多層電子密度泛函理論的發展以及鈍氣分子、激發態質子轉移反應與生命起源前胺基酸合成反應之理論研究

Development of Multi-Coefficient Density Functional Theory and Theoretical Study on Noble Gas Molecules, Excited-State Proton Transfer Reactions, and Prebiotic Synthesis of Alpha-amino Acids

彭家瑜(Chia-Yu Peng)

指導教授 ： 胡維平

國立中正大學/理學院/化學暨生物化學系/博士(2015年)

摘要

本博士論文共有五章，在第一章中我們開發了一種新的 DFT 計算方法並測試其計算效能，第二章中我們研究了一種新型鈍氣陰離子 FNgCC- 的穩定性及其各種性質，第三章我們透過理論探討在生命起源前中性環境下，透過水及對掌性分子催化合成丙胺酸化學反應的反應機制，第四章我們以理論計算探討 cyclic-O3、cyclic-S3、cyclic-Se3 的動力學穩定性，第五章我們與實驗學家配合模擬 1,8-dihydroxy-2-naphthaldehyde (DHNA) 分子在基態以及第一激發單重態質子轉移的反應機制。
在第一章的研究中我們將本實驗室過去所發表的 multi-coefficient density functional theory (MC-DFT) 與 spin- component-scaling MP2 (SCS-MP2) 理論相結合，並額外增加 E3、E4 能量校正，開發了一系列效率極高的計算方法 (MC-MP4 | MC-DFT)。我們發現此方法所搭配之 functional 若使用 DSD-BLYP ，則其計算 211 動力學及熱力學反應與準確值的 mean unsigned errors (MUE) 可降至 0.72 kcal/mol，然而其僅需花費 DSD-BLYP/aug-cc-pVTZ (MUE = 1.36 kcal/mol) 之 78% 的計算時間，上述組合亦為本研究中準確性及計算效率最高的計算方法。
第二章我們透過各種理論方法研究一種新型的鈍氣陰離子 FNgCC- (Ng = He、Ar、Kr、Xe) 的各種性質。計算結果顯示 FNgCC(Ng = Ar、Kr、Xe) 都有相當高的結合能 (17-64 kcal/mol)，而唯一的大量放熱途徑中 (FNgCC- -> FCC- + Ng) 亦包含 21-43 kcal/mol 的反應能障，而且都有相當高的 S-T gap (81 kcal/mol 以上)。我們透過理論預測這一系列的 FNgCC(Ng = Ar、Kr、Xe) 為動力學穩定的鈍氣分子，我們認為這些分子將來相當有可能在低溫的實驗條件下被觀測到。
第三章我們透過理論模擬生命起源前 (prebiotic) 中性環境下經由 Strecker reaction 合成丙胺酸 (alanine) 的反應機制。由我們的計算結果顯示此反應在沒有催化劑 (uncatalyzed) 的條件下，反應須跨越至少 33 kcal/mol 的反應能障。然而，若透過水分子催化上述反應，則所有反應能障約下降 17-27 kcal/mol，另一方面，若透過對掌性醇類分子 (R-form 或 S-form) CH3CHCl(OH)、CH3CH2CHCl(OH) 催化上述反應，則合成兩種不同對掌性丙胺酸 (D- 和 L-Alanine) 的反應能障差分別約為 0.6 和 0.9 kcal/mol，換算為 300 K 下反應速率差距分別約為 2.7 倍及 4.5 倍。顯示在生命起源前的環境下，對掌性分子的催化效應可能是造成兩種不同對掌性胺基酸比例不平衡的因素之一，此現象或許可解釋現今自然界的胺基酸對掌性為何以 L-form 為主要構型。
第四章我們透過高階理論方法計算 O3、S3、Se3 的 cyclic form -> open form 異構化反應的反應能量及其反應能障，並延續本實驗室先前 cyclic-O3 的研究，使用 VTST/MT (variational transition state theory with multidimensional tunneling) 理論計算 cyclic-S3 異構化反應的動力學性質及穿隧效應。我們發現 cyclic-O3、cyclic-S3、cyclic-Se3 的異構化反應中都有足夠的反應能障 (21.1、25.8、22.9 kcal/mol) 以維持其動力學穩定性。此外，VTST/MT 的計算結果顯示 cyclic-S3 的穿隧效應相當的弱，溫度 300 K 和 200 K 下所估計的異構化半生期分別約為 12.7 個小時和 106 年，其研究結果顯示 cyclic-S3 以及質量較重、穿隧效應較小的 cyclic-Se3 都有相當不錯的動力學穩定性。
第五章我們與實驗學家配合以理論計算模擬 1,8-dihydroxy-2-naphthaldehyde (DHNA) 在基態 (ground state, S0) 以及第一激發單重態 (1st singlet excited state, S1) 的 proton transfer 反應機制。計算結果顯示在基態下 DHNA 的 proton transfer 反應能量及能障分別約為 1.6 和 2.6 kcal/mol，我們預期在基態下 DHNA 和其 tautomer (TA) 有可能達到平衡共存。而在第一激發單重態下則存在一個低能量的反應路徑可生成 single proton transfer 以及 double proton transfer 的 tautomers (TA*、TB*)，DHNA* -> TA* 和 TA* -> TB* 的反應能障分別約為 0.3 和 2.1 kcal/mol，上述理論結果映證了實驗上放光光譜所觀測到的 TA* 與 TB* 放光波長 (520 nm、650 nm)。由理論所模擬的 2-D 位能曲面以及反應路徑亦證明在第一激發單重態的上述反應為逐步進行 (sequential、stepwise) 而非同時進行 (concerted) 的 double proton transfer 反應。

關鍵字

激發態質子轉移反應 ； 鈍氣分子 ； 密度泛函理論 ； 理論研究 ； 胺基酸合成反應

並列摘要

This thesis consists of five chapters. In chapter 1, we developed and tested several new efficient DFT methods. In chapter 2, we performed high-level theoretical study on a new type of noble-gas (Ng) containing anions FNgCC. In chapter 3, we studied the mechanisms and reaction paths of the prebiotic strecker synthesis of alanine catalyzed by water and chiral molecules in the neutral environment. In chapter 4, we studied the kinetic stability of the cyclic-O3, cyclic-S3, and cyclic-Se3. In the last chapter, we cooperated with the experimental scientists and carried out the theoretical investigation on the excited state proton transfer of 1,8-dihydroxy-2-naphthaldehyde (DHNA).
In chapter 1, we developed and tested several new efficient multi-coefficient density functional theory (MC-DFT) methods based on the DSD-BLYP functional and by including SCS-MP2 and MP4 correction energies on the performance of thermochemical kinetics against the database of 211 accurate energies. When the MP4 correlation energies were included, the new method gave an astonishingly small MUEs of 0.72 kcal/mol and cost only 78% of the DSD-BLYP/aug-cc- pVTZ method (with MUE = 1.36 kcal/mol).
In chapter 2, we made high-level theoretical study on a new type of noble-gas (Ng) containing anions FNgCC-. The results showed that FNgCC- (Ng = Ar, Kr, Xe) are kinetically stable anions in the gas phase with the three-body dissociation energies of 17-64 kcal/mol and two body-dissociation (FNgCC- -> FCC- + Ng) barriers of 21-43 kcal/mol; moreover, the S-T gaps of all the FNgCC- were over 81 kcal/mol. These results suggested that the future experimental identification of the FNgCC- anions is expected under cryogenic conditions.
In chapter 3, the mechanisms and reaction paths of the prebiotic strecker synthesis of alanine catalyzed by water and chiral molecules in the neutral environment have been studied. In this three-step reaction, the energy barriers were calculated to be over 33 kcal/mol in the uncatalyzed condition; the reaction catalyzed by water, however, could significantly reduce the barriers by 17-27 kcal/mol. When the reactions were catalyzed by the chiral molecules (R-form or S-form) CH3CHCl(OH) and CH3CH2CHCl(OH), the differences of barriers between two chiral products (D- and L-Alanine) were calculated to be 0.6 and 0.9 kcal/mol; of the rates in 300 K, 2 and 4.5 times. This result suggested that the chiral catalysts in prebiotic conditions could produce different numbers of the two different chiral (D- and L-) amino acids, which was might be a plausible reason for the dominance of L-amino acids in nature nowadays.
In chapter 4, high-level electronic structure calculations have been carried out on the kinetic stability of the cyclic-O3, cyclic-S3, and cyclic-Se3. In this study, the rate constant and tunneling effect for the isomerization reaction of cyclic-S3 was also calculated by using the VTST/MT and compared to our previous study about cyclic-O3. From our high-level calculations, the energy barriers of the isomerization reactions for O3, S3, and Se3 were predicted to be 21.1, 25.8, and 22.9 kcal/mol, respectively. The half-life of the cyclic-S3 estimated by VTST/MT was ~12.7 hours at 300 K and ∼106 years at 200 K. Since the Se3 systems were expected to show much less tunneling effects, both cyclic S3 and Se3 were expected to be kinetically stable.
In chapter 5, we studied the proton transfer reactions of 1,8- dihydroxy-2-naphthaldehyde (DHNA) on both ground state (S0) and 1st singlet excited state (S1) and estimated the wavelenths of vertical S0 -> S1 excitation and S1 -> S0 emissions. On the ground-state (S0), the normal form (N) was lower in energies than tautomer A (TA) by 1.5 kcal/mol and the barrier of N -> TA was 2.6 kcal/mol, which suggested there were equilibrium between the N and TA species in S0. The calculated S1 barriers of N* -> TA* and TA* -> TB* were 0.3 and 2.1 kcal/mol, respectively, which suggested there existed a low energy path for N* to produced TA* and TB* by single and double proton transfer reactions. A comprehensive 2-D PES plot proved that the sequential, two-step proton motion is along the minimum energetic pathway, consistent with the experimental results.

並列關鍵字

Excited-State Proton Transfer Reactions ； Noble Gas Molecules ； Density Functional Theory ； Theoretical Study ； Prebiotic Synthesis of Alpha-amino Acids

參考文獻

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