簡易檢索 / 詳目顯示

回結果列表
研究生： 許敦程
Tun-cheng Hsu
論文名稱： 質子化三甘胺酸、去質子化二甘胺酸、去質子化三甘胺酸的斷鍵反應機制之理論計算研究
Ab Initio Study of the Fragmentation Pathways of Deprotonated Diglycine、 Protonated Triglycine and Deprotonated Triglycine
指導教授： 江志強
Jyh-Chiang Jiang
口試委員: 蔡大翔
Dah-Shyang Tsai
孫英傑
Ying-Chieh Sun
張煥正
none
學位類別： 碩士
Master
系所名稱： 工程學院 - 化學工程系
Department of Chemical Engineering
論文出版年： 2005
畢業學年度： 93
語文別： 中文
論文頁數： 143
中文關鍵詞： 質子化三甘胺酸 、去質子化二甘胺酸 、去質子化三甘胺酸 、斷鍵反應機制
外文關鍵詞： protonated triglycine, deprotonated diglycine, deprotonated triglycine, Fragmentation Pathway
相關次數： 點閱：148  下載：1 
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

    • 本文使用ab initio計算，探討胜肽斷鍵的機制，研究的對象包含去質子化二甘胺酸、去質子化三甘胺酸與質子化三甘胺酸。此外也會探討質子化三甘胺酸在含一個水與二個水時，對於斷鍵機制的影響。利用B3LYP/6-31+G(d)的方法來計算反應物、中間產物、過渡態、與產物的結構、振動頻率及能量。計算顯示去質子化的結構斷鍵所需的能量，遠大於質子化的結構斷鍵所需的能量。去質子化三甘胺酸最容易斷鍵的地方是C端的碳-碳鍵，而質子化三甘胺酸中最容易斷鍵的地方是C端的胜肽鍵。質子化三甘胺酸在C端含水時，斷鍵所需的能量會升高，而當質子化三甘胺酸有兩個水時，斷鍵所需能量也會升高。

    In this thesis, ab initio calculation was used to investigate the fragmentation pathways of peptide bond in the deprotonated diglycine, deprotonated triglycine and protonated triglycine. In addition, the water effect on the fragmentation was also investigated. The molecular conformation, vibration frequency and energy of reactant, intermediate, transition state, and product were determinated by the ab initio calculation at B3LYP level using 6-31+G(d) basis set. The results show the energy barriers of the fragmentation on the deprotonated structure are much higher than those on the protonated structure. The C- C bond in C-terminal on the deprotonated triglycine is the easiest to break, otherwise, peptide bond in C-terminal on the protonated triglycine is the easiest to break. In general, the energy barriers of fragmentations are increased as the protonated triglycine surrounded with water molecules.

    中文摘要 Ⅰ 英文摘要 Ⅱ 致謝 Ⅲ 目錄 Ⅳ 圖索引 Ⅶ 表索引 XI 第一章 緒論 1.1 前言 1 1.2 蛋白質 1 1.3 胺基酸 4 1.4 胜肽 6 1.5 文獻回顧 8 1.5.1 質譜儀 9 1.5.2 胜肽的斷鍵命名規則 10 1.5.3 去質子化二甘胺酸 13 1.5.4 質子化三甘胺酸 16 1.5.4.1 a1-y2 路徑 19 1.5.4.2 b2-y1 路徑 20 1.5.4.3 diketopiperazine 路徑 22 1.5.5 去質子化三甘胺酸 23 第二章 理論計算方法 2.1 量子化學 28 2.2 計算化學的理論與方法 28 2.3 Gaussian 03 套裝軟體計算 29 2.3.1 幾何優選 30 2.3.2 振動頻率 30 2.4 分子模擬的理論及其用途 31 2.5 本論文採用的計算方法 32 第三章 結果與討論 33 3.1 去質子化二甘胺酸斷鍵的反應機制 34 3.1.1 a3離子的反應機制 35 3.1.2 b1離子的反應機制 35 3.1.3 -OCNHCH3離子的反應機制 42 3.1.4 CH3NH-離子的反應機制 43 3.2 去質子化三甘胺酸斷鍵的反應機制 49 3.2.1 a3離子的反應機制 50 3.2.2 b2離子的反應機制 52 3.2.3 a2離子的反應機制 55 3.2.4 y1離子的反應機制 55 3.3 質子化三甘胺酸的斷鍵反應機制 63 3.3.1 b2離子的斷鍵反應機制 64 3.3.2 y1離子的斷鍵反應機制 67 3.3.3 a1離子的斷鍵反應機制 69 3.3.4 y2離子的斷鍵反應機制 72 3.4 質子化三甘胺酸在C端含水的斷鍵反應機制 78 3.4.1 b2離子的斷鍵反應機制 79 3.4.2 y1離子的斷鍵反應機制 82 3.4.3 a1離子的斷鍵反應機制 85 3.4.4 y2離子的斷鍵反應機制 88 3.5 質子化三甘胺酸在N 端含水的斷鍵反應機制 92 3.5.1 b2離子的斷鍵反應機制 95 3.5.2 y1離子的斷鍵反應機制 95 3.5.3 a1離子的斷鍵反應機制 95 3.5.4 y2離子的斷鍵反應機制 98 3.6 質子化三甘胺酸含二個水的斷鍵反應機制 102 3.6.1 b2離子的斷鍵反應機制 102 3.6.2 y1離子的斷鍵反應機制 106 3.6.3 a1離子的斷鍵反應機制 107 3.6.4 y2離子的斷鍵反應機制 112 第四章 結論 120 第五章 參考文獻 122 作者介紹 126

    1. 黃蔭樨, “哈伯氏生物化學”,藝軒圖書出版 (2000)
    2.. R.F. Boyer, “Concepts in biochemistry”, 2th ed, Wiley, New York (2002)
    3. 潘家寅, “大學化學（上）”, 科技圖書股份有限公司(1990)
    4. 周延鑫, “生物物理學導論” , 華香園出版社(1987)
    5. 曾國輝, “大學生物化學”., 藝軒圖書出版社(1983)
    6. 黃蔭樨, “基礎生物化學”, 五南圖書出版公司(1982)
    7. 趙大衛, “生化學(上)”, 徐氏基金會(1980)
    8. H.R. Horton, L.A. Moran, R.S. Ochs, D.J. Rawn, and K. G. Scrimgeour, ” Principles of Biochemistry”, Prentice Hall (2001)
    9. L. Pauling, and R.B. Corey, “Configurations of polypeptide chains with favored orientations of the polypeptide around single bonds: Two pleated sheets”, Proc. Natl. Acad. Sci., 37, 729 (1951)
    10. L. Pauling, R.B. Corey, and H.R. Branson, “Two hydrogen-bonded helical configurations of the polypeptide chain“, Proc. Natl. Acad. Sci., 37, 205(1951)
    11. P. Roeostirff, and J. Fohlman, Biomed. Mass Spectrom., 11, 601 (1984)
    12. K. Biemnaa, Biomed. Environ. Mass Spectorm., 16, 99 (1988)
    13. G.A. Chass, C.N. J. Marai, A.G. Harrison, and I.G. Csizmadia, J. Phys. Chem. A, 106, 9695 (2002)
    14. M.L. Styles, and R.A.J. O’Hair, Rapid Commun. Mass Spectrom., 12, 809(1998)
    15. B. Paizs, and S. Suhaiy, Rapid Commun. Mass Spectrom., 15, 2307 (2001)
    16. R.N. Grewal, H.E. Aribi, A.G. Harrison, K.W.M. Siu, and A.C. Hopkinson, J. Phys. Chem. B, 108, 4899 (2004)
    17. R.A.J. O'Gair, and G.E. Reid, J. Am. Soc. Spectrom, 11, 244 (2000)
    18. D.G. Morgan, and M.M. Bursey, Journal of Mass Spectrometry, 30, 290 (1995)
    19. B. Paizs, and S. Suhai, Rapid Commun. Mass Spectrom., 16, 375 (2002)
    20. B. Paizs and S. Suhai, J. Am. Soc. Mass Spectrom., 15, 103 (2004)
    21. B. Pauzs, and S. Sygai, Mass Spectrom Rev.,24, 508 (2005)
    22. F. Pingitore, M. J. Polce, P. Wang, C. Wesdemiotis, and B. Paizs, J Am Soc Mass Spectrom, 15, 1025 (2004)
    23. G.E. Reid, S.E. Tichy, J. Pérez, R.A.J. O'Hair, R.J. Simpson, and H.I. Kenttämaa, J. Am. Chem. Soc., 123, 1184 (2001)
    24. M.J. Polce, Da Ren, and C. Wesdemiotis, J. Mass Spectrom. 35, 1391 (2000)
    25. R.A.J. O’Hair1, and G.E. Reid1, Rapid Commun. Mass Spectrom., 14, 1220 (2000)
    26. A. Schlosser, and W.D. Lehmann, J. Mass Spectrom. 35, 1382 (2000)
    27. H.E. Aribi, C.F. Rodriquez, D.R.P. Almeida,Y. Ling, W.W.-N. Mak,| A.C. Hopkinson, and K. W. Michael Siu, J. Am. Chrm. Soc., 125, 9229 (2003)
    28. H.E. Aribi, G. Orlova, C.F. Rodriquez, D.R.P. Almeida, A.C. Hopkinson, and K. W. Michael Siu, J. Phys. Chem., 108, 18743 (2004)
    29. T. Yalcin, I. Csizmadia, G. Imre, M.R. Peterso, Harrison, and A.G. Harrison, J Am Sot Mass Spectrom, 7, 233 (1996)
    30. B. Paizs, G. Lendvay, K. Vékey, and S. Suhai, Rapid Commun. Mass Spectrom., 13, 525 (1999)
    31. B. Paizs, Z. Szlávik, G. Lendvay, K. Vékey, and S. Suhai, Rapid Commun. Mass Spectrom., 14, 746 (2000)
    32. T.H. Tang, D.C Fang, A.G. Harrison, and I.G. Csizmadia, Journal of Molecular Structure (Theochem), 675, 79 (2004)
    33. W. Kulik, and W. Heerma, Biomed. enuiron. mass spectrorn., 18, 910.(1989)
    34. A.G. Harrison, J .Am Soc Mass Spectrom., 12,1.(2001)
    35. W. Kulik, and W. Heerma, Biomed. Env. Mass Spectrom.,18, 910. (1989)
    36. D.V. Setten, W. Kulik, and W. Heerma, Biomed. Env. Mass Spectrom.,19, 475, (1990)
    37. M. Eckersley, J.H. Bowie, and R.N. Hayes, Org. Mass Spectrom., 24, 597 (1989)
    38. R.J. Waugh, and J.H. Bowie, Rapid Commun. Mass Spectrom.,8, 169 (1994)
    39. A.G. Harrison1, K.W.M. Siu, and H.E. Aribi, Rapid Commun. Mass Spectrom., 17, 869 (2003)
    40. A. Szabo, and N.S. Ostlund, “Modern Quantum Chemistry”, Mcgraw-Hill, New York (1982)
    41. I.N. Levine, “Quantum Chemistry”, 4th ed, Prentice Hall, New York(1991)
    42. 劉東昇, “化學量子力學”, 徐氏基金會 (1998)
    43. I.N. Levine, “Quantum Chemistry” 5th ed, Prentuce-Hall, New Jersey(2000)
    44. 蘇世剛, 與牟中原, “化學”, 47(4), 308(1989)
    45. A. E. Frisch, and J.B. Foresman, “Exploring Chemistry with Electronic Structure Methods”,2 ed, Gaussian,Pittsburgh(1996)
    46. HyperChem, “Computational Chemistry”, Hypercube, Waterloo, ntario(1996)
    47. W.J. Hehre, J. Yu, P.E. Klunzinger, and L.A Lou, “A Brief Guide to Molecular Mechanics and Quantum Chemical Calculations”, Wavefunction, Irvine(1998)
    48. W.J. Hehre, L. Radom, and P.V. R, “ab initio Molecular Orbital Theory’, John Wiley & Sons, New York(1986)
    49. A. E. Frisch, and J.B. Foresman, “Exploring Chemistry with Electronic Structure Methods”,2 ed, Gaussian,Pittsburgh (1996)
    50. P. Hohenberg, and W. Kohn, Phys. Rev. B, 136, 864(1964)
    51. W. Kohn, and L.J. Sham, Phys. Rev. A, 140, 1133(1965)
    52. C.J. Cramer, “Essentials of Computational Chemistry - Theories and Models “, JohnWiley & Sons, New York (2002)
    53. R. McWeeny, and G. Dierksen, J. Chem. Phys, 49, 4852(1968)
    54. (a) J. J. P. Stewart, J. Comput. Chem, 10, 209 (1989)；(b) J. J. P. Stewart, J. Comput. Chem, 10, 221 (1989)；(c) J. J. P. Stewart, J. Comput. Chem, 11, 543 (1990)；(d) J. J. P. Stewart, J. Comput. Chem, 12, 320 (1991)
    55. A.D. Becke, J. Chem. phys, 98, 5648(1993)
    56. C.T. Lee, W. T. Yang, and R.G. Parr, Phys. Rev. A, 37, 785(1988)
    57. M.A. Frisch, J. A. Pople, and J. S. Binkley, J. Chem. Phys, 80, 3265(1984)
    58. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. 27 Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford CT (2004)
    59. S. Saebo, and J. Almlof, Chem. Phys. Lett, 154, 83(1989)
    60. M. Head-Gordon, J. A. Pople, and M. J. Frisch, Chem. Phys. Lett, 153, 503 (1988)
    61. M. J. Frisch, M. Head-Gordon and J. A. Pople, Chem. Phys. Lett, 166, 275 (1990)
    62. M. J. Frisch, M. Head-Gordon and J. A. Pople, Chem. Phys. Lett, 166, 281 (1990)
    63. J.R. Flores, J. Chem. Phys, 98, 5642 (1993)
    64. P. Pulay, and W. Meyer, Mol. Phys, 27, 473(1974)
    65. B. Paizs, and S. Suhai, Rapid Commun. Mass Spectrom., 15, 651(2001)
    66. H. Lim, D.G. Schultz, C. Yu, and L. Hanley, Analytical Chemistry, 71, 13 (1999)
    67. B. Paizs1, I.P. Csonka1, G. Lendvay, and S. Suhai1, Rapid Commun. Mass Spectrom., 15, 637 (2001)
    68. C.F. Rodriquez, A. Cunje, T. Shoeib, I.K. Chu,A.C. Hopkinson, and K. W. Michael Siu, J. Am. Chem. Soc , 123, 3006 (2001)
    69. I.P. Csonka, B. Paizs, G. Lendvay, and S. Suhai1,Rapid Commun. Mass Spectrom., 14, 417 (2000)
    70. J.S. Klassen, and P. Kebarle, J. Am. Chem. Soc., 119, 6552(1997)
    71. M. Salek, and W.D. Lehmann, J. Mass Spectrom., 38, 1143(2003)
    72. I.K. Chu, T. Shoeib, X. Guo, C.F. Rodriquez, T.C. Lau, A.C. Hopkinson, and K. W. Michael Siu, J Am Soc Mass Spectrom, 12, 163 (2001)
    73. J.M. Farrugia, R.A.J. O’Hair, and G.E. Reid, Int. J. Mass Spectrom., 210/211, 71 (2001)
    74. D.A. Skoog, F.J. Holler, and T.A. Nieman, “Principles of Instrumental Analysis”,4th ed, Harcourt Brace and Company, Olando (1998)
    75. B. Paizs, and S. Suhai, J. Am. Soc. Mass Spectrom, 14, 1454 (2003)

    QR CODE