Nucleic acid bases in anionic 2'-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities.

Protonation of nucleobases in anions of canonical 2'-deoxyribonucleotides has been investigated by the DFT computational study at the B3LYP/aug-cc-pvdz level of theory. It is demonstrated that the protonation leads to a significant decrease of conformational space of purine nucleotides while almost all conformers found for non-protonated molecules correspond to minima of the potential energy surface for protonated mdTMP and mdCMP. However, in all nucleotides, only one conformer is populated.

Dependence of deformability of geometries and characteristics of intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides on DNA conformations.

The molecular structure and deformability (with respect to average geometry) of methyl ethers of canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (mTMP), 2-deoxycytidine-5'-phosphate (mCMP), 2-deoxyadenosine-5'-phosphate (mAMP) and 2'-deoxyguanosine-5'-phosphate (mGMP) in different types of DNA have been calculated using B3LYP/cc-pvdz method. Comparison of energy at equilibrium conformations of nucleotides and conformations with torsion angles of backbone fixed to average values for different types of DNA reveals that incorporation of nucleotides to A-DNA macromolecules requires the minimum amount of deformation energy. Therefore, this type of DNA should be the least strained from viewpoint of intramolecular deformations of monomers.

1-(8-Bromo-2-methyl-4-thioxo-3,4,5,6-tetra-hydro-2H-2,6-methano-1,3-benzoxazocin-11-yl)ethanone.

In the title compound, C(14)H(14)BrNO(2)S, there are two similar non-equivalent mol-ecules in the asymmetric unit, displaying three chiral centres each. In the crystal structure, they are linked by inter-molecular N-H⋯O hydrogen bonds to form infinite chains, which are in turn connected by weak Br⋯H and S⋯H inter-actions.

Intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides: an atoms in molecules study.

The molecular structure and relative stability of different conformers of isolated canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (pdT), 2-deoxycytidine-5'-phosphate (pdC), 2-deoxyadenosine-5'-phosphate (pdA), and 2'-deoxyguanosine-5'-phosphate (pdG) were calculated using the B3LYP/6-31++G(d,p) level of theory. The results of the calculations reveal that, for all nucleotides except pdG, conformers with a syn orientation of the base do not correspond to a minimum on the potential energy surface. In the case of pdA and pdC, conformers with an orthogonal orientation of the nucleobase are located instead, north/syn conformers.