We have carried out a systematic study of hydrogen-bonded cyclic A,C,T,and mixed GCGC tetrads resembliing conformations occurring in experimental tetraplex structures,using the B3LYP hybrid density functional (DFT)method and the MMFF and AMBER force fields to determine tetrad structures and interaction energies.The results are compared to G and U tetrads analyzed previously,thereby presenting a comprehensive overview of all cyclic tetrads formed from one base type only,in addition to the GCGC data.The DFT calculations indicate that the C tetrad is planar and the GCGC tetrad is nearly planar and correspond to local minima at C_(4h) and C_i symmetry,respectively.For A tetrads with N6-H6…N7 and with N6-H6…N1 H-bonds and for T tetrads,nonplanar structures are more stable than the planar ones,and among the nonplanar structures S_4-symmetric conformations are more stable than C_4 structures.Minima confirmed by frequency calculations are found for the planar C tetrad,the C_i-symmetric GCGC tetrad,the C_4-symmetric structure of the A tetrad with N6-H6…N7 H-bonds,and the S_4-symmetric T tetrad,in addition to the already known local minima of the S_4-symmetric structure of the G tetrad and the planar U tetrad with C-H…O hydrogen bonds.The interaction energies (triangle open E~T) corrected for deformation of the bases in the tetrads range from -69.47kcal/mol for the GCGC tetrad with three pairs of strong Watson-Crick type hydrogen bonds to -11.09kcal/mol in the planar A tetrad having only a single N6-H62…N1 interbase hydrogen bond.With more than 18%,the largest cooperativity contribution to traingle open E is found for the C and G tetrads.The interaction energies,derived from the MMFF and ABVER force field are similar to the DFT data for those tetrads haveing high interaction energies,whereas the relative deviations are much larger for weakly H-bonded tetrads.
展开▼
