The Nuclear Overhauser Effect in Structural and Conformational Analysis

, by Neuhaus, David; Williamson, Michael P.

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ISBN: 9780471246756 | 0471246751
Cover: Hardcover
Copyright: 4/24/2000

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The Nuclear Overhauser Effect in Structural and Conformational Analysis, Second Edition, uniquely explains the NOE in detail, making it an indispensable resource for the novice as well as the experienced NMR researcher.

Preface

Acknowledgments

xvii

Preface To The First Edition

xix

Symbols, Abbreviations, And Units

xxi

Introduction

xxv

PART I. THEORY

(217)

Background

(20)

Energy Levels, Populations, and Intensities

(5)

Relaxation, T1 and T2

(4)

The Nature of Relaxation

(1)

The Local Field and Dipole-Dipole Relaxation

(2)

Pulses and Saturation

(8)

References

(1)

The Steady State NOE for Two Spins

(39)

The Origin and Form of the NOE

(7)

Qualitative Considerations

(4)

The Solomon Equations

(3)

Dependence of the NOE on Molecular Motion

(8)

Correlation Times, Spectral Density Functions, and Transition Probabilities

(7)

Anisotropic Tumbling

(1)

What the Symbols Mean for two Spins and for Many Spins

(8)

Relaxation Rates

(3)

T1 Measurements and Cross-Relaxation

(4)

Effects of Other Relaxation Sources

(8)

The External Relaxation Rate ρ*

(4)

Intermolecular Dipole-Dipole Relaxation

(2)

Quadrupolar Relaxation

(1)

Chemical Shift Anisotropy (CSA) Relaxation

(1)

Scalar Relaxation

(1)

Spin-Rotation Relaxation

(1)

The Heteronuclear NOE

(5)

An Extension to the Solomon Equations

(3)

References

(2)

The Steady State Noe In Rigid Multispin Systems

(36)

The Equations

(9)

The Solomon Equations for More Than Two Spins

(3)

Cross-Correlation

(2)

Two General Solutions to the Multispin Solomon Equations

(1)

Saturation of One Spin

(1)

Saturation of All Spins Except One

(2)

Internuclear Distances and Steady-State NOE Enhancements

(1)

What the Equations Mean

(19)

General: Direct Enhancements and Spin Diffusion

(4)

Interpretation at the Extreme Narrowing Limit (ωτc « 1)

(1)

Direct Effects

(3)

Indirect Effects

(1)

When Do Indirect Effects Matter?

(2)

Magnetic Equivalence

(2)

T1 and the 3/2 Effect

(1)

Chemical Equivalence

(1)

Away from the Extreme Narrowing Limit

(5)

In Practice

(7)

Incomplete Saturation

(1)

Failure to Reach Steady-State

(1)

Competition From Other Relaxation Sources

(3)

References

(1)

The Kinetics of the NOE

(31)

Introduction

(7)

Types of Kinetic NOE Experiment

(1)

Overview

100

(5)

Theory of the Kinetic NOE in a Two-Spin System

105

(3)

Theory of the Kinetic NOE in Multispin Systems

108

(3)

Multispin Kinetics in Transient NOE Experiments

108

(3)

Multispin Kinetics in TOE Experiments

111

(1)

Estimating Internuclear Distances

111

(11)

The Initial Rate Approximation

112

(1)

Distances From Enhancement Ratios

113

(2)

Errors in Distance Measurements Using the Initial Rate Approximation

115

(2)

Spin Diffusion, Nonlinear NOE Growth, and Interpretation

117

(5)

More About Experiments

122

(7)

Symmetry in Kinetic NOE Experiments

122

(2)

T1 Values as an Aid to Interpretation

124

(3)

References

127

(2)

The Effects of Exchange and Internal Motion

129

(61)

Transfer of Saturation

131

(5)

General Equations for the NOE in Systems of Two-Site Exchange

136

(12)

Exchange in a Two-Spin System

136

(7)

Exchange in Dimethylformamide

143

(5)

Applications to More Complicated Cases of Exchange

148

(10)

Averaging of Rates Rather than Enhancements

148

(2)

Analyzing Conformational Equilibria

150

(1)

Olefinic Methoxy Conformations

150

(1)

Nucleotide Conformations

151

(5)

A Statistical Approach

156

(2)

Estimating Flexibility Using Heteronuclear Relaxation Analysis

158

(9)

How Internal Motions Average Internuclear Distances

167

(7)

Internal Motions Slower Than Overall Tumbling: ``r-6 Averaging''

171

(1)

Internal Motions Faster Than Overall Tumbling

172

(2)

Allowing for Averaging

174

(4)

The Transferred NOE

178

(7)

Intermolecular NOE Enhancements Involving Water

185

(5)

References

187

(3)

Complications from Spin-Spin Coupling

190

(29)

Decoupling

(101)

Selective Population Transfer

191

(10)

Theory

192

(7)

Consequences

199

(2)

Effects of Cross-Correlation

201

(3)

Strong Coupling

204

(15)

A{B} Enhancements

206

(1)

AB{X} Enhancements

206

(7)

Scalar Relaxation

213

(1)

Scalar Relaxation of the First Kind

213

(3)

Scalar Relaxation of the Second Kind

216

(1)

References

217

(2)

PART II. EXPERIMENTAL

219

(170)

One-dimensional Experiments

221

(61)

Sample Preparation

221

(6)

Solvent

221

(3)

Solute Concentration

224

(1)

Sample Purification

225

(2)

Setting Up the Steady-State Difference Experiment

227

(20)

Introduction to the Difference Experiment

227

(3)

Minimizing Subtraction Artifacts

230

(4)

Automatic Multiple Experiments

234

(1)

Irradiation Power and Selectivity

235

(5)

Multiplet Irradiation and SPT Suppression

240

(3)

Timing

243

(4)

Processing, Display, and Calculation of Results

247

(7)

General

247

(2)

Reference Deconvolution

249

(5)

Other 1D Experiments Employing Continuous Saturation

254

(4)

CW Steady-State Integration

254

(1)

The Truncated Driven NOE (TOE) Experiment

255

(3)

Transient Experiments

258

(24)

Selective Pulses

259

(1)

Non-Gradient Transient NOE Experiments

260

(1)

Gradient-Assisted Transient NOE Experiments

261

(1)

Gradient Selection

262

(2)

DPFGSE-NOE

264

(3)

GOESY

267

(5)

Variations

272

(2)

Applications and Practicalities

274

(2)

Doubly Selective Experiments

276

(3)

References

279

(3)

The Two-dimensional Noesy Experiment

282

(49)

One Dimension or Two?

282

(3)

The Negative NOE Regime (ωτc > 1.12)

283

(1)

The Positive NOE Regime (ω&gau;c > 1.12)

283

(2)

Basic Principles

285

(8)

Acquiring a NOESY Spectrum

293

(14)

Fixed Delays and Pulse Widths

294

(2)

Acquisition Times t1 and t2 and Spectral Widths SW1 and SW2

296

(3)

Quadrature Detection in F1 and FZ

299

(5)

Phase-Sensitive NOESY

304

(3)

Phase-Cycling, Signal Selection, and Artifact Suppression

307

(9)

Rejection of Nonlongitudinal Contributions During &tum;m: J-Peak Suppression

309

(1)

Other Forms of J-Peaks: Zero Quantum Coherences and Pulse Angle Effects

310

(3)

Axial Peaks

313

(1)

Quadrature Images

313

(1)

t1 Noise

314

(2)

Data Processing

316

(6)

Zero Filling

317

(1)

Window Functions and Linear Prediction

318

(2)

Symmetrization and t1 Noise Removal

320

(1)

Integration

321

(1)

Variations

322

(9)

Semi-Selective and Network-Edited Experiments

322

(5)

Other Variants

327

(1)

References

328

(3)

Other Developments

331

(58)

Heteronuclear NOE Enhancements

331

(10)

Non-Specific Heteronuclear NOE Experiments

331

(4)

Specific Heteronuclear NOE Experiments

335

(6)

Editing and Spectral Simplification of NOE Experiments

341

(23)

Editing Using the NOE Itself

341

(5)

Editing Using Heteronuclear Scalar Couplings

346

(1)

X-Filtered NOE Experiments

347

(3)

X-Separated NOE Experiments

350

(9)

Homonuclear Three-Dimensional NOE Experiments

359

(3)

Editing Using Something Else

362

(2)

Rotating Frame NOE Experiments

364

(18)

Theory

365

(1)

Spin-Locking

365

(2)

Spin-Locked Transverse Dipole-Dipole Relaxation

367

(4)

Other Effects During Spin-Locking

371

(8)

Practicalities

379

(3)

Manipulation of ω&tum;c

382

(7)

References

384

(5)

PART III. APPLICATIONS

389

(207)

Applications of the NOE to Structure Elucidation

391

(65)

General Considerations

391

(7)

Why Structural and Conformational Problems Are the Same

391

(2)

Spectra and Assignments

393

(2)

Reporting Results and Interpretation

395

(2)

Miscellaneous

397

(1)

Aromatic Substitution and Ring Fusion Patterns: Simple Cases

398

(8)

Aromatic Substitution and Ring Fusion Patterns: More Complex Cases

406

(9)

Petroporphyrins

407

(2)

Isoquinoline and Related Alkaloids

409

(6)

Double Bond Isomers

415

(5)

Saturated Ring Systems: Simple Cases

420

(22)

Substituent Stereochemistry

422

(10)

Ring Fusion Stereochemistry

432

(10)

Saturated Ring Systems: More Complex Cases

442

(14)

Pulvomycin

444

(3)

Penitrem A

447

(3)

Other Examples

450

(3)

References

453

(3)

Applications of the NOE to Conformational Analysis

456

(29)

General Considerations

456

(3)

Why Structural and Conformational Problems are Different

456

(2)

Multiple Conformations

458

(1)

Local Conformational Detail in Small Molecules

459

(13)

Slowly Exchanging Equilibria

461

(1)

Rapidly Exchanging Equilibria: A Hypothetical Example, X-CH2OH

461

(2)

Rapidly Exchanging Equilibria: Real Examples

463

(9)

Conformational Analysis of Medium-Sized Molecules

472

(13)

References

484

(1)

Calculating Structures of Biopolymers

485

(65)

Introduction

485

(1)

Restraints

486

(29)

Assigning NOE Restraints

487

(1)

Using Only (1H, 1H) NOESY Data

488

(1)

Using Preliminary Structural Data

489

(1)

Using Heteronuclear Labeling

490

(1)

Measuring NOE Restraints

491

(2)

Calibrating NOE Restraints

493

(6)

Averaging in Equivalent Groups

499

(1)

Pseudoatom Corrections

500

(3)

Multiplicity Corrections

503

(3)

r-6 Summation

506

(1)

Stereoassignments and Torsion Angle Restraints

506

(5)

Other Types of Restraints

511

(4)

Calculating Structures

515

(15)

Distance Geometry Calculations

517

(1)

The Exact Case

518

(1)

Distance Geometry Applied to NMR Structure Determination

519

(3)

Distance Geometry in Torsion Angle Space

522

(1)

Restrained Molecular Dynamics Calculations

523

(4)

Simulated Annealing Calculations

527

(2)

Other Methods

529

(1)

Assessing and Describing NMR Structures

530

(10)

Global Precision: Overall Root Mean Squared Deviations

531

(2)

Local Precision: Local RMSD and Angular Order Parameters

533

(3)

Assessing the Quality of Structures

536

(4)

Refinement

540

(10)

General

541

(2)

Specific Protocols for Refinement

543

(3)

References

546

(4)

Biopolymers

550

(46)

Peptides and Proteins

550

(16)

Assignment: Heteronuclear Methods

554

(1)

Assignment: (1H, 1H) NOE-Based Methods

555

(1)

Structure Determination of Protein Monomers

556

(1)

Small Rigid Unlabeled Proteins

556

(2)

Larger Rigid Labeled Proteins

558

(2)

Conformationally Mobile Proteins

560

(2)

Structure Determination of Symmetric Protein Oligomers

562

(1)

Through-Space Connections by Solid-State NMR Experiments with Proteins

563

(3)

Polynucleotides

566

(17)

Structures and Conformations

567

(7)

Assignment

574

(1)

Duplex DNA

574

(2)

RNA

576

(1)

Other Nucleotides

577

(1)

Structure Calculation

577

(1)

Sequence Dependent Conformation in Duplexes

577

(4)

Non-Helical Conformations

581

(2)

Oligosaccharides

583

(4)

Sequence and Linkage Determination

584

(1)

Conformation

585

(2)

Complexes

587

(9)

Drug-Protein Complexes

589

(1)

Drug-DNA Complexes

589

(1)

Protein-Nucleic Acid Complexes

590

(2)

References

592

(4)

Appendix I. Equations for Enhancements Involving Groups of Equivalent Spins

596

(3)

Appendix II. Quantum Mechanics and Transition Probabilities

599

(12)

Index

611

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The Nuclear Overhauser Effect in Structural and Conformational Analysis

Summary

Author Biography

Table of Contents

Supplemental Materials