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用于复杂分子系统建模的VeloxChem量子-经典互操作性

VeloxChem Quantum-Classical Interoperability for Modeling of Complex Molecular Systems.

作者信息

de Gracia Triviño Juan Angel, Brumboiu Iulia Emilia, Carrasco-Busturia David, Li Xin, Li Chenxi, Linares Mathieu, Lindfeld Valentin, Rhee Young Min, Rune Julia, van Hoorn Bastiaan, Norman Patrick, Ahlquist Mårten S G

机构信息

PDC Center for High Performance Computing, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.

Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland.

出版信息

J Phys Chem A. 2025 Aug 14;129(32):7575-7587. doi: 10.1021/acs.jpca.5c03187. Epub 2025 Aug 3.

Abstract

Being a program written primarily in Python that strictly adheres to modern object-oriented software engineering and parallel programming practices, VeloxChem is shown to be suitable for the development of (semi)automatized workflows that extend its scope from first-principles quantum chemical purism to hybrid quantum-classical interoperability and some degree of semiempiricism. Methods are presented for building complex systems such as metal-organic frameworks, constructing molecular mechanics and interpolation mechanics force fields, conformer searches, system solvation, determining free energies of solvation, and determining free energy profiles of reaction pathways using the empirical valence bond method. The implementations are made intuitive with opportunities for interactive plotting and 3D molecular structure illustrations through the use of Jupyter notebooks.

摘要

VeloxChem是一个主要用Python编写的程序,严格遵循现代面向对象软件工程和并行编程实践,适用于开发(半)自动化工作流程,其范围从第一性原理量子化学纯粹主义扩展到混合量子 - 经典互操作性以及一定程度的半经验主义。文中介绍了构建复杂系统(如金属有机框架)、构建分子力学和插值力学力场、构象异构体搜索、系统溶剂化、确定溶剂化自由能以及使用经验价键方法确定反应途径自由能分布的方法。通过使用Jupyter笔记本,实现变得直观,提供了交互式绘图和3D分子结构插图的机会。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cae9/12359120/0fc76deb0eff/jp5c03187_0001.jpg

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