Combining Quantum Mechanics and Molecular Mechanics

Editorial Board......Page 2
Volume Editor......Page 3
Copyright......Page 4
Preface......Page 5
Contributors......Page 8
Introduction......Page 12
Partition of a System into QM and MM Parts......Page 14
Treatment of the QM/MM Boundary......Page 15
Interactions in the QM/MM Coupling......Page 18
Computational Aspects......Page 21
Future Prospects......Page 23
References......Page 24
Extending the Range of Computational Spectroscopy by QM/MM Approaches: Time-Dependent and Time-Independent Routes......Page 27
Introduction......Page 28
The QM/MM Framework for Spectroscopic Studies......Page 29
Time-dependent approaches for QM/MM study of complex systems in solution: the GLOB model......Page 30
Electrostatic contributions......Page 32
Nonelectrostatic contributions......Page 33
Extension to the constant presssure/flexible volume (NpT) ensemble......Page 34
Dynamic (Vibrational) effects beyond harmonic approximation......Page 36
Vibrationally resolved electronic spectra......Page 38
Vibrational properties and infrared spectra......Page 43
Electronic spectra......Page 44
Magnetic properties: electron spin resonance spectroscopy......Page 46
UV spectra of acrolein in gas phase and in aqueous solution......Page 47
ESR magnetic tensors of complex radicals in aqueous solution......Page 52
Vibrational properties beyond harmonic approximation......Page 57
Photoelectron spectrum of adenine adsorbed on Si(100)......Page 60
Final Remarks and Conclusions......Page 63
References......Page 64
Use of the Average Solvent Potential Approach in the Study of Solvent Effects......Page 68
Introduction......Page 69
The Mean Field Approximation......Page 70
The ASEP/MD Method......Page 72
The mutual solute-solvent polarization......Page 73
Location of critical points on free energy surfaces......Page 77
Calculation of free energy differences......Page 79
Validity of the Mean Field Approximation......Page 80
Anomeric effect in xylopyranose and glucopyranose......Page 83
Conformational equilibrium in a tripeptide......Page 87
Chemical reactions......Page 91
Electron transitions......Page 93
Nonradiative de-excitations in retinal......Page 100
Summary......Page 103
References......Page 104
QM/MM Approaches to the Electronic Spectra of Hydrogen-Bonding Systems with Connection to Many-Body Decomposition Schemes......Page 107
Introduction......Page 108
Statistical mechanics sampling for many-body interacting systems in condensed phases......Page 109
The QM/MM coupling schemes......Page 111
Choosing the QM system......Page 114
Truncating the MM system......Page 115
Beyond QM/MM: many-body expansions......Page 117
Wavefunction-based methods......Page 121
Time-dependent density functional theory......Page 124
UV spectra of water clusters......Page 127
Absorption spectra of liquid water......Page 131
Ionization of liquid water......Page 134
Electron binding energies of liquid ammonia......Page 137
Charge transfer to solvent in halide aqueous solutions......Page 140
Solvatochromic shifts of small organic molecules......Page 144
Final Remarks and Conclusions......Page 148
References......Page 149
Molecular Dynamics of Polypeptides and Their Inclusion Compounds with rbeta-Cyclodextrin in Aqueous Solution Using DC-SCC-DFTB/UFF Approach......Page 153
Introduction......Page 154
Density functional tight-binding method......Page 155
Self-consistent charge-density functional tight-binding......Page 159
A posteriori treatment for London dispersion in SCC-DFTB......Page 161
QM/MM approach......Page 163
Periodic boundary conditions......Page 164
rbeta-Cyclodextrin in aqueous solution......Page 165
BPP7a......Page 171
Angiotensin-(1-7) in aqueous solution......Page 175
Angiotensin-(1-7):rbeta-Cyclodextrin inclusion compound......Page 180
Final Remarks......Page 185
References......Page 186
Computer Simulations of Photobiological Processes: The Effect of the Protein Environment......Page 189
Theory......Page 190
Born-Oppenheimer approximation......Page 191
Conical intersections......Page 194
Excited state molecular dynamics......Page 201
Diabatic surface hopping......Page 203
Excited state quantum chemistry......Page 205
Mixed quantum classical molecular dynamics......Page 207
Photoactive yellow protein......Page 211
Reversibly switchable fluorescent proteins......Page 216
Final Remarks and Conclusions......Page 218
References......Page 219
Ab Initio Quantum Mechanical Charge Field Molecular Dynamics-A Nonparametrized First-Principle Approach to Liquids and Solutions......Page 221
Introduction......Page 222
Definition of subregions and the respective forces......Page 224
Electrostatic embedding and the periodic box......Page 227
Smoothing of particle migrations between the QM and MM region......Page 230
Computational effort and accuracy considerations......Page 231
Application of the QMCF MD Methodology......Page 235
Outlook......Page 250
Methodical developments......Page 251
References......Page 252
Introduction......Page 255
Mixed-Q/C Propagations Schemes......Page 257
Hydrogen Transfer in Gas Phase......Page 263
Proton and Hydride Transfer in Condensed Phase......Page 268
Vibrational Energy Relaxation......Page 278
van der Waals clusters......Page 279
Condensed phase......Page 280
References......Page 286
Development of a Quantum Chemical Method Combined with a Theory of Solutions-Free-Energy Calculation for Chemical Reactions by Condensed Phase Simulations......Page 291
Introduction......Page 292
Kohn-Sham density functional theory......Page 297
Real-space grids approach......Page 299
Hybrid quantum mechanical/molecular mechanical method......Page 307
Theory of Solutions......Page 309
Free-energy perturbation and thermodynamic integration methods......Page 310
Distribution function theory......Page 313
Kirkwood charging formula and density functional theory......Page 316
Site-site radial distribution function and reference interaction site model......Page 319
Method of energy representation......Page 323
Application to molecular binding into micelle and lipid-membrane systems......Page 330
Polarizable continuum model method......Page 334
Reference interaction site model combined with the self-consistent field calculation......Page 337
Quantum mechanical/molecular mechanical method combined with the theory of energy representation......Page 340
Calculation of solvation free energy by QM/MM-ER approach......Page 345
Calculation of reduction free energy by QM/MM-ER approach......Page 348
Conclusions and Perspectives......Page 355
References......Page 357
A Guide to QM/MM Methodology and Applications......Page 360
Introduction......Page 361
Basic Concepts of QM/MM Methodology......Page 362
Subtractive scheme......Page 363
Additive scheme......Page 364
Electrical embedding......Page 365
Electrical embedding with explicit treatment of MM region polarization......Page 366
First-principles electrostatic potential......Page 367
van der Waals interactions......Page 368
Link atom......Page 369
Frozen localized orbitals......Page 371
Performance of LA and FLO: summary......Page 372
Geometry optimization......Page 374
Microiteration......Page 375
Macroiteration......Page 377
Transition state search on the potential energy surface......Page 378
Minimum energy path (MEP)......Page 379
QM/MM Approaches to the Simulation of Kinetics and Thermodynamics in the Condensed Phase......Page 380
Free energy simulations and the QM/MM formalism......Page 382
Potential of mean force evaluation with thermodynamic integration......Page 383
Free energy perturbation techniques......Page 384
Umbrella sampling......Page 387
Replica Exchange......Page 388
Reaction coordinate-driven methods......Page 389
Transition path sampling......Page 391
Beyond Conventional QM/MM Dynamics: Explicit Account of Nuclear Quantum Effects......Page 392
Summary of Alternatives to QM/MM Methodology......Page 395
Applications to Biochemical Simulation......Page 396
DNA polymerases......Page 397
Conclusions and Perspectives......Page 399
References......Page 400