Molecular Caps for Full Quantum Mechanical Computation of Peptide-Water Interaction Energy

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

Research output: Contribution to journalArticlepeer-review

Abstract

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.

Original languageEnglish (US)
Pages (from-to)1846-1852
Number of pages7
JournalJournal of Computational Chemistry
Volume24
Issue number15
DOIs
StatePublished - Nov 30 2003

Keywords

  • Interaction energy
  • Molecular fractionation with conjugate caps (MFCC)
  • Quantum mechanical computation

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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