)-5,6,7,8-

tetrahydroisoquinolin-8-ol (95.0 mg, 0.235 mmol), NFSI (0.222 g, 0.705 mmol, 3.0 eq.), Li2CO3

(19.1 mg, 0.259 mmol, 1.1 eq.). Purified by flash chromatography using ethyl acetate – pentane

(65:35) as the eluent.. Yield determined by analysis of 1H NMR spectra of crude reaction product

using an internal standard (methyl propiolate): 34 %

1H NMR (600 MHz, MeOD): δ 8.47 (d, J = 5.4 Hz, 1H), 8.18 (s, 1H),

8.07 (d, J = 8.2 Hz 1H), 7.60 (m, 2H) 7.53, (t, J = 7.61, 1H), 7.31 (m,

5H), 7.11 (m, 2H), 5.85 (ddd, J = 50.3, 10.3, 5.6 Hz, 1H), 3.30 (m,

1H), 2.35 (m, 2H), 2.21 (m, 1H); 13C NMR (150 MHz, MeOD): δ

150.0, 149.3, 148.9, 147.9, 140.4, 140.2, 137.3, 135.1, 130.2, 130.2

(d, J = 17.4 Hz), 127.6, 127.0, 126.2, 125.3, 122.4, 121.3, 116.5, 89.1

(d, J = 172.5 Hz), 72.6, 36.2 (d, J = 11.6 Hz) , 27.2 (d, J = 18.8 Hz); 19F NMR (470 MHz, CD3CN)

–179.2.

HRMS (EI+) calcd for [C23H20FN2O3S]+ 423.1173, found 423.1170

Preparation of compound 328

Prepared following General Procedure 1: 3-(pyridin-4-yl)propyl benzoate (62.0 mg, 0.254 mmol),

NFSI (0.240 g, 0.762 mmol, 3.0 eq.), Li2CO3 (20.6 mg, 0.279 mmol, 1.1 eq.). Purified by flash

chromatography using ethyl acetate – pentane (50:50) as the eluent. Yield determined by

analysis 1H NMR spectra of crude reaction product using an internal standard (methyl propiolate):

70 %

183

1H NMR (600 MHz, CDCl3): δ 8.66 (d, J = 5.2 Hz, 2H), 7.98 (dd, J =

8.5, 1.3 Hz, 2H), 7.58 (tt, J = 7.6, 1.2 Hz, 1H), 7.45 (dd, J = 7.7, 7.7

Hz, 2H), 7.36 (d, J = 5.2 Hz, 2H), 5.72 (ddd, J = 47.9, 6.2, 6.2 Hz,

1H), 4.52 (m, 2H), 2.37 (m, 2H). 13C NMR (150 MHz, CDCl3) δ 166.4,

149.8 (d, J = 21.9 Hz), 149.3, 133.4, 129.9, 129.7, 128.6, 120.3 (d,

J = 7.4 Hz), 89.8 (d, J = 176.3 Hz), 60.4 (d, J = 4.5 Hz), 36.2 (d, J = 22.8 Hz); 19F NMR (470 MHz,

CDCl3) –187.6

HRMS (EI+) calcd for [C15H15FNO2]+ 260.1081, found 260.1109

Preparation of compound 330

Prepared following General Procedure 1: 3-(pyridin-4-yl)propyl 4-nitrobenzoate (80.0 mg, 0.280

mmol), NFSI (0.265 g, 0.840 mmol, 3.0 eq.), Li2CO3 (22.7 mg, 0.308 mmol, 1.1 eq.). Purified by

flash chromatography using ethyl acetate – pentanes (50:50) as the eluent. Yield determined by

analysis of 1H NMR spectra of crude reaction product using an internal standard (methyl

propiolate): 64 %

1H NMR (500 MHz, MeOD): δ 8.54 (d, J = 6.0 Hz, 2H), 8.32 (d, J =

8.9 Hz, 2H), 8.14 (d, J = 8.9 Hz 2H), 7.49 (d, J = 9.0 Hz, 2H) 5.84

(ddd, J = 47.8, 7.7, 4.4 Hz, 1H), 4.56 (dd, J = 6.2, 6.2 Hz, 2 H),

2.45 (m, 2H); 13C NMR (150 MHz, MeOD): δ 165.8, 151.6 (d, J =

21.0 Hz), 150.4, 136.7, 131.8, 124.6, 121.7 (d, J = 8.5 Hz), 91.2

(d, J = 174.2 Hz), 62.4 (d, J = 4.9), 36.6 (d, J = 22.5); 19F NMR (470 MHz, MeOD) –188.6

HRMS (EI+) calcd for [C15H14FN2O4]+ 305.0932, found 305.0957

Preparation of compound 331

Prepared by following General Procedure 1: 3-(pyridin-4-yl)propyl 6-((4R,5S)-5-methyl-2-

oxoimidazolidin-4-yl)hexanoate (86.0 mg, 0.255 mmol), NFSI (0.241 g, 0.765 mmol, 3.0 eq.),

Li2CO3 (20.7 mg, 0.281 mmol, 1.1 eq.). Purified by flash chromatography using dichloromethane

– methanol (95:5) as the eluent. Yield determined by analysis of 1H NMR spectra of crude reaction

product using an internal standard (methyl propiolate): 63 %.

184

1H NMR (500 MHz, MeOD): δ 8.59 (d, J = 6.0 Hz, 2H), 7.46

(d, J = 6.0 Hz, 2H), 5.73 (ddd, J = 48.1, 7.5, 4.6 Hz 1H), 4.27

(m, 2H) 3.84 (m, 1H), 3.72 (m, 1H), 2.36, 2.30 (m, 3H), 2.25

(m, 1H), 1.64 (quint., J = 7.4 Hz, 2H), 1.52 (m, 2H), 1.40 (m,

2H), 1.13 (d, J = 6.5 Hz, 3H) ; 13C NMR (150 MHz, MeOD): δ

175.3, 166.2, 151.7 (d, J = 20.5 Hz), 150.5, 121.7 (d, J = 7.9

Hz), 91.1 (d, J = 174.0 Hz), 61.0 (d, J = 5.3 Hz), 57.4, 52.7, 36.7 (d, J = 22.3 Hz), 34.8, 30.7,

30.1, 27.1, 25.8, 15.6; 19F NMR (470 MHz, MeOD) –188.8

HRMS (EI+) calcd for [C18H27FN3O3]+ 352.2031, found 352.2059

Preparation of compound 334

Prepared following General Procedure 1: 6,7-dihydro-5H-cyclopenta[c]pyridine-4-carbonitrile

(25.0 mg, 0.173 mmol), NFSI (0.164 g, 0.520 mmol, 3.0 eq.), Li2CO3 (14.0 mg, 0.190 mmol, 1.1

eq.). Purified by flash chromatography using ethyl acetate –pentane (40:60) as the eluent. Yield

determined by analysis of 1H NMR spectra of crude reaction product using an internal standard

(methyl propiolate): 60 %

1H NMR (600 MHz, CDCl3): δ 8.82 (s, 1H), 8.81 (s, 1H), 6.2 (ddd, J = 54.8, 6.7,

3.3 Hz, 1H), 3.28 (m, 1H), 3.03 (m, 1H), 2.51 (m, 2H); 13C NMR (150 MHz,

CDCl3) δ 150.5 (d, J = 16.8 Hz), 150.1, 150.0, 140.2, 114.1, 106.5, 93.5 (d, J

= 178.1 Hz), 31.3 (d, J = 22.7 Hz), 27.6; 19F NMR (CDCl3) –169.2

HRMS (ESI+) calcd for [C9H8FN2]+ 163.0666, found 165.0662

Preparation of compound 336

Prepared following General Procedure 1: 4-(2-fluoro-4-(trifluoromethyl)phenyl)-6,7-dihydro-5H-

cyclopenta[c]pyridine (30.0 mg, 0.107 mmol), NFSI (0.101 g, 0.321 mmol, 3.0 eq.), Li2CO3 (9.0

mg, 0.12 mmol, 1.1 eq.). Purified by flash chromatography using ethyl acetate – pentane (50:50)

as the eluent. Yield determined by analysis of 1H NMR spectra of crude reaction product using

an internal standard (methyl propiolate): 78 %

185

1H NMR (500 MHz, CDCl3): δ 8.71 (s, 1H), 8.57 (s, 1H), 7.61 (dd, J = 7.8,

1H) 1H), 7.56 (d, J = 7.8, 1H), 7.50 (d, J = 10.1, 1H), 5.97 (ddd, J = 54.1

Hz, 1H), 3.32 (m, 1H), 3.06 (m, 1H), 2.43 (m, 2H); 13C NMR (150 MHz,

CDCl3) δ 159.4 (d, J = 250.4 Hz), 148.5 (d, J = 17.2 Hz), 147.4, 146.0,

141.0 (d, J = 3.4 Hz), 133.0 (qd, J = 32.8, 8.0 Hz), 132.5(dq, J = 3.1, 1.5

Hz), 128.4, 127.3 (d, J = 15.4 Hz), 123.2 (qd, J = 272.6, 2.8 Hz), 121.6 (dq, J = 7.5, 3.9 Hz), 113.7

(dq, J = 25.8, 3.7 Hz), 94.9 (dd, J = 176.1, 2.9 Hz), 32.5 (d, J = 23.2 Hz), 28.1; 19F NMR (CDCl3)

–62.8, –113.3, –165.5

HRMS (EI+) calcd for [C15H11F5N]+ 300.0806, found 300.0802

Preparation of compound 338

Prepared following General Procedure 1: 3-(pyridin-4-yl)propyl 2-(4-isobutylphenyl)propanoate

(35.0 mg, 0.108 mmol), NFSI (0.102 g, 0.323 mmol, 3.0 eq.), Li2CO3 (9.0 mg, 0.12 mmol, 1.1 eq.).

Purified by flash chromatography using ethyl acetate – pentane (50:50) as the eluent. Yield

determined by analysis of 1H NMR spectra of crude reaction product using an internal standard

(methyl propiolate): 54 %.

1H NMR (500 MHz, MeOD): δ 8.53 (m, 2H), 7.27 (m, 4H), 7.15

(m, 2H), 5.38 (m, 1H), 4.23 (m, 2H), 3.73 (m, 1H), 2.46 (m, 2H),

2.20 (m, 2H), 1.83 (m, 1H), 1.47 (m, 3H), 0.88 (m, 6H); 13C NMR

(150 MHz, MeOD): δ 174.2, 149.7, 148.3, 140.1, 137.5, 128.6,

126.4, 119.8, 88.8, 59.3, 44.4, 44.1, 34.9, 29.6, 20.8, 16.7. 19F

NMR (470 MHz, MeOD) –188.8, –188.8.

HRMS (EI+) calcd for [C21H27FNO2]+ 344.2020, found 344.2021

Preparation of compound 340

To a solution of 337 ·TFA (25 mg, 0.057 mmol) in CH3CN (0.45 ml) and H2O (0.05 ml) was added

NFSI (0.054 g, 0.17 mmol, 3.0 eq) and NaDT (7.0 mg, 0.0029 mmol, 0.05 eq.) and the resulting

mixture was degassed via 3 x freeze/pump/thaw cycles. The reaction mixture was then irradiated

with long wave UV light (365 nm) for 36 h and monitored by 1H NMR spectroscopy. After this

time, the resulting suspension was diluted with CH2Cl2 and washed with saturated NaHCO3

solution. The organic layer was dried (MgSO4), concentrated, and the crude reaction product was

186

purified by column chromatography on silica gel using ethyl acetate – pentane (50:50) as the

eluent. Yield determined by analysis of 1H NMR spectra of crude reaction product using an internal

standard (methyl propiolate): 57 %.

1H NMR (600 MHz, CD3CN): δ 8.43 (d, J = 5.5 Hz, 2H), 7.37

(d, J = 7.8 Hz, 2H), 7.34 (d, J = 8.0 Hz, 2H), 7.07 (d, J = 5.3 Hz,

2H), 5.2 (dd, J = 47.6, 7.1 Hz, 1H), 4.06 (m, 2 H), 3.80 (q, J =

7.4 Hz, 1H), 2.55 (dd, J = 7.5, 7.5 Hz, 2H), 1.89 (m, 2H), 1.48

(d, J = 7.9 Hz, 3H), 1.31 (m, 1H), 1.00 (d, J = 6.8 Hz, 3H), 0.81

(d, J = 6.8 Hz, 3H); 13C NMR (150 MHz, CD3CN): δ 175.1, 151.9, 150.3, 142.2, 139.4 (d, J = 21.7

Hz), 128.5, 127.6 (d, J = 6.6 Hz), 125.0, 100.0 (d, J = 170.1 Hz), 64.3, 46.0, 34.9 (d, J = 22.6 Hz),

31.8, 29.9, 18.6, 18.5 (d, J = 6.5 Hz), 17.9 (m) ; 19F NMR (470 MHz, CD3CN) –178.9, –179.0.

HRMS (EI+) calcd for [C21H27FNO2]+ 344.2020, found 344.2019

Preparation of compound 342

Prepared following General Procedure 1: 341 (140. mg, 0.227 mmol), NFSI (0.215 g, 0.682 mmol,

3.0 eq.), Li2CO3 (18.4 mg, 0.250 mmol, 1.1 eq.). Purified by flash chromatography using ethyl

acetate – pentane (50:50) as the eluent. Yield determined by analysis of 1H NMR spectra of crude

reaction product using an internal standard (methyl propiolate): 73%.

1H NMR (500 MHz, MeOD): δ 8.51 (m, 2H), 7.81 (m, 2H), 7.68 (m, 2H),

7.39 (m, 4H) 7.31 (m, 2H), 5.68 (m, 1H), 4.39 (m, 2H), 4.31 (m, 2H),

4.22 (m, 2H), 2.23 (m, 2H), 1.73 (m, 1H), 1.61 (m, 2H), 0.97 (m, 6H);

13C NMR (150 MHz, MeOD): δ 174.6, 174.5, 158.7, 150.4, 145.2, 142.6,

128.8, 128.2, 126.2, 121.6, 120.9, 90.8, 67.9, 61.8, 54.0, 41.1, 36.9,

30.4, 25.9, 23.3, 21.7.; 19F NMR (470 MHz, MeOD) –188.5, 189.1

HRMS (EI+) calcd for [C29H32FN2O4]+ 491.2341, found 491.2358

Preparation of compound 343

To a solution of 341·2TFA (0.20 g, 0.42 mmol, 1.0 eq) in CH3CN (3.4 ml) and H2O (0.8 ml) was

added NFSI (0.40 g, 1.26 mmol,, 3.0 eq) and NaDT (51 mg, 0.021 mmol, 0.05 eq. ), and the

resulting mixture was degassed via 3 x freeze/pump/thaw cycles. The reaction mixture was

irradiated with long wave UV (365 nm) for 48 h. After this time, the resulting suspension was

187

diluted with CH2Cl2 and washed with 3 x 1.0 M NaOH. The organic layer was dried (MgSO4),

concentrated, and the crude reaction product was purified by preparative HPLC eluting with

solvent (A: 0.1 % TFA in H2O B: 0.1 % TFA in ACN) on a gradient of 2 % → 30 % solvent B over

15 minutes. Yield determined by analysis of 1H NMR spectra of crude reaction product using an

internal standard (methyl propiolate): 41 %.

1H NMR (600 MHz, D2O): δ 8.67 (d, J = 6.0 Hz, 2H), 7.96 (d, J =

6.1 Hz, 2H), 4.44 (dd, J = 8.9, 4.4 Hz 1H), 4.35 (t, J = 6.6 Hz, 2H)

3.08 (t, J = 7.9 Hz, 2H), 2.40 (ddd, J = 31.0, 15.8, 4.3 Hz, 1 H),

2.30 (ddd, J = 30.7 15.6, 9.0 Hz, 1H), 2.19 (m, 2H), 1.50 (dd, J =

22.5, 8.0 Hz, 6H) ; 13C NMR (150 MHz, D2O): δ 170.2, 163.8,

140.5, 127.3, 96.7, 66.2, 50.0, 40.1 (d, J = 21.4 Hz), 31.9, 27.5,

26.8 (d, J = 23.7 Hz), 24.7 (d, J = 24.0 Hz); 19F NMR (470 MHz, D2O) –138.7.

HRMS (EI+) calcd for [C14H22FN2O2]+ 269.1660, found 269.1649

188

Chapter 6. Direct heterobenzylic monofluorination, difluorination and trifluoromethylthiolation with dibenzenesulfonamide derivatives

The results presented in this chapter have been reported in part, see:

Meanwell, M.; Adluri, B.; Yuan, Z.; Newton, J.; Prevost, P.; Nodwell, M.; Friesen, C. M.;

Schaffer, P.; Martin, R. E.; Britton. R. Chem. Sci. 2018, 9, 5608-5613.

Other colleagues contributed to this work. Dr. Bharanishashank Adluri synthesized compounds

377, 378, 380, and 405. Dr. Zheliang Yuan developed the 18F procedure.

6.1. Direct functionalization of heterobenzylic C-H bonds

Figure 6.1. Heterobenzylic fluorides in discovery

The development of synthetic strategies that provide access to heterobenzylic fluorides is

of particular interest to medicinal chemistry and much success has been realized in

trifluoromethylation of heterocycles.271 However, introduction of heterobenzylic monofluoroalkyl

or difluoroalkyl groups remains largely reliant on cross coupling reactions80,81,84,272–277 or

deoxyfluorination of heterobenzylic alcohols278 and carbonyls,114,279 processes that require prior

189

functionalization. As a notable exception, Baran has reported innate C(sp2)–H functionalization of

heterocycles as a means to add each of the CHF2,87 CH2F88 and CF2CH3280

groups (e.g., 348 –

350) by employing the corresponding zinc sulphinate salts in Minisci-like radical addition

processes. Likewise, the introduction of difluoroacetates 351,76,281–285 difluoroacetamides 352286–

288 and difluorophosphonates 353289 has been accomplished via transition metal catalysis or

radical processes.290 Unfortunately, despite considerable advances in C(sp3)–H benzylic mono-

and difluorination, heterobenzylic C(sp3)–H fluorination278 or difluorination are largely unexplored

owing to fundamental incompatibilities between common fluorine transfer reagents (e.g., N-

fluorobenzensulfonimide (NFSI)) and nucleophilic heterocycles.248 Here, we demonstrate that

activation by transient sulfonylation is general for a range of alkylheterocycles and can be

extended to heterobenzylic difluorination and trifluoromethylthiolation. Collectively, these

convenient processes provide a platform for late-stage functionalization of drug leads and enable

direct 18F-fluorination of alkylheterocycles for the purpose of radiotracer synthesis for positron

emission tomography (PET) imaging.

entry hetero aromatic

solvent (conc. (M))

NFSI (equiv.)

temp. (°C)

product (ratio)

yield

1 354 MeCN (0.1) 3 60 357:360 (>20:1) 87 2 354 MeCN (0.5) 10 75 357:360 (1:1) 74 3 354 EtOAc (0.5) 6 75 357:360 (2:3) 82 4 355 MeCN (0.1) 3 65 358:361 (>20:1) 71 5 355 EtOAc (0.5) 10 75 358:361 (10:1) 81 6 356 MeCN( 0.1) 3 65 359:362 (1:3) 30 7 356 MeCN (0.3) 4 75 359:362 (1:8) 61 8 356 MeCN (0.5) 5 75 359:362 (1:10) 74

Table 6.1 Mono- and difluorination of 4-ethylpyridine (354) and alkyl quinolines 355 and 356

While examining the scope of the pyridylic fluorination reaction,291 we found that at

elevated temperatures (>65 C) small amounts of the corresponding difluoroalkyl derivatives were

formed and could be identified by a characteristic resonances at ~ -95 ppm in 19F NMR spectra

recorded on crude reaction mixtures. These observations prompted us to investigate the pyridylic

190

difluorination reaction as a complimentary process. As summarized in Table 6.1, heating a

solution of 4-ethylpyridine in MeCN with an excess of NFSI afforded exclusively the

monofluorinated adduct 357 at 60 C (entry 1). Increasing the reaction temperature above 80 C

(in a microwave) provided a complex mixture of products that included the corresponding

acetamide derived from displacement of fluoride by solvent (MeCN).211 However, when the

reaction was repeated at 75 C with a further increase in equivalents of NFSI, a ~1:1 mixture of

the mono- and difluorinated ethylpyridines 357 and 360 were produced in good yield (74%, entry

2) and were readily separable by flash column chromatography. Notably, for difluorination,

sequential activation by sulfonylation consumes 2 equivalents of NFSI and a further 2 equivalents

are required for fluorination. The additional excess of NFSI is required to offset its slow

decomposition over the course of the reaction (48 h). Several alternative solvents were evaluated

and a modest increase in yield was realized in EtOAc (entry 3). The fluorination of 4-ethylquinoline

(355) was also examined and we were pleased to find that heterobenzylic fluorination of this

alkylquinoline provided the monofluoroethyl product 358 in good yield (entry 4). However, despite

considerable effort, this substrate proved reluctant to undergo difluorination. Under more forcing

conditions (e.g., >90 C, microwave) decomposition occurred, and after 36 h at 75 C with a large

excess of NFSI only ~7% of the difluoroethyl quinoline 361 was produced (entry 5). Considering

the importance of both the mono- and difluoromethyl groups as bioisosteres,9 we also investigated

the fluorination of 4-methyl quinoline (356) and were surprised to find that difluorination

predominated even at low conversion, suggesting that here the second fluorination event is a

more facile process (entry 6). Increasing the equivalents of NFSI and reaction temperature (entry

7) as well as concentration (entry 8) ultimately provided the difluoromethyl quinoline 362 in

excellent yield. In both the mono- and difluorination of alkylquinolines 355 and 356, phenylsulfonyl

fluoride was observed as a by-product, suggesting that these reactions rely on activation of

quinoline through transient sulfonylation by NFSI.291 It is notable that this approach to

heterobenzylic fluorination is complimentary to the Minisci-like radical reactions described by

Baran, which favour trifluoromethylation at C7 or difluoromethylation at C2 of quinolines.87,88,280

191

Figure 6.2. Mono- and difluorination of pyridines, quinolines, pyrimidines, isoquinolines, quinazolines, and purines.

Encouraged by the susceptibility of 4-alkylquinolines 355 and 356 to undergo mono- or

difluorination, we explored the scope of these reactions with a broader range of heterocycles

including pyridines, isoquinolines, pyrimidines, quinazolines and purines. As summarized in

192

Figure 6.2, by simply modifying the equivalents of reagent and temperature, in several cases

mono- or difluorination could be effected selectively. For example, both mono- and difluoroalkyl

pyridines, quinazolines and purines could be produced in good yield following this straightforward

procedure (e.g., 357/383, 371/384, 372/385 and 373/386). As noted above, alkylquinolines were

reluctant to difluorinate but were monofluorinated in excellent yield providing 363 and 364.

Conversely, a series of methylquinolines were transformed directly into the corresponding

difluoromethylquinolines 374 – 380 in good yield. In addition to the obvious compatibility with

azaheterocycles, substituted aromatics (e.g., 377 – 382), esters (e.g., 364) and amides (e.g., 363)

were well tolerated. It is notable that 2,4-dimethylquinoline and 1-propyl-3,4-dimethlyisoquinoline

did not undergo fluorination using our standard reaction conditions. Here, we postulate that steric

hindrance from the adjacent alkyl group(s) prevents sulfonylation of the heterocycle by NFSI and

thus precludes fluorination. In several cases, complete separation of mono- and difluorinated

products by flash column chromatography proved challenging. Thus, while purified product could

be isolated this way, yields for these reactions were determined by analysis of NMR spectroscopic

data using an internal standard.

193

Figure 6.3. Trifluoromethylthiolation and chlorination of purines and quinazolines

Considering that sulfonyl transfer from NFSI is a key feature of this process (e.g., 389,

Figure 6.3),291 we examined a small collection of dibenzensulfonamide derivatives to explore their

potential in the direct heterobenzylic functionalization of alkylquinazolines and purines. As

depicted in Figure 6.3, we found that both trifluoromethylthiolation (e.g., 390 – 392 and 394 – 396)

and chlorination (e.g., 393) were facile processes. For example, 2- and 4-alkylquinazolines and

6-ethylpurine underwent heterobenzylic trifluoromethylthiolation using

N-trifluoromethylthiodibenzenesulfonimide (N(SCF3)SI).292 Surprisingly, we observed no

competing heteroaryl trifluoromethylthiolation292184 of quinazolines and purines, and attempts to

effect the equivalent transformation using trifluoromethylthiophthalimide, an electrophilic trifluoro-

methylthiolation reagent,184 delivered none of the expected trifluoromethylthiolated products. This

later result provides support for a mechanism involving activation by transient sulfonylation with

dibenzenesulfamide derivatives. Again, 2,4-disubstituted quinazolines failed to provide any

trifluoromethylthiolated product (e.g., 397 or 398) presumably due to steric hindrance impeding

sulfonylation of the heterocycle by N(SCF3)SI. Notably, this heterobenzylic

194

trifluoromethylthiolation293 reaction offers a unique opportunity to significantly alter lipophilicity

(Hansch hydrophobicity parameter = 1.44)184 and pKa of a drug lead.

Scheme 6.1 Late-stage mono- and difluorination, trifluoromethylthiolation of heterocycles

In an effort to further demonstrate the utility of this suite of transformations, we explored

the monofluorination, difluorination and trifluoromethylthiolation of quazodine (399),294 a cardiac

stimulant. As depicted in Scheme 6.1, each of these transformations proceeded smoothly and

provided access to the unique quazodine derivatives 400 – 402 in good to excellent yield. To

gauge the impact of heterobenzylic functionalization on relevant physiochemical properties, the

pKa, distribution coefficient (logD) at pH 7.4 and aqueous solubility of each compound was

measured. As summarized in Scheme 6.1, these transformations significantly affected each

property and provide a straightforward means to modulate lipophilicity and basicity. Likewise, the

195

peracetate 404 of the cytotoxic purine nucleoside analogue 403295 could be mono- or

difluorinated, affording the analogues 405 or 406, respectively, in good yield.

6.1.1. 18F-fluorination

Scheme 6.2. 18F-fluorination of heterocycle 407

Finally, we explored the direct 18F-fluorination of the annulated pyridine 407 to

demonstrate the additional utility of this transformation for rapidly generating radiotracers for

positron emission tomography (PET) imaging. We have previously exploited [18F]NFSI270 in the

direct radiofluorination of branched aliphatic amino acids296 and were pleased to find that simply

heating a solution of the annulated pyridine 407 and [18F]NFSI in MeCN at 75 C for 40 min

provided the 18F-labelled derivative 408 in good radiochemical conversion (RCC) and yield (RCY).

This streamlined heterobenzylic 18F-fluorination does not rely on prior functionalization or

sensitive reagents and thus offers certain advantages for the rapid generation of radiotracers for

PET imaging.

6.2. Conclusion

In summary, we demonstrate that transient sulfonylation of a range of nitrogen-containing

heterocycles enables direct heterobenzylic mono or difluorination using the bench stable

electrophilic fluorinating agent NFSI or radiofluorination with [18F]NFSI. Taking advantage of this

heterocycle activation process, both trifluoromethylthiolation and chlorination could also be

achieved using the corresponding dibenzenesulfonamide derivatives. This collection of late-stage

transformations should enable the rapid tuning of pKa and lipophilicty of heterocycle-containing

drug leads and provides a complimentary means to incorporate pharmaceutically relevant

bioisosteres (e.g., -CHF2, -CF2R and –CH(SCF3)R) as well as a method to rapidly generate 18F-

labelled imaging agents for PET imaging.

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6.3. Experimental

General Considerations

All reactions were carried out with commercial solvents and reagents that were used as received.

Flash chromatography was carried out with Geduran® Si60 silica gel (Merck). Concentration and

removal of trace solvents was done via a Büchi rotary evaporator using dry ice/acetone

condenser, and vacuum applied from an aspirator or Büchi V-500 pump. All reagents and starting

materials were purchased from Sigma Aldrich, Alfa Aesar, TCI America, and/or Strem, and were

used without further purification. All solvents were purchased from Sigma Aldrich, EMD,

Anachemia, Caledon, Fisher, or ACP and used without further purification, unless otherwise

specified.

Nuclear magnetic resonance (NMR) spectra were recorded using chloroform-d (CDCl3) or

acetonitrile-d3 (CD3CN). Signal positions (δ) are given in parts per million from tetramethylsilane

(δ 0) and were measured relative to the signal of the solvent (1H NMR: CDCl3: δ 7.26, CD3CN:

δ 1.96; 13C NMR: CDCl3: δ 77.16, CD3CN: δ 118.26). Coupling constants (J values) are given in

Hertz (Hz) and are reported to the nearest 0.1 Hz. 1H NMR spectral data are tabulated in the

order: multiplicity (s, singlet; d, doublet; t, triplet; q, quartet; quint, quintet; m, multiplet), coupling

constants, number of protons. NMR spectra were recorded on a Bruker Avance 600 equipped

with a QNP or TCI cryoprobe (600 MHz), Bruker 500 (500 MHz), or Bruker 400 (400 MHz).

Assignments of 1H and 13C NMR spectra are based on analysis of 1H-1H COSY, HSQC, and

HMBC spectra, where applicable. Methyl propiolate or 4-fluorotoluene was added to the crude

reaction mixtures and used as an internal standard. Yields were then calculated following

analysis of 1H NMR spectra.

High-resolution mass spectra were performed on an Agilent 6210 TOF LC/MS, Bruker MaXis

Impact TOF LC/MS, or Bruker micrOTOF-II LC mass spectrometer.

General Procedure A: Heterobenzylic monofluorination

To a solution of substrate in CH3CN (0.1-0.25 M substrate) was added N-

fluorobenzenesulfonimide (NFSI) (3.0 equiv.) and Li2CO3 (1.1 equiv.). The resulting reaction

mixture was then heated to 65 °C and maintained at this temperature for 18-24 h. The reaction

mixture was cooled, diluted with CH2Cl2 and washed with saturated NaHCO3 solution. The organic

197

layer was dried (MgSO4), concentrated and the crude reaction product was purified by column

chromatography on silica gel.

General Procedure B: Heterobenzylic difluorination

To a solution of substrate in CH3CN (0.25-0.50 M substrate) was added N-

fluorobenzenesulfonimide (NFSI) (5.0 equiv.) and Li2CO3 (5.0 equiv.). The resulting reaction

mixture was then either heated to 75 °C and maintained at this temperature for 48 h or heated to

125 °C and maintained at this temperature for 1 h in a microwave reactor. The reaction mixture

was cooled, diluted with CH2Cl2 and washed with saturated NaHCO3 solution. The organic layer

was dried (MgSO4), concentrated and the crude reaction product was purified by column

chromatography on silica gel.

General Procedure C: Heterobenzylic trifluoromethylthiolation

To a solution of substrate in CH3CN (0.20-0.50 M substrate) was added N-

trifluoromethylthiobenzenesulfonimide (2.4 equiv.) and Li2CO3 (1.1 equiv.). The resulting reaction

mixture was then either heated to 75 °C and maintained at this temperature for 48 h or heated to

125 °C and maintained at this temperature for 1 h in a microwave reactor. The reaction mixture

was cooled, diluted with CH2Cl2 and washed with saturated NaHCO3 solution. The organic layer

was dried (MgSO4), concentrated and the crude reaction product was purified by column

chromatography on silica gel.

Preparation of compound 363

Following General Procedure A, to a solution of N-pentyl-3-(quinolin-4-yl)propenamide (0.0485 g,

0.179 mmol) in 1.2 mL of CH3CN (0.15 M substrate) was added NFSI (0.170 g, 0.538 mmol, 3.0

equiv.) and Li2CO3 (0.015 g, 0.197 mmol, 1.1 equiv.). The resulting reaction mixture was then

heated to 65 °C and maintained at this temperature for 24 h. Purification of the crude 363 by flash

chromatography (pentane-ethyl acetate 4:6) afforded 363 (32.5 mg, 63%)

1H NMR (600 MHz, CDCl3): δ 8.95 (d, J = 4.5 Hz, 1H), 8.22 (d, J =

8.4 Hz, 1H), 8.00 (d, J = 8.4 Hz, 1H), 7.78 (dd, J = 8.4, 7.1 Hz, 1H),

7.63 ( dd, J = 8.4, 7.1 Hz, 1H), 7.55 (d, J = 4.5 Hz, 1H), 6.73 (ddd, J

= 46.8, 9.1, 2.6 Hz, 1H), 5.63 (br s, 1H), 3.32 (m, 2H), 2.90 (ddd, J

= 37.1, 15.4, 2.8 Hz, 1H), 2.78 (ddd, J = 17.5, 15.3, 9.1, 4.4 Hz 1H),

1.52 (m, 2H), 1.31 (m, 4H), 0.90 (dd, J = 7.3, 7.3 Hz, 3H); 13C NMR (150 MHz, CDCl3): δ 168.2,

198

149.8, 130.9, 130.2, 130.1, 129.9, 127.7, 124.4 (d, J = 5.1 Hz), 122.9, 116.9 (d, J = 11.4 Hz), 88.5

(d, J = 175.5 Hz), 44.5 (d, J = 24.8 Hz), 40.1, 29.3, 29.1, 22.5, 14.1; 19F NMR (470 MHz, CDCl3):δ

–183.6

HRMS (EI+) calcd for [C17H22FN2O]+ 289.1711, found 289.1724.

Preparation of compound 364

Following General Procedure A, to a solution of substrate (0.040 g, 0.070 mmol) in 0.35 mL of

CH3CN (0.20 M substrate) was added NFSI (0.066 g, 0.21 mmol, 3.0 equiv.) and Li2CO3 (6.0 mg,

0.077 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to 65 °C and maintained

at this temperature for 24 h. Purification of the crude 364 by flash chromatography (pentane-ethyl

acetate 5:5) afforded 364 as a 1:1 mixture of diastereomers (37.0 mg, 90%).

IR (neat): = 2939, 2868, 1724, 1178, 905, 730 cm-

1; 1H NMR (600 MHz, CDCl3): δ 8.96 (1H), 8.17 (1H),

7.93 (1H), 7.76 (1H), 7.62 (1H), 7.53 (1H), 6.66 (1H),

4.84 (1H), 3.66 (3H), 2.99(1H), 2.34 (1H), 2.21 (1H),

1.96 (1H), 1.91-0.98 (25H), 0.94 (3H), 0.91 (3H),

0.65 (3H); 13C NMR (150 MHz, CDCl3): δ 174.9,

169.0, 150.5, 148.5, 144.1, 130.8, 129.7, 127.4, 124.5, 122.7, 117.3, 87.8, 75.8, 56.6, 56.2, 51.6,

42.9, 42.4, 42.1, 42.1, 40.6, 40.3, 36.0, 35.5, 35.1, 34.7, 32.4, 32.3, 31.2, 31.2, 28.3, 27.1, 26.8,

26.7, 26.5, 24.3, 23.5, 21.0, 18.4, 12.2; 19F NMR (470 MHz, CDCl3):δ –182.9, –182.9.

HRMS (EI+) calcd for [C37H51FNO4]+ 592.3797, found 592.3793.

Preparation of compound 365

Following General Procedure A, to a solution of 4-ethylquinoline (0.025 g, 0.159 mmol) in 1.60

mL of CH3CN (0.10 M substrate) was added NFSI (0.150 g, 0.478 mmol, 3.0 equiv.) and Li2CO3

(13.0 mg, 0.175 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to 65 °C and

maintained at this temperature for 24 h. Purification of the crude 365 by flash chromatography

(pentane-EtOAc 7:3) afforded 365 (17.3 mg, 62%).

199

1H NMR (600 MHz, CDCl3): δ 8.95 (d, J = 4.5 Hz, 1H), 8.17 (d, J = 8.5 Hz, 1H), 7.90

(d, J = 8.5 Hz, 1H), 7.74 (dd, J = 8.2, 8.2 Hz, 1H), 7.59 (dd, J = 7.9, 7.9 Hz, 1H),

7.51 (d, J = 4.4 Hz, 1H), 6.33 (dq, J = 46.8, 6.5 Hz, 1H), 1.81 (dd, J = 24.3, 6.5 Hz,

3H) 13C NMR (150 MHz, CDCl3): δ 150.6 (d, J = 22.5 Hz), 148.4, 146.9 (d, J = 19.1

Hz), 130.7, 129.4, 127.0, 124.7 (d, J = 4.8 Hz), 122.9, 116.6 (d, J = 10.9 Hz) 87.8 (d, J = 172.3

Hz), 22.7 (d, J = 25.1 Hz); 19F NMR (470 MHz, CDCl3): δ –176.7

HRMS (ESI+) calcd for [C11H11FN]+ 176.0870, found 176.0841

Preparation of compound 366

A solution of 5-bromo-4-ethylpyrimidine (35.0 mg, 0.187 mmol, 1.0 eq.), NFSI (0.177 g, 0.56

mmol, 3.0 eq.), and Li2CO3 (15.2 mg, 0.206 mmol, 1.1 eq.) in 1.2 mL CH3CN was added to a

microwave vial. The vial was sealed in a CEM Discover LabMate microwave reactor and the

resulting mixture was heated to 120 °C (as monitored by a vertically focused infrared temperature

sensor) for 75 min. The reaction was concentrated under reduced pressure and the crude product

366 was purified by column chromatography on silica gel using ethyl acetate – pentanes (5:95)

as the eluent. Yield determined by analysis of 1H NMR spectra of crude reaction product using an

internal standard (methyl propiolate): 59 %.

1H NMR (500 MHz, CDCl3): δ 9.18 (s, 1H), 8.85 (s, 1H), 5.96 (dq, J = 47.0, 6.5

Hz, 1H), 1.73 (dd, J = 24.1, 6.5 Hz, 3H); 13C NMR (150 MHz, SO(CD3)2) δ 163.1

(d, J = 18.8 Hz), 160.0, 157.0, 119.2 (d, J = 2.5 Hz), 88.2 (d, J = 171.3 Hz), 18.6

(d, J = 24.6 Hz); 19F NMR (470 MHz, CDCl3) δ –179.5

HRMS (ESI+) calcd for [C6H7BrFN2]+ 204.9771, found 204.9798

Preparation of compound 367

A solution of 2-chloro-4-ethylpyrimidine (35.0 mg, 0.245 mmol, 1.0 eq.), NFSI (0.233 g, 0.74

mmol, 3.0 eq.), and Li2CO3 (20.0 mg, 0.270 mmol, 1.1 eq.) in 1.0 mL CH3CN was added to a

microwave vial. The vial was sealed in a CEM Discover LabMate microwave reactor and the

resulting mixture was heated to 150 °C (as monitored by a vertically focused infrared temperature

sensor) for 75 min. The reaction was concentrated under reduced pressure and the crude product

367 was purified by column chromatography on silica gel using ethyl acetate – pentanes (5:95)

as the eluent. Yield determined by analysis of 1H NMR spectra of crude reaction product using an

internal standard (methyl propiolate): 44 %.

200

1H NMR (500 MHz, CDCl3): δ 8.69 (d, J = 4.9 Hz, 1H), 7.48 (d, J = 5.0, 1H), 5.6 (dq,

J = 48.1, 6.8 Hz, 1H), 1.71 (dd, J = 24.6, 6.8 Hz, 3H); 13C NMR (150 MHz, SO(CD3)2)

δ 171.8 (d, J = 23.7 Hz), 161.7, 159.8 (d, J = 2.6 Hz), 115.9 (d, J = 6.8 Hz), 89.2 (d,

J = 170.6 Hz), 20.3 (d, J = 25.0); 19F NMR (470 MHz, CDCl3) δ –184.0

HRMS (ESI+) calcd for [C6H7ClFN2]+ 161.0276, found 161.0299

Preparation of compound 368

Following General Procedure A, to a solution of 4-(3-phenylpropyl)pyrimidine (0.025 g, 0.126

mmol) in 1.25 mL of CH3CN (0.10 M substrate) was added NFSI (0.238 g, 0.756 mmol, 6.0 equiv.)

and Li2CO3 (10.0 mg, 0.139 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to

125 °C and maintained at this temperature for 25 minutes in a microwave reactor. The yield for

368 (48%) was determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-

fluorotoluene as an internal standard. Purification of the crude material by flash column

chromatography (pentane-ethyl acetate; 6:4) provided an analytical sample of 368.

IR (neat): = 2829, 1582, 1350, 1056, 750 cm-1;1H NMR (600 MHz, CDCl3): δ

9.16 (s, 1H), 8.78 (d, J = 4.8 Hz, 1H), 7.52 (d, J = 4.9 Hz, 1H), 7.29 (dd, J = 7.4,

7.4 Hz, 1H), 7.22 (d, J = 7.4 Hz, 1H), 7.20 (dd, J = 7.4, 7.4 Hz, 1H), 5.49 (ddd,

J = 48.4, 8.6, 2.3 Hz, 1H), 2.84 (dd, J = 8.3, 8.3 Hz, 2H), 2.39 (m, 1H), 2.22 (m,

1H); 13C NMR (150 MHz, CDCl3) δ 168.8 (d, J = 26.0 Hz), 158.1 (d, J = 2.9 Hz), 157.5 (d, J = 1.6

Hz), 140.6, 128.7, 128.6, 126.4, 117.0 (d, J = 8.3 Hz), 92.5 (d, J = 175.9 Hz), 36.9 (d, J = 21.7

Hz), 31.0 (d, J = 3.2 Hz); 19F NMR (470 MHz, CDCl3): δ –193.4

HRMS (EI+) calcd for [C13H14FN2]+ 217.1136, found 217.1128

Preparation of compound 369

Following General Procedure A, to a solution of 1-ethylisoquinoline (0.025 g, 0.159 mmol) in 1.60

mL of CH3CN (0.25 M substrate) was added NFSI (0.150 g, 0.478 mmol, 3.0 equiv.) and Li2CO3

(13.0 mg, 0.175 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to 75 °C and

maintained at this temperature for 24 h. Purification of the crude 369 by flash chromatography

(pentane-EtOAc 85:15) afforded 369 (19.3 mg, 69%).

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IR (neat): = 3055, 2989, 1624, 1586, 1378, 1055, 827 cm-1;1H NMR (600 MHz,

CDCl3): δ 8.52 (d, J = 5.7 Hz, 1H), 8.38 (d, J = 8.6 Hz, 1H), 7.87 (d, J = 8.3 Hz, 1H),

7.71 (dd, J = 7.8, 7.8 Hz, 1H), 7.65 (d, J = 5.5 Hz, 1H), 7.64 (dd, J = 7.6 Hz, 1H),

6.35 (dq, J = 48.0, 6.6 Hz, 1H), 1.93 (dd, J = 24.0 Hz, 6.6 Hz, 3H); 13C NMR (150

MHz, CDCl3) δ 157.8 (d, J = 19.7 Hz), 141.5, 136.9, 130.2, 127.6 (d, J = 1.7 Hz), 127.6, 126.2,

125.3 (d, J = 5.8 Hz), 121.6 (d, J = 1.7 Hz), 91.2 (d, J = 168.2 Hz), 20.5 (d, J = 23.6 Hz); 19F NMR

(470 MHz, CDCl3): δ –169.5

HRMS (EI+) calcd for [C11H11FN]+ 176.0870, found 176.0887

Preparation of compound 370

Following General Procedure A, to a solution of 1-propylisoquinoline (0.025 g, 0.146 mmol) in

0.60 mL of CH3CN (0.25 M substrate) was added NFSI (0.138 g, 0.438 mmol, 3.0 equiv.) and

Li2CO3 (12.0 mg, 0.161 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to 75

°C and maintained at this temperature for 24 h. The yield for 28 (78%) was determined by analysis

of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an internal standard.

Purification of the crude material by flash chromatography (pentane-EtOAc 85:15) provided an

analytical sample of 370.

IR (neat): = 2957, 1604, 1499, 1119, 900 cm-1;1H NMR (600 MHz, CDCl3): δ

8.51 (d, J = 5.5 Hz, 1H), 8.37 (d, J = 8.3 Hz, 1H), 7.86 (d, J = 8.3 Hz, 1H), 7.70

(dd, J = 7.4, 7.4 Hz, 1H), 7.64 (d, J = 5.5 Hz, 1H), 7.62 (dd, J = 7.4, 7.4 Hz, 1H),

6.04 (ddd, J = 48.1, 8.6, 5.2 Hz, 1H), 2.35 (m, 1H), 2.20 (m, 1H), 1.12 (dd, J = 7.4,

7.4 Hz, 3H); 13C NMR (150 MHz, CDCl3) δ 157.4 (d, J = 19.8 Hz), 141.5, 136.8, 130.1, 127.5,

127.4 (d, J = 1.4 Hz), 126.2, 125.2 (d, J = 6.2 Hz), 121.3 (d, J = 1.4 Hz), 96.2 (d, J = 173.4 Hz),

28.2 (d, J = 22.7 Hz), 9.9 (d, J = 5.7 Hz); 19F NMR (470 MHz, CDCl3): δ –178.0

HRMS (EI+) calcd for [C12H13FN]+ 190.1027, found 190.1027

Preparation of compound 371

Following General Procedure A, to a solution of 2-ethylquinazoline (0.025 g, 0.158 mmol) in 0.60

mL of CH3CN (0.25 M substrate) was added NFSI (0.100 g, 0.50 mmol, 3.0 equiv.) and Li2CO3

(0.026 g, 0.348 mmol, 2.2 equiv.). The resulting reaction mixture was then heated to 125 °C and

maintained at this temperature for 60 minutes in a microwave reactor. The yield for 371 (72%)

202

was determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as

an internal standard. Purification of the crude material by flash column chromatography (pentane-

ethyl acetate; 7.5:2.5) provided an analytical sample of 371.

IR (neat): = 2959, 1620, 1585, 1490, 1379, 1077, 765 cm-1;1H NMR (600

MHz, CDCl3): δ 9.45 (s, 1H), 8.10 (d, J = 8.2 Hz, 1H), 7.96 (m, 2H), 7.69 (dd, J

= 7.6, 7.6 Hz, 1H), 5.91 (dq, J = 48.5, 6.6 Hz), 1H), 1.85 (dd, J = 24.1, 6.7 Hz,

3H); 13C NMR (150 MHz, CDCl3): δ 164.5 (d, J = 19.6 Hz), 161.1, 150.2, 134.7,

128.7, 128.2, 127.4, 124.2, 91.2 (d, J = 173.9 Hz), 20.9 (d, J = 24.1 Hz); 19F NMR (470 MHz,

CDCl3): δ –177.1

HRMS (EI+) calcd for [C10H10FN2]+ 177.0823, found 177.0817

Preparation of compound 372

Following General Procedure A, to a solution of 6-bromo-4-ethylquinazoline (0.025 g, 0.106

mmol) in 1.1 mL of CH3CN (0.10 M substrate) was added NFSI (0.040 g, 0.127 mmol, 1.2 equiv.)

and Li2CO3 (9.0 mg, 0.117 mmol, 1.1 equiv.). The resulting reaction mixture was then left room

temperature and maintained at this temperature for 96 hours. Purification of the crude 372 by

flash chromatography (pentane-ethyl acetate; 85:15) afforded 372 (24.0 mg, 91%).

IR (neat): = 3975, 2254, 1498, 903, 726 cm-1;1H NMR (600 MHz, CDCl3): δ

9.32 (s, 1H), 8.01 (dd, J = 9.0, 2.0 Hz, 1H), 7.99 (d, J = 9.0 Hz, 1H), 6.18 (dq,

J = 48.1, 6.9 Hz, 1H), 1.91 (dd, J = 24.2, 6.6 Hz, 3H); 13C NMR (150 MHz,

CDCl3): δ 166.3 (d, J = 21.3 Hz), 154.5, 149.8, 137.7, 131.2, 127.6 (d, J = 9.2

Hz), 123.3, 122.1, 91.2 (d, J = 172.1 Hz), 20.7 (d, J = 23.1 Hz); 19F NMR (470 MHz, CDCl3): δ –

174.2

HRMS (EI+) calcd for [C10H9BrFN2]+ 254.9928, found 254.9949

Preparation of compound 373

Following General Procedure A, to a solution of 6-ethyl-9-methyl-9H-purine (0.015 g, 0.093 mmol)

in 0.40 mL of CH3CN (0.25 M substrate) was added NFSI (0.096 g, 0.303 mmol, 3.3 equiv.) and

Li2CO3 (8.2 mg, 0.111 mmol, 1.2 equiv.). The resulting reaction mixture was then heated to 75

°C and maintained at this temperature for 36 hours. Purification of the crude 373 by flash

chromatography (CH2Cl2-MeOH 96:4) afforded 373 (11.1 mg, 70%).

203

IR (neat): = 2978, 2262, 1039, 832 cm-1;1H NMR (600 MHz, CD3CN): δ 8.92

(s, 1H), 8.21 (s, 1H), 6.18 (dq, J = 47.3, 6.6 Hz, 1H), 1.81 (dd, J = 24.7, 6.7 Hz,

3H); 13C NMR (150 MHz, CD3CN): δ 157.5 (d, J = 19.4 Hz), 153.7, 152.8, 147.8,

131.7, 88.8 (d, J = 168.8 Hz), 30.2, 20.2 (d, J = 24.4 Hz); 19F NMR (470 MHz,

CD3CN): δ –176.6

HRMS (EI+) calcd for [C8H10FN4]+ 181.0884, found 181.0890

Preparation of compound 374

Following General Procedure B, to a solution of 4-methylquinoline (0.030 mL, 0.226 mmol) in 0.45

mL of CH3CN (0.50 M substrate) was added NFSI (0.357 g, 1.13 mmol, 5.0 equiv.) and Li2CO3

(0.084 g, 1.13 mmol, 5.0 equiv.). The resulting reaction mixture was then heated to 75 °C and

maintained at this temperature for 48 hours. The yield for 374 (68%) was determined by analysis

of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an internal standard.

Purification of the crude material by flash column chromatography (pentane-ethyl acetate; 6:4)

provided an analytical sample of 374.

1H NMR (600 MHz, CDCl3): δ 9.03 (d, J = 4.3 Hz, 1H), 8.21 (d, J = 8.5 Hz, 1H),

8.10 (d, J = 8.5 Hz, 1H), 7.80 (dd, J = 7.5, 7.5 Hz, 1H), 7.67 (dd, J = 7.5 Hz, 1H).

7.60 (d, J = 4.3 Hz, 1H), 7.17 (t, J = 54.6 Hz, 1H) ; 13C NMR (150 MHz, CDCl3): δ

150.1, 148.8, 138.0 (t, J = 21.8 Hz), 130.6, 130.1, 128.0, 124.3 (t, J = 3.1 Hz),

123.4, 118.1 (t, J = 7.7 Hz), 113.4 (t, J = 241.0 Hz); 19F NMR (470 MHz, CDCl3): δ –115.1

HRMS (EI+) calcd for [C10H8F2N]+ 180.0619, found 180.0600.

Preparation of compound 375

Following General Procedure B, to a solution of 6-bromo-4-methylquinoline (0.030 g, 0.136 mmol)

in 0.30 mL of CH3CN (0.50 M substrate) was added NFSI (0.214 g, 0.679 mmol, 5.0 equiv.) and

Li2CO3 (0.050 g, 0.679 mmol, 5.0 equiv.). The resulting reaction mixture was then heated to 75

°C and maintained at this temperature for 48 hours. The yield for 375 (64%) was determined by

analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an internal standard.

Purification of the crude material by flash column chromatography (pentane-ethyl acetate; 6:4)

provided an analytical sample of 375.

204

1H NMR (600 MHz, CDCl3): δ 9.03 (d, J = 4.3 Hz, 1H), 8.26 (s, 1H), 8.08 (d, J =

, 9.0 Hz, 1H), 7.88 (dd, J = 9.1, 1.8 Hz, 1H), 7.61 (d, J = 4.5 Hz, 1H), 7.10 (t, J

= 54.4 Hz, 1H); 13C NMR (150 MHz, CDCl3): δ 150.4, 147.4, 137.2 (t, J = 22.4

Hz), 133.7, 132.2, 126.0, 125.3 (t, J = 2.7 Hz), 122.4, 119.0 (t, J = 7.5 Hz), 113.2

(t, J = 241.1 Hz); 19F NMR (470 MHz, CDCl3):δ –114.9

HRMS (EI+) calcd for [C10H7BrF2N]+ 257.9724, found 257.9711

Preparation of compound 376

Following General Procedure B, to a solution of 4-methyl-6-phenylquinoline (0.046 g, 0.210 mmol)

in 0.42 mL of CH3CN (0.50 M substrate) was added NFSI (0.331 g, 1.05 mmol, 5.0 equiv.) and

Li2CO3 (0.078 g, 1.05 mmol, 5.0 equiv.). The resulting reaction mixture was then heated to 75 °C

and maintained at this temperature for 48 hours. The yield for 376 (41%) was determined by

analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an internal standard.

Purification of the crude material by flash column chromatography (pentane-ethyl acetate; 1:1)

provided an analytical sample of 376.

1H NMR (600 MHz, CDCl3): δ 9.06 (d, J = 4.4 Hz, 1H), 8.31 (d, J = 8.8 Hz, 1H),

8.29 (s, 1H), 8.10 (dd, J = 8.8, 1.9 Hz, 1H), 7.77 (d, J = 7.7 Hz, 2H), 7.66 (d, J =

4.3 Hz, 1H), 7.57 (dd, J = 7.7, 7.7 Hz, 2H), 7.48 (dd, J = 7.7, 7.7 Hz, 1H), 7.25

(t, J = 54.6 Hz, 1H) ; 13C NMR (150 MHz, CDCl3): δ 150.0, 148.1, 140.8, 140.3,

138.0 (t, J = 21.6 Hz), 130.9, 129.9, 129.2, 128.3, 127.8, 124.5 (t, J = 2.9 Hz), 121.2, 118.5 (t, J

= 7.8 Hz), 113.5 (t, J = 240.8 Hz); 19F NMR (470 MHz, CDCl3):δ –115.0

HRMS (EI+) calcd for [C16H12F2N]+ 256.0932, found 256.0930

Preparation of compound 377

Following General Procedure B, to a solution of 4-(methyl)-6-(4-fluorophenyl)quinoline (0.035 g,

0.147 mmol) in 0.29 mL of CH3CN (0.50 M substrate) was added NFSI (0.232 g, 0.735 mmol, 5.0

equiv.) and Li2CO3 (0.059 g, 0.735 mmol, 5.0 equiv.). The resulting reaction mixture was then

heated to 75 °C and maintained at this temperature for 48 hours. The yield for 377 (63%) was

determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an

internal standard. Purification of the crude material by flash column chromatography (pentane-

ethyl acetate; 1:1) provided an analytical sample of 377.

205

1H NMR (600 MHz, CDCl3): δ 9.02 (s, 1H), 8.27 (d, J = 8.8 Hz, 1H), 8.19

(s, 1H), 8.00 (dd, J = 8.8, 1.9 Hz, 1H), 7.68 (m, 2H), 7.62 (d, J = 3.9 Hz,

1H), 7.57 (dd, J = 7.7, 7.7 Hz, 2H), 7.21 (dd, J = 8.7, 8.7 Hz, 1H), 7.19 (t, J

= 54.6 Hz, 1H) ; 13C NMR (150 MHz, CDCl3): δ 163.1 (d, J = 248.7 Hz),

150.0, 148.0, 139.8, 138.0 (t, J = 21.7 Hz), 136.4 (d, J = 3.2 Hz), 131.0, 129.8, 129.4 (d, J = 8.2

Hz) 124.5, 121.1, 118.7 (t, J = 7.0 Hz), 116.2 (d, J = 21.1 Hz), 113.6 (t, J = 241.3 Hz); 19F NMR

(470 MHz, CDCl3):δ –114.2, –114.7

HRMS (EI+) calcd for [C16H11F3N]+ 274.0838, found 274.0813

Melting point: 111-114 ˚C

Preparation of compound 378

Following General Procedure B, to a solution of 4-methyl-6-(4-(trifluoromethyl)phenyl)quinoline

(0.035 g, 0.122 mmol) in 0.24 mL of CH3CN (0.50 M substrate) was added NFSI (0.192 g, 0.610

mmol, 5.0 equiv.) and Li2CO3 (0.045 g, 0.610 mmol, 5.0 equiv.). The resulting reaction mixture

was then heated to 75 °C and maintained at this temprature for 48 hours. The yield for 378 (60%)

was determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as

an internal standard. Purification of the crude material by flash column chromatography (pentane-

ethyl acetate; 1:1) provided an analytical sample of 378.

IR (neat): = 2948, 1680, 1173, 722 cm-1; 1H NMR (600 MHz, CDCl3): δ

9.08 (s, 1H), 8.35 (d, J = 8.8 Hz, 1H), 8.29 (s, 1H), 8.06 (dd, J = 8.8, 1.8 Hz,

1H), 7.83 (d, J = 8.2 Hz, 2H), 7.78 (d, J = 8.2 Hz, 2H), 7.68 (d, J = 3.7 Hz,

1H), 7.20 (t, J = 54.7 Hz, 1H); 13C NMR (150 MHz, CDCl3): δ 150.1, 147.8,

143.7, 139.6, 138.7 (t, J = 22.5 Hz), 130.8, 130.5 (q, J = 32.6 Hz), 129.9, 128.2, 126.2 (q, J = 3.7

Hz), 124.6, 124.2 (q, J = 272.4 Hz), 122.0, 119.0, 113.5 (t, J = 241.2 Hz) 121.1, 118.7 (t, J = 7.0

Hz), 116.2 (d, J = 21.1 Hz), 113.6 (t, J = 241.3 Hz); 19F NMR (470 MHz, CDCl3):δ –62.5, –114.6

HRMS (EI+) calcd for [C17H11F5N]+ 324.0806, found 324.0813

206

Preparation of compound 379

Following General Procedure B, to a solution of 7-bromo-4-methylquinoline (0.025 g, 0.113 mmol)

in 0.22 mL of CH3CN (0.50 M substrate) was added NFSI (0.178 g, 0.566 mmol, 5.0 equiv.) and

Li2CO3 (0.042 g, 0.566 mmol, 5.0 equiv.). The resulting reaction mixture was then heated to 75

°C and maintained at this temperature for 48 hours. The yield for 379 (68%) was determined by

analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an internal standard.

Purification of the crude material by flash column chromatography (pentane-ethyl acetate; 1:1)

provided an analytical sample of 379.

IR (neat): = 2971, 2254, 1604, 902, 724 cm-1; 1H NMR (600 MHz, CDCl3): δ 9.03

(d, J = 4.3 Hz, 1H), 8.41 (d, J = 2.0 Hz, 1H), 7.99 (d, J = 9.0 Hz, 1H), 7.76 (dd, J

= 9.0 Hz, 1H) 7.61 (d, J = 4.3 Hz, 1H), 7.12 (t, J = 54.2 Hz, 1 H); 13C NMR (150

MHz, CDCl3): δ 151.1, 149.4, 138.2 (t, J = 22.4 Hz), 132.9, 131.5, 124.9, 124.4,

118.5 (t, J = 7.6 Hz), 113.3 (t, J = 241.3 Hz); 19F NMR (470 MHz, CDCl3):δ –114.6

HRMS (EI+) calcd for [C10H7BrF2N]+ 257.9724, found 257.9739

Melting point: 68-72˚C

Preparation of compound 380

Following General Procedure B, to a solution of 4-methyl-7-(4-(trifluoromethyl)phenyl)quinoline

(0.035 g, 0.122 mmol) in 0.24 mL of CH3CN (0.50 M substrate) was added NFSI (0.192 g, 0.61

mmol, 5.0 equiv.) and Li2CO3 (0.045 g, 0.61 mmol, 5.0 equiv.). The resulting reaction mixture

was then heated to 75 °C and maintained at this temperature for 48 hours. The yield for 380 (46%)

was determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as

an internal standard. Purification of the crude material by flash column chromatography (pentane-

ethyl acetate; 1:1) provided an analytical sample of 380.

IR (neat): = 2925, 1617, 1326, 1119, 1071, 729 cm-1; 1H NMR (600

MHz, CDCl3): δ 9.07 (d, J = 4.2 Hz, 1H), 8.44 (d, J = 1.7 Hz, 1H), 8.21

(d, J = 8.6 Hz, 1H), 7.92 (dd, J = 8.8, 1.8 Hz, 1H) 7.87 (d, J = 8.2 Hz,

2H), 7.87 (d, J = 8.2 Hz, 2H), 7.63 (ddd, J = 4.2 Hz, 1H), 7.18 (t, J =

54.5 Hz, 1H); 13C NMR (150 MHz, CDCl3): δ 150.9, 148.9, 143.3, 141.3,

138.1 (t, J = 22.7 Hz), 136.0, 130.5 (q, J = 32.7), 128.5, 128.0, 127.3, 126.2 (q, J = 3.7 Hz), 124.4,

207

123.8 (t, J = 3.1 Hz), 118.5 (t, J = 7.9 Hz), 113.4 (t, J = 241.3 Hz); 19F NMR (470 MHz, CDCl3):δ

–62.5, –114.8

HRMS (EI+) calcd for [C17H11F5N]+ 324.0806, found 324.0806

Preparation of compound 381

Following General Procedure B, to a solution of 3-(pyridin-4-yl)propyl 4-nitrobenzoate (0.025 g,

0.087 mmol) in 0.17 mL of ethyl acetate (0.50 M substrate) was added NFSI (0.274 g, 0.87 mmol,

10 equiv.) and Li2CO3 (0.033 g, 0.44 mmol, 5.0 equiv.). The resulting reaction mixture was then

heated to 75 °C and maintained at this temperature for 48 hours. Purification of the crude 381 by

flash chromatography (pentanes: ethyl acetate 1:1) afforded 381 (13.1 mg, 49%).

1H NMR (600 MHz, CDCl3): δ 8.80 (d, J = 3.8 Hz, 1H), 8.28 (d, J = 8.5

Hz, 2H), 8.05 (d, J = 8.5, 1H), 7.64 (d, J = 3.8 Hz, 2H), 4.60 (dd, J = 6.3,

6.3 Hz, 2H), 2.69 (m, J = 3.7 Hz, 2H); 13C NMR (150 MHz, CDCl3): δ

164.4, 150.9, 149.4, 149.3, 135.0, 130.8, 123.8, 120.3, 120.2, 59.3,

37.8 (t, J = 26.7 Hz); 19F NMR (470 MHz, CDCl3):δ –97.9.

HRMS (EI+) calcd for [C15H13F2N2O4]+ 323.0838, found 323.0845.

Preparation of compound 382

Following General Procedure B, to a solution of 3-(pyridin-4-yl)propyl 4-bromobenzoate (0.025 g,

0.078 mmol) in 0.16 mL of ethyl acetate (0.50 M substrate) was added NFSI (0.247 g, 0.78 mmol,

10 equiv.) and Li2CO3 (0.029 g, 0.39 mmol, 5.0 equiv.). The resulting reaction mixture was then

heated to 75 °C and maintained at this temperature for 48 hours. Purification of the crude 382 by

flash chromatography (pentanes: ethyl acetate 1:1) afforded 382 (12.1 mg, 47%).

IR (neat): = 2973, 1723, 1272, 1118, 732 cm-1;1H NMR (600 MHz,

CDCl3): δ 8.73 (d, J = 3.8 Hz, 2H), 7.68 (d, J = 7.8 Hz, 2H), 7.56 (d, J =

7.8 Hz, 2H), 7.42 (d, J = 3.8 Hz, 2H), 4.51 (t, J = 5.9 Hz, 2H), 2.66 (tt, J

= 15.7, 6.2 Hz, 2H); 13C NMR (150 MHz, CDCl3): δ 165.5, 150.6, 144.9

(t, J = 26.8 Hz), 131.9, 131.1, 128.6, 128.5, 120.5 (t, J = 242.9 Hz),

119.6 (t, J = 6.3 Hz), 58.8 (t, J = 5.4 Hz), 37.9 (t, J = 27.2 Hz); 19F NMR (470 MHz, CDCl3):δ –

97.6

208

HRMS (EI+) calcd for [C15H13BrF2NO2]+ 356.0092, found 356.0091

Preparation of compound 383

Following General Procedure B, to a solution of 4-ethylpyridine (0.025 mL, 0.22 mmol) in 0.45 mL

of ethyl acetate (0.50 M substrate) was added NFSI (0.694 g, 2.20 mmol, 10 equiv.) and Li2CO3

(0.081 g, 1.10 mmol, 5 equiv.). The resulting reaction mixture was then heated to 75 °C and

maintained at this temperature for 48 hours. The yield for 383 (43%) was determined by analysis

of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an internal standard. TFA

was added to the reaction mixture prior to concentration under reduced pressure. Purification of

the crude material by flash column chromatography (pentane-ethyl acetate; 1:1) provided an

analytical sample of 383.297

IR (neat): = 3085, 2923, 1666, 1293, 1150, 720 cm-1;1H NMR (600 MHz, CDCl3): δ

11.11 (br s, 1H), 9.02 (d, J = 6.2 Hz, 2H), 7.95 (d, J = 6.3 Hz, 2H), 2.00 (t, J = 18.4

Hz, 3H); 19F NMR (470 MHz, CDCl3):δ –75.9, –92.2

HRMS (EI+) calcd for [C7H8F2N]+ 144.0619, found 144.0623

Melting point: 86-89˚C

Preparation of compound 384

Following General Procedure B, to a solution of 2-ethylquinazoline (0.025 g, 0.158 mmol) in 0.65

mL of CH3CN (0.25 M substrate) was added NFSI (0.249 g, 0.791 mmol, 5.0 equiv.) and Li2CO3

(0.026 g, 0.348 mmol, 2.2 equiv.). The resulting reaction mixture was then heated to 125 °C and

maintained at this temperature in a microwave reactor for 1 hour. The yield for 384 (86%) was

determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an

internal standard. Purification of the crude material by flash column chromatography (pentane-

ethyl acetate; 4:6) provided an analytical sample of 384.

IR (neat): = 2977, 1620, 1584, 905, 729 cm-1; 1H NMR (600 MHz, CDCl3): δ

9.52 (s, 1H), 8.17 (d, J = 8.7 Hz, 1H), 8.01 (m, 2H), 7.76 (dd, J = 7.3 Hz, 1H),

2.19 (t, J = 18.7 Hz, 3H); 13C NMR (150 MHz, CDCl3) δ 161.4, 159.3 (t, J = 28.1

Hz), 149.9, 135.0, 129.2, 129.2, 127.3, 124.7, 119.8 (t, J = 239.7 Hz), 23.4 (t,

J = 26.8 Hz); 19F NMR (CDCl3): δ –92.8

209

HRMS (EI+) calcd for [C10H9F2N2]+ 195.0728, found 195.0725

Preparation of compound 385

Following General Procedure B, to a solution of 6-bromo-4-ethylquinazoline (0.025 g, 0.106

mmol) in 0.22 mL of CH3CN (0.50 M substrate) was added NFSI (0.100 g, 0.318 mmol, 3.0 equiv.)

and Li2CO3 (9.0 mg, 0.117 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to

125 °C and maintained at this temperature in a microwave reactor for 1 hour. The yield for 385

(74%) was determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-

fluorotoluene as an internal standard. Purification of the crude material by flash column

chromatography (pentane-ethyl acetate; 8:2) provided an analytical sample of 385.

IR (neat): = 3059, 2976, 1394, 1117, 1036, 759 cm-1; 1H NMR (600 MHz,

CDCl3): δ 9.36 (s, 1H), 8.66 (d, J = 1.2 Hz, 1H), 8.04 (dd, J = 9.0, 1.8 Hz, 1H)

1H), 8.02 (d, J = 9.0, 1H), 2.23 (t, J = 19.4, 1H); 13C NMR (150 MHz, CDCl3) δ

160.6 (d, J = 32.2 Hz), 153.8, 150.7, 138.1, 131.1, 128.5 (t, J = 6.1 Hz), 123.0 (t,

J = 240.7 Hz), 123.0, 122.2, 22.7 (t, J = 25.7 Hz); 19F NMR (CDCl3): δ –84.4

HRMS (EI+) calcd for [C10H8BrF2N2]+ 272.9833, found 272.9833

Preparation of compound 386

Following General Procedure B, to a solution of 6-ethyl-9-methyl-9H-purine (0.025 g, 0.169 mmol)

in 0.68 mL of CH3CN (0.25 M substrate) was added NFSI (0.266 g, 0.843 mmol, 5.0 equiv.) and

Li2CO3 (0.027 g, 0.372 mmol, 2.2 equiv.). The resulting reaction mixture was then heated to 125

°C and maintained at this temperature in a microwave reactor for 1 hour. The yield for 386 (69%)

was determined by analysis of a 1H NMR spectrum (500 MHz, CD3CN) using 4-fluorotoluene as

an internal standard. Purification of the crude material by flash column chromatography (pentane-

ethyl acetate; 1:9) provided an analytical sample of 386.

IR (neat): = 2975, 1594, 1328, 1119, 907, 731 cm-1; 1H NMR (600 MHz, CDCl3):

δ 9.05 (s, 1H), 8.19 (s, 1H), 3.96 (s, 3H) 1H), 2.20 (t, J = 19.4, 3H); 13C NMR (150

MHz, CDCl3) δ 153.7, 152.9 (t, J = 30.1 Hz), 152.1, 146.7, 130.1, 120.4 (t, J = 240.2

Hz), 30.1, 23.6 (t, J = 26.4 Hz); 19F NMR (CDCl3): δ –90.8

HRMS (EI+) calcd for [C8H9F2N4]+ 199.0790, found 199.0784

210

Preparation of compound 390

Following General Procedure C, to a solution of 6-bromo-4-ethylquinazoline (0.025 g, 0.106

mmol) in 0.53 mL of CH3CN (0.20 M substrate) was added N-

trifluoromethylthiobenzenesulfonimide (0.100 g, 0.252 mmol, 2.4 equiv.) and Li2CO3 (9.0 mg,

0.117 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to 75 °C and maintained

at this temperature for 48 hours. Purification of the crude 390 by flash chromatography (pentanes:

ethyl acetate; 85:15) afforded 390 (33.0 mg, 92%).

IR (neat): = 2977, 1557, 1485, 1115, 731 cm-1;1H NMR (600 MHz, CDCl3): δ

9.30 (s, 1H), 8.28 (d, J = 1.8 Hz, 1H), 8.02 (dd, J = 9.0, 2.0 Hz, 1H), 8.00 (d, J

= 9.0 Hz, 1H) 5.25 (q, J = 7.1 Hz, 1H), 1.94 (d, J = 7.1 Hz, 3H); 13C NMR (150

MHz, CDCl3): δ 167.9, 154.7, 149.4, 138.0, 131.6, 130.9 (q, J = 307.8 Hz),

125.9, 122.7, 122.6, 41.4, 22.9; 19F NMR (470 MHz, CDCl3):δ –40.3

HRMS (EI+) calcd for [C11H9BrF3N2S]+ 336.9616, found 336.9621

Preparation of compound 391

Following General Procedure C, to a solution of 6-ethyl-9-methyl-9H-purine (0.025 g, 0.169 mmol)

in 0.68 mL of CH3CN (0.25 M substrate) was added N-trifluoromethylthiobenzenesulfonimide

(0.147 g, 0.372 mmol, 2.2 equiv.) and Li2CO3 (0.015 g, 0.20 mmol, 1.1 equiv.). The resulting

reaction mixture was then heated to 125 °C and maintained at this temperature in a microwave

reactor for 50 minutes. The yield for 391 (56%) was determined by analysis of a 1H NMR spectrum

(500 MHz, CD3CN) using 4-fluorotoluene as an internal standard. Purification of the crude material

by flash column chromatography (pentane-ethyl acetate; 1:1) provided an analytical sample of

391.

IR (neat): = 2953, 1750, 1591, 1331, 1223, 1114 cm-1; 1H NMR (600 MHz, CDCl3):

δ 8.96 (s, 1H), 8.08 (s, 1H), 5.28 (q, J = 7.1 Hz, 1H), 3.93 (s, 3H), 1.90 (d, J = 7.4,

1H); 13C NMR (150 MHz, CDCl3) δ 159.9, 152.8, 152.2, 145.4, 130.9 (q, J = 304.2

Hz), 40.7 (q, J = 1.8 Hz), 30.1, 21.7; 19F NMR (CDCl3): δ –40.4

HRMS (EI+) calcd for [C9H10F3N4S]+ 263.0573, found 263.0573

211

Preparation of compound 392

Following General Procedure C, to a solution of 2-propylquinazoline (0.025 g, 0.158 mmol) in 0.65

mL of CH3CN (0.25 M substrate) was added N-trifluoromethylthiobenzenesulfonimide (0.249 g,

0.791 mmol, 5.0 equiv.) and Li2CO3 (0.026 g, 0.348 mmol, 2.2 equiv.). The resulting reaction

mixture was then heated to 125 °C and maintained at this temperature in a microwave reactor for

1 hour. The yield for 392 (74%) was determined by analysis of a 1H NMR spectrum (500 MHz,

CD3CN) using 4-fluorotoluene as an internal standard. Purification of the crude material by flash

column chromatography (pentane-ethyl acetate; 1:1) provided an analytical sample of 392.

IR (neat): = 2973, 1624, 1113, 905, 731 cm-1; 1H NMR (600 MHz, CDCl3): δ

8.52 (d, J = 5.7 Hz, 1H), 8.17 (d, J = 8.7 Hz, 1H), 7.88 (dd, J = 7.3, 7.3 Hz, 1H),

7.67 (dd, J = 7.3, 7.3 Hz, 1H), 7.62 (d, J = 5.5 Hz, 1H), 5.25 (dd, J = 5.9, 5.7

Hz, 1H), 2.42 (m, 1H), 2.32 (m, 1H), 0.91 (t, J = 7.6 Hz, 3H); 13C NMR (150

MHz, CDCl3) δ 158.7, 141.9, 136.7, 131.3 (q, J = 307.7 Hz), 130.6, 128.0, 126.0, 124.2, 120.8,

47.7, 30.0, 11.4; 19F NMR (CDCl3): δ –40.3

HRMS (EI+) calcd for [C12H12F3N2S]+ 273.0668, found 273.0688

Preparation of compound 393

To a solution of 6-bromo-4-ethylquinazoline (0.020 g, 0.085 mmol) in 0.35 mL of CH3CN (0.25 M

substrate) was added N-chlorobenzenesulfonimide (0.034 g, 0.102 mmol, 1.2 equiv.) and Li2CO3

(6.9 mg, 0.093 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to and

maintained at 75 °C for 48 hours. Purification of the crude 393 by flash chromatography

(pentanes: diethyl ether; 6:4) afforded 393 (17.7mg, 78%).

IR (neat): = 2925, 1558, 1484, 905, 837, 729 cm-1; 1H NMR (600 MHz,

CDCl3): δ 9.35 (s, 1H), 8.44 (d, J = 1.9 Hz, 1H), 8.01 (dd, J = 8.9, 1.9 Hz, 1H),

7.99 (d, J = 8.9 Hz, 1H) 5.75 (q, J = 6.7 Hz, 1H), 2.08 (d, J = 6.7 Hz, 3 H); 13C

NMR (150 MHz, CDCl3): δ 166.4, 154.8, 149.7, 137.7, 131.4, 126.7, 123.4,

122.3, 52.7, 22.1

Melting point: 107-108˚C

HRMS (EI+) calcd for [C10H9BrClN2]+ 270.9632, found 270.9642.

212

Preparation of compound 394

To a solution of 4-ethyl-6-phenylquinazoline (0.030 g, 0.128 mmol) in 0.60 mL of CH3CN (0.20 M

substrate) was added N-trifluoromethylthiobenzenesulfonimide (0.102 g, 0.256 mmol, 2.0 equiv.)

and Li2CO3 (10.0 mg, 0.141 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to

and maintained at 75 °C for 36 hours. Purification of the crude 394 by flash chromatography

(pentanes: diethyl ether; 6:4) afforded 394 (20.9 mg, 49%).

1H NMR (500 MHz, CDCl3): δ 9.29 (s, 1H), 8.26 (d, J = 1.5 Hz, 1H), 8.21

(dd, J = 8.7, 1.5 Hz, 1H), 8.18 (d, J = 8.7 Hz, 1H) 5.42 (q, J = 7.0 Hz, 1H),

1.98 (d, J = 7.0 Hz, 3H); 13C NMR (125 MHz, CDCl3): δ 168.7, 154.4, 150.1,

141.6, 139.7, 134.2, 131.2 (d, J = 307.6 Hz), 130.3, 129.4, 128.7, 127.7,

121.9, 121.1, 41.4, 22.9; 19F NMR (470 MHz, CDCl3): δ -40.3

HRMS (EI+) calcd for [C17H14F3N2S]+ 335.0824, found 335.0844

Preparation of compound 395

To a solution of 4-ethyl-6-(4-fluorophenyl)quinazoline (0.030 g, 0.119 mmol) in 0.60 mL of CH3CN

(0.20 M substrate) was added N-trifluoromethylthiobenzenesulfonimide (0.095 g, 0.240 mmol, 2.0

equiv.) and Li2CO3 (9.7 mg, 0.13 mmol, 1.1 equiv.). The resulting reaction mixture was then

heated to and maintained at 75 °C for 36 hours. Purification of the crude 395 by flash

chromatography (pentanes: diethyl ether; 6:4) afforded 395 (33.3 mg, 79%).

1H NMR (500 MHz, CDCl3): δ 9.28 (s, 1H), 8.21 (d, J = 1.5 Hz, 1H), 8.19

(d, J = 8.6 Hz, 1H), 8.14 (dd, J = 8.6, 1.8 Hz, 1H), 7.67 (m, 2H), 7.24 (m,

2H), 5.40 (q, J = 7.0 Hz, 1H), 1.98 (d, J = 7.0 Hz, 3 H); 13C NMR (125

MHz, CDCl3): δ 168.8, 160.3 (d, J = 248.5 Hz), 154.5, 150.1, 140.5, 135.8

(d, J = 2.8 Hz), 134.0, 131.1 (q, J = 307.2), 130.4, 129.4 (d, J = 8.0 Hz), 121.9, 120.9, 116.4 (d, J

= 21.7 Hz), 41.3, 22.9; 19F NMR (470 MHz, CDCl3): δ -40.3, -113.4

HRMS (EI+) calcd for [C17H13F4N2S]+ 353.0730, found 353.0711.

213

Preparation of compound 396

To a solution of 4-ethyl-6-(4-ethylphenyl)quinazoline (0.030 g, 0.115 mmol) in 0.55 mL of CH3CN

(0.20 M substrate) was added N-trifluoromethylthiobenzenesulfonimide (0.091 g, 0.230 mmol, 2.0

equiv.) and Li2CO3 (9.3 mg, 0.270 mmol, 1.1 equiv.). The resulting reaction mixture was then

heated to and maintained at 75 °C for 48 hours. Purification of the crude 396 by flash

chromatography (pentanes: diethyl ether; 6:4) afforded 396 (28.3 mg, 68%).

1H NMR (500 MHz, CDCl3): δ 9.27 (s, 1H), 8.23 (d, J = 1.6 Hz, 1H),

8.20 (dd, J = 9.1, 1.8 Hz, 1H), 8.16 (d, J = 9.1 Hz, 1H), 7.63 (d, J = 8.2

Hz, 2H), 7.38 (d, J = 8.2 Hz, 2H), 5.41 (q, J = 7.0 Hz, 1H), 2.75 (q, J =

7.6 Hz, 2H), 1.98 (d, J = 7.0 Hz, 3H), 1.31 (t, J = 7.6Hz, 3H); 13C NMR

(150 MHz, CDCl3): δ 168.2, 154.3, 150.0, 145.1, 141.5, 137.0, 134.2,

131.1 (q, J = 309.0 Hz), 130.2, 129.0, 127.6, 122.0, 120.7, 41.5, 28.7, 23.0, 15.7; 19F NMR (470

MHz, CDCl3): δ -40.3.

HRMS (EI+) calcd for [C19H18F3N2S]+ 363.1137, found 363.1119.

Preparation of compound 400

Following General Procedure A, to a solution of quazodine (0.025 g, 0.115 mmol) in 1.2 mL of

CH3CN (0.10 M substrate) was added NFSI (0.044 g, 0.138 mmol, 1.2 equiv.) and Li2CO3 (10.0

mg, 0.127 mmol, 1.1 equiv.). The resulting reaction mixture was then left room temperature and

maintained at this temperature for 120 hours. Purification of the crude 400 by flash

chromatography (pentane-ethyl acetates; 1:1) afforded 400 (14.0 mg, 50%).

IR (neat): = 2957, 1617, 1501, 1233, 1133, 905, 729 cm-1; 1H NMR (600

MHz, CDCl3): δ 9.12 (s, 1H), 7.56 (s, 1H), 7.38 (s, 1H), 6.15 (dq, J = 48.1, 6.6

Hz, 1H), 4.08 (s, 3H), 4.06 (s, 3H), 1.90 (dd, J = 24.2, 6.7 Hz, 3H); 13C NMR

(150 MHz, CDCl3) δ 163.6 (d, J = 20.8 Hz), 156.1, 153.0, 150.5, 149.5, 118.2,

107.3, 102.2 (d, J = 9.2 Hz), 91.7 (d, J = 171.5 Hz), 56.6, 56.4, 20.5 (d, J = 23.2 Hz); 19F NMR

(470 MHz, CDCl3): δ –174.1

HRMS (EI+) calcd for [C12H14FN2O2]+ 237.1034, found 237.1042

Melting point: 111-114˚C

214

Preparation of compound 401

Following General Procedure B, to a solution of quazodine (0.025 g, 0.115 mmol) in 0.23 mL of

CH3CN (0.50 M substrate) was added NFSI (0.108 g, 0.344 mmol, 3.0 equiv.) and Li2CO3 (9.0

mg, 0.127 mmol, 1.1 equiv.). The resulting reaction mixture was then heated to 125 °C in a

microwave reactor and maintained at this temperature for 1 hour. Purification of the crude 401 by

flash chromatography (pentanes: ethyl acetate; 7:3) afforded 401 (17.8 mg, 62%).

1H NMR (600 MHz, CDCl3): δ 9.14 (s, 1H), 7.68 (s, 1H), 7.39 (s, 1H), 4.09 (s,

1H), 4.07 (s, 1H), 2.22 (t, J = 19.6 Hz, 3H); 13C NMR (150 MHz, CDCl3) δ

158.0 (t, J = 30.3 Hz), 156.4, 152.3, 150.9, 150.3, 123.5 (t, J = 239.9 Hz),

117.2, 107.1, 103.0, 56.6, 56.4, 22.7 (t, J = 25.5 Hz); 19F NMR (470 MHz,

CDCl3): δ –85.3

HRMS (ESI+) calcd for [C12H15F2N2O2]+ 255.0940, found 255.0949

Preparation of compound 402

Following General Procedure C, to a solution of quazodine (0.025 g, 0.115 mmol) in 0.60 mL of

CH3CN (0.20 M substrate) was added N-trifluoromethylthiobenzenesulfonimide (0.108 g, 0.275

mmol, 2.4 equiv.) and Li2CO3 (9.0 mg, 0.127 mmol, 1.1 equiv.). The resulting reaction mixture

was then heated to 75 °C and maintained at this temperature for 48h. Purification of the crude

402 by flash chromatography (pentanes: ethyl acetate; 1:1) afforded 402 (34.0 mg, 94%).

1H NMR (600 MHz, CDCl3): δ 9.12 (s, 1H), 8.18 (s, 1H), 7.38 (s, 1H), 7.25 (s,

1H), 5.20, (q, J = 7.0, 1H), 4.08 (s, 3H), 4.08 (s, 3H), 1.96 (d, J = 6.9 Hz, 3H);

13C NMR (150 MHz, MeOD): δ 164.7, 156.4, 153.4, 151.1, 149.0, 131.2 (q, J

= 307.7 Hz), 117.5, 107.7, 100.7, 56.7, 56.4, 41.4, 22.4; 19F NMR (470 MHz,

CDCl3):δ –40.4

HRMS (EI+) calcd for [C13H14F3N2O2S]+ 319.0723, found 319.0725

Melting point: 104-107˚C

Preparation of compound 405

Following General Procedure A, to a solution of 404 (0.020 g, 0.049 mmol) in 0.20 mL of CH3CN

(0.25 M substrate) was added NFSI (0.047 g, 0.148 mmol, 3.0 equiv.) and Li2CO3 (4.0 mg, 0.054

215

mmol, 1.1 equiv.). The resulting reaction mixture was then heated to 75 °C and maintained at

this temperature for 48 hours. The yield for 405 (69%) was determined by analysis of a 1H NMR

spectrum (500 MHz, CD3CN) using 4-fluorotoluene as an internal standard. Purification of the

crude material by flash column chromatography (pentane-ethyl acetate; 25:75) provided an

analytical sample of 405 as a 1:1 mixture of diastereomers.

IR (neat): = 2971, 1748, 1592, 1223, 1057 cm-1; 1H NMR (600 MHz,

CDCl3): δ 9.00 (1H), 8.26 (1H), 6.25 (1H), 6.19 (1H), 5.98 (1H), 5.68

(1H), 4.48 (1H), 4.46 (1H), 4.39 (1H), 2.16 (3H), 2.12 (3H), 2.09 (3H),

1.88 (3H); 13C NMR (150 MHz, CDCl3): δ 170.4, 169.7, 169.5, 159.2,

152.8, 151.7, 143.4, 131.5, 88.4, 86.7, 80.6, 73.2, 70.7, 63.1, 20.9, 20.7,

20.7, 20.5; 19F NMR (470 MHz, CDCl3):δ –180.2, 180.2.

HRMS (EI+) calcd for [C18H22FN4O7]+ 425.1467, found 425.1459

Preparation of compound 406

Following General Procedure B, to a solution of 404 (0.010 g, 0.025 mmol) in 0.10 mL of CH3CN

(0.25 M substrate) was added NFSI (0.039 g, 0.123 mmol, 5.0 equiv.) and Li2CO3 (9.1 mg, 0.123

mmol, 5.0 equiv.). The resulting reaction mixture was then heated to 75 °C and maintained at

this temperature for 48 hours. Purification of the crude 406 by flash chromatography (pentanes:

ethyl acetate 25:75) afforded 406 (6.3 mg, 57%).

IR (neat): = 2952, 1749, 1590, 1224, 1133 cm-1; 1H NMR (600 MHz,

CDCl3): δ 9.05 (s, 1H), 8.35 (s, 1H), 6.28 (d, J = 5.1 Hz 1H), 5.98 (t,

J = 5.2, 5.2 Hz, 1H), 5.66 (dd, J = 5.1, 5.1 Hz, 1H), 4.49 (m, 1H), 4.46

(dd, J = 13.1, 1.8 Hz, 1H), 4.40 (dd, J = 13.1 Hz, 4.1 Hz, 1H), 2.20 (t,

J = 18.8 Hz, 3H), 2.17 (s, 3H), 2.13 (s, 3H), 2.09 (s, 3H); 13C NMR

(150 MHz, CDCl3): δ 170.3, 169.6, 169.3, 153.4 (t, J = 30.9 Hz), 152.7, 152.2, 144.3, 130.8, 120.0

(t, J = 239.6 Hz), 86.7, 80.5, 73.1, 70.6, 62.9, 23.4 (t, J = 25.9 Hz), 20.8, 20.5, 20.4; 19F NMR (470

MHz, CDCl3):δ –90.9.

HRMS (EI+) calcd for [C18H21F2N4O7]+ 443.1373, found 443.1370

216

Radiochemistry

Production of [18F]F2 gas

[18F]F2 gas was produced on TRIUMF’s TR13 cyclotron via the 18O(p,n)18F nuclear reaction in an

aluminum-body target using two proton irradiations. First [18O]O2 was loaded into the target to

~270 psi and irradiated with 25 A of 13 MeV protons for 5-10 minutes. The gas was removed

under reduced pressure and cryogenically trapped for recycling. F2 gas (3 % in Ar) was filled into

the target to 14 psi and topped with Ar to 290 psi. The target was then irradiated for 2-5 min with

20 A of 13 MeV protons. The target was emptied to the chemistry lab carried by Ar.

Synthesis of [18F]N-fluorodibenzenesulfonamide ([18F]NFSI)

Sodium dibenzenesulfonamide (40 mg, 125 µmol) was dissolved in 1 mL of 4:1 CH3CN:H2O and

placed in a conical vial. [18F]F2 produced in the cyclotron target was then passed through the

solution over a period of ~10 min. The waste gas was trapped by saturated KI solution. Typically

3-4 GBq was trapped in the reaction mixture. The resulting solution was then passed through a

SepPak (Waters tC18 SepPak Plus Long Cartridge). The cartridge was washed with 10 mL H2O

followed by 600 µL CH3CN. [18F]NFSI was then eluted from the SepPak cartridge in 2.4 mL

CH3CN. Typically, 50 ± 8 µmol of purified NFSI with an activity of 0.3-0.5 GBq is produced from

this process. The amount of NFSI generated in each reaction was calculated following HPLC

analysis of the reaction mixture and comparison with a calibration curve prepared from NFSI.

Synthesis of [18F] 408

The [18F]NFSI solution was concentrated under vacuum at 75 oC, then 360 µL CH3CN was added.

The mixture of 407 (6.70 mg, 50 µmol), Li2CO3 (4.2 mg, 57 µmol) and [18F]NFSI (180 µL CH3CN

solution) were place in a 5 mL conical vial and reacted at 75 oC for 40 min. After this time, a

fraction of the resulting mixture was subjected to HPLC analysis to get the radiochemical

conversion (RCC). Analytical HPLC was carried out on a Phenomenex Luna C18 (4.6 x 100 mm,

1 mL/min) using a gradient of 100% solvent A (0.1% TFA in H2O) to 100% solvent B (0.1% TFA

in CH3CN) over 15 min. A fraction of 15 µL reaction mixture was used for the purification, the

mixture was subjected to semi-preparatory HPLC purification. Semi-preparatory HPLC condition:

Phenomenex Luna C18 (4.6 x 100 mm, 1 mL/min) using a gradient of 100% solvent A (0.1% TFA

in H2O) to 100% solvent B (0.1% TFA in CH3CN) over 15 min. The radiochemical yield (RCY) is

217

reported as a percentage and represents the total activity present in the purified 18F-labeled 408

divided by the total activity present in the purified [18F]NFSI x 100 (decay corrected).

Figure 6.1: HPLC radio trace of purified [18F]NFSI (top), HPLC radio trace of crude

(middle) and HPLC radio trace of purified 408 (bottom, blue line) overlaid with HPLC UV trace

(220 nm) of authentic reference (bottom, red line).

HPLC radio trace of purified

[18F]NFSI

HPLC radio trace of

crude 408

Blue line: HPLC radio

trace of

Purified 408

Red line: HPLC UV

trace of

authentic reference

218

Chapter 7. Future Work

7.1. Synthesis of NA and CA Screening-Libraries

High-throughput screening of chemical libraries represents a powerful tool for drug-lead

identification.298 However, these libraries often suffer from poor structural and stereochemical

diversity thus limiting their effectiveness in drug discovery.298 The chemical methods established

in Chapters 2-4 of this thesis provide a platform for the efficient synthesis of a broad variety of

different nucleoside and carbohydrate scaffolds and thus should facilitate future efforts in

generating NAs and CAs for screening libraries.

Scheme 7.1. Synthesis of C2’/C4’-modified NA and ProTide libraries

Libraries of carbacycles, iminosugars, fluorosugars, and numerous NA scaffolds can

readily be accessed for screening against targets associated with cancer, viral and bacterial

infections, and other diseases. Of particular interest to medicinal chemistry, would be a library

consisting of NAs that incorporate modifications at both the C2’ and C4’-positions (Scheme 7.1A),

a subclass of antiviral NAs whose syntheses were previously lengthy and unamenable to rapid

diversification.107 Furthermore, utilizing chemistry developed at Merck, NAs 409 can be readily

219

converted into their corresponding phosphoramidate prodrugs (ProTide) 411 which are also used

as antiviral and anticancer therapies.299

7.2. Incorporating NAs into Antisense Oligonucleotides

Antisense Oligonucleotides (ASO) consist of single stranded DNA or RNA and function by

targeting genes that are linked to disease.300 Incorporation of nucleoside analogues into an

oligonucleotide can prevent its degradation by nucleases and improve its potency.300 For

example, Damha reported the synthesis of 4’-modified-2’-deoxy-2’-fluorouridine nucleoside

analogues where he demonstrated 4’-methoxy analogues significantly improved oligomer stability

against nucleases.301 As mentioned previously, our NA synthesis allows for the rapid synthesis of

a variety of novel NAs. Observing the effects of these NAs on oligomer stability and potency may

provide new structural insights for the further development of ASO therapies. As shown in Figure

7.1, concurrent modifications to the phosphate ester backbone, such as a phosphorothiolate

linkage (413 and 414), may also be investigate to improve nuclease resistance.

Figure 7.1. C2’/C4’-modified NAs for incorporation into oligonucleotides

220

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242

Appendix A. Liquid-Chromatography Chromatograms

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257

(+/-)-224-Bis-PNB

(-)-224-Bis-PNB

258

(+/-)-227-Bis-PNB

(+)-227-Bis-PNB

259

(+/-)-229-Bis-PNB

(-)-229-Bis-PNB

260

(+/-)-220-Bis-PNB

(-)-220-Bis-PNB

261

(+/-)-222-Bis-PNB

(-)-222-Bis-PNB

262

(+/-)-200-Bis-PNB

(-)-200-Bis-PNB

263

(+/-)-200-Bis-PNB

(-)-200-Bis-PNB derived from 223

264

(+/-)-200-Bis-PNB

(-)-200-Bis-PNB derived from 225

265

(+/-)-221-Bis-PNB

(-)-221-Bis-PNB

266

(+/-)-219-Bis-PNB

(-)-219-Bis-PNB

267

(+/-)-230-Bis-PNB

(-)-230-Bis-PNB

268

(+/-)-228

(-)-228

269

(+/-)-237-Bis-PNB

(+/-)-237-Bis-PNB

270

(+/-)-238

238

271

(+/-)-239-Bis-PNB

239-Bis-PNB

272

(+/-)-241

241

273

(+/-)-242

242

274

(+/-)-243-Bis-PNB

243-Bis-PNB

275

(+/-)-243-Bis-PNB

243-Bis-PNB derived

from 244

276

(+/-)-246-diol

246-diol

277

(+/-)-247-Bis-PNB

247-Bis-PNB