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Theory and Applications of Computational Chemistry the First Forty Years

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Theory and Applications of Computational Chemistry the First Forty Years Theory and Applications of Computational Chemistry The First Forty Years Editors CLIFFORD E. DYKSTRA Department of Chemistry Indiana University-Purdue University Indianapolis (IUPUI) Indianapolis, IN, U.S.A. GERNOT FRENKING Fachbereich Chemie Phillips- Universität Marburg Marburg, Germany KWANG S. KIM Department of Chemistry Pohang University of Science and Technology Pohang, Republic of Korea GUSTAVO E. SCUSERIA Department of Chemistry Rice University Houston, TX, U.S.A. Amsterdam - Boston - Heidelberg - London - New York - Oxford Paris - San Diego - San Francisco - Singapore - Sydney - Tokyo vii Contents Chapter 1. Computing technologies, theories, and algorithms. The making of 40 years and more of theoretical and computational chemistry Clifford E. Dykstra, Gernot Frenking, Kwang S. Kim and Gustavo E. Scuseria 1 1.1 Introduction 1 1.2 Technology and methodology 2 1.3 Outlook 6 1.4 Acknowledgements 7 1.5 References 7 Chapter 2. Dynamical, time-dependent view of molecular theory Yngve Öhrn and Erik Deumens 9 2.1 Introduction 9 2.2 Molecular Hamiltonian 12 2.3 The time-dependent variational principle in quantum mechanics 18 2.4 Coherent states 21 2.4.1 Gaussian wave packet as a coherent State 21 2.4.1.1 Gaussian wave packet with evolving width 25 2.4.2 The determinantal coherent State for N electrons 29 2.5 Minimal electron nuclear dynamics (END) 32 2.6 Rendering of dynamics 37 2.7 Acknowledgements 39 2.8 References 39 Chapter 3. Computation of non-covalent binding affinities J. Andrew McCammon 41 3.1 Introduction 41 3.2 Current methods 42 VIII Contents 3.3 Future prospects 43 3.4 Concluding perspective: molecular dynamics simulations and drug discovery 44 3.5 Acknowledgements 45 3.6 References 45 Chapter 4. Electrodynamics in computational chemistry Liniin Zhao, Shengli Zou, Encai Hao and George C. Schatz 47 4.1 Introduction 47 4.2 Electrodynamics of metal nanoparticles 49 4.2.1 Methods 49 4.2.2 Dielectric constants 50 4.2.3 Spherical particles 51 4.2.4 Effects of particle shape 51 4.2.5 Effects of solvent and of surrounding layers 52 4.2.6 Local electric fields and SERS 55 4.3 Electronic structure studies of surface enhanced Raman spectra 59 4.3.1 Surface modeis and electronic structure methods 59 4.3.2 Applications 60 4.4 Acknowledgements 63 4.5 References 64 Chapter 5. Variational transition State theory Bruce C. Garrett and Donald G. Truhlar 67 5.1 Introduction 67 5.2 Gas phase reactions 68 5.2.1 Classical mechanical theory 68 5.2.2 Inclusion of quantum mechanical effects 72 5.2.3 Improved prescriptions for the reaction coordinate and dividing surface 75 5.2.4 Spectroscopy of the transition State 77 5.2.5 Applications 77 5.3 Reactions in Condensed phases 77 5.3.1 Reactions in rigid environments and application to reactions in crystals or at crystal-vapor interfaces 78 5.3.2 Reactions in fluid environments with a Single reaction coordinate 79 5.3.3 Reactions in fluid environments with an ensemble of reaction coordinates 82 5.4 Summary and conclusions 83 5.5 Acknowledgements 84 5.6 References 84 Contents ix Chapter 6. Computational chemistry: attempting to simulate large molecular Systems Enrico Clementi 89 6.1 Introduction 89 6.2 The long preparation and the seeding time: 1930-1960 90 6.3 Quantum Chemistry and the Laboratory of Molecular Structure and Spectra, Chicago, 1960 92 6.4 My Hartree-Fock, MC-SCF and density functional period: the 1960 decade 95 6.5 From Schrödinger to Newton; my second Simulation period 103 6.6 Statistical and fluid dynamic simulations, and also Computers hardware development in the Hudson Valley 105 6.7 Back to the beginning: a new approach to an old problem 108 6.8 Conclusions 111 6.9 Acknowledgements 111 6.10 References 111 Chapter 7. The beginnings of coupled-cluster theory: an eyewitness account Josef Paldus 115 7.1 'Prehistory' 116 7.2 Gestation 119 7.3 Birth 124 7.4 Growing pains 129 7.5 Maturation 132 7.6 Quovadis? 134 7.7 Acknowledgements 140 7.8 References 140 Chapter 8. Controlling quantum phenomena with photonic reagents Herschel Rabitz 149 8.1 How can control of quantum dynamics phenomena be achieved?. ... 149 8.2 Why does quantum control with photonic reagents appear to be so easy? 156 8.3 What is occurring during the process of Controlling quantum dynamics phenomena? 158 8.4 Conclusion 162 8.5 References 162 Chapter 9. First-principles calculations of anharmonic vibrational spectroscopy of large molecules R.B. Gerber, GM. Chaban, B. Brauer and Y. Miller 165 9.1 Introduction 165 x Contents 9.2 Anharmonic vibrational spectroscopy methods 167 9.2.1 Perturbation theory 168 9.2.2 The vibrational self-consistent field approach 169 9.2.3 Grid methods 172 9.2.4 Diffusion quantum Monte Carlo 172 9.2.5 Semiclassical methods 173 9.3 Ab initio vibrational spectroscopy 173 9.3.1 Fitting ab initio potentials versus direct ab initio spectroscopy calculations 173 9.3.2 Ab initio VSCF and CC-VSCF 174 9.3.2.1 VSCF equations 174 9.3.2.2 Representations of the potential 175 9.3.2.3 CC-VSCF equations 177 9.3.2.4 Anharmonic infrared intensities 178 9.3.2.5 Electronic structure methods used with VSCF 178 9.3.2.6 Improvements and extensions of VSCF and CC-VSCF 179 9.3.3 Ab initio anharmonic calculations using perturbation theory 180 9.4 Applications and Performance 180 9.4.1 Performance for large molecules 180 9.4.2 Spectroscopy calculations as a test of ab initio and DFT force fields 182 9.4.3 Vibrational spectroscopy of hydrogen-bonded Clusters 182 9.4.4 Ab initio spectroscopy and the identification of new molecular species 185 9.4.5 Ab initio spectroscopy and the elucidation of complex spectra 186 9.4.6 Overtones and combination mode transitions 186 9.4.7 Open-shell Systems 187 9.5 Future directions 188 9.5.1 Larger Systems 188 9.5.2 Quest for increased accuracy 189 9.5.3 Time-domain spectroscopy 189 9.6 Acknowledgements 189 9.7 References 190 Chapter 10. Finding minima, transition states, and following reaction pathways on ab initio potential energy surfaces Hrant P. Hratchian and H. Bernhard Schlegel 195 10.1 Introduction 195 10.2 Background 196 Contents xi 10.2.1 Potential energy surfaces 196 10.2.2 Analytic PES derivatives 198 10.2.3 Coordinate Systems 201 10.3 Minimization 202 10.3.1 Newton methods 203 10.3.2 GDIIS 207 10.3.3 QM/MM optimizations 209 10.3.4 Finding surface intersections and points of dosest approach 210 10.3.5 Practical considerations 212 10.3.5.1 Starting structure 212 10.3.5.2 Coordinate System 213 10.3.5.3 Minimization algorithm 215 10.3.5.4 Hessian quality 215 10.3.5.5 Tips for difficult minimizations 217 10.4 Transition State optimization 218 10.4.1 Local methods 219 10.4.2 Climbing, bracketing, and interpolation methods 220 10.4.3 Path optimization methods 224 10.4.4 Practical considerations 227 10.4.4.1 Building an initial structure 227 10.4.4.2 Coordinate System 228 10.4.4.3 Algorithm choice 229 10.4.4.4 Hessian quality 230 10.4.4.5 Verifying TSs 230 10.5 Reaction path following 230 10.5.1 First-order methods 232 10.5.2 Second-order methods 234 10.5.3 Higher order integrators 236 10.5.4 Dynamic reaction path 237 10.5.5 Practical considerations 238 10.5.5.1 Algorithm choice 238 10.5.5.2 Projected frequencies and coupling matrix elements 241 10.5.5.3 Bifurcation 242 10.5.5.4 Tips for difficult reaction path calculations 242 10.6 Summary and outlook 243 10.7 References 243 Chapter 11. Progress in the quantum description of vibrational motion of polyatomic molecules Joel M. Bowman, Stuart Carter and Nicholas C. Handy. ... 251 11.1 Introduction 251 11.2 Beyond the harmonic approximation 252 xii Contents 11.3 Vibrational CI theory 254 11.3.1 The n-mode representation of the potential 255 11.3.2 Results of selected calculations 257 11.3.3 The 'Reaction Path' Version of MULTIMODE 260 11.4 Current bottlenecks and future progress 263 11.5 Acknowledgements 265 11.6 References 265 Chapter 12. Toward accurate computations in photobiology Adalgisa Sinicropi and Massimo Olivucci 269 12.1 Introduction 269 12.2 Ab initio quantum chemical methods for excited states 272 12.3 Fate of light energy in photobiology 276 12.3.1 GFP spectroscopy 278 12.3.2 Rh spectroscopy 279 12.3.3 The photoisomerization path of Rh 282 12.3.4 Nature of the energy storage 284 12.4 From photobiology to biomimetic molecular switches 285 12.5 Conclusions 287 12.6 Acknowledgements 288 12.7 References 288 Chapter 13. The nature of the chemical boncl in the light of an energy decomposition analysis Matthias Lein and Gernot Frenking 291 13.1 Introduction 291 13.2 Energy decomposition analysis 295 13.3 Bonding in main-group Compounds 296 13.3.1 Diatomic molecules H2, N2, CO, BF 297 13.3.2 Dipnicogens N2-Bi2 302 13.3.3 Dihalogens F2-I2 303 13.3.4 Nonpolar Single bonds of the first octal row H„E-EH„ (E = Li-F; n = 0-3) 305 13.3.5 Nonpolar multiple bonds HB=BH, H2C=CH2, HN=NH andHC^CH 308 13.3.6 Nonpolar group-14 bonds H3E-EH3 (E = C-Pb) 310 13.3.7 Donor-acceptor bonds Y3B-NX3 and Y3B-PX3 (X, Y = H, Me, Cl) 311 13.3.8 Main group metallocenes ECp2 (E = Be-Ba, Zn, Si-Pb) and ECp (E = Li-Cs, B-Tl) 314 13.3.9 Bonding in SF6 and XeF6 and a comparison with WF6 ...
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