Density functional theory has been used to calculate harmonic normal mode vibrational frequencies for unlabeled and isotope-labeled 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 and 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. 1. Introduction Ubiquinones ( : 2,3-dimethoxy-5-methyl-6-polyprenyl-1,4-benzoquinones) play an important role in biological electron and proton transfer processes that occur in both respiration and photosynthesis [1]. In photosynthetic reaction centers from purple bacteria, two UQ molecules, called and , act as terminal electron acceptors [2]. In purple bacterial reaction centers (PBRCs) (see Abbreviations) from Rhodobacter (Rb.) sphaeroides, and are both ubiquinone-10 (UQ10) molecules. and have very different functions; however, is an intermediary cofactor involved in transferring electrons from bacteriopheophytin to , while couples electron and proton transfer processes [3, 4]. The very different redox functions of and are testimony to the flexibility of UQs in biological processes. Since and are both UQ10 molecules, pigment-protein interactions must modulate the functional properties of UQ10 in PBRCs. Elucidation of these pigment-protein interactions is at the heart of much current research in photosynthesis [5, 6]. Fourier transform infrared (FTIR) difference spectroscopy (DS) is a sensitive molecular-level probe of pigment-protein interactions, and it is widely used to study both the neutral and reduced states of the quinones occupying the and binding sites in PBRCs [7]. Although and FTIR difference spectra
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