哌啶基氨基酸离子液体的结构和动力学:计算研究

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2025-01-08 DOI:10.1007/s00894-024-06266-8
Khusboo Dubey, Raghu Nath Behera
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引用次数: 0

摘要

与传统离子液体相比,氨基酸离子液体因其合成成本低、生物可降解性和生物相容性好而受到越来越多的关注。在这项研究中,我们研究了由n -丁基n -甲基哌啶[Pip]阳离子和氨基酸(赖氨酸[Lys]、组氨酸[His]和精氨酸[Arg])阴离子组成的三种离子液体的结构和动力学。采用径向分布函数、空间分布函数和配位数对体相结构进行了分析。计算了氢键、离子对和离子笼形成的时间相关函数,分析了其动力学性质。在离子对之间发现的氢键大多具有中等到较弱的静电优势。[Pip][His]体系表现出离子对之间最强的相互作用能,而[Pip][Lys]体系表现出与其更高的扩散和离子电导率一致的更快的动力学。方法采用M06-2X/ 6-311 + + G(d,p)水平的密度泛函理论进行几何优化和波函数计算。利用分子内原子理论对电子密度进行了拓扑分析。采用经典的分子动力学模拟方法,结合OPLS-AA力场对系统动力学进行了研究。图形抽象
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Structure and dynamics of piperidinium based amino acid ionic liquids: a computational investigation

Context

There has been growing interest in amino acid ionic liquids because of their low-cost synthesis and superior biodegradability and biocompatibility compared to traditional ionic liquids. In this study, we have investigated the structure and dynamics of three ionic liquids consisting of N-butyl N-methyl piperidinium [Pip] cation with amino acid (lysine [Lys], histidine [His], and arginine [Arg]) anions. The radial distribution functions, the spatial distribution functions, and the coordination numbers have been used to analyze the structure in the bulk phase. The time-correlation functions for hydrogen bonds, ion pairs, and ion cage formation have been calculated to analyze the dynamic properties. The hydrogen bonds found between the ion pairs are mostly electrostatically dominant with moderate to weaker strengths. The [Pip][His] system showed the strongest interaction energy between the ion pairs, while the [Pip][Lys] system demonstrated faster dynamics consistent with its higher diffusion and ion conductivity.

Method

The density functional theory at M06-2X/6–311 + + G(d,p) level was employed for geometry optimization and wave function calculations. The theory of atoms-in-molecule was used for the topological analysis of electron density. The classical molecular dynamics simulations with OPLS-AA force field were employed to study the dynamics of the systems.

Graphical Abstract

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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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