Contemporary computer-assisted approaches to molecular structure elucidation / Mikhail Elyashberg, Antony Williams, Kirill Blinov
- Author
- Elyashberg, Mikhail
- Published
- Cambridge : RSC Publishing, [2012]
- Copyright Date
- ©2012
- Physical Description
- xxii, 482 pages : illustrations (some color) ; 24 cm.
- Additional Creators
- Williams, Antony and Blinov, Kirill
- Series
- Contents
- Machine generated contents note: pt. I Computer-Assisted Structure Elucidation: Fundamentals -- ch. 1 General Principles of CASE Systems -- 1.1.Statement of the Problem of Structure Elucidation -- 1.2.A Molecule as a "Machine" for Coding Structural Information -- 1.3.Quantification of Structural Information -- 1.4.Straightforward CASE Strategy -- 1.5.Structure Elucidation as an Inverse Problem of Modeling -- 1.6.A Practical Approach to Solution of the CASE Problem -- 1.7.Detection of Molecular Fragments -- 1.7.1.Spectrum-Structure Correlation Method -- 1.7.2.Methods for Recognition of Large Fragments -- 1.8.Structure Generation: Descriptive Explanation -- 1.8.1.Elements of Chemical Informatics -- 1.8.2.The Generation of Structural Formulae of Isomers -- 1.8.3.Typical Structural Constraints Used in Structure Generators -- 1.8.4.Structure Verification -- References -- ch. 2 Cognitive Peculiarities of the Structure Elucidation Problem -- 2.1.Axioms and Hypotheses Based on Characteristic Spectral Features -- 2.2.Axioms and Hypotheses of 2D NMR Spectroscopy -- 2.3.Structural Hypotheses Necessary for the Assembly of Structures -- 2.4.Properties of Information Used for the Structure Elucidation -- References -- ch. 3 Methods of NMR Spectrum Prediction and Structure Verification -- 3.1.Methods of 13C NMR Chemical Shift Prediction -- 3.1.1.Additive Rules-based Methods -- 3.1.2.Fragment-based Methods -- 3.1.3.Artificial Neural Networks (ANNs) -- 3.1.4.A New Fast and Accurate Algorithm for 13C Chemical Shift Prediction -- 3.2.Prediction of 1H NMR spectra -- 3.2.1.Incremental Approach: Linear Models -- 3.2.2.Structural Database Approach: ACD/HNMR Predictor -- 3.2.3.NN and PLS Algorithms for 1H Chemical Shift Prediction -- 3.2.4.ACD/Labs NN and PLS Algorithms for 1H Chemical Shift Prediction -- 3.3.Empirical and DFT GIAO QM Methods of 13C Chemical Shifts Prediction: Competitors or Collaborators? -- 3.3.1.Data selection and Processing -- 3.3.2.Statistical Comparison of Methods -- 3.3.3.Outliers and Unusual Structures -- 3.3.4.Synergistic Interaction between Empirical and Non-Empirical Methods -- 3.4.Heteronuclear NMR Spectrum Prediction -- 3.4.1.Phosphorus-31 NMR Spectrum Prediction -- 3.4.2.Fluorine-19 NMR Spectrum Prediction -- 3.4.3.Nitrogen-15 NMR Spectrum Prediction -- 3.4.4.Other Heteronuclear NMR Predictions -- 3.5.Prediction of 2D NMR Spectra -- References -- ch. 4 Methods of Relative Stereochemistry Determination in CASE Systems -- 4.1.Selection of the Most Probable Stereoisomer Set -- 4.2.Computer-aided Determination of Relative Stereochemistry and 3D Models of Complex Organic Molecules from 2D NMR Spectra -- 4.2.1.3D Structure Optimization with Molecular Mechanics -- 4.2.2.NOE Penalty Function Calculation -- 4.2.3.Search by Running Over All Stereoisomer Structures -- 4.2.4.The Genetic Algorithm (GA) Approach -- 4.2.5.An Example of a Genetic Run and Parameter Optimization for Taxol -- 4.2.6.A Challenging Example: Brevetoxin B -- References -- pt. II Examples of Case Expert Systems -- ch. 5 CASE Expert Systems Based on 1D NMR Spectra -- 5.1.Introduction -- 5.2.The X-PERT System -- 5.2.1.Knowledge Base of X-PERT -- 5.2.2.Structural Group Analysis -- 5.2.3.Structure Generation and Verification -- 5.3.The SpecSolv Program -- 5.4.The 1D ACD/Structure Elucidator System -- 5.4.1.Operation in OCA Mode -- 5.4.2."Classic" Structure Generation -- 5.5.Expert System GENIUS -- References -- ch. 6 CASE 2D NMR-based Expert Systems -- 6.1.Introduction -- 6.2.SESAMI-C -- 6.3.SESAMI-H -- 6.4.The Expert System CISOC-SES -- 6.5.The LSD Expert System -- 6.6.The COCON Expert System -- 6.7.The LUCY Expert System -- 6.8.Stochastic Algorithms for Structure Generation in 2D NMR-Based Expert Systems -- References -- pt. III Expert System: Structure Elucidator -- ch. 7 The Knowledge Base of the Structure Elucidator CASE System -- 7.1.Structure and Content of Factual Knowledge ACD/NMR Database -- 7.2.Structural Searching Using a 13C NMR Spectrum -- 7.3.Methods of Spectral and Structural Search Optimization -- 7.4.Fragment Library -- 7.4.1.The Algorithm for Creating the Library of Fragments with 13C NMR Subspectra -- 7.4.2.Fragment Searching in the Fragment Library Using a 13C NMR Spectrum -- 7.5.Composition of Axiomatic Knowledge -- 7.5.1.Fragment Libraries -- 7.5.2.Universal Libraries -- 7.5.3.Specialized Libraries -- 7.5.4.Fragment "Visit Card" -- 7.6.Structural Filter -- 7.7.Atom Property Correlation Table (APCT) -- 7.8.Library of Typical Functional Groups -- References -- ch. 8 Primary Data Processing: Preparation, Input and Checking -- 8.1.Data used for Structure Elucidation -- 8.2.Molecular Formula -- 8.3.Molecular Connectivity Diagram (MCD) -- 8.4.NMR Spectra -- 8.4.1.1D NMR Spectra -- 8.4.2.2D NMR spectra -- 8.5.Complex Problems -- 8.5.1.When Carbon Spectra are Unavailable -- 8.5.2.When Spectral Data is not Sufficient to Elucidate Structures -- 8.6.Checking MCD for Consistency -- 8.6.1.Forming the MCD -- 8.6.2.Checking MCD for Consistency -- 8.7.Fuzzy Structure Generation -- References -- ch. 9 Approaches to Algorithmic Structure Elucidation -- 9.1.Introduction -- 9.2.Functional Scheme of the System -- 9.2.1.System Operation with 1D NMR Spectra -- 9.2.2.Molecular Structure Elucidation from 2D NMR Spectra -- 9.3.How Does the System Work? -- 9.3.1.Utilization of 1D NMR Spectra -- 9.3.2.Application of 2D NMR Data Analysis -- 9.4.Examples of Structure Elucidation in the Common Mode -- 9.5.Examples of Structure Elucidation in Fragment Mode -- 9.5.1.Azadirachtin -- 9.5.2.Cycloshermilamine D -- 9.5.3.Lyngbyabellin A -- 9.5.4.Paradisin C -- 9.6.Utilization of Both UFs and FFs -- 9.6.1.Apramide G -- 9.6.2.Hetcochlorin -- 9.7.Application of a User Database for the Structure Elucidation of Challenging Problems -- 9.7.1.Creating a User Database -- 9.7.2.Solving Challenging Problems -- 9.8.Elucidation of Symmetric and Ionic Structures -- 9.9.Challenges for Empirical and GIAO DFT NMR Prediction -- References -- ch. 10 The Challenge of Non-Standard Spectral Responses and the Role of Fuzzy Structure Generation -- 10.1.Examples of Successful Removal of Contradictions -- 10.2.Resolving Contradictions in More Complicated Cases -- 10.3.Solving Problems Using FSG -- 10.3.1.Modes of FSG -- 10.3.2.The Strategy of Applying FSG -- 10.3.3.Problem Solution using FSG in the Common Mode -- 10.3.4.Problem Solution using FSG in the Fragment Mode -- 10.4.Is There an Alternative to FSG? -- 10.5.FSG as an Analytical Tool -- References -- ch. 11 Challenging Structure Elucidator -- 11.1.Structure Elucidation of a Degradant of Cryptospirolepine -- 11.2.Solution of a Cryptolepine Family "Puzzle" -- 11.3.Structure Elucidation of Two Unexpected Reaction Products in a Reaction of an α, β-Unsaturated Pyruvates -- 11.4.CASE Application for Identification of Drug Impurities in Mixture -- 11.4.1.Structure Elucidation and Quantification -- 11.5.Structure Elucidation of Crizotinib -- References -- ch. 12 Structural Revisions of Natural Products with the Aid of the Structure Elucidator System -- 12.1.Introduction -- 12.2.Examples of Structure Revision Using an Expert System -- 12.2.1.Revision of Structures by Reinterpretation of Experimental Data -- 12.2.2.Revision of Structures with Application of Chemical Synthesis -- 12.3.Revision of Structures by the Re-examination of 2D NMR Data -- 12.4.Structure Selection on the Basis of Spectrum Prediction -- 12.5.Discussion -- References -- ch. 13 Comparison of Systematic CASE Systems versus a Traditional Approach -- 13.1.Introduction -- 13.2.Problems Solved in the Common Mode of the StrucEluc Expert System -- 13.3.Problems Solved in Fragment Mode -- 13.4.The Combined Application of Empirical and Non-Empirical Methods of Chemical Shift Assignment -- 13.5.Elucidating "Undecipherable" Chemical Structures Using Computer-Assisted Structure Elucidation Approaches -- 13.6.Discussion -- References -- ch. 14 An Evaluation of the Performance of the Structure Elucidator System -- 14.1.Time Required to Solve Problem -- 14.2.Efficiency of Filtering Generated Structures -- 14.3.Evaluation of Methods for Selection of the Most Probable Structure -- References -- ch. 15 Conclusions.
- Subject(s)
- ISBN
- 1849734321
9781849734325 - Bibliography Note
- Includes bibliographical references and index.
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