RadicalPy:自旋动力学模拟工具

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2024-11-12 Epub Date: 2024-10-29 DOI:10.1021/acs.jctc.4c00887
Lewis M Antill, Emil Vatai
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引用次数: 0

摘要

自由基对(电子-空穴对、极子对)是瞬时反应的中间产物,在科学的各个领域都有发现和利用,从物理学的硬领域,如有机半导体、自旋电子学、量子计算和太阳能电池,到化学和生物学的软领域,如溶液中的化学反应、仿生系统和量子生物学。对自由基对现象的定量分析历来只有少数几个小组取得了成功。有鉴于此,我们用 Python 编程语言提出了一个直观的开源框架,提供经典、半经典和量子模拟方法。我们实现了自由基对动力学速率方程求解器、基于蒙特卡洛的自旋去相速率估计和分子数据库功能。我们引入了动力学量子方法,这是一种融合了经典速率方程、半经典和量子技术的新方法。这种方法在实现更高精度的同时,还解决了量子方法内存要求过大的问题,而且还提供了波长分辨模拟,可进行时间和波长分辨磁场效应模拟。模型示例说明了该软件的多功能性和易用性,包括应用于黄素腺嘌呤二核苷酸光化学的磁敏吸收和荧光的新方法、通过分子动力学模拟对反向胶束内自由基对的自旋-自旋相互作用的估计、蛋白质内自由基对的各向异性以及蒽晶体中的三重激子对。直观的界面也使该软件成为自旋化学领域感兴趣者的教学辅助工具。此外,该软件还具有模块化和可扩展性的特点,旨在实现自旋动力学模拟的标准化。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
RadicalPy: A Tool for Spin Dynamics Simulations.

Radical pairs (electron-hole pairs, polaron pairs) are transient reaction intermediates that are found and exploited in all areas of science, from the hard realm of physics in the form of organic semiconductors, spintronics, quantum computing, and solar cells to the soft domain of chemistry and biology under the guise of chemical reactions in solution, biomimetic systems, and quantum biology. Quantitative analysis of radical pair phenomena has historically been successful by a few select groups. With this in mind, we present an intuitive open-source framework in the Python programming language that provides classical, semiclassical, and quantum simulation methodologies. A radical pair kinetic rate equation solver, Monte Carlo-based spin dephasing rate estimations, and molecule database functionalities are implemented. We introduce the kine-quantum method, a new approach that amalgamates classical rate equations, semiclassical, and quantum techniques. This method resolves the prohibitively large memory requirement issues of quantum approaches while achieving higher accuracy, and it also offers wavelength-resolved simulations, producing time- and wavelength-resolved magnetic field effect simulations. Model examples illustrate the versatility and ease of use of the software, including the new approach applied to the magnetosensitive absorption and fluorescence of flavin adenine dinucleotide photochemistry, spin-spin interaction estimation from molecular dynamics simulations on radical pairs inside reverse micelles, radical pair anisotropy inside proteins, and triplet exciton pairs in anthracene crystals. The intuitive interface also allows this software to be used as a teaching or learning aid for those interested in the field of spin chemistry. Furthermore, the software aims to be modular and extensible, with the aim to standardize how spin dynamics simulations are performed.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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