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Slideshow

New Tools for Making Computational Quantum Chemistry Simpler

Anthony Schaefer, speaker
Anthony Schaefer
Graduate Student, Department of Chemistry
University of Georgia
Chemistry Building, Room 400
Organic Seminar

Computational quantum chemistry can be used to gain insight into reactivity and simulate properties or spectra. However, conducting computational studies often requires using command line interfaces, which have a steep learning curve. A simpler alternative to command line interfaces is graphical user interfaces. Existing graphical interfaces are often insufficient to handle every task that one encounters during a computational study: building structures, setting up computations, viewing calculated properties, and creating publication-quality graphics. I have built SEQCROW1 : a collection of tools with a graphical interface for facilitating computational chemistry studies. SEQCROW allows for structures to be built and modified quickly. My tools also allow for computations to be set up, run, and processed. With SEQCROW, users can analyze Fukui functions 2 , vibrational modes, simulated spectra, and several structure-based parameters: Sterimol 3 , ligand cone angles 4,5 , and buried volume 6 . SEQCROW will also enable users to automate transition state searches. SEQCROW is built as a plugin for UCSF ChimeraX 7.

Illustration of images generated by SEQCROW computational quantum chemistry interface

References

  1. Schaefer, A. J.; Ingman, V. M.; Wheeler, S. E. SEQCROW: A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems. J Comput Chem 2021, 42, 1750-1754.
  2. Pino-Rios, R.; Inostroza, D.; Cárdenas-Jirón, G.; Tiznado, W. Orbital-Weighted Dual Descriptor for the Study of Local Reactivity of Systems with (Quasi-) Degenerate States. J Phys Chem A 2019, 123, 10556-10562
  3. Verloop, A. Drug Design; Medicinal chemistry; Acad. Press: New York, 1976; Vol. 3.
  4. Tolman, C. A.; Seidel, W. C.; Gosser, L. W. Formation of three-coordinate nickel(0) complexes by phosphorus ligand dissociation from NiL4. J. Am. Chem. Soc. 1974, 96, 53-60.
  5. Bilbrey, J. A.; Kazez, A. H.; Locklin, J.; Allen, W. D. Exact ligand cone angles. J. Comput. Chem. 2013, 34, 1189-1197.
  6. Poater, A.; Ragone, F.; Giudice, S.; Costabile, C.; Dorta, R.; Nolan, S. P.; Cavallo, L. Thermodynamics of N-Heterocyclic Carbene Dimerization: The Balance of Sterics and Electronics. Organometallics 2008, 27, 2679-2681.
  7. Goddard, T. D.; Huang, C. C.; Meng, E. C.; Pettersen, E. F.; Couch, G. S.; Morris, J. H.; Ferrin, T. E. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018, 27, 14-25.

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