| Supermolecule is a multiplex system which is combined by the weak interaction between molecules, which usually includes two or more subordinate-systems. At present, it is one of the scientific issues to study the essence of the interactions. The supermolecule system building on the weak interactions between molecules has always been the focus on chemistry, bionomy, material science and informatics theoretically and experimentally. However, because the experiments fail to provide varied information in detail, quantum-chemical computation has an important effect on supplementing their structures, energies and infrared spectrum. Amino acid and peptide are the most simple structures of molecules that are usually chosen as a good model for studying biological systems exhibiting the amino acid type of bonding and DNA structures. In a way, it may explain the deeply theoretical problems of some life phenomena, evolution progress, even bionomy.On the other hand, viewing the studying state home and abroad in length and breadth, we have found that the computations of the weak interactions are almost restricted to gas phase. Nevertheless, of many physical and chemical phenomena, the interactions of molecules happen in solution phase. And solvent effect is a ubiquitous phenomenon. Therefore, it plays an important role on understanding life phenomenon, interface and molecular polymerization to probe into the solvent effect on the geometric structures' stability, polarity and ultraviolet absorption of supermolecules. We take the supermolecules of cysteine-water, cysteine-hydrazine and cysteine dimmer as an example to study their stability in water as well as the characters mentioned above.At present, the study for the supermolecules of amino and peptide with other molecules is still at the primary stage and there are only a few reports about it. For instance, the Japanese scientist S. Yamebe has studied thesupermolecular system of glycin molecule with more than one water molecules, and Germanic scientist P. Hobza has analyzed glycin dimmer and considered the hydrogen-bonded interaction and the vibrational frequency shifts. But all of them have not studied the supermolecules from the point of view of chiral structure and of solution phase.In a word, this is a new field worth studying intensively. Based on the supermolecules of cysteine-water, cysteine-hydrazine and cysteine dimmer, the paper has discussed their geometric parameters, hydrogen bonding and its intensity, chiral discrimination and helical structures caused by chirality, interaction energies, infrared spectrum, vibrational frequency shifts, IR intensity and so on, which will to some extent illustrate some life phenomena, even deeply theoretical problems of bionomy.The paper includes six chapters. The first chapter is the preface, and it is composed of the brief introduction of the conception of supermolecule and hydrogen-bonded complex, of the chiral discrimination in complex , of the main work, and of academic value and practical meanings of this paper. The second chapter introduces the harmonic oscillator model, normal mode vibration types and frequency characteristics of infrared spectra. The third chapter recommends the related calculating methods which are used in this paper. By comparing the methods, finally we think that the DFT method is the best and we use it throughout the research. In brief, the former chapters mainly discuss the theoretical surrounding and bases, so that they offer the reliable quantum chemistry methods.On the basis of these theories, using density functional theory (DFT), Hartree-Fock method and second-order Moller-Plesset Perturbation (MP2) method, the hydrogen bonding of the complexes formed between cysteine and water molecules has been completely investigated in the fourth chapter. Six reasonable geometries on the potential energy hypersurface of the cysteine-water system are calculated by varied basis sets. The optimizedgeometric parameters and interaction energies for various isomers at different levels are estimated. The infrared spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. Finally the solution phase studies are also carried out using the Onsager reaction field model in water solvent at B3LYP/6-311++G(d,p) level.In the fifth part, we investigate the hydrogen bonding of 1:1 complexes formed between cysteine and hydrazine molecules. We employed the same method as that of the fourth chapter and calculated the equilibrium structures, total energies and vibrational frequencies of all the species. Six reasonable geometries on the potential energy hypersurface of cysteine-hydrazine system are considered with the global minimum, and the structure CW3 is the most stable. At the same time, the optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported. Finally the solvent effects on the geometries of the cysteine-water complexes have also been investigated using self-consistent reaction-field (SCRF) calculations at the B3LYP/6-31+G(d,p) level. The results indicate that the polarity of the solvent has played an important role on the structures.On the basis of the foresaid parts, it is concluded that B3LYP is superior to other methods of DFT because its results are the best agreement with the experimental values. Therefore, B3LYP is used to study the helical structure caused by chirality of cysteine dimer in the sixth chapter. Two reasonable geometric structures on the potential energy hypersurface of cysteine-cysteine system are considered with the global minimum. Similarly, the optimized geometric parameters and interaction energies for various isomers at 6-31G basis set level are estimated. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported. Additionally, the solvent effects on the geometries of the cysteine-cysteine complexes have also been investigated using self-consistent reaction-field (SCRF)... |
PDF Full Text Request