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

• Main Authors: Chia-Yu Peng, 彭家瑜
• Other Authors: Wei-Ping Hu
• Format: Others
• Language: zh-TW
• Published: 2015
• Online Access: http://ndltd.ncl.edu.tw/handle/02494196428647060097

博士 === 國立中正大學 === 化學暨生物化學研究所 === 104 === 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.