SEQCROW: A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems

Area of Science:

• Computational Chemistry
• Structural Biology
• Organic Chemistry

Background:

• UCSF ChimeraX is a powerful molecular visualization tool.
• Complex organic and organometallic compounds require specialized editing and analysis tools.
• Efficient generation of publication-quality figures and computational input is crucial.

Purpose of the Study:

• Introduce SEQCROW, a UCSF ChimeraX bundle.
• Provide advanced molecular structure editing capabilities.
• Integrate quantum chemistry utilities for complex compounds.

Main Methods:

• Developed graphical presets and bond editing tools for molecular structures.
• Implemented ligand mapping for efficient structure building.
• Integrated visualization of vibrational modes and simulated IR spectra.
• Included computation and visualization of molecular descriptors (e.g., percent buried volume, ligand cone angles, Sterimol parameters).
• Added functionality for processing thermochemical corrections from quantum mechanical computations.
• Enabled generation of input files for ORCA, Psi4, and Gaussian.
• Facilitated running and managing computational jobs.

Main Results:

• SEQCROW facilitates rapid and efficient building of molecular structures.
• Users can generate publication-quality molecular structure figures.
• Advanced computational chemistry tasks are streamlined within ChimeraX.
• SEQCROW supports analysis of complex organic and organometallic compounds.

Conclusions:

• SEQCROW enhances UCSF ChimeraX with advanced structure editing and quantum chemistry tools.
• The bundle accelerates the creation of molecular figures and computational workflows.
• SEQCROW is a valuable resource for researchers working with complex organic and organometallic chemistry.