Vibalizer: A free, web‐based tool for rapid, quantitative comparison and analysis of calculated vibrational modes

Abstract

This report describes the development and applications of a software package called Vibalizer, the first and only method that provides free, fast, interactive, and quantitative comparison and analysis of calculated vibrational modes. Using simple forms and menus in a web-based interface, Vibalizer permits the comparison of vibrational modes from different, but similar molecules and also performs rapid calculation and comparison of isotopically substituted molecules' normal modes. Comparing and matching complex vibrational modes can be completed in seconds with Vibalizer, whereas matching vibrational modes manually can take hours and gives only qualitative comparisons subject to human error and differing individual judgments. In addition to these core features, Vibalizer also provides several other useful features, including the ability to automatically determine first-approximation mode descriptions, to help users analyze the results of vibrational frequency calculations. Because the software can be dimensioned to handle almost arbitrarily large systems, Vibalizer may be of particular use when analyzing the vibrational modes of complex systems such as proteins and extended materials systems. Additionally, the ease of use of the Vibalizer interface and the straightforward interpretation of results may find favor with educators who incorporate molecular modeling into their classrooms. The Vibalizer interface is available for free use at http://www. compchem.org, and it is also available as a locally-installable package that will run on a Linux-based web server.

Hydrogen Bonding and Solvent Polarity Markers in the UV Resonance Raman Spectrum of Tryptophan: Application to Membrane Proteins

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Spectroscopic identification of reactive porphyrin motions

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Probing Heme Vibrational Anisotropy: An Imidazole Orientation Effect?

“…In Figures 3 to 5, we compare modes in [Fe(OEP)] and [Fe(OEP)(2-MeHIm)] that involve similar atomic motions on the basis of vibrational correlational analysis. 62, 81, 82 In all illustrations the iron motion is exactly in the porphyrin plane, or nearly so, and the porphyrin plane is parallel to the page. We note that in [Fe(OEP)] the iron motion is exactly along the Fe–N p bond directions, as expected, but in [Fe(OEP)(2-MeHIm)] the motion deviates from these directions.…”