Modern NMR Approaches To The Structure Elucidation of Natural Products Volume 1: Instrumentation and Software

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2 Modern NMR Approaches To The Structure Elucidation of Natural Products Volume 1: Instrumentation and Software

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4 Modern NMR Approaches to the Structure Elucidation of Natural Products Volume 1: Instrumentation and Software Edited by Antony J. Williams ChemConnector Inc., USA Gary E. Martin Merck Research Laboratories, USA and David Rovnyak Bucknell University, USA

5 Print ISBN: PDF eisbn: A catalogue record for this book is available from the British Library r The Royal Society of Chemistry 2016 All rights reserved Apart from fair dealing for the purposes of research for non-commercial purposes or for private study, criticism or review, as permitted under the Copyright, Designs and Patents Act 1988 and the Copyright and Related Rights Regulations 2003, this publication may not be reproduced, stored or transmitted, in any form or by any means, without the prior permission in writing of The Royal Society of Chemistry or the copyright owner, or in the case of reproduction in accordance with the terms of licences issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of the licences issued by the appropriate Reproduction Rights Organization outside the UK. Enquiries concerning reproduction outside the terms stated here should be sent to The Royal Society of Chemistry at the address printed on this page. The RSC is not responsible for individual opinions expressed in this work. The authors have sought to locate owners of all reproduced material not in their own possession and trust that no copyrights have been inadvertently infringed. Published by The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF, UK Registered Charity Number Visit our website at Printed in the United Kingdom by CPI Group (UK) Ltd, Croydon, CR0 4YY, UK

6 AJW dedicates this volume to his mother Eirlys, his sister Rae and his sons Taylor and Tyler. DR is grateful to Jennifer, Henry and Holly for their support. GEM dedicates this volume to his wife Linda and his sons Joshua and Casey.

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8 Contents Part 1 Hardware Chapter 1 New Directions in Natural Products NMR: What Can We Learn by Examining How the Discipline Has Evolved? 3 Gary E. Martin, Antony J. Williams and David Rovnyak References 22 Chapter 2 NMR Magnets: A Historical Overview 26 Razvan Teodorescu 2.1 Introduction Field Strength and NMR Sensitivity and Resolution Magnetic Field Homogeneity Magnetic Field Stability Minimizing Stray Magnetic Fields Mitigating External Magnetic Field Disturbances Reducing the Physical Size and Weight Cryogen Conservation and Future Outlook 34 Acknowledgements 37 References 37 Chapter 3 Small-volume NMR: Microprobes and Cryoprobes 38 Clemens Anklin 3.1 Introduction Theoretical and Practical Aspects of Small-volume Probes 39 Modern NMR Approaches To The Structure Elucidation of Natural Products, Volume 1: Instrumentation and Software Edited by Antony J. Williams, Gary E. Martin and David Rovnyak r The Royal Society of Chemistry 2016 Published by the Royal Society of Chemistry, vii

9 viii Contents 3.3 Conventional Small-volume Probes Cryogenically Cooled Small-volume Probe 51 References 56 Chapter 4 Cryogenically Cooled NMR Probes: a Revolution for NMR Spectroscopy 58 Kimberly L. Colson 4.1 Introduction Historical Perspective Sensitivity Impact on Samples of Limited Supply Experimental Options Expand Magnetic Resonance Imaging Future Developments Conclusion 68 Acknowledgements 68 References 68 Chapter 5 Application of LC-NMR to the Study of Natural Products 71 Manfred Spraul, Ulrich Braumann, Markus Godejohann, Cristina Daolio and Li-Hong Tseng 5.1 Introduction LC-NMR Technology On-flow LC-NMR Direct Stop-flow Loop Collection Post-column Solid-phase Extraction (LC-SPE-NMR) Integration of Mass Spectrometric Detection of Peaks of Interest for LC-(SPE)-NMR Cryogenic Probes and Their Advantages for LC-(SPE)-NMR SPE-LC-SPE-NMR/MS Application Examples from Natural Product-related Samples Integration of Metabonomics Routines and LC-SPE-NMR/MS Example of the Total Analysis Concept SPE-LC-SPE-NMR/MS Conclusion 91 References 92

10 Contents Chapter 6 Application of Non-uniform Sampling for Sensitivity Enhancement of Small-molecule Heteronuclear Correlation NMR Spectra 93 Melissa R. Palmer, Riju A. Gupta, Marci E. Richard, Christopher L. Suiter, Tatyana Polenova, Jeffrey C. Hoch and David Rovnyak ix 6.1 Exponential Non-uniform Sampling and Sensitivity Signal Enhancement by Non-uniform Versus Uniform Sampling Signal Enhancement of an Exponentially Decaying Signal by NUS Evaluating NUS Weighting Functions Validation Using Linear Transforms Application of NUS Enhancement to 2D Heteronuclear Correlations Critique and Outlook Methods and Materials 114 Acknowledgements 115 References 115 Chapter 7 NMR Spectroscopy Using Several Parallel Receivers 119 Ray Freeman and Ēriks Kupče 7.1 Introduction Multiple Receivers PANACEA Structure of Small Molecules Long-range Couplings Fast Measurements Biochemical Samples Conclusion 142 Acknowledgements 143 References 143 Part 2 Data Processing and Informatics Chapter 8 1 H-NMR Spectroscopy: The Method of Choice for the Dereplication of Natural Product Extracts 149 John Blunt, Murray Munro and Antony J. Williams 8.1 Natural Product Chemistry 149

11 x Contents 8.2 Dereplication Concept and Definitions Why Dereplication is Necessary Approaches to Dereplication Time, Scale, Cost Existing Methodologies Databases Taxonomic Information Biological Data UV Spectral Data Mass Spectrometric Data H-NMR Data Pattern-matching Approach to Dereplication Searchable 1 H-NMR Features and the MarinLit Database Development of the AntiMarin Database Extension of 1 H NMR Searching to the Dictionary of Natural Products Why 1 H-NMR Dereplication is Discriminatory Searchable Fields and 1 H-NMR Dereplication Data Entry Examples of the 1 H NMR Approach to Dereplication H-NMR Pattern Matching Search Strategies Chemical Shift-matching Approach to Dereplication The ACD/Labs NMR Database MarinLit and AntiBase Databases and 13 C Chemical Shift Matching The Chemical Shift-matching Databases Recognition of New Compounds: Arbiter of Novelty The Costs Associated With Dereplication Conclusion 182 References 183 Chapter 9 Application of Computer-assisted Structure Elucidation (CASE) Methods and NMR Prediction to Natural Products 187 M. E. Elyashberg, Antony J. Williams and K. A. Blinov 9.1 Introduction 187

12 Contents 9.2 Axiomatic Theory of Structure Elucidation Axioms and Hypotheses Based on Characteristic Spectral Features Axioms and Hypotheses of 2D-NMR Spectroscopy Structural Hypotheses Necessary for the Assembly of Structures General Principles of the CASE Systems Methods of NMR Spectral Prediction Expert System Structure Elucidator Knowledgebase of the StrucEluc System Molecular Connectivity Diagram (MCD) Structure Generation and Verification Structure Generation in the Presence of NSCs Determination of Relative Stereochemistry of Identified Structures Challenging StrucEluc Structure Elucidation of a Cryptospirolepine Degradant Solution of a Cryptolepine Family Puzzle Systematic CASE Approach Versus Traditional Methods Advantages of the CASE Approach in the Creation and Verification of Structural Hypotheses Example CASE as an Aid to Avoid Pitfalls During Structure Elucidation Performance and Limitations of StrucEluc Conclusion 238 References 239 xi Chapter 10 Multi-dimensional Spin Correlations by Covariance NMR 244 David A. Snyder and Rafael Brüschweiler 10.1 Introduction Theory of Covariance NMR Homonuclear NMR via Indirect and Doubly Indirect Covariance Unsymmetrical and Generalized Indirect Covariance 251

13 xii Contents 10.5 Computational Aspects Applications of Covariance NMR to Natural Product Structure Elucidation NMR Analysis of Mixtures of Natural Products Conclusion and Outlook 255 Acknowledgements 256 References 256 Chapter 11 Future Approaches for Data Processing 259 Kirill Blinov and Antony J. Williams 11.1 General Description of the Structure Elucidation Process General Features of Natural Product Spectra Common Problems with Spectral Data Missing Signals Signal Overlap Extra Signals Main Approaches for Improved Processing Improving Spectral Quality or Reducing the Acquisition Time Peak Picking Combining Information from Different Spectra. Unsymmetrical Indirect Covariance Automated Data Processing for Structure Identification Conclusion 274 References 275 Chapter 12 NMR: The Emerging New Analytical Tool for Nutraceutical Analysis 277 Kimberly L. Colson, Jimmy Yuk and Christian Fischer 12.1 Introduction Nutraceuticals Unique Strengths of NMR Highly Complex Mixtures and the Metabolomics Approach Sample Evaluation Procedures Example Bruker SOP Considerations Used for Nutraceutical Analysis Selection of Experiments and NMR Optimization 288

14 Contents xiii 12.3 Analysis Methods Targeted Methods of Qualitative and Quantitative Assessment: Identity, Purity Strength, and Composition Non-targeted NMR Approaches of Qualitative Assessment Conclusion 302 References 302 Chapter 13 Prospects and Challenges in Molecular Structure Identification by Atomic Force Microscopy 306 Bruno Schuler, Fabian Mohn, Leo Gross, Gerhard Meyer and Marcel Jaspars 13.1 Structure Determination Using Spectroscopic Methods Atomic Resolution on Molecules with Atomic Force Microscopy Experimental Setup Sample and Tip Preparation Amount of Material Needed Origin of Atomic Contrast AFM-aided Structure Determination Polycyclic Aromatic Hydrocarbons Cephalandole A Breitfussin A Conclusion and Outlook 319 References 320 Subject Index 321

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