本研究主要利用量子力學之密度泛函理論，第一原理模擬計算粒線體中電子傳遞鏈的第四個複合物，即細胞色素c氧化酶（Cytochrome c oxidase）的氧氣還原反應，以了解粒線體複雜產能機制中的一環。細胞色素c氧化酶中含有幾個重要的機制，例如電子傳遞、質子幫浦（proton pump）、氧氣還原反應等等，彼此之間是相互影響且密切相關的，本研究則主要著重在電子傳遞流程的部分，以觀察細胞色素c氧化酶活性中心的材料性質與電子轉移的整體能量分析。
研究目的與能源環保議題相關，如何使能源獲得最有效率的應用，為目前研究的關鍵點與方向，常見的燃料電池效率約40至60%，然而在生物體中化學能轉換成ATP的效率卻高達90%，故若能了解生物體高效率轉換能量的機制，也許能成為未來解決環境問題的契機，減低對於石化能源過度依賴的目的，進而減少二氧化碳的排放，減緩溫室效應所造成的氣候變遷。
本研究之分析結果，包含對細胞色素c氧化酶中的電子傳遞流程所含結構，進行幾何結構最佳化與頻率的計算、分析結構的最穩定態之能量值、能隙值、HOMO與LUMO之分子軌域圖（molecular orbital）、紅外線光譜圖（IR spectrum）、鍵長等資訊，以及計算速率決定步驟（rate-determining step）的反應速率與活性。
根據研究結果分析，我們獲得以下幾項結論。第一，分子結構受Jahn-teller effect影響，使得原始分子結構以三重態為最低能量態，也就是說三重態結構為最穩定之多重態。第二，能隙部分的資料顯示出分子結構的化學穩定性，本研究得到結論為四個結構中，以Fe-OO為活性最高的結構。第三，由反應速率與活性值計算，本研究之細胞色素c活化中心模擬物，其還原反應速率與活性遠高於無機觸媒(如Pt, Pd, Ag, Co etc.)，故未來可參考此分子結構結合生物酵素與傳統觸媒，有可能繼續改進現有燃料電池性能。

摘要 I
ABSTRACT II
致謝 III
目錄 IV
圖目錄 IV
表目錄 VI
符號表 VII
第一章 緒論 1
1.1 前言 1
1.2 粒線體簡介 2
1.2.1 粒線體的結構 3
1.2.2 粒線體DNA 4
1.2.3 粒線體的功能 4
1.3 細胞色素與細胞色素C氧化酶 7
1.4 氧氣還原反應 12
1.5 文獻回顧 14
1.5.1 粒線體 14
1.5.2 細胞色素c氧化酶 14
1.6 研究動機與目的 18
第二章 理論與計算 19
2.1 前言 19
2.2 密度泛函理論 20
2.2.1 Hohenberg-Kohn理論 21
2.2.2 Kohn-Sham方法 24
2.2.3 Self-Consistent Field（SCF, 自洽場）計算 26
2.3 交換─相關泛函理論 29
2.3.1 B3LYP交換─相關泛函理論 30
2.4 基底函數組理論 30
2.4.1基底函數6-31G簡介 32
2.5 反應速率 32
第三章 模型建構與模擬方法 35
3.1 模擬流程 35
3.2 模擬模型建構 36
3.3 模擬設定 38
3.3.1. 原子軌域與能隙. 38
3.3.2. 吉布斯自由能（Gibbs Free Energy） 39
3.3.3. 紅外光譜與拉曼光譜 41
第四章 結果與討論 44
4.1 細胞色素C氧化酶 44
4.1.1 Fe為中心 44
4.1.2 Fe-OO為中心 48
4.1.3 Fe-OOH為中心 50
4.1.4 Fe-OOH2為中心 52
4.2 氧分子 54
4.3 反應速率計算 55
第五章結論與未來工作 62
5.1 結論 62
5.2 未來工作 63
參考文獻 64

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