Suppr超能文献

通过该界面自动执行像素计算。

: automated execution of Pixel calculations via the interface.

作者信息

Reeves Matthew G, Wood Peter A, Parsons Simon

机构信息

EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3FJ, Scotland.

Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England.

出版信息

J Appl Crystallogr. 2020 Jul 30;53(Pt 4):1154-1162. doi: 10.1107/S1600576720008444. eCollection 2020 Aug 1.

Abstract

The interpretation of crystal structures in terms of intermolecular interaction energies enables phase stability and polymorphism to be rationalized in terms of quantitative thermodynamic models, while also providing insight into the origin of physical and chemical properties including solubility, compressibility and host-guest formation. The Pixel method is a semi-empirical procedure for the calculation of intermolecular interactions and lattice energies based only on crystal structure information. Molecules are represented as blocks of undistorted molecular electron and nuclear densities subdivided into small volume elements called pixels. Electrostatic, polarization, dispersion and Pauli repulsion terms are calculated between pairs of pixels and nuclei in different molecules, with the accumulated sum equating to the intermolecular interaction energy, which is broken down into physically meaningful component terms. The procedure enables Pixel calculations to be carried out with minimal user intervention from the graphical interface of , which is part of the software distributed with the Cambridge Structural Database (CSD). Following initial setup of a crystallographic model, one module assigns atom types and writes necessary input files. A second module then submits the required electron-density calculation either locally or to a remote server, downloads the results, and submits the Pixel calculation itself. Full lattice energy calculations can be performed for structures with up to two molecules in the crystallographic asymmetric unit. For more complex cases, only molecule-molecule energies are calculated. The program makes use of the CSD Python API, which is also distributed with the CSD.

摘要

根据分子间相互作用能对晶体结构进行解释,能够依据定量热力学模型来阐释相稳定性和多晶型现象,同时还能深入了解包括溶解度、压缩性和主客体形成在内的物理和化学性质的起源。像素法是一种仅基于晶体结构信息来计算分子间相互作用和晶格能的半经验方法。分子被表示为未变形的分子电子和核密度块,这些块被细分为称为像素的小体积元素。在不同分子中的像素对和原子核之间计算静电、极化、色散和泡利排斥项,累积总和等于分子间相互作用能,该能量又被分解为具有物理意义的组成项。该程序能够在用户最少干预的情况下,通过 (它是随剑桥结构数据库(CSD)分发的软件的一部分)的图形界面进行像素计算。在晶体学模型的初始设置之后,一个模块会指定原子类型并编写必要的输入文件。然后第二个模块会在本地或向远程服务器提交所需的电子密度计算,下载结果,并提交像素计算本身。对于晶体学不对称单元中包含多达两个分子的结构,可以进行完整的晶格能计算。对于更复杂的情况,只计算分子 - 分子能量。该程序使用了同样随 CSD 分发的 CSD Python API。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c24/7401789/ca62ada277ef/j-53-01154-fig1.jpg

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验