CH ⃛ O hydrogen bonding in solutions of methylated nucleic acid base analogs as revealed by nmr

Abstract

Formation and thermodynamic characteristics of C-H ... O hydrogen bonding of methylated uracils and caffeine have been studied by nmr along two lines. 1. The concentration and temperature dependencies of the PMR spectra of 1,3-dimethyluracil (m2 1,3Ura), 1,3-dimethylthymine (m2 1,3Thy), and 1,3,6-trimethyluracil (m3 1,3,6Ura) in chloroform at high concentrations of base analogs indicated the self-association of m2 1,3Ura and m2 1,3Thy via C(6)H ... O hydrogen bonding and the competitive formation of C-H ... O bonds between carbonyl oxygens and chloroform. The intermolecular interaction energy and the arrangement of molecules in the local minima of various m2 1,3Ura dimers were calculated by the method of atom-atom potentials. The deepest minimum for the m2 1,3Ura coplanar dimer corresponds to a C(6)-H ... O hydrogen-bond formation. 2. At low concentration of m2 1,3Ura and caffeine in CCl4, C(6)-H ... O bonding for m2 1,3Ura and C(8)-H ... O bonding for caffeine with oxygens of dimethyl sulfoxide (DMSO) and acetone were observed. The association constants of these complexes were obtained at different temperatures. The enthalpies delta H, of the m2 1,3Ura-DMSO, m2 1,3Ura-accetone, caffeine-DMSO, and caffeine-acetone complexes were -2 +/- 0.1 kcal/mol. The calculations showed that the deepest minimum of the caffeine-acetone coplanar complex corresponds to C(8)-H ... O bonding with energy of -3.5 kcal/mol and that of the m2 1,3Ura-acetone complexes corresponds to C(6)-H ... O bonding with energy of -3.4 kcal/mol. The approximate correction for the solvent effect provides good agreement of the experimental data with the calculations.

The Role of C–H···O Interactions in the Solid and Liquid‐Phase Structures of Methyltrioxo Rhenium

“…without negative eigenvalues from the frequency calculations – was found to be the most stable configuration among the several MTO dimers tested, and presents three C–H ··· O hydrogen bond contacts. The dimerisation energy is –21.8 kJ · mol –1 (without corrections) and –15.9 kJ · mol –1 (after CP and ZPVE corrections), falling in the expected range for this type of interaction 7–14. These values show that a C–H ··· O bonded dimer is clearly more stable than the previously reported dimers based on oxygen bridges 6.…”

Identification of specific contacts in T3 RNA polymerase-promoter interactions: Kinetic analysis using small synthetic promoters

“…It is intriguing to propose that the 4-amino group of cytosine at position -11 may be a normal recognition contact but that, in a UA pair (replacing the cytosine amino group by a carbonyl), the 5-hydrogen of uracil might serve as an alternate contact. Although weak hydrogen bond donation of the 5-hydrogen is theoretically possible, model studies of nucleic acid base analogs have been unable to observe such interactions (Bruskov et al, 1989).…”

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

“…In structures with Watson-Crick and Hoogsteen type hydrogen bonded TATA tetrads (Fig. 6 a-e) the methyl hydrogens of thymines remain close (-3.0 A) to N7 or Ni of adenine, thus giving rise to the additional possibility of C-H-N hydrogen bond formation, similar to C-H-O hydrogen bonds (Taylor and Kennard, 1982;Bruskov et al, 1989;Zhurkin et al, 1994). In all the structures shown in Fig.…”