The role of the reaction force to characterize local specific interactions that activate the intramolecular proton transfers in DNA basis

Abstract

MP2/6-311G** and B3LYP/6-311G** studies of the intramolecular proton transfer in adenine, cytosine, guanine, and thymine has been performed, with the aim of evaluating the role of the reaction force as a global descriptor of the process. It turns out that the reaction force profile is quite an interesting tool to characterize reaction mechanisms. Indeed, in adenine and cytosine the proton transfer is assisted by an increasing electronic delocalization in the adjacent ring, whereas in guanine and thymine the attractive electrostatic interaction with the acceptor oxygen atom is strong enough to promote the transfer.

A noteworthy feature of bond dissociation/formation reactions

“…The dissociation of a bond XY is divided by the minimum of F ( R c ) into two phases, as seen in Figure 2(b). These can be interpreted in terms of what was observed earlier 1–7 for processes having V ( R c ) and F ( R c ) profiles such as those in Figure 1. The first phase, as the bond is being stretched from R c = R e to R c = α, is characterized by a growing (negative) restoring force.…”

“…The reaction force F ( R c ) that is associated with any chemical or physical process A → B can provide considerable insight into its mechanism. This has been demonstrated for a series of chemical reactions and conformational transformations 1–7, all of them characterized by energy barriers in both the forward and reverse directions. We shall now address the dissociation or formation of an individual bond, having a barrier in only one direction.…”

“…The general picture that we have presented is based upon our analyses of variations in structural and electronic properties along the intrinsic reaction coordinates of a number of different processes 1–7. Structural changes take place in all three phases—preparative, transition to products, and relaxation.…”

“…However, the electronic properties that are affected by the process tend to show a strikingly different pattern: they change rather slowly and gradually during the preparative and relaxation portions, but very rapidly and extensively in the intervening transition phase between R c = α and R c = γ. This consistent pattern, a pronounced variation largely localized between the minimum and the maximum of F ( R c ), has been observed for the electrostatic potentials, local ionization energies, atomic charges, Fukui functions, etc., of the atoms involved in the process 1–7.…”

The mechanism of double proton transfer in dimers of uracil and 2‐thiouracil—The reaction force perspective

“…The existence of these molecules in many tautomeric forms has been revealed to be crucial to explain the mutation occurring during DNA duplication. 6 These tautomeric structures can be obtained through intramolecular hydrogen transfer in the monomeric structure [6][7][8] or by intermolecular hydrogen transfer in the dimer system formation. 9 Recently it has been shown that the intramolecular tautomerization of the monomeric structures of 2,4-diketo and 2-thio,4-keto uracil present quite high energy barriers of about 40 kcal/mol, so we explore in this article the way to obtain the enol or thiol tautomers from the intermolecular proton transfer reactions of dimeric structures of uracil and 2-thiouracil.…”