Molecular Dynamics Simulations Based Applications And Theory,

As a rapidly growing up method of molecular simulation, molecular dynamics (MD) has been widely used to calculate thermodynamic and dynamic properties as well as structures of many systems, and has wider developing space and higher application foreground. This thesis focuses on the applications of MD in the studies on some elemental and theoretical researches such as host-guest inclusion, molecular interaction in nanoparticles, cracking of chemical bonds as well as physical properties of some substances. A lot of useful results have been obtained by making many new attempts and systematic researches.The studies on the host-guest inclusion such as those of host cyclodextrin (CD) and guest cresol isomers demonstrate that van der Waals force, H-bonding force, hydrophobicity as well as solvent effect will make an important impact on behaviors of the inclusions, movement of the guests inside CD, as well as dynamic structures of both the host and the inclusions. The simulation results show that, by MD simulation with some proper programming techniques, one can 'sees' many microscopic visions especially the pictures of dynamic structures which can not be seen by today's experimental techniques, and can also validate or explain some experimental phenomena.The studies on molecular interactions in a kind of nanoparticle formed by gold cluster adsorbing some thiol terminated hydroquinonyl ether chains demonstrate that the nanoparticle is stable whether adsorption is physical or chemical and whether the gold core is in crystal or pseudo-crystal or amorphous. The explanations are that, the gold core is stable because of its crystal-like structure, and the corona is also stable because most chains adopt relatively bending conformation to reduce their energies, and the system energy is favorable as well as the nanoparticle has showed some heat stability. Meanwhile, the chains in the corona had been found forming several correlated groups, and in each group the phenylene rings correlate each other in either parallel or perpendicular forms. This correlation may increase the probability of inter-chain electron transfer.To make MD succeed in studying the breaking of chemical bonds, a novel reactive potential RPMD and the corresponding force field CRACK has been put forward. With CRACK force field, pyrolysis behaviors of n-octane and n-decane had been studied by MD technique. The results show that RPMD can certainly describe breaking and forming of chemical bonds. The distribution of pyrolysis products was found to be comparable with the experimental ones. Although some simulation results were quantitatively rough, most of them can be acceptable which shows that the idea of RPMD is feasible. The development of this novel reactive potential can provide a new tool to study some simple reactions by MD technique.Finally, some physical properties of substances such as solidification process and mechanism of diesel and mechanical properties of an anisotropic material TATB had been studied by MD technique. The following viewpoints have been brought forward for the first time that: the jump of atomic self-diffusion constant with temperature can be used to judge the solidification point of liquid;mechanical properties of an anisotropic material can be calculated by a new method of the constant pressure MD.The above studies have enhanced our understanding to many microscopic processes as well as the characters of some phenomena, and also have enriched the research means of MD and expanded the application fields of MD. I believe that, in the coming future, these studies will support strongly the widely use of MD technique in many fields.