生物系統中電子與質子傳遞之理論研究：針對環境影響與量子效應作探討

電子與質子傳遞在許多化學反應及生物系統中均扮演著重要的角色，例如光合作用、綠色螢光蛋白、粒線體膜蛋白引發的代謝反應乃至半導體工業所需的光蝕刻製程，其影響範圍之廣、作用之深，也因此，該如何透過實驗與理論，有效地在定性、定量上分析可能影響電子/質子傳遞機制的因素，無庸置疑地便成為長年來最重要的研究主題之一。本論文中，將運用時變性密度泛函理論（Time-dependent density functional theory）、量子朗之萬方程（quantum Langevin equation）及直接性耦合計算（Direct coupling）等方法，針對不同系統中的電子、質子傳遞反應進行理論計算研究，以期更深入了解此類反應的化學動力學機制。本論文主要分為三個篇章，分別針對不同的電子/質子傳遞問題作探討：（ㄧ）粒線體膜蛋白（細胞色素bc1）中，電子在血基質網絡之間的傳遞機制與速率分析；（二）類光合作用系統中，激發態的質子與電子耦合傳遞反應機制；（三）利用計算分子中特定位置的電位，發展高效率的激發態酸性預測方法。由本論文得出之結果，將有助於揭示生物系統中電子、質子傳遞的動力學過程，了解環境與其他系統自由度是如何透過與電子/質子的耦合來影響粒子傳遞，另一方面確認了以量子力學方法處理相似類型問題的必要性。更進一步，我們期望未來能以此研究為基礎，提高設計仿生功能分子的效率。

關鍵字

電子傳遞；質子傳遞；光合作用；粒線體；光酸；電子耦合質子傳遞；量子效應

並列摘要

Electron and proton transfer are at the heart of many chemical and biological systems, such as photosynthesis, mitochondria, and light-sensitized dyes. Quantitative identification of different factors that affect the electron/proton-transfer dynamics, including quantum effects in biological systems and couplings with environment, remain to be critical issues. In this thesis, we utilize time-dependent density functional theory, quantum Langevin equation, and direct coupling calculations to examine the electron/proton-transfer dynamics in biological systems. Three topics are independently studied: (a) determining the electronic couplings and electron-transfer rates within the heme network in a mitochondria membrane protein, cytochrome bc1 complex (b) examining the mechanism behind excited-state proton-coupled electron transfer in a hydrogen-bonded molecular pair mimicking the key step of light reaction in photosynthesis, and (c) developing an excited-state-acidity descriptor based on strong correlation between photoacidity and local electrostatic potential at the proton-donating atom. From the results, couplings of the electron/proton-transferring motion with environment and other degrees of freedom are demonstrated to play important roles affecting the reaction dynamics. Quantum-mechanical treatments must be applied to achieve qualitatively-correct pictures illustrating the mechanism. Knowledge learned from our results can serve as basis for understanding the dynamical behavior of biological electron/proton transfer, which can be further applied to design artificial compounds mimicking the functionalities of natural species.

並列關鍵字

electron transfer ； proton transfer ； photosynthesis ； mitochondria ； photoacid ； proton coupled electron transfer

參考文獻

[1] J. W. Cooley. Protein conformational changes involved in the cytochrome bc1 complex catalytic cycle. Biochim. Biophys. Acta - Bioenergetics, 1827:1340, 2013.

[2] C. J. Gagliardi, B. C. Westlake, C. A. Kent, J. J. Paul, J. M. Papanikolas, and T. J. Meyer. Integrating proton coupled electron transfer (PCET) and excited states. Coord. Chem. Rev., 254:2459, 2010.

[3] B. Kok, B. Forbush, and M. McGloin. Cooperation of charges in photosynthetic o2 evolution-i. a linear four step mechanism. Photochem. Photobiol., 11:457, 1970.

[5] D. Pines, S. Keinan, P. M. Kiefer, J. T. Hynes, and E. Pines. Effect of solvent dielectric constant and acidity on the OH vibration frequency in hydrogen-bonded complexes of fluorinated ethanols. J. Phys. Chem. B, 119:9278, 2015.

[6] G. Renger and T. Renger. Photosystem ii: The machinery of photosynthetic water splitting. Photosyn. Res., 98:53, 2008.

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生物系統中電子與質子傳遞之理論研究：針對環境影響與量子效應作探討

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