Dna Bases And The Peptide Chain Hydrogen Bonds Between The Theoretical Research

DNA occupies a central role in the development and functioning of living organisms for its functions of storing and transfer of genetic information.However,it is notable that all the performances of the functions must depend on the interactions with proteins.Among so-called protein-nucleic acid interactions,the hydrogen(H)-bonding interactions play a crucial role for on one hand its contribution to the structural stabilities of DNA and proteins,so the formation and/or breaking of hydrogen bonds(HBs)are intimately involved in nearly all these interactions. On the other hand,some of the interactions are directly dominated by HBs in such processes of DNA repair and molecular recognition etc.The H-bonding interactions between protein and nucleic acid have been found to be a vital actor in the process of repairing oxidative damage to the purines and mediating glycosidic-bond cleavage.Multiple H-bonging has been proposed to be the driving force in the molecular recognition process in protein-nucleic acid complexes. Besides,Multiple HBs between an amino acid side chain and bases are expected to alter in different ways the electronic properties of nucleic acid bases,which act an important role in understanding DNA and RNA damages.So it is of great important to carry out some investigations on the H-bonding interactions between DNA and proteins.It is due to the facts above that we endeavor in our present work to make an investigation on the H-bonding interactions of adenine-formamide(A-F)complexes.In the present paper,adenine and formamide have been adopted as a model for the study of the H-bonding interactions between DNA and proteins.The whole paper is made up of six parts.The first chapter includes a brief introduction of development of quantum chemistry theory and an elucidation of the matter that intrigues our interests and the value of our investication.The second chapter referring to HBs and ionization potentials(IP)and electron affinities(EA)is something about the contents we seriously investigate in the system.In the third part,related calculation methods used in the present paper have been succinctly introduced.In brief,the first three chapters are the basis and background of our studies,which offer us useful and reliable quantum methods.Based upon the mentioned work,a systemic investigation has been carried out in chapter four.Nine stable double-hydrogen bonded cyclic complexes have been obtained at B3-LYP/6-311++G(d,p)basis level.And we found,for the complexes,those which have the N atom of formamide as their hydrogen donors are more stable the others with C atom hydrogen donor of formamide.In chapter 5,we increase the number of formamide molecules on the basis of work of chapter four to eventually form a locked chain around adenine.The structures of hydrogen-bonded complexes A-F_n(n=2-7)of adenine with polyformamide molecules have been fully optimized at B3LYP/6-31G(d)basis set level.A displacement of formamide molecules to one side of adenine mean plane happened with an increasing number of formamide molecules for the hydrophobic character of the C-H bonds and the cooperativity of H bonds. The most interesting geometrical change of adenine upon the co:mplex is the shortening of the bond C4-N6 resulting from the strengthening of the conjugation between theπsystem of the adenine ring and the lone pair of the nitrogen atom.An existence of weak N-H…πbonding interaction between theπsystem of adenine with N-H bond of F7 is found and further conformed by an NBO analysis specially carried out on A - F₇.The last part sets off with the probation of how the electronic properties of nucleic acid bases change and,sequentially,what effects these chances will make on the mutation of DNA. The geometric and energetic chances of adenine monomer and adenine-formamide complexes have been investigated using B3LYP methold,and ionization potentials(IP)and electron affinities(EA)of the system have also been calculated.Both the detachment and attachment of one electron have an impact on the structures of the complexes.The former merely has influence on the intermolecular geometries while the later on both the intermolecular and intramolecular geometries.As far as energies is concerned,the system become unstable during the process of electron detachment as well as electron attachment,and the cations is more unstable than the anions.Furthermore,we found the H-bonding interactions interactions between adenine and formamide would facilitate adiabatical electron detachment and attachment but have different effects on vertical electron detachment and attachment.As is mentioned above,we concluded that the impact on the properties of bases made by the H-bonding interactions should not to be ignored,which will make a further influence upon the functions on DNA in living organisms.We hope the present work would provide other investigators in the same field with valuable references.