Low-frequency parameterization of hydrogen bonding

We review the model of the hydrogen bond developed by Lippincott and Schroeder and discuss the frequency range in which it is valid, specifically in the optical and near infrared range. We then show why and how to modify the Lippincott and Schroeder formulate to apply to the far infrared and lower ranges. The contrasts between the old and modified systems, particularly with respect to the effective force constants are worked out and plotted for an example.     

Intramolecular hydrogen bonding in cardiolipin

Fourier transform infrared (FT-IR) spectroscopy was used to determine whether intramolecular hydrogen bonding between the C-OH and P-OH groups exists in beef heart cardiolipin (CL) or in hydrogenated beef heart cardiolipin (18:0-CL) as compared to the synthetic 2'-deoxy analogue of cardiolipin (16:0-dCL). Such intramolecular hydrogen bonding would provide a structural basis for proton conduction on the molecular level. In aqueous dispersions at 20 degrees C, both 18:0-CL and 16:0-dCL exist in the gel phase as bilayers with gel to liquid-crystalline transitions (Tm) at 61 and 56 degrees C, respectively, whereas the unsaturated CL exists in the non-bilayer (hexagonal II) state. Evidence for intramolecular hydrogen bonding of the C-OH group in aqueous dispersions of 18:0-CL is provided by the large increase in Tm observed on changing the aqueous medium from H2O to D2O but specific hydrogen-bonded C-OH...PO2- species cannot be identified because water molecules also compete for the PO2- binding sites. However, C-OH...PO2- hydrogen bonds can be identified in dry films of the sodium salt of 18:0-CL or in CCl4 solution. In contrast, such hydrogen bonds cannot be formed in the deoxy analogue (16:0-dCL) indicating that the central C-OH group in 18:0-CL could provide a structural basis for proton conduction, involving the phosphate groups.     

Characterisation of hydrogen bonding networks in RNAs via magic angle spinning solid state NMR spectroscopy

It is demonstrated that the spatial proximity of ¹H nuclei in hydrogen bonded base-pairs in RNAs can be conveniently mapped via magic angle spinning solid state NMR experiments involving proton spin diffusion driven chemical shift correlation of low gamma nuclei such as the imino and amino nitrogens of nucleic acid bases. As different canonical and non-canonical base-pairing schemes encountered in nucleic acids are characterised by topologically different networks of proton dipolar couplings, different base-pairing schemes lead to characteristic cross-peak intensity patterns in such correlation spectra. The method was employed in a study of a 100 kDa RNA composed of 97 CUG repeats, or (CUG)₉₇ that has been implicated in the neuromuscular disease myotonic dystrophy. ¹⁵N–¹⁵N chemical shift correlation studies confirm the presence of Watson–Crick GC base pairs in (CUG)₉₇.     

Cooperative hydrogen bonding in amyloid formation

Amyloid diseases, including Alzheimer's and prion diseases, are each associated with unbranched protein fibrils. Each fibril is made of a particular protein, yet they share common properties. One such property is nucleation-dependent fibril growth. Monomers of amyloid-forming proteins can remain in dissolved form for long periods, before rapidly assembly into fibrils. The lag before growth has been attributed to slow kinetics of formation of a nucleus, on which other molecules can deposit to form the fibril. We have explored the energetics of fibril formation, based on the known molecular structure of a fibril-forming peptide from the yeast prion, Sup35, using both classical and quantum (density functional theory) methods. We find that the energetics of fibril formation for the first three layers are cooperative using both methods. This cooperativity is consistent with the observation that formation of amyloid fibrils involves slow nucleation and faster growth.     

Cooperative aspects of hydrogen bonding in carbohydrates

Various compounds related to the antibacterial, sulfanilamide drugs have been prepared from dehydro-l-ascorbic acid or its d-erythro analog by reaction with hydrazines related to sulfanilamide, sulfadiazine, sulfamerazine, sulfamethazine, and sulfamethoxydiazine, whereby the 2-mono- and 2,3-bis-(hydrazone) were isolated. After opening of the lactone ring in the bis(hydrazones) with alkali, nucleophilic attack, on the carbonyl group, of the imino nitrogen atom of the 3-hydrazone residue afforded 3-(l-threo-glycerol-1-yl)-1-phenyl- and -1-(p-sulfamylphenyl)-4,5-pyrazole-dione 4-(p-sulfamylphenlhydrazone) and the related 3-(d-erythro-glycerol-1-yl)compounds. Whereas acetylation of l-threo-2,3-hexodiulosono-1,4-lactone 2,3-bis(p-sulfamylphenylhydrazone) (9) and 3-(l-threo-glycerol-1-yl)-1-(p-sulfamylphenyl)-4,5-pyrazoledione 4-(p-sulfamylphenylhydrazone) (15) gave the O-acetyl derivatives, benzoylation of 15 gave the di-N-benzoy ltri-O-benzoyl compound. Reaction of 9 with cupric chloride gave 3,6-anhydro-3-(p-suIfamylphenylazo) -l-xylo-2-hexulosono-1,4-lactone 2-(p-sulfamylphenylhydrazone). The 3-(l-threo-glycerol-1-yl)-1-(p-sulfamylphenyl)flavazole (35) was prepared by the rearrangement of 3-[(1-p-sulfamylphenyl)hydrazono-l-threo-trihydroxybutyl]-2-quinoxalinont (33). Periodate oxidation of 15,33, and 35 gave 3-formyl-1-(p-sulfamylphenyl)-4,5-pyrazoledione 4-(p-sulfamylphenylhydrazone), 3-1-[(p-sulfamylphenyl)hydrazono]glyoxal-1-yl]-2-quinoxalinone, and 3-formyl-1-(p-sulfamylphenyl)flavazole, respectively. The i.r. and n.m.r. spectral data for some of these derivatives are reported.     

Apparent hydrogen bonding by strongly immobilized spin-labels

The hyperfine separations of nitroxide spin-labels which are tightly bound within hemoglobin exhibit a substantial temperature dependence even when the hemoglobin is immobilized by freezing or precipitation. It is shown that NO.--HX hydrogen bond formation by the spin-label within its binding site is a good explanation for the observed temperature dependence. Comparative studies using different hemoglobin derivatives and two different spin-labels suggest that the HX group may be some element of the protein matrix and that this hydrogen bond may be a factor in the stabilization of the label within its binding site. The hyperfine separation of a fatty acid spin probe incorporated into aqueous bilayer dispersons of dipalmitoylphosphatidylcholine also exhibits a temperature dependence at low temperature which is qualitatively similar to that of the spin-labeled hemoglobin systems. Saturation transfer electron paramagnetic resonance measurements indicate that label motion is not the source of this temperature dependence. A hydrogen-bond equilibrium between water molecules and the nitroxide NO. group appears to be a plausible source of the temperature-dependent hyperfine separation in the lipid bilayer system. Small amplitude torsional oscillation or librational motion by the nitroxide may also produce additional changes in the hyperfine separation which are difficult to distinguish from hydrogen-bonding effects under some circumstances. The apparent hydrogen-bond equilibrium exhibits a strong thermal and environmental dependence which may be of importance in a number of biophysical spin-label measurements.     

Hydrogen bonding isosteres: bimolecular carboxylic acid and amine-N-oxide interactions mediated via CH...O hydrogen bonds

The X-ray structures of cocrystals between 2,2'-dipyridyl-N,N'-dioxide (1) with fumaric acid (2), itaconic acid (3), succinic acid (4), and oxalic acid (5) were solved to determine if concurrent CH...O interactions were capable of orienting the bimolecular association of the two molecules. Cocrystals 1.2, 1.3 and 1.4 produce cyclic hydrogen bonded motifs employing pair-wise OH...O and CH...O hydrogen bonds, whereas cocrystal 1.5 forms analogous OH...O hydrogen bonds with a different set of intermolecular CH...O hydrogen bonds. Evidence of cocrystal formation was also observed for these complexes by differential scanning calorimetry and FT-IR spectroscopy. The structures of 1.2, 1.3 and 1.4 demonstrate the potential of the pair-wise OH...O and CH...O hydrogen bonding interactions and serve to illustrate their use as hydrogen bonding isosteres in crystal engineering, molecular recognition, and drug design.     

Three new supramolecular networks formed via hydrogen bonding interactions: Syntheses, crystal structures and magnetic properties

Three new iron(III) citrate complexes [Fe₂(cit)₂(H₂O)₂](H₂bpa) (1), [Fe₂(cit)₂(H₂O)₂](H₂bpe) (2) and [Fe₄(cit)₄(H₂O)₄](H₂bpp)₂(H₂O) (3) (cit = C(O⁻)(COO⁻)(CH₂COO⁻)₂, bpa = 1,3-bis(4-pyridyl)ethane, bpe = 1,3-bis(4-pyridyl)ethene, bpp = 1,3-bis(4-pyridyl)propane) were synthesized and characterized by elemental analysis, spectroscopic techniques and magnetic properties. Single X-ray diffraction analyses in the 1-3 complexes reveal that the iron ion is six-coordinated and is bound by two deprotonated citrates and a pair of aqua ligands in a distorted octahedral fashion. The anionic complex contains a centro-symmetrical planar of four-membered Fe₂O₂ ring. There are significant contributions to the stabilities of the assembled lattices in 1-3 arising from the protonated pyridine analogue counterions neutralizing the anionic charges of the complexes. The units in the complexes are connected together via hydrogen bonding to form 3D supramolecular networks. The supramolecular structures of 1-2 show alternating and motif linking the anionic moieties which are in turn interwoven with cationic moieties, while 3 shows alternating and motif. The magnetic properties of 1-3 are investigated and discussed in detail.     

An M-H…H-C hydrogen bonding interaction

Study of several X-ray and neutron diffraction crystal structures of aryl phosphine hydride complexes shows that abnormally close CH…HM contacts (1.6–2.1 Å) commonly occur between the arene CH bonds and the hydride. The data suggest that weak CH…HM hydrogen bonds are involved, resembling those we have previously characterized for the NH…HN case. Based on these results, a new mechanism is suggested for cyclometallation.     

The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction

To study the role of hydrogen bonding via interfacial water molecules in protein-protein interactions, we examined the interaction between hen egg white lysozyme (HEL) and its HyHEL-10 variable domain fragment (Fv) antibody. We constructed three antibody mutants (l-Y50F, l-S91A, and l-S93A) and investigated the interactions between the mutant Fvs and HEL. Isothermal titration calorimetry indicated that the mutations significantly decreased the negative enthalpy change (8-25 kJ mol(-1)), despite some offset by a favorable entropy change. X-ray crystallography demonstrated that the complexes had nearly identical structures, including the positions of the interfacial water molecules. Taken together, the isothermal titration calorimetric and x-ray crystallographic results indicate that hydrogen bonding via interfacial water enthalpically contributes to the Fv-HEL interaction despite the partial offset because of entropy loss, suggesting that hydrogen bonding stiffens the antigen-antibody complex.