Molecular Dynamics Simulation Studies On The Properties Of Several Soft Materials Due To Environmental Confinements

Soft matter is a subfield of condensed matter comprising a variety of physicalstates that are easily deformed by thermal stresses or thermal fluctuations. In spite ofthe various forms of soft materials, many of their properties have commonphysicochemical origins, such as a large number of internal degrees of freedom, weakinteractions between structural elements, and a delicate balance between entropic andenthalpic contributions to the free energy. These properties lead to large thermalfluctuations, a wide variety of forms, sensitivity of equilibrium structures to externalconditions, macroscopic softness, and metastable states. The space in which softmatter exists is referred to external environment. The structures, properties anddynamics of soft matter are strongly affected by the environment, such as irradiationwith light, surface adsorption, confined space, and so forth. Though many ofexperimental techniques have been widely used to study the soft materials, there arestill some problems to be resolved. In fact, the understanding of the micro-processesand the detailed morphological features of soft matter can be advanced throughcomputer simulations. In this thesis, we investigated the photo-isomerization of liquidcrystals formed by azobenzene and (1-cyclohexenyl)phenyldiazene, the ionic liquidfilm based on [emim][Tf2N] and [emim][TfO] adsorbed on highly oriented pyrolyticgraphite using atomistic molecular dynamics (MD) simulations, and the Free energyand scalings for polymer translocation through a nanopore using coarse-graind MD (CGMD) method. The main results are as follows:(1) Atomistic molecular dynamics simulations have been used to investigatethe liquid crystal systems based on[4-pentyl-(1-cyclohexenyl)]-(4-cyanophenyl)diazene (5CPDCN) and4-cyano-4′-pentylazobenzene (5AZCN). The results show the growth process of anematic phase from a disordered phase. Then the phase transition caused byisomerization reaction is studied based on a temporary modification of the dihedralpotential. The properties of5AZCN and5CPDCN are compared, showing that theorientation of trans-5CPDCN is more highly ordered than trans-5AZCN. This can beattributed to that the more extended dihedral angles2(i.e. the dihedral anglebetween the ring system and the terminal chain) in trans-5CPDCN enhance therod-like conformation of the molecules. The orientational correlation functionsgl(r)(l=1,2) are also calculated, by which we find that both5CPDCN and5AZCN systemsin nematic phase present parallel and anti-parallel dipole correlations. Theanti-parallel dipole correlation is localized for the5CPDCN system; on the contrary,the parallel dipole correlation is weakly localized for the5AZCN system.(2)Molecular dynamics simulations have been used to study the ionic liquid (IL)crystalline film based on1-ethyl-3-methylimidazoliumbis[trifluoromethylsulfonyl]imide ([emim][Tf2N]) and1-ethyl-3-methylimidazoliumtrifluoromethanesulfonate ([emim][TfO]) on the graphite surface. Our results showthat the cations are distributed parallel to the surface in the1/2monolayer (ML)crystalline film. The [Tf2N] anions are parallel to the surface with the oxygen atoms atthe bottom, whereas the [TfO] anions are distributed perpendicular to the surface alsowith the oxygen atoms at the bottom in the1/2ML crystalline film. It is found that theIL-vapor interface strongly influences the arrangement of ions at the interface. Theanions in the top layer with the oxygen atoms outmost turn to be with the F atomsoutmost to form C–H···O hydrogen bonds with the cations. The calculatedorientational ordering shows that in the outmost layer at the IL-vapor interface, the cation rings present both parallel and perpendicular to the surface at350K.(3)Coarse-grained molecular dynamics simulations combined with milestoningmethod are used to study the stochastic process of polymer chain translocation thougha nanopore. We find that the scalings for polymer translocation process (the chain isinitialized with the first monomer in the nanopore) and for polymer escape process(the chain is initialized with the middle monomer in the nanopore) are different. Thetranslocation process is mainly controlled by the entropic barrier, while the polymerescape process is driven by the effective force due to free energy difference.