探索显性相互作用:通过DFT和从头算研究揭示可可碱-水配合物的稳定结构

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Tanvi, Mohd Tauheed Ilyas, G. S. S. Saini, Anamika Mukhopadhyay
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引用次数: 0

摘要

溶质-溶剂相互作用对生命过程至关重要,因为生物反应主要发生在液体环境中。水,由于其显著的氢键能力,在这些生物系统中作为溶剂起着关键作用。本研究计算研究了可可碱的水合作用,可可碱是一种具有显著治疗潜力和良好安全性的分子。重点研究1:1的可可碱-水配合物的分子间相互作用,以便全面鉴定当可可碱溶解在水中时,水的潜在相互作用位点。此外,该研究扩展到研究多达三个水分子的物种,以探索合作结合现象的潜力。方法采用MP2/6-311++G(d,p)和\(\omega \) B97XD/6-311++G(d,p)两种高斯理论水平,优化几何结构,计算可可碱-水配合物的能量。在1:1的可可碱-水势能表面上确定了8个不动点,其中大多数表现出双氢键基序和线性偏差。在MP2/6-311++G(d,p)和\(\omega \) B97XD/6-311++G(d,p)两个理论能级上测定的相互作用能分别为7.78 kcal/mol和9.29 kcal/mol,整体最小结构以O-H-O和N-H-O氢键同时存在为特征。MP2/6-311++G(d,p)水平的自然键轨道(NBO)分析被用于量化供体-受体电荷和超共轭能。相互作用能、电荷密度和键长延伸率之间存在线性关系,这突出了这些关键参数之间复杂的相互作用。为了研究合作氢键,我们模拟了最多三个水分子的配合物。利用分子原子(AIM)分析和降低密度梯度(RDG)方法进一步表征了弱相互作用。我们发现,当水合作用增加到两个水分子时,可显著降低互变异构势垒,从46.09 kcal/mol降低到20.47 kcal/mol。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Exploring the dominant interactions: unveiling the stable structure of theobromine-water complexes through DFT and ab initio investigations

Context

Solute-solvent interactions are crucial for life processes, as biological reactions primarily take place in liquid environments. Water, owing to its remarkable capacity for hydrogen bonding, plays a pivotal role as a solvent in these biological systems. This study computationally investigates the hydration of theobromine, a molecule with significant therapeutic potential and a favorable safety profile. It focuses on the intermolecular interactions within 1:1 theobromine-water complexes in order to provide a comprehensive identification of the potential interaction sites for water when theobromine is dissolved in it. In addition, the research extends to investigate species with up to three water molecules to explore the potential for cooperative binding phenomena.

Methods

In this work, we have employed MP2/6-311++G(d,p) and \(\omega \)B97XD/6-311++G(d,p) levels of theory within Gaussian09 to optimize geometries and calculate the energies of theobromine-water complexes. Eight stationary points have been identified on the 1:1 theobromine-water potential energy surface, with the majority exhibiting dual hydrogen bond motifs and deviations from linearity. The global minimum structure is characterized by the simultaneous presence of O-H—O and N-H—O hydrogen bonds, with interaction energies of 7.78 kcal/mol and 9.29 kcal/mol determined at the MP2/6-311++G(d,p) and \(\omega \)B97XD/6-311++G(d,p) levels of theory, respectively. Natural bond orbital (NBO) analysis at the MP2/6-311++G(d,p) level has been used to quantify donor-acceptor charges and hyperconjugation energies. A linear correlation between interaction energy, charge density, and bond length elongation has been observed, highlighting the intricate interplay of these key parameters. To investigate cooperative hydrogen bonding, we have modeled complexes with up to three water molecules. Weak interactions have been further characterized using atoms in molecules (AIM) analysis and reduced density gradient (RDG) approach. We have found that increasing the hydration up to two water molecules significantly reduces the tautomerization barrier from 46.09 to 20.47 kcal/mol.

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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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