New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology.
New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology.
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DOI：
10.1021/acs.jctc.0c00247
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发表时间：
2020-08-11
影响因子：
5.5
通讯作者：
Faraldo-Gómez JD
中科院分区：
文献类型：
--
作者：
Orabi EA;Faraldo-Gómez JD
氟化氢（HF）是极性最强的双原子分子，也是能够形成氢键的最简单的分子之一。HF在气相和溶液中都偏离理想状态，因此从基本观点来看是非常有趣的。纯HF和HF水溶液也广泛用于化学和工业过程，尽管它们具有高毒性。HF在某些生物条件下也是一种稳定的物种，因为它不像其他卤化氢那样容易在水中解离;然而，关于HF如何与生物分子相互作用知之甚少。在这里，我们着手开发一个分子力学模型，使计算机模拟HF在化学和生物学应用。该模型是基于一个全面的高层次从头计算量子化学调查的HF单体和二聚体的结构和能量;（HF）n集群，n = 3-7;各种集群的HF和水;和复合物的HF与类似物的所有20种氨基酸和几种常见的脂质，中性和离子化。这种系统的分析解释了这种分子的独特性质;例如，尽管是双原子的，但相互作用的HF分子有利于非线性几何形状，HF是一种强氢键供体，但却是一种差的受体。从头算的数据也使我们能够校准一个三站点的分子力学模型，我们调查的结构和热力学性质的气体，液体和超临界HF在很宽的温度和压力范围内; HF在水中的溶剂化结构和H2O在液体HF;和HF的自由扩散穿过脂质双层，一个关键的过程中潜在的高细胞毒性的HF。尽管其固有的简化，提出的模型显着改善了以前的努力，以捕捉纯和含水HF流体的性质，分子力学方法，并根据我们的知识构成了第一个参数集校准的生物分子模拟。
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution, and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are also broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino-acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule; for example, that interacting HF molecules favor non-linear geometries despite being diatomic, and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods, and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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影响因子：
15
作者：
Bauer, SH;Beach, JY;Simons, JH
通讯作者：
Simons, JH
影响因子：
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ROTHMAN, LS
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