Hyperchem Computation Chemistry

Part 2 Theory and Methods......Page 1 All rights reserved......Page 2 Who Should Read this Guide?......Page 17 Annotated Bibliography......Page 18 Practical Guide......Page 21 What is Computational Chemistry?......Page 23 Investigating the Reactivity of Molecules......Page 24 Evaluating Chemical Pathways and Mechanisms......Page 25 Studying the Dynamic Behavior of Molecules......Page 26 Exploring Potential Energy Surfaces......Page 27 Complexity of Potential Energy Surfaces......Page 30 Geometry Optimization......Page 32 Transition State Search......Page 33 Langevin Dynamics......Page 34 Monte Carlo Simulations......Page 35 Molecular Mechanics......Page 37 Bonds and Angles......Page 39 Torsions......Page 41 van der Waals Interactions and Hydrogen Bonding......Page 42 Electrostatic Potential......Page 43 United versus All Atom Force Fields......Page 44 Cutoffs......Page 45 Quantum Mechanics......Page 47 Calculating Electronic Potential Energy......Page 48 Exclusion Principle......Page 50 Simplified Wave Functions......Page 52 Configuration Interaction......Page 53 Møller-Plesset Perturbation Theory......Page 56 Orbital Occupancy......Page 57 Atomic Orbitals and Their Interactions......Page 58 SCF Technique......Page 59 RHF and UHF......Page 60 Multiplicity Considerations......Page 61 RHF Half-Electron Technique......Page 62 SCF Convergence......Page 63 Calculation Results......Page 64 Quantitative Results......Page 65 Single Point Calculations......Page 67 Total Spin Density......Page 68 Examples of Single Point Calculations......Page 69 Geometry Optimizations......Page 73 Steepest Descent......Page 74 Conjugate Gradient......Page 75 Setting Convergence Criteria......Page 76 Examples of Geometry Optimizations......Page 77 Solvation and Periodic Boundary Conditions......Page 78 2. Characterize a potential energy surface for a c.........Page 81 Eigenvector Following......Page 82 Synchronous Transit......Page 83 Molecular Dynamics......Page 85 Integration Algorithm......Page 86 Conservation of Energy......Page 87 Temperature Control......Page 88 Initial Conditions and Heating......Page 89 Equilibration and Data Collection......Page 90 Collecting Data......Page 91 Examples of Molecular Dynamics Simulations......Page 92 Constant Temperature versus Constant Energy......Page 93 Quenched Dynamics......Page 94 Randomization During Molecular Dynamics......Page 95 When is Conformational Space Adequately Sampled?......Page 96 Using Geometric Restraints......Page 97 Limiting Conformational Changes during High Temper.........Page 98 Freezing Part of a System......Page 99 Choice of Dielectric Constant......Page 100 Collecting Averages from Simulations......Page 101 9. Calculate the ratio.......Page 102 Conformational Searches......Page 103 Simulation or Run Time......Page 104 Step Size......Page 105 Bond Breaking......Page 106 Langevin Dynamics......Page 107 Integration Algorithm......Page 108 Time Step......Page 109 Friction coefficient......Page 110 Introduction......Page 111 Background and Method......Page 112 Temperature......Page 113 Equilibration and Statistical Averaging......Page 114 Heating and Cooling......Page 115 MM+......Page 117 Dielectric Function......Page 119 Nonbonded Cutoffs......Page 120 Restraints......Page 121 OPLS......Page 122 Obtaining a Starting Structure......Page 123 Calculating Part of a Molecular System......Page 124 Choosing a Basis Set......Page 125 Charge and Spin Multiplicity......Page 127 Convergence Acceleration......Page 128 Two-electron Integral Cutoff......Page 129 Raffenetti Two-Electron Integral Format......Page 130 Number of d Orbitals......Page 131 Ghost-Atoms......Page 132 Hückel Constant......Page 133 Convergence Criteria......Page 134 Configuration Interaction......Page 135 Types of Calculations......Page 136 Single Point Calculations and CI......Page 137 Transition State Search......Page 138 Energy Conservation in Molecular Dynamics Calculat.........Page 139 Vibrational Spectrum......Page 140 Extended Hückel Method......Page 141 Defining Electron-Electron Interactions......Page 142 CNDO, INDO, MINDO/3, ZINDO/1, and ZINDO/S Methods......Page 143 Parameterization......Page 144 Energies of Molecules......Page 146 Geometries of Molecules......Page 148 Energies of Transition States......Page 149 Dipole Moments......Page 150 Electrostatic Potential......Page 151 Atomic Charges......Page 153 Chemical Reactivity......Page 154 Atomic Charges and Reactivity......Page 156 Frontier Molecular Orbitals......Page 157 Vibrational Analysis and Infrared Spectroscopy......Page 159 Experimental Characteristic IR Fundamental Frequen.........Page 160 UV-visible Spectra......Page 163 Extended Hückel......Page 164 MINDO/3......Page 165 PM3......Page 166 ZINDO/S......Page 167 Further Reading......Page 168 Theory and Methods......Page 169 HyperChem Architecture......Page 171 The Back Ends......Page 172 HyperChem Philosophy......Page 173 Potential Energy Surfaces......Page 174 Single Point......Page 176 The Born-Oppenheimer Approximation......Page 177 The Hamiltonian of a Collection of Nuclei and Elec.........Page 178 The Nuclear Hamiltonian......Page 179 Molecular Mechanics versus Quantum Mechanics......Page 180 Classical Mechanics on a Potential Energy Surface......Page 181 Force-Energy Generators......Page 182 Molecular Mechanics......Page 183 Background......Page 184 Definition of Atom Type......Page 185 The Typing Rules......Page 186 Redefining or Adding Types......Page 188 Force Fields......Page 189 Energetic Terms in the Potential......Page 190 Dihedrals......Page 191 van der Waals......Page 192 Hydrogen Bonding......Page 195 Effective Dielectric Constants......Page 196 Cutoffs......Page 197 MM+......Page 198 Bond Stretching......Page 199 Bond Dipoles......Page 200 Angle Bending......Page 201 Out-of-Plane Bending......Page 202 van der Waals......Page 203 AMBER......Page 204 Dihedrals......Page 205 Electrostatic......Page 206 OPLS......Page 207 Electrostatic......Page 208 Bond Stretching......Page 209 Improper Dihedrals......Page 210 van der Waals......Page 211 Parameter Sets......Page 212 Modifying Existing Parameter Sets......Page 213 Creating New Parameter Sets......Page 214 Chem.ini or Registry Setup of Force Field Options......Page 215 Periodic Boundary Conditions and Solvent......Page 216 The Periodic Boundary Conditions......Page 217 Details of Solvation Methodology......Page 218 2. Use Restraints in the Setup menu to bring up th.........Page 219 The Default MM+ Force Field......Page 220 The Wild Card Approach......Page 221 The Default Force Field......Page 222 1. If the number of valence electrons is 0 or 8, t.........Page 223 12. If the number of electrons is 6 (O, S, etc.), .........Page 224 Bond Stretching......Page 225 Parameters for Butadiene and Related Molecules......Page 226 Torsions......Page 227 2. Aromatic bonds (as in benzene) have a two-fold .........Page 228 van der Waals......Page 229 Quantum Mechanics......Page 231 Background......Page 232 Approximate Solutions of the Schrödinger equation......Page 233 Charge and Multiplicity......Page 234 Molecular Orbitals......Page 235 Orbital Energy Diagrams......Page 236 The MO-LCAO Approximation......Page 237 The Matrix equations for the Molecular Orbitals......Page 238 Solving for the Molecular Orbitals......Page 239 1. Guess the position of each electron, that is, y.........Page 240 The Roothaan equations......Page 241 Spin Pairing......Page 242 Pople-Nesbet Unrestricted equations......Page 243 Convergence......Page 245 Spin Pairing—Restricted or Unrestricted?......Page 246 Electronic States......Page 248 4. Request configuration interaction, if you want .........Page 250 Configuration Interaction......Page 251 MP2 Correlation Energy......Page 252 The Neglect of Differential Overlap Approximation......Page 254 Contour Plots......Page 256 Total Electron Density......Page 257 Orbital Plots......Page 259 Electrostatic Potential......Page 260 Choosing the Classical–Quantum Boundary......Page 262 Capping Atoms and their Parameters......Page 264 Supported Methods......Page 266 Ab Initio Method......Page 267 Normalized Primitive Gaussian Functions......Page 269 Minimal Basis Sets: STO-3G......Page 270 Split-Valence Basis Sets......Page 273 Polarized Basis Sets......Page 276 Two-Electron Integrals......Page 278 Regular Integral Format......Page 279 Raffenetti Integral Format......Page 280 Direct SCF Calculation......Page 281 Projected CNDO/INDO......Page 282 Ghost-Atoms......Page 283 Basic Method......Page 284 Valence Atomic Orbitals......Page 285 Hamiltonian Matrix Elements......Page 286 Mixed Model......Page 288 The CNDO equations......Page 289 Mixed Model (CNDO and INDO)......Page 292 Exchange Phenomena......Page 293 Differences Between INDO and CNDO......Page 294 Spin Interactions in INDO......Page 295 MINDO/3......Page 296 One-Center One-Electron Integral Hmm......Page 297 One-Center Two-Electron Integral......Page 298 Mixed Model......Page 299 MNDO......Page 300 Two-Center Two-Electron Integrals......Page 302 One-Center One-Electron Integral Hmm......Page 305 One-Center Two-Electron Integrals......Page 306 Core-Core Repulsion Integrals......Page 307 AM1 and PM3......Page 308 ZINDO/1......Page 310 Mixed Model......Page 311 Mixed Model......Page 312 Single Points on a Potential Energy Surface......Page 315 Local Minima on a Potential Energy Surface......Page 317 Unconstrained Geometry Optimization......Page 318 Steepest Descent......Page 319 Conjugate Gradient Methods......Page 320 Fletcher-Reeves......Page 321 Block Diagonal Newton-Raphson......Page 322 Transition Structures on a Potential Energy Surfac.........Page 323 Eigenvector Following Method......Page 324 Synchronous Transit Method......Page 325 Temperature......Page 326 Leap-frog Algorithm......Page 327 Random Velocities or Restart Velocities......Page 328 The Basic Phases of a Trajectory......Page 329 Heating and Cooling......Page 330 Collecting Data......Page 332 Free Dynamics or Constant Temperature Dynamics......Page 333 The Snapshot Collection Period......Page 334 Averaging Energetic and Structural Data......Page 335 Averaging Energetic Values......Page 336 Deviations from the Average......Page 337 The CSV File......Page 338 Obtaining and Understanding MD Graphs......Page 339 Collecting Trajectory for Subsequent Playback......Page 340 Creating a Snapshot (SNP) file......Page 341 Reading a (HIN, SNP) File for Playback......Page 342 Simple Reactions on a Potential Energy Surface......Page 343 Trajectory Analysis......Page 344 Setting Initial Coordinates and Velocities......Page 345 RHF/UHF Considerations......Page 346 UV Visible Spectroscopy......Page 347 Vibrational Calculation......Page 348 Normal Coordinate Analysis......Page 349 Infrared Absorption......Page 352 Acknowledgments......Page 355 Index......Page 357