苯硼酸的微水化及其水化自由能。

IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Doungous Sale, Alhadji Malloum, Mama Nsangou, Jean Jules Fifen, Jeanet Conradie
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引用次数: 0

摘要

背景:了解苯硼酸与周围水分子的相互作用对于溶剂化系统中的几种应用是必不可少的。本文研究了苯基硼酸(PBA)的微水化反应,并利用簇连续溶剂化模型计算了其水化自由能。PBA的微水化在以前的文献中没有被研究过。它要求PBA的结构被n个外显水分子(PBA- wn)包围。结果表明,苯硼酸的B(OH) 2单元与水分子形成类似中性水分子的团簇。QTAIM分析表明,苯硼酸-水簇的结构被强OH⋯O和弱CH⋯O氢键稳定。除了QTAIM分析外,还对最稳定的构型进行了NBO分析,以更好地了解化合物内电子密度从给体到合适受体的离域。此外,我们发现在20 ~ 400 K的温度范围内,最稳定的结构占据了团簇的总体。最后,利用微水合苯硼酸的结构,估算了PBA的水化自由能和水化焓。在室温下,苯硼酸的水化焓和自由能分别为- 72.1 kcal/mol和- 85.5 kcal/mol。温度对水化自由能和水化焓的影响表明,水化焓与温度无关,而自由能随温度线性增加。方法:采用经典分子动力学方法生成PBA-W - n的初始构型,并用理论水平ω B97X-D/def2-TZVP进行优化。优化,频率计算和NBO分析使用高斯16套件的程序执行。在最稳定的构型上,我们进行了分子中原子的量子理论(QTAIM)分析,以深入了解PBA-W n的氢键网络。QTAIM使用AIMAll软件执行。热力学性质作为温度的函数计算使用自制的FORTRAN代号为TEMPO。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Microhydration of phenylboronic acid and its hydration free energy

Microhydration of phenylboronic acid and its hydration free energy

Microhydration of phenylboronic acid and its hydration free energy

Microhydration of phenylboronic acid and its hydration free energy

Context

Understanding the interactions of phenylboronic acid with its surrounding water molecules is essential for several applications in solvated systems. In the present work, we investigated the microhydration of the phenylboronic acid (PBA) and calculated its hydration free energy using the cluster continuum solvation model. Microhydration of PBA has not been investigated previously in the literature. It requires the structures of PBA to be surrounded by n explicit water molecules (PBA-W\(_n\)). The results show that the B(OH)\(_2\) unit of phenylboronic acid forms clusters with water molecules that are similar to those of neutral water clusters. The QTAIM analysis shows that the structures of phenylboronic acid-water clusters are stabilized by strong OH\(\cdots \)O and weak CH\(\cdots \)O hydrogen bonds. In addition to QTAIM analysis, NBO analysis was also performed on the most stable configurations to better understand the delocalization of electron density from donor to proper acceptor within the compound. In addition, we found that the most stable structures dominate the population of the clusters for temperatures from 20 to 400 K. Finally, using the structures of the microhydrated phenylboronic acid, we estimated the free energy of hydration and the enthalpy of hydration of PBA. At room temperature, the phenylboronic acid’s free energy and enthalpy of hydration are respectively evaluated to be \(-\)72.1 kcal/mol and \(-\)85.5k cal/mol. Assessment of temperature effects on the free energy and the enthalpy of hydration shows that the enthalpy is temperature-independent, while the free energy increases linearly with temperature.

Methods

Initial configurations of PBA-W\(_n\) have been generated using classical molecular dynamics and subsequently optimized using the level of theory, \(\omega \)B97X-D/def2-TZVP. Optimizations, frequency calculations, and NBO analysis are performed using the Gaussian 16 suite of programs. On the most stable configurations, we have performed the quantum theory of atoms in molecules (QTAIM) analysis to get insights into the hydrogen bond network of PBA-W\(_n\). QTAIM is performed using AIMAll software. Thermodynamic properties as a function of temperature are evaluated using a homemade FORTRAN code-named TEMPO.

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来源期刊
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
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