Theoretical Study The Mechanism Of Single-Site Ruthenium Catalyst For Water Oxidation And Predict Double-Strand Thymine-Mercury(Ⅱ)-Thymine Base Pair DNA Structue

Recently, with the progress in the relative density functional theory and its numerical methods, and the computer capacity, DFT based first principles calculation and the combined quantum mechanics and molecular mechanics method have becomed main research tools for biology, chemistry and materials science. The dissertation have two research parts:the first content is devoted to study the mechanism of single-site ruthenium catalyst for water oxidation by means of the combined quantum mechanics and molecular mechanics method (QM/MM) and the first principles calculation, the calculation result reveal the reaction mechanism of water oxidation. This understanding is helpful in the design of new catalysts for water oxidation. The second content predicts the double-strand thymine-mercury (Ⅱ)-thymine base pair DNA structure by Oniom (QM/MM) method. The innovative points of research as follwing:we show the details reaction circle path and microscope details of single-site ruthenium catalyst for water oxidation from atom level, our calculation results and the theory explanations are consist with the experiment data. And predicting to show the structure of the double-strand thymine-mercury (Ⅱ)-thymine base pair DNA structure, the calculation results support the previous experiment study. The concerned properties include geometry, electron structure, reaction path, frequency calculation.The first chapter is basic theory method, we introduction density functional method, perturbation theory, electron configuration interaction theory. For the rapid development and applied widely density functional theory, the main idea can find the right exchange-correlation functional. Many functional have been proposed to improve the calculation chemistry precision as local density and generalized gradient approximation functional, non-local and self-interaction correction functional, the description strongly correlation and weak interaction system functional. Finally, we introduce some bases with selective strategy.The second chapter introduces QM/MM minimum free energy path method. This method has the great advantage to deal the biology and the great number atoms molecules with the good precision and simulation the chemistry reaction with the bond formation and break. Currently, many QM/MM methods can not give the reasonable reaction barrier compared with the experiment. Therefore, we develop QM/MM method to optimize the reaction free energy path as "QM/MM MFEP". The optimization iteration time is less, and, the computer cost is cheap. Finall, we show two real examples with QM/MM MFEP method.The third chapter studies the detail water oxidation mechanism of single-site ruthenium catalyst [Ru"(tpy)(bpm)(OH2)]2+([RuⅡ-OH2]2+:tpy=2,2’:6’,2"-terpyridine; bpm=2,2’-bipyrimidine) for oxygen release:water oxidation is a key reaction step in nature and artificial photosynthesis. Combined several theoretical tools, we have studied the entire catalytic cycle of water oxidation for this single-site ruthenium catalyst. The calculation results suggest that spin state of the ruthenium complex play a key role in some key reaction steps of the entire cycle. The redox potentials and pKa. calculations for the first two proton-coupled electron transfers (PCETs) from [RuⅡ-OH2]2+to [RuⅣ-O]2+and the following electron-transfer process to [Ruv-O]3+suggest that these processes can proceed readily in acidic or weakly basic conditions. The subsequent water splitting process involves two water molecules,[RuⅤ-O]3+to generate [RuⅢ-OOH]2+, and H3O+with a low activation barrier (～10kcal/mol). After the key O-O bond forming step in the single-site Ru catalysis, another PECT process oxidizes [RuⅢ-oOH]2+to [RuⅣ-OO]2+, when the pH is lower than3.7. Two possible forms of [RuⅣ-OO]2+, open and closed, can exist and interconvert with a low activation barrier (<7kcal/mol) due to strong spin-orbital coupling effects, and the spin state of [RuⅣ-OO]2+was changed from singlet flipping to triplet during the open and closed structure interconverting process. In Pathway1at pH=1.0, oxygen release is rate-limiting with an activation barrier～12kcal/mol while the electron-transfer step from [RuⅣ-OO]2+to [Ruv-00]3+becomes rate-determining at pH=O (Pathway2) with Ce(IV) as oxidant. The results of these theoretical studies with atomistic details have revealed subtle details of reaction mechanisms at several stages during the catalytic cycle. This understanding is helpful in the design of new catalysts for water oxidation.The fourth chapter theoretical predicted the thymine-mercury (Ⅱ)-Thymine base pair stacking DNA structure by Oniom method. We calculated the structure parameters of thymine-mercury (Ⅱ)-Thymine base pair DNA by3DNA algorithm, these structure parameters indicate that the stacking conformation of thymine-mercury (Ⅱ)-Thymine base pair DNA similar to nature DNA. The metal-nucleobase bond as mercury link the thymine is very stability. The stability becomes better with the numbers of thymine-mercury (Ⅱ)-Thymine base pair addition. These theoretical results are helpful to design new DNA functional materials, also further understand the toxicity of mercury.