In order to elucidate roles of the 2'-O-methylation of pyrimidine nucleotide residues of tRNAs, conformations of 2'-O-methyluridylyl(3'----5')uridine (UmpU), 2'-O-methyluridine 3'-monophosphate (Ump), and 2'-O-methyluridine (Um) in 2H2O solution were analyzed by one- and two-dimensional proton NMR spectroscopy and compared with those of related nucleotides and nucleoside. As for UpU and UmpU, the 2'-O-methylation was found to stabilize the C3'-endo form of the 3'-nucleotidyl unit (Up-/Ump-moiety). This stabilization of the C3'-endo form is primarily due to an intraresidue effect, since the conformation of the 5'-nucleotidyl unit (-pU moiety) was only slightly affected by the 2'-O-methylation of the 3'-nucleotide unit. In fact even for Up and Ump, the 2'-O-methylation significantly stabilizes the C3'-endo form by 0.8 kcal/.mol-1. By contrast, for nucleosides (U and Um), the C3'-endo form is slightly stabilized by 0.1 kcal/.mol-1. Accordingly, the stabilization of the C3'-endo form by the 2'-O-methylation is primarily due to the steric repulsion among the 2-carbonyl group, the 2'-O-methyl group and the 3'-phosphate group in the C2'-endo form. For some tRNA species, 2-thiolation of pyrimidine residues is found in positions where the 2'-O-methylation is found for other tRNA species.(ABSTRACT TRUNCATED AT 250 WORDS)

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The air/liquid interface of 1-alkyl-3-methylimidazolium tetrafluoroborates with the general formula [C(n)mim]BF(4) (n = 4-11) was studied using infrared-visible sum frequency generation (SFG) vibrational spectroscopy. The probability of the gauche defect per CH2-CH2 bond in the alkyl chain decreases as the number of carbon atoms in the alkyl chain increases. This observation suggests that the interaction between the alkyl chains is enhanced as the alkyl chain length becomes longer. The frequencies of the C-H stretching vibrational modes observed in the SFG spectra are higher than those of the corresponding peak positions observed in the infrared spectra of the bulk liquids. This shift is consistent with a structure in which the alkyl chain protrudes from the bulk liquid into the air. A local structure, which originates from the intermolecular interaction between the ionic liquid molecules, is proposed to explain these observations.