Parameterization and validation of Gromos force field to use in conformational analysis of epoxidic systems

Reynier Suardiaz; Mitchell Maestre; Ernesto Suárez; Carlos Pérez

doi:10.1016/j.theochem.2006.08.030

Parameterization and validation of Gromos force field to use in conformational analysis of epoxidic systems

Reynier Suardiaz^*, Mitchell Maestre, Ernesto Suárez, Carlos Pérez

^*Corresponding author for this work

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

In order to study the conformational space of new natural products derivatives using molecular mechanics (MM) and molecular dynamics (MD), the Gromos force field has been expanded to include epoxidic systems. The parameterization and validation of Gromos were done to simulate 22, 23 epoxides in brassinosteroids analogs. The parameters were derived with an emphasis on the dependence between energy and dihedral angle due to its relevance in the conformational analysis. Molecular dynamics simulations of two model systems similar to those of interest were performed to validate the force field with the proposed parameters. Excellent agreement has been obtained between the MD simulation and the results of a potential energy surface (PES) calculated at B3LYP/6-31G^** level.

Original language	English
Pages (from-to)	21-25
Number of pages	5
Journal	Journal of Molecular Structure: THEOCHEM
Volume	778
Issue number	1-3
DOIs	https://doi.org/10.1016/j.theochem.2006.08.030
Publication status	Published - 11 Dec 2006

Keywords

Conformational analysis
Epoxidic systems
Force field
Gromos
Parameterization

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10.1016/j.theochem.2006.08.030

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title = "Parameterization and validation of Gromos force field to use in conformational analysis of epoxidic systems",

abstract = "In order to study the conformational space of new natural products derivatives using molecular mechanics (MM) and molecular dynamics (MD), the Gromos force field has been expanded to include epoxidic systems. The parameterization and validation of Gromos were done to simulate 22, 23 epoxides in brassinosteroids analogs. The parameters were derived with an emphasis on the dependence between energy and dihedral angle due to its relevance in the conformational analysis. Molecular dynamics simulations of two model systems similar to those of interest were performed to validate the force field with the proposed parameters. Excellent agreement has been obtained between the MD simulation and the results of a potential energy surface (PES) calculated at B3LYP/6-31G** level.",

keywords = "Conformational analysis, Epoxidic systems, Force field, Gromos, Parameterization",

author = "Reynier Suardiaz and Mitchell Maestre and Ernesto Su{\'a}rez and Carlos P{\'e}rez",

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doi = "10.1016/j.theochem.2006.08.030",

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TY - JOUR

T1 - Parameterization and validation of Gromos force field to use in conformational analysis of epoxidic systems

AU - Suardiaz, Reynier

AU - Maestre, Mitchell

AU - Suárez, Ernesto

AU - Pérez, Carlos

PY - 2006/12/11

Y1 - 2006/12/11

N2 - In order to study the conformational space of new natural products derivatives using molecular mechanics (MM) and molecular dynamics (MD), the Gromos force field has been expanded to include epoxidic systems. The parameterization and validation of Gromos were done to simulate 22, 23 epoxides in brassinosteroids analogs. The parameters were derived with an emphasis on the dependence between energy and dihedral angle due to its relevance in the conformational analysis. Molecular dynamics simulations of two model systems similar to those of interest were performed to validate the force field with the proposed parameters. Excellent agreement has been obtained between the MD simulation and the results of a potential energy surface (PES) calculated at B3LYP/6-31G** level.

AB - In order to study the conformational space of new natural products derivatives using molecular mechanics (MM) and molecular dynamics (MD), the Gromos force field has been expanded to include epoxidic systems. The parameterization and validation of Gromos were done to simulate 22, 23 epoxides in brassinosteroids analogs. The parameters were derived with an emphasis on the dependence between energy and dihedral angle due to its relevance in the conformational analysis. Molecular dynamics simulations of two model systems similar to those of interest were performed to validate the force field with the proposed parameters. Excellent agreement has been obtained between the MD simulation and the results of a potential energy surface (PES) calculated at B3LYP/6-31G** level.

KW - Conformational analysis

KW - Epoxidic systems

KW - Force field

KW - Gromos

KW - Parameterization

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DO - 10.1016/j.theochem.2006.08.030

M3 - Article

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JO - Journal of Molecular Structure: THEOCHEM

JF - Journal of Molecular Structure: THEOCHEM

SN - 0166-1280

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ER -

Parameterization and validation of Gromos force field to use in conformational analysis of epoxidic systems

Abstract

Keywords

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