Chemistry Reference
In-Depth Information
In quantum mechanics methods, electrons are included explicitly. In MD the
electrons are not included explicitly due to the Born-Oppenheimer approximation
(BO). This approach assumes that that it is possible to uncouple nuclear and
electronic motion. In molecular mechanics it is considered that the electrons of the
system find their optimum distribution. Chemical problems can be investigated
considering the nucleus. Molecules are a collection of masses that interact with
each other using almost harmonic forces. This is analogous to a ball and spring
model,
i.e.
weights joined by springs. Positive increments are reflected by
thermodynamically unfavorable contribution (distortions) to the molecule's
potential energy.
The potential energy of the system is given as the sum of the potential energies of
all the atoms involved. For each atom, a sum of energy terms (individual
interactions that are a function of the coordinates). Parameters called force field
and internal coordinates are often used. The force fields are often classified as
bonded or non-bonded (non-covalent).
The function for molecular mechanics potential energy can be expressed as the
sum of terms, which accounts for stretching of bonds, angles and dihedrals from
equilibrium. There are also terms corresponding to sums over all pairs of atom
pairs separated by at least three bonds. The electrostatic energy is calculated with
a Coulomb potential. A 12-6 Lennard-Jones potential is used to calculate van der
Waals energies.
In order to mimic the screening of electrostatic interactions by solvent both
approximate (variations with distance) and more realistic (explicit ions and
solvents) schemes can be used. Often the manner in which the parameters
involved are derived determine the differences in the force fields. MD programs
include GROMOS, CHARMM, AMBER, CVV, NAMD and others [559-563].
The ensemble method is a general statistical procedure for obtaining
thermodynamics properties. The average of corresponding quantum state values
with the same statistical weight yields the macroscopic thermodynamic properties
introducing the concept of 'ensemble' of Gibbs. A great number of replicas
(representing different values for positions and moments) of a system are
