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
1. [1]
  Jie ZHAO , Sen LIU , Qikang YIN , Xiaoqing LU , Zhaojie WANG . Theoretical calculation of selective adsorption and separation of CO₂ by alkali metal modified naphthalene/naphthalenediyne. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 515-522. doi: 10.11862/CJIC.20230385
2. [2]
  Maitri Bhattacharjee , Rekha Boruah Smriti , R. N. Dutta Purkayastha , Waldemar Maniukiewicz , Shubhamoy Chowdhury , Debasish Maiti , Tamanna Akhtar . Synthesis, structural characterization, bio-activity, and density functional theory calculation on Cu(Ⅱ) complexes with hydrazone-based Schiff base ligands. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1409-1422. doi: 10.11862/CJIC.20240007
3. [3]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026
4. [4]
  Qin Li , Kexin Yang , Qinglin Yang , Xiangjin Zhu , Xiaole Han , Tao Huang . Illuminating Chlorophyll: Innovative Chemistry Popularization Experiment. University Chemistry, 2024, 39(9): 359-368. doi: 10.3866/PKU.DXHX202309059
5. [5]
  Yunting Shang , Yue Dai , Jianxin Zhang , Nan Zhu , Yan Su . Something about RGO (Reduced Graphene Oxide). University Chemistry, 2024, 39(9): 273-278. doi: 10.3866/PKU.DXHX202306050
6. [6]
  Jizhou Liu , Chenbin Ai , Chenrui Hu , Bei Cheng , Jianjun Zhang . 六氯锡酸铵促进钙钛矿太阳能电池界面电子转移及其飞秒瞬态吸收光谱研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2402006-. doi: 10.3866/PKU.WHXB202402006
7. [7]
  Zhihuan XU , Qing KANG , Yuzhen LONG , Qian YUAN , Cidong LIU , Xin LI , Genghuai TANG , Yuqing LIAO . Effect of graphene oxide concentration on the electrochemical properties of reduced graphene oxide/ZnS. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1329-1336. doi: 10.11862/CJIC.20230447
8. [8]
  Zhuo WANG , Junshan ZHANG , Shaoyan YANG , Lingyan ZHOU , Yedi LI , Yuanpei LAN . Preparation and photocatalytic performance of CeO₂-reduced graphene oxide by thermal decomposition. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1708-1718. doi: 10.11862/CJIC.20240067
9. [9]
  Hui Shi , Shuangyan Huan , Yuzhi Wang . Ideological and Political Design of Potassium Permanganate Oxidation-Reduction Titration Experiment. University Chemistry, 2024, 39(2): 175-180. doi: 10.3866/PKU.DXHX202308042
10. [10]
  Tong Zhou , Jun Li , Zitian Wen , Yitian Chen , Hailing Li , Zhonghong Gao , Wenyun Wang , Fang Liu , Qing Feng , Zhen Li , Jinyi Yang , Min Liu , Wei Qi . Experiment Improvement of “Redox Reaction and Electrode Potential” Based on the New Medical Concept. University Chemistry, 2024, 39(8): 276-281. doi: 10.3866/PKU.DXHX202401005
11. [11]
  Ji-Quan Liu , Huilin Guo , Ying Yang , Xiaohui Guo . Calculation and Discussion of Electrode Potentials in Redox Reactions of Water. University Chemistry, 2024, 39(8): 351-358. doi: 10.3866/PKU.DXHX202401031
12. [12]
  Xiaofeng Zhu , Bingbing Xiao , Jiaxin Su , Shuai Wang , Qingran Zhang , Jun Wang . Transition Metal Oxides/Chalcogenides for Electrochemical Oxygen Reduction into Hydrogen Peroxides. Acta Physico-Chimica Sinica, 2024, 40(12): 2407005-. doi: 10.3866/PKU.WHXB202407005
13. [13]
  Junli Liu . Practice and Exploration of Research-Oriented Classroom Teaching in the Integration of Science and Education: a Case Study on the Synthesis of Sub-Nanometer Metal Oxide Materials and Their Application in Battery Energy Storage. University Chemistry, 2024, 39(10): 249-254. doi: 10.12461/PKU.DXHX202404023
14. [14]
  Tingting Jiang , Jing Chang . Application of Ideological and Political Education in Chemical Analysis Experiment under the Background of Emerging Engineering Education: Taking the Redox Titration Experiment as an Example. University Chemistry, 2024, 39(2): 168-174. doi: 10.3866/PKU.DXHX202308007
15. [15]
  Yunxin Xu , Wenbo Zhang , Jing Yan , Wangchang Geng , Yi Yan . A Fascinating Saga of “Energetic Materials”. University Chemistry, 2024, 39(9): 266-272. doi: 10.3866/PKU.DXHX202307008
16. [16]
  Xiao Liu , Guangzhong Cao , Mingli Gao , Hong Wu , Hongyan Feng , Chenxiao Jiang , Tongwen Xu . Seawater Salinity Gradient Energy’s Job Application in the Field of Membranes. University Chemistry, 2024, 39(9): 279-282. doi: 10.3866/PKU.DXHX202306043
17. [17]
  Xinxin JING , Weiduo WANG , Hesu MO , Peng TAN , Zhigang CHEN , Zhengying WU , Linbing SUN . Research progress on photothermal materials and their application in solar desalination. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1033-1064. doi: 10.11862/CJIC.20230371
18. [18]
  Yuanyin Cui , Jinfeng Zhang , Hailiang Chu , Lixian Sun , Kai Dai . Rational Design of Bismuth Based Photocatalysts for Solar Energy Conversion. Acta Physico-Chimica Sinica, 2024, 40(12): 2405016-. doi: 10.3866/PKU.WHXB202405016
19. [19]
  Qi Wang , Yicong Gao , Feng Lu , Quli Fan . Preparation and Performance Characterization of the Second Near-Infrared Phototheranostic Probe: A New Design and Teaching Practice of Polymer Chemistry Comprehensive Experiment. University Chemistry, 2024, 39(11): 342-349. doi: 10.12461/PKU.DXHX202404141
20. [20]
  Yixuan Gao , Lingxing Zan , Wenlin Zhang , Qingbo Wei . Comprehensive Innovation Experiment: Preparation and Characterization of Carbon-based Perovskite Solar Cells. University Chemistry, 2024, 39(4): 178-183. doi: 10.3866/PKU.DXHX202311091

Get Citation

PDF

XML

Metrics

PDF Downloads(1298)
Abstract views(3486)
HTML views(6)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142