簡易檢索 / 詳目顯示

回結果列表
研究生： 溫淑如
論文名稱： 含鎳超氧化物歧化酶擬態化合物之理論計算反應機制之探討
Computational Mechanism Study for Superoxide Disproportionation of a Model Complex for Nickel Superoxide Dismutase
指導教授： 李位仁
Lee, Way-Zen
蔡明剛
Tsai, Ming-Kang
學位類別： 碩士
Master
系所名稱： 化學系
Department of Chemistry
論文出版年： 2013
畢業學年度： 101
語文別： 中文
論文頁數： 93
中文關鍵詞： 理論計算 、超氧化物歧化酶擬態化合物 、反應機制
英文關鍵詞： DFT calculation, NiSOD model complex, reaction mechanism
論文種類： 學術論文
相關次數： 點閱：131  下載：3 
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報

    • 含脯胺酸衍生物之五牙基二價鎳錯合物[Ni(H2BDPP)- (tBuNC)](BF4)2 (1-tBuNC)，藉由二價及三價鎳之間的氧化態轉換，具有將超氧離子進行歧化反應之能力，使其生成氧氣及過氧化氫分子。衍生物[Ni(BDPP)](PF6) (3)則具有將超氧離子氧化生成氧氣之能力。為了瞭解此擬態化合物之反應機制，本研究利用DFT理論計算的方法，提出四種可能路徑，並針對各反應過程中的過渡態及其電子組態之改變進行分析及探討。根據各反應之能量，推得出最合理的反應機構如下：二價鎳錯合物[Ni(H2BDPP)]2+ (1m)被超氧離子去質子化生成四配位平面四方構型的[Ni(HBDPP)]+ (2m)及超氧化氫自由基，接著超氧化氫自由基與錯合物2m的鎳中心鍵結，並進行氫原子轉移(HAT)反應生成[Ni(BDPP)]+ (3m)及過氧化氫，隨後錯合物3m再與第二個超氧離子反應，經由電子轉移生成[Ni(BDPP)] (4m)及氧氣。在此機制中，鎳錯合物是以高自旋組態(high spin state)下進行反應，速率決定步驟為超氧化氫鍵結到錯合物2m之二價鎳中心進行氫原子轉移反應。此理論計算的結果，使我們對於此擬態化合物之歧化反應有更進一步的瞭解。

    A NiII complex, Ni(H2BDPP)(tBuNC)](BF4)2 (1-tBuNC), supported by a prolinol-containing pentadentate ligand, 2,6-bis(((S)-2- (diphenylhydroxymethyl)-1-pyrrolidinyl)methyl)pyridine (H2BDPP), is able to catalyze the disproportionation of O2− into O2 and H2O2 through a cycle of NiII and NiIII oxidation states. Its derivative, [Ni(BDPP)](PF6) (3), has shown the capability to oxide O2− to form O2. To understand the mechanism of this process, a series of density functional theory (DFT) calculations and analysis were carried out. Four possible reaction mechanisms are proposed, and the activation energy and detail for the change of the electron distribution for each mechanism are analyzed. The most energetically reasonable mechanism is described as following. First, the NiII complex, [Ni(H2BDPP)]2+ (1m), reacts with O2−, which acts as a base to deprotonate the prolinol of the ligand, to form a deprotonated square-planar intermediate, [Ni(HBDPP)]+ (2m), with the formation of HOO• radical. The produced HOO• radical further coordinates to the NiII center of 2m and proceeds hydrogen atom transfer (HAT) to generate [Ni(BDPP)]+ (3m) and H2O2. Once complex 3m is formed, it immediately reacts with the second O2− and electron transfer occurred to generate [Ni(BDPP)] (4m) and O2. This mechanism proceeds under high spin state of Ni cmplexes and the rate determining step is the coordination of HOO• to the NiII center of 2m for the HAT reaction. This theoretical investigation provides a useful insight into the mechanism of our NiSOD mimics.

    中文摘要 I 英文摘要 II 圖索引 III 表索引 IX 第一章 緒論 第一節 超氧化物歧化酶之相關文獻探討 1 一、銅/鋅超氧化物歧化酶，Cu/ZnSOD 3 二、含錳及含鐵超氧化物歧化酶，MnSOD and FeSOD 4 三、含鎳超氧化物歧化酶，NiSOD 4 第二節 含鎳超氧化物歧化酶擬態化合物的研究 11 第二章 計算原理 第一節 量子力學 16 第二節 計算化學的理論與方法 18 一、分子力學 18 二、初始法(ab initio) 19 三、半經驗法 20 四、密度泛函理論 21 第三節 基底函數(Basis Sets) 22 第四節 計算方法 28 一、單點能量 28 二、幾何優化 28 三、振動頻率 30 四、溶劑效應 30 第五節 本篇論文的計算方法 33 第三章 結果與討論 前言 34 第一節 幾何結構比較 37 一、錯合物[Ni(H2BDPP)(tBuNC)](BF4)2 (1-tBuNC)的優化結構比較 37 二、錯合物[Ni(HBDPP)](ClO4) (2)的優化結構比較 40 三、錯合物[Ni(BDPP)](PF6) (3)的優化結構比較 42 四、錯合物[Ni(BDPP)] (4)的優化結構比較 45 第二節 計算分析之反應架構 48 第三節 氧化階段之可能機構及其計算分析 49 一、路徑A的能量圖及反應機制之探討 54 二、路徑B的能量圖及反應機制之探討 59 三、路徑C的能量圖及反應機制之探討 62 四、氧化階段各反應機制之能量比較 66 第四節 氧化階段中路徑A之各電子結構探討 67 第五節 還原階段的反應機制探討 73 第六節 本研究與酵素反應機制之比較 80 第四章 結論 第一節 結論 85 第二節 未來展望 86 參考文獻 87

    1. McCord, J. M.; Fridovich, I. J. Biol. Chem. 1969, 244, 6049.
    2. (a) Bryngelson, P. A.; Maroney, M. J. Met. Ions Life Sci. 2007, 2, 417. (b) Imlay, J. A. Annu. Rev. Microbiol. 2003, 349, 331. (c) McCord, J. M. Superoxide Dismutase 2002, 349, 331. (d) Wallace, D. C. Science 1992, 256, 628. (e) Valentine, J. S.; Wertz, D. L.; Lyons, T. J.; Liou, L. L.; Goto, J. J.; Gralla, E. B. Curr. Opin. Chem. Biol. 1998, 2, 253. (f) Miller, A.-F.; Sorkin, D. L. Comments Mol. Cell. Biophys. 1997, 9, 1.
    3. Velazquez, E.; Winocour P. H.; Kesteven P.; Alberti K. G.; Laker M. F.; Diabet Med 1991, 8, 752.
    4. Iovine, N. M.; Pursnani, S.; Voldman, A.; Wasserman, G.; Blaser, M. J.; Weinrauch, Y. Infection and Immunity 2008, 986.
    5. (a) Rosen, D. R.; Siddique, T.; Patterson, D.; Figlewicz, D. A.; Sapp, P.; Hentati, A.; Donaldson, D.; Goto, J.; O’Regan, J. P.; Deng, H. X. Nature 1993, 362, 59. (b) Orrell, R. W. Neuromuscular Disord. 2000, 10, 63. (c) Stathopulos, P. B.; Rumfeldt, J. A.; Scholz, G. A.; Irani, R. A.; Frey, H. E.; Hallewell, R. A.; Lepock, J. R.; Meiering, E. M. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7021. (d) Liochev, S. I.; Fridovich, I. Free Radical Biol. Med. 2003, 34, 1383.
    6. Heinrich, L. P. Biochemie & Pathobiochemie, 2007, 123.
    7. (a) Chandran, K.; McCracken, J.: Peterson, F. C.; Antholine, W. E.; Volkman, B. F.; Kalyanaraman. B. Biochemistry 2010, 49, 10616. (b) Lippard, S. J. Acc. Chem. Res. 1982, 15, 318. (c) Current Opinion in Chemical Biology 2004, 8,162.
    8. (a) Quint, P. S.; Domsic, J. F.; Cabelli, D. E.; McKenna, R.; Silverman, D. N. Biochemistry 2008, 47, 4621. (b) Miller, A.-F. Curr. Opin. Chem. Biol. 2004, 8, 162. (c) Youn, H.; Kim, E.; Roe, J.; Hah, Y. C.; Kang, S. Biochem. J. 1996, 318, 889. (d) Wuerges, J.; Lee, J.-W.; Yim, Y.-I.; Yim, H.-S.; Kang, S.-O.; Carugo, K. D. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 8569. (e) Keele, B. B. Jr.; McCord, J. M.; Fridovich, I. J. Biol. Chem. 1970, 245, 6176. (f) Edwards, R. A.; Baker, H. M.; Whittaker, M. M.; Whittaker, J. W.; Jameson, G. B,; Baker, E. N. J. Biol. Inorg. Chem. 1998, 3, 161. (g) Lah, M. S.; Dixon, M. M.; Pattridge, K. A.; Stallings, W. C.; Fee, J. A.; Ludwig, M. L. Biochemistry 1995, 34, 1646.
    9. (a) Youn, H.-D.; Youn, H.; Lee, J.-W.; Yim, Y.-I.; Lee, J.-K.; Hah, Y. C.; Kang, S-O. Arch. Biochem. Biophys. 1996, 334, 341. (b) Youn, H.-D.; Kim, E.-J.; Roe, J.-H., Hah, Y. C.; Kang, S.-O. Biochem. J. 1996, 318, 889. (c) Kim, E.-J.; Chung, H.-J.; Suh, B.; Hah, Y. C.; Roe, J.-H. Mol. Microbiol. 1998, 27, 187. (d) Kim, E.-J.; Kim, H.-P.; Hah, Y. C.; Roe, J.-H. Eur. J. Biochem. 1996, 241, 178.
    10. Pelmenschikov, V.; Siegbahn, Per E. M., J. Am. Chem. Soc. 2006, 128, 7466.
    11. Shearer J. Angew. Chem. Int. Ed. 2013, 52, 2569.
    12. Lee, W. Z.; Chiang, C. W.; Lin, T. H.; Kuo, T. S. Chem. Eur. J. 2012, 18, 50.
    13. Cramer, C. J. Essentials of Computational Chemistry West Sussex, England; New York, 2002.
    14. Levine, I. N. Quantum Chemistry; 3th ed. Brooklyn, New York, 1970.
    15. Lewars, E. Computational Chemistry:Introduction to the Theory and Applications of Molecular and Quantum Mechanics Boston, 2004.
    16. Lewars, E. G. Computational Chemistry Introduction to the Theory and Applications; 2th ed. Peterborough Ontario Canada, 2011.
    17. Young, D. Computational Chemistry:A Practical Guide for Applying Techniques to Real World Problems; 2th ed. New York, 2001.
    18. Rode, B. M.; Hofer, T. S.; Kugler, M. D. The Basics of Theoretical and Computational Chemistry Weinheim, 2007.
    19. (a) Parr, R. C.; Yang, W. Annu. Rev. Phys. Chern. 1995, 46, 701. (b) Kohn, W.; Sham, L. J. Phys. Rev. 1965, 140, A1133. (c) Castro, A.; Marques, M. A. L.; Rubio, A. J. Chem. Phys. 2004, 121, 3425. (d) Leach, A. R. Molecular Modelling:Principles and Applications; 2th ed. Harlow, England, 2001.
    20. Hartree, D. R. Proc. Cambridge Phil. Soc. 1928, 24, 89.
    21. (a) Moller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618. (b) Binkley, J. S.; Pople, J. A. Int. J. Quant. Chem. 1975, 9, 229.
    22. Shavitt, I. Mol. Phys. 1998, 94, 3.
    23. Crawford, T. D.; III, H. F. S. Rev. Comput. Chem 2000, 14, 33.
    24. (a) Pariser, R.; Parr, R. G. J. Chem. Phys. 1953, 21, 466. (b) Pariser, R.; Parr, R. G. J. Chem. Phys. 1953, 21, 767. (c) Pople, J. A. Trans Faraday Soc 1953, 49, 1375.
    25. J. A. Pople , G. A. S. J. Chem. Phys. 1966, 44, 3289.
    26. (a) Baird, N. C.; Dewar, M. J. S. J. Chem. Phys. 1969, 50, 1262. (b) Bingham, R. C.; Dewar, M. J. S.; LO, D. H. J. Am. Chem. Soc. 1975, 97, 1285.
    27. (a) Dewar, M. J. S.; Thiel, W. J. Am. Chem. Soc. 1977, 99, 4899. (b) Dewar, M. J. S.; Thiel, W. J. Am. Chem. Soc. 1977, 99, 4907. (c) Dewar, M. J. S.; McKee, M. L. J. Am. Chem. Soc. 1977, 99, 5231.
    28. (a) J. A. Pople , D. L. B., P. A. Dobosh J. Chem. Phys. 1967, 47, 2026. (b) Dixon, R. N. Mol. Phys. 1967, 12, 83. (c) Kotzian, M.; Rosch, N.; Zerner, M. C. Theor. Chim. Acta. 1992, 81, 201.
    29. Dewar, M. J. S.; Klopman, G. J. Am. Chem. Soc. 1967, 89, 3089.
    30. Dannenberg, J. J.; Evleth, E. M. Int. J. Quant. Chem. 1992, 44, 869.
    31. (a) Stewart, J. J. P. J. Comp. Chem. 1989, 10, 209. (b) Stewart, J. J. P. J. Comp. Chem. 1991, 12, 320. (c) Stewart, J. J. P. J. Comp. Chem. 1992, 10, 221.
    32. (a) Holder, A. J.; II, R. D. D.; Jie, C. Tetrahedron 1994, 50, 627. (b) Dewar, M. J. S.; Jie, C.; Yu, J. Tetrahedron 1993, 49, 5003.
    33. Hohenberg, P.; Kohn, W. Phys. Rev. B 1964, 136, B864.
    34. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. J. Phys. Chem. A 2007, 111, 10439.
    35. Ullrich, C. A.; Kohn, W. Phys. Rev. Lett. 2001, 87, 093001.
    36. (a) Becke, A. D. J. Chem. Phys. 1993, 98, 5648. (b) Perdew, J. P.; Ruzsinszky, A.; Tao, J.; Staroverov, V. N.; Scuseria, G. E.; Csonka, G. I. J. Chem. Phys. 2005, 123, 062201.
    37. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623.
    38. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157.
    39. (a) Slater, J. C. Phys. Rev. 1930, 36, 57. (b) Bouferguene, A.; Fares, M.; Hoggan, P. E. Int. J. Quant. Chem. 1996, 57, 801.
    40. (a) Gill, P. M. W. Adv Quantum Chem 1994, 25, 141. (b) Boys, S. F. Proc. R. Soc. London. Ser. A 1950, 200, 542. (c) Gill, P. M. W.; Pople, J. A. Int. J. Quant. Chem. 1991, 40, 753.
    41. (a) Hehre, W. J.; Stewart, R. F.; Pople, J. A. J. Chem. Phys. 1969, 51, 2657. (b) Newton, M. D.; Lathan, W. A.; Hehre, W. J.; Pople, J. A. J. Chem. Phys. 1969, 51, 3927.
    42. (a) Dunning, T. H. J. Chem. Phys. 1989, 90, 1007. (b) Woon, D. E.; Dunning, T. H. J. Chem. Phys. 1993, 98, 1358. (c) Woon, D. E.; Dunning, T. H. J. Chem. Phys. 1995, 103, 4572.
    43. (a) Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 270. (b) Wadt, W. R.; Hay, P. J. J. Chem. Phys. 1985, 82, 284. (c) Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 299.
    44. (a) Roy, L. E.; Hay, P. J.; Martin, R. L. J. Chem. Theory Comput. 2008, 4, 1029. (b) Foresman, J. B. Exploring Chemistry with Electronic Structure Methods; 2th ed. Pittsburgh, 2000.
    45. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, N. J.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J.; Gaussian 09, Revision A.1; Gaussian, Inc: Wallingford, CT, 2009.
    46. (a) Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999. (b) Mennucci, B.; Tomasi, J.; Cammi, R.; Cheeseman, J. R.; Frisch, M. J.; Devlin, F. J.; Gabriel, S.; Stephens, P. J. J. Phys. Chem. A 2002, 106, 6102.
    47. Grey, A. D.N.J., DNA And Cell Biology 2002, 21, 251.
    48. Fukui, K. Acc. Chem. Res. 1981, 14, 363.
    49. Firdler, A. T.; Bryngelson, P. A.; Maroney, M. J.; Brunold, T. C. J. Am. Chem. Soc. 2005, 127, 5449.
    50. (a) Krause, M. E.; Glass, A.M.; Jackson, T. A.; Laurence, J. S. Inorg. Chem. 2010, 49, 362. (b) Shearer, J.; Long, L. M. Inorg. Chem. 2006, 45, 2358. (c) Neupane, K. P.; Shearer, J. Inorg. Chem. 2006, 45, 10552. (d) Pierre, J.-L.; Chautemps, P.; Refaif, S.; Beguin, C.; El Mazouki, A.; Serratrice, G.; Saint-Aman, E.; Rey, P. J. Am. Chem. Soc. 1995, 117, 1965. (e) Tabbi, G.; Driessen, W. L.; Reedijk, J.; Bonomo, R. P.; Veldman, N.; Spek, A. L. Inorg. Chem. 1997, 36, 1168.

    下載圖示
    QR CODE