Flexibility and Vibrational Frequencies

Scheiner ° who considered various different basis sets. Not only is the energetic preference affected by correlation and basis set particulars, but also by orbital exponent and by the superposition error. 

The prior section discussed the general shape of the potential energy surfaces of H-bonded complexes, the possible occurrence of multiple minima, and transition states that connect them. It was pointed out that these surfaces tend to be rather flat. We focus in this section on smaller regions of the surface which lie in the vicinity of the equilibrium geometry. 

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As it is now very well known, accurate studies of the water-water interaction by means of ab-initio techniques require the use of larger and flexible basis sets and methods which consider correlation effects [85,94-96], Since high level ab-initio post-Hartree-Fock calculations are unfeasible because of their high computational cost for systems with many degrees of freedom, Density Functional Theory, more economical from the computational point of view, is being more and more considered as a viable alternative. Recently, we have presented [97] results of structural parameters and vibrational frequencies for the water clusters (H20) , n=2 to 8, using the DFT method with gradient corrected density functionals. 

Calculating partition functions for the activated complex, however, involves an estimation of its structure (to obtain 7, ly, I ) and vibrational frequencies. How this can be done approximately will be discussed in Section 3.2.3. These estimations are the weakest point of the theory and lead to the sometimes unfavorable reputation of TST as being so flexible that it can explain almost any k expression by making adjustments to the structural parameters assumed for the activated complex. 

The most complete picture of conformational flexibility of pyrimidine rings in nucleic acid bases has been provided by molecular dynamics study of isolated molecules using ab initio Carr-Parinello method [45]. According to these studies, the population of planar conformation of heterocycle does not exceed 20% for thymine, cytosine, and guanine and amounts to about 30% for adenine (Table 21.4). These values are considerably smaller as compared to estimations based on vibrational frequencies mentioned above. Such difference is quite natural because in the case of vibrational analysis, only the lowest ring out-of-plane normal mode is considered. However, there are also smaller contributions of the other ring out-of-plane vibrations not included in this analysis. Therefore, such estimation should be considered as an upper limit for assessment of population of planar conformation of ring. 

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