Stereodynamics of Molecular Systems (eBook)

Front Cover 1
Stereodynamics of Molecular Systems 4
Copyright Page 5
Table of Contents 8
Preface 6
Inaugural Address by Nobel Laureate Ivar Giaever 12
Part I: Methodology NMR Spectroscopy and Crystallography 14
Chapter 1. Nuclear Magnetic Resonance Spectroscopy Chemical Shifts, Coupling Constants and Molecular Geometry 16
Introduction 16
Constitutional Features of Nucleic Acids 16
Assignments and Analysis of the NMR Spectra of Nucleic Acids 17
The Vicinal Coupling Constants 27
The Four Bond Coupling Constants 32
The Five Bond Coupling Constants 34
The Chemical Shifts 35
Recent Developments 44
Summary 48
Acknowledgement 49
References and Footnotes 49
Chapter 2. Nuclear Magnetic Resonance Spectroscopy Stereodynamics of Small Molecules 52
References and Footnotes 64
Chapter 3. Nuclear Magnetic Resonance Spectroscopy Solution Dynamics of Polymer Chains 66
Introduction 66
Mechanisms of Spin-Lattice Relaxation 66
Measurement of T1 
70 
Nuclear Overhauser Enhancement 71
Carbon-13 Relaxation in Macromolecules 74
More Realistic Models: Polybutene-1 81
References and Footnotes 85
Chapter 4. Single Crystal Crystallography1 88
Introduction 88
A Crystal is a Periodic Array of Material 89
The Scattering of X-rays by a Crystal Depends on The Superposition of Waves 94
The Total Scattering From An Object Is Defined Within A Sphere Called Reciprocal Space 
97 
Scattering Factors for Individual Atoms Characterize Molecular Scatterin 97
Scattering From A Crystal Samples The Complete Scattering Pattern 98
The Quality of the Structure Depends on the Extent of the Data 104
The Phase Problem Complicates Crystallography Enormously 109
Short Nucleic Acid Fragments May Be Solved Directly From the Intensity Data 112
Macromolecules Must Be Derivatized To Be Solved 114
Refinement Is The Acid Test For A Structure 118
Concluding Remarks 119
Acknowledgements 120
References and Footnotes 120
Part II: Small Molecules and Ions 124
Chapter 5. The Rotation-Inversion Dichotomy in Trialkylamines Diethylmethylamine and Triethylamine 126
References and Footnotes 142
Chapter 6. Pyramidal Carbanions? 144
Direct Evidence for Pyramidal Methyl Anion 145
The Inversion Barrier in Methyl Anion 146
Carbanion Inversion in Solution 149
Measurement of Anion Inversion Rates by Carbon-13 NMR 150
Carbanion Inversion in the Gas Phase 153
Conclusion 156
Acknowledgements 156
References and Footnotes 156
Chapter 7. Delocalization in Diarylmethyl Anions Probe of Solution Ion States? 160
Static NMR Spectra: Results and Discussion 161
Dynamic NMR Spectra: Results and Discussion 166
Acknowledgements 174
References and Footnotes 174
Chapter 8. Steric Effects on Electron-Transfer Reactions of Sulfonamides 176
Introduction 176
Results and Discussion 178
References and Footnotes 182
Chapter 9. The Effect of Isotopic Perturbation on NMR Spectra 184
Introduction 184
Carbonium Ions and their Rearrangement 185
Rapid, Degenerate 1,2-Hydride and Methide Shifts in Carbonium Ions 186
The Effect of Deuterium Perturbation on Rapidly Equilibrating Systems 188
Deuterium Perturbation of the NMR Spectra of Symmetric (Single Energy Minimum) Cases 189
The Deuterium Perturbation Method for Distinguishing Rapidly Equilibrating from Symmetric Cases 191
Acknowledgements 196
References and Notes 196
Part III: Medium Size Molecular Systems 198
Chapter 10. Conf ormational Mobility of the Backbone of Cyclic Tripeptides1 200
Introduction 200
The "Crown" 201
The Dynamics of the Backbone 203
Cyclic Tripeptides Containing Chiral Amino Acids 203
Conclusions 208
Acknowledgements 209
References and Notes 209
Chapter 11. Multinuclear NMR Studies of Crown and Cryptand Complexes 210
Introduction 210
Proton Magnetic Resonance 210
Carbon-13 NMR 212
AiJtaiiMete NMR 213
References and Footnotes 220
Chapter 12. Frontier Orbital Models for and Rearrangements of Organotransition Metal Compounds 222
Introduction 222
Structures of Organotransition Metal Pi Complexes 222
Molecular Rearrangements 229
Summary 235
Acknowledgements 236
References and Footnotes 236
Chapter 13. Spectroscopic and X-ray Crystallographic Structural Studies of Mo(IV), Mo(V), and Mo(VI) Complexes with Linear Thiolate Ligands 240
Complexes with Bidentate Thiolate Ligands 242
Tridentate Thiolate Ligands 246
Tetradentate Ligands 252
Conclusions 259
Acknowledgement 260
References and Footnotes 260
Part IV: Systems of Higher Order Nucleic Acid Statics and Dynamics 262
Chapter 14. The Diverse Spatial Configurations of DNA Evidence for a Vertically Stabilized Double Helix 264
Introduction 264
The Controversy 265
The Resolution of the Controversy 266
Vertical Double Helices for Naturally Occurring Polynucleotidesl 290
Acknowledgment 292
References and Footnotes 292
Chapter 15. Does DNA Have Two Structures in Solution That Coexist At Equilibrium? 294
Nature of Normal Mode Oscillation in DNA Structure that Gives Rise to the Formationof ß Kinked DNA 295
Structure of DNA In Solution At Equilibrium 296
Wave Propagation (Phonons) In DNA 296
Discussion 297
Acknowledgements 298
Appendix 298
References and Footnotes 299
Chapter 16. Structure, Fluctuations and Interactions of the Double Helix 300
Exchange Chemistry 301
Evidence for An Open State in Poly (A.U) And Identity of the Exchanging Protons 302
New Applications of Exchange Methods 307
Acknowledgements 310
References and Footnotes 311
Chapter 17. Internal Twisting of Short DNA Segments 312
Introduction 312
Fiber Studies 313
Solution Studies 314
Torsional Rigidity of DNA 322
Acknowledgements 324
References and Footnotes 324
Chapter 18. The Flexible DNA Double Helix 326
Residue Flexibility 328
Polymer Flexibility 334
Circle and Loop Formation 336
Summary 340
Acknowledgement 342
References and Notes 342
Chapter 19. Conformational Flexibility of the Polynucleotide Chain 344
The Double Helix and Ring Pucker 344
Polynucleotide Chain May Turn Corners With Changes in Ring Pucker 347
The Double Helix Changes Conformation Upon Intercalation 349
Conformational Flexibility in Nucleic Acid Macromolecules: Yeast tRNAphe 351
Intercalation in Yeast tRNAPhe 354
Discussion 357
Acknowledgements 358
References and Footnotes 358
Chapter 20. Accessible Surface Areas of Nucleic Acids and Their Relation to Folding, Conformational Transition, and Protein Recognition 360
Introduction 360
Calculation of "Static" Accessible Surface Area 361
Polarity of Exposed Atoms 364
Surface of DNA Double Helices 364
Surfaces for RNA Double Helix and Single Helix 371
Transfer RNA 372
Two-Thirds of Nucleic Acid Surfaces are Buried on Folding 373
Driving Force in Nucleic Acid Folding is Quite Different from That of Proteins 374
Correlation of A.B Helical Transitions to DNA Hydration 374
Major Groove of B-DNA and Minor (Shallow) Groove ofA-DNA Are Primary Recognition Surfaces for Proteins 377
Acknowledgements 378
References and Footnotes 378
Chapter 21. The Coil Form of Poly(rU): A Model Composed of Minimum Energy Conformers That Matches Experimental Properties 380
Introduction 380
Methods 382
Results and Discussion 384
Characteristic Ratios 387
Conclusion 391
Acknowledgement 394
References and Footnotes 394
Chapter 22. Modelling of Drug-Nucleic Acid Interactions Intercalation Geometry of Oligonucleotides 396
Introduction 396
The Crystallographic Data 397
Models for Binding to RNA Duplexes 398
Binding to Single Strands 409
Conclusions 410
Acknowledgement 410
References and Footnotes 410
Chapter 23. DNA Structure and its Distortion by Drugs 412
Electric Dichroism of DNA 412
Dichroism of Intercalated Drugs 418
Kinking of DNA by Irehdiamine 419
Allosteric Transformation of Calf Thymus DNA by Distamycin 420
References and Footnotes 423
Chapter 24. Structure and Dynamics of Poly(dG-dC) in Solution Steroid Diamine.Nucleic Acid Complexes and Generation of an "Alternating B-DNA" Conformation in High Salt 426
Introduction 426
Poly(dG-dC) in Low Salt Solution 426
Backbone Phosphates 434
Poly(dG-dC) in High Salt Solution 436
Steroid Diamine · Poly(dG-dC) Complex 442
Summary 449
References and Footnotes 450
Chapter 25. Spectroscopic Studies of Drug Nucleic Acid Complexes 452
Ethidium and Actinomycin Bind Non-competitively to Calf Thymus DNA at Low r Values 454
Fluorescence Lifetime Measurements of Ethidium Complexes in Solution and in the Solid State 455
Daunorubicin and Adriamycin Facilitate Actinomycin Binding to poly(dA-dT).poly(dA-dT) 456
Enzyme Inhibition Studies 458
Actinomycin Dissociation Kinetics 458
Acknowledgments 463
References and Notes 463
Part V: Intact Biological Systems 466
Chapter 26. Carbon-13 Cross-Polarization Magic-Angle NMR Studies of Biological Systems1 468
Introduction 468
13C Spectra For Selected Tissues 469
Acknowledgments 480
References and Notes 480
Chapter 27. NMR Zeugmatographic Imaging of Organs and Organisms 482
Acknowledgements 484
References and Notes 484
Index to Subjects 486