An efficient approach for ab initio energy calculation of biopolymers.
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 CH3CO-(GLY)n-NHCH3(n = 3-25) and excellent results are obtained.
Chen
Xihua
X
Department of Chemistry, New York University, New York, New York 10003, USA.
Zhang
Yingkai
Y
Zhang
John Z H
JZ
D001704:Biopolymers / Q000737:chemistry*; D002627:Chemistry, Physical / Q000379:methods*; D004247:DNA / Q000737:chemistry; D004583:Electrons; D005998:Glycine / Q000737:chemistry; D008024:Ligands; D008956:Models, Chemical; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry
D001704:Biopolymers; D008024:Ligands; D010455:Peptides; D011506:Proteins; C011080:polyglycine; D004247:DNA; D005998:Glycine