Computational and experimental trans-Hbond deuterium isotope shifts suggest that Hbonding and electronic base-stacking interactions, although largely orthogonal, are coupled in B-form DNA duplexes. For an A:T base pair, the Hbond is shorter and stronger in the RAR:YTY than YAY:RTR context. This difference is due to the greater anharmonicity of the N3−H3 vibrational potential of the thymine in RAR:YTY, which arises from electronic interactions between A:T and adjacent bases. As predicted by the calculations, reduction of the base stacking propensity using ethanol abolishes the experimental sequence dependence of 2hΔ13C2.

Solvent-induced effects on nitrogen NMR shielding of 1,2,4,5-tetrazine and two isomeric tetrazoles are calculated using density functional theory combined with the polarizable continuum model and using the continuous set gauge transformation. Direct and indirect solvent effects on shielding are also calculated. It has been shown that the observed solvent-induced shielding variation is more strongly related to the intensity of the solvent reaction field rather than on the change of molecular geometry induced by the solvent.

Density functional theory calculations of isolated Watson-Crick A:U and A:T base pairs predict that adenine 13C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, (2h)Delta13C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that (2h)Delta13C2 is sensitive to hydrogen-bond strength. Calculated (2h)Delta13C2 values at a given N1-N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical (2h)Delta13C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on (2h)Delta13C2 values. Furthermore, (2h)Delta13C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that (2h)Delta13C2 is context dependent and that this dependence is similar for RNA and DNA.

Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the 15 N chemical shift of backbone amides of proteins, 1 D 15 N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for 1 D 15 N(D) including the backbone dihedral angles, U and W, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length. Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio. The N-H stretching anharmonicity contribution falls off with the cosine of the N-HÁÁÁO bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, 1 D 15 N(D) can provide insights into hydrogen bonding geometries.

Here, we show that 1JNH values are on average 0.4 Hz less negative for double-stranded RNA A:U than for DNA A:T base pairs, which, according to existing theory, suggests that RNA N1...N3 hydrogen bond distances are about 0.02 A shorter than those of DNA. Also, there is a statistically relevant trend between 1JNH and 2hDelta13C2 values, which supports the original hypothesis that 2hDelta13C2 values are also sensitive to hydrogen bond distances. Finally, a context dependence is observed for these values, which suggests that hydrogen-bonding and base-stacking interactions are coupled.

Malonic anhydrides decompose at or below room temperature, to form a ketene and carbon dioxide. Rate constants for the thermal decomposition of malonic, methylmalonic, and dimethylmalonic anhydrides were measured by NMR spectroscopy at various temperatures, and activation parameters were evaluated from the temperature dependence of the rate constants. Methylmalonic anhydride is the fastest, with the lowest ΔH(‡), and dimethylmalonic anhydride is the slowest. The nonlinear dependence on the number of methyl groups is discussed in terms of a concerted [2(s) + (2(s) + 2(s))] or [2(s) + 2(a)] cycloreversion that proceeds via a twisted transition-state structure, supported by computations.

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Hydrogen-bond lengths of nucleic acids are (1) longer in DNA than in RNA, and (2) sequence dependent. The physicochemical basis for these variations in hydrogen-bond lengths is unknown, however. Here, the notion that hydration plays a significant role in nucleic acid hydrogen-bond lengths is tested. Watson-Crick N1...N3 hydrogen-bond lengths of several DNA and RNA duplexes are gauged using imino 1J(NH) measurements, and ethanol is used as a cosolvent to lower water activity. We find that 1J(NH) values of DNA and RNA become less negative with added ethanol, which suggests that mild dehydration reduces hydrogen-bond lengths even as the overall thermal stabilities of these duplexes decrease. The 1J(NH) of DNA are increased in 8 mol% ethanol to those of RNA in water, which suggests that the greater hydration of DNA plays a significant role in its longer hydrogen bonds. The data also suggest that ethanol-induced dehydration is greater for the more hydrated G:C base pairs and thereby results in greater hydrogen-bond shortening than for the less hydrated A:T/U base pairs of DNA and RNA.