Matrix isolation infrared spectroscopic and theoretical study of the reactions of tantalum oxide molecules with methanol

The reactions of tantalum monoxide (TaO) and dioxide (TaO(2)) molecules with methanol in solid neon were investigated by infrared absorption spectroscopy. The ground-state TaO molecule reacted with CH(3)OH in forming the CH(3)OTa(O)H molecule via the hydroxylic hydrogen atom transfer from methanol to the metal center spontaneously on annealing. The observation of the spontaneous reaction is consistent with theoretical predictions that the OH bond activation process is both thermodynamically exothermic and kinetically facile. In contrast, the TaO(2) molecule reacted with CH(3)OH to give primarily the TaO(2)(CH(3)OH) complex, which further rearranged to the CH(3)OTa(O)OH isomer via the hydroxylic hydrogen atom transfer from methanol to one of oxygen atom of metal dioxide upon visible light excitation.     

(R)‐(6,6′‐Dihydroxybiphenyl‐2,2′‐diyl)bis(diphenylphosphine oxide) methanol solvate

The title compound, C₃₆H₂₈O₄P₂·CH₄O, was synthesized directly from the methoxy analogue. The crystal structure shows that one OH group interacts with an O atom of a phosphine oxide group in an adjacent mol­ecule, while the other OH group complexes with the methanol solvent molecule via intermolecular hydrogen bonds. An O atom of one phosphine oxide group interacts with the hydroxy H atom of methanol via a hydrogen bond. There are intra‐ and intermolecular π–π interactions between the phenyl rings. All these interactions result in the formation of supramolecular chiral parallelogram channels via self‐assembly.     

Overtone spectroscopy of sulfonic acid derivatives

Vapor-phase OH-stretching overtone spectra of methanesulfonic acid and trifluoromethanesulfonic acid were recorded in the Deltav(OH) = 4 and 5 regions using cavity ring-down spectroscopy. We compare these spectra to those of sulfuric acid to consider the effect on vibrational overtone spectra of replacing one of the OH groups with a more or less electronegative group. We complement our experimental work with anharmonic oscillator local mode calculations of the OH-stretching frequencies and intensities. The presence of a weak intramolecular interaction between the hydrogen atom of the OH group and the oxygen atom of the adjacent S=O group in methanesulfonic acid lowers its OH-stretching frequency from what would otherwise be predicted based on the electronegativity of the methyl group.     

IR-UV double resonance spectroscopic investigation of phenylacetylene-alcohol complexes. Alkyl group induced hydrogen bond switching

The electronic transitions of phenylacetylene complexes with water and trifluoroethanol are shifted to the blue, while the corresponding transitions for methanol and ethanol complexes are shifted to the red relative to the phenylacetylene monomer. Fluorescence dip infrared (FDIR) spectra in the O-H stretching region indicate that, in all the cases, phenylacetylene is acting as a hydrogen bond acceptor to the alcohols. The FDIR spectrum in the acetylenic C-H stretching region shows Fermi resonance bands for the bare phenylacetylene, which act as a sensitive tool to probe the intermolecular structures. The FDIR spectra reveal that water and trifluoroethanol interact with the pi electron density of the acetylene C-C triple bond, while methanol and ethanol interact with the pi electron density of the benzene ring. It can be inferred that the hydrogen bonding acceptor site on phenylacetylene switches from the acetylene pi to the benzene pi with lowering in the partial charge on the hydrogen atom of the OH group. The most significant finding is that the intermolecular structures of water and methanol complexes are notably distinct, which, to the best of our knowledge, this is first such observation in the case of complexes of substituted benzenes.     

Low variance energy estimators for systems of quantum Drude oscillators: treating harmonic path integrals with large separations of time scales

In the effort to develop atomistic models capable of accurately describing nanoscale systems with complex interfaces, it has become clear that simple treatments with rigid charge distributions and dispersion coefficients selected to generate bulk properties are insufficient to predict important physical properties. The quantum Drude oscillator model, a system of one-electron pseudoatoms whose "pseudoelectrons" are harmonically bound to their respective "pseudonuclei," is capable of treating many-body polarization and dispersion interactions in molecular systems on an equal footing due to the ability of the pseudoatoms to mimic the long-range interactions that characterize real materials. Using imaginary time path integration, the Drude oscillator model can, in principle, be solved in computer operation counts that scale linearly with the number of atoms in the system. In practice, however, standard expressions for the energy and pressure, including the commonly used virial estimator, have extremely large variances that require untenably long simulation times to generate converged averages. In this paper, low-variance estimators for the internal energy are derived, in which the large zero-point energy of the oscillators does not contribute to the variance. The new estimators are applicable to any system of harmonic oscillators coupled to one another (or to the environment) via an arbitrary set of anharmonic interactions. The variance of the new estimators is found to be much smaller than standard estimators in three example problems, a one-dimensional anharmonic oscillator and quantum Drude models of the xenon dimer and solid (fcc) xenon, respectively, yielding 2-3 orders of magnitude improvement in computational efficiency.     

Exploring the transfer of hydrogen atom from kaempferol-based compounds to hydroxyl radical at ground state using PCM-DFT approach

Thermodynamic and kinetic studies of the hydrogen atom transfer (HAT) from hydroxyl (OH) groups of four kaempferol-based compounds, namely kaempferol, morin, morin-5^*-sulfonate and morin-7-O-sulfate to hydroxyl radical (·OH), have been carried out using density functional theory (DFT) methods at the CAM-B3LYP/6–311++G(d,p) level equipped with polarizable continuum model (PCM) of solvation. All HAT reactions in aqueous solution are exothermic and spontaneous. For most compounds, the most preferable OH group for HAT is situated at position C3 (O3-H3) on the pyrone ring. The reaction potential of such a reactive group is found to be highest in morin-7-O-sulfate. The rate constants for the HAT reactions at different OH groups of each compound have been determined based on the transition state theory. The presence of substituents leads to the variation in either the characteristic interactions at the reactive site or the charge distribution on transition-state geometries, hence significantly affecting the kinetics of HAT. The highest rate of HAT is resulted for the OH group at position C4^* (O4^*-H4^*) on the phenyl ring (ring B) of morin-5^*-sulfonate because a hydrogen bond between ·OH and the sulfonate group favors the formation of transition state. However, for most compounds under study, the HAT reaction at O3-H3 initiated by ·OH is highly favorable both thermodynamically and kinetically.

     

Calculation of the characteristics of ethanol and methanol adsorbed in a pore of activated carbon by the density functional method

Density functional theory was used to perform quantum-chemical calculations of changes in the energy and structure characteristics of methanol and ethanol molecules caused by their adsorption in model slitlike pores of activated carbon. The conclusion was made that changes in these characteristics (bond lengths, angles, charges on atoms, and harmonic vibration frequencies) is additional evidence of the validity of the Tolmachev thermodynamic model, in which adsorption is treated as a quasi-chemical reaction of the addition of adsorbate molecules to adsorption centers of an adsorbent. It was shown that the arrangement of alcohol molecules, when the C-O and C-C bonds were approximately parallel to pore walls and the hydrogen atom was directed toward a nearer pore wall, was most favorable energetically. Two adsorbed alcohol molecules are also arranged parallel to pore walls and form a hydrogen bond.     

A DFT-based study of the hydrogen-bonding interactions between epicatechin and methanol/water

Tea polyphenols are essential components that give tea its medicinal properties. Methanol and water are frequently used as solvents in the extraction of polyphenols. Hydrogen-bonding interactions are significant in the extraction reaction. Density functional theory (DFT) techniques were used to conduct a theoretical investigation on the hydrogen-bonding interactions between methanol or water and epicatechin, an abundant polyphenol found in tea. After first analyzing the epicatechin monomer's molecular geometry and charge characteristics, nine stable epicatechin (EC) H₂O/CH₂OH complex geometries were discovered. The presence of hydrogen bonding in these improved structures has been proven. The calculated hydrogen bond structures are very stable, among which the hydrogen bond bonded with a hydroxyl group has higher stability. The nine complex structures’ hydrogen bonds were thought to represent closed-shell-type interactions. The interaction energy with 30O-31H on the epicatechin benzene ring is the strongest in the hydrogen bond structure. While the other hydrogen bonds were weak in strength and mostly had an electrostatic nature, the hydrogen bonds between the oxygen atoms in H₂O or CH₂OH and the hydrogen atoms of the hydroxyl groups in epicatechin were of moderate strength and had a covalent character. Comparing the changes in the hydrogen bond structure vibration peak, the main change in concentration peak is the hydrogen bond vibration peak in the complex. Improved the study on the hydrogen bond properties of CH₂OH and H₂O of EC.     

Methanol adsorption on the beta-Ga2O3 surface with oxygen vacancies: theoretical and experimental approach

Methanol adsorption on beta-Ga2O3 surface has been studied by Fourier transform infrared spectroscopy (FTIR) and by means of density functional theory (DFT) cluster model calculations. Adsorption sites of tetrahedral and octahedral gallium ions with different numbers of oxygen vacancies have been compared. The electronic properties of the adsorbed molecules have been monitored by computing adsorption energies, optimized geometry parameters, overlap populations, atomic charges, and vibrational frequencies. The gallia-methanol interaction has different behaviors according to the local surface chemical composition. The calculations show that methanol can react in three different ways with the gallia surface giving rise to a nondissociative adsorption, a dissociative adsorption, and an oxidative decomposition. The surface without oxygen vacancies is very reactive and produces the methanol molecule decomposition. The molecule is nondissociatively adsorbed by means of a hydrogen bond between the alcoholic hydrogen atom and a surface oxygen atom and a bond between the alcoholic oxygen atom and a surface gallium atom. Two neighbor oxygen vacancies on tetrahedral gallium sites produce the dissociation of the methanol molecule and the formation of a bridge bond between two surface gallium atoms and the methoxy group.     

Quantum Drude oscillator model for describing the interaction of excess electrons with water clusters: an application to (H2O)13(-)

Cluster anions for which the excess electron occupies an extended nonvalence orbital can be described by use of a model Hamiltonian employing quantum Drude oscillators to represent the polarizable charge distributions of the monomers. In this work, a Drude model for water cluster anions is described and used to investigate the (H2O)13(-) cluster. Several low-energy isomers are characterized, and the finite-temperature properties of the cluster are investigated by means of parallel tempering Monte Carlo simulations. Two structural motifs, one with double-acceptor water monomers and the other with four-membered rings of double-acceptor single-donor monomers with four free OH groups pointed in the same direction, are found to lead to large (approximately > eV) electron binding energies. The distributions of the computed vertical detachment energies qualitatively reproduce the experimentally measured photoelectron spectrum, and our simulations indicate that both of the main peaks in the measured spectrum derive from several isomers.     

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA)(2)] and [(o-TOL)(CA)(2)] have been prepared. The (13)C NMR, (1)H NMR, (1)H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H?N intermolecular hydrogen bond between 2NH(2) groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.     

Determination of the entropy of formation of the Pt(111)∣ perchloric acid solution interface. Estimation of the entropy of adsorbed hydrogen and OH species

The entropy of formation of the interface between a Pt(111) electrode and a 0.1-M HClO₄ solution is calculated here for the first time from the temperature dependence of total charge vs potential curves following a thermodynamic analysis based on the electrocapillary equation. From this quantity, the absolute entropies of specifically adsorbed species (hydrogen and OH) can be estimated. The present method is an alternative treatment of data that overcomes some of the limitations involved in the approach that uses a generalized isotherm. However, it requires additional experimental data: the temperature coefficient of the potential of zero total charge of the working electrode and the temperature coefficient of the reference electrode. Comparison of the results obtained by both approaches shows that, for hydrogen adsorption, the agreement is reasonable, but the differences are larger for OH adsorption, thus showing the limitations inherent in the treatment based on the generalized isotherm. Dedicated to Professor Oleg Petrii on the occasion of his 70th birthday on August 24, 2007.     

Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment

Dimethyl phosphate (DMP) anion has been used extensively as a model compound to simulate the properties of phosphate group. A 35-point DMP anion potential model is constructed based on the atom-bond electronegativity equalization fluctuating charge molecular force field (ABEEM/MM), and it is employed to study the properties of gas-phase DMP anion and DMP-(H₂O) _n (n = 1–3) clusters. The ABEEM/MM model reproduces well the properties obtained by available experiments and QM calculations, including charge distributions, geometries, and conformational energies of gas-phase DMP-water complexes. Furthermore, molecular dynamics simulation on the DMP anion in aqueous solution based on the ABEEM/MM shows that a remarkable first hydration shell around the nonesterified oxygen atom of DMP anion is formed with a coordination number of 5.2. It is also found that two hydrogen atoms of one water molecule form two hydrogen bonds with two nonesterified oxygen atoms of DMP anion simultaneously. This work could be used as a starting point for us to establish the ABEEM/MM nucleic acid force field.     

Characterization of intramolecular hydrogen bonds by atomic charges and charge fluxes

The electronic charge redistribution and the infrared intensities of the two types of intramolecular hydrogen bonds, O-H···O and O-H···π, of o-hydroxy- and o-ethynylphenol, respectively, together with a set of related intermolecular hydrogen bond complexes are described in terms of atomic charges and charge fluxes derived from atomic polar tensors calculated at the B3LYP/cc-pVTZ level of theory. The polarizable continuum model shows that both the atomic charges and charge fluxes are strongly dependent on solvent. It is shown that their values for the OH bond in an intramolecular hydrogen bond are not much different from those for the "free" OH bond, but the changes are toward the values found for an intermolecular hydrogen bond. The intermolecular hydrogen bond is characterized not only by the decreased atomic charge but also by the enlarged charge flux term of the same sign producing thus an enormous increase in IR intensity. The overall behavior of the charges and fluxes of the hydrogen atom in OH and ≡CH bonds agree well with the observed spectroscopic characteristics of inter- and intramolecular hydrogen bonding. The main reason for the differences between the two types of the hydrogen bond lies in the molecular structure because favorable linear proton donor-acceptor arrangement is not possible to achieve within a small molecule. The calculated intensities (in vacuo and in polarizable continuum) are only in qualitative agreement with the measured data.     

Plasmon resonances and plasmon‐induced charge transport in linear atomic chains

In linear hydrogen atomic chains, plasmon resonances and plasmon‐induced charge transport are studied by time‐dependent density functional theory. For the large linear chain, it is a general phenomenon that, in the longitudinal excitation, there are high‐energy resonances and a large low‐energy resonance. The energy of the large low‐energy resonance conforms to the results calculated by the classical Drude model. In order to explain the formation mechanism of the high‐energy resonances, we present a simple harmonic oscillator model. This model may reasonably account for the relationship between low‐energy and high‐energy resonances, and has a certain degree of universality. As the interatomic distance decreases, the current shows a gradual transition from insulator to metal. The current enhancement mainly depends on the local field enhancement associated with plasmon excitation, and the enhanced electron delocalization effect as a result of the decrease of the interatomic distance. © 2013 Wiley Periodicals, Inc.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

Intramolecular O―H⋯O and C―H⋯O hydrogen bond cooperativity in D‐glucopyranose and D‐galactopyranose—A DFT/GIAO,QTAIM/IQA,and NCI approach

Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom–atom interaction energies, and atomic charges for partial structures and conformers of α‐D‐glucopyranose, β‐D‐glucopyranose, and α‐D‐galactopyranose built up by introducing OH groups into 2‐methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3‐diol motif. Variations in the interaction energies reveal that a “new” hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C―H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O―H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O―H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom–atom distances are shorter, and interaction energies are enhanced.     

Bond properties using a modern version of the Drude model

Using a mixture of classical and quantum mechanics, Drude model formulas for the polarizability and magnetic susceptibility of an atom or molecule and the dispersion coefficient for intermolecular forces between atoms and molecules are obtained both when the same frequency of oscillation is used for all the electrons and when different frequencies are used. The latter case allows us to discuss bond properties. The frequencies involved can be determined in a nonempirical way when it is recognized that the Frost model can be regarded as giving an ab initio quantitative justification for the Drude model. © 1996 John Wiley & Sons, Inc.     

The complexes between CH3OH and CF4. Infrared matrix isolation and theoretical studies

The complex formed between methanol and tetrafluoromethane has been identified in argon and neon matrixes by help of FTIR spectroscopy. Three fundamentals (nu(OH), nu(FCF), and nu(CO)) were observed for the complex isolated in the two matrixes, and the OH stretch was red shifted in a neon matrix and blue shifted in an argon matrix with respect to the corresponding vibration of the methanol monomer. The theoretical studies of the structure and spectral characteristics of the complexes formed between CH(3)OH and CF(4) were carried out at the MP2 level of theory with the 6-311+G(2df,2pd) basis set. The calculations resulted in three stationary points from which two (I-1, I-2) corresponded to structures involving the O-H...F hydrogen bond and the third one (I-3) to the non-hydrogen-bonded structure. The topological analysis of the distribution of the charge density (AIM theory) confirmed the existence of the hydrogen bond in I-1, I-2 complexes and indicated weak interaction between the oxygen atom of CH(3)OH and three fluorine atoms of CF(4) in the I-3 complex. The comparison of the experimental and theoretical data suggests that in the matrixes only the non-hydrogen-bonded complex I-3 is trapped. The blue/red shift of the complex OH stretching vibration with respect to the corresponding vibration of CH(3)OH in argon/neon matrixes is explained by the different sensitivity of the complex and monomer vibrations to matrix material. The ab initio calculations performed for the ternary CH(3)OH-CF(4)-Ar systems indicated a negligible effect of an argon atom on the binary complex frequencies.     

Density functional study of hydrogen bond formation between methanol and organic molecules containing Cl, F, NH2, OH, and COOH functional groups

Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides < fluorides < alcohols < amines, while the contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups.