Nucleic acid bases , pyrimidine ring flexibility

Conformational Flexibility of Pyrimidine Ring in Nucleic Acid Bases... 

An analysis of character and frequencies of normal vibrations and scan of relaxed potential energy surface represents two complementary approaches to investigation of conformational flexibility of pyrimidine rings in nucleic acid bases. A combined application of these approaches allows estimating population of conformations with nonplanar rings for each molecule. 

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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