OH-stretching Frequencies Research Articles

A theoretical study of the anionic intermolecular hydrogen bonding between dihydroxy tetrahydrofuran and phosphate ions

The formation of strong hydrogen bonds between 3,4- cis-dihydroxy tetrahydrofuran (DHTHF) and diphosphate anion (H 2PO 4 −) and between DHTHF and phosphate dianion (HPO 4 2−) was detected by quantum chemical studies. Quantum chemical calculations done using the ab initio MP2 level of theory and using the density functional theory with the B3LYP/6-311+G(d,p) basis set showed that the hydrogen bond distances are rather short, the dissociation energies of the hydrogen bonds are quite large, and the red shifts of the OH-stretching frequencies of DHTHF in the adducts are very large. Based on these theoretical results, a mechanism has been proposed to interpret the catalytic activity of the ribose containing polymers for the cleavage of DNA.

Orientation of OH groups in kaolinite and dickite: Ab initio molecular dynamics study

Ab-initio density-functional molecular dynamics simulations and full relaxation of all atomic positions are used to reconcile the crystal structures with IR spectra of dickite and kaolinite. The relaxation of atomic positions preserves the accepted space group symmetries. A pair of two hydroxyl groups oriented parallel to the layer is formed in structures of both dickite and kaolinite producing the high-frequency components of the OH-stretching frequencies. Other hydroxyls make relatively strong interlayer hydrogen bonds and produce down-shifted stretching bands. All hydroxyl groups are involved in effective hydrogen bonds. The OH-stretching frequencies depend linearly on the strength of the hydrogen bond.

Ab initio investigation of the adsorption of benzene in mordenite

The adsorption of benzene in pure-silica and acid mordenite has been investigated using density functional theory, both in the local density approximation and including generalized-gradient corrections. Benzene acts as a test molecule for studying the interaction between an aromatic hydrocarbon and a zeolite. Different adsorption modes have been studied for several acid sites. All configurations have been optimized by minimizing the total energy with respect to all lattice parameters and to the atomic coordinates. The strength of the adsorption is directly correlated to the local structural distortion of the zeolitic framework, especially of the acid site. Only if strong adsorption occurs, the molecule itself is slightly deformed. Furthermore, an analysis of the differential charges has been performed, indicating substantial polarization effects for the acid site as well as for the molecule. Finally, the red-shift of the OH-stretching frequencies due to the adsorption has been calculated.

Surface vibrational spectroscopic study of surface melting of ice.

Surface melting on the (0001) face of hexagonal ice ( I(h)) was studied by sum-frequency vibrational spectroscopy in the OH stretch frequency range. The degree of orientational order of the dangling OH bonds at the surface was measured as a function of temperature. Disordering sets in around 200 K and increases dramatically with temperature. The results show that the disordered (quasiliquid) layer on ice is structurally different from normal liquid water.

Water structure changes induced by hydrophobic and polar solutes revealed by simulations and infrared spectroscopy

A combination of simulations and Fourier transform infrared spectroscopy was used to examine the effect of three ionic solutes (KCl, NaCl, and KSCN), the polar solute urea, and the osmolyte trimethylamine-N-oxide (TMAO) on a water structure. The ionic solutes increase the mean water–water H-bond angle in their first hydration shell concomitantly shifting the OH stretching mode to higher frequency, and shifting the HOH bending mode to lower frequency. TMAO decreases the mean water–water H-bond angle in its first hydration shell, shifts the OH stretching mode frequency down, and shifting the HOH bending mode frequency up. Urea has no effect on the mean H-bond angle, OH stretch, and HOH bend frequencies. These results can be explained in terms of changes in the relative proportions of two H-bond angle populations: Ionic solutes increase the population of more distorted (larger angle) H bonds relative to the less distorted population, TMAO has the reverse effect, while urea does not affect the H-bond angle probability distribution. The negligible effect of urea on water structure supports the direct binding model for urea-induced protein denaturation.

Theoretical study of structure and spectra of cage clusters (H 2O) n, n=11,12

The optimal structures, interaction energies and OH stretch frequencies of water cage clusters, (H 2O) n , n=11,12 have been investigated, employing an empirical polarizable potential and MP2 ab initio calculations. The new spectral feature at the OH stretch region for (H 2O) 12 clusters in comparison with the octamer is the presence of new border spectral lines due to four-coordinated double donor–double acceptor (DDAA) water molecules (D-donor, A-acceptor) in the gap between the two distinct relatively narrow spectral range corresponding, as in the octamer, to double donor–single acceptor (DDA) and single donor–double acceptor (DAA) water molecules.

Autoionization-detected infrared spectroscopy of intramolecular hydrogen bonds in aromatic cations. II. Unconventional intramolecular hydrogen bonds

A newly developed infrared spectroscopic technique, called autoionization-detected infrared (ADIR) spectroscopy, was applied for a study on hydroxyl–alkyl interactions in cresol and ethylphenol cations. In this technique, vibrational transitions in the ion core of high Rydberg states, which has almost the same vibrational structure as the corresponding bare molecular ion, are measured by detecting the vibrational autoionization signal. The OH stretching vibrations in the rotational isomers of the ortho-, meta-, and para-cresol cations and those of the ethylphenol cations were observed. Remarkable low-frequency shifts of the OH vibration were found only for the cis rotational isomers of the ortho-cresol and ortho-ethylphenol cations, whereas no such shift was found for all the other rotational and structural isomer cations. On the other hand, no remarkable shift of the OH stretch frequency was found for all the isomers in the neutral ground state. These results indicate that an intramolecular hydrogen bond is formed between the hydroxyl and alkyl groups in the cationic ground state of ortho-cresol and ortho-ethylphenol. The remarkable low-frequency shift of the OH vibration also indicates that the alkyl group acts as a proton acceptor in the hydrogen bond. This is a new type of intramolecular hydrogen bond, and the origin of such unconventional hydrogen bond in the cations is discussed.

Theoretical Study of Structure and Spectra of Cage Clusters (H2O)n, n = 7−10

The optimal structures, interaction energies, and OH stretch frequencies of water cage clusters, (H2O)n, n = 7−10, have been investigated theoretically. The study consisted of MP2 level ab initio c...

Periodic B3-LYP calculations on H-Edingtonites, both alone and interacting with acetylene

The EDI framework has been adopted, for the first time, to define a series of zeolites derived from the all-silica Edingtonite, featuring a tetragonal lattice with five SiO2 groups per unit cell, by substitution of a single Si atom per unit cell by an Al atom and the addition of a charge-compensating acidic proton. Four different H-EDI structures have been considered, the geometries of which have been obtained by minimizing the mechanical energy defined in terms of a model ion potential force field. The relative stability and the anharmonic OH-stretching frequency have been computed for the resulting optimized geometries by an abinitio periodic method using the B3-LYP hamiltonian and polarized basis set of double zeta quality. The electrostatic potential and the electric field within the zeolite cavity have also been computed abinitio. The interaction of acetylene with a given H-EDI structure has then been studied at the abinitio B3-LYP level, by optimizing selected degrees of freedom. The binding energy and the OH frequency shift due to interaction with acetylene have been computed and compared with those from molecular cluster models containing the Brønsted site. From energetic and vibrational data of the interaction with acetylene, the periodic structure appears more acidic than the adopted model clusters. The H-EDI zeolite appears to be an attractive model system for its structural simplicity which allows one to study the interaction of small probe molecules using moderate computational resources.

Differing Effects of Particle Size and Shape in the Infrared and Raman Spectra of Kaolinite

A B S T R ACT : Infrared (IR) spectra of well-ordered kaolinites generally show four OH-stretching frequencies, near 3697, 3670, 3652 and 3620 cm i. Raman spectra of the same kaolinites mostly show an additional band near 3686 cm -~, which, in the coarsely crystalline Keokuk kaolinite, largely replaces the 3695 cm -I band. It is shown that the 3686 cm ~ band can be ascribed to a transverse optical crystal vibration involving the in-phase stretching vibration of the three inner-surface hydroxyl groups in the unit-cell. Raman exciting radiation, commonly of wavelength near 500 nm, can excite this crystal vibration in crystals of comparable and greater thickness. Infrared studies are usually made on clay-size (<2 ~tm) particles, which have mean thicknesses of 30-150 nm. Infrared radiation of wavelength near 2.7 gm can only excite whole crystal vibrations perpendicular to the plates. The in-phase vibration of inner-surface OH groups in the whole-crystal mode lies at 3697 cm -1, which is the same frequency as that of the longitudinal optical mode in macroscopic crystals.

Differing Effects of Particle Size and Shape in the Infrared and Raman Spectra of Kaolinite

Infrared (IR) spectra of well-ordered kaolinites generally show four OH-stretching frequencies, near 3697, 3670, 3652 and 3620 cm (super -1) . Raman spectra of the same kaolinites mostly show an additional band near 3686 cm (super -1) , which, in the coarsely crystalline Keokuk kaolinite, largely replaces the 3695 cm (super -1) band. It is shown that the 3686 cm (super -1) band can be ascribed to a transverse optical crystal vibration involving the in-phase stretching vibration of the three inner-surface hydroxyl groups in the unit-cell. Raman exciting radiation, commonly of wavelength near 500 nm, can excite this crystal vibration in crystals of comparable and greater thickness. Infrared studies are usually made on clay-size (

Conformational analysis of alkoxyalcohols A combined IR and molecular mechanics study

The conformational behaviour of one branched and three linear alkoxyalcohols has been investigated by IR spectroscopy and molecular mechanics (MM). The OH-stretching region (3750–3150 cm-1) has been studied in dilute apolar solution. In the MM calculations, for each compound all unique staggered conformations have been analysed, both with and without contributions to the steric energy from rotational and vibrational energy and entropy. The corrections enhance the amount of non-bonded conformers and significantly improve the agreement between theoretical and experimental populations. Calculated H-bond geometries are seen to be related with observed OH-stretching vibrations. The agreement between theoretical and experimental frequency shifts (ΔOH, i.e. the difference between free and bonded) is poor, especially for short H-bond contacts, thus making calculated OH-stretching frequencies unsuitable for assignment purposes.

Infrared Spectroscopy of Hydrogen-Bonded Phenol−Amine Clusters in Supersonic Jets

We report infrared spectra of hydrogen-bonded phenol−amine clusters, phenol−NH3, −N(CH3)3, −NH(C2H5)2, and −N(C2H5)3, prepared in jet expansions. The OH, NH, and CH stretching fundamentals were studied. Infrared−ultraviolet double-resonance techniques were utilized for vibrational spectroscopy of size-selected clusters. The OH stretch frequencies of the phenol moieties showed extremely large red-shifts from that of bare phenol, reflecting the strong proton affinities of the amines. Moreover, non-proton-transferred structures of the clusters were confirmed. The detailed structure of phenol−NH3 was examined by ab initio calculations, which reproduced the observed infrared spectrum.

How reliable is the Lippincott-Schroeder potential for the OH…N hydrogen bonded fragment in the gas phase?

Ab initio calculations at the MP2 level of theory, with a 6–31 G basis set which includes polarization functions on the atoms involved in the H bond, are performed on the hydrogen-bonded phenol-NH 3 complex. The equilibrium O…N distance ( R e) is equal to 2.837 Å. The potential profile along the proton coordinate at a fixed O…N distance V( r, R e) only one minimum. Its shape is verified by calculation of the OH stretch frequency. The Lippincott-Schroeder potential is able to reproduce the shape of the V( r, R e) function for systems with an OH…N fragment in the gas phase only if some its parameters are calibrated to fit high-level ab initio data.

A study of bernalite, Fe(OH)3, using M�ssbauer spectroscopy, optical spectroscopy and transmission electron microscopy

To study the crystal chemistry of bernalite, Fe(OH)3, and the nature of the octahedral Fe3+ environment, Mossbauer spectra were recorded from 80 to 350 K, optical spectra were recorded at room temperature and a sample was studied using transmission electron microscopy. The Mossbauer spectrum of bernalite consists of a single six-line magnetic spectrum at 80 K. A broadened six-line magnetic spectrum with significantly less intensity is observed at higher temperatures, and is attributed to a small fraction of bernalite occurring as small particles. The variation of hyperfine magnetic field data for bulk bernalite with temperature is well described by the Weiss molecular field model with parameters of H0 = 55.7±0.3 T and TN = 427±5K. The centre shift data were fitted to the Debye model with parameters δ0=0.482±0.005 mm/s (relative to α-Fe) and ΘM=492±30 K. The quadrupole shift is near zero at 300 K, and does not vary significantly with temperature. Absorption spectra in the visible and near infrared range show three crystal field bands of Fe3+ at 11 300, 16000 and 23 200 cm-1, giving a crystal field splitting of 14 570 cm-1 and Racah parameters of B=629 cm-1 and C=3381 cm-1. Infrared reflection spectra show two distinct OH-stretching frequencies, which could correspond to two structurally different types of OH groups. A band was also observed at 2250 cm-1, suggesting the presence of molecular CO2 in the large cation site. Analytical transmission electron microscopy indicates that Si occurs within the bernalite structure as well as along domain boundaries. Electron diffraction and imaging show that bernalite is polysynthetically twinned along {100} planes with twin domains ranging from 3 to 20 nm in thickness. Results are discussed with respect to the nature of the octahedral Fe3+ site, and compared with values for other iron oxides and hydroxides.

Computer Simulation of Cation Distribution in Dioctahedral 2:1 Layer Silicates Using IR-Data: Application to Mössbauer Spectroscopy of a Glauconite Sample

AbstractA new approach is described to computer simulate cation distribution in octahedral sheets of dioctahedral 2:1 layer silicates with vacant trans-octahedra. This approach makes use of the information on cation distribution at the one-dimensional level provided by integrated IR optical densities for the region of OH-stretching frequencies. By using this program it is possible to show that (1) the Mössbauer spectrum of glauconite B. Patom conforms to the structural model composed of celandonite-like and illite-like domains whose dimensions are limited by approximately 2 or 4 unit cells; (2) non-equivalency of “left” and “right” cis-positions (with fixed b-direction) with respect to R2+ and R3+ occupancy is a characteristic feature of a celadonite-like domain.

On long and short hydrogen-bonds

Abstract Experimental results of OH-stretching frequencies, O-O- and O-H-distances are compared with each other and are discussed in connection with results of the same characteristic parameters as well as their complexation energies as determined on the basis of the theoretical ab initio calculations of Almlof for [Cl ⋯H⋯ Cl]− complexes. The comparison of the various results shows that the deviation of the X-H-distance ΔrOH and ΔrClH, respectively, from the central position seems to be a helpful tool in order to distinguish between asymmetric H-bond potentials and potentials in which the lowest energy level is above the potential barrier (more or less symmetric H-bonds). The theoretical results support the idea that the vOH−ROO correlation is not continuous at ROO ⋍ 2.44 A - the O-O-distance where the strongest H-bonds are to be expected. The theoretical results indicate, that the correlation of the H-bond energy ΔE(v=0) with the XH-frequency (or frequency shift) is not linear and is different for asymmetric and more or less symmetric H-bonds. However, for relative frequency shifts of more than approximately 30% the change in H-bond energy is expected to be of the order of kT. This indicates, that the influence of the surrouding of a H-bond will become very important for comparatively strong H-bonds (approx. −22kcal/mol H-bond for ClH-complexes).

Bridged calix[4]arenes; X-ray crystal and molecular structures and spectroscopic studies

Single crystals of two macrocyclic compounds of the calix[4] arene type, in which two opposite para-positions are connected by an additional aliphatic chain where n= 5 (1a) or n= 7 (1c) respectively, were obtained from acetone without incorporation of solvent. Crystals of compound (1a) are monoclinic, space group P21/n, a= 8.879(1), b= 17.216(4), c= 18.167(3)A, β= 98.16(1)°, V= 2 748.2 A3, Z= 4, Dx= 1.258 g cm–3, final R-value 0.046 (2 476 unique reflections); crystals of compound (1c) are monoclinic, space group P21/c, a= 18.105(3), b= 9.117(2), c= 19.123(2)A, β= 97.84(1)°, V= 3127.0 A–3, Z= 4, Dx= 1.166 g cm–13, final R-value 0.043 (4 470 unique reflections). In both cases the arrangement of the four phenolic residues corresponds to the cone conformation. This cone is strongly distorted in the case of compound(1a), where two aromatic rings are nearly parallel. For the whole series of bridged calix[4]arenes (n= 5–14) FTIR spectra were measured in CCl4. A decreasing OH-stretching frequency with increasing chain length n shows an increasing strength of the intramolecular hydrogen bonds. These results, which are also supported by the 1H NMR data, are discussed in connection with the molecular conformations found in the crystalline state.

Etude par spectroscopic Raman et infrarouge des verres de pseudo-spin Rb 0,65(NH 4) 0,35H 2PO 4

Raman and infrared spectra of RbH 2PO 2 and NH 4H 2PO 4 crystals and of the solid solution Rb 0.65(NH 4) 0.35H 2PO 4 have been studied at room and liquid helium temperatures. The paraelectric→ ferroelectric transition of RbH 2PO 4 is characterized by the increased number of bands and to some extent by band narrowing. The paraelectric→antiferroelectric transition of NH 4H 2PO 4 has a much more profound effect on the Raman and infrared spectra, mainly because of the dynamic orientational disorder of ammonium ions in the paraelectric phase. The solid solution Rb 0.65(NH 4) 0.35H 2PO 4 spectra at 20 K containing a frustrated OH·O bonded system in the competing ferroelectric and antiferroelectric interactions show that the hydrogen bonds are not much modified with respect to those of pure crystals as far as OH-stretching frequencies (and thus distances) and band shapes are concerned. The bands associated with the vibrations of ammonium ions also remain broad at low temperature indicating a frozen-in NH 4 + orientational disorder in the solid solution. This is probably the factor determining the overall characteristics of the spectra.

Calculation of the effect of shock and temperature on hydrogen bonding in water

Previously developed empirical potentials which well describe H bonding in a variety of materials have been used to calculate the effect of shock on H bonding in water. The calculations account for the anomalous decrease of the internal OH stretch frequency of the water molecule with increasing shock pressure, and also can account for the temperature-dependent decrease in the number of H bonded water complexes. A new form of water which is symmetrically H bonded is predicted to exist in a shock front above 9 GPa of shock pressure.