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研究生: 黃莉雯
Huang, Li-Wen
論文名稱: 以第一原理計算胜肽分子之導電性質變化
First Principle Calculation of Changes in the Con-ductance of Single Peptide Molecules
指導教授: 蘇彥勳
Su, Yen-Hsun
共同指導教授: 關肇正
Kaun, Chao-Cheng
學位類別: 碩士
Master
系所名稱: 工學院 - 材料科學及工程學系
Department of Materials Science and Engineering
論文出版年: 2015
畢業學年度: 103
語文別: 中文
論文頁數: 52
中文關鍵詞: 第一原理胜肽非平衡格林函數生物感測器
外文關鍵詞: first principle, peptide, biosensor
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  • 胜肽分子組成有相當多種變化性,可藉由相異單體分子以不同的次序排列,因此我們可以得到特定長度、特定鍵結強度、對離子有專一性等性質。由於尺度上的優勢,胜肽可以用來發展分子電子元件,且可利用其對離子與有機分子的吸附特性,用來作為微型生物感應檢測器。
    本研究利用第一原理對胜肽進行結構優化及電性分析,研究針對四種胜肽cysteamine-Cys、cysteamine-Gly-Cys、Cys-Gly-Cys、cysteamine-Gly-Gly-Cys (Cys=cysteine, Gly=glycine),四種胜肽兩端皆為巰基使其與金電極相接進行討論,討論內容包含拉伸胜肽至斷裂對於系統能量以及電性的影響,拉伸量與電導值之間的趨勢;胜肽上吸附環境賀爾蒙雙酚A後之結構及電導值的變化;胜肽與銅離子結合形成錯合物的電性分析;胜肽以不同的螯合位置與連接銅離子連接形成錯合物,其結構是否會穩定存在。研究首先會將各系統結構優化在進行分析討論,其中的電性分析主要是觀察各系統的Transmission spectra、Fermi energy附近的Density of States分布情形及Fermi energy位置之Local Density of States,藉由這些結果計算出電導值以及分析。
    根據研究結果,胜肽之電導值會隨著伸長而上升直至斷裂,其系統總能也會隨之升高,胜肽吸附雙酚A後電導會是原本胜肽電導的26倍左右,而胜肽-銅離子錯合物其結構可能性相當多故其電導值變化範圍也非常大,本研究針對部分可能結構進行討論實際穩定存在的可能性。

    Silicon-based electronics are hard to head towards the nanoscale, the construction of electronic devices with individual molecules becomes an attractive alternative and has aroused interests in the study of the electronic properties of single molecules. Peptides are chosen as the object in the study because of the unlimited choice of different se-quences that can be tuned to obtain optimal binding strength and specificity for a metal ion or organic molecule. Based on the biochemical properties of peptide, it can be used as miniature biosensor. Four peptides are studied in our work, cysteamine-Cys, cysteam-ine-Gly-Cys, Cys-Gly-Cys, and cysteamine-Gly-Gly-Cys (Cys=cysteine, Gly=glycine), which each have two thiol termini that can form reproducible contact to Au electrodes. We analyze peptide and its systems by using first-principles calculations based on the density functional theory and the nonequilibrium Green’s function approach. Our re-search includes that conductance changing by stretching peptide, the conductance of pep-tide attached by Bisphenol A or copper ion, possible structures of peptide-Cu2+ complex-es. According to the results, the conductance of the peptide and the total energy of the system rise up with the elongation until breaking. After peptide adsorbing Bisphenol A, the conductance becomes about 26 times of the original peptide conductance. The con-ductance ranges of peptide-Cu2+ complexes are very large because there are considerable numbers of possible complexes structures. This study discusses some possible structures whether they stably exist or not.

    摘要 I 英文摘要 II 誌謝 V 目錄 VI 表目錄 VII 圖目錄 VIII 第一章 緒論 1 1-1 前言 1 1-2 研究動機 5 第二章 理論與計算方式 6 2-1 第一原理計算與應用 6 2-2 薛丁格方程式 7 2-3多電子系統與 Hartree-Fock 近似 9 2-4 密度泛函理論(Density Functional Theory) 10 2-5 贋勢法 14 2-6 非平衡格林函數理論(non-equilibrium Green´s functions)[23, 24] 16 2-7 自洽場方法(self-consistent field method) 22 第三章 模擬軟體介紹 24 第四章 模擬結果與分析 26 4-1 電極與胜肽接合 26 4-2 胜肽拉伸對於電性之影響 29 4-3 胜肽吸附Bisphenol A對於電性之影響 40 4-4胜肽吸附金屬離子對於電性之影響 42 4-5 胜肽-金屬離子錯合物結構 46 第五章 結論 48 參考文獻 50

    [1] C. Joachim, J.K. Gimzewski, A. Aviram, Electronics using hybrid-molecular and mono-molecular devices, Nature, 408 (2000) 541-548.
    [2] P.A. Hunt, C. Lawson, M. Gieske, B. Murdoch, H. Smith, A. Marre, T. Hassold, C.A. VandeVoort, Bisphenol A alters early oogenesis and follicle formation in the fetal ovary of the rhesus monkey, Proceedings of the National Academy of Sciences of the United States of America, 109 (2012) 17525-17530.
    [3] E. Chow, J.J. Gooding, Peptide modified electrodes as electrochemical metal ion sensors, Electroanalysis, 18 (2006) 1437-1448.
    [4] Peptide bond. In Wikipedia, the free encyclopedia. From http://en.wikipedia.org/wiki/Peptide_bond
    [5] X. Xiao, B. Xu, N. Tao, Changes in the conductance of single peptide molecules upon metal-ion binding, Angewandte Chemie, 43 (2004) 6148-6152.
    [6] P. Hohenberg, W. Kohn, Inhomogeneous Electron Gas, Physical Review B, 136 (1964) B864.
    [7] W. Kohn, L.J. Sham, Self-Consistent Equations Including Exchange and Correlation Effects, Physical Review, 140 (1965) 1133.
    [8] J.P. Perdew, K. Burke, M. Ernzerhof, Generalized gradient approximation made simple, Physical Review Letters, 77 (1996) 3865-3868.
    [9] E. Schrödinger, An Undulatory Theory of the Mechanics of Atoms and Molecules, Physical Review 28 (1926) 1049-1070.
    [10] M. Born, Zur Quantenmechanik der Stoßvorgänge, Zeitschrift für Physik, 37 (1926) 863-867.
    [11] M. Born, R. Oppenheimer, Zur Quantentheorie der Molekeln, Annalen der Physik, 389 (1927) 457-484.
    [12] J.C. Slater, A Simplification of the Hartree-Fock Method, Physical Review, 81 (1951) 385-390.
    [13] P.A.M. Dirac, Quantum mechanics of many-electron systems, P R Soc Lond a-Conta, 123 (1929) 714-733.
    [14] L.H. Thomas, The calculation of atomic fields, Proc. Cambridge Phil. Soc., 23 (1927) 542-548.
    [15] E. Fermi, Un Metodo Statistico per la Determinazione di alcune Prioprietà dell'Atomo, Rend. Accad. Naz. Lincei, 6 (1927) 602-607.
    [16] D.M. Ceperley, B.J. Alder, Ground-State of the Electron-Gas by a Stochastic Method, Physical Review Letters, 45 (1980) 566-569.
    [17] J.P. Perdew, J.A. Chevary, S.H. Vosko, K.A. Jackson, M.R. Pederson, D.J. Singh, C. Fiolhais, Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation, Physical review. B, Condensed matter, 46 (1992) 6671-6687.
    [18] A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Physical review. A, 38 (1988) 3098-3100.
    [19] D.C. Langreth, M.J. Mehl, Beyond the Local-Density Approximation in Calculations of Ground-State Electronic-Properties, Physical Review B, 28 (1983) 1809-1834.
    [20] H. Hellmann, A new approximation method in the problem of many electrons, Journal of Chemical Physics, 3 (1935) 61-61.
    [21] H. Hellmann, W. Kassatotschkin, Metallic binding according to the combined approximation procedure, Journal of Chemical Physics, 4 (1936) 324-325.
    [22] M.C. Payne, M.P. Teter, D.C. Allan, T.A. Arias, J.D. Joannopoulos, Iterative minimization techniques forab initiototal-energy calculations: molecular dynamics and conjugate gradients, Reviews of Modern Physics, 64 (1992) 1045-1097.
    [23] J. Taylor, H. Guo, J. Wang, Ab initiomodeling of quantum transport properties of molecular electronic devices, Physical Review B, 63 (2001).
    [24] Y.V.N.a.Y.M. Blanter, Quantum transport: Introduction to Nanoscience, Cambridge University Press, (2009) 29-41.
    [25] L.V. Keldysh, Diagram technique for nonequilibrium processes, SOVIET PHYSICS JETP 20 (1965) 1018–1026.
    [26] Nanodcal Theory by NanoAcademic Technologies Inc.
    [27] I.N. Levine, Quantum Chemistry, Prentice Hall.
    [28] J. Taylor, H. Guo, J. Wang, Ab initiomodeling of open systems: Charge transfer, electron conduction, and molecular switching of aC60device, Physical Review B, 63 (2001).
    [29] D. Waldron, L. Liu, H. Guo, Ab initio simulation of magnetic tunnel junctions, Nanotechnology, 18 (2007) 424026.
    [30] J.M. Soler, E. Artacho, J.D. Gale, A. Garcia, J. Junquera, P. Ordejon, D. Sanchez-Portal, The SIESTA method for ab initio order-N materials simulation, J Phys-Condens Mat, 14 (2002) 2745-2779.
    [31] H. Sellers, A. Ulman, Y. Shnidman, J.E. Eilers, Structure and Binding of Alkanethiolates on Gold and Silver Surfaces - Implications for Self-Assembled Monolayers, Journal of the American Chemical Society, 115 (1993) 9389-9401.
    [32] S. Datta, Electronic Transport in Mesoscopic Systems, Cambridge University Press, (1995).
    [33] Y.H. Tang, V.M.K. Bagci, J.H. Chen, C.C. Kaun, Conductance of Stretching Oligothiophene Single-Molecule Junctions: A First-Principles Study, J Phys Chem C, 115 (2011) 25105-25108.
    [34] Y. Wang, J. Lv, L. Zhu, Y. Ma, Crystal structure prediction via particle-swarm optimization, Physical Review B, 82 (2010).

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