SEQCROW: A ChimeraXbundle to facilitate quantum chemical applications to complex molecular systems

• Published in: Journal of Computational Chemistry
• Main Authors: Schaefer, Anthony J., Ingman, Victoria M., Wheeler, Steven E.
• Other Authors: Division of Chemistry, National Science Foundation
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2021
• Subjects: Orca
• Online Access: http://dx.doi.org/10.1002/jcc.26700; https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.26700; https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26700; https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jcc.26700

Abstract We describe a bundle for UCSF ChimeraX called SEQCROW that provides advanced structure editing capabilities and quantum chemistry utilities designed for complex organic and organometallic compounds. SEQCROW includes graphical presets and bond editing tools that facilitate the generation of publication‐quality molecular structure figures while also allowing users to build molecular structures quickly and efficiently by mapping new ligands onto existing organometallic complexes as well as adding rings and substituents. Other capabilities include the ability to visualize vibrational modes and simulated IR spectra, to compute and visualize molecular descriptors including percent buried volume, ligand cone angles, and Sterimol parameters, to process thermochemical corrections from quantum mechanical computations, to generate input files for ORCA, Psi4, and Gaussian, and to run and manage computational jobs.