### 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 language | English |
---|---|

Pages (from-to) | 830-836 |

Number of pages | 7 |

Journal | Canadian Journal of Chemistry |

Volume | 95 |

Issue number | 8 |

DOIs | |

Publication status | Published - Jan 1 2017 |

### Fingerprint

### Keywords

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

### ASJC Scopus subject areas

- Catalysis
- Chemistry(all)
- Organic Chemistry

### Cite this

*Canadian Journal of Chemistry*,

*95*(8), 830-836. https://doi.org/10.1139/cjc-2017-0124

**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.

Research output: Contribution to journal › Article

*Canadian Journal of Chemistry*, vol. 95, no. 8, pp. 830-836. https://doi.org/10.1139/cjc-2017-0124

}

TY - JOUR

T1 - Dimension reduction in conformational analysis

T2 - A two-rotor mathematical model of amino acid diamide conformational potential energy surface

AU - Villar, John Justine S.

AU - Valdez, Adrian Roy L.

AU - Setiadi, David H.

AU - Fiser, Béla

AU - Viskolcz, B.

AU - Csizmadia, I.

AU - Rágyanszki, Anita

PY - 2017/1/1

Y1 - 2017/1/1

N2 - 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.

AB - 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.

KW - Analytical fitting

KW - Conformational analysis

KW - Parameter search

KW - Potential energy surfaces

UR - http://www.scopus.com/inward/record.url?scp=85026834079&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85026834079&partnerID=8YFLogxK

U2 - 10.1139/cjc-2017-0124

DO - 10.1139/cjc-2017-0124

M3 - Article

VL - 95

SP - 830

EP - 836

JO - Canadian Journal of Chemistry

JF - Canadian Journal of Chemistry

SN - 0008-4042

IS - 8

ER -