Theoretical Investigations Into The Interaction Between Nucleic Bases And Small Active Inorganic Molecules

The studies about the interaction between nucleic acid bases and small inorganic molecules are helpful to investigate the micro-mechanism of the biological function of nucleic acids and to explain the physiology process of small inorganic molecules. This thesis presents a systematical investigation to complexes formed between various nucleic acid bases and BH3,BF3,BC13,CO,NO et. al. using the ab initio methods, density functional theory (DFT) calculations.Geometries and combination energies are predicated at B3LYP/6-31G(d) and MP2/6-31G(d) level for thymine-BH3 complexes and 5 geometries have been obtained. The charge transference exists in all the conformers and the combination energies have a good line relationship with their charge transference. The calculated results showed that when the complex formed their IR spectrum moved to the red side and the frequency shifts are relative to the stabilities of the complexes.Seven configurations with no imaginary frequencies have been obtained for the guanine-BH3 systems. The results indicate that four of the seven configuration are relatively stable ones in which the pyridine-type nitrogen atoms or carbonyl oxygen or nitrogen of amino group offers its lone pair electron to the empty p orbital of born atom. According to the AIM analysis, dihydrogen bonds have been formed in most of them. The frequencies analysis showed that all the stretching vibrations of BH3 undergo red shifts in complexes, and the shifts are relatively to the combining energies of complexes.Geometries and binding energies are predicted for adenine-BH3 complexes and 6 optimized configurations have been obtained. The results indicate that the three configurations in which the pyridine-type nitrogen atoms offer their lone pair electrons to the empty p orbital of born atom are the most stable ones and the 3 pyridine-type nitrogen atoms have the similar abilities to combine with B atom. The vibration analysis showed that the stretching frequencies of BH3, NH2 and N9-H suffered red shifts while that of the bending of NH2 and the stretching of C-H bond showed blue shifts. The charge transferences from adenine to BH3 existed in the complexes according to the results of NBO analysis.Geometries and combination energies are predicated at B3LYP/6-31G and MP2/6-31Glevel for cytosine-BH3 complexes and 5 geometries have been obtained. The outcome indicates that the configurations with the boron atom combines with N or O directly are relative stable ones. The stabilities of the remainders that formed with n-p interaction are weaker. The stabilities of all configurations are relative to their charge transference.Five configurations have been obtained in the calculations for uracil-BH3 complexes. The vibrational analysis and natural bond orbital analysis are carried out for the obtained configurations. The phenomena of charge transference exist in all the conformers. The style and amount of charge transference are varied with the configurations.Geometries and binding energies are predicted at B3LYP/6-311+G* level for the guanine-BX3 (X=F,C1) systems and four conformers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BC^ respectively. The formation for all the configurations are based on the o-p action that pyridine-type N or carbonyl O offers its lone electron pair to the empty p orbital of B. In the most stable configuration of guanine-BF3, BF3 connected to N3 of guanine. While in the most stable configuration of BCI3 complexes, BCI3 connected to O10 of guanine. Guanine-BF3 complexes are more stable than guanine-BCb ones. Besides a-p actions, hydrogen bonds between guanine and BX3 were formed according to the AIM analysis.Geometries and binding energies are predicted for the adenine-BX3 (X=F,C1) systems and four configurations have been obtained for both adenine-BF3 and adenine-BCb respectively. The most stable conformer is BF3 or BCI3 connected to N3 of adenine and with the stabilization energy of 94.39 or 86.19 kJ/mol at B3LYP/6-311+G* level. Three of four configurations are relatively stable as they are formed with the fact that pyridine-type N offer lone electron pair to the empty orbital of B for both BF3 and BC13 complexes. Just as guanine-BX3 systems, adenine-BF3 complexes are more stable than adenine-BCl3 ones and the concomitances of charge transference from adenine to BX3 were occurred.For the cytosine-BX3(X=F,Cl) systems, geometries and binding energies were using the B3LYP method of DFT and MP2 method of ab initio with 6-311+G* or 6-311++G* bases sets. Three configurations were found for each system. In the most stable conformer of cytosine-BF3 or cytosine-BCl3, boron atom of BX3(X=F,C1) connected to carbonyl oxygen Og of cytosine with a stabilization energy of-78.71 and -69.62 kJ/mol respectively. The analyses for the combining interaction between BX3 and cytosine with the...