Indication of water droplet formation in hydrated clusters of cytosine and adenine: An electronic structure study using B3LYP, LMP2 and PM6

Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study

“…Such effect is possible only in isolated complexes of nucleobases with only several water molecules. In the case of water solutions or polyhydrated complexes, water molecules are strongly bonded to bulk water than to a base molecule [17,18]. Therefore, they are virtually not involved in ring out-of-plane vibrations of pyrimidine rings.…”

“…Investigations of hydrated complexes of nucleobases indicated that geometries of these molecules are sensitive enough to polarizing influence of neighboring fragments [11][12][13][14][15] as it was predicted by Cramer and Truhlar [16]. Some deformation of geometry of bases was observed in small hydrated clusters [17,18]. The ability of bases to change their geometries under influence of water environment was demonstrated most clearly in the case of formation of closed chains of water molecules around nucleobases.…”

PM6 quantum chemical study of the H-bonded and stacked associates of the adenine and thymine DNA bases: The nature of base stacking

“…In contrast, the base-stacking reaction in water is work. For example, we recently found that, although PM6 predicted the correct relative stability of different hydrated clusters of adenine and thymine, there were notable differences in the water network arrangement in the PM6-and B3LYP-optimised structures [24]. Quantum chemical methods that explicitly take into account electron correlation are expected to more accurately describe the dispersion energy, which plays a major role in the base-base interactions in the stacked structures.…”

“…We used the PM6 method recently to investigate hydrated complexes of thymine and adenine [24]. In contrast to the previous MC simulations, the base geometries can be fully optimised in the PM6 calculations, thereby allowing more realistic estimates of the baseassociate geometry.…”

Calculating interaction energies in transition metal complexes with local electron correlation methods

“…11 Demonstrations of the power of this approach are increasingly common, with applications in many areas of chemistry. [12][13][14][15][16][17][18][19][20][21] Recently, DF-LMP2 has been shown to produce excellent results for weak, noncovalent interactions such as hydrogen bonding and stacking interactions at a fraction of the cost of conventional methods. [20][21][22] Coupled with spin-component scaling ͑SCS͒, 23 this method compares well with benchmark coupled-cluster data.…”