An efficient approach for ab initio energy calculation of biopolymers

Research output: Contribution to journalArticle

Abstract

We present a new method for efficient total-energy calculation of biopolymers using the density-matrix (DM) scheme based on the molecular fractionation with conjugate caps (MFCC) approach. In this MFCC-DM method, a biopolymer such as a protein is partitioned into properly capped fragments whose density matrices are calculated by conventional ab initio methods which are then assembled to construct the full system density matrix. The assembled full density matrix is then employed to calculate the total energy and dipole moment of the protein using Hartree-Fock or density-functional theory methods. Using this MFCC-DM method, the self-consistent-field procedure for solving the full Hamiltonian problem is avoided and an efficient approach for ab initio energy calculation of biopolymers is achieved. Two implementations of the approach are presented in this paper. Systematic numerical studies are carried out on a series of extended polyglycines CH3 CO- (GLY)n - NHCH3 (n=3-25) and excellent results are obtained.

Original languageEnglish (US)
Article number184105
JournalJournal of Chemical Physics
Volume122
Issue number18
DOIs
StatePublished - May 8 2005

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Biopolymers
biopolymers
Fractionation
caps
fractionation
matrix methods
energy
proteins
Hamiltonians
Dipole moment
Carbon Monoxide
Density functional theory
self consistent fields
Proteins
dipole moments
fragments
density functional theory
moments

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

An efficient approach for ab initio energy calculation of biopolymers. / Chen, Xihua; Zhang, Yingkai; Zhang, John.

In: Journal of Chemical Physics, Vol. 122, No. 18, 184105, 08.05.2005.

Research output: Contribution to journalArticle

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