Practical Aspects of Computational Chemistry IV (eBook)

Prof. J Leszczynski - Series Editor of COCH, Prof. of Chem at Jackson State University Dr. Manoj Shukla, US Army Engineer, R&D Centre

Preface 5
Contents 7
1 Relativistic Effects and Quantum Electrodynamics in Chemistry 9
1.1 Introduction 9
1.2 The Infinite Order IOTC and DKHn Theories 11
1.3 Potential Energy Curves in the Spin-Free Relativistic DKHn and IOTC Theory 13
1.4 Electronic States in the Spin Dependent Relativistic Theory 16
1.5 Spin-Dependent Two-Component Theories 18
1.6 Quantum Electrodynamic 20
1.7 X-Ray Spectroscopy and the Relativistic and QED Corrections 24
1.8 Concluding Remarks 29
References 31
2 How Can One Locate the Global Energy Minimum for Hydrogen-Bonded Clusters? 33
2.1 Introduction 33
2.2 Basin Hopping and Minima Hopping 35
2.3 Finding the Optimal Hydrogen Bond Topology 37
2.3.1 Representation of H-Bonded Clusters 37
2.3.2 Why Is Topology Optimization Needed? 37
2.3.3 Comparing and Storing Water Cluster Minima 39
2.3.4 Filters to Screen Topologies 39
2.3.5 Topology Optimization by Enumeration 41
2.3.6 Short Topology-Altering Optimization 44
2.3.7 Extended Topology-Altering Optimization 46
2.3.8 Genetic Topology Optimization 48
2.3.9 Comparison of Topology Optimization Methods 50
2.4 Global Optimization of Water Clusters 51
2.4.1 Improved Minima Hopping 51
2.4.2 Accept or Reject? 52
2.4.3 Operator Call Sequences 53
2.4.4 How the Operators Work 54
2.4.5 Performance Tests 59
2.5 General Version of Improved Minima Hopping 61
2.6 Concluding Remarks 61
References 62
3 Optical Parameters of ?-Conjugated Oligomer Chains from the Semiempirical Local Coupled-Cluster Theory 64
3.1 Introduction 64
3.2 Semiempirical Local cue-CCSD Theory 66
3.3 Semiempirical cue-CCSD Calculations of (Hyper)polarizabilities 72
3.3.1 Justification of ?-Electron CCSD Theory 74
3.3.2 The Wave Function Structure in cue-CCSD Approach 76
3.3.3 (Hyper)polarizabilities of ?-Conjugated Systems 81
3.4 Conclusion 105
References 107
4 A Critical Look at Methods for Calculating Charge Transfer Couplings Fast and Accurately 110
4.1 Introduction 110
4.2 DFT Based Methods 112
4.2.1 The Frozen Density Embedding Formalism 112
4.2.2 Constrained Density Functional Theory Applied to Electron Transfer Simulations 119
4.2.3 Fragment Orbital DFT 122
4.2.4 Ultrafast Computations of the Electronic Couplings: The AOM Method 125
4.2.5 Note on Orthogonality 126
4.2.6 A Fully Semiempirical Method: Pathways 127
4.3 High-Accuracy Electronic Couplings 128
4.3.1 GMH Method 129
4.3.2 Other Adiabatic-to-Diabatic Transformation Methods 131
4.3.3 Fragment Charge Difference 132
4.4 Practical Aspects: A Protocol for Running FDE-ET Calculations 133
4.5 Conclusions and Future Directions 137
References 137
5 Methods for Computing Ro-vibrational Energy Levels 142
5.1 Introduction 142
5.2 Deriving the Kinetic Energy Operator 143
5.3 Basis Functions 146
5.3.1 Vibrational Basis Functions 146
5.3.2 Ro-vibrational Basis Functions 148
5.4 Eigensolvers 149
5.4.1 Direct Methods 149
5.4.2 Iterative Methods 149
5.5 Using Iterative Methods with a Product Basis Set 149
5.6 Using Contracted Bases with the Lanczos Method 151
5.6.1 Matrix-Vector Products for ?V 153
5.7 Conclusion 154
References 154
6 Effectively Unpaired Electrons for Singlet States: From Diatomics to Graphene Nanoclusters 157
Abstract 157
6.1 Introduction 158
6.2 General Definitions and Yamaguchi’s Index 159
6.3 Head-Gordon’s Index 162
6.4 Unpairing Indices from Collectivity and Entropy Numbers 163
6.5 Hole-Particle Densities and Head-Gordon’s Index 166
6.6 Using the High-Order Density Matrices 170
6.7 Algorithmic Aspects 172
6.8 Spin Correlations 173
6.9 Spin-Polarization Indices and Antiferromagnetic Image of Molecule 175
6.10 Unpairing in Excited States 180
6.11 Conjugated Hydrocarbons in ?-Electron Schemes 184
6.12 Giant Hydrocarbons and Nanographenes in a Spin-Polarized Hückel-like Scheme 190
6.13 Electron Unpairing in Strong Fields 196
6.14 In Search of Better EUE Measures 198
6.15 Concluding Remarks 200
Acknowledgment 201
Appendix A: Duality Symmetry and Generalized EUE Indices 202
Appendix B: Density Matrix and NOON for QCTB 204
Appendix C: Generalized Hole-Particle Indices 206
References 208
7 In Silico Assembly of Carbon-Based Nanodevices 213
Abstract 213
7.1 Introduction 214
7.1.1 Engineering Carbon Nanostructures 214
7.1.2 A Peptide Covalent Bond Between Carbon Nanotube and DNA 214
7.1.3 A Carbon Nanotube-DNA Origami Junction 215
7.1.4 Observation of Electrical Gating by ssDNA Upon Binding to Carbon Nanotube 215
7.1.5 Carbon Nanotubes for Drug-Delivery 216
7.2 Irradiation-Induced Defects in a Silica-Supported Carbon Nanotube 216
7.3 Gating Mechanism of DNA Wrapping on Carbon Nanotube 219
7.4 Assembly and Electron Transport Characteristic of a DNA-Graphene Junction 222
7.5 The Hydrodynamic Volume of Maximum PEGylated Carbon Nanotube 228
7.6 Summary and Conclusions 234
References 235
8 Computational Mechanochemistry 239
8.1 Introduction to Mechanochemistry. What Is It? 239
8.2 Computations 240
8.2.1 Explicit External Force Approach 241
8.2.2 Explicit External Force at Finite Temperatures 241
8.3 Isotensionl Ab Initio Molecular Dynamics 242
8.3.1 Mechano-Stereochemistry of Cyclopropane Ring-Opening Reactions 242
8.3.2 SN2 at Sulfur: Disulfide Bond Reduction 244
8.3.3 From Simple Diethyl Disulfide Model into Protein 245
References 248
9 Hydrogen Bond and Other Lewis Acid–Lewis Base Interactions—Mechanisms of Formation 250
Abstract 250
9.1 Which Interactions Are Classified as the Lewis Acid–Lewis Base Ones? 250
9.2 Mechanisms of Hydrogen Bond Formation 260
9.3 Mechanisms Accompanying Formation of Lewis Acid–Lewis Base Links 266
9.4 The Electron Charge Shifts in a Case of Cooperativity Effects 275
9.5 Summary 279
Acknowledgments 280
References 280
10 Iodine Containing Drugs: Complexes of Molecular Iodine and Tri-iodide with Bioorganic Ligands and Lithium Halogenides in Aqueous Solutions 283
Abstract 283
10.1 Introduction 284
10.2 Computational Details 287
10.3 Results and Discussion 288
10.4 The Mechanism of Anti-HIV Action 300
10.5 Conclusion 303
References 303
11 Detailed Atomistic Modeling of Si(110) Passivation by Atomic Layer Deposition of Al2O3 306
Abstract 306
11.1 Introduction 307
11.2 Computational Details 309
11.3 Results and Discussion 313
11.3.1 Si Slabs 313
11.3.2 Oxidation 316
11.3.2.1 Atomic Oxygen 316
11.3.2.2 Oxidation via Joining with Al16O30 with or Without Pre-oxidation Using Oxygen Atoms 322
11.3.3 Al Deposition 325
11.3.4 Junction with the Al16O30 Fragment After Al Deposition 336
11.4 Discussion 344
11.4.1 Structural Distortion of the Defects 345
11.4.2 Boehmite Formation 346
11.4.3 Joining Procedure: Pros et Cons 347
11.5 Conclusions 350
Acknowledgments 351
References 352
12 Development of the Latest Tools for Building up “Nano-QSAR”: Quantitative Features—Property/Activity Relationships (QFPRs/QFARs) 355
Abstract 355
12.1 Introduction 356
12.2 Methods 368
12.2.1 Data 368
12.2.1.1 Thermal Conductivity of Micro-Electro-Mechanical Systems 368
12.2.1.2 Mutagenicity of Fullerene Under Various Conditions 368
12.2.1.3 Prediction of Membrane Damage by Various TiO2 Nanoparticles 372
12.2.1.4 Prediction of Membrane Damage by ZnO and TiO2 Nanoparticles 374
12.2.1.5 Prediction of Membrane Damage by Nano Metal Oxides 376
12.2.2 Principles of Building up Optimal Descriptors 381
12.2.3 Calculation of the Optimal Descriptors 386
12.3 Results and Discussion 386
12.3.1 QFPR for Thermal Conductivity of MEMS 386
12.3.2 QFAR for Mutagenicity (TA100) of Fullerene 387
12.3.3 QFAR for Membrane Damage by Various TiO2 Nanoparticles 388
12.3.4 QFAR for Membrane Damage by Means of Various TiO2 and ZnO Nanoparticles 389
12.3.5 QFAR for Cellular Membrane Damage (CMD) by Metal Oxide Nanoparticles 390
12.4 Conclusions 396
Acknowledgments 397
References 397
Index 399