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用于分子动力学模拟的薄荷醇力场的参数化与优化

Parameterization and optimization of the menthol force field for molecular dynamics simulations.

作者信息

Jasik Mateusz, Szefczyk Borys

机构信息

Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.

出版信息

J Mol Model. 2016 Oct;22(10):234. doi: 10.1007/s00894-016-3082-1. Epub 2016 Sep 7.

DOI:10.1007/s00894-016-3082-1
PMID:27604277
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5014899/
Abstract

Menthol's various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field.

摘要

薄荷醇的多种生物学特性使其成为医学和美容应用中的有用成分,而其三个不对称中心意味着它可用于一系列有机反应。已发现薄荷醇取代的离子液体(ILs)具有良好的抗菌和抗静电性能,并且在有机催化和生化研究中也很有用。然而,到目前为止,尚未构建专门针对薄荷醇分子设计和验证的力场。在本工作中,展示了关于力场参数在再现薄荷醇宏观性质能力方面的验证和优化。测试并仔细调整了与全原子液体模拟优化势(OPLS-AA)兼容的参数集。参数的细化包括部分原子电荷的拟合、 Lennard-Jones参数的优化以及为再现量子能量分布所需的二面角参数的重新计算。为了验证力场,计算了液态薄荷醇的各种物理化学性质。同时考虑了热力学和动力学性质,包括密度、表面张力、汽化焓和剪切粘度。所获得的力场被证明能够准确再现所研究化合物的性质,同时与OPLS-AA力场完全兼容。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/4f9484f8f5cb/894_2016_3082_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/4443bb70fc62/894_2016_3082_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/e087322a3bd6/894_2016_3082_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/290994433d77/894_2016_3082_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/4f9484f8f5cb/894_2016_3082_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/4443bb70fc62/894_2016_3082_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/e087322a3bd6/894_2016_3082_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/290994433d77/894_2016_3082_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f7a7/5014899/4f9484f8f5cb/894_2016_3082_Fig4_HTML.jpg

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Menthol--pharmacology of an important naturally medicinal "cool".薄荷醇——一种重要天然药用“清凉”物质的药理学。
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