An empirical potential for the O-H ⋯ O hydrogen bond: Part 2. Comparison with observed hydrogen bond geometries

The room temperature distribution of O-H ? O hydrogen bond geometries has been predicted by a Monte Carlo calculation, with an empirical potential energy function for the hydrogen bond. The results are compared with a recent survey of hydrogen bonds in carbohydrate crystal structures. The calculated and observed distributions of the O-H ? O angle have mean values of 165.5° and 167.1° respectively. Both the theoretical and experimental results suggest that short O ? H hydrogen bonds tend to be more linear than long O ? H bonds. The distribution of hydrogen bonding within the lone pair plane of the acceptor oxygen atom is predicted to be broader than the distribution perpendicular to this plane, in agreement with the experimental data. The empirical hydrogen bond function, in conjunction with the molecular mechanics program MMI, has also been used to predict the geometries of inter-residue hydrogen bonds in five disaccharides. The O ? H distances and O-H ? O angles are reproduced with r.m.s. deviations of 0.06 Å and 9° respectively.     

Description of collective effects in computer models of water

The dynamics of a system containing 3456 water molecules in a cubic cell with periodic boundary conditions at 297 K was simulated. The time dependence of distances between oxygen atoms was examined for many pairs of molecules. These distances often oscillate around a certain average value over long periods of time (10 ps and longer). These average values can be about 2.8 Å (hydrogen bond) or much larger, up to 12–13 Å and more. This suggests that big groups of molecules are involved in a concerted motion. Lists of hydrogen bonds in 50 configurations divided by an interval of about 1 ps are compared. The average lifetime of a hydrogen bond is about 7 ps. The network of hydrogen bonds is colored according to their lifetimes for one of the configurations. The bonds that live longer than 7 ps form an infinite cluster. The bonds that live longer than 8 ps join to form a great number of finite clusters including several hundreds of nodes (molecules). These clusters contain few closed cycles. Even the bonds that live longer than 20 ps are united into clusters each containing two or three nodes (molecules). The self-diffusion coefficient for molecules involved in long-lived bonds is likely to be slightly smaller than that for molecules which do not participate in these bonds.     

Hydrogen bond and residence dynamics of ion-water and water-water pairs in supercritical aqueous ionic solutions: dependence on ion size and density

We have carried out a series of molecular dynamics simulations to investigate the hydrogen bond and residence dynamics of X(-)-water (X=F, Cl, and I) and pairs in aqueous solutions at a temperature of 673 K. The calculations are done at six different water densities ranging from 1.0 to 0.15 g cm(-3). The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The F(-)-water hydrogen bonds are found to have a longer lifetime than all other hydrogen bonds considered in the present study. The lifetime of Cl(-)-water hydrogen bonds is shorter than that of F(-)-water hydrogen bonds but longer than the lifetime of water-water hydrogen bonds. The lifetimes of I(-)-water and water-water hydrogen bonds are found to be very similar. Generally, the lifetimes of both anion-water and water-water hydrogen bonds are found to be significantly shorter than those found under ambient conditions. In addition to hydrogen bond lifetimes, we have also calculated the residence times and the orientational relaxation times of water molecules in ion(water) hydration shells and have discussed the correlations of these dynamical quantities with the observed dynamics of anion(water)-water hydrogen bonds as functions of the ion size and density of the supercritical solutions.     

The hydrogen bond in the solid state

The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.     

Density functional theory and atoms-in-molecules investigation of intramolecular hydrogen bonding in derivatives of malonaldehyde and implications for resonance-assisted hydrogen bonding

A density functional theory (DFT) and atoms-in-molecules (AIM) analysis has been applied to the intramolecular hydrogen bonding in the enol conformers of malonaldehyde and its fluoro-, chloro-, cyano-, and nitro-substituted derivatives. With the B3LYP/6-311++G(2d,p) method, good agreement between the DFT geometries and published experimental structures has been found. The donor-acceptor distance was also varied in a series of constrained optimizations in order to determine if energetic, structural, and topological trends associated with intermolecular hydrogen bonding remain valid in the intramolecular case. At very short donor-acceptor distances (<2.24 A), the hydrogen is symmetrically located between donor and acceptor; at distances longer than this, the hydrogen bonding is no longer symmetric. The AIM methodology has been applied to explore the topology of the electron density in the intramolecular hydrogen bonds of the chosen model systems. Most AIM properties for intramolecular hydrogen bond distances longer than 2.24 A show smooth trends, consistent with intermolecular hydrogen bonds. Integrated AIM properties have also been used to explore the phenomenon of resonance-assisted hydrogen bonding (RAHB). It is shown that as the donor-acceptor distance is varied, pi-electron density is redistributed among the carbon atoms in the intramolecular hydrogen bond ring; however, contrary to prior studies, the integrated atomic charges on the donor-acceptor atoms were found to be insensitive to variation of hydrogen-bonding distance.     

Hydrogen bonding of water, hydrogen sulphide and related acceptors with electron donors

Properties of hydrogen bonds formed by 1:1 interaction of H₂O with oxygen, nitrogen, sulphur and other electron donors have been evaluated by extended Hückel and CNDO methods and the results are discussed in relation to the experimental data. A detailed analysis of the variation of the dissociation energies and charge densities with bond distances is presented for the amine-water system. 1:2 complexes of water with donors are found to contain weaker hydrogen bonds than 1:1 complexes. Results of molecular orbital calculations on the hydrogen bonding of H₂S and CH₃SH with some donors are presented. The theoretical value of hydrogen bond dissociation energy varies linearly with the overlap population, and stretching force constant of the hydrogen bond as well as with the experimental O—H frequency shift.     

Raman spectroscopy of newberyite Mg(PO3OH)·3H2O: a cave mineral

Newberyite Mg(PO3OH)·3H2O is a mineral found in caves such as from Moorba Cave, Jurien Bay, Western Australia, the Skipton Lava Tubes (SW of Ballarat, Victoria, Australia) and in the Petrogale Cave (Madura, Eucla, Western Australia). Because these minerals contain oxyanions, hydroxyl units and water, the minerals lend themselves to spectroscopic analysis. Raman spectroscopy can investigate the complex paragenetic relationships existing between a number of 'cave' minerals. The intense sharp band at 982 cm(-1) is assigned to the PO4(3-)ν1 symmetric stretching mode. Low intensity Raman bands at 1152, 1263 and 1277 cm(-1) are assigned to the PO4(3-)ν3 antisymmetric stretching vibrations. Raman bands at 497 and 552 cm(-1) are attributed to the PO4(3-)ν4 bending modes. An intense Raman band for newberyite at 398 cm(-1) with a shoulder band at 413 cm(-1) is assigned to the PO4(3-)ν2 bending modes. The values for the OH stretching vibrations provide hydrogen bond distances of 2.728 ? (3267 cm(-1)), 2.781 ? (3374 cm(-1)), 2.868 ? (3479 cm(-1)), and 2.918 ? (3515 cm(-1)). Such hydrogen bond distances are typical of secondary minerals. Estimates of the hydrogen-bond distances have been made from the position of the OH stretching vibrations and show a wide range in both strong and weak bonds.     

New thermochemical parameter for describing solvent effects on IR stretching vibration frequencies. Communication 2. Assessment of cooperativity effects

Solvent effects on O-H stretching vibration frequency of methanol in hydrogen bond complexes with different bases, CH3OH...B, have been investigated by FTIR spectroscopy. Using chloroform as a solvent results in strengthening of CH3OH...B hydrogen bonding due to cooperativity between CH3OH...B and Cl3CH...CH3OH bonds. A method is proposed for quantifying the hydrogen bond cooperativity effect. The determined cooperativity factors take into account all specific interactions of the solute in proton-donor solvents. In addition, a method of estimation of cooperativity factors Ab and AOX in system (CH3OH)2...B is proposed. It is demonstrated that in such systems, the cooperativity factor of the OH...B bond decreases and that of the OH...O bond increases with increasing the acceptor strength of the base B. The obtained results are in a good agreement with the data obtained previously from matrix-isolation FTIR spectroscopy.     

Probing the acidity of p-substituted phenols in the excited state: electronic spectroscopy of the p-cyanophenol-water cluster.

The hydrogen bond structure of the p-cyanophenol-water cluster has been determined in the ground and first excited electronic state by rotationally resolved UV spectroscopy. The water molecule is trans-linearly bound to the hydroxy group of the p-cyanophenol moiety, with hydrogen bond distances considerably shorter in both electronic states than in the similar phenol-water cluster. The structure of the cluster has been elucidated by ab initio calculations at various levels of theory and compared to the experimental findings. The barriers to internal rotation of the water moiety were determined experimentally to be 275 and 183 cm(-1) for the ground and excited state, respectively. Hydrogen bond distances and the energy barrier to water torsion correlate with the pK(a) values of different substituted phenols for both electronic states.     

Estimates of the energy of intramolecular hydrogen bonds

A method for the estimation of the energy of intramolecular hydrogen bonds in conjugated systems existing in a variety of conformations is presented. The method is applied to determine the intramolecular hydrogen bond energy in 3-aminopropenal and 3-aminopropenthial. According to the proposed estimation scheme, the intramolecular H-bond energies are found to be of the order of 5-7 kcal/mol. These results are compared with those obtained by using other estimation schemes as well as with the recent results by other authors. Also, the H-bond energies in dimers and trimers of the two molecules are calculated and compared with the corresponding data for internally hydrogen-bonded monomers. This comparison shows that the bond equalization effect is primarily due to proton donor-proton acceptor proximity. In comparison with intermolecular hydrogen bonds, the rigidity of the chelate skeleton enhances this proximity effect. The same effect can be seen in systems with intermolecular hydrogen bonds, although its magnitude is diminished because of the absence of additional forces which pull the proton donor and proton acceptor groups toward each other. No specific resonance-assisted origin of the intramolecular hydrogen bond energy seems to be needed to elucidate the energetics of these bonds.     

Theoretical study of the symmetry of the (OH...O)- hydrogen bonds in vinyl alcohol-vinyl alcoholate systems

The interactions between substituted vinyl alcohols and vinyl alcoholates (X = NH(2), H, F, Cl, CN) are studied at the B3LYP/6-311++G(d,p) level of theory. In a first step, the conformation of the monomers is investigated and the proton affinities (PA(A(-))) of the enolates are calculated. The enols and enolates are held together by strong (OH...O)(-) hydrogen bonds, the hydrogen bond energies ranging from 19.1 to 34.6 kcal mol(-1). The optimized O...O distances are between 2.414 and 2.549 A and the corresponding OH distances from 1.134 and 1.023 A. The other geometry parameters such as C[double bond]C or CO distances also indicate that, in the minimum energy configuration, the hydrogen bonds are characterized by a double well potential. The Mulliken charges on the different atoms of the proton donors and proton acceptors and the frequencies of the nu(OH) stretching vibrations agree with this statement. All the data indicate that the hydrogen bonds are the strongest in the homomolecular complexes. The transition state for hydrogen transfer is located with the transition barrier estimated to be about zero. Upon addition of the zero-point vibration energies to the total potential energy, the barrier vanishes. This is a characteristic feature of low-barrier hydrogen bonds (LBHBs). The hydrogen bond energies are correlated to the difference 1.5 PA(AH) - PA(A(-)). The correlation predicts different energies for homomolecular hydrogen bonds, in agreement with the theoretical calculations. Our results suggest that a PA (or pK(a)) match is not a necessary condition for forming LBHBs in agreement with recent data on the intramolecular hydrogen bond in the enol form of benzoylacetone (J. Am. Chem. Soc. 1998, 120, 12117).     

Synthesis,Crystal and Molecular Structure of Mono- and Diaquadi(acetato-O)-Bis(2,4′-Bipyridyl) Copper(II)

The title compound has been synthesized and characterized by elemental analysis and conductivity studies. The crystal and molecular structure has been determined. There are two different types of molecules in the crystal: mono- and diaquadi(acetato-O)-bis(2,4'-bipyridyl) copper (II). Both copper atoms occupy special positions. The copper atoms show almost ideal square pyramidal (4 + 1) and square bipyramidal (4 + 2) coordination. Due to the Jahn-Teller effect, the axial Cu-O(water) bond distances are longer than respective equatorial Cu-O(acetate) bond distances. The bond valences of the copper were computed. An intramolecular strong hydrogen bond linking O(water) and O(acetate) atoms exists in the molecule. The differences of geometrical environment for copper in mono- and diaquadi(acetato-O)-bis(2,4'-bipyridyl) copper(II) are imposed by strong intermolecular hydrogen bonds creating a linear infinite chain structure along crystallographic x axis. Also weak intramolecular hydrogen bonds are present in the molecule.     

Peisleyite an unusual mixed anion mineral--a vibrational spectroscopic study

The mineral peisleyite has been studied using a combination of electron microscopy and vibrational spectroscopy. Scanning electron microscope (SEM) photomicrographs reveal that the peisleyite morphology consists of an array of small needle-like crystals of around 1 microm in length with a thickness of less than 0.1 microm. Raman spectroscopy in the hydroxyl stretching region shows an intense band at 3506 cm(-1) assigned to the symmetric stretching mode of the OH units. Four bands are observed at 3564, 3404, 3250 and 3135 cm(-1) in the infrared spectrum. These wavenumbers enable an estimation of the hydrogen bond distances 3.052(5), 2.801(0), 2.705(6) and 2.683(6)A. Two intense Raman bands are observed at 1023 and 989 cm(-1) and are assigned to the SO(4) and PO(4) symmetric stretching modes. Other bands are observed at 1356, 1252, 1235, 1152, 1128, 1098 and 1067 cm(-1). The bands at 1067 cm(-1) is attributed to AlOH deformation vibrations. Bands in the low wavenumber region are assigned to the nu(4) and nu(2) out of plane bending modes of the SO(4) and PO(4) units. Raman spectroscopy is a useful tool in determining the vibrational spectroscopy of mixed hydrated multianion minerals such as peisleyite. Information on such a mineral would be difficult to obtain by other means.     

A bond by any other name

A hydrogen bond is an interaction wherein a hydrogen atom is attracted to two atoms, rather than just one, and acts like a bridge between them. The strength of this attraction increases with the increasing electronegativity of either of the atoms, and in the classical view, all hydrogen bonds are highly electrostatic and sometimes even partly covalent. Gradually, the concept of a hydrogen bond has become more relaxed to include weaker and more dispersive interactions, provided some electrostatic character remains. A great variety of very strong, strong, moderately strong, weak, and very weak hydrogen bonds are observed in practice. Weak hydrogen bonds are now invoked in several matters in structural chemistry and biology. While strong hydrogen bonds are easily covered by all existing definitions of the phenomenon, the weaker ones may pose a challenge with regard to nomenclature and definitions. Recently, a recommendation has been made to the International Union of Pure and Applied Chemistry (IUPAC) suggesting an updated definition of the term hydrogen bond. This definition will be discussed in greater detail.     

A vibrational spectroscopic study of perhamite, an unusual silico-phosphate

The silico-phosphate mineral perhamite has been studied using a combination of electron and vibrational spectroscopy. SEM photomicrographs reveal that perhamite morphology consists of very thin intergrown platelets that can form a variety of habits. Infrared spectroscopy in the hydroxyl-stretching region shows a number of overlapping bands which are observed in the range 3581-3078 cm(-1). These wavenumbers enable an estimation to be made of the hydrogen bond distances in perhamite: 3.176(0), 2.880(5), 2.779(6), 2.749(3), 2.668(1) and 2.599(7)A. Intense Raman bands are observed in the region 1110-1130 and 966-996 cm(-1) and are assigned to the SiO(4) and PO(4) symmetric stretching modes. Other bands are observed in the range 1005-1096 cm(-1) and are attributed to the nu(3) antisymmetric bending modes of PO(4). Some low intensity bands around 874 cm(-1) were discovered and remain unclassified. Bands in the low-wavenumber region are assigned to the nu(4) and nu(2) out-of-plane bending modes of the OSiO and PO(4) units. Raman spectroscopy is a useful tool in determining the vibrational spectroscopy of mixed hydrated multi-anion minerals such as perhamite. Information on such a mineral would be difficult to obtain by other means.     

Investigating pressure effects on structural and dynamical properties of liquid methanol with many-body interactions

Molecular-dynamics simulations utilizing a many-body potential was used to study the pressure dependence of structural and dynamical properties for liquid methanol. The liquid density as a function of pressure agreed well with experiment, and a combination of radial and angular distribution functions were used to analyze molecular structure. From these distribution functions, it was observed that hydrogen bond strength increased with increasing pressure. This observation coincided with an increase in the molecular dipole as a function of pressure, having a significant effect on the observed increased hydrogen bond strength. Also, methanols were found to more strongly favor exactly two hydrogen bonds, with fewer methanols of zero, one, or three hydrogen bonds present at higher pressures. Furthermore, a majority of the compression with increased pressure was found to occur in regions perpendicular to the methanol hydrogen-oxygen bond vector. This was the case despite hydrogen-oxygen nonbonded distances between hydrogen bonding species being shorter, but their stiffer oxygen-hydrogen-(nonbonded) oxygen angle offsets this, resulting in their oxygen-oxygen distances being relatively unaffected. The methanol translational diffusion decreased significantly with increased pressure, while the rotational diffusion decreased at a similar magnitude around the oxygen-hydrogen and oxygen-carbon bond vectors, despite having very different overall diffusion. Finally, the hydrogen bond lifetime increased significantly with pressure, owing to the increased hydrogen bond strength, and the slower translational and rotational dynamics.     

Thermo-Raman spectroscopic study of the natural layered double hydroxide manasseite

Raman and thermo-Raman spectroscopy have been applied to study the natural hydrotalcite manasseite Mg(6)Al(2)(OH)(16)(CO(3)).4H(2)O. Hydrogen bond distances calculated using a Libowitzky-type empirical function varied between 2.61 and 3.00A. Stronger hydrogen bonds were formed by water units as compared to the hydroxyl units. Thermo-Raman spectroscopy enabled the identification of bands attributed to the hydroxyl units. Two Raman bands at 1062 and 1058 cm(-1) are assigned to symmetric stretching modes of the carbonate anion. Thermal treatment shifts these bands to higher wavenumbers indicating a change in the carbonate bonding.     

Dynamics of halide ion-water hydrogen bonds in aqueous solutions: dependence on ion size and temperature

We have carried out a series of molecular dynamics simulations to investigate the dynamics of X(-)-water (X = F, Cl, Br, and I) and water-water hydrogen bonds in aqueous alkali halide solutions at room temperature and also of Cl(-)-water and water-water hydrogen bonds at seven different temperatures ranging from 238 to 318 K. The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The results of the hydrogen bond dynamics are obtained for two different cutoff values for the angular criterion. In both cases, similar dynamical behavior of the hydrogen bonds is found with respect to their dependence on ion size and temperature. The fluoride ion-water hydrogen bonds are found to break at a much slower rate than water-water hydrogen bonds, while the lifetimes of chloride and bromide ion-water hydrogen bonds are found to be shorter than those of fluoride ion-water ones but still longer than water-water hydrogen bonds. The short-time dynamics of iodide ion-water hydrogen bonds is found to be slightly faster, while its long-time dynamics is found to be slightly slower than the corresponding water-water hydrogen bond dynamics. Correlations of the observed dynamics of anion(water)-water hydrogen bonds with those of rotational and translational diffusion and residence times of water molecules in ion(water) hydration shells are also discussed. With variation of temperature, the lifetimes of both Cl(-)-water and water-water hydrogen bonds are found to show Arrhenius behavior with a slightly higher activation energy for the Cl(-)-water hydrogen bonds.     

Raman and infrared spectroscopy of arsenates of the roselite and fairfieldite mineral subgroups

Raman spectroscopy complimented with infrared spectroscopy has been used to determine the molecular structure of the roselite arsenate minerals of the roselite and fairfieldite subgroups of formula Ca(2)B(AsO(4))(2).2H(2)O (where B may be Co, Fe(2+), Mg, Mn, Ni and Zn). The Raman arsenate (AsO(4))(2-) stretching region shows strong differences between the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. In the infrared spectra complexity exists with multiple (AsO(4))(2-) antisymmetric stretching vibrations observed, indicating a reduction of the tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong Raman bands around 450 cm(-1) are assigned to nu(4) bending modes. Multiple bands in the 300-350 cm(-1) region assigned to nu(2) bending modes provide evidence of symmetry reduction of the arsenate anion. Three broad bands for roselite are found at 3450, 3208 and 3042 cm(-1) and are assigned to OH stretching bands. By using a Libowitzky empirical equation hydrogen bond distances of 2.75 and 2.67 A are estimated. Vibrational spectra enable the molecular structure of the roselite minerals to be determined and whilst similarities exist in the spectral patterns, sufficient differences exist to be able to determine the identification of the minerals.     

Studies on the Effect of Structure to Property Stability of Glucomannan

1 INTRODUCTION Directive action of hydrogen bond paves the way for new fields of biological activity, molecular re- cognition and crystal engineering[1]. Hydrogen bond plays an important role in the physical and chemical properties, such as melting point, boiling point, solu- bility, acid strength, viscosity and hardness degree[2]. At present, the popular tools used to investigate hy- drogen bond include wet melting point method, chromatography analysis method, spectrum method and diffract…