Molecular Modelling: Principles and Applications
A broad and practical introduction to the major techniques employed in molecular modelling and computational chemistry. Split into two parts, the first covers the two major methods used to describe the interactions within a system - quantum mechanics and molecular mechanics. The second deals with the techniques that use such energy models, including minimisation, molecular dynamics, Monte Carlo simulations and conformational analysis.Molecular Modelling also discusses the use of more advanced methods, such as the calculation of free energies, simulation of chemical reactions and the use of database searching to design new molecules. Visit the accompanying website now at http://www.booksites.net/leach .
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Useful Concepts in Molecular Modelling
Quantum Mechanical Models
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algorithm amino acids approach appropriate approximately atoms basis functions basis set calculated carbon cell chain charge Chemical Physics coefficients components Computational Chemistry configuration conformational space considered constant constraint contribution coordinates correlation corresponds cutoff derivatives determined dielectric dipole distance distance geometry distribution eigenvalues electron density electrostatic potential energy minimisation energy surface ensemble equation example experimental Fock matrix force field Gaussian Gaussian functions geometry gradient Hamiltonian Hartree-Fock hydrogen bonding initial integrals iteration Journal of Chemical kcal/mol large number Lennard-Jones Lennard-Jones potential ligand linear matrix minimum molecular dynamics molecular dynamics simulation molecular mechanics molecular modelling molecular orbital molecules Monte Carlo method Monte Carlo simulation multipole non-bonded nuclei obtained parameters particles performed pharmacophore phase polarisation potential energy predict problem properties protein quantum mechanics random number reaction rotation shown in Figure solute solvent step theory thermodynamic torsion angle transition structure vector velocities Waals wavefunction zero