The effect of intramolecular hydrogen bond on the N-glycosidic bond strength in 3-methyl-2′-deoxyadenosine: a quantum chemical study

Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches

Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol^-1 . This value increases by ca. 1 kcal mol^-1 on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol^-1 depending on the structure of the β-diketone in question.

QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine

The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 10²-10⁴-fold faster rate than that of purine nucleoside substrates, such as inosine. Such a remarkable substrate specificity and the plausible hydrolytic mechanisms of uridine have been explored by using QM/MM and MM MD simulations. The present calculations show that the relatively stronger hydrogen-bond interactions between uridine and the active-site residues Gln227 and Tyr231 in CU-NH play an important role in enhancing the substrate binding and thus promoting the N-glycosidic bond cleavage, in comparison with inosine. The estimated energy barrier of 30 kcal/mol for the hydrolysis of inosine is much higher than 22 kcal/mol for uridine. Extensive MM MD simulations on the transportation of substrates to the active site of CU-NH indicate that the uridine binding is exothermic by ∼23 kcal/mol, more remarkable than inosine (∼12 kcal/mol). All of these arise from the noncovalent interactions between the substrate and the active site featured in CU-NH, which account for the substrate specificity. Quite differing from other nucleoside hydrolases, here the enzymatic N-glycosidic bond cleavage of uridine is less influenced by its protonation.

Estimating the energy of intramolecular hydrogen bonds from 1H NMR and QTAIM calculations

The values of the downfield chemical shift of the bridge hydrogen atom were estimated for a series of compounds containing an intramolecular hydrogen bond O-HO, O-HN, O-HHal, N-HO, N-HN, C-HO, C-HN and C-HHal. Based on these values, the empirical estimation of the hydrogen bond energy was obtained by using known relationships. For the compounds containing an intramolecular hydrogen bond, the DFT B3LYP/6-311++G(d,p) method was used both for geometry optimization and for QTAIM calculations of the topological parameters (electron density ρ^BCP and the density of potential energy V in the critical point of the hydrogen bond). The calculated geometric and topological parameters of hydrogen bonds were also used to evaluate the energy of the hydrogen bond based on the equations from the literature. Comparison of calibrating energies from the ¹H NMR data with the energies predicted by calculations showed that the most reliable are the linear dependence on the topological ρ^BCP and V parameters. However, the correct prediction of the hydrogen bond energy is determined by proper fitting of the linear regression coefficients. To obtain them, new linear relationships were found between the calculated ρ^BCP and V parameters and the hydrogen bond energies obtained from empirical ¹H NMR data. These relationships allow the comparison of the energies of different types of hydrogen bonds for various molecules and biological ensembles.

Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2'-Hydroxy Group and Acid-Base Catalysis

Despite the inherent stability of glycosidic linkages in nucleic acids that connect the nucleobases to sugar-phosphate backbones, cleavage of these bonds is often essential for organism survival. The current study uses DFT (B3LYP) to provide a fundamental understanding of the hydrolytic deglycosylation of the natural RNA nucleosides (A, C, G, and U), offers a comparison to DNA hydrolysis, and examines the effects of acid, base, or simultaneous acid-base catalysis on RNA deglycosylation. By initially examining HCOO^-···H₂O mediated deglycosylation, the barriers for RNA hydrolysis were determined to be 30-38 kJ mol^-1 higher than the corresponding DNA barriers, indicating that the 2'-OH group stabilizes the glycosidic bond. Although the presence of HCOO^- as the base (i.e., to activate the water nucleophile) reduces the barrier for uncatalyzed RNA hydrolysis (i.e., unactivated H₂O nucleophile) by ∼15-20 kJ mol^-1, the extreme of base catalysis as modeled using a fully deprotonated water molecule (i.e., OH^- nucleophile) decreases the uncatalyzed barriers by up to 65 kJ mol^-1. Acid catalysis was subsequently examined by selectively protonating the hydrogen-bond acceptor sites of the RNA nucleobases, which results in an up to ∼80 kJ mol^-1 barrier reduction relative to the corresponding uncatalyzed pathway. Interestingly, the nucleobase proton acceptor sites that result in the greatest barrier reductions match sites typically targeted in enzyme-catalyzed reactions. Nevertheless, simultaneous acid and base catalysis is the most beneficial way to enhance the reactivity of the glycosidic bonds in RNA, with the individual effects of each catalytic approach being weakened, additive, or synergistic depending on the strength of the base (i.e., degree of water nucleophile activation), the nucleobase, and the hydrogen-bonding acceptor site on the nucleobase. Together, the current contribution provides a greater understanding of the reactivity of the glycosidic bond in natural RNA nucleosides, and has fundamental implications for the function of RNA-targeting enzymes.

Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability

N3 protonation induces base rotation and stabilizes the syn orientation of the adenine nucleobase of [dAdo+H]⁺ and [Ado+H]⁺via formation of a strong intramolecular N3H⁺⋯O5′ hydrogen-bonding interaction, which in turn influences the mechanisms and energetics for N-glycosidic bond cleavage.

Intramolecular OH⋅⋅⋅Fluorine Hydrogen Bonding in Saturated, Acyclic Fluorohydrins: The γ-Fluoropropanol Motif

Fluorination is commonly exercised in compound property optimization. However, the influence of fluorination on hydrogen-bond (HB) properties of adjacent functional groups, as well as the HB-accepting capacity of fluorine itself, is still not completely understood. Although the formation of OH⋅⋅⋅F intramolecular HBs (IMHBs) has been established for conformationally restricted fluorohydrins, such interaction in flexible compounds remained questionable. Herein is demonstrated for the first time-and in contrast to earlier reports-the occurrence of OH⋅⋅⋅F IMHBs in acyclic saturated γ-fluorohydrins, even for the parent 3-fluoropropan-1-ol. The relative stereochemistry is shown to have a crucial influence on the corresponding (h1) JOH⋅⋅⋅F values, as illustrated by syn- and anti-4-fluoropentan-2-ol (6.6 and 1.9 Hz). The magnitude of OH⋅⋅⋅F IMHBs and their strong dependence on the overall molecular conformational profile, fluorination motif, and alkyl substitution level, is rationalized by quantum chemical calculations. For a given alkyl chain, the "rule of shielding" applies to OH⋅⋅⋅F IMHB energies. Surprisingly, the predicted OH⋅⋅⋅F IMHB energies are only moderately weaker than these of the corresponding OH⋅⋅⋅OMe. These results provide new insights of the impact of fluorination of aliphatic alcohols, with attractive perspectives for rational drug design.