THE NUCLEAR OVERHAUSER EFFECT IN STRUCTURAL AND CONFORMATIONAL ANALYSIS

Transcription

1 THE NUCLEAR OVERHAUSER EFFECT IN STRUCTURAL AND CONFORMATIONAL ANALYSIS David Neuhaus and Michael P. Williamson VCH

2 CONTENTS Preface v Acknowledgments vii Symbols, Abbreviations, and Units xvii Introduction xxi PART THEORY C H A P T E R 1 Background Energy Levels, Populations, and Intensities Relaxation, T, and T The Nature of Relaxation The Local Field and Dipole-Dipole Relaxation Pulses and Saturation References 22 CHAPTER 2 The Steady-State NOE for Two Spins The Origin and Form of the NOE Qualitative Considerations The Solomon Equations Dependence of the NOE on Molecular Motion Correlation Times, Spectral Density Functions, and Transition Probabilities Anisotropie Tumbling What the Symbols Mean for Two Spins and for Many Spins Relaxation Rates ", Measurements and Cross-Relaxation 43 ix

3 X CONTENTS 2.4 Effects of Other Relaxation Sources The External Relaxation Rate p* Intermolecular Dipole-Dipole Relaxation Quadrupolar Relaxation Chemical Shift Anisotropy (CSA) Relaxation Scalar Relaxation Spin-Rotation Relaxation The Heteronuclear NOE References 60 CHAPTER 3 The Steady-State NOE in Rigid Multispin Systems The Equations The Solomon Equations for More Than Two Spins Cross-Correlation Two General Solutions to the Multispin Solomon Equations Saturation of One Spin Saturation of All Spins Except One Internuclear Distances and Steady-State NOE Enhancements What the Equations Mean General; Direct Enhancements and Spin Diffusion Interpretation at the Extreme Narrowing Limit (an c < 1) Direct Effects Indirect Effects When Do Indirect Effects Matter? Magnetic Equivalence T, and the 3/2 Effect Chemical Equivalence Away from the Extreme Narrowing Limit In Practice Incomplete Saturation Failure to Reach Steady State Competition from Other Relaxation Sources References WO CHAPTER 4 The Kinetics of the NOE The Initial Rate Approximation The Truncated Driven NOE (TOE) The Reference Distance 109

4 CONTENTS xi Noninstantaneous Saturation Correlation Times Internal Motion Noninitial Conditions Practical Implications Further Implications for Interpretation What Is the Steady State? r, Values as an Aid to Interpretation Transient and NOESY Experiments Calculated Examples of Multispin Systems References 139 CHAPTER 5 The Effects of Exchange and Internal Motion Transfer of Saturation General Equations for the NOE in Systems of Two-Site Exchange Exchange in a Two-Spin System Exchange in Dimethylformamide Applications to More Complicated Cases of Exchange Averaging of Rates Rather Than Enhancements Two-Site Exchange in a Multispin System Olefinic Methoxy Conformations Nucleotide Conformations: A Simple Model Nucleotide Conformations: The "Best Fit" Approach Allowing for Averaging Exchange Rates Faster Than Molecular Tumbling The Transferred NOE References 181 CHAPTER 6 Complications from Spin-Spin Coupling Decoupling Selective Population Transfer Theory Consequences Strong Coupling A{B} Enhancements AB{X} Enhancements Scalar Relaxation Scalar Relaxation of the First Kind Scalar Relaxation of the Second Kind References 208

5 xii CONTENTS EXPERIMENTAL 209 CHAPTER 7 One-Dimensional Experiments Sample Preparation Solvent Solute Concentration Sample Purification Setting Up the Steady-State Difference Experiment Introduction to the Difference Experiment Minimizing Subtraction Artifacts Automatic Multiple Experiments Irradiation Power and Selectivity Multiplet Irradiation and SPT Suppression Timing Display and Calculation of Results Other 1D Experiments CW Steady-State Integration The Truncated Driven NOE (TOE) Experiment Transient Experiments Selective Pulses Other Considerations References 251 CHAPTER 8 The Two-Dimensional NOESY Experiment One Dimension or Two? The Negative NOE Regime (an c > 1.12) The Positive NOE Regime (COT C < 1.12) Basic Principles Acquiring a NOESY Spectrum Fixed Delays and Pulse Widths Acquisition Times?, and t 2 and Spectral Widths SW\ and SW Quadrature Detection in F, and F Phase-Sensitive NOESY Phase Cycling, Signal Selection, and Artifact Suppression Rejection of Nonlongitudinal Contributions during t m ; /-Peak Suppression Other Forms of 7-Peaks; Zero Quantum Coherences and Pulse Angle Effects Axial Peaks 288

6 CONTENTS xiii Quadrature Images ?, Noise Data Processing Zero Filling Window Functions Symmetrization and f, Noise Removal Integration Variations 2P Combination with Other 2D Experiments Semiselective Experiments Heteronuclear Experiments Other Variants References 304 CHAPTER 9 Other Developments Heteronuclear Experiments Rotating Frame NOE Experiments Theory Spin Locking and Transverse Cross-Relaxation Other Effects during Spin Locking Practice Summary Variation of u>x c Editing and Spectral Simplification Coping with Large Solvent Signals Methods That Suppress the Solvent Signal Methods That Do Not Excite the Solvent Signal Data Processing Special Problems of 2D Experiments References 347 PART III APPLICATIONS 351 CHAPTER 10 Applications of the NOE to Structure Elucidation General Considerations Why Structural and Conformational Problems Are the Same Spectra and Assignments 355

7 xiv CONTENTS Reporting Results and Interpretation Miscellaneous Aromatic Substitution and Ring Fusion Patterns: Simple Cases Aromatic Substitution and Ring Fusion Patterns: More Complex Cases Petroporphyrins Isoquinoline and Related Alkaloids Double Bond Isomers Saturated Ring Systems: Simple Cases Substituent Stereochemistry Ring Fusion Stereochemistry Saturated Ring Systems: More Complex Cases Pulvomycin Penitrem A Other Examples References 419 CHAPTER 11 Applications of the NOE to Conformational Analysis General Considerations Why Structural and Conformational Problems Are Different Multiple Conformations Local Conformational Detail in Small Molecules Slowly Exchanging Equilibria Rapidly Exchanging Equilibria: A Hypothetical Example, X CH 2 OH Rapidly Exchanging Equilibria: Real Examples Conformational Analysis of Medium-Sized Molecules References 448 CHAPTER 12 Biopolymers 12.1 Peptides and Proteins Assignment: General Sequential Assignment Method Crystal/Sequence Method Techniques Requiring No Structural Assumptions Techniques Requiring Structural Assumptions 459 4SI

8 CONTENTS Structure Determination Small Cyclic Peptides Acyclic Peptides Small Proteins: General BUSI IIA: Distance Geometry Metallothionein Lac Repressor Headpiece: Molecular Dynamics Large Proteins Polynucleotides Structures and Conformations A, B, or Z? Sequential Assignment Sequence-Dependent Conformation Interactions with Other Molecules Oligosaccharides Sequence and Linkage Determination Conformation References 498 APPENDIX I Equations for Enhancements Involving Groups of Equivalent Spins 503 APPENDIX II Quantum Mechanics and Transition Probabilities 505 Index 515