Theoretical Study of Proton Tunneling in the Imidazole-Imidazolium Complex.

Proton tunneling in the hydrogen-bonded imidazole-imidazolium complex ion has been studied theoretically. Ab initio CASSCF/6-311++G(d,p) calculations concerning geometry optimization and vibrational frequencies have been carried out for equilibrium and transition state structures of the system. Two-dimensional double-well model potentials were constructed on the basis of ab initio results and used to analyze the proton dynamics in the hydrogen bond and the influence of the excitation of low-frequency hydrogen-bond vibrations on the proton tunneling splittings. The energy of tunneling-split vibrational sublevels of the high-frequency tunneling mode have been calculated for its ground and first excited vibrational state for the series of excitations of the coupled low-frequency intramolecular hydrogen-bond modes. The promoting and suppressing effect of the low-frequency modes on the proton splittings was shown in the ground and first excited vibrational state of the tunneling mode. The vibrational sublevels form the two separate semicontinuous bands between which the absorption transitions may occur. This mechanism explains the experimentally observed splitting and doublet-component broadening of the high-frequency N-H stretching infrared (IR) absorption band.

A comparison of the hydrogen bond interaction dynamics in the adenine and thymine crystals: BOMD and spectroscopic study.

In this work we present the comparison study of Adenine and Thymine crystals based on the hydrogen bond dynamics. The ab initio molecular dynamics have been used as the base for the further studied interactions observed inside crystals. The generated power spectra, as well as the fluctuation of the interaction energies, showed large differences between hydrogen bond networks in the considered crystals. The analysis of intermolecular interactions have been done base on the reactivity descriptors as well frontiers orbitals along trajectories. The main results showed that in adenine crystals the intermolecular interactions have three directions and fluctuate, while in the thymine crystal have only two directions and are weak but stable. These results explain also on the difference between adenine and thymine melting temperature.

Path Integral Calculation of the Hydrogen/Deuterium Kinetic Isotope Effect in Monoamine Oxidase A-Catalyzed Decomposition of Benzylamine.

Monoamine oxidase A (MAO A) is a well-known enzyme responsible for the oxidative deamination of several important monoaminergic neurotransmitters. The rate-limiting step of amine decomposition is hydride anion transfer from the substrate α-CH2 group to the N5 atom of the flavin cofactor moiety. In this work, we focus on MAO A-catalyzed benzylamine decomposition in order to elucidate nuclear quantum effects through the calculation of the hydrogen/deuterium (H/D) kinetic isotope effect. The rate-limiting step of the reaction was simulated using a multiscale approach at the empirical valence bond (EVB) level. We applied path integral quantization using the quantum classical path method (QCP) for the substrate benzylamine as well as the MAO cofactor flavin adenine dinucleotide. The calculated H/D kinetic isotope effect of 6.5 ± 1.4 is in reasonable agreement with the available experimental values.

Comparison of the Hydrogen Bond Interaction Dynamics in the Guanine and Cytosine Crystals: Ab Initio Molecular Dynamics and Spectroscopic Study.

In this work, we present the comparison study of guanine and cytosine crystals based on the hydrogen bond (HB) dynamics. The ab initio molecular dynamics gave us a base for detailed analysis. The analysis of the trajectories by power spectrum generation, as well as the fluctuation of the interaction energies, showed large differences between HB networks in the considered crystals. The charge flow is present in the guanine molecule which forms the flat surfaces in the crystals. In the cytosine zigzag structure, the charge flow is blocked. The interaction energy is significantly less stabilizing in the cytosine structure than in the guanine. Finally, the possible influence of charge transfer on the melting temperature has been discussed.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Infrared Spectroscopy and Born-Oppenheimer Molecular Dynamics Simulation Study on Deuterium Substitution in the Crystalline Benzoic Acid.

In this study we present complementary computational and experimental studies of hydrogen bond interaction in crystalline benzoic acid and its deuterated and partially deuterated derivatives. The experimental part of the presented work includes preparation of partially deuterated samples and measurement of attenuated total reflection (ATR)-FTIR spectra. Analysis of the geometrical parameters and time course of dipole moment of crystalline benzoic acid and its deuterated and partially deuterated derivatives by Born-Oppenheimer molecular dynamics (BOMD) enabled us to deeply analyze the IR spectra. Presented simulations based on BOMD gave us opportunity to investigate individual motion and its contribution to the IR spectra. The band contours calculated using Fourier transform of autocorrelation function are in quantitative agreement with the experimental spectra. Characterization of single bands was carried out by "normal coordinate analysis". The salient point of our study is a comparison of the spectra of the deuterated and partially deuterated crystalline benzoic acid with that of the nondeuterated one. Furthermore, we have applied the principal component analysis for analysis of the number of components in partially deuterated systems. In this study, we reveal that the arrangements of hydrogen and deuterium atoms in partially deuterated samples are random.

Born-Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms.

In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II. Quantization of the O-H stretching modes allows a detailed discussion on the strength of hydrogen-bonding interactions. The focal point of our study is examination of the hydrogen bond characteristics in the crystal structure and clarification of the influence of hydrogen bonding on the presence of the two crystalline forms of aspirin. In the BOMD method, thermal motions were taken into account. Solving the Schrödinger equation for the snapshots of 2D proton potentials, extracted from MD, gives the best agreement with IR spectra. The character of medium-strong hydrogen bonds in Form I of aspirin was compared with that of weaker hydrogen bonds in aspirin Form II. Two proton minima are present in the potential function for the hydrogen bonds in Form I. The band contours, calculated by using one- and two-dimensional O-H quantization, reflect the differences in the hydrogen bond strengths between the two crystalline forms of aspirin, as well as the strong hydrogen bonding in the cyclic dimers of Form I and the medium-strong hydrogen bonding in Form II.

Quantum-mechanical study of energies, structures, and vibrational spectra of the H(D)Cl complexed with dimethyl ether.

Interaction energies, molecular structure and vibrational frequencies of the binary complex formed between H(D)Cl and dimethyl ether have been obtained using quantum-chemical methods. Equilibrium and vibrationally averaged structures, harmonic and anharmonic wavenumbers of the complex and its deuterated isotopomer were calculated using harmonic and anharmonic second-order perturbation theory procedures with Density Functional Theory B3LYP and B2PLYP-D and ab initio Møller-Plesset second-order methods, and a 6-311++G(3d,3p) basis set. A phenomenological model describing anharmonic-type vibrational couplings within hydrogen bonds was developed to explain the unique broadening and fine structure, as well as the isotope effect of the Cl-H and Cl-D stretching IR absorption bands in the gaseous complexes with dimethyl ether, as an effect of hydrogen bond formation. Simulations of the rovibrational structure of the Cl-H and Cl-D stretching bands were performed and the results were compared with experimental spectra.

Car-Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds.

We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car-Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid.

Investigation of hydrogen bonds properties in the terephthalic acid crystal, using molecular dynamics method.

The aim of this study was to perform calculations using the method of Car-Parrinello molecular dynamics, leading to the optimized geometry of the molecules of 1,4-benzenedicarboxylic acid (terephthalic acid) in crystals, for the hydrogen form and three variants of substitution of deuterium atoms inside a carboxyl group. Based on the results, trajectories and dipole moments were calculated, what makes possible to simulate vibrations in different systems, and to make calculation of theoretical infrared spectra and atomic power spectra. Theoretical results were compared with the experimental spectra, which verifies the correctness of the method and also was compared with the results obtained by quantum-mechanical calculations using DFT for the isolated dimer. Comparison of the spectra of different forms, allowed for in-depth analysis of the effect of isotopic substitution on the frequency of vibrations and shapes of bands, and confirm the presence of possible coupling effects and intra- and intermolecular interactions. Comparison with the DFT results for the dimer show influence of the crystal structure on the spectra.

Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide.

The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment. We calculated the spectra by using harmonic approximation, the time course of the dipole moment function as obtained from the Car-Parrinello simulation, and the quantization of the nuclear motion of the proton for an instantaneous snapshot of the structures in one and two dimensions. Although quantitative assessment of the agreement between the computed and experimental band contour is difficult due to the fact that the experimental band is very broad, we feel that the most reasonable qualitative agreement with the experiment is obtained from snapshot structures and two-dimensional quantization of the proton motion. We have also critically examined the methods of constructing the one-dimensional proton potential. Perspectives are given for the treatment of nuclear quantum effects in biocatalysis.

Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV).

In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and ß, were considered. The deformation density contributions originating from NOCV's revealed that the formation of hydrogen bonding is associated with the electronic charge deformation in both the σ-(Δρ(σ)) and π-networks (Δρ(π)). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the empty P*(H-O) orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component (Δρ(π)), is based on the transfer of electron density from the π-orbital localized on the oxygen of OH on one oxalic acid monomer to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔE(elstat)) is equally as important as orbital interaction term (ΔE(orb)). Finally, comparing ß-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO bonds, neither qualitative nor quantitative.

Theoretical study of proton tunneling in the excited state of tropolone.

Ab initio CIS/6-311++G(d,p) calculations of geometry and vibrational frequencies have been carried out in the A state of tropolone. The grids of potential energy surfaces along the coordinates of high frequency tunneling vibration and the low-frequency coupled vibration have been calculated. Two-dimensional model potentials, formed from symmetric mode coupling potential and squeezed double well potential, have been fitted to the calculated potential energy surfaces and used to analyze proton dynamics. The tunneling splittings for different vibrationally excited states have been calculated and compared with the available experimental data. The model potential energy surfaces, based on the CIS/6-311++G(d,p) calculations, give good estimation of the tunneling energy splittings in the vibrationally ground and excited states of tropolone and explain monotonic decrease in tunneling splittings with the excitation of low-frequency out-of-plane modes and increase in the tunneling splittings with the excitation of low-frequency planar modes.

Theoretical and spectroscopic study of infrared spectra of hydrogen-bonded 1-methyluracil crystal and its deuterated derivative.

Theoretical simulation of the band shape and fine structure of the N-H(D) stretching band is presented for 1-methyluracil and its deuterated derivative taking into account anharmonic coupling between the high-frequency N-H(D) stretching and the low-frequency N...O stretching vibrations, resonance interaction between two equivalent hydrogen bonds in the dimer, anharmonicity of the potentials for the low-frequency vibrations in the ground and excited state of the N-H(D) stretching mode, Fermi resonance between the N-H(D) stretching and the first overtone of the N-H(D) bending vibrations, and electrical anharmonicity. The effect of deuteration has been successfully reproduced by our model calculations. Infrared, far-infrared, Raman, and low-frequency Raman spectra of the polycrystalline 1-methyluracil have been recorded. The geometry and experimental frequencies are compared with the results of harmonic and anharmonic B3LYP6-311++G(**) calculations.

Theoretical modeling of the O-H stretching IR bands of hydrogen-bonded dimers of benzoic acid in S(0) and S(1) electronic states.

Theoretical model for vibrational interactions in the hydrogen-bonded dimer of benzoic acid is presented. The model takes into account anharmonic-type couplings between the high-frequency O-H and the low-frequency O[cdots, three dots, centered]O stretching vibrations in two hydrogen bonds, resonance interactions (Davydov coupling) between two hydrogen bonds in the dimer, and Fermi resonance between the O-H stretching fundamental and the first overtone of the O-H in-plane bending vibrations. The vibrational Hamiltonians and selection rules for the C(2h) geometry in the S(0) state and for the C(s) in-plane bent geometry in the S(1) state of the dimer are derived. The model is used for theoretical simulation of the O-H stretching IR absorption bands of benzoic acid dimers in the gas phase in the electronic ground and first excited singlet states. Ab initio CIS and CIS(D)6-311++G(d,p) calculations have been performed to determine geometry, frequencies, and excited state energies of benzoic acid dimer in the S(1) state.

Theoretical model of infrared spectra of hydrogen bonds in molecular crystals and its application to interpretation of infrared spectra of 1-methylthymine.

A theoretical model for vibrational interactions in the hydrogen bonds in molecular crystals with four molecules forming two centrosymmetric dimers in the unit cell is presented. The model takes into account anharmonic-type couplings between the high-frequency N-H(D) and the low-frequency N...O stretching vibrations in each hydrogen bond, resonance interactions (Davydov coupling) between equivalent hydrogen bonds in each dimer, resonance interdimer interactions within a unit cell, and Fermi resonance between the N-H(D) stretching fundamental and the first overtone of the N-H(D) in-plane bending vibrations. The vibrational Hamiltonian, selection rules, and expressions for the integral properties of an absorption spectrum are derived. The model is used for theoretical simulation of the NH stretching bands of 1-methylthymine and its ND derivative at 300 K. The effect of deuteration is successfully reproduced by our model. Infrared, far-infrared, Raman, and low-frequency Raman spectra of 1-methylthymine and its deuterated derivative have been measured. Experimental geometry and frequencies are compared with the results of density functional theory calculations performed at the B3LYP6-311++G**, B3LYP/cc-pVTZ, B3PW916-311++G**, and B3PW91/cc-pVTZ levels.

Theoretical model for a tetrad of hydrogen bonds and its application to interpretation of infrared spectra of salicylic acid.

Theoretical model of vibrational interactions in hydrogen-bonded salicylic acid dimer is presented which takes into account the adiabatic couplings between high- and low-frequency O-H and O...O stretching vibrations, resonance interactions between both intermolecular hydrogen bonds and between inter- and intramolecular hydrogen bonds, and Fermi resonance between the O-H stretching fundamental and the first overtone of the O-H in-plane bending vibrations. The model is used for theoretical simulation of the nu(s) stretching bands of salicylic acid and its OD derivative at 300 K. The effect of deuteration is successfully reproduced by our model. Infrared, far infrared, Raman, and low-frequency Raman spectra of the polycrystalline salicylic acid and its deuterated derivative have been measured. The geometry and experimental frequencies are compared with the results of density-functional theory calculations performed at the B3LYP6-31 ++ G**, B3LYP/cc-pVTZ, B3PW916-31 ++ G**, and B3PW91/cc-pVTZ levels. O-H, O-D, and O...O stretching frequencies are used in theoretical simulation of the nu(s) stretching bands.

Theoretical modeling of infrared spectra of hydrogen-bonded crystals of salicylic acid.

A theoretical model for the infrared spectra in the O-H stretching region of hydrogen-bonded salicylic acid is presented. Based on the model, infrared spectrum in the O-H stretching region is calculated for salicylic acid and compared with the experimental one. The experimental and theoretical spectra are in good agreement.