Chemistry Reference
In-Depth Information
There are various levels of theory to study structures and properties of bio
molecular systems. The systems can be described in quantum mechanical methods
by wave functions of the Schrodinger equation, which relates the Hamiltonian
operator to the stationary states, and energies of the system. However,
approximations should be made since the Schrodinger equation cannot be solved
exactly in practice.
With the exception of using fundamental constants of nature,
i.e.
Planck's
constants and the mass of the electron, approximations of the solution of the
Schrodinger equation are called
ab initio
. It is possible to use these methods to
determine quite accurately electrostatic potential and molecular structures.
However, the applications of these methods are limited to small systems due to
heavy computational demands.
Biomolecular systems have too many electronic degrees of freedom for solving
the Schrodinger's equation. The sophisticated molecular modeling techniques are
too computational demanding when large systems comprising hundreds/thousands
of atoms are involved, in contrast to molecular dynamics simulations.
MD is a method based on molecular mechanics, which calculates the molecular
system's behavior in a time dependent procedure. It is considered as a virtual
experiment or an interface between theory and laboratory experiment. These
methods can be used to get a better understanding of biophysical and biochemical
processes. They also yield a better comprehension of factors determining
structural stability by sampling efficiently the configuration space. These methods
are useful for understanding small molecules (drugs), biomolecular structures as
well as their interactions.
In molecular mechanical methods it is assumed that at every set of positions the
potential energy of a collection of atoms is defined. MD begins with the
fundamental assumption that matter consists of atoms. The collections of atoms
are treated as a mechanical system (moving with the potential energy). It is then
possible to calculate the vibrational spectrum, thermodynamic properties,
equilibrium structures, reaction rates and equations of state for the system
investigated.
