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

Abstract

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。

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.