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Modern NMR Approaches to the Structure Elucidation of Natural Products

Modern NMR Approaches to the Structure Elucidation of Natural Products

Antony Williams | Gary Martin | David Rovnyak

(2016)

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Abstract

The Ghanian plant Cryptolepis sanguinolenta is the source of a series of fascinating indoloquinoline alkaloids. The most unusual member of this alkaloid series was initially proposed to be a spiro nonacyclic structure, named cryptospirolepine, and was elucidated in 1993 based on the technologies available at that time. There were, however, several annoying attributes to the structure that bothered analysts for the ensuing 22 years. During the two decades that followed the initial work there have been enormous developments in NMR technology. Using new experimental approaches, specifically homodecoupled 1,1- and 1,n-HD-ADEQUATE NMR experiments developed in 2014, the structure of only a 700 µg sample of cryptospirolepine has been revised and is shown on the cover of this volume. The confluence of the NMR technological and methodological advances that allowed the revision of the structure of cryptospirolepine using a submilligram sample seems a fitting example for this book, which is dedicated to the NMR characterization of various classes of natural products.

Volume 2 considers data processing and algorithmic based analyses tailored to natural product structure elucidation and reviews the application of NMR to the analysis of a series of different natural product families including marine natural products, terpenes, steroids, alkaloids and carbohydrates. Volume 1 discusses contemporary NMR approaches including optimized and future hardware and experimental approaches to obtain both the highest quality and most appropriate spectral data for analysis. These books, bringing together acknowledged experts, uniquely focus on the combination of experimental approaches and modern hardware and software applied to the structure elucidation of natural products. The volumes will be an essential resource for NMR spectroscopists, natural product chemists and industrial researchers working on natural product analysis or the characterization of impurities and degradation products of pharmaceuticals that can be as scarce as natural product samples.


Antony J. Williams graduated with a BSc and PhD in chemistry from the University of Liverpool and University of London respectively. He subsequently became a Post-doctoral Fellow at the National Research Council in Ottawa and then an NMR Facility Director at the University of Ottawa. He has also worked as an NMR Technology Leader at Eastman-Kodak Company in Rochester and held a number of positions, including Chief Science Officer, at ACD/Labs. In 2007, he established ChemZoo, Inc and became host of ChemSpider, one of the primary internet portals for chemistry. ChemSpider was acquired by the Royal Society of Chemistry (RSC) in 2009 and Dr Williams is currently Vice-President of Strategic Development at the RSC. He presently holds an adjunct position at UNC-Chapel Hill and has been a member of the ACS since 1996.

Gary E. Martin graduated with a BS in Pharmacy in 1972 from the University of Pittsburgh and a PhD in Pharmaceutical Sciences from the University of Kentucky in 1975, specializing in NMR spectroscopy. He was a Professor at the University of Houston from 1975 to 1989, assuming the position of Section Head responsible for US NMR spectroscopy at Burroughs Wellcome, Co. in Research Triangle Park, NC, eventually being promoted to the level of Principal Scientist. In 1996 he assumed a position at what was initially the Upjohn Company in Kalamazoo, MI and held several positions there through 2006 by which time he was a Senior Fellow at what was then Pfizer, Inc. In 2006 he assumed a position as a Distinguished Fellow at Schering-Plough responsible for the creation of the Rapid Structure Characterization Laboratory. He is presently a Distinguished Fellow at Merck Research Laboratories.

David Rovnyak earned his BS from the University of Richmond, and his PhD studying high resolution NMR of quadrupolar nuclei at MIT. He transitioned to solution phase biomolecular NMR in postdoctoral work at the Harvard Medical School before joining the Chemistry Department at Bucknell University, where he has been recognized with Bucknell's Excellence in Teaching Award. He currently serves as Assistant Editor of Concepts in Magnetic Resonance. His lab pursues interdisciplinary topics in biophysical research including bile acid aggregation, methods in protein NMR, nonuniform sampling and small molecule profiling.


Table of Contents

Section Title Page Action Price
Cover Cover
Contents ix
Foreword v
Dedication viii
Part 1 1
Chapter 1 Application of the Nuclear Overhauser Effect to the Structural Elucidation of Natural Products 3
1.1 The Historical Origin of the Term ‘‘Nuclear Overhauser Effect 3
1.2 The Theory Behind the NOE 6
1.3 Multispin Systems 15
1.4 The Kinetic NOE 16
1.5 Transient NOE 17
1.6 ROE and ROESY 18
1.7 Scalar Couplings–Zero-quantum Filters 21
1.8 NOE Experiments for the Structural Elucidation of Dimeric Compounds 24
1.9 Fully Quantitative NOE in Small Molecules 26
1.10 NOE Deconvolution–NAMFIS 30
1.11 Conclusions 35
References 36
Chapter 2 Assigning Molecular Configuration by Nuclear Magnetic Resonance 39
2.1 Assigning Relative Configuration 39
2.1.1 Coupling Constants and NOEs 40
2.1.2 Acetonides 43
2.1.3 J-Based Analysis–The Murata Method 44
2.1.4 Universal Database 51
2.1.5 Computational Methods 55
2.1.6 Residual Chemical Shift Anisotropy 56
2.2 Assigning Absolute Configuration 60
2.2.1 Chiral Anisotropic Reagents 60
2.3 Conclusions 66
References 68
Chapter 3 Nuclear Magnetic Resonance Experiments Applicable to the Elucidation and Characterization of Nitrogenous Natural Products: 1H-15N Heteronuclear Shift Correlation Methods 71
3.1 1H-15N Direct and Long-range Heteronuclear Shift Correlation 71
3.2 15N Chemical Shift Referencing 72
3.3 The Range of 15N Chemical Shifts 73
3.4 15N Pulse Widths 74
3.5 15N Chemical Shift Prediction 76
3.5.1 Validating 15N Chemical Shift Prediction 80
3.5.2 Setting F1 Spectral Windows 82
3.5.3 Structure Verification using a 15N Content Database 83
3.5.4 Enhancing 15N Chemical Shift Prediction with a ‘‘User-trained\" Database 83
3.6 Computer-assisted Structure Elucidation–The Impact of 15N Data 84
3.7 1JNH and nJNH Coupling Constants 86
3.8 1H-15N Results Obtained Using Various Experiments 86
3.8.1 1H-15N Experiments Employing an Initial 1JNH Magnetization Transfer 87
3.8.2 1H-15N Experiments Employing an Initial nJNH Magnetization Transfer 91
3.8.3 1H-15N HSQMBC 95
3.8.4 1H-15N HSQMBC-TOCSY: A Hyphenated Long-range 1H-15N Experiment 98
3.8.5 Triple-resonance 1H-15N Experiments 107
3.9 Conclusions 113
References 113
Chapter 4 Application of Residual Dipolar Couplings to the Structural Analysis of Natural Products 117
4.1 Introduction 117
4.2 Alignment Media 130
4.3 The Nature of the Alignment Process 142
4.4 How RDCs are Measured 143
4.5 Data Analysis–How the RDCs are used in the Structural Analysis of Small Molecules 148
4.5.1 Possible Scenarios 148
4.5.2 How to Manage Experimental Uncertainties in RDC Analysis 153
4.5.3 The Conformational Problem 156
4.5.4 How to Handle Symmetrical Rotors 158
4.5.5 Software 159
4.6 RDCs in the Structural Elucidation of Natural Products 159
4.6.1 Dimeric Products 166
4.7 Conclusions 172
References 172
Chapter 5 Applications of High-resolving Power, High-accuracy Mass Spectrometry for the Structural Elucidation of Natural Products 177
5.1 Introduction 177
5.1.1 Mass Spectrometry for the Structural Elucidation of Unknowns 177
5.1.2 Brief Description of FT-ICR 185
5.2 Examples from Literature 190
5.2.1 Ultra-high Resolving Power to Separate the Isotopic Fine Structures 190
5.2.2 Study of Biosynthesis Processes by Measuring Stable Isotopic-labeled Precursors using FT-ICR MS 194
5.2.3 Metabolite Profiling of Triterpene Saponins by Combined Accurate Mass Measurement and MSn Experiments using LC FT-ICR MS 195
5.3 Conclusions 197
References 197
Chapter 6 Current Pulse Sequence Developments in Small-molecule Nuclear Magnetic Resonance Spectroscopy 199
6.1 Introduction 199
6.2 Fast NMR 202
6.3 Pure Shift NMR 206
6.3.1 The ZS Experiment 209
6.3.2 Sensitivity, Strong Coupling Effects, and Spectral Quality 210
6.3.3 ZS Applications 216
6.3.4 Implementing Homodecoupling in 1D and 2D NMR Experiments 218
6.4 Perfect NMR 227
6.4.1 Perfect Spin-echo 228
6.4.2 Using ZQFs 233
6.5 Ultra-long-range Correlation NMR 234
6.5.1 Long-range HSQMBC 236
6.5.2 HSQMBC-TOCSY 237
6.5.3 ADEQUATE 240
6.6 Future Perspectives 243
Acknowledgments 244
References 244
Part 2 251
Chapter 7 Terpenes: Mono-, Sesqui-, and Higher Terpenes 253
7.1 Introduction 253
7.2 Types of Terpenes and Related Compounds 254
7.3 Basic Approach to Terpene Structure Elucidation by NMR Spectroscopy 257
7.4 Avoiding Determining the Wrong Structure 261
7.5 Specialized Techniques that are Useful for Different Types of Terpenes 267
7.6 Conclusions 272
Acknowledgments 272
References 273
Chapter 8 Nuclear Magnetic Resonance of Steroids 275
8.1 Prologue 275
8.2 An Introduction to Steroids 275
8.3 Modern and ‘‘Rare\" NMR Methods in the Steroid Field 284
8.3.1 Recent General NMR Developments 284
8.3.2 Covariance NMR and Steroids 284
8.3.3 The HSQC-TOCSY Experiment 287
8.3.4 13C-Detected Experiments 287
8.3.5 1D and High-resolution 1D 1H Methods 288
8.3.6 19F NMR 290
8.3.7 Residual Dipolar Couplings 294
8.4 Considerations 298
8.5 Conclusions 307
Acknowledgments 308
References 308
Chapter 9 Nuclear Magnetic Resonance Experiments Applicable to the Elucidation and Characterization of Alkaloid Structures Part I: Direct 1H-13C Heteronuclear Shift Correlation and Establishing Contiguous Protonated Carbon Spin Systems 315
9.1 Introduction 315
9.2 ‘‘First-tier\" NMR Methods for Alkaloid Structure Characterization 316
9.2.1 Sample Preparation 317
9.2.2 Probe Selection 317
9.2.3 Parameter Choices 318
9.3 Acquiring NMR Spectra 319
9.4 1D Reference Spectra 319
9.5 Fundamental or ‘‘First-tier\" 2D NMR Spectra 322
9.5.1 Conventional HSQC 322
9.5.2 Multiplicity-edited HSQC 324
9.5.3 Incorporating BIRD-based Homonuclear Decoupling in the HSQC Experiment: PS-HSQC 324
9.5.4 Summary of One-bond Heteronuclear Correlation Methods 327
9.6 Intentionally Folding HSQC Spectra in Limited-sample Situations 329
9.7 Non-uniform Sampling 332
9.8 Long-range Heteronuclear Shift Correlation 335
9.8.1 HMBC 335
9.8.2 LR-HSQMBC 338
9.9 Defining the Proton-Proton Connectivity Network 342
9.9.1 COSY and TOCSY Spectra 342
9.9.2 HSQC-TOCSY Spectra 346
9.9.3 HSQMBC-COSY and HSQMBC-TOCSY Spectra 349
9.9.4 Strategy for Employing Hyphenated 2D Experiments 354
References 354
Chapter 10 Nuclear Magnetic Resonance Experiments Applicable to the Elucidation and Characterization of Alkaloid Structures Part II: Advanced Techniques for the Identification of Adjacent Carbons Using H2BC, 1,1-ADEQUATE, and Variants 358
10.1 Identification of Adjacent Carbons Using H2BC and 1,1-ADEQUATE Data 358
10.1.1 Identification of Adjacent Protonated Carbons Using the H2BC Experiment 359
10.1.2 Identifying Adjacent Carbons Using 1,1- and 1,1-HD-ADEQUATE 361
10.2 1,n-ADEQUATE and Advanced Variants 371
10.2.1 1,n-ADEQUATE 373
10.2.2 1,n-HD-ADEQUATE 374
10.2.3 Edited 1,n-HD-ADEQUATE 378
10.3 Examples of the Application of Advanced NMR Methods in Structure Elucidation Studies 380
10.3.1 Staurosporine–Is the Crew's Rule Obsolete? 383
10.3.2 Cryptospirolepine–Resolution of a Long-standing Structural Ambiguity Using 1,1- and 1,n-HD-ADEQUATE Spectra 386
10.3.3 Eudistidine-C 397
10.4 Conclusions 399
References 400
Chapter 11 Nuclear Magnetic Resonance Case Studies in Marine Natural Products 403
11.1 Introduction 403
11.1.1 Case Studies 404
11.1.2 Snapshots 405
11.2 Marine Natural Product Case Studies 405
11.2.1 Trachycladindoles 405
11.2.2 Franklinolides 406
11.2.3 Bistellettazines 409
11.2.4 Phorbasins 412
11.2.5 Ircinialactams 417
11.2.6 Fascioquinols 420
11.3 Marine Natural Product Snapshots 426
References 438
Chapter 12 Nuclear Magnetic Resonance Case Studies in Microbial Natural Products 440
12.1 Introduction 440
12.1.1 Case Studies 441
12.1.2 Snapshots 441
12.2 Microbial Natural Product Case Studies 442
12.2.1 Aspergillazines 442
12.2.2 Nocardioazines 444
12.2.3 Heronamides 447
12.2.4 Kibdelones 452
12.2.5 Reveromycins 457
12.3 Microbial Natural Product Snapshots 463
12.3.1 Macrocyclic Lactones 463
12.3.2 Cyclic Peptides 463
12.3.3 Caged Structures 463
12.3.4 Miscellaneous 475
12.4 Conclusion 483
References 483
Chapter 13 Nuclear Magnetic Resonance in Saponin Structure Elucidation 486
13.1 Introduction 486
13.2 General Considerations 487
13.3 Structure and Relative Stereochemistry of the Aglycone 489
13.4 Identity of Component Monosaccharides 493
13.5 Linkage Position and Sequence of the Oligosaccharide Chain 497
13.6 Concluding Remarks 499
13.6.1 Experimental 500
References 500
Chapter 14 Increasing the Adoption of Advanced Techniques for the Structure Elucidation of Natural Products 502
References 506
Subject Index 508