Fragmentation: Toward Accurate Calculations on Complex Molecular Systems (eBook)

Mark S. Gordon (Herausgeber)

eBook Download: PDF

2017
John Wiley & Sons (Verlag)
978-1-119-12925-7 (ISBN)

Infos

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system.

Topics covered include:

• Fragmentation methods
• Embedding methods
• Explicitly correlated local electron correlation methods
• Fragment molecular orbital method
• Methods for treating large molecules

This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Edited by
MARK S. GORDON, Department of Chemistry, Iowa State University, Ames, USA

Inhalt

Fragmentation 3
Contents 7
List of Contributors 13
Preface 17
1 Explicitly Correlated Local Electron Correlation Methods 19
1.1 Introduction 19
1.2 Benchmark Systems 21
1.3 Orbital-Invariant MP2 Theory 24
1.4 Principles of Local Correlation 27
1.5 Orbital Localization 28
1.6 Local Virtual Orbitals 30
1.6.1 Pseudo-Canonical Pair-Specific Orbitals 30
1.6.2 Projected Atomic Orbitals 34
1.6.3 Pair Natural Orbitals 36
1.6.4 Linear Scaling PNO Generation 40
1.6.5 Orbital-Specific Virtuals (OSVs) 41
1.7 Choice of Domains 42
1.8 Approximations for Distant Pairs 44
1.8.1 Bipolar Multipole Approximations of Electron Repulsion Integrals 44
1.8.2 Approximations of Distant Pair Energies 47
1.9 Local Coupled-Cluster Methods (LCCSD) 51
1.9.1 Weak Pair Approximations 53
1.9.2 Long-Range Cancellations of Terms in the LCCSD Equations 54
1.9.3 Projection Approximations 57
1.10 Triple Excitations 59
1.11 Local Explicitly Correlated Methods 59
1.11.1 PNO-LMP2-F12 60
1.11.2 PNO-LCCSD-F12 67
1.12 Technical Aspects 71
1.12.1 Local Density Fitting 71
1.12.2 Parallelization 74
1.13 Comparison of Local Correlation and Fragment Methods 75
1.14 Summary 78
Appendix A: The LCCSD Equations 81
Appendix B: Derivation of the Interaction Matrices 83
References 85
2 Density and Potential Functional Embedding: Theory and Practice 99
2.1 Introduction 99
2.2 Theoretical Background 100
2.3 Density Functional Embedding Theory 102
2.3.1 Basic Theory 102
2.3.1.1 Definition of the Embedding Potential 103
2.3.1.2 Optimization Procedure 103
2.3.2 Embedding Potential Construction—Implementations in Planewave Codes 104
2.3.2.1 Implementation with Pseudopotentials in ABINIT 105
2.3.2.2 Implementation with PAW in VASP 105
2.3.2.3 Penalty Functions—Damping the Unphysical Oscillations 109
2.3.2.4 Illustrative Example 111
2.3.3 Embedded Cluster Calculations 112
2.3.3.1 Calculation of Embedding Integrals 112
2.3.3.2 Evaluation of the Total Energy 114
2.3.3.3 Examples 115
2.4 Potential Functional EmbeddingTheory 119
2.4.1 Basic Theories and Technical Details 120
2.4.1.1 Definition of Energies 120
2.4.1.2 Optimized Effective Potential (OEP) Scheme for Exact Kinetic Energy 121
2.4.1.3 Energy Gradient 122
2.4.1.4 Summary of the Code Structure 123
2.4.2 Illustrative Examples 124
2.4.2.1 AlP Diatomic 125
2.4.2.2 H2O on MgO (001) 126
2.5 Summary and Outlook 127
Acknowledgments 129
References 129
3 Modeling and Visualization for the Fragment Molecular Orbital Method with the Graphical User Interface FU, and Analyses of Protein–Ligand Binding 137
3.1 Introduction 137
3.2 Overview of FMO 138
3.3 Methodology 138
3.3.1 FMO/PCM Formulation in the Presence of Dummy Atoms 138
3.3.2 New Analyses Defining the Desolvation Penalty in the Protein–Ligand Binding 140
3.3.2.1 Asymmetric Binding Analysis (ABA) 140
3.3.2.2 Symmetric Binding Analysis (SBA) 141
3.3.2.3 Symmetric Binding Analysis with Separated Cavitation (SBAC) 141
3.3.2.4 Fragment-Wise Elaboration of SBA in FMO 142
3.3.2.5 Fragment-Wise Elaboration of SBAC 145
3.3.3 Application of Analyses to Protein–Ligand Binding 145
3.4 GUI Development 146
3.4.1 Outline of FU 146
3.4.2 Modeling and Result Visualization 147
3.4.2.1 Modeling of an FKBP Protein Complex 147
3.4.2.2 Creating FMO Input 147
3.4.2.3 Running FMO in GAMESS 149
3.4.2.4 Visualizing FMO Results 149
3.4.3 An Overview of Using FU for a Complex System 151
3.4.4 Examples of Scripting in FU 151
3.4.4.1 Converting Multiple PDB Files into Z-matrix Files 151
3.4.4.2 Drawing Dipole Moments with Arrows 153
3.5 Conclusions 154
Acknowledgments 155
References 155
4 Molecules-in-Molecules Fragment-Based Method for the Accurate Evaluation of Vibrational and Chiroptical Spectra for Large Molecules 159
4.1 Introduction 159
4.2 Computational Methods and Theory 160
4.3 Results and Discussion 164
4.3.1 MIM Method for Geometry Optimization 164
4.3.2 MIM Method for Evaluating IR Spectra (MIM-IR) 164
4.3.3 MIM Method for Evaluating Raman Spectra (MIM-Raman) 167
4.3.4 MIM Method for Evaluating VCD Spectra (MIM-VCD) 169
4.3.5 MIM Method for Evaluating ROA Spectra (MIM-ROA) 172
4.3.6 Two-Step-MIM Scheme for Evaluating Raman and ROA Spectra 174
4.4 Summary 175
4.5 Conclusions 176
Acknowledgments 177
References 177
5 Effective Fragment Molecular Orbital Method 183
5.1 Introduction 183
5.1.1 Effective Fragment Potentials 184
5.1.2 Fragment Molecular Orbital Method 185
5.2 Effective Fragment Molecular Orbital Method 186
5.2.1 Correlation Energies in the EFMO Method 188
5.2.2 The EFMO Gradient 190
5.2.3 Timings and Computational Efficiency 191
5.2.4 Biochemistry with EFMO 192
5.2.5 Fully Integrated EFMO 196
5.2.6 Remarks, Notes, and Comments 197
5.3 Summary and Future Developments 198
References 198
6 Effective Fragment Potential Method: Past, Present, and Future 201
6.1 Overview of the EFP Method 201
6.2 Milestones in the Development of the EFP Method 203
6.2.1 EFP1 Water Model 203
6.2.2 EFP (EFP2) General Model 205
6.3 Present: Chemistry at Interfaces and Photobiology 210
6.3.1 OH Radical Solvated inWater 210
6.3.2 EFP for Macromolecules and Polymers 216
6.4 Future Directions and Outlook 220
References 221
7 Nucleation Using the Effective Fragment Potential and Two-Level Parallelism 227
7.1 Introduction 227
7.2 Methods 229
7.2.1 Brief Overview of DNTMC 229
7.2.2 Brief Overview of EFP 231
7.2.3 Overview of the Two-Level Parallelism Approach 233
7.3 Results 235
7.3.1 Evaporation Rate of Water Hexamer Cluster at 243K 235
7.3.2 Ion Mediated Nucleation 236
7.3.3 Evaporation Rate of Sulfuric Acid from Neutral Sulfuric Acid Dimer Clusters 237
7.3.4 Two-Level Parallel DNTEFP Performance Analysis 239
7.4 Conclusions 241
Acknowledgments 241
References 242
8 Five Years of Density Matrix Embedding Theory 245
8.1 Quantum Entanglement 245
8.2 Density Matrix EmbeddingTheory 246
8.3 Bath Orbitals from a Slater Determinant 248
8.4 The Embedding Hamiltonian 250
8.5 Self-Consistency 252
8.6 Green’s Functions 254
8.7 Overview of the Literature 255
8.8 The One-Band Hubbard Model on the Square Lattice 255
8.9 Dissociation of a Linear Hydrogen Chain 258
8.10 Summary 258
Acknowledgments 259
References 259
9 Ab initio Ice, Dry Ice, and Liquid Water 263
9.1 Introduction 263
9.2 Computational Method 265
9.2.1 Internal Energy 266
9.2.2 Structure and Phonons 268
9.2.3 Spectra 269
9.2.4 Pressure Effects 270
9.2.5 Temperature Effects 271
9.2.6 Born–Oppenheimer Molecular Dynamics 273
9.3 Case Studies 274
9.3.1 Ice-Ih 274
9.3.2 Ice-HDA 277
9.3.3 Ice-VIII 280
9.3.4 Liquid Water 284
9.3.5 CO2-I: Pressure Tuning of Fermi Resonance 290
9.3.6 CO2-I and III: Solid–Solid Phase Transition 295
9.3.7 CO2-I: Thermal Expansion 298
9.4 Concluding Remarks 302
9.5 Disclaimer 302
Acknowledgments 302
References 303
10 A Linear-Scaling Divide-and-Conquer Quantum Chemical Method for Open-Shell Systems and Excited States 315
10.1 Introduction 315
10.2 Theories for the Divide-and-Conquer Method 316
10.2.1 Review of DC-SCF and DC-Based Correlation Theories 316
10.2.1.1 DC-HF/DFT 316
10.2.1.2 DC-Based Correlation Theory 318
10.2.1.3 Dual-Buffer DC-Based Correlation Method 319
10.2.2 Linear-Scaling Divide-and-Conquer Method for Open-Shell Systems 320
10.2.2.1 DC-USCF and DC-UMP2 320
10.2.2.2 Expected Value of the Squared Spin Operator ?S2 322
10.2.3 Linear-Scaling Divide-and-Conquer Method for Excited-State Calculations 322
10.2.3.1 DC-CIS/TDDFT 322
10.2.3.2 DC-SAC/SACCI 323
10.3 Assessment of the Divide-and-Conquer Method 325
10.3.1 Divide-and-Conquer Calculations for Open-Shell Systems 325
10.3.1.1 DC-USCF and DC-UMP2 325
10.3.2 Excited-State Calculations based on the Divide-and-Conquer Method 331
10.3.2.1 Conjugated Aldehyde 331
10.3.2.2 Photoactive Yellow Protein 333
10.4 Conclusion 336
References 337
11 MFCC-Based Fragmentation Methods for Biomolecules 341
11.1 Introduction 341
11.2 Theory and Applications 342
11.2.1 The MFCC Approach 342
11.2.2 Electron Density and Total Energy 344
11.2.3 The EE-GMFCC Method for Energy Calculation 346
11.2.4 The EE-GMFCC-CPCM Method for Protein Solvation Energy 349
11.2.5 The EE-GMFCC-CPCM Method for Protein–Ligand Binding Energy 355
11.2.6 The EE-GMFCC Method for Geometry Optimization and Vibrational Spectrum of Proteins 356
11.2.7 The EE-GMFCC-Based Ab Initio Molecular Dynamics for Proteins 358
11.3 Conclusion 363
Acknowledgments 364
References 364
Index 367
EULA 377

Produkt-Details

• Erscheint lt. Verlag: 2.8.2017
• Sprache: englisch
• Themenwelt: Mathematik / Informatik ► Informatik ► Theorie / Studium
• Themenwelt: Naturwissenschaften ► Biologie
• Themenwelt: Naturwissenschaften ► Chemie ► Organische Chemie
• Themenwelt: Naturwissenschaften ► Chemie ► Physikalische Chemie
• Themenwelt: Technik ► Maschinenbau
• Schlagworte: Bioinformatics & Computational Biology • Bioinformatik • Bioinformatik u. Computersimulationen in der Biowissenschaften • Biowissenschaften • charge transfer • Chemie • Chemistry • Computational Chemistry & Molecular Modeling • Computational Chemistry u. Molecular Modeling • Coupled Cluster • EFP • Embedding • FMO • Fragment • Fragmentation • Life Sciences • LMO • Local • Materials Science • Materialwissenschaften • Materialwissenschaften / Theorie, Modellierung u. Simulation • Monte Carlo • Theory, Modeling & Simulation • Water
• ISBN-10: 1-119-12925-7 / 1119129257
• ISBN-13: 978-1-119-12925-7 / 9781119129257