Starikov / Lewis / Tanaka Modern Methods for Theoretical Physical Chemistry of Biopolymers

1. Auflage 2011
ISBN: 978-0-08-046101-4
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 604 Seiten

Modern Methods for Theoretical Physical Chemistry of Biopolymers provides an interesting selection of contributions from an international team of researchers in theoretical chemistry. This book is extremely useful for tackling the complicated scientific problems connected with biopolymers' physics and chemistry.
The applications of both the classical molecular-mechanical and molecular-dynamical methods and the quantum chemical methods needed for bridging the gap to structural and dynamical properties dependent on electron dynamics are explained. Also included are ways to deal with complex problems when all three approaches need to be considered at the same time. The book gives a rich spectrum of applications: from theoretical considerations of how ATP is produced and used as 'energy currency' in the living cell, to the effects of subtle solvent influence on properties of biopolymers and how structural changes in DNA during single-molecule manipulation may be interpreted.
· Presents modern successes and trends in theoretical physical chemistry/chemical physics of biopolymers
· Topics covered are of relevant importance to rapidly developing areas in science such as nanotechnology and molecular medicine
· Quality selection of contributions from renowned scientists in the field

Autoren/Hrsg.

Starikov, Evgeni

Lewis, James P.

Tanaka, Shigenori

Inhaltsverzeichnis

1;Cover;1
2;List of Contributors;6
3;Contents;14
4;Section 1 Quantum chemistry;34
4.1;Chapter 1 Theoretical development of the fragment molecular orbital (FMO) method;36
4.1.1;1.1 Introduction;36
4.1.2;1.2 The Theory of the FMO Method;39
4.1.2.1;1.2.1 Basic ideas;39
4.1.2.2;1.2.2 Fragmentation;39
4.1.2.3;1.2.3 Mathematical formulation;42
4.1.2.4;1.2.4 Computational scheme and property calculation;44
4.1.2.5;1.2.5 Many-body treatment;46
4.1.2.6;1.2.6 Electron correlation;47
4.1.2.7;1.2.7 Interfragment separation;48
4.1.2.8;1.2.8 The multilayer approach;50
4.1.2.9;1.2.9 Pair interaction analysis;51
4.1.2.10;1.2.10 An example of the FMO interaction analysis: ethanol and water;54
4.1.3;1.3 Accuracy of the FMO Method;57
4.1.4;1.4 Parallelization;62
4.1.5;1.5 Scaling;65
4.1.6;1.6 Guidelines to Applications;67
4.1.7;1.7 Conclusions;69
4.1.8;1.8 Acknowledgements;70
4.1.9;1.9 References;70
4.2;Chapter 2 Developments and applications of ABINIT-MP software based on the fragment molecular orbital method;72
4.2.1;2.1 Introduction;72
4.2.2;2.2 ABINIT-MP Software;73
4.2.3;2.3 An Application of FMO-HF Method: Prediction of Ligand Binding Affinities of Estrogen Receptor a;74
4.2.4;2.4 Implementation of the MP2 Method;79
4.2.5;2.5 CIS Calculations;81
4.2.6;2.6 Summary;84
4.2.7;2.7 Acknowledgements;84
4.2.8;2.8 References;84
4.3;Chapter 3 Combined DFT and electrostatic calculations of pKas in proteins: study of cytochrome c oxidase;86
4.3.1;3.1 Introduction;86
4.3.2;3.2 Structure and Function of CcO;89
4.3.3;3.3 The Proton Pumping Mechanism;90
4.3.4;3.4 Computational Methods for pKa Calculations;92
4.3.4.1;3.4.1 Overview;92
4.3.4.2;3.4.2 Density functional calculations;95
4.3.4.3;3.4.3 Continuum Electrostatic Calculations;96
4.3.4.4;3.4.4 Solvation Calculations;97
4.3.5;3.5 Results and Discussion;98
4.3.5.1;3.5.1 Computational models;98
4.3.5.2;3.5.2 The calculation of pKa in water;99
4.3.5.3;3.5.3 The pKa of His291 in CcO;101
4.3.5.4;3.5.4 The dielectric constant of protein cavities;105
4.3.6;3.6 Conclusions;106
4.3.7;3.7 Acknowledgements;109
4.3.8;3.8 References;109
4.4;Chapter 4 Watson–Crick hydrogen bonds: nature and role in DNA replication;112
4.4.1;4.1 Introduction;112
4.4.2;4.2 Accuracy of DFT for Hydrogen Bonds: Water Dimer;114
4.4.3;4.3 Structure of Hydrogen Bonds of DNA;114
4.4.3.1;4.3.1 Watson–Crick base pairs;114
4.4.3.2;4.3.2 Effect of the backbone;116
4.4.3.3;4.3.3 Effect of the crystal environment;118
4.4.4;4.4 The Nature of Hydrogen Bonds in DNA;119
4.4.4.1;4.4.1 Electrostatic interactions;119
4.4.4.2;4.4.2 Orbital interactions;121
4.4.4.3;4.4.3 Charge redistribution;121
4.4.4.4;4.4.4 Bond energy decomposition;122
4.4.4.5;4.4.5 Cooperativity between hydrogen bonds and resonance assistance;124
4.4.5;4.5 DNA Replication: Steric Factors Versus Hydrogen Bonding;125
4.4.6;4.6 Conclusions;129
4.4.7;4.7 Acknowledgements;129
4.4.8;4.8 References;129
4.5;Chapter 5 Quantum chemical modeling of charge transfer in DNA;132
4.5.1;5.1 Introduction;132
4.5.2;5.2 Basics of the Electron Transfer Theory;135
4.5.3;5.3 Quantum Mechanical Models;135
4.5.3.1;5.3.1 Driving force .G0;136
4.5.3.2;5.3.2 Estimation of the electronic coupling Vda;137
4.5.3.3;5.3.3 Intra- and inter-strand electronic couplings;138
4.5.3.4;5.3.4 Effect of conformational dynamics on Vda;140
4.5.3.5;5.3.5 Superexchange paths;140
4.5.3.6;5.3.6 Parameters for excess electron transfer;143
4.5.4;5.4 Charge Transfer in DNA Stacks and Chromophore–DNA Complexes;146
4.5.4.1;5.4.1 Quantum chemical study of DNA p-stacks;146
4.5.4.2;5.4.2 Photoinduced charge separation in DNA hairpins;147
4.5.5;5.5 Charge Localization in DBA .-Stacks;148
4.5.6;5.6 Concluding Remarks;149
4.5.7;5.7 References;150
5;Section 2 Molecular mechanics;154
5.1;Chapter 6 Solvent effects on biomolecular dynamics simulations:A comparison between TIP3P, SPC and SPC/E water models acting on the Glucocorticoid receptor DNA-binding domain ;156
5.1.1;6.1 Introduction;156
5.1.2;6.2 Methods;157
5.1.2.1;6.2.1 Analysis;158
5.1.2.1.1;6.2.1.1 Atomic displacement and fluctuations;158
5.1.2.1.2;6.2.1.2 Order parameters;159
5.1.2.1.3;6.2.1.3 Hydration;159
5.1.2.1.4;6.2.1.4 Energies;159
5.1.2.1.5;6.2.1.5 Rotational times;160
5.1.3;6.3 Results and Discussion;161
5.1.3.1;6.3.1 Protein stability and rotational diffusion;161
5.1.3.2;6.3.2 Structural fluctuations in the protein;161
5.1.3.3;6.3.3 Entropy and energy;164
5.1.4;6.4 Conclusion;166
5.1.5;6.5 Acknowledgement;167
5.1.6;6.6 References;167
5.2;Chapter 7 Computer simulations of DNA stretching;170
5.2.1;7.1 Introduction;170
5.2.1.1;7.1.1 Straining biopolymers one by one;171
5.2.1.2;7.1.2 The highly flexible DNA;171
5.2.1.3;7.1.3 The highly robust DNA;172
5.2.1.4;7.1.4 Pulling the cord;172
5.2.1.5;7.1.5 Early mechano-chemical w;173
5.2.2;7.2 Structural Changes in DNA During Single-Molecule Manipulations;174
5.2.2.1;7.2.1 Computer modelling of the stretched structure of DNA;174
5.2.3;7.3 Computer Simulation of a Single DNA Stretching Experiment;175
5.2.3.1;7.3.1 Computational details;176
5.2.3.2;7.3.2 Tensile load versus elongation;177
5.2.3.3;7.3.3 Path of least resistance;178
5.2.3.4;7.3.4 Can we rely on a stretched force field?;180
5.2.3.5;7.3.5 Internal interactions short and long range;180
5.2.3.6;7.3.6 Fast transition in sugar-phosphate backbone;181
5.2.3.7;7.3.7 Sugar–phosphate chains zipped up by the bases;183
5.2.3.8;7.3.8 Comparison with experiment;184
5.2.3.9;7.3.9 Biological relevance?;185
5.2.4;7.4 Conclusions;185
5.2.5;7.5 References;188
5.3;Chapter 8 On the art of computing the IR spectra of molecules in the condensed phase;192
5.3.1;8.1 Introduction;192
5.3.2;8.2 Methods to Calculate IR Spectra of Molecules in the Condensed Phase from DFT/MM-MD Simulations;195
5.3.2.1;8.2.1 FTTCF;196
5.3.2.2;8.2.2 INMA;197
5.3.2.3;8.2.3 TF-GV;198
5.3.2.4;8.2.4 Summary of Methods;200
5.3.2.5;8.2.5 IR spectra of molecules in a protein environment;200
5.3.3;8.3 Recent Results and Accuracy Issues;202
5.3.3.1;8.3.1 DFT/MM partitioning;202
5.3.3.2;8.3.2 Modelling of the environment;203
5.3.3.3;8.3.3 Non-resonant interactions between DFT- and MM-fragment;206
5.3.4;8.4 Conclusion;207
5.3.5;8.5 Acknowledgement;208
5.3.6;8.6 References;208
5.4;Chapter 9 High throughput in-silico screening of large ligand databases for rational drug design;212
5.4.1;9.1 Drug Activity and Key-Lock Principle;212
5.4.2;9.2 Rational Drug Design and Database Screening;213
5.4.3;9.3 Anatomy of a Virtual Screening Tool;214
5.4.3.1;9.3.1 The scoring function;215
5.4.3.2;9.3.2 The global optimization engine;215
5.4.4;9.4 A Practical Example: Database Screen to a Rigid MTX Recept;216
5.4.5;9.5 Target Degrees of Freedom: Specificity Versus Diversity;218
5.4.5.1;9.5.1 Screens using various rigid TK receptor conformations;218
5.4.5.2;9.5.2 Flexible receptor screens;220
5.4.5.3;9.5.3 Comparison: Rigid screen versus flexible screen;220
5.4.6;9.6 Conclusions;221
5.4.7;9.7 Acknowledgements;221
5.4.8;9.8 References;222
5.5;Chapter 10 Enzymatic recognition of radiation-produced oxidative DNA lesion. Molecular dynamics approach;224
5.5.1;10.1 Introduction;224
5.5.2;10.2 Computational Studies and Radiation Risk;225
5.5.3;10.3 DNA Repair;226
5.5.4;10.4 Method;227
5.5.4.1;10.4.1 Analysis of electrostatic energy;228
5.5.5;10.5 Results and Discussions;229
5.5.5.1;10.5.1 Cytosinyl radical (5-hydroxy-6-cytosinyl radical);229
5.5.5.2;10.5.2 Thymine dimer (5,6 cis.sin cyclobuthane thymine dimer);230
5.5.5.3;10.5.3 Thymine glycol (5,6-dihydroxy-5,6-dihydro-pyrimidine);232
5.5.5.4;10.5.4 8-oxoguanine (7,8-dihydro-8-oxoguanine);233
5.5.5.5;10.5.5 Role of electrostatic energy in recognition;235
5.5.6;10.6 Conclusion;239
5.5.7;10.7 Acknowledgements;240
5.5.8;10.8 Appendix;240
5.5.8.1;10.8.1 Computational details;240
5.5.8.2;10.8.2 Supercomputers used in simulations;240
5.5.8.3;10.8.3 Performance parameters;241
5.5.9;10.9 References;242
5.6;Chapter 11 Nucleation of polyglutamine amyloid fibres modelling using molecular dynamics;244
5.6.1;11.1 Introduction;245
5.6.1.1;11.1.1 Polyglutamine sequences in nature;245
5.6.1.2;11.1.2 Huntington’s disease;246
5.6.1.3;11.1.3 Protein conformations;247
5.6.1.3.1;11.1.3.1 Ramachandran diagrams;247
5.6.1.3.2;11.1.3.2 Polyglutamine amyloid nuclei;248
5.6.2;11.2 Simulation Methodology;250
5.6.3;11.3 Results;251
5.6.3.1;11.3.1 Relative stability of different polyQ nuclei;251
5.6.3.2;11.3.2 Stability of Perutz model with glutamine repeat length;253
5.6.4;11.4 Discussion and Conclusions;255
5.6.5;11.5 Acknowledgements;258
5.6.6;11.6 References;258
5.7;Chapter 12 Drug discovery using grid technology;260
5.7.1;12.1 Introduction;261
5.7.2;12.2 Grid-Based Exhaustive Conformational Search;262
5.7.2.1;12.2.1 OmniRPC system;262
5.7.2.2;12.2.2 CONFLEX as an exhaustive conformational search algorithm;264
5.7.2.3;12.2.3 Parallelized and grid-based CONFLEX;264
5.7.2.4;12.2.4 Application of CONFLEX to peptide folding;267
5.7.3;12.3 Replica Exchange Molecular Dynamics Toolkit for Drug-Receptor Docking;268
5.7.3.1;12.3.1 Object-oriented framework for statistical mechanics simulations;270
5.7.3.2;12.3.2 Performance evaluation;270
5.7.4;12.4 DNA and Estrogen Receptor Interaction Revealed by Fragment Molecular Orbital Calculation;273
5.7.4.1;12.4.1 DNA and estrogen receptor interaction;273
5.7.4.2;12.4.2 Analysis of DNA-ERE and ER-DBD systems by FMO;274
5.7.5;12.5 Drug Markup Language and Virtual Screening on Grid;277
5.7.5.1;12.5.1 Drug ML database;277
5.7.5.2;12.5.2 Virtual screening on the grid environment;278
5.7.6;12.6 Concluding Remarks;279
5.7.7;12.7 Acknowledgements;280
5.7.8;12.8 References;280
5.8;Chapter 13 Thermodynamics and kinetic analysis of FoF1-ATPase;282
5.8.1;13.1 Introduction;282
5.8.2;13.2 Understanding the Structures using Molecular Dynamics Simulations;285
5.8.3;13.3 Thermodynamics of ATP Hydrolysis;286
5.8.4;13.4 Implication on the Kinetics of ATP Hydrolysis by F1-ATPase;288
5.8.5;13.5 Thermodynamics in ATP Synthesis;289
5.8.6;13.6 ATP Hydrolysis Versus ATP Synthesis by FoF1-ATP Synthase;291
5.8.6.1;13.6.1 An E1 E2 mechanism;291
5.8.6.2;13.6.2 Kinetics;292
5.8.7;13.7 Summary;293
5.8.8;13.8 Acknowledgements;295
5.8.9;13.9 References;295
6;Section 3 Statistical methods;298
6.1;Chapter 14 Monte Carlo method: some applications to problems in protein science;300
6.1.1;14.1 Introduction;300
6.1.2;14.2 Background;301
6.1.2.1;14.2.1 The Monte Carlo method;301
6.1.2.1.1;14.2.1.1 Main idea of the Monte Carlo method;301
6.1.2.1.2;14.2.1.2 Essentials of the Metropolis Monte Carlo algorithm;304
6.1.2.2;14.2.2 Some other necessary background;306
6.1.2.2.1;14.2.2.1 Electrostatic energy of a microscopic state of a protein;306
6.1.2.2.2;14.2.2.2 Electrostatic part of the protein Gibbs free energy;308
6.1.2.2.3;14.2.2.3 Hendersson–Hasselbalch titration;309
6.1.3;14.3 Monte Carlo Simulations of Ionization Properties for Unfolded Proteins;310
6.1.3.1;14.3.1 Importance of accounting for electrostatic interactions in unfolded proteins;310
6.1.3.2;14.3.2 Spherical model of unfolded proteins;311
6.1.3.2.1;14.3.2.1 Basic concepts;311
6.1.3.2.2;14.3.2.2 Electrostatic energy in the spherical model;312
6.1.3.2.3;14.3.2.3 Coding of protein sequence;314
6.1.3.2.4;14.3.2.4 Calculation of free energy profile;316
6.1.3.3;14.3.3 Details of the Monte Carlo algorithm;318
6.1.3.4;14.3.4 Applications of the spherical model of unfolded proteins;320
6.1.3.4.1;14.3.4.1 Barnase;320
6.1.3.4.2;14.3.4.2 N-terminal domain of the ribosomal protein L9;321
6.1.3.4.3;14.3.4.3 Staphylococcal nuclease;322
6.1.3.4.4;14.3.4.4 N-terminal SH3 domain of the Drosophila protein drk;323
6.1.3.5;14.3.5 Concluding remarks;326
6.1.4;14.4 Monte Carlo Studies of Dimensions of Unfolded Proteins;327
6.1.4.1;14.4.1 Generic-chain representation of unfolded proteins;327
6.1.4.1.1;14.4.1.1 Basic concepts;327
6.1.4.1.2;14.4.1.2 Charge distribution and dielectric properties of the medium;328
6.1.4.2;14.4.2 Details of the Monte Carlo algorithm;328
6.1.4.3;14.4.3 Dimensions of non-charged chains;330
6.1.4.4;14.4.4 Dimensions of flexible charged chains;331
6.1.4.4.1;14.4.4.1 Zero net charge;331
6.1.4.4.2;14.4.4.2 Non-zero net charge;333
6.1.4.5;14.4.5 Comparison with experimental data;334
6.1.4.5.1;14.4.5.1 Cytochrome c;335
6.1.4.5.2;14.4.5.2 SNase;335
6.1.4.5.3;14.4.5.3 Hen-egg white lysozyme;336
6.1.4.6;14.4.6 Concluding remarks;336
6.1.5;14.5 References;337
6.2;Chapter 15 Protein structure generation and elucidation: applications of automated histogram filtering cluster analysis;340
6.2.1;15.1 Introduction;340
6.2.2;15.2 AHF-Clustering: Fundamental Concepts;341
6.2.3;15.3 Overview of Principal Component Analysis;343
6.2.4;15.4 AHF Clustering: The Algorithm;344
6.2.5;15.5 Efficient Generation of Low-Energy Protein Conformations;346
6.2.6;15.6 Collective Coordinates for an All-Atom Protein Model;347
6.2.7;15.7 Overview and Summary;349
6.2.8;15.8 Acknowledgements;350
6.2.9;15.9 References;351
6.3;Chapter 16 All-atom protein folding with stochastic optimization methods;352
6.3.1;16.1 Introduction;352
6.3.1.1;16.1.1 Force field;353
6.3.1.2;16.1.2 Optimization methods;354
6.3.1.2.1;16.1.2.1 Stochastic tunneling method;354
6.3.1.2.2;16.1.2.2 Parallel tempering;355
6.3.1.2.3;16.1.2.3 Basin hopping technique;355
6.3.1.2.4;16.1.2.4 Evolutionary strategies;356
6.3.2;16.2 Results;357
6.3.2.1;16.2.1 The trp-cage protein;357
6.3.2.2;16.2.2 The HIV accessory protein;359
6.3.2.3;16.2.3 The bacterial ribosomal protein L20;360
6.3.3;16.3 Conclusion;361
6.3.4;16.4 Discussion;362
6.3.5;16.5 Acknowledgements;363
6.3.6;16.6 References;363
7;Section 4 Model Hamiltonians;364
7.1;Chapter 17 Simple models for nonlinear states of double-helix DNA;366
7.1.1;17.1 Introduction;366
7.1.2;17.2 Englander Model – Base Twist around the Backbone;367
7.1.3;17.3 Yomosa Model;369
7.1.4;17.4 Takeno-Homma Model;370
7.1.5;17.5 Zhang Model;371
7.1.6;17.6 Yakushevich Model;373
7.1.7;17.7 Peyrard–Bishop Model of DNA Denaturation;374
7.1.8;17.8 The Prohofsky Branch of the Peyrard–Bishop Model;376
7.1.9;17.9 Dauxois–Peyrard–Bishop DNA Denaturation Model;377
7.1.10;17.10 Further Analyses of the DPB Models;379
7.1.11;17.11 Simple Helicoidal Model of dsDNA;383
7.1.12;17.12 Concluding Remarks;386
7.1.13;17.13 References;387
7.2;Chapter 18 The effects of bridge motion on electron transfer reactions mediated by tunneling;390
7.2.1;18.1 Introduction;390
7.2.2;18.2 The General Nonadiabatic Rate Expression;390
7.2.3;18.3 Semi-Classical Rate Equation in the Franck–Condon (Static Bridge) Approximation;392
7.2.4;18.4 Distance Dependence of the Electronic Coupling (Tunneling Matrix Element) in the Static Bridge Approximation;393
7.2.5;18.5 Methods for the Computation of Tunneling Matrix Elements;393
7.2.6;18.6 Bridge Mediated Electron Transfer Rates for Fluctuating Bridges;394
7.2.7;18.7 Influence of Tunneling Matrix Element Fluctuations on the ET Rate;396
7.2.8;18.8 Qualitative Picture of Tunneling Matrix Element Fluctuation Effects on the ET Rate;397
7.2.9;18.9 Quantum Nuclear Motion and Inelastic Tunneling;401
7.2.10;18.10 Tunneling Through a Bridge with Large Conformational Freedom;406
7.2.11;18.11 Bimolecular ET Kinetics: Exploring Numerous Protein–Protein Conformations;408
7.2.12;18.12 Aqueous Coupling Pathways Between Proteins;410
7.2.13;18.13 Prospects;412
7.2.14;18.14 Acknowledgement;412
7.2.15;18.15 References;412
7.3;Chapter 19 Modelling molecular conduction in DNA wires: charge transfer theories and dissipative quantum transport;416
7.3.1;19.1 Introduction;416
7.3.2;19.2 Environmental Effects within AB Initio Approaches;417
7.3.3;19.3 Modelling the System–Environment Interaction;419
7.3.3.1;19.3.1 Modelling the system–environment interaction: a DNA-wire in a dissipative bath;420
7.3.4;19.4 Conclusions and Outlook;423
7.3.5;19.5 Acknowledgements;423
7.3.6;19.6 References;423
7.4;Chapter 20 Electronic structure theory of DNA: from semi-empirical theory of the p-stack to ab initio calculations of the optical conductivity;426
7.4.1;20.1 Introduction;426
7.4.2;20.2 Ab Initio Density Functional Theory;428
7.4.3;20.3 Modeling DNA p-orbitals within Slater–Koster–Hückel theory;428
7.4.4;20.4 Electronic Structure and Optical Conductivity of Wet DNA;431
7.4.5;20.5 Conclusions;437
7.4.6;20.6 Acknowledgements;437
7.4.7;20.7 Appendix A. Slater–Koster Inter-Atomic Matrix Elements;437
7.4.8;20.8 Appendix B. Parameter Fitting;438
7.4.9;20.9 References;439
7.5;Chapter 21 Electronic transport and localization in short and long DNA;440
7.5.1;21.1 Introduction;440
7.5.2;21.2 Quantum Chemical Methods for Short DNA Strands;441
7.5.2.1;21.2.1 Generating the poly(dA)–poly(dT) DNA structures;442
7.5.2.2;21.2.2 Electronic structure calculations of molecular dynamics snapshots;443
7.5.2.3;21.2.3 Quantifying the degree of localization;443
7.5.2.4;21.2.4 Electronic states of a periodic poly(dA)–poly(dT) DNA;444
7.5.2.5;21.2.5 Electronic states of sampled poly(dA)–poly(dT) DNA configurations;445
7.5.3;21.3 Effective Tight-Binding Hamiltonians for Long DNA Strands and Complete Sequences;448
7.5.3.1;21.3.1 The ladder model;449
7.5.3.2;21.3.2 The numerical approach to localization in a Hamiltonian tight-binding model;452
7.5.3.3;21.3.3 Long DNA sequences: .-DNA, centromers and (super-)promoters;452
7.5.3.4;21.3.4 Results for localization lengths;453
7.5.3.5;21.3.5 Promoter sequences and E. coli binding sites;454
7.5.4;21.4 Summary;457
7.5.5;21.5 Acknowledgements;457
7.5.6;21.6 References;457
7.6;Chapter 22 Polaronic charge transport mechanism in DNA;462
7.6.1;22.1 Introduction;462
7.6.2;22.2 Model Hamiltonian for Polaron-Like Charge Transfer along DNA;463
7.6.3;22.3 Localized Polaron-Like States;467
7.6.4;22.4 Charge Transport Established by Mobile Polarons;470
7.6.5;22.5 Charge Transport in Poly(dA)–Poly(dT) and Poly(dG)– Poly(dC) DNA Polymers;473
7.6.6;22.6 Control of ET in DNA;477
7.6.7;22.7 Summary;481
7.6.8;22.8 Acknowledgements;482
7.6.9;22.9 References;482
7.7;Chapter 23 Atomistic models of biological charge transfer;484
7.7.1;23.1 Introduction;484
7.7.2;23.2 Methods;486
7.7.3;23.3 Applications;488
7.7.3.1;23.3.1 DNA oligomers;488
7.7.3.2;23.3.2 Complex arrangements of nucleobases;490
7.7.3.3;23.3.3 Model proteins;490
7.7.4;23.4 Conclusions;491
7.7.5;23.5 Acknowledgements;492
7.7.6;23.6 References;492
7.8;Chapter 24 Nonlinear models in DNA conductivity;494
7.8.1;24.1 Introduction;494
7.8.2;24.2 Quantum Mechanical Model;496
7.8.3;24.3 Band Structure of Polynucleotide Chains;498
7.8.4;24.4 Fröhlich Hamiltonian in Holstein Model;500
7.8.5;24.5 Weak Coupling;501
7.8.6;24.6 Particle Motion in an Electric Field in a Weak Coupling Limit;502
7.8.7;24.7 Case of Strong Coupling;503
7.8.8;24.8 Particle Motion in an Electric Field, at the Limit of the Strong Coupling;505
7.8.9;24.9 Temperature Dependence of Particle Mobility;507
7.8.10;24.10 Low-Temperature Phenomena. Bloch Oscillations;510
7.8.11;24.11 Conclusions;513
7.8.12;24.12 Acknowledgements;513
7.8.13;24.13 References;513
8;Section 5 Electric properties;516
8.1;Chapter 25 Electronic structure of DNA derivatives and mimics by density functional theory;518
8.1.1;25.1 Motivation and Background;518
8.1.1.1;25.1.1 G4-wires;519
8.1.1.2;25.1.2 CuHy-wire;520
8.1.1.3;25.1.3 State-of-the-art DFT calculations of DNA structures;521
8.1.2;25.2 Computational Details;524
8.1.2.1;25.2.1 Method;524
8.1.2.2;25.2.2 Systems;524
8.1.2.2.1;25.2.2.1 G4-wires;524
8.1.2.2.2;25.2.2.2 CuHy-wire;526
8.1.3;25.3 Results and Discussion on G4-Wires;526
8.1.3.1;25.3.1 K(I)-trapping and empty G4-wires;526
8.1.3.2;25.3.2 What are the effects of metal substitution?;530
8.1.3.3;25.3.3 What are the effects of structural deformations?;532
8.1.4;25.4 Results and Discussion on the CuHy-Wire;534
8.1.5;25.5 Perspectives on Other Promising Strategies for Structural Manipulation of DNA: Metal Complexation and Aromatic Expansion;536
8.1.6;25.6 Summary;537
8.1.7;25.7 Acknowledgements;538
8.1.8;25.8 References;538
8.2;Chapter 26 Embedding method for conductance studies of large molecules;542
8.2.1;26.1 Introduction;542
8.2.2;26.2 The Embedding Method;543
8.2.2.1;26.2.1 The embedding potential;543
8.2.2.2;26.2.2 Sub-volume embedding;546
8.2.2.3;26.2.3 Transmission and the embedding potential;548
8.2.3;26.3 Localized Orbitals and Embedding;551
8.2.3.1;26.3.1 The embedding potential as a self-energy;551
8.2.3.2;26.3.2 Localized orbitals and sub-volume embedding;553
8.2.3.3;26.3.3 Density of states;554
8.2.3.4;26.3.4 Transmission through the molecule;555
8.2.4;26.4 Embedding Studies of DNA;557
8.2.4.1;26.4.1 Extended Hückel theory;558
8.2.4.2;26.4.2 Density of states;559
8.2.4.3;26.4.3 Transmission and conductance;562
8.2.5;26.5 References;565
8.3;Chapter 27 Ballistic conductance for all-atom models of native and chemically modified DNA: a review of a Kubo-formula based approach;568
8.3.1;27.1 Introduction;568
8.3.2;27.2 Method of Calculation;569
8.3.3;27.3 Duplexes Under Study;575
8.3.4;27.4 Results and Discussion;575
8.3.5;27.5 Conclusions;577
8.3.6;27.6 Acknowledgements;578
8.3.7;27.7 References;578
9;Subject Index;580
10;Color Plate Section;584