OH Bond Length Research Articles

Systematic Design-of-Experiments, factorial-design approaches for tuning simple empirical water models

ABSTRACT Using systematic Design-of-Experiments, factorial-design approaches, we identify how five variables (site charge, sigma, epsilon, OH bond length and HOH bond angle) affect the diffusivity and radial distribution function accuracy within the framework of the Simple Point Charge water model. From this (by a full-functional DoX-effects model), we glean response equations for the effects of these systematic variations on both estimation of site-site radial distribution functions, in addition to self-diffusivities, allowing scope to estimate more precisely optimal parameters for use in tailored force-fields for particular purposes (e.g. improved fidelity towards particular desired structural or dynamical properties). To this end, the diffusivity error was reduced from an initial value of 35.2–0.64%, whilst the radial distribution function was more difficult to improve, with a reduction in error of 2.83%.

Prediction of the infrared spectrum of water on graphene substrate using hybrid classical/quantum simulation

IR spectroscopy is one of the most important methods for clarifying the microscopic behavior of surficial water. We theoretically predict the IR spectrum of water molecules on a graphene substrate using a hybrid method that combines classical molecular dynamics and density functional theory. The IR spectrum of surficial water is characterized by a blue shift of the stretching mode compared to the spectrum of bulk water, and by the appearance of a small sub-peak at around 2950 cm−1. These changes are related to differences in the OH bond length and bonding pattern for hydrogen bonds.

Beyond Badger's Rule: The Origins and Generality of the Structure-Spectra Relationship of Aqueous Hydrogen Bonds.

The structure of hydrogen bonded networks is intimately intertwined with their dynamics. Despite the incredibly wide range of hydrogen bond strengths encountered in water clusters, ion-water clusters, and liquid water, we demonstrate that the previously reported correlation between the change in the equilibrium bond length of the hydrogen bonded OH covalent bond and the corresponding shift in its harmonic frequency in water clusters is much more broadly applicable. Surprisingly, this correlation describes the ratios for both the equilibrium OH bond length/harmonic frequency and the vibrationally averaged bond length/anharmonic frequency in water, hydronium water, and halide water clusters. Consideration of harmonic and anaharmonic data leads to a correlation of -19 ± 1 cm-1/0.001 Å. The fundamental nature of this correlation is further confirmed through the analysis of ab initio Molecular Dynamics (AIMD) trajectories for liquid water. We demonstrate that this simple correlation for both harmonic and anharmonic systems can be modeled by the response of an OH bond to an external field. Treating the OH bond as a Morse oscillator, we develop analytic expressions, which relate the ratio of the shift in the vibrational frequency of the hydrogen-bonded OH bond to the shift in OH bond length, to parameters in the Morse potential and the ratio of the first and second derivatives of the field-dependent projection of the dipole moment of water onto the hydrogen-bonded OH bond. Based on our analysis, we develop a protocol for reconstructing the AIMD spectra of liquid water from the sampled distribution of the OH bond lengths. Our findings elucidate the origins of the relationship between the molecular structure of the fleeting hydrogen-bonded network and the ensuing dynamics, which can be probed by vibrational spectroscopy.

Dipotassium tetrahydroxidopentaoxidotetraborate monohydrate

In the tetraborate anion of the title compound, K2[B4O5(OH)4]·H2O, the bridging B—O bond lengths of the tetrahedral BO4 and the trigonal-planar BO3 units are slightly longer than the corresponding terminal B—OH bond lengths. The crystal structure is stabilized by intermolecular O—H...O, O—H...Owater and Owater—H...O hydrogen bonds, generating a three-dimensional network. The two potassium cations both show a coordination number of 9.

An accurate full-dimensional permutationally invariant potential energy surface for the interaction between H2O and CO.

The interaction between H2O and CO has been the subject of numerous experimental and theoretical investigations for a long time due to their important roles in various environments, such as the atmosphere, combustion of hydrocarbons, and the interstellar medium. In this work, the first full-dimensional accurate potential energy surface (PES) was developed for the CO + H2O system based on ca. 102 000 points calculated at the level of an explicitly correlated coupled-cluster method with single, double, and perturbative triple excitations with the augmented correlation-consistent polarized triple zeta basis set (CCSD(T)-F12a/AVTZ) using the permutation invariant polynomial-neural network (PIP-NN) method. The geometries, energies, and frequencies of the two complex wells, CO-H2O and OC-H2O, and one transition state connecting them, as well as some interconversions between different conformers, are accurately reproduced by the PES, thanks to the small fitting error of only 1.08 meV. With full-dimensional degrees of freedom considered in the PES, we found that there exist strong dependences of the CO and OH bond lengths on the OC-H2O and CO-H2O interaction energies, which is not possible in reduced dimensional PESs. Finally, classical dynamics was carried out to study the energy transfer between H2O and CO with different initial vibrational energies in H2O and different vibrational states in CO.

ATR-FTIR study of the isosbestic point in water solution of electrolytes

Here we report an ATR-FTIR study on aqueous electrolytic solutions aimed to investigate the nature of the isosbestic point observed in the stretching mode broad band. This feature reveals that the properties of the system are described by the superposition of two components at equilibrium whose relative abundance depends on the running parameter. Here we show that the OH intramolecular bond length changes differently in the two components. It has been observed that, surprisingly, the OH bond length of highly correlated water molecules decreases with the concentration of the solute. On the opposite, it expands in molecules belonging to small cluster. As the shortening of the OH bond shows that the water-water interaction prevails on water-ion interaction, we make the hypothesis that the decrease of the bond length is due to a collective behaviour of the water molecules replacing the classic concept of H-bond in water.

Effect of ionic charge on O[formula omitted]H⋯Se hydrogen bond: A computational study

Complexes between para-substituted cationic phenol and SeH2 have been investigated in electronic ground state at the B3LYP, B3PW91, and ωB97xD levels of theory using 6-311++G(3df,3pd) basis set. Various electron-donating and withdrawing substituents (NH2, OH, CH3, H, F, Cl, CN, and NO2) are used to characterize electronic substituent effect on intermolecular +OH⋯Se hydrogen bond. Electron withdrawing substituent increases hydrogen bond stabilization energy and red shift in OH stretching frequency. Introduction of a positive charge transforms weak hydrogen bond of neutral OH⋯Se type into a strong hydrogen bond. Complexation induced changes on various hydrogen bond parameters, such as, stabilization energy, change in OH bond length, change in OH stretching frequency, extent of charge transfer from hydrogen bond acceptor to donor, hydrogen bond orders, electron density at the hydrogen bond critical point exhibit conventional electronic substitution effect. Stabilization energy of +OH⋯Y hydrogen bond are similar in the complexes between cationic phenol and SH2/SeH2, whereas it is almost twice with OH2 in case of +OH⋯Y hydrogen bond.

ChemInform Abstract: Structural Studies on Mannich Bases of 2‐Hydroxy‐3,4,5,6‐tetrachlorobenzene. An UV, IR, NMR and DFT Study. A Mini‐Review

AbstractReview: 30 refs.

Structural studies on Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene. An UV, IR, NMR and DFT study. A mini-review

Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene are chosen as an exemplary case for tautomeric Mannich bases. Molecular structures are calculated. OH stretching frequencies are rationalized based on DFT calculations. Intrinsic deuterium isotope effects on 13C chemical shifts in the M-form are estimated based on OH bond lengths. The observed deuterium isotope effects on 13C chemical shifts are demonstrated to be largely of equilibrium type except at ambient temperatures.

Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein

Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21Å by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440–4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effect have so far underestimated the bond length by more than 0.07Å. To elucidate the origin of the difference, we performed a vibrational analysis of the H bond on potential energy curve with O…O distance of 2.47Å on the equilibrium structure, and that with O…O distance of 2.56Å on the experimental crystal structure. While the vibrationally averaged OH bond length for equilibrium structure was underestimated, the corresponding value for crystal structure was in reasonable agreement with the corresponding experimental values. The elongation of the O…O distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP.

Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

Neutron diffraction structures of water in crystalline hydrates of metal salts.

Neutron diffraction structures of water molecules in crystalline hydrates of metal salts have been collected from the literature up to December 2011. Statistical methods were used to investigate the influence on the water structures of the position and nature of hydrogen bond acceptors and cations coordinated to the water oxygen. For statistical modelling the data were pruned so that only structures with oxygen as hydrogen acceptors, single hydrogen bonds, and no more than two metals or hydrogens coordinated to the water oxygen were included. Multiple linear regression models were fitted with the water OH bond length and bond angle as response variables. Other variables describing the position and nature of the acceptors and ions coordinated to the waters were taken as explanatory variables. These variables were sufficient to give good models for the bond lengths and angles. There were sufficient structures involving coordinated Mg(2+) or Cu(2+) for a separate statistical modelling to be done for these cases.

Tunneling isomerization of small carboxylic acids and their complexes in solid matrixes: a computational insight.

We have studied hydrogen-atom tunneling in the cis-to-trans conformational change of some carboxylic acid monomers and formic acid (FA) complexes and dimers at the MP2(full) and CCSD(T) levels of theory within the Wentzel-Kramers-Brillouin approximation. The barrier for the minimum energy path, where the OH bond length and the COH bending angle are optimized, is found to be a good approximation for providing the highest barrier transparency. The matrix effect on the transmission coefficients of cis-FA monomer, trans-cis FA dimer (tc1), and cis-acetic acid monomer are modeled by the polarizable continuum model (PCM) at the MP2(full) level of theory in different environments. For the cis-FA monomer and trans-cis FA dimer (tc1), the calculated transmission coefficients agree with the experimental lifetimes observed in noble-gas solids. However, this method cannot reproduce the experimental results obtained for cis-acetic acid. Moreover, the long lifetime of cis-FA and cis-acetic acid in the N2 environment cannot be reproduced either, which is most probably due to specific interactions that are not included in the PCM. The calculation for cis-HCOOD shows a strong decrease of the barrier transparency compared to that for cis-HCOOH, which is consistent with the experiments. In general, good agreement is observed between the calculated barrier transparency (including PCM) and experimental tunneling rate. However, some exceptions are found, which shows that additional factors influence the tunneling rate.

Periodic, vdW-corrected density functional theory investigation of the effect of Al siting in H-ZSM-5 on chemisorption properties and site-specific acidity

Twelve crystallographically distinct Al substitution sites of H-ZSM-5 are modeled by periodic density functional theory using the vdW-DF functional. While the stability of Al substitution and Brønsted acid OH bond length at different active site positions are similar, the OH stretch frequency, SiOAl bond angle, and adsorption energies of various probe molecules differ notably without observable correlations between these properties. Comparison of adsorption energy values with and without van der Waals corrections demonstrates the significance of the inclusion of dispersion interactions. Our data indicate that theoretical investigations of H-ZSM-5 require a careful selection of the location of the active site.

Effect of molecular structure on fluid transport through carbon nanotubes

We perform molecular dynamics simulations to study the transport of geometrically modified water models through channels of carbon nanotube (CNT) membranes. We use two modifications to an existing water model (extended simple point charge SPC/E) as representative surrogates of molecular fluids: (1) bent model (model B) in which the HOH angle is varied while keeping the dipole moment constant by adjusting the OH bond length and (2) modified bent model (model MB) in which the HOH angle changes without any change in OH bond length thereby changing the dipole moment. Interestingly, we find that the fluid transport is a nonmonotonic function of the bond angle for both fluid models. This observed trend is not anticipated based on the fluid density as a function of the bond angle inside and outside of the nanotube channel. However, the average residence time of transmitted molecules through the channel provides an approximately inverse linear correlation with the observed flux, independent of the fluid model. Based on these correlations, we have developed an empirical design parameter connecting fluid transport through CNTs as a function of average occupancy (number of fluid molecules inside the nanotube) and the average residence time. Our results suggest that transport through carbon nanotubes can be sensitive to small changes in the structure of fluid molecules that can potentially be utilised for mixture separation.

Compositional effects on Si–OH bond length in hydrous silicates with implications for trends in the SiOH acidity

Theoretical calculations of the structure and Brønsted acidity of SiOH groups in silica clusters have never addressed the question if these vary with the degree of SiOH deprotonation. In this connection, a statistical analysis is presented of Si–OH bond lengths in crystalline hydrogen silicates with well-determined structures with a special emphasis placed on effects of the silicate composition. It is found that among hydrogen silicates of large cations with low charges the Si–OH bonds are always longer than terminal Si–O bonds in the same anion and correlate in length with the anionic charge per tetrahedron. The findings are explained by steric limitations on charge balancing at oxygen atoms by hydrogen bonds and/or cations. It is suggested that similar limitations and imbalances may underlie the well-known trends in the Brønsted acidity of silicic acids and silicas in aqueous media: decreased acidity with increased SiOH deprotonation and increased acidity with increased tetrahedra connectivity.

TDDFT study of excitation of water molecules with short laser pulses

We explore the excitation of water molecules subject to short and intense laser pulses in the frame of time-dependent density function theory (TDDFT) at the level of the time-dependent local-density approximation (TDLDA), applied to valence electrons, coupled non-adiabatically to molecular dynamics (MD) of ions. We first study the optical absorption spectra of the water molecule as an observable in the “linear" domain and results are in good agreement with experiments. We then explore the influence of the laser frequency on the excitation. It is found that when the laser frequency is off-resonant or highly above the resonant region, the excitations are weak whereas for the resonant frequency case, the ionization is enhanced and bond lengths are enlarged. Furthermore, a direct coupling of ions with the laser pulse with the off-resonant frequency is found when investigating the OH bond lengths. We finally study the effect of laser intensity on the excitation of H2O and it is found that ionization increases when the laser intensity varies from low to high and we observe stable vibrations to Coulomb fragmentation when the ionization is up to typically two more charge units.

Crystal chemistry, thermal expansion, and Raman spectra of hydroxyl-clinohumite: implications for water in Earth’s interior

Two samples of hydroxyl-clinohumite, sample SZ0407B with approximate composition Mg8.674(14)Fe0.374(4)(Si0.99(1)O4)4(OH)2 and sample SZ0411B with composition Mg9(SiO4)4(OH)2, were synthesized at 12 GPa and 1,250 °C coexisting with olivine. Unit-cell parameters determined by single-crystal X-ray diffraction are given as follows: a = 4.7525(4) A, b = 10.2935(12) A, c = 13.7077(10) A, α = 100.645(9)°, V = 659.04(9) A3 for SZ0407B, and a = 4.7518(6) A, b = 10.2861(12) A, c = 13.7008(9) A, α = 100.638(9)°, V = 658.15(9) A3 for SZ0411B. Single-crystal X-ray intensity data were collected for crystal structure refinements of both samples. Relative to the pure-Mg sample, Fe decreases M3–OH bond lengths by ~0.010(3) A, consistent with some ferric iron ordering into M3. Raman spectroscopy shows two strong bands in the lattice-mode region at 650 and 690 cm−1 in the Fe-bearing sample, which are not observed in the pure-Mg sample. Spectra in the H2O region show at least five bands, which are deconvolved into seven distinct O–H-stretching modes. Thermal expansion measurements were carried out for both samples from 153 to 787 K by single-crystal X-ray diffraction. The average a-, b-, c-axial and volumetric thermal expansion coefficients (10−6 K−1) are 10.5(1), 12.3(2), 12.5(2) and 34.9(5) for SZ0407B, respectively, and 11.1(1), 12.6(3), 13.7(3), 36.8(6) for SZ0411B, respectively. After heating, the unit-cell parameters were refined again for each sample at ambient condition, and no significant changes were observed, indicating no significant oxidation or dehydration during the experiment. For the DHMS phases along the brucite–forsterite join, linear regression gives a systematic linear decrease in expansivity with increasing density. Further, substitution of ferrous iron into these structures decreases thermal expansivity, making the Fe-bearing varieties slightly stiffer.

Pressure-induced hydrogen bond symmetrisation in guyanaite, β-CrOOH: evidence from spectroscopy and ab initio simulations

Guyanaite, β-CrOOH, is a structural analogue of the high-pressure oxyhydroxide phases δ-AlOOH and ɛ-FeOOH. Here, it was synthesized in piston-cylinder and multi-anvil press experiments at 4–13.5 GPa and 900–1100 °C. The deuterated phase β-CrOOD was synthesized at 4 GPa and 600 °C. The samples were characterized at ambient conditions by X-ray diffraction, diffuse optical reflectance spectroscopy and infrared absorption (IR) spectroscopy. In addition, the structural evolution of β-CrOOH and β-CrOOD with increasing pressure up to about 20 GPa was studied by in situ IR spectroscopy in a diamond anvil cell (DAC). This investigation was complemented by first-principles calculations in the framework of the density-functional theory (DFT). A pronounced geometric isotope effect and very short O-H. . .O bond lengths of 2.497(3) A for β-CrOOH and 2.541(3) A for β-CrOOD are observed at ambient pressure. In the IR spectra, no bands show up above 2000 cm−1, which indicates strong hydrogen bonding. The evolution of OH- and OD-related vibrational bands with pressure studied by IR spectroscopy shows a discontinuity at about 5 GPa. The DFT calculations suggest that this change in compression mechanism is related to a second-order phase transition from the low-pressure phase with asymmetric hydrogen positions (space group P 21 nm or Pnnm ) to a high-pressure phase with space group Pnnm that is characterized by symmetric hydrogen bonds with two identical OH bond lengths of 1.20(1) A. Using density functional perturbation theory, the most prominent high-frequency modes observed in the IR spectra are assigned to O-H-O bending vibrations. The transition pressure for hydrogen bond symmetrisation in β-CrOOH is considerably lower than in other hydrous phases of recent interest, such as δ-AlOOH or phase D.

Reactive quenching of OH A 2Σ+ by O2 and CO: Experimental and nonadiabatic theoretical studies of H- and O-atom product channels

The outcomes following collisional quenching of electronically excited OH A (2)Σ(+) by O(2) and CO are examined in a combined experimental and theoretical study. The atomic products from reactive quenching are probed using two-photon laser-induced fluorescence to obtain H-atom Doppler profiles, O ((3)P(J)) atom fine structure distributions, and the relative yields of these products with H(2), O(2), and CO collision partners. The corresponding H-atom translational energy distributions are extracted for the H + O(3) and H + CO(2) product channels, in the latter case revealing that most of the available energy is funneled into internal excitation of CO(2). The experimental product branching ratios show that the O-atom producing pathways are the dominant outcomes of quenching: the OH A (2)Σ(+) + O(2) → O + HO(2) channel accounts for 48(3)% of products and the OH A (2)Σ(+) + CO → O + HCO channel yields 76(5)% of products. In addition, quenching of OH A (2)Σ(+) by O(2) generates H + O(3) products [12(3)%] and returns OH to its ground X (2)Π electronic state [40(1)%; L. P. Dempsey, T. D. Sechler, C. Murray, and M. I. Lester, J. Phys. Chem. A 113, 6851 (2009)]. Quenching of OH A (2)Σ(+) by CO also yields H + CO(2) reaction products [26(5)%]; however, OH X (2)Π (v" = 0,1) products from nonreactive quenching are not observed. Theoretical studies characterize the properties of energy minimized conical intersections in four regions of strong nonadiabatic coupling accessible from the OH A (2)Σ(+) + CO asymptote. Three of these regions have the O-side of OH pointing toward CO, which lead to atomic H and vibrationally excited CO(2) products and/or nonreactive quenching. In the fourth region, energy minimized points are located on a seam of conical intersection from the OH A (2)Σ(+) + CO asymptote to an energy minimized crossing with an extended OH bond length and the H-side of OH pointing toward CO in a bent configuration. This region, exoergic with respect to the reaction asymptote, is likely to be the origin of the dominant O + HCO product channel.