• Views 1,196
• Citations 0
• ePub 35
• PDF 456
`Computational Biology JournalVolume 2013 (2013), Article ID 807592, 11 pageshttp://dx.doi.org/10.1155/2013/807592`
Research Article

## Calculated Vibrational Properties of Ubisemiquinones

Department of Physics and Astronomy, Georgia State University, 29 Peachtree Center Avenue, Atlanta, GA 30303, USA

Received 15 October 2012; Accepted 27 November 2012

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.

1. B. Trumpower, Function of Quinones in Energy Conserving Systems, Academic Press, 1982.
2. B. Ke, “The bacterial photosynthetic reaction center: chemical composition and crystal structure,” in Photosynthesis: Photobiochemistry and Photobiophysics, pp. 47–62, Kluwer Academic Publishers, Dordrecht, The Netherlands, 2001.
3. B. Ke, “The, “Stable” primary electron acceptor (${\text{Q}}_{\text{A}}$) of photosynthetic bacteria,” in Photosynthesis: Photobiochemistry and Photobiophysics, pp. 101–110, Kluwer Academic Publishers, Dordrecht, The Netherlands, 2001.
4. B. Ke, “The secondary electron acceptor (${\text{Q}}_{\text{B}}$) of photosynthetic bacteria,” in Photobiochemistry and Photobiophysics, pp. 111–128, Kluwer Academic Publishers, Dordrecht, The Netherlands, 2001.
5. N. Srinivasan and J. H. Golbeck, “Protein-cofactor interactions in bioenergetic complexes: the role of the A1A and A1B phylloquinones in Photosystem I,” Biochimica et Biophysica Acta, vol. 1787, no. 9, pp. 1057–1088, 2009.
6. C. A. Wraight and M. R. Gunner, “The acceptor quinones of purple photosynthetic Bacteria-structure and spectroscopy,” in The Purple Photosynthetic Bacteria, C. N. Hunter, F. Daldal, M. C. Thurnauer, and J. T. Beatty, Eds., pp. 379–405, Springer, 2009.
7. J. Breton and E. Nabedryk, “Protein-quinone interactions in the bacterial photosynthetic reaction center: light-induced FTIR difference spectroscopy of the quinone vibrations,” Biochimica et Biophysica Acta, vol. 1275, no. 1-2, pp. 84–90, 1996.
8. M. Bauscher and W. Mäntele, “Electrochemical and infrared-spectroscopic characterization of redox reactions of p-quinones,” Journal of Physical Chemistry, vol. 96, no. 26, pp. 11101–11108, 1992.
9. M. Bauscher, E. Nabedryk, K. Bagley, J. Breton, and W. Mantele, “Investigation of models for photosynthetic electron acceptors. Infrared spectroelectrochemistry of ubiquinone and its anions,” FEBS Letters, vol. 261, no. 1, pp. 191–195, 1990.
10. X. Zhao, T. Ogura, M. Okamura, and T. Kitagawa, “Observation of the resonance raman spectra of the semiquinones QA·- and QB·- in photosynthetic reaction centers from Rhodobacter sphaeroides R26,” Journal of the American Chemical Society, vol. 119, pp. 5263–5264, 1997.
11. G. Balakrishnan, P. Mohandas, and S. Umapathy, “Ab initio studies on structure and vibrational spectra of ubiquinone and its radical anion,” Spectrochimica Acta A, vol. 53, no. 10, pp. 1553–1561, 1997.
12. M. Nonella, “A density functional investigation of model molecules for ubisemiquinone radical anions,” Journal of Physical Chemistry B, vol. 102, no. 21, pp. 4217–4225, 1998.
13. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., 2004.
14. K. M. Bandaranayake, V. Sivakumar, R. Wang, and G. Hastings, “Modeling the A1 binding site in photosystem. I. Density functional theory for the calculation of “anion—neutral“ FTIR difference spectra of phylloquinone,” Vibrational Spectroscopy, vol. 42, no. 1, pp. 78–87, 2006.
15. E. Cancès, C. Le Bris, B. Mennucci, and J. Tomasi, “Integral equation methods for molecular scale calculations in the liquid phase,” Mathematical Models and Methods in Applied Sciences, vol. 9, no. 1, pp. 35–44, 1999.
16. E. Cancès, B. Mennucci, and J. Tomasi, “A new integral equation formalism for the polarizable continuum model: theoretical background and applications to Isotropic and anisotropic dielectrics,” Journal of Chemical Physics, vol. 107, no. 8, pp. 3032–3041, 1997.
17. J. Tomasi, B. Mennucci, and E. Cancès, “The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level,” Journal of Molecular Structure, vol. 464, no. 1–3, pp. 211–226, 1999.
18. J. Tomasi, R. Cammi, B. Mennucci, C. Cappelli, and S. Corni, “Molecular properties in solution described with a continuum solvation model,” Physical Chemistry Chemical Physics, vol. 4, no. 23, pp. 5697–5712, 2002.
19. J. Tomasi, B. Mennucci, and R. Cammi, “Quantum mechanical continuum solvation models,” Chemical Reviews, vol. 105, no. 8, pp. 2999–3093, 2005.
20. J. M. L. Martin and C. Van Alsenoy, GAR2PED, University of Antwerp, 1995.
21. H. Lamichhane, R. Wang, and G. Hastings, “Comparison of calculated and experimental FTIR spectra of specifically labeled ubiquinones,” Vibrational Spectroscopy, vol. 55, no. 2, pp. 279–286, 2011.
22. C. Cappelli, C. O. Silva, and J. Tomasi, “Solvent effects on vibrational modes: ab-initio calculations, scaling and solvent functions with applications to the carbonyl stretch of dialkyl ketones,” Journal of Molecular Structure, vol. 544, pp. 191–203, 2001.
23. G. Hastings, K. M. P. Bandaranayake, and E. Carrion, “Time-resolved FTlR difference spectroscopy in combination with specific isotope labeling for the study of A1, the secondary electron acceptor in photosystem 1,” Biophysical Journal, vol. 94, no. 11, pp. 4383–4392, 2008.
24. J. Breton, J. R. Burie, C. Berthomieu, G. Berger, and E. Nabedry, “The binding sites of quinones in photosynthetic bacterial reaction centers investigated by light-induced FTIR difference spectroscopy: assignment of the ${\text{Q}}_{\text{A}}$ vibrations in Rhodobacter sphaeroides using 18O- Or13C-labeled ubiquinone and vitamin K1,” Biochemistry, vol. 33, no. 16, pp. 4953–4965, 1994.
25. R. Brudler, H. J. M. De Groot, W. B. S. Van Liemt et al., “Asymmetric binding of the 1- and 4- $\text{C}=\text{O}$ groups of ${\text{Q}}_{\text{A}}$ in Rhodobacter sphaeroides R26 reaction centres monitored by Fourier transform infra-red spectroscopy using site-specific isotopically labelled ubiquinone-10,” EMBO Journal, vol. 13, no. 23, pp. 5523–5530, 1994.
26. J. Breton, C. Boullais, G. Berger, C. Mioskowski, and E. Nabedryk, “Binding sites of quinones in photosynthetic bacterial reaction centers investigated by light-induced FTIR difference spectroscopy: symmetry of the carbonyl interactions and close equivalence of the QB vibrations in Rhodobacter sphaeroides and Rhodopseudomonas viridis probed by isotope labeling,” Biochemistry, vol. 34, no. 36, pp. 11606–11616, 1995.
27. R. Brudler, H. J. M. De Groot, W. B. S. Van Liemt et al., “FTIR spectroscopy shows weak symmetric hydrogen bonding of the ${\text{Q}}_{\text{B}}$ carbonyl groups in Rhodobacter sphaeroides R26 reaction centres,” FEBS Letters, vol. 370, no. 1-2, pp. 88–92, 1995.