Theoretical Studies On Several Typical Molecular Aggregates

Molecular aggregate is an aggregated structure with unique structural features and characteristics. The structure is based on the weak interaction between the molecule and its synergy effects. Self-assembly is an important approach to creat ordered molecular aggregate with novel structure and function. Self-assembly is a technology which means the ordered structure is formed spomtaneously by the basic structure unit, and in the non-covalent interaction, the basic unit is aggregated as a stable structure with the appearance of certain rules of geometry. Molecular aggregation is a common phenomenon in nature. Many researchers use a variety of modern experimental techniques to study the microstructure and aggregation patterns of molecular aggregation system, especially its dynamic properties’detecting. Its deficiencies are not able to provide the microscopic structure and dynamic properties of molecular aggregation system at the molecular level or micro level. Therefore, the development and use of the knowledge of theoretical chemistry, which is used to study the aggregation structure of aggregation systems and molecular interactions between different molecules, have become one of the important directions of molecular aggregates chemistry.In this thesis, a series of theoretical studies have been carried out for several tipical molecular aggregation systems. On the one hand, by performing quantum mechanism calculations, we investigated the properties of the single molecule which decided the ohysic-chemical characteristics of the aggregation systems. On the other hand, we performed molecular dynamics on the aggregation systems to investigate the interior micro-evironment of the aggregates, and the influence of external conditions on the aggregation architecture. The important results in this thesis can be summarized as follows:1. Molecular dynamics was performed to explore the structure and dynamical properties of the LDH-MO hybrid systems. According to the specific information of the simulations, the38MO-LDH system was considered to be more appropriate. The concentration profiles, mean square displacement (MSD) and self-diffusion coefficient were calculated using the trajectory files on the basis of MD simulations. The results indicated that the MO molecules were much more stable when intercalated into the LDH layers. The tilt angle was about74.15°, which was consistent with the experiment results. Different aggregation and orientation in the LDH layers had different photophysical properties.2. Molecular dynamic simulations have been performed to show the detail in the structure characteristic of the hydrogels of Fmoc-dipeptides. It is found that the Fmoc-dipeptides molecules are formed the hydrogels structure in the water and it can be influenced by the quantity of the solvent and the temperature. The network structure is mainly due to the interaction of the π-π stacking, and the face to face orientation and offset stacked orientation are indicated to play a key role in the interaction between Fmoc planes. The interaction between different molecules in the system also investigated, and it suggested that regions with a lower water density around the Fmoc-dipeptide have a corresponding higher hydrogels density, and the hydrogen bonds between different molecules also play an important role in forming the network hydrogel structure.3. The direct hydrodesulfurization (DDS) of dibenzothiophene (DBT) has been theoretically studied using density functional theory method. The energy and main geometry parameters of the intermediates and transition states of DBT molecules during reaction process are calculated by means of quantum chemistry calculation. Consequently, it is validated that the cleavage of C-S bond in DBT can be happened to achieve ring opening over acidic catalyst. From the results of energy-analysis, it is shown that the cleavage of C-S bond needs high energy, it is the key step, as well as the most difficult step. The active hydrogen atoms exiting in the system play an important role in reaction process.