Vibrational analysis of the H5O2+ infrared spectrum using molecular and driven molecular dynamics

Standard molecular and driven molecular dynamics are used to analyze prominent spectral features in the H5O2+ infrared spectrum. In the driven method, the molecular Hamiltonian is augmented with a time-dependent term, mu x epsilon(0) sin(omegat), where mu is the dipole moment of H5O2+, epsilon0 is the electric field, and omega is the frequency. The magnitude of the electric field determines whether the driving is mild (the harmonic limit) or strong (anharmonic motion and mode coupling). We analyze the spectrum in the wavenumber range from 600 to 1900 cm(-1), where recent experimental measurements are available for H5O2+. On the basis of the simulations, we have assigned the broad feature around 1000 cm(-1) to the proton transfer coupled with the torsion motion. Intense absorption near 1780 cm(-1) is assigned to the H2O monomer bend coupled with proton transfer.     

Domain catalyzed chemical reactions: a molecular dynamics simulation of isomerization kinetics

The model for domain catalyzed isomerization kinetics in condensed fluids is applied for a diluted mixture of a chiral solute with a consolute temperature. The solution is quench to phase separation at temperatures below the consolute temperature. The droplet coalescence enhances the isomerization kinetics due to the substantial excess pressure inside the small droplets given by the Laplace equation. The domain catalyzed isomerization kinetics breaks the symmetry, and the droplets end with only one dominating species. We argue that D-glyceraldehyde which is only moderately solvable in water and which has played a crucial role in the evolution is a candidate for the stereo specific ordering in bio-organic matter.     

Aggregation of FeCl2 clusters in supercritical water investigated by molecular dynamics simulations

We have carried out molecular dynamics (MD) simulations of the aggregation of FeCl 2 clusters in supercritical water. The particle formation in systems of 2048 water molecules (rigid SPC/E-model) and 120 Fe (2+) ions and 240 Cl (-) ions has been investigated for 250 ps at five different state points at temperatures from 798 to 873 K and system densities from 0.18 g/cm (3) to 0.13 g/cm (3). We describe the particle growth by means of properties of the largest cluster in a system as well as cluster size averaged and time averaged observables. From preexisting or immediately formed units of Fe (2+)-Cl (-), Fe (2+)-Cl (-) 2, Fe (2+)-Cl (-) 3 etc., the further growth of clusters is dominated by aggregation of such small building blocks. Clusters up to 10 ions in size with large charge imbalances are found during the growth process while a balanced positive to negative charge ratio is found on the average with time and cluster size development. Water molecules are found within the FeCl 2 clusters during the whole time interval covered by the simulations, which is in agreement with the existence of crystal water in FeCl 2 crystals grown from aqueous solutions. The radial distribution functions obtained from the simulation data are in good agreement with experimental results of slightly distorted FeCl 2.4H 2O crystals.     

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach

Electron attachment dynamics of excess electron in water cluster (H2O)n (n = 2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP26-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n = 3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by -1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by -5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100-300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n = 2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results.     

Vibrational density of states of the hydrogen sites in hydrogen-bonded molecular solids

Inelastic neutron scattering measurements of the incoherent dynamical structure factor of hydrogen-bonded molecular solids are reviewed. Particular attention is devoted to ice and ice-like polycrystalline samples. Their vibrational density of states is discussed in terms of the influence of proton disorder, anharmonicity and fluctuations of the force constants on the width and shape of the band.     

Infinite dilution activity coefficients in hydrogen-bonded mixtures via molecular dynamics: the water/methanol system

The single charging integral method, recently employed to calculate residual chemical potential differences between water and methanol due to size, energy, and partial charge parameters, is extended to include the contributions due to the differences in molecular model geometry. The calculated infinite dilution activity coefficients for the binary are compared to their experimental values at 298 K. With the SPC water model and the methanol model of Van Leeuwen [Van Leeuwen and Smit, J. Phys. Chem. 99 (1995) 831], the total calculated residual chemical potential difference between water and methanol agrees to within 2% of the experimental value. The residual chemical potential differences in the infinite dilution systems, however, disagree with experiment by 20 to 100%. The effect of deviations from the Lorentz–Berthelot combining rules for unlike site–site interactions is addressed. The delicate balance between electrostatic attraction and overlap repulsion is implicated in the disagreement between the calculated and experimental chemical potential differences.     

Ab initio molecular dynamics simulations of elimination reactions in water solution: exploring the borderline region between the E1cb and E2 reaction mechanisms

We report a theoretical study, based on ab initio molecular dynamics simulations in water solution, of the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Recent theoretical and experimental evidence points toward the lack of a net distinction between the E1cb and E2 reaction paths, which seem to merge smoothly into each other in these borderline cases (Alunni, S.; De Angelis, F.; Ottavi, L.; Papavasileiou, M.; Tarantelli, F. J. Am.Chem. Soc. 2005, 127, 15151-15160). In this study, we explore the dynamics on the potential energy surface for the reaction of 2-(2-fluoroethyl)-1-methyl pyridinium with OH- by means of Car-Parrinello simulations in water solution. Our results indicate that the reaction mechanism effectively evolves through the potential energy region of the carbanion: the carbon-fluoride bond breaks only after the carbon-hydrogen bond, confirming the conclusions of a recently reported study of the potential energy surface for this system.     

Stability of cyclic (H2O)n clusters within molecular solids: Role of aromaticity

Cyclic water clusters (H₂O)_n (n = 3–12) trapped inside organic/inorganic hosts do not correspond to the global energy minimal structures. Their closed loop connections through the H‐bonds, although weakly interacting, result in diamagnetic ring currents leading to what we term “H‐bonded aromaticity.” Such H‐bonded aromaticity in supramolecular structures generalizes the formation of such stable (H₂O)_n molecules confined within various host systems. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Electronic spectra of hydrogen-bonded 2-fluoropyridine clusters with water in a supersonic free jet

Fluorescence excitation, multiphoton ionization, and dispersed fluorescence spectra of bare and hydrogen-bonded 2-fluoropyridine with water were measured in a supersonic free jet. For bare 2-fluoropyridine, fluorescence quantum yield decrease in the higher vibronic levels was observed even under collision-free conditions. The inter-system crossing channel was probed experimentally by two color R2PI and found to be negligible. The non-radiative relaxation process of 2-fluoropyridine is mainly governed by the relaxation to the electronic ground state. Electronic spectra of 2-fluoropyridine-(water)(n) (n=1 approximately 3) were also obtained. The hydrogen bond formation with water increases the quantum yield in the higher vibronic levels. Rather low frequency vibrations were observed in the hole burning spectrum of bare 2-fluoropyridine; however, these vibronic bands disappeared with the hydrogen bond formation with water. The appearance of low frequency vibronic bands observed for bare 2-fluoropyridine is ascribed to the existence of closely lying (n,pi) state.     

Reactions of NH+2 ions with H2O and with CH3CHO. Association and exchange reactions involving clusters of the H+(H2O)n(

Kinetic energy dependence of rate constants and branching ratios for reactions of NH₂⁺ ions with water and with acetaldehyde have been studied at 297 K using the drift tube technique. The rate coefficients for two-body and three-body reactions are presented together with the ionized products. Several types are apparent, such as proton transfer, association and exchange reactions.     

Double quantum 1H MAS NMR studies of hydrogen-bonded protons and water dynamics in materials

Two-dimensional double quantum (DQ) 1H MAS NMR was used to investigate different proton environments in a series of alkali (Na, K, Rb, Cs) [Nb6O19]8- Lindqvist salts, with the water and hydrogen-bound intercluster protons being clearly resolved. Through the analysis of the DQ 1H NMR spinning sideband pattern, it is possible to extract both the mean and distribution of the motionally averaged intramolecular homonuclear 1H-1H dipolar coupling for the different water environments and the intercluster protons. Motional order parameters for the water environments were then calculated from the averaged dipolar couplings. The influence of additional intermolecular dipolar couplings due to multispin interactions were simulated and discussed.     

Theoretical study of the dynamics of the H+CH4 and H+C2H6 reactions using a specific-reaction-parameter semiempirical Hamiltonian

We present a theoretical study of the reactions of hydrogen atoms with methane and ethane molecules and isotopomers. High-accuracy electronic-structure calculations have been carried out to characterize representative regions of the potential-energy surface (PES) of various reaction pathways, including H abstraction and H exchange. These ab initio calculations have been subsequently employed to derive an improved set of parameters for the modified symmetrically-orthogonalized intermediate neglect of differential overlap (MSINDO) semiempirical Hamiltonian, which are specific to the H+alkane family of reactions. The specific-reaction-parameter (SRP) Hamiltonian has then been used to perform a quasiclassical-trajectory study of both the H+CH4 and H+C2H6 reactions. The calculated values of dynamics properties of the H+CH4-->H2+CH3 reaction and isotopologues, including alkyl product speed distributions, diatomic product internal-state distributions, and cross sections, are generally in good agreement with experiment and with the results provided by the ZBB3 PES [Z. Xie et al., J. Chem. Phys. 125, 133120 (2006)]. The results of trajectories propagated with the SRP Hamiltonian for the H+C2H6-->H2+C2H5 reaction also agree with experiment. The level of agreement between the results calculated with the SRP Hamiltonian and experiment in both the H+methane and H+ethane reactions indicates that semiempirical Hamiltonians can be improved for not only a specific reaction but also a family of reactions.     

Direct MP2 molecular dynamics studies of H atom reaction with CD4 and CH4

The mechanism and dynamics of the H + CD₄ → CD₃ + HD (I) and H + CH₄ → CH₃ + H₂ (II) reactions have been investigated by electronic structure methods. The minimum‐energy path and vibrational frequencies along the intrinsic reaction coordinate are calculated at MP2/cc‐pVDZ level. Energy distributions of the products are also obtained by the direct classical trajectory calculations at the MP2/ cc‐pVDZ level. It is found that most of the available energy appears as product translational energy, and very little of the available energy is partitioned into internal excitation of the HD (H₂) product for reaction I (II), which is in agreement with the experimental evidence. The results indicate that the experimental results could be reproduced by the direct MP2 molecular dynamics calculations. The rotational state distributions of the products show the HD (H₂) products are formed with lower rotational quantum numbers than the CD₃ (CH₃) products. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Vibrational relaxation of the H2O bending mode in liquid water

We have studied the vibrational relaxation of the H(2)O bending mode in an H(2)O:HDO:D(2)O isotopic mixture using infrared pump-probe spectroscopy. The transient spectrum and its delay dependence reveal an anharmonic shift of 55+/-10 cm(-1) for the H(2)O bending mode, and a value of 400+/-30 fs for its vibrational lifetime.     

Ab initio study of the isomeric equilibrium of the HCN...H2O and H2O...HCN hydrogen-bonded clusters

An ab initio study of the stability, spectroscopic properties, and isomeric equilibrium of the hydrogen-bonded HCN...H2O and H2O...HCN isomers is presented. Density functional theory and perturbative second-order MP2 and coupled-cluster CCSD(T) calculations were carried out and binding energies obtained with correlation-consistent basis sets including extrapolation to the infinity basis set level. At the best theoretical level, CCSD(T), the H2O...HCN complex is more stable than the HCN...H2O complex by ca. 6.3 kJ mol(-1). Rotational and vibrational spectra, including anharmonic corrections, are calculated. These calculated spectroscopic data are used to obtain thermochemical contributions to the thermodynamic functions and hence the Gibbs free energy. The relative free energies are used to estimate the equilibrium constant for isomerism. We find that under typical conditions of supersonic expansion experiments (T < 150 K) H2O...HCN is essentially the only isomer present. Furthermore, our calculations indicate that the hydrogen-bonded cluster becomes favorable over the separated moieties at temperatures below 200 K.     

Kinetics of the reactions of CH2Br and CH2I radicals with molecular oxygen at atmospheric temperatures

The kinetics of the reactions of CH2Br and CH2I radicals with O2 have been studied in direct measurements using a tubular flow reactor coupled to a photoionization mass spectrometer. The radicals have been homogeneously generated by pulsed laser photolysis of appropriate precursors at 193 or 248 nm. Decays of radical concentrations have been monitored in time-resolved measurements to obtain the reaction rate coefficients under pseudo-first-order conditions with the amount of O2 being in large excess over radical concentrations. No buffer gas density dependence was observed for the CH2I + O2 reaction in the range 0.2-15 x 10(17) cm(-3) of He at 298 K. In this same density range the CH2Br + O2 reaction was obtained to be in the third-body and fall-off area. Measured bimolecular rate coefficient of the CH2I + O2 reaction is found to depend on temperature as k(CH2I + O2)=(1.39 +/- 0.01)x 10(-12)(T/300 K)(-1.55 +/- 0.06) cm3 s(-1)(220-450 K). Obtained primary products of this reaction are I atom and IO radical and the yield of I-atom is significant. The rate coefficient and temperature dependence of the CH2Br + O2 reaction in the third-body region is k(CH2Br + O2+ He)=(1.2 +/- 0.2)x 10(-30)(T/300 K)(-4.8 +/- 0.3) cm6 s(-1)(241-363 K), which was obtained by fitting the complete data set simultaneously to a Troe expression with the F(cent) value of 0.4. Estimated overall uncertainties in the measured reaction rate coefficients are about +/-25%.     

On the strength of hydrogen bonding within water clusters on the coordination limit

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18 , 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice I_h). The strongest HBs within H₂O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange-correlation to discriminate among the different examined types of HBs within H₂O clusters, (b) the use of the above-mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri- and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H₂O clusters.     

Spectrum and dynamics of the CH chromophore in CD2HF. I. Vibrational Hamiltonian and analysis of rovibrational spectra

We have measured the complete rovibrational spectrum of dideutero-fluoro-methane (CD₂HF) from the far-infrared (20 cm⁻¹) to the visible (14000 cm⁻¹) largely at Doppler-limited resolution. Rovibrational parameters are reported for CH-stretching and bending fundamentals and overtones. The spectra of the coupled stretching and bending modes of the CH chromophore are analyzed quantitatively both in terms of effective Hamiltonians and a three-dimensional model Hamiltonian. A new numerical method for solving the corresponding eigenvalue problem is described briefly. The strong Fermi and Darling—Dennison resonances lead to fast vibrational redistribution on the femtosecond time scale.     

On the kinetic mechanism of the hydrogen abstraction reactions of the hydroxyl radical with CH3CF2Cl and CH3CFCl2: A dual level direct dynamics study

By means of the dual‐level direct dynamics method, the mechanisms of the reactions, CH₃CF₂Cl + OH → products (R1) and CH₃CFCl₂ + OH → products (R2), are studied over a wide temperature range 200–2000 K. The optimized geometries and frequencies of the stationary points are calculated at the MP2/6‐311G(d,p) level, and then the energy profiles of the reactions are refined with the interpolated single‐point energy method at the G3(MP2) level. The canonical variational transition‐state theory with the small‐curvature tunneling (SCT) correction method is used to calculate the rate constants. For the title reactions, three reaction channels are identified and the H‐abstraction channel is the major pathway. The results indicate that F substitution has a significant (reductive) effect on hydrochlorofluorocarbon reactivity. Also, for all H‐abstraction reaction channels the variational effect is small and the SCT effect is only important in the lower temperature range on the rate constants calculation. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010