分子模拟的原理和应用(英文影印版)

.2.3 polyelectronic atoms and molecules
2.4 molecular orbital calculations
2.5 the hartree-fock equations
2.6 basis sets
2.7 open-shell systems
2.8 electron correlation
2.9 practical considerations when performing ab initio calculations
2.10 approximate molecular orbital theories
2.11 semi-empirical methods
2.12 huckel theory
2.13 valence bond theories
2.14 calculating molecular properties using quantum mechanics
2.15 perfonnance of semi-empirical methods
2.16 energy component analysis
further reading
references
3 empirical force field models: molecular mechamcs
3.1 introduction
3.2 some general features ofmolecular mechanics force fields
3.3 bond stretching
3.4 angle bending
3.5 torsional terms
3.6 improper torsions and out-of-plane bending motions
3.7 cross tenns and non-bonded interactions
3.8 electrostatic interactions
3.9 van der waals interactions
3.10 many-body effects in empirical potentials
3.11 effective pair potentials
3.12 hydrogen bonding in molecular mechanics
3.13 force field modeis for the simulation ofliquid water
3.14 united atom force fields and reduced representations
3.15 derivatives ofthe molecular mechanics energy function
3.16 calculating thennodynamic properties using a force field
3.17 force field parametrisation
3.18 transferability offorce field parameters
3.19 the treatment of delocalised π-systems
3.20 foree fields for metals and inorganic systems
appendix 3.1 the interaction between two drude molecules
further reading
references
4 energy minimisation and related methods for exploring the energy surface
4.1 introduction
4.2 non-derivative minimisation methods
4.3 introduction to derivative minimisation methods
4.4 first-order minimisation methods
4.5 second derivative methods: the newton-raphson method
4.6 quasi-newton methods
4.7 which minimisation method should i use?
4.8 applications of energy minimisation
4.9 determination of transition structures and reaction pathways
further reading
references
5 computer slmulation methods
5.1 introduction
5.2 calculation of simple thermodynamic properties
5.3 phase space
5.4 practical aspects ofcomputer simulation
5.5 boundaries
5.6 monitoring the equilibration
5.7 tmncating the potential and the minimum image convention ..
5.8 long-range forees
5.9 the cell-multipole method for non-bonded interactions
5.10 analysing the results ofa simulation and estimating errors
appendix 5.1 basic statistical mechanics
appendix 5.2 heat capacity and energy fluctuations
appendix 5.3 the real gas contribution to the virial
appendix 5.4 translating particle back into central box
further reading
references
6 molecular dvnamics simulation methods
6.1 introduction
6.2 molecular dynamics using simple models
6.3 molecular dynamics with continuous potentials
6.4 setting up and mnning a molecular dynamics simulation
6.5 constraint dynamics
6.6 time-dependent properties
6.7 molecular dynamics at constant temperature and pressure
6.8 incorporating solvent effects into molecular dynamics: potentials of mean force and stochastic dynamics
6.9 conformational changes from molecular dynamics simulations
6.10 molecular dynamics simulations ofchain amphiphiles
appendix 6.1 energy conservation in molecular dynamics
appendix 6.2 fourier series and fourier analysis
further reading
references
7 monte carlo simulation methods
7.1 introduction
7.2 calculating properties by integration
7.3 some theoretical background to the metropolis method
7.4 implementation of the metropolis monte carlo method
7.5 monte carlo simulation of molecules
7.6 models used in monte carlo simulations of polymers
7.7 'biased' monte carlo methods
7.8 monte carlo sampling from different ensembles
7.9 calculating the chemical potential
7.10 the configurational bias monte carlo method
7.11 simulating phase equilibria by gibbs ensemble monte carlo method
7.12 monte carlo or molecular dynamics?
appendix 7.1 the marsaglia random number generator
further reading
references
8 conformational analysis
8.1 introduction
8.2 systematic methods for exploring conformational space
8.3 model-building approaches
8.4 random search methods
8.5 gerietic algorithms
8.6 distance geometry
8.7 exploring conformational space using simulation methods
8.8 which conformational search method should i use?
8.9 stmctural databases
8.10 molecular fitting
8.11 clustering algorithms and pattem recognition techniques
8.12 reducing the dimensionality of a data set
8.13 the role of conformational analysis in predicting the structures of peptides and proteins
further reading
references
9 three challenges in molecular modelling: free energies solvation and slmulating reactions
9.1 the difficulty of calculating free energies by computer
9.2 the calculation of free energy differences
9.3 applications ofmethods for calculating free energy differences
9.4 the calculation ofenthalpy and entropy differences
9.5 partitioning the free energy
9.6 potential pitfalls with free energy calculations
9.7 potentials of mean force
9.8 continuum representations ofthe solvent
9.9 the electrostatic contribution to the free energy ofsolvation: the bom and onsager models
9.10 non-electrostatic contributions to the solvation free energy
9.11 very simple solvation models
9.12 modelling chemical reactions
9.13 density functional theory
appendix 9.1 calculating free energy differences using thennodynamic integration
appendix 9.2 using the slow growth method for calculating free energy differences
further reading
references
10 the use of molecular modelling to discover and design new molecules
10.1 molecular modelling in drug discovery
10.2 deriving and using three-dimensional pharmacophores
10.3 molecular docking
10.4 structure-based methods to identify lead compounds
10.5 de novo ligand design
10.6 molecular similarity
10.7 quantitative structure-activity relationships
further reading
references
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