Theoretical Study On The H-bonded Dimmers For Some Biological Systems

The H-bonded dimmers of the five bases in DNA and RNA and four H-bonded complexes between 2,4-dithiothymine and water were studied in our research. The 61 H-bonded dimmers of the five bases in DNA and RNA were optimized at the B3LYP/6-311++G** computational level, and then the vibrational frequencies were studied at the same level. The interaction energies were computed at both the B3LYP/6-311++G** and MP2/6-311++G** computational level with the configurations got at B3LYP method. Then the natural bond orbital (NBO) analysis, atoms in molecules (AIM) analysis, NMR, and molecular electrostatic potential (MESP) were studied to clarify the properties and characteristics of the hydrogen bonds in all these dimmers. The H-bonded complexes between 2,4-dithiothymine and water were optimized at the MP2/6-31G(d) computational level. Then the natural bond orbital (NBO) analysis, atoms in molecules (AIM) analysis, and NMR were studied for the four complexes. The main results are as follows:1,The ten H-bonded dimmers of uracil are studied at first. There are two types of hydrogen bonds in all these dimmers: N–H…O and C–H…O complexes. The N–H…O interaction is much stronger than the C–H…O interaction, whereas both are proved to be the classic, red-shifting H-bonds. The dimmer with two N–H…O interactions is the most stable, whereas the dimmer with two C–H…O interactions is most instable one. The research scheme is proves to be precise and effective as our results are agreed with the previous references. Thus the research scheme is used for the following investigation.2,The seven H-bonded dimmers of cytosine are studied and there are four hydrogen bonds in them: N–H…O, N–H…N, C–H…O, and C–H…N interactions. The N–H…O and N–H…N interactions are stronger than the C–H…O and C–H…...