MFCC-downhill simplex method for molecular structure optimization

X. H. Chen, John Zhang

Research output: Contribution to journalArticle

Abstract

In this paper, a MFCC-downhill simplex method is proposed to study binding structures of small molecules or ions in large molecular complex systems. This method employs the Molecular Fractionation with Conjugated Caps (MFCC) approach in computing inter-molecular energy and implements the downhill simplex algorithm for structural optimization. The method is numerically tested on a system of [KCp(18-crown-6)] to optimize the position of the potassium cation in a fixed coordination sphere. The result of MFCC-downhill simplex optimization method shows good agreement with both the crystal structure and with the full-system downhill simplex optimized structure. The effect of the initial structure of the simplex and the method/basis-set levels of the quantum chemical calculation on the MFCC-downhill simplex optimization are also discussed. This method should be applicable to structure optimization of large complex molecular systems such as proteins or other biopolymers.

Original languageEnglish (US)
Pages (from-to)277-289
Number of pages13
JournalJournal of Theoretical and Computational Chemistry
Volume3
Issue number3
DOIs
StatePublished - Sep 2004

Fingerprint

simplex method
Fractionation
caps
fractionation
Molecular structure
molecular structure
optimization
Biopolymers
Structural optimization
biopolymers
complex systems
Potassium
Cations
Large scale systems
potassium
Crystal structure
Positive ions
Ions
proteins
Proteins

Keywords

  • [KCp(18-crown-6)]
  • MFCC-downhill simplex method
  • Molecular Fragmentation with Conjugated Caps (MFCC)
  • Quantum chemical computation
  • Structural optimization

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

MFCC-downhill simplex method for molecular structure optimization. / Chen, X. H.; Zhang, John.

In: Journal of Theoretical and Computational Chemistry, Vol. 3, No. 3, 09.2004, p. 277-289.

Research output: Contribution to journalArticle

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