A Theoretical Study On The Catalytic Reaction Mechanisms Of Metal Complexes And Enzymes

Based on quantum chemistry and molecular mechanics, this thesis explored the chemical and biochemical catalytic reaction mechanisms by organometallic compounds and metal enzymes through the theoretical calculation method. For transition-metal organometallic compounds, the reaction mechanisms of small molecules activation by transition-metal organometallic compounds was researched, especial the activation of carbon dioxide. For metal enzymes, the internal hydrogen transfer mechanism above the redox site was reasearched. In addition, we also compared to the reaction mechanism of small molecules activation by nonmetallic compound.For the researches with sub-topic of small molecules activation by organometallic compounds, two notable carbon dioxide activation chemical reactions by transition-metal compunds are selected. One is the reduction of carbon dioxide in iron biocatalyst [FeH（PP3）]BF4 catalytic hydrogenation reaction, the other is copper（I）-NHC-catalyzed C-H carboxylation of terminal alkynes with carbon dioxide. Due to the restrictions in experimental condition, the details of the reaction mechanisms are both unclear.For the former reaction discussed in Chapter three, it is calculated that the reduction of carbon dioxide could be carried out via two spin states, the high-spin（HS） triplet state and the low-spin（LS） singlet state. The minimum energy crossing points（MECPs） on the seam of two intersecting PESs were searched out. Some interesting phenomena, such as the open-loop phenomenon, and the O-rebound process, were demonstrated to be the important causes of the spin crossover. For the latter reaction discussed in Chapter four, three types of reaction mechanisms were designed, explored and compared. The optimal reaction channels of corresponding pathways were selected. It was noting that in the insertion process of activated CO₂ by NHC, the Cu-O bond formed firstly, and then induced the formation of new C-C bond, but not as a universal speculated that the formation of the new C-C bond induced the transfer of the CO₂ unit from the carbene center to the copper center. The essence is the formation of CO₂-NHC-Cu cocatalyst promotes the reaction process. Also, the functions of NHC were determined. Our calculations investigated that（1） the special difunctional roles of NHC can indeed facilitate the reaction process after the formation of CO₂-NHC-Cu cocatalyst, whereas the unexpected low energy of this cocatalyst results in its ultrastability and then hinders the dropping of energy barrier in the whole reaction and（2） the additional interaction of NHC with the same metal atom will promote the insertion process of CO₂ through increasing the electrophilicity of the metal center.In order to compared with the reaction mechanisms of small molecules activation reactions by transition-metal organometallic compounds, another reaction was selected using a nonmetal catalyst, Frustrated Lewis pairs（FLPs） to activate small molecules. In Chapter five, DFT calculations were carried out to explore the reaction mechanisms for the reaction between a classical FLP compound, boron amidinate HC（i PrN）2B（C6F5）2 and small molecules, including carbon dioxide, carbon monoxide and two terminal alkynes, methylacetylene and phenylacetylene. All these reactions can be regarded as following the concerted addition mechanism.Compared to transition-metal organometallic compounds, though metal enzymes belong to biological macromolecules, they always performed better catalytic effect and the reaction conditions are always more moderate. In Chapter six, the detailed reaction mechanism of a metal redox enzyme, ba3-type Cytochrome c oxidese（CcO） from Thermus thermophilus, was explored by molecular dynamic simulation method. CcO is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. A potential mechanism for proton transport in the region above the dinuclear center（DNC） is proposed, with residue His376 as proton-loading site. Two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane were identified, which can likely also act as proton exit transport pathways. In addition, we also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151 II and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected byprotonation of residue His376.Our research works get insight into the reaction mechanism essence of small molecules, especial carbon dioxide, activated by metal organometallic compounds, which is also compared to the mechamisms activated by nonmetal compounds. The detail proton pump mechanism in the process of redox oxygen molecules to water in a redox metal enzyme, ba3-type CcO from Thermus thermophilus was also investigated, as well as two interal water exit pathways indenfied. These works would supply theoretical guide and help advance the development of novel related catalyst.