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Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Wydawnictwo Wiley & Sons
Data wydania
Liczba stron 376
Forma publikacji książka w twardej oprawie
Język angielski
ISBN 9781119129240
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Opis książki

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 moleculesThis 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.

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Spis treści

List of Contributors xiPreface xv1 Explicitly Correlated Local Electron Correlation Methods 1Hans-Joachim Werner, Christoph Koppl, Qianli Ma, and Max Schwilk1.1 Introduction 11.2 Benchmark Systems 31.3 Orbital-Invariant MP2 Theory 61.4 Principles of Local Correlation 91.5 Orbital Localization 101.6 Local Virtual Orbitals 121.7 Choice of Domains 241.8 Approximations for Distant Pairs 261.9 Local Coupled-Cluster Methods (LCCSD) 331.10 Triple Excitations 411.11 Local Explicitly Correlated Methods 411.12 Technical Aspects 531.13 Comparison of Local Correlation and Fragment Methods 571.14 Summary 60Appendix A: The LCCSD Equations 63Appendix B: Derivation of the Interaction Matrices 65References 672 Density and Potential Functional Embedding: Theory and Practice 81Kuang Yu, Caroline M. Krauter, Johannes M. Dieterich, and Emily A. Carter2.1 Introduction 812.2 Theoretical Background 822.3 Density Functional Embedding Theory 842.4 Potential Functional Embedding Theory 1012.5 Summary and Outlook 109Acknowledgments 111References 1113 Modeling and Visualization for the Fragment Molecular Orbital Method with the Graphical User Interface FU, and Analyses of Protein-Ligand Binding 119Dmitri G. Fedorov and Kazuo Kitaura3.1 Introduction 1193.2 Overview of FMO 1203.3 Methodology 1203.4 GUI Development 1283.5 Conclusions 136 Acknowledgments 137 References 1374 Molecules-in-Molecules Fragment-Based Method for the Accurate Evaluation of Vibrational and Chiroptical Spectra for Large Molecules 141K. V. Jovan Jose and Krishnan Raghavachari4.1 Introduction 1414.2 Computational Methods and Theory 1424.3 Results and Discussion 1464.4 Summary 1574.5 Conclusions 158 Acknowledgments 159 References 1595 Effective Fragment Molecular Orbital Method 165Casper Steinmann and Jan H. Jensen5.1 Introduction 1655.2 Effective Fragment Molecular Orbital Method 1685.3 Summary and Future Developments 180References 1806 Effective Fragment Potential Method: Past, Present, and Future 183Lyudmila V. Slipchenko and Pradeep K. Gurunathan6.1 Overview of the EFP Method 1836.2 Milestones in the Development of the EFP Method 1856.3 Present: Chemistry at Interfaces and Photobiology 1926.4 Future Directions and Outlook 202References 2037 Nucleation Using the Effective Fragment Potential and Two-Level Parallelism 209Ajitha Devarajan, Alexander Gaenko, Mark S. Gordon, and Theresa L. Windus7.1 Introduction 2097.2 Methods 2117.3 Results 2177.4 Conclusions 223Acknowledgments 223References 2248 Five Years of Density Matrix Embedding Theory 227Sebastian Wouters, Carlos A. Jime´nez-Hoyos, and Garnet K.L. Chan8.1 Quantum Entanglement 2278.2 Density Matrix Embedding Theory 2288.3 Bath Orbitals from a Slater Determinant 2308.4 The Embedding Hamiltonian 2328.5 Self-Consistency 2348.6 Green's Functions 2368.7 Overview of the Literature 2378.8 The One-Band Hubbard Model on the Square Lattice 2378.9 Dissociation of a Linear Hydrogen Chain 2408.10 Summary 240Acknowledgments 241References 2419 Ab initio Ice, Dry Ice, and Liquid Water 245So Hirata, Kandis Gilliard, Xiao He, Murat Kec¸eli, Jinjin Li, Michael A. Salim, Olaseni Sode, and Kiyoshi Yagi9.1 Introduction 2459.2 Computational Method 2479.3 Case Studies 2569.4 Concluding Remarks 2849.5 Disclaimer 284 Acknowledgments 284 References 28510 A Linear-Scaling Divide-and-Conquer Quantum Chemical Method for Open-Shell Systems and Excited States 297Takeshi Yoshikawa and Hiromi Nakai10.1 Introduction 29710.2 Theories for the Divide-and-Conquer Method 29810.3 Assessment of the Divide-and-Conquer Method 30710.4 Conclusion 318References 31911 MFCC-Based Fragmentation Methods for Biomolecules 323Jinfeng Liu, Tong Zhu, Xiao He, and John Z. H. Zhang11.1 Introduction 32311.2 Theory and Applications 32411.3 Conclusion 345 Acknowledgments 346 References 346Index 349

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