Hydrogen bonding in polymer mixtures

The enthalpy–infrared frequency shift correlation for simple acids and bases is extended to study hydrogen bonding in polymer systems. The acidity of a polymer is calibrated by comparing the shifts in hydroxyl absorption frequency of the acidic polymer when mixed with a series of bases with the corresponding spectral shifts of known acids with the same bases. The basicity of a polymer is calibrated by measuring the hydroxyl frequency shifts of known acids when mixed with the basic polymer. For polymers containing carbonyl groups, the shift in carbonyl absorption is also a measure of basicity. The acidity and basicity constants obtained for polymers are in good agreement with the values for small-molecule analogs. The enthalpies of hydrogen bond formation in polymer mixtures are calculated from the acidity or basicity constants.     

Hydrogen bonding and anaesthesia

General anaesthetics act by perturbing intermolecular associations without breaking or forming covalent bonds. These associations might be due to a variety of van der Waals interactions or hydrogen bonding. Neurotransmitters all contain OH or NH groups, which are prone to form hydrogen bonds with those of the neurotransmitter receptors. These could be perturbed by anaesthetics.

Aromatic rings in amino acids can act as weak hydrogen bond acceptors. On the other hand the acidic hydrogen in halothane type anaesthetics are weak proton donors. These two facts together lead to a probable mechanism of action for all general anaesthetics.     

Hydrogen bond-assisted macrocyclic oligocholate transporters in lipid membranes

Three macrocyclic oligocholates containing a carboxyl group, a guanidinium ion, and a Cbz-protected amine, respectively, were studied as membrane transporters for hydrophilic molecules. To permeate glucose across lipid bilayers, the macrocycles stacked over one another to form a transmembrane nanopore, driven by a strong tendency of the water molecules in the internal cavities of the amphiphilic macrocycles to aggregate in a nonpolar environment. To transport larger guests such as carboxyfluorescein (CF), the macrocycles acted as carriers to shuttle the guest across the membrane. Hydrogen-bonds between the side chains of the macrocycles strongly affected the transport properties. Surprisingly, the carboxyl group turned out to be far more effective at assisting the aggregation of the oligocholate macrocycles in the membrane than the much stronger carboxylate-guanidinium salt bridge, likely due to competition from the phosphate groups of the lipids for the guanidinium.     

Hydrogen bonding in ethanol under shear

We study the dependence of viscosity of ethanol on shear rate using constant volume and constant pressure nonequilibrium molecular dynamics simulations, with the emphasis of the interrelationship between breaking, stability, and alignment of hydrogen bonds and shear thinning at high shear rates. We find that although the majority of hydrogen bond breakings occur at low shear rates, we do not observe shear thinning until there is some shear-induced alignment of the hydrogen bonds with the direction of shear.     

Hydrogen bonding in acetylene containing dichlorodiazaalkadienes

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Hydrogen bonding in vitamin B6

Double-well potential energy surfaces for hydrogen bonding in crystalline vitamin B₆ have been associated with molecular environmental effects. New calculations, involving improved representations of a fragmentation model, include the introduction of a second pyridoxinium chloride system within the model in a “dimer-like” configuration. The new results confirm the double-well potential and the prediction of the experimentally observed position for the proton as being due essentially to environmental effects. Atomic difference maps are presented for the charge density distributions, which reflect the nature of the bonding as it depends on the proton position. Mulliken populations are examined particularly in relation to the “intermolecular” transfer of electrons.     

Anion binding versus intramolecular hydrogen bonding in neutral macrocyclic amides

Although amide groups are important hydrogen-bond donors in natural and synthetic anion receptors, studies on structure-affinity relationships of amide-based macrocyclic receptors are still very limited. Therefore, we synthesized a series of macrocyclic tetraamides 5-8 derived from 1,3-benzenedicarboxylic (isophthalic) acid and aliphatic alpha,omega-diamines of different lengths. (1)H NMR titrations in DMSO solution show that the anion affinity of these receptors decreases with increasing size of the macrocycle irrespective of the anion, and this suggests a minor role of geometric complementarity. Comparison with their previously studied pyridine congeners reveals that the isophthalic acid based macrocycles are less potent, in contrast to what was found for simple model diamides. Combined theoretical and experimental structural studies were carried out to determine the reasons behind this behaviour. The results show that the unexpectedly low anion binding ability of the isophthalic acid-based receptors is due to the self-complementary nature of the isophthalic bis-amide fragments: when two such moieties are present within a sufficiently flexible macrocycle, they adopt syn-anti conformations and bind each other by two strong intramolecular hydrogen bonds that close the macrocyclic cavity. Nevertheless, anion binding is able to break these hydrogen bonds and switch a macrocycle into a convergent all-syn conformation. Despite the ill-preorganized conformation, 20-membered receptor 6 is better than either its open-chain analogue (macrocyclic effect) and/or its isomer having differently placed carbonyl groups. The crystal structures of four anion complexes of the macrocyclic receptors are reported. X-ray studies and solution NMR data confirmed the inclusive nature of the complexes and pointed to strong involvement of aromatic CH hydrogen atoms in anion binding.     

Hydrogen bonding to divalent sulfur

A combination of vapor phase infrared spectroscopy and ab initio calculations has been used to show that sulfur is weaker than, but nearly equivalent to, oxygen as a hydrogen bond acceptor. Enthalpies of hydrogen bond formation were obtained for the hydrogen bonded complexes formed between methanol and either dimethyl sulfide or dimethyl ether by temperature dependence studies of the infrared spectra.     

Hydrogen bonding incis-2,3-epoxycyclooctanol

Hydrogen bonding and the electron-withdrawing or electron-donating characteristics of substituent groups that are neighboring to epoxide groups can affect the reactivity of the epoxide ring. The crystal structure ofcis-2,3-epoxycyclooctanol has been determined as a saturated eight-membered ring compound in which a hydroxyl group is attached to the C(1) atom that is adjacent to a 2,3-fused epoxy ring. The findings are that the longer epoxide C-O bond (and hence the one expected to be more readily broken) is the one farther from the hydroxyl group [1.462(1) å versus 1.447(1) å] and that the optimal hydrogen bonding is to an adjacent molecule radier than within the molecule. The shortest C-C bond is that of the epoxide group; the bond adjacent to it (on the side farther from the hydroxyl group) is the next shortest.     

A computer-designed macrocyclic zinc receptor

A macrocycle containing a pair of bipyridine moieties with a linker designed using the computer program CAVEAT exhibits unique selectivity in the binding of zinc ion relative to other metals.     

Hydrogen bonding in transition metal carbonyl complexes

Conclusions The formation of a previously unknown type of hydrogen bonding OH...OC-M involving the oxygen atom of the CO group at the metal atom was observed upon the interaction of CpMn(CO)₂-P(i-Pr)₃ with (CF₃)₃COH in liquid xenon solution at low temperatures.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2605–2608, November, 1986.     

Hydrogen bonding in substituted formic acid dimers

The hydrogen-bonded dimers of formic acid derivatives XCOOH (X = H, F, Cl, and CH3) have been investigated using density functional theory (B3LYP) and second-order M?ller-Plesset perturbation (MP2) methods, with the geometry optimization carried out using 6-311++G(2d,2p) basis set. The dimerization energies calculated using aug-cc-pVXZ (with X = D and T) basis have been extrapolated to infinite basis set limit using the standard methodology. The results indicate that the fluorine-substituted formic acid dimer is the most stable one in comparison to the others. Topological analysis carried out using Bader's atoms in molecules (AIM) theory shows good correlation of the values of electron density and its Laplacian at the bond critical points (BCP) with the hydrogen bond length in the dimers. Natural bond orbital (NBO) analysis carried out to study the charge transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes reveals that most of the dimers are associated with conventional H-bonding except a few, where improper blue-shifting hydrogen bonds are found to be present.     

Hydrogen bonding pathways in human dihydroorotate dehydrogenase

Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.