Theoretical Studies Of The Self-Assembly On Metal Surfaces And In Solutions By Using Quantum Mechanics And Molecular Mechanics Models

Self-assembly is a phenomenon that disordered pre-existing components form an organized structure by certain interactions between these components in the absence of external driving forces. It is commonly present in living biological systems, ranging from microscopic bacteria to macroscopic living organisms. Formed by self-assembly of a great number of organic molecules, numerous organic molecular devices emerge with the electric properties easily tuned by attaching different chemical groups. It is es-sential to understand the connection between self-assembly packing conformations and the performance of organic films by theoretical calculations. In this dissertation, quan-tum mechanics (QM) and molecular mechanics (MM) are combined to study packing conformations of self-assembly on metal surfaces and the aggregates in solutions by the modified force field. The results and conclusions of this dissertation are summa-rized as follows:1. The role of substrate in packing structures of oligothiophenes on the Ag(111) surfacePacking structures and orientation of oligothiophene (nT, n-4and6) molecules on Ag (111) surface are investigated by molecular dynamics (MD) simulations and quantum chemical calculations. The MD simulations show that average adsorption height of the first nT layer is3.2A, close to the experimental observation3.4A. The first two layers are separated by3.5A, falling in a distance range of the π-π stacking. The nT monolayer tends to be more ordered with the increase of the coverage and the arrangement of6T molecules is more ordered than that in the4T film on the Ag(111) surface. Comparing to the packing conformations of6T in the amorphous solid, the Ag(111) substrate makes the6T molecules lie flat to form an ordered arrangement.2. Sexithiophene template effects on packings and orientations of C60molecules on the Ag(111) surfaceThe packing conformations and the orientations of C60molecules on top of the preadsorbed6T monolayer on the Ag(111) surface have been investigated by the molec-ular dynamics simulations. For the absorbed C60molecules on the Ag(111) surface, most of C60molecules take the orientations with hexagon or6:6bond facing to the sur-face, which agrees well with experimental observation. Simulated scanning tunneling microscope (STM) images of C60monolayer calculated by density functional theo-ry (DFT) with different molecular orientations are also close to those obtained from experimental measurements.It is also shown that the underlying6T stripes make C60molecules aggregate in chainlike arrays on the6T covered Ag(111) surface, showing significant template ef-fect on the directed self-assembly of C60cages. Most of C60molecules on the6T prepatterned Ag(111) surface have the configurations with6:6bond or5:6bond facing to the substrate. When the deposition order is changed, the6T stripes are shown to tilt with corrugation on the underlying C60carpet, revealing the important role of the deposition order in modulation of the ordered supramolecular nanostructures.3. Modulating morphology of thiol-based monolayers in honeycomb hydrogen-bonded nanoporous template on the Au(111) surfaceThe difference in monolayer morphology caused by different functional thiol-s (ASH, BP3SH, and C12SH) within the surface-supported porous network of NDI and MEL molecules has been investigated by molecular dynamics simulations with the modified force field. Classical Lennard-Jones potential with the newly fitted pa-rameters is used to treat the nonbonded interfacial interaction, and the Morse potential is used to describe the Au… S binding. Force field parameters of intermolecular and interfacial interactions are modified to reproduce MP2adsorption height and binding energies.Within the framework of modified force field, molecular dynamics simulations show that NDI-MEL network lies flat in an ordered hexagonal pattern on the sub- strate. The packing morphology and unit cell parameters of the triple hydrogen-bonded network obtained from molecular dynamics simulations and quantum chemical calcu-lations match the image and measurements from the STM. The backbone flexibility, which varies with the length and shape of thiol chains, is demonstrated to affect the monolayer morphology. The subsequently deposited thiols also disturb the bicompo-nent nanoporous to different extent, originating from the subtle balance between the thiol-thiol, thiol-template, and the intra-template hydrogen-bonding interactions. The understanding of nanotemplate effect on the thiol-based monolayer growth is helpful for fabricating novel surface-supported host-guest hybrid nano-devices at single molec-ular level.4. Light and electric field induced switching of thiolated azobenzene self-assembled monolayerThe photoisomerization mechanism of thiolated azobenzene (AZO) and its deriva-tives has been studied by TD-DFT calculations. There is a conical intersection in the N=N rotation mechanism with low energy barrier (less than5.0kcal/mol) between the ground state and the first excited state. The presence of electric field indicates charge transfer between AZOs monolayer and the Au(111) surface. In AZO and AZO(NH2), the trans conformation is presented under both E+and E_electric field along the molecular long axis. Interestingly, the cis/trans isomerization is evoked by different di-rections of electric field for AZO(NO2) monolayer. The Au(111)-SAMAZO//SAMC12-Hg junction is further simulated by our modified force field. It is found that height of Hg drop is reduced by1.0A when the AZO SAM switches from trans to cis form. Our simulation results open a new perspective in designing the switchable SAM molecules in a tunable fashion.5. Molecular dynamics simulations of self-assembled aggregates in solutionMolecular dynamics simulations are employed to study the conformations of a Pt-coordination prism, CB11Me12-aggregates, and cryptophane molecules in various polar and non-polar solvents. The solvent polarity affects the shape of the prism molecule with different number of solvent molecules inside of the cage. The radial distribution of CB11Me12-aggregation is affected by the addition of sulfolane. The selectivity in the encapsulation of guest molecule for these cage-shaped cryptophane supramolecules is sensitive to the counterions. The thermodynamic properties are also estimated by calculations. These results are of importance for the understanding of the function of certain biological ion channels and the host-guest chemistry in aqueous solutions.