Article,
Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method
J. Comput. Chem., 21 (16): 1494-1504 (December 2000)
Abstract
A ``linear-scaling revolution'' is occurring in quantum chemistry.
This development is allowing for the first time the routine examination
of large molecular assembles (e.g., proteins and DNA in water) using
electronic structure methods. One of these approaches is the divide
and conquer method and, in this article, we review the implementation
of this approach for semiempirical Hamiltonians. This is then followed
by brief reviews of three application areas. First, we will discuss
the charge distribution of biological molecules in solution as described
by quantum mechanics. In particular, the role polarization and charge
transfer plays in affecting the charge distribution of proteins will
be discussed. Next, we will examine the energetic consequences of
charge transfer and polarization on biomolecular solvation. The final
section will describe the computation of solvation free energies
using a combined divide and conquer/Poisson-Boltzmann approach. The
application of linear scaling quantum mechanical methods to biology
is only just beginning, but the future is very bright, and it is
our opinion that quantum mechanics will have a profound influence
on our understanding of biological systems in the coming years. (C)
2000 John Wiley & Sons, Inc.
Tags
- and
- biological
- calculations;
- conquer}
- divide
- molecular
- orbital
- scaling
- semiempirical
- systems;
- {linear
