Citation: HU Qiong, WANG Guo-Ying, OU Jia-Ming, WANG Rui-Li. Effect ofWater Ligation on the Redox Potential and Infrared Spectra of Chlorophyll-a[J]. Acta Physico-Chimica Sinica, ;2010, 26(11): 3035-3040. doi: 10.3866/PKU.WHXB20101116 shu

Effect ofWater Ligation on the Redox Potential and Infrared Spectra of Chlorophyll-a

1.
College of Physics and Electronic Information, Yunnan Normal University, Kunming 650092, P. R. China

Received Date: 18 May 2010
Available Online: 23 September 2010
Fund Project: 国家自然科学基金(10764006)资助项目 (10764006)

In the reaction center of photosystem I the accessory electron transfer cofactors are two monomeric chlorophyll-a molecules that are ligated to two water molecules. To study the effect of water ligation on the redox potential and vibrational properties of chlorophyll-a, we built three molecular models of water ligation of chlorophyll-a based on the X-ray crystal structure of photosystem I. Then, we systematically calculated the geometries, vibrational frequencies, bond dissociation energies, and redox potentials of these models using density functional theory. The calculations were conducted in the gas phase, water, and a simulated protein environment. In addition, three different basis sets were employed to investigate the influence of the basis set on the calculation results. ¹⁵N, ²H, and ¹³C labeled spectra of the models in the gas phase were also calculated. Our results show that the water ligand causes the Mg ion of chlorophyll-a to move away fromthe center of the porphyrin ring so that the Mg—N bond lengths increase and the Mg centered angles decrease. When a nearby amino acid, asparagine (ASNB591), provides a hydrogen bond to the water that is axial ligand to the chlorophyll-a, these changes increase further. Additionally, the Mg—O bond distance decreases, the dissociation energy increases, and the redox potential also decreases. Furthermore, the redox potentials of the molecules and their bond dissociation energies decrease as the relative dielectric constant of the media and the basis sets increase. However, differences in the frequencies of the corresponding carbonyl groups and the C=C vibrations of the porphyrin ring in the three models are less than 7 cm^-1, and the differences in frequency shift upon isotope labeling between the models are less than 3 cm^-1. These results provide useful information for further studies of the structural and functional properties of chlorophyll-a in the photosynthetic reaction center.
- Density functional theory,
- Chlorophyll-a,
- Redox potential,
- Dissociation energy,
- Infrared spectrum,
- Basis set
1. [1]
  
  1. Jordan, P.; Fromme, P.; Witt, H. T.; Klukas, O.; Saenger, W.; Krauss, N. Nature, 2001, 411: 909
2. [2]
  2. Wang, R.; Parameswaran, S.; Hastings, G. Vibrational Spectroscopy, 2007, 44: 357
3. [3]
  3. Vernon, L. P.; Seely, G. R. The chlorophylls. NewYork: Academic Press, 1966: 187-251
4. [4]
  4. Dolphin, D. The porphyrins. NewYork: Academic Press, 1978: 430-455
5. [5]
  5. Fromme, P.; Jordan, P.; Krauβ, N. Biochimica et Biophysica Acta, 2001, 1507: 5
6. [6]
  6. Matyushov, D. V. J. Phys. Chem. B, 2006, 110: 10095
7. [7]
  7. Webber, A. N.; Lubitz, W. Biochimica et Biophysica Acta, 2001, 1507: 61
8. [8]
  8. Krabben, L.; Schlodder, E.; Jordan, R.; Carbonera, D.; Giacometti, G.; Lee, H.; Webber, A. N.; Lubitz, W. Biochemistry, 2000, 39: 13012
9. [9]
  9. Ramesh, V. M.; Gibasiewicz, K.; Su, L.; Bingham, S. E.;Webber, A. N. Biochimica et Biophysica Acta, 2007, 1767: 151
10. [10]
  10. Holzwarth, A. R.; Muller, M. G.; Niklas, J.; Lubitz, W. Biophysical Journal, 2006, 90: 552
11. [11]
  11. Giera, W.; Ramesh, V. M.; Webber, A. N.; Stokkum, I. V.; Grondelle, R. V.; Gibasiewicz, K. Biochimica et Biophysica Acta, 2010, 1797: 106
12. [12]
  12. Zhao, G. J.; Han, K. L. Biophysical Journal, 2008, 94: 38
13. [13]
  13. Zhao, G. J.; Han, K. L. ChemPhysChem, 2008, 9: 1842
14. [14]
  14. Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J. Phys. Chem. B, 2007, 111: 8940
15. [15]
  15. Zhao, G. J.; Han, K. L. J. Phys. Chem. A, 2007, 111: 9218
16. [16]
  16. Heimdal, J.; Jensen, K. P.; Devarajan, A.; Ryde, U. J. Biol. Inorg. Chem., 2007, 12: 49
17. [17]
  17. O'Malley, P. J. Am. Chem. Soc., 2000, 122: 7798
18. [18]
  18. Parameswaran, S.; Wang, R.; Hastings, G. J. Phys. Chem. B, 2008, 112: 14056
19. [19]
  19. Frisch, A.; Dennington II, R. D.; Keith, T. A.; Millam, J. GaussView4.1.2.Wallingford, CT: Gaussian Inc., 2007
20. [20]
  20. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; et al. Gaussian 03. Revision D.01. Pittsburg, PA: Gaussian Inc., 2004
21. [21]
  21. Foresman, J. B.; Frisch, A. Exploring chemistry with electronic s tructuremethods. 2nd ed. Pittsburg, PA: Gaussian Inc., 1996: 1-302
22. [22]
  22. Hasegawa, K.; Noguchi, T. Biochemistry, 2005, 44: 8865
23. [23]
  23. Shen,Y.; Ryde, U. Journal of Inorganic Biochemistry, 2004, 98: 878
24. [24]
  24. Reiss, H.; Heller, A. J. Phys. Chem., 1985, 89: 4207
25. [25]
  25. Nakato, Y.; Chiyoda, T.; Tsubomura, H. Bull. Chem. Soc. Jpn., 1974, 47: 3001
26. [26]
  26. Sheer, H. Chlorophylls. Boca Raton: CRC Press, 1991: 855-902
27. [27]
  27. Wheeler, R. A.; Eriksson, L. A. Theoretical biochemistry-processes and properties of biological systems. Amsterdam: Elsevier, 2001: 655-690
28. [28]
  28. Noguchi, T. Photosynth. Res., 2010, 104: 321
29. [29]
  29. Berezin, K. V.; Nechaev, V. V.; Ziganshina, O. D. Journal of Structural Chemistry, 2004, 45: 217
30. [30]
  30. Nabedryk, E.; Leonhard, M.; Mantele, W.; Breton, J. Biochemistry, 1990, 29: 3242
31. [31]
  31. Breton, J.; Nabedryk, E.; Clerici, A. Biochimica et Biophysica Acta, 2001, 1507: 180
32. [32]
  32. Wang, R.; Sivakumar, V.; Johnson, T. W.; Hastings, G. Biophysical Journal, 2004, 86: 1061
33. [33]
  33. Schmid, E. D.; Schneider, F. W.; Siebert, F. Spectroscopy of biological molecules-newadvance. Chichester: Wiley&Sons 1988: 297-300
34. [34]
  34. Breton, J.; Nabedryk, E.; Leibl, W. Biochemistry, 1999, 38: 11585
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