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Advanced Chemistry Development, Inc. (ACD/Labs)

NMR Workshop

Brent LefebvreNMR Product Manager

European User’s Meeting – Obernai, FranceOctober 23, 2007

2

Application and Technical Notes

Application Application Notes and Notes and Technical NotesTechnical Notes

3

Outline

Secrets of Version 11 Revealed!What’s New in NMR

Automatic Quantitation Using Macros and ChemBasic

Database Searching TipsBe a DB search guru

Macro PossibilitiesMeet “Joe Macro”


Secrets of Version 11 Revealed


NMR Workshop Topic #1

5

Version 11

What’s New?New development in all productsThis is not a complete listModular products, check your modules

6

1D NMR Processor

Improved Multiplet AnalysisMultiplet Report TemplatesSmarter Integral PositionsMore flexible OverlayWith HNMR or CNMR

Assignment Quality PreviewVerification DiagnosticsCalculation ProtocolSolvent Specific Verification

7

Improved Multiplet Analysis

ASCI Data Set• 30 Samples• Good S/N• 400 MHz• Pharma type Structures

8

Improved Multiplet Analysis

ASCI Data Set• 30 Samples• Poor S/N• 300 MHz• Pharma type Structures

ASCI-1_A1_25_1D1H HNMR Match Factor: HNMR Structure Purity:

1.95 1.90 1.85 1.80 1.75 1.70 1.65 1.60 1.55 1.50 1.45 1.40Chemical Shift (ppm)

0

0.01

0.02

0.03

0.04

0.05

0.06

0.07

0.08

0.09

0.10

0.11

0.12

0.13

0.14

0.15

0.16

0.17

0.18

0.19

0.20

Nor

mal

ized

Inte

nsity

ASCI-1_B2_25_1D1H HNMR Match Factor: HNMR Structure Purity:

1.95 1.90 1.85 1.80 1.75 1.70 1.65 1.60 1.55 1.50 1.45 1.40Chemical Shift (ppm)

0

0.005

0.010

0.015

0.020

0.025

0.030

0.035

0.040

0.045

0.050

0.055

0.060

Nor

mal

ized

Inte

nsity

400400 300300

9

Multiplet Report Templates

Custom TemplatesBased on JournalsOr based on your own requirements

Virtually limitless customization

10

Smart Integral Positions

11

Flexible Overlay

12

Assignment Quality Preview

13

Assignment Quality Preview

14

Verification Diagnostics

Major InconsistencyAssignment is missing, error must be fixed manually

15

Verification Diagnostics

Minor InconsistencyAssignment is present, error can be dismissed if desired

16

And More…

Calculation ProtocolNow available in 1D NMR Processor

For Predicted or Verified Experimental

Solvent-Specific PredictionAnd VerificationNow possible in 1D NMR Processor

17

2D NMR Processor

Faster Spectrum DisplayAutomatically attach 1D to axesAutomatic Gridline CreationREAL Correlation SearchPick picking and gridline countWith 2D Predictor

View Calculation Protocol

18

Auto-attach 1D

19

Auto-Gridline Creation

20

Correlation Search

21

And Much More…

Peak Picking & Gridline CountNo need to add these up manually any more!

Calculation protocol as in 1DFor Predicted or Verified spectra

22

NMR Predictors

Improved Stereo-encodingIntegration of Neural NetworkImproved accuracy – AGAIN!Expanded databasesC-H and C-X coupling predicted and available for trainingHit data highlighting

23

Improved Stereo-Encoding

Flaws existed in old stere-encoding schemeNew scheme is much more robustImproved accuracy results

Different isomers give different results in more cases

24

Neural Network Integrated

Neural Nets properly integratedNow default prediction uses hybrid value of Neural Net, Incremental scheme and HOSE code

25

Improved Accuracy

No “official” numbers yetSmall datasets only so farNew numbers coming soon!

Should show significant improvement in Proton accuracy…

26

Expanded Databases

Year 2003 2004 2005 2006 2007Release Version 7.0 Version 8.0 Version 9.0 Version 10 Version 11# of Chemical Shifts

1,320,000 1,384,000 1,440,000 1,578,505 1,666,199

HNMR Database

Year 2003 2004 2005 2006 2007Release Version 7.0 Version 8.0 Version 9.0 Version 10 Version 11# of Chemical Shifts

1,850,000 2,017,000 2,160,000 2,351,827 2,430,218

CNMR Database

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C-H and C-X Coupling

28

Hit Data Highlighting

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Spectrum Databasing

Lots of new Database featuresDate SearchExport to ExcelData Hit Highlighting

30

Structure Elucidator

Work with FragmentsImproved Generation Algorithm

Faster and smarterBetter Screen LayoutsUse Prediction DatabasesBetter tools for faster work-up

31

“What’s New” Documents

See website for complete “What’s New” documentsWill be available shortly

Or I can send them upon request

32

Outline






A Prototype System for Automated Quantitation and Purity Analysis with

NMR



34

What was the problem being solved?

The results of activity screening depends on two things:

ActivityConcentration

Need a test for HT automated quantitation

35

What tools were available to solve it?

ACD/Automation ServerACD/1D NMR Processor, ACD/HNMR Predictor and ACD/ChemSketch

Macro process in the ProcessorChemBasic in ChemSketch

Enough processing tricks here to do it

36

Solution Design

Option #1Assign structure to spectrum# of Protons per peak knownAccurate quantitation possible against all peaks in spectrum

ConsError proneAssignment needs to be perfectSolvents or impurities cause problems

37

Solution Design

Option #2Same as #1, but use only 1 peakLess interference from impurities

ConsInaccurateDependence on a single integration area is too high risk

38

Solution Design

Option #3Use Aromatic regionSum # of aromatic protonsMeasure total integral of region

ProsAccurate and more robust than other approachesAccurate assignment not needed

39

Details of the Design

Integration measured against referenceExternal calibration of Eretic peak necessary

Number of aromatic and exchangeable protons counted on proposed structure‘Best’ number of protons per integral foundQuantity determined and reported

40

Quantitation Spectra

M4HBA90

7.5 5.0 2.5 0Chemical Shift (ppm)

41452827

OH

O CH3

Eretic Signal(Quantitation Reference)

41

Integral Value per Proton = ?

In this case two protons contribute to each resonance.

So:

Integral (per proton) = 13.7

How can this be Automated?

M4HBA90

8.0 7.5 7.0 6.5 6.0Chemical Shift (ppm)

2827

OH

O CH3

42

How Many Protons Contribute to Each Integral?

M4HBA90


2827

OH

O CH3

Correct Answer (Hopefully)

Possible Answers

Testing Funnel

1

2 5

36 4

78

43

M4HBA90


2827

Proton Count per Integral RegionExample #1

1

2 5

36 4

78

O H

O C H 3

Here: estimate 4-5 protons in this region

An acceptable analysis has to:

1. duplicate the 1:1 intensity ratio

2. fit 4-5 proton expectation

Test #1

1. Proton counts have to be in the same ratio as the measured integral values.

2. Sum of protons has to be in a reasonable range

44

Example #1

1

2 5

36 4

78

1 1 sum=2

2 2 sum=4

3 3 sum=6

4 4 sum=8

M4HBA90


2827

OH

O CH3

Protons per Integral

Trial Values

Correct Analysis Found

45

Example #2

8.5 8.0 7.5Chemical Shift (ppm)

171360172169

N O

CH3

OH

N

HH

H

Estimated 5-6 protons in this region

A proposed analysis has to:

1. duplicate the 1:1:2:1 intensity ratio

2. fit 5-6 proton expectation

1

2 5

36 4

78

46

Example #2protons per integral – trial values


171360172169

1 1 2 1 sum = 5

2 2 4 2 sum = 10

3 3 6 3 sum = 15

4 4 8 4 sum = 20

N O

CH3

OH

N

HH

H

Protons per Integral -

Trial Values

Correct Analysis Found

47

Automatic Reality Check


171360172169

Compare results with a dependable but less accurate method

– require agreement within a range

– (169+172+360+171)/5.5 = 159 vs. 173

– 173 is close enough to the alternative estimate of 159 to pass

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How well does it work?

These results need to be validated against

NMR by handExternal gold standard

Tests are ongoingResults will be available soon

49

Other Tests

Remove OutliersAnalyses that passed are screened for consistency - Outliers are removed

Special CasesIdentify and skip special casesReport an error for failed analyses

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Automation

All of these calculations are done in the ACD/Labs macro language and ChemBasicThis can then be automated with ACD/Automation ServerThe goal being:

Unattended Automated Quantitation

51

What’s Next?

Extend the Quantitation capabilities by building it into the software

If there is enough interest…

Continue to use ChemBasic and Macros to solve similar problems

Any suggestions?

52

Acknowledgements

ACD/LabsRobin MartinArvin Moser

PfizerClaude JonesTom O’ConnellPatrick WheelerShen YangWei WangHong WangTorren Peakman

53

Outline






Database Searching Tips

- Be a DB Search Guru



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Database Searching Tips

Database SearchingHighlight hit dataUsing lists to do intersecting and subtraction searchesPull hits directly into Specman for comparisonRetrieve all hits automatically before a search

56

Data Hit Highlighting

Data found is highlightedHelps locate relevant hits when scrolling through list

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Data Hit Highlighting

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Using Lists

The List menu in SpecDB is very powerfulAllows you to do all sorts of thing with multiple searches

59

List Commands

MergeIntersectSubtractDuplicateSubtract and DuplicateSubtract Current IDAdd Current ID to BSet IDsSwitchUndoLoadSave

60

Aldrich Database

35,164 records in Version 11!

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Aldrich Database Search

Here is what we know:Benzene group is presentCarbonyl is notOnly interested in chloroform spectraNo HalogensCarbon peak at 165 PPMProton peak at 5.5 PPM

62


Substructure SearchBezeneLimits list to only aromatics

List A: 25,743 recordsList B: 35,164 records

63


Duplicate ListPut result of search step 1 into B list as well.


64


Substructure SearchCarboxylLimit A list to Carboxyl and benzene containing structures


65


Subtract List A from List BReturns all structures with bezene ring, but not carboxyl group


66


Parameter SearchSearch for records with Chloroform as the solventLimit A list to records in that solvent


67


Duplicate List A to BJust in case. ☺


68


Formula SearchWe know there are no halogens

Search “F” in formula searchSubtract and Duplicate

Search “Cl” in formula searchSubtract and Duplicate

Search “Br” in formula searchSubtract and Duplicate

List A and B: 3,674 records remain

69


Carbon peak SearchPeak observed at 165 PPM

Search between 160-170 PPM

List A: 1023 recordsList B: 3674 records

70


Peak Search1H NMR Peak observed at 5.5 PPMSearch between 5 and 6 to be safe

71


Peak Search1H NMR Peak observed at 5.5 PPMSearch between 5 and 6 to be safe

List A: 158 recordsList B: 6,109 records

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Now scroll through your hits!

73



74



75

Pull Hits into Processor

Get search hits directly in Processor windowCompare hit spectrum easily to search spectrum

83

Outline






The Joe MacroWhat is possible with

Macros?



85

Joe Macro

Designed by Arvin Moser Upon special requestUtilizes Chembasic, Chembasic forms, Report Template forms and a Macro

86

Joe Macro System Files

87

How Does it Work?

User chooses to activate macroOr it is activated automatically when a spectrum is imported

User a walked through the process…

95

ChemSketch Report – Page 1

ASCI-1_A1_15_1D1H.esp

18 16 14 12 10 8 6 4 2 0 -2 -4 -6 -8Chemical Shift (ppm)

3.03

2.01

0.96

10.0

1

7.66 7.

667.

63 7.51

7.40

3.87

3.78

3.75

Acquisition Time (sec) 4.5001 Comment T.Spitzer u0002-5-15_d5xf_H1Date Jun 3 2007 Date Stamp Jun 3 2007File Name C:\Work\My Documents\Product Management\ASCI\Test_1

Data\Data_A1_400V_HSQC-DEPT\ASCI-1_A1_15_1D1HFrequency (MHz) 400.10 Nucleus 1HNumber of Transients 16 Original Points Count 49506Points Count 65536 Pulse Sequence s2pulSolvent DMSO-d6 Spectrum Offset (Hz) 2000.4858Sweep Width (Hz) 11001.10 Temperature (degree C) 29.000

1H NMR (400 MHz, DMSO-d6) δ ppm 3.78 (3 H, s), 3.86 (9 H, m), 7.40 (2 H, s), 7.51 (1 H, d, J=7.9 Hz), 7.65 (2 H, m), 10.01 (1 H, s)

22 10 2007Date:11 4 1

6

2

O15

16 5

3

17

O12

18

21

O25

1924

O7

O9

O13

20

O22

CH38

CH314

CH310

CH323

H24a

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ChemSketch Report – Page 2ASCI-1_A1_15_1D1H.esp

5.5 5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0Chemical Shift (ppm)

0

0.25

0.50

0.75

1.00

Nor

mal

ized

Inte

nsity

3.03

9.12

M01(s)

M02(m)

3.87

3.86

3.78

3.78

3.75

ASCI-1_A1_15_1D1H.esp

9.5 9.0 8.5 8.0 7.5 7.0 6.5 6.0Chemical Shift (ppm)

0

0.25

0.50

0.75

1.00

Nor

mal

ized

Inte

nsity

2.01

0.96

1.93

M03(s)

M04(d)

M05(m)

7.66 7.

667.

65

7.63

7.63 7.

517.

507.

40

97

Possibilities Abound

Macros can do wondrous thingsFrom advanced automatic processingTo wizardsTo manual processes in a specific order

98

Enter Manual Mode

99

Enter Manual Mode

100

Enter Manual Mode

Modes that are available:Integration, BaseLine, Phase, Peak Picking, Annotation, Edit Spectrum, Reference, Assignment, Multiplets, Peak Fitting.

Place this command in the middle of a macro

Macro then pauses and lets a user perform a manual operation

101

Increase your Efficiency

A macro can undoubtedly increase your efficiencyAnalyze what you do to your spectraIf there are common threads, try to macro-ize it!

102

Outline



