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Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method
Author(s) -
van der Vaart Arjan,
Gogonea Valentin,
Dixon Steven L.,
Merz Kenneth M.
Publication year - 2000
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/1096-987x(200012)21:16<1494::aid-jcc6>3.0.co;2-4
Subject(s) - solvation , divide and conquer algorithms , statistical physics , linear scale , scaling , quantum , charge (physics) , electronic structure , quantum chemistry , implicit solvation , charge density , physics , quantum mechanics , computer science , molecule , mathematics , algorithm , supramolecular chemistry , geodesy , geography , geometry
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. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1494–1504, 2000