Dimension reduction in conformational analysis

A two-rotor mathematical model of amino acid diamide conformational potential energy surface

John Justine S. Villar, Adrian Roy L. Valdez, David H. Setiadi, Béla Fiser, B. Viskolcz, I. Csizmadia, Anita Rágyanszki

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The conformational potential energy surface (PES) of a molecule provides insights into the relative stability of the possible foldamers. However, the time and space complexity of electronic structure calculations, commonly used to generate PES, increases exponentially with an increasing number of atoms. The use of mathematical functions to model the topology of conformational PES is an alternative to more computer-intensive quantum chemical calculations, but the choice and complexity of functions used are crucial in achieving more accurate results. This paper presents a method to illustrate the topology of amino acid diamide PESs through a linear combination of a Fourier series and a mixture of Gaussian functions. Results yield a significantly small error, with an average RMSE of 4.9946 kJ mol-1 for all fits, which suggest that these functions may be used to represent the topology of the PESs, with around twofold order of magnitude decrease in computational time, with respect to DFT electronic structure calculations. This study ultimately aims to provide a foundation for a framework on building polypeptide PES from individual amino acid PESs.

Original languageEnglish
Pages (from-to)830-836
Number of pages7
JournalCanadian Journal of Chemistry
Volume95
Issue number8
DOIs
Publication statusPublished - Jan 1 2017

Fingerprint

Diamide
Potential energy surfaces
Amino acids
Rotors
Mathematical models
Amino Acids
Topology
Electronic structure
Polypeptides
Fourier series
Discrete Fourier transforms
Atoms
Peptides
Molecules

Keywords

  • Analytical fitting
  • Conformational analysis
  • Parameter search
  • Potential energy surfaces

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Organic Chemistry

Cite this

Dimension reduction in conformational analysis : A two-rotor mathematical model of amino acid diamide conformational potential energy surface. / Villar, John Justine S.; Valdez, Adrian Roy L.; Setiadi, David H.; Fiser, Béla; Viskolcz, B.; Csizmadia, I.; Rágyanszki, Anita.

In: Canadian Journal of Chemistry, Vol. 95, No. 8, 01.01.2017, p. 830-836.

Research output: Contribution to journalArticle

Villar, John Justine S. ; Valdez, Adrian Roy L. ; Setiadi, David H. ; Fiser, Béla ; Viskolcz, B. ; Csizmadia, I. ; Rágyanszki, Anita. / Dimension reduction in conformational analysis : A two-rotor mathematical model of amino acid diamide conformational potential energy surface. In: Canadian Journal of Chemistry. 2017 ; Vol. 95, No. 8. pp. 830-836.
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