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WIREs Comput Mol Sci
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QChASM: Quantum chemistry automation and structure manipulation

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Abstract As the tools of computational quantum chemistry have continued to mature, larger and more complex molecular systems have become amenable to computational study. However, studies of these complex systems often require the execution of enormous numbers of computations, which can be a tedious and error‐prone process if done manually. We have developed a suite of free, open‐source tools to facilitate the automation of quantum chemistry workflows. These tools are collected under the organization QChASM (Quantum Chemistry Automation and Structure Manipulation) and include functionality for building and manipulating complex molecular structures and performing routine tasks (AaronTools), a toolkit for automating TS optimizations and predictions of the outcomes of selective homogeneous catalytic reactions, and a plug‐in for UCSF ChimeraX that provides a graphical interface for building complex molecular structures and representing output from quantum chemistry computations. These tools are described below, with a focus on the recent Python implementation of AaronTools. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Software > Quantum Chemistry
Main components of QChASM
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Screenshots of SEQCROW showing the QM input generator allowing users to save “Presets” of common input file types for Gaussian, Orca, and Psi4, the calculation of Sterimol parameters, and the normal mode visualization and IR spectra plotting
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Use of the function map_ligand to replace the ligand in a TS for an enantioselective Markovnikov hydroboration (from Reference 16) of a terminal alkene with (S,S)‐Me‐DuPhos
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(a) Dimer of 3‐methylindole and 3,9‐dihydro‐purine‐2,6‐dione from Reference 9 before and after rotation of 3,9‐dihydro‐purine‐2,6‐dione by 60° around the vector normal to the ring plane; (b) TS for a stereoselective epoxide ring opening catalyzed by the chiral phosphoric acid TRIP, from Reference 10, highlighting the six iPr and one OMe that will be rotated by makeConf (selected hydrogen atoms removed for clarity); (c) TS for an Ir‐catalyzed CH activation reaction before and after substitution of atoms 11 and 13 with Me groups and replacement of the Me group at atom 25 with a Ph ring using substitute; (d) use of mapLigand to replace a model ZDMP ligand with (S)‐BINAP in a TS structure for a Noyori asymmetric hydrogenation of acetaldehyde
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Software > Quantum Chemistry
Structure and Mechanism > Reaction Mechanisms and Catalysis

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