Full ab initio computation of protein-water interaction energies

D. W. Zhang, J. Z.H. Zhang

Research output: Contribution to journalArticle

Abstract

A method to perform full quantum mechanical (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been developed. This new scheme, named molecular fractionation with conjugate caps (MFCC), decomposes a protein molecule into amino acid-based fragments. These individual fragments are properly treated to preserve the chemical property of the bonds that are cut. Through proper combination of interaction energies between the molecule and individual fragments and their conjugate caps, the full protein-molecule interaction energy can be obtained to a high degree-of-accuracy by full ab initio calculations. Here we report a benchmark full ab initio calculation of interaction energy between a HIV-1 gp41 protein (with 982 atoms) and a water molecule at various geometries using HF (Hartree Fock), DFT (density functional theory) and MP2 (second-order Moller-Plesset perturbation theory) methods on a standard workstation.

Original languageEnglish (US)
Pages (from-to)43-49
Number of pages7
JournalJournal of Theoretical and Computational Chemistry
Volume3
Issue number1
DOIs
StatePublished - Mar 1 2004

Keywords

  • Ab initio calculation
  • Interaction
  • MFCC
  • Protein-water

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics

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