Topological analysis potential energy surfaces

Figures 1.12 and 1.13 readily explain, without quantitative calculation, some key features of the photodissociation of H2O through excitation in the A and in the B absorption bands. Multi-dimensional potential energy surfaces are the cornerstones for a trustworthy analysis of molecular dynamics. Knowing the general topology of the PES often suffices for a qualitative explanation of the main experimental observations. However, in order to perform realistic calculations we need potential energy surfaces which are as accurate and complete as possible.

Before analysis of the interactions of the nucleic acid bases with the clay minerals in the presence of water and cation one needs to understand the individual interactions of NAs with isolated water and with a cation. Such theoretical study was performed for 1 -methylcytosine (MeC) [139]. The study revealed influence of water and cation in the proton transfer for this compound. This leads to the formation of imino-oxo (MeC ) tautomer. Topology of the proton transfer potential surface and thermodynamics of stepwise hydration of MeCNa+ and MeC Na+ complexes is further discussed. The one dimensional potential energy profile for this process followed by the proton transfer with the formation of hydrated MeC Na+ is presented in Fig. 21.2. One-dimensional potential energy profile for amino-imino proton transfer in monohydrated N1-methylcytosine (this represents the situation when tautomerization is promoted by a single water molecule without the influence of Na+ cation) and for the case of pure intramolecular proton transfer (tautomerization is not assisted by any internal interactions) is also included. The most important features of this profile do not depend on the presence or absence of Na+ cation. All the potential energy curves have local minima corresponding to MeC and MeC. However, the significant difference is observed in the relative position of local minima and transition state, which results in a different thermodynamic and kinetic behavior for all presented cases (see Fig. 21.2). 

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