NMR parameters and geometries of OHN and ODN hydrogen bonds of pyridine-acid complexes

In this paper, equations are proposed which relate various NMR parameters of OHN hydrogen-bonded pyridine-acid complexes to their bond valences which are in turn correlated with their hydrogen-bond geometries. As the valence bond model is strictly valid only for weak hydrogen bonds appropriate empirical correction factors are proposed which take into account anharmonic zero-point energy vibrations. The correction factors are different for OHN and ODN hydrogen bonds and depend on whether a double or a single well potential is realized in the strong hydrogen-bond regime. One correction factor was determined from the known experimental structure of a very strong OHN hydrogen bond between pentachlorophenol and 4-methylpyridine, determined by the neutron diffraction method. The remaining correction factors which allow one also to describe H/D isotope effects on the NMR parameters and geometries of OHN hydrogen bond were determined by analysing the NMR parameters of the series of protonated and deuterated pyridine- and collidine-acid complexes. The method may be used in the future to establish hydrogen-bond geometries in biologically relevant functional OHN hydrogen bonds.     

The quasi-symmetric OHN and ODN bridges in the adducts of 3,5-dimethylpyridine with 3,5-dinitrobenzoic acid

The crystal structure of the adduct of 3,5-dimethylpyridine and 3,5-dinitrobenzoic acid (DMP-DNB) has been determined at room temperature and 80 K for both undeuterated and deuterated compounds. The monoclinic crystals are isomorphous, space group P2₁/c and Z = 4. Very strong OHN hydrogen bonds are almost linear with fully disordered (1:1) bridge hydrogen atoms between oxygen and nitrogen atoms. This is well reflected in the difference in electron density maps the contours of which depend both on cooling and deuteration. The intramolecular hydrogen bond lengths are 2.550(2) Å for the (OHN) and 2.563(2) Å for (ODN) at room temperature and 2.529(2) Å for (OHN) and 2.531(2) Å for (ODN) at 80 K. Therefore, there is a small but meaningful isotope effect upon the O…N hydrogen bridge length at room temperature and no Ubbelohde isotope effect is observed at 80 K. The infra-red spectra show very broad stretching protonic bands in the 200–1600 cm⁻¹ range. The isotopic ratio v(H)/v(D) at room temperature is about 1.1.     

NMR studies of solid state—solvent and H/D isotope effects on hydrogen bond geometries of 1:1 complexes of collidine with carboxylic acids

¹H and ¹⁵N NMR spectra of 10 complexes exhibiting strong OHN hydrogen bonds formed by ¹⁵N-labeled collidine and different proton donors, partially deuterated in mobile proton sites, have been observed by low-temperature NMR spectroscopy using a low-freezing CDF₃/CDF₂Cl mixture as polar aprotic solvent. The following proton donors have been used: HCl, formic acid, acetic acid, various substituted benzoic acids and HBF₄. The slow hydrogen bond exchange regime could be reached below 140 K, which allowed us to resolve ¹⁵N signal splittings due to H/D isotopic substitution. The valence bond order model is used to link the observed NMR parameters to hydrogen bond geometries. The results are compared to those obtained previously [Magn. Reson. Chem. 39 (2001) S18] for the same complexes in the organic solids. The increase of the dielectric constant from the organic solids to the solution (30 at 130 K) leads to a change of the hydrogen bond geometries along the geometric correlation line towards the zwitterionic structures, where the proton is partially transferred from oxygen to nitrogen. Whereas the changes of spectroscopic and, hence, geometric parameters are small for the systems which are already zwitterionic in the solid state, large changes are observed for molecular complexes which exhibit almost a full proton transfer from oxygen to nitrogen in the polar liquid solvent.     

Structure of AuCN determined from total neutron diffraction

The structure of gold cyanide, AuCN, has been determined at 10 and 300 K using total neutron diffraction. The structure consists of infinite [bond]Au[bond](CN)[bond]Au[bond](CN)[bond] linear chains, hexagonally packed, with the gold atoms in sheets. The Au-C and Au-N bond lengths are found to be identical, with d(Au(-C/N) = 1.9703(5) A at 300 K. This work supersedes a previous study, by others, which used Rietveld analysis of neutron Bragg diffraction in isolation, and found these bonds to have significantly different lengths (Delta d = 0.24 A) at 300 K. The total correlation function, T(r), at 10 and 300 K, has been modeled using information derived from total diffraction. The broadening of inter- and intrachain correlations differs markedly due to random displacements of the chains in the direction of the chain axes. This is a consequence of the relatively weak bonding between the chains. An explanation for the negative thermal expansion in the c-direction, which occurs between 10 and 300 K, is presented.     

Incoherent inelastic neutron scattering of the strong (NHN) bond in H3Co(CN)6

The vibrations of the strong symmetric NHN hydrogen bond in H₃Co(CN)₆ have been investigated by inelastic neutron scattering spectroscopy at 80 K. The two deformation modes δ(NH) and γ(NH) have been identified. A strong protonic mode is observed in the low energy transfer region and is assigned to the antisymmetric stretching vibration of the hydrogen bond. Relative intensities of the ν(NH) fundamental, its first overtone and bending fundamentals are interpreted as suggesting a strongly anisotropic Debye-waller factor. At 5 K the ν(NH) fundamental shows a complex structure which is interpreted in terms of coupling with low frequency lattice modes.     

Electron and nuclear positions in the short hydrogen bond in urotropine-N-oxide.formic acid

The crystal structure of urotropine-N-oxide.formic acid, as determined from multiple temperature single-crystal X-ray diffraction experiments in the range 123-295 K and from neutron diffraction at 123 K, is reported. There is a strong hydrogen bonding interaction between the OH of formic acid and the N-oxide of urotropine, with the oxygen-oxygen distance ranging from 2.4300(10) to 2.4469(10) A. The electron density of the hydrogen atom associated with this interaction was located in the Fourier difference maps of the spherical atom refinement after all heavy atom positions were determined. The maximum of the electron density associated with the hydrogen bond is located approximately 1.16 A from the formate segment, though the distribution of electron density is very broad. The electron density associated with the H atom is thus shown by these accurate X-ray diffraction experiments to be approximately centered at all temperatures studied. This was conclusively confirmed by single-crystal neutron diffraction data obtained at 123 K, from which statistically equivalent O-H distances of 1.221(7) and 1.211(7) A were obtained.     

Variable temperature neutron diffraction and X-ray charge density studies of tetraacetylethane

Single crystal neutron diffraction data have been collected on a sample of enolized 3,4-diacetyl-2,5-hexanedione (tetraacetylethane, TAE) at five temperatures between 20 and 298 K to characterize the temperature-dependent behavior of the short, strong, intramolecular hydrogen bond. Upon decreasing the temperature from 298 K to 20 K, the O2-H1 distance decreases from 1.171(11) to 1.081(2) A and the O1...H1 distance increases from 1.327(10) to 1.416(6) A. The convergence of the C-O bond lengths from inequivalent distances at low temperature to identical values (1.285(4) A) at 298 K is consistent with a resonance-assisted hydrogen bond. However, a rigid bond analysis indicates that the structure at 298 K is disordered. The disorder vanishes at lower temperatures. Short intermolecular C-H...O contacts may be responsible for the ordering at low temperature. The intramolecular O...O distance (2.432 +/- 0.006 A) does not change with temperature. X-ray data at 20 K were measured to analyze the charge density and to gain additional insight into the nature of the strong hydrogen bond. Quantum mechanical calculations demonstrate that periodic boundary conditions provide significant enhancement over gas phase models in that superior agreement with the experimental structure is achieved when applying periodicity. One-dimensional potential energy calculations followed by quantum treatment of the proton reproduce the location of the proton nearer to the O2 site reasonably well, although they overestimate the O-H distance at low temperatures. The choice of the single-point energy calculation strategy for the proton potential is justified by the fact that the proton is preferably located nearer to O2 rather than being equally distant to O1 and O2 or evenly distributed (disordered) between them.     

Coupling of functional hydrogen bonds in pyridoxal-5'-phosphate-enzyme model systems observed by solid-state NMR spectroscopy

We present a novel series of hydrogen-bonded, polycrystalline 1:1 complexes of Schiff base models of the cofactor pyridoxal-5'-phosphate (PLP) with carboxylic acids that mimic the cofactor in a variety of enzyme active sites. These systems contain an intramolecular OHN hydrogen bond characterized by a fast proton tautomerism as well as a strong intermolecular OHN hydrogen bond between the pyridine ring of the cofactor and the carboxylic acid. In particular, the aldenamine and aldimine Schiff bases N-(pyridoxylidene)tolylamine and N-(pyridoxylidene)methylamine, as well as their adducts, were synthesized and studied using 15N CP and 1H NMR techniques under static and/or MAS conditions. The geometries of the hydrogen bonds were obtained from X-ray structures, 1H and 15N chemical shift correlations, secondary H/D isotope effects on the 15N chemical shifts, or directly by measuring the dipolar 2H-15N couplings of static samples of the deuterated compounds. An interesting coupling of the two "functional" OHN hydrogen bonds was observed. When the Schiff base nitrogen atoms of the adducts carry an aliphatic substituent such as in the internal and external aldimines of PLP in the enzymatic environment, protonation of the ring nitrogen shifts the proton in the intramolecular OHN hydrogen bond from the oxygen to the Schiff base nitrogen. This effect, which increases the positive charge on the nitrogen atom, has been discussed as a prerequisite for cofactor activity. This coupled proton transfer does not occur if the Schiff base nitrogen atom carries an aromatic substituent.     

NMR studies of solvent-assisted proton transfer in a biologically relevant Schiff base: toward a distinction of geometric and equilibrium H-bond isotope effects

The tautomeric equilibrium in a Schiff base, N-(3,5-dibromosalicylidene)-methylamine 1, a model for the hydrogen bonded structure of the cofactor pyridoxal-5'-phosphate PLP which is located in the active site of the enzyme, was measured by means of 1H and 15N NMR and deuterium isotope effects on 15N chemical shifts at variable temperature and in different organic solvents. The position of the equilibrium was estimated using the one-bond 1J(OHN) and vicinal 3J(H(alpha)CNH) scalar coupling constants. Additionally, DFT calculations of a series of Schiff bases, N-(R1-salicylidene)-alkyl(R2)amines, were performed to obtain the hydrogen bond geometries. The latter made it possible to investigate a broad range of equilibrium positions. The increase of the polarity of the aprotic solvent shifts the proton in the intramolecular OHN hydrogen bond closer to the nitrogen. The addition of methanol and of hexafluoro-2-propanol to 1 in aprotic solvents models the PLP-water interaction in the enzymatic active site. The alcohols, which vary in acidity and change the polarity around the hydrogen bond, also stabilize the equilibrium, so that the proton is shifted to the nitrogen.     

Intrinsic proton-donating power of zinc-bound water in a carbonic anhydrase active site model estimated by NMR

Using liquid-state NMR spectroscopy we have estimated the proton-donating ability of Zn-bound water in organometallic complexes designed as models for the active site of the metalloenzyme carbonic anhydrase (CA). This ability is important for the understanding of the enzyme reaction mechanism. The desired information was obtained by (1)H and (15)N NMR at 180 K of solutions of [Tp(Ph,Me)ZnOH] [1, Tp(Ph,Me) = tris(2-methyl-4-phenylpyrazolyl)hydroborate] in CD(2)Cl(2), in the absence and presence of the proton donors (C(6)F(5))(3)BOH(2) [aquatris(pentafluorophenyl)boron] and Col-H(+) (2,4,6-trimethylpyridine-H(+)). Col-H(+) forms a strong OHN hydrogen bond with 1, where the proton is located closer to nitrogen than to oxygen. (C(6)F(5))(3)BOH(2), which exhibits a pK(a) value of 1 in water, also forms a strong hydrogen bond with 1, where the proton is shifted slightly across the hydrogen-bond center toward the Zn-bound oxygen. Finally, a complex between Col and (C(6)F(5))(3)BOH(2) was identified, exhibiting a zwitterionic OHN hydrogen bond, where H is entirely shifted to nitrogen. The comparison with complexes of Col with carboxylic acids studied previously suggests that, surprisingly, the Zn-bound water exhibits in an aprotic environment a similar proton-donating ability as a carboxylic acid characterized in water by a pK(a) of 2.2 ± 0.6. This value is much smaller than the value of 9 found for [Zn(OH(2))(6)](2+) in water and those between 5 and 8 reported for different forms of CA. Implications for the biological function of CA are discussed.     

Intramolecular hydrogen bonds in 3-diethylaminomethyl-5-R-salicylic aldehydes

Two 3-diethylaminomethyl-5-R-salicylic aldehydes were obtained and studied in chloroform solutions by FTIR and NMR spectroscopy. The existence of an equilibrium between the structures with OHO=C and NHO intramolecular hydrogen bonds was suggested. In the case of compound 1 (R=OCH₃) the OHO=C intramolecular hydrogen bond was more favorable whereas in the case of compound 2 (R=Br) the structure with the OHN intramolecular hydrogen bond was predominant.     

Localization of hydrogen in the layer oxide HTiNbO5

The structure of HTiNbO₅ at 10 and 300 K and of DTiNbO₅ at 300 K has been investigated by neutron powder diffraction. The TiNbO₅ framework and the octahedral distortions previously found for the alkalititanoniobates by X-ray diffraction are confirmed. The position of hydrogen (or deuterium) has been determined: very strong OH … O hydrogen bonds with O … O distances ranging from 2.51 to 2.63 Å are observed. The similarity of these compounds with acids is shown, explaining their ion exchange properties. The absence of protonic conductivity can be explained from structural arguments. The open character of this structure, which can play a part in intercalation and deintercalation reactions is also discussed.     

Ions in water: the microscopic structure of concentrated NaOH solutions

A neutron diffraction experiment with isotopic H/D substitution on four concentrated NaOH/H(2)O solutions is presented. The full set of partial structure factors is extracted, by combining the diffraction data with a Monte Carlo simulation. These allow to investigate both the changes of the water structure in the presence of ions and their solvation shells. It is found that the interaction with the solute affects the tetrahedral network of hydrogen bonded water molecules in a manner similar to the application of high pressure to pure water. The solvation shell of the OH(-) ions has an almost concentration independent structure, although with concentration dependent coordination numbers. The hydrogen site coordinates a water molecule through a weak bond, while the oxygen site forms strong hydrogen bonds with a number of molecules that is on the average very close to four at the higher water concentrations and decreases to about three at the lowest one. The competition between hydrogen bond interaction and Coulomb forces in determining the orientation of water molecules within the cation solvation shell is visible in the behavior of the g(NaHw)(r) function     

Origin of the monoclinic-to-monoclinic phase transition and evidence for the centrosymmetric crystal structure of BiMnO3

Structural properties of polycrystalline single-phased BiMnO3 samples prepared at 6 GPa and 1383 K have been studied by selected area electron diffraction (SAED), convergent beam electron diffraction (CBED), and the Rietveld method using neutron diffraction data measured at 300 and 550 K. The SAED and CBED data showed that BiMnO3 crystallizes in the centrosymmetric space group C2/c at 300 K. The crystallographic data are a = 9.5415(2) A, b = 5.61263(8) A, c = 9.8632(2) A, beta = 110.6584(12) degrees at 300 K and a = 9.5866(3) A, b = 5.59903(15) A, c = 9.7427(3) A, beta = 108.601(2) degrees at 550 K, Z = 8, space group C2/c. The analysis of Mn-O bond lengths suggested that the orbital order present in BiMnO3 at 300 K melts above TOO = 474 K. The phase transition at 474 K is of the first order and accompanied by a jump of magnetization and small changes of the effective magnetic moment and Weiss temperature, mueff = 4.69 microB and theta = 138.0 K at 300-450 K and mueff = 4.79 microB and theta = 132.6 K at 480-600 K.     

Structural and EPR study of the dependence on deuteration of the Jahn-Teller distortion in ammonium hexaaquacopper(II) sulfate, (NH4)

The variation of the EPR spectra with degree of deuteration of the partially deuterated Tutton salt ammonium hexaaquacopper(II) sulfate, (NH4)2[Cu(H2O)6](SO4)2, has been measured at 293 K. The measurements indicate that the structure changes quite abruptly from that of the pure hydrogenous salt to that of the fully deuterated salt at approximately 50% deuteration. The structure of a crystal in which approximately 42% of the hydrogen atoms were replaced by deuterium was elucidated at 15 K by single-crystal time-of-flight neutron diffraction. The hexaaquacopper(II) complex exhibits an orthorhombically distorted, tetragonally elongated octahedral coordination geometry (Cu-O bond distances of 2.281(1), 2.007(1), and 1.975(1) A). The structure is very similar to that reported for the undeuterated salt at 9.6 K, and markedly different from that of the fully deuterated compound at 15 K, which has similar Cu-O bond lengths but with the directions of the long and intermediate bonds interchanged. There is no evidence for disorder or partial switching of the Cu-O bond directions. This is consistent with the temperature dependence of the EPR spectrum of the approximately 42% deuterated compound, which indicates a thermal equilibrium between the two structural forms close to room temperature similar to that reported for the undeuterated compound, but complete reversion to the low-temperature phase on cooling to 5 K. The possible influence of deuteration upon the hydrogen-bonding distances and the bearing of this upon the structural modifications of the compound are discussed.     

The crystal structure of RbHSeO4: A neutron diffraction study of the paraelectric phase

The structure of the paraelectric phase of RbHSeO₄ has been determined at 387 K by neutron diffraction. The structure consists of chains of hydrogen bonded SeO₄ groups extending along the crystallographic b axis. Two different hydrogen bonds have been characterized, with OO distances of 2.524(4) and 2.583(3) Å. In the shorter OHO hydrogen bond the hydrogen atom is disordered, suggesting that the ordering of hydrogen participates directly in the phase transition to the ferroelectric phase.     

First principles molecular dynamics study of filled ice hydrogen hydrate

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and∕or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and∕or low temperatures.     

Hydrogen-bond dynamics and Fermi resonance in high-pressure methane filled ice

High-pressure, variable temperature infrared spectroscopy and first-principles calculations on the methane filled ice structure (MH-III) at high pressures are used to investigate the vibrational dynamics related to pressure induced modifications in hydrogen bonding. Infrared spectroscopy of isotopically dilute solutions of H(2)O in D(2)O is employed together with first-principles calculations to characterize proton dynamics with the pressure induced shortening of hydrogen bonds. A Fermi resonance is identified and shown to dominate the infrared spectrum in the pressure region between 10 and 30 GPa. Significant differences in the effects of the Fermi resonance observed between 10 and 300 K arise from the double-well potential energy surface of the hydrogen bond and quantum effects associated with the proton dynamics.     

Bindungsverhältnisse in den kristallinen Phasen von Rubidiumhydroxid und -deuterohydroxid,RbOH und RbOD

Bonding Conditions in Crystalline Phases of RbOH and RbOD The crystalline modifications of RbOH and RbOD have been investigated between 16 K and melting point employing X-ray, neutron diffraction and calorimetric methods as well as IR and Raman spectroscopy. The results elucidate the bonding interactions in these phases. For crystal data see ?Inhaltsubersicht”?. The structurally distinct influence of the asymmetric charge distribution of the hydroxide ion decreases with increasing temperatures: In the TlI-type structure the anions are hydrogen bonded forming infinite chains at low temperatures. The hydrogen bonds break open by warming up. Phase transformations above 300 K (RbOD) resp. 265 K (BbOH) are associated with the discontinous expansion of rocking vibrations of the anions. In the high temperature form with KaCI-type structure the anions rotate quasi-freely     

On the variation of the structure of liquid deuterium fluoride with temperature

The structure of liquid deuterium fluoride has been measured using pulsed neutron diffraction and high energy x-ray diffraction techniques as a function of temperature. The neutron experiments were performed at T=296+/-2 K, 246+/-2 K, and 193+/-2 K and the x-ray measurements carried out at 296+/-2 K and 195+/-2 K. The x-ray pair correlation functions, which are dominated by fluorine-fluorine interactions, show the first peak at approximately 2.53+/-0.05 A remains very nearly invariant with decreasing temperature. Peaks around 4.5 and 5.0 A also appear at both temperatures in the x-ray data. In contrast, the intermolecular peaks in the total neutron pair correlation function show that significant systematic local structural changes occur as the temperature is lowered. The first intermolecular peak position shortens from 1.64+/-0.05 A at 296 K to 1.56+/-0.05 A at 195 K. Although there are overlapping contributions from the intermolecular hydrogen-fluorine and hydrogen-hydrogen correlations, it is clear that the temperature dependent structural changes are largely due to a rearrangement of the deuterium atom positions in the fluid. By comparison with partial structure factor data the hydrogen bonds appear to become more linear at lower temperatures.