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Density functional theory has been used to calculate harmonic normal mode vibrational frequencies for unlabeled and isotopelabeled ubisemiquinones in both the gas phase and in several solvents. It is shown that four methoxy group conformations are likely to be present in solution at room temperature. Boltzmann weighted infrared and Raman spectra for the four conformers were calculated, and composite spectra that are the sum of the Boltzmann weighted spectra were produced. These composite spectra were compared to experimental FTIR and resonance Raman spectra, and it is shown that the calculated band frequencies, relative band intensities, and 13C and 18O isotope-induced band shifts are in excellent agreement with experiment. The calculations show that the C=O and C=C modes of ubisemiquinone strongly mix with methoxy methyl CH bending vibrations, and that the degree of mixing is altered upon isotope labeling, resulting in complicated changes in mode frequencies, intensities, and composition upon isotope labeling. Upon consideration of the calculated potential energy distributions of the normal modes of ubisemiquinone, and how they change upon isotope labeling, an explanation of some puzzling features in previously published Raman spectra is provided.


This article was originally published in Computational Biology Journal and is reposted here with the permission of the authors. Copyright © 2013 Hari P. Lamichhane and Gary Hastings. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Creative Commons Attribution 3.0 License
This work is licensed under a Creative Commons Attribution 3.0 License.