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In this paper we calculate the relative conformer populations of the tryptamine molecule. Our approach combines high level electronic structure conformer energies with harmonic frequencies and an anharmonic treatment of the torsional motions using the torsional path integral Monte Carlo method. We have developed a 3-D potential energy surface as a function of the torsional coordinates at the B3LYP/6-31+G(d) level using 2535 grid points. Eight conformers of tryptamine were found to be significantly populated at 430 K as opposed to the experimental observation of seven. This, along with further comparisons with various experimental data, leads us to suppose that conformer interconversion occurs during the cooling phases of many of the experiments. The ordering of the calculated populations fits well with available experimental data. Torsional anharmonicity is found to affect conformer populations more significantly at 430 K than at 100 K (although overall the effects are small), while quantum mechanical effects are not important at either temperature.

A reduced dimensionality (RD) approximation is developed for the title reaction which treats the angle of approach of the hydroxyl radical to the nitrogen dioxide molecule and the radial distance between the two species explicitly. All other degrees of freedom are treated adiabatically. Electronic structure calculations at the complete active space self-consistent field level are used to fit a potential energy surface (PES) in these two coordinates. Within this RD model the adiabatic capture centrifugal sudden approximation is used to calculate the high pressure limit rate constant. A correction for reflection from the PES due to rotationally nonadiabatic transitions is applied using the wave packet capture approximation. The branching ratio for the title reaction is calculated for the atmospherically significant temperature range of 200-400 K at 20 Torr without distinguishing between the conformers of HOONO. The result is k(HOONO)k(HNO(3) )=0.051 at 20 Torr and 300 K, which is in good agreement with the measured branching ratio between cis-cis-HOONO and nitric acid. This suggests that most of the different conformers of HOONO were converted to the most stable cis-cis conformer on the time scale of the measurements made.

We study the reaction Cl + CH(4)--> HCl + CH(3) using a 2-D potential energy surface obtained by fitting a double Morse analytical function to high level (CCSD(T)/cc-pVTZ//MP2/cc-pVTZ)ab initio data. Dynamics simulations are performed in hyperspherical coordinates with the close-coupled equations being solved using R-matrix propagation. Quantum contributions from spectator modes are included via a harmonic zero-point correction to the ab initio data prior to fitting the potential. This is the first time this method has been applied to a heavy-light-heavy reaction and the first time it has been used to study differential cross sections. We find thermal rate constants and state-to-state differential cross sections which are in good agreement with experimental data. We discuss the applicability of our method to the study of kinetic isotope effects (KIEs), which we derive for the CH(4)/CD(4) substitution. The calculated KIE compares favourably with experiment. Finally, we discuss the sensitivity of the results of dynamics simulations on the accuracy of the fitted potential.

Here, we give a full account of a large collaborative effort toward an atomic-scale understanding of modern industrial ammonia production over ruthenium catalysts. We show that overall rates of ammonia production can be determined by applying various levels of theory (including transition state theory with or without tunneling corrections, and quantum dynamics) to a range of relevant elementary reaction steps, such as N(2) dissociation, H(2) dissociation, and hydrogenation of the intermediate reactants. A complete kinetic model based on the most relevant elementary steps can be established for any given point along an industrial reactor, and the kinetic results can be integrated over the catalyst bed to determine the industrial reactor yield. We find that, given the present uncertainties, the rate of ammonia production is well-determined directly from our atomic-scale calculations. Furthermore, our studies provide new insight into several related fields, for instance, gas-phase and electrochemical ammonia synthesis. The success of predicting the outcome of a catalytic reaction from first-principles calculations supports our point of view that, in the future, theory will be a fully integrated tool in the search for the next generation of catalysts.

Different ruthenium clusters of various sizes are constructed with the aim to model the Ru(0001) surface with a sufficient accuracy for predicting catalysis by hybrid density functional methods (B3LYP). As an example reaction the hydrogenation step N(ads) + H(ads) --> NH(ads) from the catalytic production cycle of ammonia is chosen. A cluster of 12 ruthenium atoms is found to reproduce experimental geometries and frequencies of the various reactants on the surface satisfyingly. To get the geometries of adsorbed hydrogen qualitatively correct it is shown that second layer atoms have to be included in the model cluster. Boundary effects are believed to have minor effects on optimized geometries, whereas the effects on reaction barriers are significant. A comparison of model cluster calculations to a periodic supercell approach employing plane waves and density functional methods (RPBE) reveals similar barriers for reaction. The influence of tunneling in this reaction is determined by the small curvature tunneling approach on the electronic surfaces.

Schemes to include a treatment of torsional anharmonicity in the conformational analysis of biological molecules are introduced. The approaches combine ab initio electronic energies and harmonic frequencies with anharmonic torsional partition functions calculated using the torsional path integral Monte Carlo method on affordable potential energy surfaces. The schemes are applied to the conformational study of the monosaccharide beta-d-galactose in the gas phase. The global minimum structure is almost exclusively populated at 100 K, but a large number of conformers are present at ambient and higher temperatures. Both quantum mechanical and anharmonic effects in the torsional modes have little effect on the populations at all temperatures considered, and it is, therefore, expected that standard harmonic treatments are satisfactory for the conformational study of monosaccharides.

A practical quantum-dynamical method is described for predicting accurate rate constants for general chemical reactions. The ab initio potential energy surfaces for these reactions can be built from a minimal number of grid points (average of 50 points) and expressed in terms of analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimised using the MP2 method with a cc-pVTZ basis set. Single point energies are calculated on the optimised geometries at the CCSD(T) level of theory with the same basis set. The dynamics of these reactions occur on effective reduced dimensionality hyper-surfaces accounting for the zero-point energy of the optimised degrees of freedom. Bonds being broken and formed are treated with explicit hyperspherical time independent quantum dynamics. Application of the method to the H + CH(4)--> H(2)+ CH(3), H + C(2)H(6)--> H(2)+ C(2)H(5), H + C(3)H(8)--> H(2)+n-C(3)H(7)/H(2)+i-C(3)H(7) and H + CH(3)OH --> H(2)+ CH(3)O/H(2)+ CH(2)OH reactions illustrate the potential of the approach in predicting rate constants, kinetic isotope effects and branching ratios. All studied reactions exhibit large quantum tunneling in the rate constants at lower temperatures. These quantum calculations compare well with the experimental results.

An extended version of the torsional path integral Monte Carlo (TPIMC) method is presented and shown to be useful for studying the conformation of flexible molecules in solvated clusters. The new technique is applied to the hydrated clusters of the 2-amino-1-phenyl-ethanol (APE) molecule. APE + nH2O clusters with n = 0-4 are studied at 100 and 300 K using both classical and quantum simulations. Only at the lower temperature is the hydration number n found to impact the conformational distribution of the APE molecule. This is shown to be a result of the temperature-dependent balance between the internal energy and entropy contributions to the relative conformer free energies. Furthermore, at 100 K, large quantum effects are observed in the calculated conformer populations. A particularly large quantum shift of 30% of the total population is calculated for the APE + 2H2O cluster, which is explained in terms of the relative zero point energy of the lowest-energy hydrated structures for this cluster. Finally, qualitative agreement is found between the reported calculations and recent spectroscopy experiments on the hydrated clusters of APE, including an entropically driven preference for the formation of AG-type hydrated structures and the formation of a water "droplet" in the APE + 4H2O cluster.

We present a three-dimensional quantum scattering model to treat reactions of the type H + C2H6 --> H2 + C2H5. The model allows the torsional and the stretching degrees of freedom to be treated explicitly. Zero-point energies of the remaining modes are taken into account in electronic structure calculations. An analytical potential-energy surface was developed from a minimal number of ab initio geometry evaluations using the CCSD(T,full)/cc-pVTZ//MP2(full)/cc-pVTZ level of theory. The reaction is endothermic by 1.5 kcal mol(-1) and exhibits a vibrationally adiabatic barrier of 12.0 kcal mol(-1). The results show that the torsional mode influences reactivity when coupled with the vibrational C-H stretching mode. We also found that ethyl radical products are formed internally excited in the torsional mode.

We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes (III-->I and IV-->I), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the IV-->I conformer interconversion process. However, our calculations present little indication that IV-->I interconversion occurs more readily than III-->I interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne- and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric -CH(2) stretch of conformer IV provides a means for its conclusive experimental detection.

The energetics and structure of the protonated water hexamer (H2O)6H+ have been examined employing both model potentials and high-level ab initio methods. To select candidate structures for this cluster, Parallel-Tempering and the OSS2 potential were used as devices to complement the set of stationary points previously optimized by Hodges and Wales, Chem. Phys. Lett., 2000, 324, 279. Structures of these local minima were successively re-optimized using OSS3, B3LYP/aug-cc-pVDZ, and MP2/aug-cc-pVDZ, the latter providing a reference to benchmark the performance of the empirical models and B3LYP method. We found that both OSS2 and OSS3 require a re-parameterization to adequately describe the energetics of some isomers. Zero point energy was found to be important in defining the relative stability of the optimized isomers. The effect of the anharmonicity on the vibrational ground state of (H2O)6H+ was also examined by means of diffusion Monte Carlo (DMC) and the OSS3 potential, and we found that it accounts for a decrease in total energy of roughly 0-4.4 mE(h). This is a significant effect on the energetics considering that many isomers are nearly degenerate. Including the anharmonic corrections computed with DMC, the branched species were found to be the most stable isomers. The height of the barriers separating a cage or cyclic isomer from a branched one was found to vary from 1.5 to 5.8 mE(h).

The hydrogenation of nitrogen (N(ads)+H(ads)-->NH(ads)) on metal surfaces is an important step in ammonia catalysis. We investigate the reaction dynamics of this hydrogenation step by time independent scattering theory and variational transition state theory (VTST) including tunneling corrections. The potential energy surface is derived by hybrid density functional theory on a model cluster composed of 12 ruthenium atoms resembling a Ru(0001) surface. The scattering calculations are performed on a reduced dimensionality potential energy hypersurface, where two dimensions are treated explicitly and all others are included implicitly by the zero-point correction. The VTST calculations include quantum effects along the reaction coordinate by applying the small curvature tunneling scheme. Even at room temperature (where ruthenium already shows catalytic activity) we find rate enhancement by tunneling by a factor of approximately 70. Inspection of the reaction probabilities shows that the major contribution to reactivity comes from the vibrational ground state of the reactants into vibrationally excited product states. The reaction rates are higher than determined in previous studies, and are compatible with experimental overall rates for ammonia synthesis.

The dynamics and kinetics of the abstraction reactions of H atoms with ethane and methanol have been studied using a quantum mechanical procedure. Bonds being broken and formed are treated with explicit hyperspherical quantum dynamics. The ab initio potential energy surfaces for these reactions have been developed from a minimal number of grid points (average of 48 points) and are given by analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimized using the second order perturbation theory method with a correlation consistent polarized valence triple zeta basis set. Single point energies are calculated on the optimized geometries with the coupled cluster theory and the same basis set. The reaction of H with C2H6 is endothermic by 1.5 kcal/mol and has a vibrationally adiabatic barrier of 12 kcal/mol. The reaction of H with CH3OH presents two reactive channels: the methoxy and the hydroxymethyl channels. The former is endothermic by 0.24 kcal/mol and has a vibrationally adiabatic barrier of 13.29 kcal/mol, the latter reaction is exothermic by 7.87 kcal/mol and has a vibrationally adiabatic barrier of 8.56 kcal/mol. We report state-to-state and state-selected cross sections together with state-to-state rate constants for the title reactions. Thermal rate constants for these reactions exhibit large quantum tunneling effects when compared to conventional transition state theory results. For H+CH3OH, it is found that the CH2OH product is the dominant channel, and that the CH3O channel contributes just 2% at 500 K. For both reactions, rate constants are in good agreement with some measurements.

We extend the technique of quantum propagation on a grid of trajectory guided coupled coherent states to simulate experimental absorption spectra. The approach involves calculating the thermally averaged dipole moment autocorrelation function by means of quantum propagation in imaginary time. The method is tested on simulation of the far infrared spectrum of water trimer based on a three-dimensional model potential. Results are in good agreement with experiment and with other calculations., ((c) 2004 American Institute of Physics)

A quantum-mechanical model is designed for the calculation of termolecular association reaction rate coefficients in the low-pressure fall-off regime. The dynamics is set up within the energy transfer mechanism and the kinetic scheme is the steady-state approximation. We applied this model to the formation of ozone O + O2 + M --> O3 + M for M = Ar, making use of semiquantitative potential energy surfaces. The stabilization process is treated by means of the vibrational close-coupling infinite order sudden scattering theory. Major approximations include the neglect of the O3 vibrational bending mode and rovibrational couplings. We calculated individual isotope-specific rate constants and rate constant ratios over the temperature range 10-1000 K and the pressure fall-off region 10(-7)-10(2) bar. The present results show a qualitative and semiquantitative agreement with available experiments, particularly in the temperature region of atmospheric interest.

A general and practical procedure is described for calculating rate constants for chemical reactions using a minimal number of ab initio calculations and quantum-dynamical computations. The method exploits a smooth interpolating functional developed in the hyperspherical representation. This functional is built from two Morse functions and depends on a relatively small number of parameters with respect to conventional functionals developed to date. Thus only a small number of ab initio points needs to be computed. The method is applied to the H + CH4 --> H2 + CH3 reaction. The quantum scattering calculations are performed treating explicitly the bonds being broken and formed. All the degrees of freedom except the breaking and forming bonds are optimized ab initio and harmonic vibrational frequencies and zero-point energies for them are calculated at the MP2(full) level with a cc-pVTZ basis set. Single point energies are calculated at a higher level of theory with the same basis set, namely CCSD(T, full). We report state-to-state cross sections and thermal rate constants for the title reaction and make comparisons with previous results. The calculated rate constants are in good agreement with experiments., (Copyright 2004 American Institute of Physics)

This review discusses recent quantum scattering calculations on bimolecular chemical reactions in the gas phase. This theory provides detailed and accurate predictions on the dynamics and kinetics of reactions containing three atoms. In addition, the method can now be applied to reactions involving polyatomic molecules. Results obtained with both time-independent and time-dependent quantum dynamical methods are described. The review emphasises the recent development in time-dependent wave packet theories and the applications of reduced dimensionality approaches for treating polyatomic reactions. Calculations on over 40 different reactions are described.

We have developed an anisotropic atom-atom intermolecular potential model for the interaction of uracil with water. The potential consists of a distributed multipole analysis (DMA) model for the electrostatic energy, and a 6-exp potential to represent the repulsion-dispersion term. The repulsion-dispersion potential parameters are adjusted to yield good agreement with accurate ab initio data on the minima and transition states of the uracil-water complex. We have used this potential in diffusion Monte Carlo simulations of uracil-water, uracil-(water)2 and uracil-(water)3. The uracil-water simulations show that the theoretically based potential gives a qualitatively different picture of uracil hydration than that provided by a standard isotropic atom-atom point charge model, which is shown to underestimate the delocalized motion of the water hydrogen atoms. Plots of the vibrational probability density of the hydrogen atoms show the delocalized motion of the water hydrogen atoms that are not involved in hydrogen bonding.

It is common to represent molecules by "ball-and-stick" models that represent static positions of atoms. However, the vibrational states of water molecules involved in hydrogen bonding have wide amplitudes, even in their ground states. Here we introduce a new representation of this wide-amplitude vibrational motion: H-density plots. These plots represent the delocalized zero-point vibrational motion of terminal hydrogen atoms of water molecules weakly bound to other molecules. They are a vibrational analogy to electron densities. Calculations of the H-densities for complexes of water with water, benzene, phenol, and DNA bases are presented. These are obtained using the quantum diffusion Monte Carlo method. Comparisons of measured and calculated rotational constants provide experimental evidence of the new concept.

It is now possible to use rigorous quantum scattering theory to perform accurate calculations on the detailed state-to-state dynamics of chemical reactions in the gas phase. Calculations on simple reactions, such as H + D2 --> HD + D and F + H2 --> HF + H, compete with experiment in their accuracy. Recent advances in theory promise to extend such accurate predictions to more complicated reactions, such as OH + H2 --> H2O + H, and even to reactions of molecules on solid surfaces. New experimental techniques for probing reaction transition states, such as negative-ion photodetachment spectroscopy and pump-probe femtosecond spectroscopy, are stimulating the development of new theories.

The average dipole moment of a water molecule in the condensed phase is enhanced by around 40 percent relative to that of an isolated monomer. This enhancement results from the large polarization caused by the electric field induced by surrounding monomers. A quantitative molecular description of this polarization is essential for modeling aqueous solvation phenomena. This combined theoretical and experimental study of dipole moments in small water clusters provides such a description and also gives insights into the structure of liquid water.