The nature and energy characteristics of intramolecular hydrogen bonds in crystals

Intermolecular head-to-head interaction of carbonyl groups in bicyclic hydrogen-bonded synthon based on β-hydroxy ketones

In this study, we report a counterintuitive carbonyl–carbonyl interaction explored for crystalline (2RS,3RS)-1-aryl-2-bromo-3-hydroxy-3-(2-nitrophenyl)-propan-1-ones.

Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines

Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in ¹⁵N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.

Resonance-assisted stabilisation of hydrogen bonds probed by NMR spectroscopy and path integral molecular dynamics

Path integral molecular dynamics and experimental NMR data are used to investigate resonance-assisted hydrogen bonds (RAHBs). When nuclear delocalisation is included in chemical shift calculations, the agreement with experiment is excellent, while static calculations show very poor performance. The results support the concept of RAHB, which has recently been questioned.

Tuning of the double-well potential of short strong hydrogen bonds by ionic interactions in alkali metal hydrodicarboxylates

The influence of the cation nature on the peculiarities of short strong H-bonds within hydrocarboxylate crystals is revealed.

Separation of planar rotamers through intramolecular hydrogen bonding in polysubstituted 5-nitrosopyrimidines

Unique isolation of pairs of planar rotamers, planamers, as chemical species differing only in nitroso group orientation, separable through the presence of a single intramolecular hydrogen bond, is reported.

Hydrogen-bridged chelate ring-assisted π-stacking interactions

A salicylideneaniline (SA) derivative, (6Z)-6-({[2-(hydroxymethyl)phenyl]amino}methylidene)-3,5-dimethoxycyclohexa-2,4-dien-1-one monohydrate, has an increased aromaticity within its hydrogen-bridged chelate ring owing to its NH character. In the reported crystal structure, nonconventional π-stacking interactions, which are referred to as hybrid π-stacking interactions, are observed between a quasiaromatic chelate ring, formed as a result of the resonance-assisted intramolecular hydrogen bond and ordinary aromatic rings. Besides, π-stacking interactions are also seen between two hydrogen-bridged quasiaromatic chelate rings, which are referred to as pure π-stacking interactions. A CSD search has revealed that both kinds of interactions are frequently observed in molecular crystals of SA derivatives in fully or partially NH tautomeric form, and aromaticity levels of certain fragments of SA derivatives have dramatic effects on their stacking arrangements. These interactions are distinguished from the usual π...π interactions by their formation character, i.e. both σ- and π-deficient and σ-deficient character of pure interactions is more pronounced than that of the hybrid ones.

Geometry and spectral properties of the protonated homodimer of pyridine in the liquid and solid states. A combined NMR, X-ray diffraction and inelastic neutron scattering study

The structure and spectral signatures of the protonated homodimer of pyridine in its complex with a poorly coordinating anion have been studied in solution in CDF(3)/CDClF(2) down to 120 K and in a single crystal. In both phases, the hydrogen bond is asymmetric. In the solution, the proton is involved in a fast reversible transfer that determines the multiplicity of NMR signals and the sign of the primary H/D isotope effect of --0.95 ppm. The proton resonates at 21.73 ppm that is above any value reported in the past and is indicative of a very short hydrogen bond. By combining X-ray diffraction analysis with model computations, the position of the proton in the crystal has been defined as d(N-H) = 1.123 Å and d(H···N) = 1.532 Å. The same distances have been estimated using a (15)N NMR correlation. The frequency of the protonic out-of-plane bending mode is 822 cm(-1) in agreement with Novak's correlation.

Effect of a pH change on the conformational stability of the modified nucleotide queuosine monophosphate

The naturally occurring modified nucleotide queuosine 5'-monophosphate (QMP) related to biochemical regulatory pathways in the cell was investigated using quantum chemical approaches. The relative stability of biologically relevant conformations of QMP in solvent under a pH change was predicted at the BVP86/TZVP and MP2/TZVP levels of theory. Hydrogen bonding in QMP was studied using Bader's approach. The acidity constants of QMP were estimated using the COSMO-RS theory. It has been found that the neutral and anionic forms of QMP are the most stable in the physiological pH range. These forms correspond to the anti/north conformation and exist as zwitterionic tautomers having a negatively charged phosphate group (-1 for neutral and -2 for anionic) and a positively charged secondary amine group in the side chain. It was also found that QMP possesses the syn conformation in the cationic state at pH < 5.0 and undergoes syn to anti conformation transition when the pH increases, remaining in the anti conformation at the higher pH values. The marker IR bands specific for the anionic and neutral QMP forms in the 2300-2700 cm(-1) region were assigned to H-bonded NH groups of the QMP side chain. The bands between 800 and 1300 cm(-1) of the "fingerprint" (400-1500 cm(-1)) region were assigned to the vibrations of the ribose ring, the phosphate group and the side chain of QMP. The predicted IR spectra can be useful for the assignment of vibration bands in the experiential spectra of QMP or identification of the QMP forms. The revealed peculiarities of the QMP conformation sensitivity to a pH change as well as additional formed H-bonds could be responsible for specific nucleotide interactions with enzymes.

Non-resonance-assisted hydrogen bonding in hydroxymethylene and aminomethylene cyclobutanones and cyclobutenones and their nitrogen counterparts

The characteristics of intramolecular hydrogen bonds (IMHB) have been systematically analyzed for a series of 32 different enols of derivatives of cyclobutane, cyclobutene, and cyclobutadiene bearing oxygen and nitrogen functionalities, at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. In those cases where two tautomers (interconnected by a hydrogen shift through the IMHB) exist, tautomer a, in which the HB-donor group (YH) is attached to the four-membered ring, is less stable than tautomer b, in which is the HB-acceptor (X) is the one attached to the four-membered ring. As expected the OH group behaves as a better HB-donor than the NH(2) group and the C==NH group as a better HB-acceptor than the C==O group, although the first effect clearly dominates. Accordingly, the expected IMHB strength follows the [donor, acceptor] trend: [OH,C==NH]>[OH,C==O]>[NH(2),C==NH]>[NH(2),C==O]. Quite unexpectedly, in all those compounds in which the functionality exhibiting the IMHB is unsaturated, the IMHB is weaker than in their saturated counterparts, verifying that the primary effect on the strength of the IMHB is the structure of the sigma-skeleton of the system. In the conjugated systems investigated here, the severe constraints imposed by the four-membered ring force the HB donor and acceptor to be far apart and the IMHB is rather weak. These geometrical constraints are less severe for the saturated analogues and the IMHB becomes stronger, confirming that the characteristics of the sigma-skeleton, and not the resonance-assisted hydrogen bond (RAHB) phenomenon, are the primary contributors to the strength of the IMHB in conjugated compounds.

Resonance-assisted hydrogen bonds: a critical examination. Structure and stability of the enols of beta-diketones and beta-enaminones

The characteristics of the intramolecular hydrogen bond (IMHB) for a series of 40 different enols of beta-diketones and their nitrogen counterparts have been systematically analyzed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. In some cases, two tautomers may exist which are interconnected by a hydrogen shift through the IMHB. In tautomer a the HB donor group (YH) is attached to the six-membered ring, while in tautomer b the HB acceptor (X) is the one that is attached to the six-membered ring. We found that changing an O to a N favors the a tautomer when the atom is endo and the contrary when it is exo, while the presence of a double bond favors the a tautomers. As expected, the OH group behaves as a better HB donor than the NH2 group and the C=NH group as a better HB acceptor than the C=O group, although the first effect clearly dominates. Accordingly, the expected IMHB strength follows the [donor, acceptor] trend: [OH, C=NH] > [OH, C=O] > [NH2, C=NH] > [NH2, C=O]. For all those compounds in which the functionality exhibiting the IMHB is unsaturated (I-type), the IMHB is much stronger than in their saturated counterparts (II-type). However, when the systems of the II-type subset, which are saturated, are constrained to have the HB donor and the HB acceptor lying in the same plane and at the same distance as in the corresponding unsaturated analogue, the IMHB is of similar or even larger strength. Hence, we conclude that, at least for this series of unsaturated compounds, the resonance-assisted hydrogen bond effect is not the primary reason behind the strength of their IMHBs, which is simply a consequence of the structure of the sigma-skeleton of the system that keeps the HB donor and the HB acceptor coplanar and closer to each other.