Division of Theoretical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1083, Amsterdam 1081 HV, the Netherlands.
Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Genova, Via Dodecaneso 31, Genova 16146, Italy.
J Chem Inf Model. 2022 Nov 28;62(22):5525-5535. doi: 10.1021/acs.jcim.2c00690. Epub 2022 Oct 31.
The continuous improvement of computer architectures allows for the simulation of molecular systems of growing sizes. However, such calculations still require the input of initial structures, which are also becoming increasingly complex. In this work, we present CAT, a Compound Attachment Tool (source code available at https://github.com/nlesc-nano/CAT) and Python package for the automatic construction of composite chemical compounds, which supports the functionalization of organic, inorganic, and hybrid organic-inorganic materials. The CAT workflow consists in defining the anchoring sites on the reference material, usually a large molecular system denoted as a scaffold, and on the molecular species that are attached to it, , the ligands. Usually, ligands are pre-optimized in a conformation biased toward more linear structures to minimize interligand(s) steric interactions, a bias that is important when multiple ligands are attached onto the scaffold. The resulting superstructure(s) are then stored in various formats that can be used afterward in quantum chemical calculations or classical force field-based simulations.
计算机体系结构的不断改进使得模拟越来越大的分子系统成为可能。然而，这样的计算仍然需要输入初始结构，而这些结构也变得越来越复杂。在这项工作中，我们提出了 CAT，一个复合附着工具（源代码可在 https://github.com/nlesc-nano/CAT 获得）和一个用于自动构建复合化学化合物的 Python 包，它支持有机、无机和有机-无机混合材料的功能化。CAT 工作流程包括在参考材料（通常是一个大的分子系统，称为支架）和与之附着的分子物种（配体）上定义附着点。通常，配体在构象上被预优化，以偏向更线性的结构，以最小化配体之间的空间相互作用，当多个配体附着在支架上时，这种偏向是很重要的。然后将得到的超结构以各种格式存储，这些格式可以在以后的量子化学计算或基于经典力场的模拟中使用。
