KLD: a program to elucidate the localization of the Fermi and Coulomb holes in molecular systems.

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2024-07-29 DOI:10.1007/s00894-024-06070-4
Valeria Bedoya, Vladimir Rodríguez, Luis Rincón, Cesar Zambrano, Luis Seijas, F Javier Torres
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Abstract

Context: The electron localization is a concept that allows scientists to better understand the physical and chemical properties of electronic systems. It is associated with the propensity of electron pairs with opposite spins to accumulate as well as with their response to external perturbations. This paper contains a detailed description of the design and implementation of the program KLD, which was primarily developed in our research group to elucidate electron localization in molecular systems by evaluating the information content of electron-pair density functions. KLD employs two information-based functions as a real space measure of the Fermi and Coulomb holes for same-spin electrons and shows a better resolution as compared to other methods (i.e., ELF). Information about the acceleration of the code is also included in the present work, being noticeable the reduction of wall-time calculation and the error calculation between versions.

Methods: KLD was designed to be easy to use, extend, and maintain; thus, many principles of modern software development, extensive testing, and package management were adopted. The latest version of the KLD program was created utilizing the Compute Unified Device Architecture (CUDA) version, which allows it to use the computational capacity of NVIDIA Graphics Processing Units (GPUs) for processing purposes. The electron-pair conditional density was calculated from the canonical molecular orbitals obtained at the HF/6-31G(2df,p) level, or alternatively the natural orbitals in the case of explicit correlated wavefunctions computed at the MP2/6-31G(2df,p)//HF/6-31G(2df,p) level.

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KLD:阐明分子系统中费米孔和库仑孔定位的程序。
背景:电子定位是一个能让科学家更好地理解电子系统物理和化学特性的概念。它与具有相反自旋的电子对的聚集倾向及其对外部扰动的反应有关。本文详细介绍了 KLD 程序的设计与实现,该程序主要由我们的研究小组开发,目的是通过评估电子对密度函数的信息含量来阐明分子系统中的电子定位。KLD 采用两个基于信息的函数作为同旋电子的费米空穴和库仑空穴的实空间度量,与其他方法(如 ELF)相比,具有更好的分辨率。有关代码加速的信息也包含在本研究中,其中值得注意的是壁时间计算的减少和不同版本之间的误差计算:KLD 的设计宗旨是易于使用、扩展和维护,因此采用了许多现代软件开发、广泛测试和软件包管理的原则。最新版本的KLD程序采用了计算统一设备架构(CUDA)版本,可以利用英伟达™(NVIDIA®)图形处理器(GPU)的计算能力进行处理。电子对条件密度是根据在 HF/6-31G(2df,p)水平上获得的标准分子轨道计算得出的,或者根据在 MP2/6-31G(2df,p)//HF/6-31G(2df,p)水平上计算的显式相关波函数计算出的自然轨道计算得出的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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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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