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基于经典德鲁德振子的己吡喃糖单糖的可极化经验力场。

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator.

作者信息

Patel Dhilon S, He Xibing, MacKerell Alexander D

机构信息

Department of Pharmaceutical Sciences, University of Maryland , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States.

出版信息

J Phys Chem B. 2015 Jan 22;119(3):637-52. doi: 10.1021/jp412696m. Epub 2014 Feb 24.

Abstract

A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute-water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins.

摘要

基于经典德鲁德振子提出了一种可极化经验力场,用于选定单糖的六元吡喃糖形式。参数优化针对量子力学(QM)偶极矩、溶质 - 水相互作用能、振动频率和构象能。该模型的验证基于晶体实验数据、糖水溶液密度、葡萄糖扩散常数、d - 葡萄糖和d - 半乳糖在水溶液中外环羟甲基的旋转偏好以及其他QM数据。值得注意的是,最终模型对单糖的所有十六种非对映异构体采用单一静电模型,这表明可极化模型具有可转移性。预计所提出的参数将为糖类的综合可极化力场奠定基础,该力场将与脂质和蛋白质的可极化德鲁德参数兼容,从而能够模拟糖脂和糖蛋白。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e5fe/4306497/0673c56409d3/jp-2013-12696m_0001.jpg

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