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NATURAL SCIENCES TRIPOS Part III

Thursday 29th May 2014 9.00 to 12.10

CHEMISTRY: PAPER 1A

Candidates should attempt SIX questions.

Where a question is divided into sections, the approximate division of marks betweensections is indicated at the end of the question.

Linear graph paper is available if required.

A Periodic Table, the structures of the amino acids and nucleotide bases, the values ofphysical constants, character tables and selected mathematical formulae will be found inthe data book provided.

Write on ONE side of the paper only.

The answers to each question should be returned separately.

A separate cover sheet for each question should be completed.

Calculator students are permitted to use an approved calculator.

STATIONERY REQUIREMENTS SPECIAL REQUIREMENTS

Graph paper (2 sheets) Department of Chemistry Data BookLined paper Question record cardRough work pad

You may not start to read the questions printed on

the subsequent pages of this question paper until

instructed that you may do so by the Invigilator.

During the first 10 minutes of the examination

you are permitted to read the paper, but you may

not start writing your answers until this time has

elapsed.

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CHEMISTRY: PAPER 1B

Candidates should attempt FIVE questions.
















elapsed.

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CHEMISTRY: PAPER 1C

Candidates should attempt FOUR questions.
















elapsed.

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M2 Advanced Diffraction Methods

Answer allparts of the question.

1

(a) What are the two main advantages of powder diffraction methods, and why are theyso useful in neutron diffraction studies?

(b) A specimen of nanocrystalline CaZrO3 is studied by x-ray diffraction, using CuKradiation (= 1.5418 ). The positions of the first ten diffraction lines are:

line 1 2 3 4 5 6 7 8 9 10

2(deg.) 21.68 30.84 38.01 44.18 49.72 54.85 64.26 68.68 72.97 77.16

Assuming that this is a cubic material, determine the lattice type and index the lines,and hence determine the unit cell dimension. Which of the lines will give the mostaccurate value, and why ?

(c) In a related experiment particles of composition BaxCa(1x)ZrO3 are prepared, andgive very similar powder x-ray diffraction patterns, as shown in the figure below.

15 25 35 45 55 65 75

2(degrees)

CaZrO3

(Ca,Ba)ZrO3

BaZrO3

intensity

The line positions are unchanged from those in CaZrO3, suggesting that the unit cellis unaltered, but there are subtle changes in the line intensities. In particular, therelative intensities of lines 5 and 9 are dramatically reduced as barium is substitutedfor calcium, but this reduction is most marked at the intermediate composition shownabove, rather than in pure BaZrO3.

[Qu.1continued on next page]

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[Continuation of Qu.1]

If it is assumed that all these phases have the perovskite structure, with atomicpositions:

Zr @ (0,0,0) : Ba or Ca @ ( 12 , 12 ,

12 ) : O @ (

12 ,0,0), (0,

12 ,0) and (0,0,

12 )

derive an expression for the structure factor, assuming that the site at ( 12 , 12 ,

12 ) is

occupied by a fraction xof barium and (1 x) of calcium atoms. Bearing in mindthat the atomic scattering factor is proportional to atomic number, show how partialsubstitution of calcium by barium could produce the observed intensity variations.

(d) X-ray emission analysis of individual CaZrO3 nanocrystals indicates an averageCaK/ZrKintensity ratio of 2.6, whereas in BaZrO3 the BaL/ZrKrato is 3.3.

The corresponding values in the BaxCa(1x)ZrO3specimen above are 1.17 and 1.82.

Evaluate the composition of this phase and explain if it is in accordance with theexplanation for the intensity variations described above.

[Atomic numbers Ca 20 : Zr 40 : Ba 56]

Approximate division of marks: (a) 20%, (b) 20%, (c) 40%, (d) 20%.

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M3 Magnetic Materials

2


(a) Briefly explain the reasons why nickel metal is a ferromagnet.

(b) Show how different MLM bridging angles may give rise to either ferromagnetic orantiferromagnetic superexchange.

A new cluster containing octahedral Ni2+, [Ni6(LH)4(MeO)4(MeOH)6] has a NiOcore as shown below, where the numbers 16 represent the six different nickel ions.

OHOOH OH

LH3

6

O1

5

O3

O O4

OO

O O

O O2

Analysis of the susceptibility values gives the following values for the differentexchange interactions:

J1,6 = J6,2 = J2,5 = J5,3 = J3,4 = +1.7 KJ6,5 = J2,3 = +35.5 K

J1,2 = J5,4 = 2.5 K

Use these values to derive the most energetically favourable arrangement of spins forthe cluster, write down the spin Hamiltonian for this cluster and hence calculate itsdegree of magnetic frustration.

Approximate division of marks: (a) 40%, (b) 60%.

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M4 Energy Landscapes and Soft Materials

3


(a) Consider two identical, charged colloidal spheres with radius R in a monovalentelectrolyte solution. We assume that the interaction energy between the spheres canbe approximated as:

Uel(r) = R

22

2

er,

whereris the surface-to-surface distance of the spheres, is the surface charge den-sity,the dielectric permittivity of the fluid, and is the inverse of the DebyeHuckelscreening lengthDH.

(i) Sketch the interaction potentialUel(r).

On the same graph sketch U

el(r) for the case of a divalent electrolyte solutionof the same concentration in the same solvent. Clearly label both functions andindicate the value ofdivalent/monovalent.

(ii) Now consider that the colloids are also subject to the dispersion interaction:

Udisp(r) C

r

where Cdenotes a constant which depends on the material from which thespheres are made, and the properties of the solvent. IsCpositive or negative?Explain your answer.

Sketch the dispersion interaction energy Udisp(r). On the same graph sketchthe dispersion interaction energyU

disp(r) if the absolute difference between therefractive index of the solvent and the spheres is decreased. Clearly label bothfunctions.

(iii) Sketch the total interaction energy Utot = Uel(r)+Udisp(r) for the case wherethe absolute value of the dispersion interaction is everywhere stronger than the

absolute value of the electrostatic repulsion, and for a case where that is nottrue.


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(b) (i) Prove the uniqueness theorem for a steepest-descent pathway on the energylandscapeV(X), where X is a vector of 3NCartesian coordinates for a moleculewithNatoms. Explain how this result enables basins of attraction to be definedfor local minima ofV(X).

(ii) For the two-dimensional potentialV(x,y) =y4 + 3x2 4y2 find and classify allthe stationary points. Derive analytical solutions for the steepest-descent pathsin the neighbourhood of the transition state and sketch contours for the functiontogether with the pathways.

Approximate division of marks: (a) (i) 15%, (ii) 15%, (iii) 20%, (b) (i) 20%, (ii) 30%.

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M5 Stereocontrolled Organic Synthesis

4


(a) Account mechanistically for the following transformations and assign the configura-tion at the labelled stereocentres (*).

StBu

OSiMe3

BF3-OEt2,

CH2Cl2, 78oC

O

O

HO

O

*

LDA, Me3SiCl,

THF, 78 to 60 oC;

aqueous HCl

*

H

O OMe OH OMe

tBuS

O

*

(b) Give a mechanistic account of this transformation, including a conformational draw-

ing of the tricyclic product.

O

NCl

H AIBN

Bu3SnHtricyclic product


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M6 Computer Simulation Methods in Chemistry and Physics

5


The one-dimensional Ising model in an external magnetic field is defined by

E=Ji j

si sj B

i

si

whereEis the energy of a system of spins si, Jis a coupling constant and Bis an externalmagnetic field, and for which sican take the values +1 and 1. In one dimension eachspin has two neighbours, one on the left and the other on the right. The symbol i jin thefirst sum indicates that the sum is restricted to immediate neighbouring pairs of spins.

(a) Write a pseudo-code to simulate the one-dimensional Ising model withNspins andwithB =0.

(b) Extend the pseudo-code to the case with non-zero B, and with periodic boundaryconditions (i.e. for which spin 1 is a neighbour of spin N). You may visualize thissituation by arranging the Nspins in a circle.

(c) Define the radial distribution functiong(r) for a two-dimensional Lennard-Jones fluidand describe its limiting behaviour for small and for large values ofr.

(d) Compare the behaviour of the radial distribution functiong(r) for a two-dimensionalLennardJones fluid for two different volume fractions.

Approximate division of marks: equal for each part.

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M7 Nano Science and Colloid Science Chemistry at small length scales

6


(a) (i) Give an enthalpic and an entropic reason for the stability of vesicle structuresrelative to lamella surfactant mesophases.

(ii) With reference to the concept of preferred interfacial curvature of a surfactant,explain why di-chain lipids are usually to be found in cell membranes and invesicles.

(iii) Where in the bilayer structure would you expect to find (i) a small hydrophobicsolute and (ii) a hydrophilic solute?

(b) If an ionic lipid is used to make a vesicle, describe what you expect to happen if theionic strength of the interior of the vesicle is increased.

(c) Discuss the relative importance of the major interactions in self-assembly ofamphiphiles into micelles. Your answer should include hydrogen bonding, thehydrophobic effect and electrostatic considerations.

Approximate division of marks: (a) 50%, (b) 20%, (c) 30%.

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M8 Protein folding, misfolding and disease

7


It has been suggested that the mechanism of folding of any protein will fall on a spectrumbetween two extremes: diffusion-collision and nucleation-condensation.

(a) Explain the differences between these two mechanisms, and explain how you mightexpect the pattern of-values to differ.

(b) What properties of a protein are likely to determine the mechanism by which it folds?Give examples.

(c) If a protein folds by nucleation-condensation what are the possible consequences ofmaking a destabilizing mutation of one of the residues in (i) the obligate nucleus or(ii) the critical nucleus? Explain your reasoning.


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M9 Supramolecular Chemistry and self-organisation

8


An equimolar mixture of the three molecules shown below (A, B and C) forms threeproducts (1,2and3) upon self-assembly in dichloromethane.

N N

NNN

N

N

N

N

N

N

N

N

N

C

A

N

N

B

Zn

N N

NN

Zn


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(a) Show schematically the structures of products1, 2and 3, and predict in what ratio

you would expect them to be formed. Briefly explain your reasoning.(b) Upon addition of two equivalents (per A) of copper(I) tetrafluoroborate to the mixture

noted above, a single product 4is formed. Schematically show the structure of thisproduct, and briefly explain its formation.

(c) The 1H NMR spectrum of 4at 25 C is consistent with four-fold symmetry: onlyone -pyrrolic proton resonance is observed, for example. Upon cooling to 75 C,this symmetry appears to break, with two -pyrrolic proton resonances replacing thesingle one observed at room temperature. Briefly explain these observations.

(d) Predict what happens to the1H NMR spectra of4at 25 C and75 C following theaddition of two additional equivalents of copper(I) tetrafluoroborate.

Approximate division of marks: equal for each part.

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M10 Medicinal Chemistry

9


(a) Erlotinib is a quinazoline treatment for advanced lung cancer. It can be made from atrisubstituted benzene starting material as summarised below:

HO

HO

OEt

OO

Br

K2CO3, TBAI

Acetone, , 64 hours

(93%)TBAI = tetrabutyl ammonium iodide

A

O

O

OEt

O

B

O

O

(excess)

?

O

O

N

NHR

O

ON

Erlotinib (C)

(i) Give reaction mechanisms for the formation ofB, explaining the role of each

of the reagents and the solvent.(ii) Erlotinib itself (C, abbreviated structure) is then synthesised fromB. Propose

a synthetic pathway that would allow you to do this (mechanisms are notrequired).


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(b) One of the key steps in the synthesis of the pyrrole ring in Lipitor uses chemistryshown in the scheme below. Suggest a mechanism for this reaction.

F

N

HO2C O

OO

CONHPh

Ac2O, reflux

N

CONHPh

OO

F

Approximate division of marks: (a) (i) 30%, (ii) 30%, (b) 40%.

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L1 Catalysis for chemical synthesis

10


(a) Propose a synthesis ofC from A and B that uses asymmetric catalysis. Your synthesiscan involve multiple steps and you may use any common reagents. Provide a detaileddescription of how the stereochemistry is controlled as part of your answer.

N

Boc

OH

N

OH

SHS

A B C

(b) Propose a concise synthetic route to racemicF, starting from Dand E. All of thecarbon atoms required are supplied by one equivalent ofD and two equivalents ofE;you may use multiple synthetic steps in your answer. Provide detailed mechanismsin support of your answer.

Br

SO2

DF

N

SO2

H2N Br

E


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L2 Solid electrolytes

11


(a) Describe briefly the direct-exchange diffusion mechanism. Give an example ofdiffusion by this mechanism.

(b) Consider an ion diffusing in a simple cubic lattice by the direct interstitial mecha-nism. The distance between nearest-neighbour interstitial sites in all directions isa.Assume, for simplicity, that diffusional jumps occur instantaneously at discrete times,withbeing the time interval between jumps.

(i) Derive expressions for the time dependence of the square root of the mean-squared displacement, s(t), and of the length of the trajectory, (t), covered bya diffusing ion fort.

(ii) Sketch the graph ofs(t)/(t) fort.

(iii) Assuming =108 s anda =3 , estimate s(t) and(t) fort=1 s; commenton their relative difference .

(c) The fluorite (CaF2) structure can be regarded as a face-centred-cubic array of Ca2+

ions, with the F ions located at the corners of a cube within the unit cell, each F ionbeing at a distance of one quarter of the body-diagonal length of the unit cell from thenearest corner Ca2+ ion.

Assuming that the ions are spherical, that the ionic radii of Ca2+ and F ions areequal, and nearest neighbour Ca2+ and F ions touch, calculate the atomic packingfraction (the proportion of volume in the unit cell actually occupied by the ions) forthis structure.

The atomic packing fraction for the rocksalt (NaCl) structure is 0.65. What does acomparison of the values of packing fractions for the two structures indicate aboutthe likely mode of F ion diffusion in CaF2?


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L3 Electronic structure of solid surfaces

12


Pyrrole-1-carboxylic acid (below) is deposited below room temperature on the {110}surface of anfccmetal.

N

OOH

(a) Briefly explain the XPS (X-ray Photoemission Spectroscopy) and NEXAFS (Near-

Edge X-ray Absorption Fine Structure) techniques, highlighting their similarities anddifferences, and discussing the type of information obtainable from each.

(b) XPS reveals a single N 1s peak, but the O 1s peak may be resolved into twodistinct components. Upon heating above room temperature, hydrogen is evolvedfrom the surface in a quantity consistent with one liberated H2 molecule per twoadsorbed molecules of pyrrole-1-carboxylic acid; the N 1s XPS peak retains itsoriginal lineshape, but the O 1speak can no longer be resolved into two components.

What can be deduced from this information about the structure of the adsorbed

molecules in the low temperature (i.e. below room temperature) and high temperature(i.e. above room temperature) regimes?

(c) NEXAFS experiments are performed on the same system. Examining the O 1sedgereveals a strong peak that may be interpreted as arising from excitation of electronsinto an unoccupied molecular orbital ofsymmetry; a similar peak is also observedat the N 1sedge, which may likewise be interpreted as involving an unoccupied state. In the low temperature regime, both peaks reach their maximum intensity whenpolarised X-rays are employed with their electric field vector perpendicular to thesurface, and both disappear whenever the electric field vector lies within the surface

plane.Based upon these observations, what may be deduced about the conformation andorientation of the adsorbed molecules in the low temperature regime?


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(d) Further NEXAFS data are obtained in the high temperature regime, in which case thepeak at the O 1sedge is found to vanish when the electric field vector of polarisedX-rays is either perpendicular to the surface or parallel to the close-packed rows, andto reach its maximum intensity when the electric field vector lies within the surfaceplane but perpendicular to the close-packed rows of the surface. The peak at the N1sedge is similarly minimised when polarised X-Rays have their electric field vectorperpendicular to the surface, but it is maximised when the electric field vector liesparallel to the close-packed rows and minimised when it lies perpendicular to them inthe surface plane.

What do these data imply about the orientation and/or conformation of the adsorbedmolecules in the high temperature regime?

(e) It is subsequently found that higher coverages of adsorbed molecules may be obtainedby depositing above room temperature (rather than depositing below room tempera-ture and subsequently heating). At saturation, scanning tunnelling microscopy revealsthat the overlayer adopts a (21) periodicity with one molecule per such surface unitcell.

How might we expect the NEXAFS data to vary with polarisation in this case?

Approximate division of marks: (a) 30%, (b) 20%, (c) 20%, (d) 20%, (e) 10%.

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L4 Organic Solids

13


(a) Molecules X and Y form a cocrystal that is found to dissociate partially at highhumidity. Explain this observation and draw a ternary phase diagram for this system,describing its main features and any assumptions or simplifications that you havemade. What phase(s) would you expect to exist at equilibrium at high humidity?

[The solubility of compoundXin water at room temperature is 20 mg/ml and that ofcompoundYis 50 mg/ml.]

(b) Outline the advantages and disadvantages of using the following techniques in the

preparation of cocrystals: (i) solution crystallisation, (ii) solid-state grinding (withand without the addition of a few drops of liquid) and (iii) freeze-drying.

(c) MoleculesIandII(shown below) form a cocrystal that is observed, by powder X-raydiffraction, to dissociate upon heating. The dissociation is endothermic as determinedby DSC analysis.

Discuss these observations in terms of the free energies and likely crystal structuresof the relevant crystal forms, including a free energy against temperature diagram inyour answer.

N

N N

N

O

O

I

N

N N

HN

O

O

II

Approximate division of marks: (a) 35% (b) 30%, (c) 35%.

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L5 Chemical Dynamics

14

Answer bothparts of the question.

(a) (i) Explain why the scattering of particles takes place in a plane.

(ii) Derive the expression

= 2b

a

dr

r2

1b2/r2 V(r)/E1/2

relating thedeflection angle to the impact parameter band the total energyE, whereais the distance of closest approach of the particles.

(b) Sodium atoms can be ionized in aqueous solution with the electron remaining insolution

Naaq Na+aq + e

aq

The solvated electron eaqcan be treated as a large halide-like aqueous anion. Using theBorn approximation for the solvation free energy, estimate the change in the reactionfree energy compared to ionization in vacuum.

[The radius of the sodium cation is 1.6 and that of the solvated electron 4.8 . Therelative dielectric constant of water is 80. The solvation free energy of the neutral

atom can be ignored.]


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L6 Main group organometallics

15


(a) Suggest the identities and aggregation states of the complexes formed whenAandBare monolithiated in the presence of one equivalent of Et2O.

Ph But

NH

Ph

HN

But

A B

(b) Compound C reacts in toluene with 100% 6Li enriched nBuLi (1 eq.) to givecrystallineDand a gas.

Ph

P

Me

O

C

Ph

The 13 C{1H}NMR spectrum ofDreveals aromatic signals as well as a multiplet at32 ppm. X-ray crystallography reveals an aggregate in which each Li interacts withone C-centre and multiple O-centres.

(i) Propose a structure forD.

(ii) Explain the appearance of the 13C{1H} NMR spectrum of D and predict themultiplicity of the32 ppm resonance.

[6Li,I=1; 31P, natural abundance 100%, I= 12 ]


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(c) Semiconductor materials such as GaAs are prepared by Organometallic ChemicalVapour Deposition (OMCVD). Precursors such as GaMe3 and AsH3are fed into areactor where they form GaAs on a heated target.

GaMe3

AsH3

reactor underreduced pressure

film forms ontarget surface

target heated

What kinds of problems arise from the use of these types of precursors and howcan some of these difficulties be alleviated by using alternative precursors? Whatparticular problems are encountered when trying to make GaN and what solutionshave been developed?

Approximate division of marks: (a) 25 %, (b) 25%, (c) 50%.

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L8 Total Synthesis

16


The following schemes contains key transformations from the total synthesis of a numberof natural products.

(a) Provide a detailed mechanism for the reaction betweenAandBto formC, giving anexplanation of how the stereochemistry of the reaction is controlled.

OBoc O

OPh

CH3

N

O

OBnOO

H

OTBS

N(CH3)2

LDA, TMEDA

-78 C to 0 CN

O

OBnOOH

H

OTBS

N(CH3)2

O

HCH3

OBoc

A B C

(b) Explain the mechanism of the following bromination reaction to formE. Accountfor why there is no tetrahydrofuran formation involving the carbon atom that isbrominated and the proximal hydroxyl group.

[Hint: PhI(OAc)2 + Br2 = AcOBr]

O

O

O

CH3

H

HO

H

CH3

ONH

O

OH

O

O

O

CH3

H

HO

H

ONH

O

OHBrBr

PhI(OAc)2, Br2, h

D E


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(c) Provide a detailed mechanism of the reaction shown below, giving an explanation ofhow the stereochemistry of the reaction is controlled.

N

NHCO2Me

Br H

I

NH2

N

Br H

NH

NCO2Me

I

H

F G H

N

O

O

I

Et3N


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L9 Biosynthesis

17

Answer bothparts of the question.

(a) Neoxanthin and capsanthin are among the many carotenoids produced by plants forlight-harvesting and protection from photochemical damage. Isopentenyl pyrophos-phate (IPP) is a known precursor.

HO

O

C

OHHO

Neoxanthin

HO Capsanthin

O

OH

OP2O63-

IPP

+

(i) Give detailed mechanisms for the steps leading from IPP to the first commonprecursor of the carotenoids that has the full number of carbons atoms.

(ii) Give mechanisms for the reactions that form the terminal ring-systems ofneoxanthin and capsanthin.

(b) Thromboxane A2is derived from arachidonic acid and O2. Propose a mechanism forthis transformation.

CO2H

Arachidonic acid

OH

CO2H

O

O

Thromboxane A2


END OF PAPER

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