关于静水压力对肌氨酸晶体结构和电子特性影响的 DFT 研究。

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Geanso M. de Moura, Mateus R. Lage, Adenilson Santos, Rodrigo Gester, Stanislav R. Stoyanov, Tarciso Andrade-Filho
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引用次数: 0

摘要

背景:我们进行了密度泛函理论计算,以研究氨基酸肌氨酸晶体结构的结构和电子特性与静水压力应用的关系。我们对计算结果进行了分析,并与现有的实验数据进行了比较。我们的研究结果表明,在高达 3.7 GPa 的静水压力下,使用 Grimme 弥散校正 PBE 函数(PBE-D3)计算的肌氨酸晶体结构和性质与现有的实验结果最为吻合。根据实验结果研究并阐明了关键的结构重排,如单胞压缩、头尾压缩和分子旋转。此外,还介绍了带隙能的调整和状态密度的偏移,这些都表明了高压引起的结构变化。计算得出的特性表明,肌氨酸在涉及压力引起的结构变化的电子设备中大有可为:采用了三种广泛使用的广义梯度近似函数--PBE、PBEsol 和 revPBE,并进行了 Grimme 的 D3 分散修正。此外,还对非局部范德瓦耳斯密度函数 vdW-DF 进行了评估。计算使用 Quantum Espresso 软件套件中的投影仪增强波方法进行。几何优化结果使用 VMD 可视化。Multiwfn 和 NCIPlot 程序用于波函数和分子间相互作用分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A DFT study of the effect of hydrostatic pressure on the structure and electronic properties of sarcosine crystal

Context

We perform density functional theory calculations to study the dependence of the structural and electronic properties of the amino acid sarcosine crystal structure on hydrostatic pressure application. The results are analyzed and compared with the available experimental data. Our findings indicate that the crystal structure and properties of sarcosine calculated using the Grimme dispersion-corrected PBE functional (PBE-D3) best agree with the available experimental results under hydrostatic pressure of up to 3.7 GPa. Critical structural rearrangements, such as unit cell compression, head-to-tail compression, and molecular rotations, are investigated and elucidated in the context of experimental findings. Band gap energy tuning and density of state shifts indicative of band dispersion are presented concerning the structural changes arising from the elevated pressure. The calculated properties indicate that sarcosine holds great promise for application in electronic devices that involve pressure-induced structural changes.

Methods

Three widely used generalized gradient approximation functionals—PBE, PBEsol, and revPBE—are employed with Grimme’s D3 dispersion correction. The non-local van der Waals density functional vdW-DF is also evaluated. The calculations are performed using the projector-augmented wave method in the Quantum Espresso software suite. The geometry optimization results are visualized using VMD. The Multiwfn and NCIPlot programs are used for wavefunction and intermolecular interaction analyses.

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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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