Applications Of Multi-scale Simulation On Life Science And Material

Multi-scale simulation can take advantage of different simulation methods to investigate system properties at different scales. In this work, Quantum chemistry calculation,force field method and molecular dynamics method were applied to perform simulation at electronic and atomic scales to investigate bonding mechanism and electronic structure of heme with ligands,solvation free energy and reaction mechanism of energetic materials.Heme is a prosthetic group playing important roles in biological processes. To investigate how heme bonds with ligands is of great value for understanding its functions. Oil/water partition coefficient and infinite-dilution activity coefficient are important thermodynamic properties being widely applied in pharmaceutical and chemical industries. They are directly related to solvation free energy, which has been an important research field for computational chemistry. FOX-7 is a new kind of energetic material with both high explosive property and low sensitivity. It has been believed to be a promising replacement for RDX. Energetic material reaction mechanism attracts more and more attention because it is crucial for production, transportation, storage and usage of energetic material.Results and conclusions are in the following:1. DFT method was applied to investigate bonding mechanism of heme with CO, NO as well as O2 and effects of electronic configuration on complex properties. The bonding mechanisms areσdonation andπback-donation.σdonation is important in Fe-CO bond but not in Fe-NO or Fe-O2 bond. Imidazole bonds with heme throughσdonation involving lone pair of electron on coordinate nitrogen atom. As a result, Fe-CO bond is weakened while Fe-NO and Fe-O2 bonds are strengthened. After imidazole binding, there is more electron increasement on dioxygen with open shell singlet state than that with close shell singlet state. Open shell singlet state is in favor of electronπback-donation. With open shell singlet state, the Fe-O2 vibrational frequency increases by 63 cm-1 after imidazole binding. On the contrary, with close shell singlet state, the Fe-O2 vibrational frequency decreases by 22 cm-1 after imidazole binding. The results indicate that electronic configuration has significant effects on molecular properties.2. Molecular dynamics based on force field method and thermodynamic integration method are used to perform precise solvation free energy calculation to predict oil/water partition and infinite-dilution activity coefficients. The precision of free energy calculation can reach 0.5kJ/mol,which is the highest level in the world. The deviation from experiment result using force field method independent from experimental data is less than 2.7kJ/mol, which has the same accuracy level with that of quantitative structure property relationship (QSPR) method dependent on experimental data. It has been pointed out that solvation free energy result with higher accuracy can be obtained with improved force field, especially intermolecular interaction term. Based on this work, the honor of performing best among molecular simulation results in the Fifth Industrial Fluid Properties Simulation Challenge has been received.3. Ab initio molecular dynamics was performed to investigate reaction mechanism of FOX-7 in condensed phase and at different temperatures. C-NO2 bond fission and hydrogen transfer are initial reaction mechanisms of FOX-7. There are both inter- and intra-molecular hydrogen transfer reactions. Besides, the oxygen atom of nitro group and nitrogen atom of amino group can be served as the hydrogen acceptor. It has been found out that temperature has a significant effect on initial reaction mechanism of FOX-7. That is because either reaction enthalpy or entropy increasement for hydrogen transfer is less than that of C-NO2 bond fission. At low temperature, hydrogen transfer is main reaction because enthalpy change is dominant in free energy change. At high temperature, C-NO2 bond fission is main reaction because entropy change is dominant in free energy change. Polymers found in the reaction process indicate reaction mechanism involving more than one FOX-7 molecule. Main stable products are H2O, N2 and CO2. 690 species in the reaction process of FOX-7 have been identified which are reasonable models for development and validation of ReaxFF parameters. Besides, investigation on nitromethane reaction at high temperature and pressure indicate that the products are urea and other polymers. After enlarging system size, the polymers break up into water and other small molecules. Investigation results are of value for understanding reaction mechanism of energetic materials and design of new energetic materials with better properties.