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通过分子支架的自动化功能化探索化学空间

: exploration of chemical space by automated functionalization of molecular scaffold.

作者信息

Kalikadien Adarsh V, Pidko Evgeny A, Sinha Vivek

机构信息

Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands

出版信息

Digit Discov. 2022 Jan 6;1(1):8-25. doi: 10.1039/d1dd00017a. eCollection 2022 Feb 14.

Abstract

Exploration of the local chemical space of molecular scaffolds by post-functionalization (PF) is a promising route to discover novel molecules with desired structure and function. PF with rationally chosen substituents based on known electronic and steric properties is a commonly used experimental and computational strategy in screening, design and optimization of catalytic scaffolds. Automated generation of reasonably accurate geometric representations of post-functionalized molecular scaffolds is highly desirable for data-driven applications. However, automated PF of transition metal (TM) complexes remains challenging. In this work a Python-based workflow, , that is aimed at automating the PF of a given molecular scaffold with special emphasis on TM complexes, is introduced. In three representative applications of by comparing with DFT and DFT-B calculations, we show that the generated structures have a reasonable quality for use in computational screening applications. Furthermore, we show that generated geometries can be used in machine learning applications to accurately predict DFT computed HOMO-LUMO gaps for transition metal complexes. is open-source and aims to bolster and democratize the efforts of the scientific community towards data-driven chemical discovery.

摘要

通过后功能化(PF)探索分子支架的局部化学空间是发现具有所需结构和功能的新型分子的一条有前途的途径。基于已知电子和空间性质合理选择取代基进行后功能化是催化支架筛选、设计和优化中常用的实验和计算策略。对于数据驱动的应用而言,自动生成后功能化分子支架合理准确的几何表示非常必要。然而,过渡金属(TM)配合物的自动后功能化仍然具有挑战性。在这项工作中,引入了一种基于Python的工作流程,旨在自动实现给定分子支架的后功能化,特别强调过渡金属配合物。在通过与密度泛函理论(DFT)和DFT-B计算进行比较的三个代表性应用中,我们表明生成的结构在计算筛选应用中具有合理的质量。此外,我们表明生成的几何结构可用于机器学习应用,以准确预测过渡金属配合物的密度泛函理论计算的最高已占分子轨道-最低未占分子轨道(HOMO-LUMO)能隙。该工作流程是开源的,旨在支持科学界在数据驱动的化学发现方面的努力并使其民主化。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c61/8887922/053d818b8fc4/d1dd00017a-f1.jpg

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