| In present paper is using the quantum chemistry density functional (B3LYP) method, in DNA and RNA of these base pairs configuration, theoretical research on different acting sites of hydrogen bonding mechanism and electronic characteristics. Through the analysis of these base pairs there are main exist N-H…N、N-H…O,C-H… N and C-H…O four types of hydrogen bonds, systematically studied the essence of intermolecular interaction and wheather the bond belongs to redshift or blueshift hydrogen bonding between them. This thesis mainly includes the following three parts:1. Using quantum chemistry method of coupled cluster (CCSD/aug-cc-pVDZ) studied the interaction between pyrimidine and purine in nucleic acid and geometric structure optimization. There are exist N-H…N, N-H…O and C-H--O three types of hydrogen bond in these base pairs, Because the C-H…O bond length is longer and the bond angle is smaller than other types of hydrogen bond, belonging to abnormal blueshift curved hydrogen bond, does not meet the hydrogen bond formation of the judgment standard, cannot be regarded as a normal hydrogen bond, so can ignore its effects. Due to the N-H…N and N-H…O the proton donor N-H lengths elongation, vibration frequency decreases, and shows the redshift hydrogen bond. The C-H…O type hydrogen bond has a small contribution to the stability of systems, C-H bond to shorten, the vibration frequency increase, showing the blue shift of hydrogen bonds. Whether the redshift or blueshift hydrogen bond, C-H or N-H the stretching vibration of the infrared intensity relative to the monomer are increase, Proton donor intrinsic dipole moment of the first derivative is greater than zero. Natural bonding orbital (NBO) analysied indicate that the hyperconjugation and rehybrid theory can well explain the reasons for the formation of hydrogen bonds. The interaction energies were corrected with basis function equilibrium correction method (BSSE) eliminated the base group of overlapping error. The second-order stabilization energies and NBO analyze used the program in Gaussian03program package. In order to further explore these type of interaction, using graphical analyses for systems were performed the reduced density gradient (RDG) color-filled isosurface, RDG graphical analyses were performed to visualize the positions and the strengths of hydrogen bonding. AIM analysis has been disclosed that the nature of all the hydrogen bonding interactions, molecule belong to the closed-shell electrostatic interactions, the stabilities of these complexes with the charge transfer value are correlated positively. Electron density transition matrix analysis shows that the excitation areas are main focu on the N,O atoms, involving the breadth of space is very big. The first excited state mainly involves the frontier molecules orbital, belonging to σ'π*or n*'π*type transition.2. Using the quantum chemistry density functional method, at the theory of B3LYP/6-311++G(d,p) level theoretical studied hydrogen-bond interaction on thymine and adenine different action parts, and also calculated the interaction energy of these systems, the change of bond length and bond energy of the relate bonds. Results indicate that the strong electron-withdrawing group and conjugation effect are contributed to the formation of hydrogen bonds. X-H bond length elongation and stretch vibration frequency reduce, belonging to the common red shift of hydrogen bond. Intermolecular hyperconjugation effect caused by the intramolecular conjugated effect was weaked. Polarization effect make the X atomic orbital hybridization, the change of molecular dipole moment indicate that the infrared spectrum activity, actioning position infrared absorption enhanced obviously, it is consistent with the correlation energy of bonds, indicating that there is really exist stronger interaction between base pairs. Molecular frontier orbital theory defin the highest energy electrons occupying orbital (HOMO) and the lowest energy empty orbital (LUMO) which are generally referred to as the frontier molecular orbital. The intermolecular interaction only relate to the front molecular orbitals, reaction conditions and the paths depends on the frontier orbital symmetry, the red part of the frontier orbital are the outermost electron density N and O atoms, indicating that H…Y happened charge transfer from H to Y atom., but it’s energy level is much lower than the lone pair electrons. The two orbitals decide the electron gain and loss of molecules and the size of the transfer capability, determine the spatial orientation of intermolecular reaction. Infrared spectra mainly belong to the ground state to first excited state vibration signal, the strongest infrared absorption peaks of the vibrating energy level transition. The vibration of the molecule between the ground state and excited vibration in the transition, the change of dipole moment caused by the vibration means that the infrared activity, IR activity is proportional to the change of dipole moment.3. Using quantum chemistry density functional method (B3LYP) theoretical study the hydrogen bonds feature of guanine with cytosine on different paired, at the6-311++G (d, p) basis set optimized base pair ground state structure, electronic characteristics and energy analysis. Frequency analysis indicate X-H bonds widespread elongation and belong to common redshift hydrogen bonds, Hydrogen bond the impact on the vibration frequency of the base ring was significantly less than that of X-H. Ring vibration frequency increases to some extent, while the bond stretching vibration frequency was significantly reduced. Natural bond orbital analysis indicate that both strong electron-withdrawing group and conjugated effect are all conducive to the formation of hydrogen bonds; electrostatic attraction effect causes charge transfer to the hydrogen bonding position, leading to the increasing of atomic rehybridization effects. Electron donor orbital of the electrostatic effect caused by the change in electron distribution change the bond force constants, increases the s orbital characteristics coverage of X atom with the adjacent atom. AIM through the electronic density of the scalar field to describe the topological properties of molecules in the bonding properties, by analyzing the bond critical point of Laplace values, we found that they are all positive, indicating that the existence of hydrogen bonds between the base pairs is weak interactions, These interactions are essentially electrostatic attraction or van der Waals interaction, not by unshared electron pair to achieve, thus bonding position electron density area do not aggregate. |
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