New Developments in NMR

By: Antony Williams, Mikhail E Elyashberg, Kirill Blinov

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Hardcover | 30 November 2011

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504 Pages

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Computer-Assisted Structure Elucidation (CASE) systems are a combination of software algorithms and tools to support and enable chemists and spectroscopists engaged in the process of molecular structure elucidation via the analysis of spectroscopic data. These expert systems dramatically reduce the time associated with structure elucidation and improve the reliability of the results. Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation describes the principles on which these expert systems for spectroscopic structure elucidation are based and concisely explains the algorithmic concepts behind the programs. The authors use their own personal experiences in the development of the Structure Elucidator (StrucEluc) CASE software system to discuss the present state-of-the-art in computer-assisted structure elucidation. Scientists that are presently using CASE systems will be interested in the algorithms and modern approaches and for organizations that are currently using the StrucEluc platform the book is designed to help researchers understand the strategies behind CASE as well as details regarding the StrucEluc platform. For scientists that have never used CASE systems they will now have access to all necessary information to understand CASE systems for mastering this new and very effective approach to structure elucidation. The authors overall goal is writing this book is to produce the 'must read' definitive text that will represent the results of decades of work to develop computer-assisted structure elucidation software systems. CASE systems are now powerful software tools commonly outperforming and correcting human interpretations of data. This book will also provide an historical perspective of the work of the founding fathers of the technique and identify the challenges that have been overcome to produce modern CASE systems.

Industry Reviews

"Computer-assisted structure elucidation (CASE) aims to provide users in chemistry, molecular biology, or other areas dealing with structures of small molecules with suggestions on the structural identity of molecules based on spectroscopic, chromatographic and other boundary information. With "Contemporary computer-assisted approaches to molecular structure elucidation", Mikhail Elyashberg, Anthony Williams and Kirill Blinov, all world-renowned experts on the topic, have recently written a normative standard text-book on the topic. Published by RSC publishing in 2012 and on 481 pages, the book provides a comprehensive overview on computer-assisted structure elucidation. The book is divided into three parts (Basics of CASE, Overview of CASE systems, and a comprehensive discussion of their own system, Structure Elucidator) comprised of overall 14 chapters. As the authors point out, the CASE process can be reduced to logically interfering `the most probable structural hypothesis from a set of statements reflecting the interrelation between a spectrum and structure'. Given that every human expert in structure elucidation will be biased by his or her own education, history of certain compound classes worked on, or types of spectroscopy used, CASE systems can be incredibly valuable by suggesting solutions to the structure elucidation problem outside of our range of experience. The book delivers what the title promises. I have been working on CASE systems in the last 15 years and wrote a number of reviews on the topic. This is clearly the most comprehensive book on the topic on the market and generally a valuable resource for anyone working in the area of structure elucidation of small molecules." -- C. Steinbeck * Amazon review *

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Non-Fiction Science Chemistry Analytical Chemistry Magnetic Resonance

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Non-Fiction Science Chemistry Analytical Chemistry Magnetic Resonance

Acknowledgments	p. xxi
Computer-Assisted Structure Elucidation: Fundamentals
General Principles of CASE Systems	p. 3
Statement of the Problem of Structure Elucidation	p. 3
A Molecule as a "Machine" for Coding Structural Information	p. 5
Quantification of Structural Information	p. 8
Straightforward CASE Strategy	p. 9
Structure Elucidation as an Inverse Problem of Modeling	p. 12
A Practical Approach to Solution of the CASE Problem	p. 14
Detection of Molecular Fragments	p. 17
Spectrum-Structure Correlation Method	p. 17
Methods for Recognition of Large Fragments	p. 24
Structure Generation: Descriptive Explanation	p. 25
Elements of Chemical Informatics	p. 25
The Generation of Structural Formulae of Isomers	p. 28
Typical Structural Constraints Used in Structure Generators	p. 30
Structure Verification	p. 31
References	p. 33
Cognitive Peculiarities of the Structure Elucidation Problem	p. 37
Axioms and Hypotheses Based on Characteristic Spectral Features	p. 38
Axioms and Hypotheses of 2D NMR Spectroscopy	p. 42
Structural Hypotheses Necessary for the Assembly of Structures	p. 45
Properties of Information Used for the Structure Elucidation	p. 47
References	p. 49
Methods of NMR Spectrum Prediction and Structure Verification	p. 50
Methods of ¹³C NMR Chemical Shift Prediction	p. 52
Additive Rules-based Methods	p. 52
Fragment-based Methods	p. 53
Artificial Neural Networks (ANNs)	p. 56
A New Fast and Accurate Algorithm for ¹³C Chemical Shift Prediction	p. 67
Prediction of 1H NMR spectra	p. 82
Incremental Approach: Linear Models	p. 82
Structural Database Approach: ACD/HNMR Predictor	p. 83
NN and PLS Algorithms for ¹H Chemical Shift Prediction	p. 86
ACD/Labs NN and PLS Algorithms for ¹H Chemical Shift Prediction	p. 89
Empirical and DFT GIAO QM Methods of ¹³C Chemical Shifts Prediction: Competitors or Collaborators?	p. 90
Data selection and Processing	p. 93
Statistical Comparison of Methods	p. 94
Outliers and Unusual Structures	p. 99
Synergistic Interaction between Empirical and Non-Empirical Methods	p. 101
Heteronuclear NMR Spectrum Prediction	p. 102
Phosphorus-31 NMR Spectrum Prediction	p. 102
Fluorine-19 NMR Spectrum Prediction	p. 104
Nitrogen-15 NMR Spectrum Prediction	p. 104
Other Heteronuclear NMR Predictions	p. 106
Prediction of 2D NMR Spectra	p. 106
References	p. 107
Methods of Relative Stereochemistry Determination in CASE Systems	p. 112
Selection of the Most Probable Stereoisomer Set	p. 113
Computer-aided Determination of Relative Stereochemistry and 3D Models of Complex Organic Molecules from 2D NMR Spectra	p. 122
3D Structure Optimization with Molecular Mechanics	p. 123
NOE Penalty Function Calculation	p. 124
Search by Running Over All Stereoisomer Structures	p. 126
The Genetic Algorithm (GA) Approach	p. 127
An Example of a Genetic Run and Parameter Optimization for Taxol	p. 129
A Challenging Example: Brevetoxin B	p. 134
References	p. 136
Examples of Case Expert Systems
CASE Expert Systems Based on 1D NMR Spectra	p. 141
Introduction	p. 141
The X-PERT System	p. 142
Knowledge Base of X-PERT	p. 142
Structural Group Analysis	p. 144
Structure Generation and Verification	p. 145
The SpecSolv Program	p. 146
The ID ACD/Structure Elucidator System	p. 149
Operation in OCA Mode	p. 150
"Classic" Structure Generation	p. 152
Expert System GENIUS	p. 154
References	p. 160
CASE 2D NMR-based Expert Systems	p. 162
Introduction	p. 162
SESAMI-C	p. 164
SESAMI-H	p. 169
The Expert System CISOC-SES	p. 172
The LSD Expert System	p. 179
The COCON Expert System	p. 183
The LUCY Expert System	p. 188
Stochastic Algorithms for Structure Generation in 2D NMR-Based Expert Systems	p. 190
References	p. 191
Expert System: Structure Elucidator
The Knowledge Base of the Structure Elucidator CASE System	p. 197
Structure and Content of Factual Knowledge ACD/NMR Database	p. 198
Structural Searching Using a ¹³C NMR Spectrum	p. 201
Methods of Spectral and Structural Search Optimization	p. 203
Fragment Library	p. 205
The Algorithm for Creating the Library of Fragments with ¹³C NMR Subspectra	p. 206
Fragment Searching in the Fragment Library Using a ¹³C NMR Spectrum	p. 210
Composition of Axiomatic Knowledge	p. 212
Fragment Libraries	p. 212
Universal Libraries	p. 213
Specialized Libraries	p. 213
Fragment "Visit Card"	p. 214
Structural Filter	p. 215
Atom Property Correlation Table (APCT)	p. 216
Library of Typical Functional Groups	p. 219
References	p. 219
Primary Data Processing: Preparation, Input and Checking	p. 220
Data used for Structure Elucidation	p. 220
Molecular Formula	p. 221
Molecular Connectivity Diagram (MCD)	p. 222
NMR Spectra	p. 223
1D NMR Spectra	p. 224
2D NMR spectra	p. 227
Complex Problems	p. 233
When Carbon Spectra are Unavailable	p. 234
When Spectral Data is not Sufficient to Elucidate Structures	p. 238
Checking MCD for Consistency	p. 241
Forming the MCD	p. 241
Checking MCD for Consistency	p. 243
Fuzzy Structure Generation	p. 250
References	p. 251
Approaches to Algorithmic Structure Elucidation	p. 253
Introduction	p. 253
Functional Scheme of the System	p. 254
System Operation with 1D NMR Spectra	p. 256
Molecular Structure Elucidation from 2D NMR Spectra	p. 257
How Does the System Work?	p. 263
Utilization of 1D NMR Spectra	p. 264
Application of 2D NMR Data Analysis	p. 265
Examples of Structure Elucidation in the Common Mode	p. 269
Examples of Structure Elucidation in Fragment Mode	p. 271
Azadirachtin	p. 271
Cycloshermilamine D	p. 273
Lyngbyabellin A	p. 276
Paradisin C	p. 279
Utilization of Both UFs and FFs	p. 280
Apramide G	p. 280
Hetcochlorin	p. 283
Application of a User Database for the Structure Elucidation of Challenging Problems	p. 286
Creating a User Database	p. 288
Solving Challenging Problems	p. 290
Elucidation of Symmetric and Ionic Structures	p. 292
Challenges for Empirical and GIAO DFT NMR Prediction	p. 294
References	p. 297
The Challenge of Non-Standard Spectral Responses and the Role of Fuzzy Structure Generation	p. 300
Examples of Successful Removal of Contradictions	p. 302
Resolving Contradictions in More Complicated Cases	p. 308
Solving Problems Using FSG	p. 315
Modes of FSG	p. 316
The Strategy of Applying FSG	p. 320
Problem Solution using FSG in the Common Mode	p. 324
Problem Solution using FSG in the Fragment Mode	p. 332
Is There an Alternative to FSG?	p. 336
FSG as an Analytical Tool	p. 342
References	p. 343
Challenging Structure Elucidator	p. 346
Structure Elucidation of a Degradant of Cryptospirolepine	p. 346
Solution of a Cryptolepine Family "Puzzle"	p. 349
Structure Elucidation of Two Unexpected Reaction Products in a Reaction of an ,ß-Unsaturated Pyruvates	p. 354
CASE Application for Identification of Drug Impurities in Mixture	p. 356
Structure Elucidation and Quantification	p. 357
Structure Elucidation of Crizotinib	p. 362
References	p. 364
Structural Revisions of Natural Products with the Aid of the Structure Elucidator System	p. 366
Introduction	p. 366
Examples of Structure Revision Using an Expert System	p. 367
Revision of Structures by Reinterpretation of Experimental Data	p. 368
Revision of Structures with Application of Chemical Synthesis	p. 384
Revision of Structures by the Re-examination of 2D NMR Data	p. 394
Structure Selection on the Basis of Spectrum Prediction	p. 407
Discussion	p. 410
References	p. 416
Comparison of Systematic CASE Systems versus a Traditional Approach	p. 419
Introduction	p. 419
Problems Solved in the Common Mode of the StrucEluc Expert System	p. 422
Problems Solved in Fragment Mode	p. 427
The Combined Application of Empirical and Non-Empirical Methods of Chemical Shift Assignment	p. 437
Elucidating "Undecipherable" Chemical Structures Using Computer-Assisted Structure Elucidation Approaches	p. 440
Discussion	p. 450
References	p. 450
An Evaluation of the Performance of the Structure Elucidator System	p. 453
Time Required to Solve Problem	p. 453
Efficiency of Filtering Generated Structures	p. 454
Evaluation of Methods for Selection of the Most Probable Structure	p. 457
References	p. 462
Conclusions	p. 463
Subject Index	p. 469
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New Developments in NMR

At a Glance

Hardcover

Industry Reviews

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