Theoretical Research Of Hydrogen Bond In Self-Assembly System Containing Aromatic Acid And Aromatic Acid Derivative

The molecular surface self-assembly system means a kind of two-dimensional spontaneous aggregation formed by weak interacitons, it’s stable in thermodynamics, certain in structure, specific in performance, and it plays an important role in host-guest self-assembly, molecular electronics, and chiral recognition. It is generally accepted that weak interactions is primary factor of assembing into specific structure. In experimental method, scanning tunneling microscopic (STM) is employed to research the self-assembly system. In order to find out the reason of forming self-assembly structure, theoretical simulation is gradually employed. In self-assembly system containing structures of aromatic acid, Hydrogen bond is important to final structures, which can not be proved by experimental method. In this thesis, theoretical simulation is employed to research the self-assembly of TPA on HOPG and BIC/C8H18O on HOPG by fisrt principles, molecular mechanics and molecular dynamic calcualtions. In two researched system, the similarity is the structure of benzene linked to carboxylic acid functional group. The role of Hydrogen bond is researched in the simulation process.In this paper, firstly BIC is divided into molecular segments, fisrt principles and molecular mechanics calculations is performed to benzoic acid which is expected to from Hydrogen bond in surface self-assembly. The exact geometry, vibration frequency and Hydrogen bond energy can be got. Based on the first principles results, field parameters of MMFF94force field is optimized to make molecular mechanics calculations and first principles calculations results consistent. After optimizing the field parameters, two results is basically same to each other:geometry of benzoic acid molecule is the same, there are both39kinds of vibration mode, the maximum frequency difference does not exceed3%, the energy of Hydrogen bond does not exceed1kcal/mol. The results of molecular mechanic is accurate.Molecular dynamics simulation is performed on TPA self-assembly with the MMFF94force field optimized to research the role of Hydrogen bond in TPA self-assembly process. Molecular dynamics results show that, the higher the temperature, the more regularly TPA tends to arrange, trimeric structure of Hydrogen bond is more unstable; the larger coverage, the more ordered structure of TPA self-assembly is, and the dimer form of Hydrogen bond is predominant. Different Hydrogen bond form lead to different TPA self-assembly structures on HOPG directly and Hydrogen bond is primary factor of affecting TPA self-assembly structure. The effect of Van der Waal’s force is weaker than Hydrogen bond. The results of TPA self-assembly simulation further verify that the optimization of MMFF94force field parameters is reasonable.Energy of BIC/C8H18O self-assembly system is computed with the MMFF94force field optimized, and two kinds of configuration are considered:clockwise (CW) and counterclockwise (CCW) networks. Energy of network formed by BIC/OA is the lowest, it is easier for BIC to form CW network with R-OA, and it is the opposite case for S-OA. Energy of BIC/R-OA and BIC/S-OA is27kcal/mol higher than BIC/OA system. Different chirality of C8H18O lead to different energy of self-assembly structure, with the changes of chiral position in the carbon chain, the energy of self-assembly show odd-even effect. The results of molucular dynamic simulation of BIC/C8H18O system show that using solvent model is conducive to make self-assembly structure stable. When CW network is got, Hydrogen bond length concentrate most in BIC/OA, better in BIC/R-OA, worst in BIC/S-OA. The stablity among three system reduce in turn. From the results of molecular dynamic, circle Hydrogen bond structure of BIC/C8H18O is governing factor for forming network, the final chiral structure is formed by the circle Hydrogen bond structure gruadually.