Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site

Abstract

Previously we have shown that ONIOM type (QM/MM) calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and 18O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0), 2,3,5,6-tetramethyl-1, 4-benzoquinone (duroquinone, DQ), and 2,3-dimethyl-l,4-naphthoquinone (DMNQ) incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites. The normal modes that contribute to the bands in the calculated spectra, their composition, frequency, and intensity, and how these quantities are modified upon 18O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10–13 cm−1 separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry in H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are “tail-less.” Spectra were also calculated for reaction centers with corresponding “tail” containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated spectra.

Vibrational spectroscopy of photosystem I

“…To help confirm the validity of the QM/MM vibrational frequency calculations that were undertaken [64], further similar QM/MM calculations were undertaken for the neutral state of several different quinones incorporated into the Q A binding site and, again, the calculated isotope edited FTIR DS were found to agree well with experimental spectra [67]. In all of the experimental spectra, and in the QM/MM calculated spectra, two separate bands due to the neutral quinone C_O modes were well resolved.…”

Additive Engineering in Perovskite Solar Cells: Effect of Basicity of Benzoquinone Additives Controlled by Substituent

“…However, the mixture of 4Cl-BQ/PbI 2 shows a blue shift in the C�O stretching from 1679.8 to 1689.6 cm −1 , suggesting little interaction between C�O and Pb 2+ . A pronounced red shift in C�O stretching from 1635.6 cm −1 in pure 4Me-BQ to 1587.8 cm −1 in the 4Me-BQ/PbI 2 composite confirms the strong interaction between 4Me-BQ and PbI 2 , 31 which also implies enhanced Lewis basicity of oxygen in the carbonyl group by the electron-donating methyl substituent.…”

Current challenges in photosynthesis: from natural to artificial

“…The computational calculation (ONIOM) is increasingly critical in interpreting the FTIR data in elucidating the structural and functional relationship in photosynthesis. Zhao et al using ONIOM type calculation to simulate isotope edited FTIR difference spectra for reaction centers with a variety of foreign quinones in the Q A site and allows a direct assessment of the appropriateness of previous IR assignments and suggestions (Zhao et al, 2013 ). The protein kinases STN7 and STN8 are predominately responsible for the thylakoid phosphorylation in PS II.…”