A Genetic Algorithm for Conformational Search of Organic Molecules

Implications for Materials Chemistry

Milan Keser, Samuel I Stupp

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

A genetic algorithm was designed in order to predict the low-energy conformations of organic molecules, particularly those of interest in the study of self assembly. The molecules of interest typically have many degrees of freedom so that it is difficult to minimize their conformational energies by conventional means. This has been our motivation in developing a genetic algorithm tailored specifically for efficient conformational search. The algorithm incorporates binary coding, fitness proportional selection, full generational replacement, N-point crossover, fitness scaling and niching. The algorithm was able to predict the minimum energy conformation of tricosane (C23H48) after only several thousand energy evaluations. Furthermore, the algorithm found low-energy conformations of self assembling molecules synthesized in our laboratory which match predictions based on X-ray and electron diffraction data.

Original languageEnglish
Pages (from-to)345-351
Number of pages7
JournalComputers and Chemistry
Volume22
Issue number4
Publication statusPublished - Jun 20 1998

Fingerprint

Chemistry
Conformations
Genetic algorithms
Molecules
Genetic Algorithm
Conformation
Energy
Fitness
Electron diffraction
Self assembly
Niching
Predict
Self-assembly
X ray diffraction
X-Ray Diffraction
Replacement
Crossover
Diffraction
Coding
Degree of freedom

Keywords

  • Genetic algorithm
  • Organic molecules
  • Self assembly

ASJC Scopus subject areas

  • Biotechnology
  • Chemical Engineering(all)
  • Applied Microbiology and Biotechnology

Cite this

A Genetic Algorithm for Conformational Search of Organic Molecules : Implications for Materials Chemistry. / Keser, Milan; Stupp, Samuel I.

In: Computers and Chemistry, Vol. 22, No. 4, 20.06.1998, p. 345-351.

Research output: Contribution to journalArticle

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