The interaction of OH- with the sugar beta-D-galactose is studied computationally, with Ab Initio Molecular Dynamics (AIMD) as the prime tool. The main findings are: (1) the OH- abstracts a proton from the sugar in a barrier-less process, yielding H2O and a Deprotonated beta-D-Galactose anion, (Dep-beta-D-G)(-). (2) This reaction can be reversed when two additional H2O molecules are present in the sugar. (3) At 500 K, a ring-opening reaction occurs in (Dep-beta-D-G)(-) within a timescale of 10 ps. The (neutral) sugar itself is stable over this timescale, and well beyond. This indicates that OH- can catalyze the degradation of beta-D-galactose. Implications of this process are briefly discussed.

Noble-gas hydrides, generally prepared in noble-gas matrices, have fascinating chemical bonding and properties. However, very little is known on the kinetic stability of these compounds, and how it can be affected by different molecular environments and conditions. In this Letter, recent computational and experimental results bearing on this topic are discussed and analyzed. For the important case of HXeOH, there appears to be a gap between the predicted long lifetime for the isolated molecule and much shorter lifetime observed experimentally in a Xe matrix. Understanding of this gap is an important challenge in this field. (C) 2012 Elsevier B. V. All rights reserved.

Isomerization and ionization of N2O4 on model ice and silica surfaces, hypothesized as key steps in atmospheric HONO formation, were studied using B3LYP and MP2 methods. The models employed are (H2O)(20) for ice and Si8O16H12 for silica. It is found that dangling surface -OH bonds play a key role in the isomerization to generate the ‘active’, asymmetric ONONO2. However, the computed barrier is high. Potential catalytic effects due to additional water molecules or local heating caused by photoabsorption are discussed. The results suggest that the isomerization of N2O4 into the active ONONO2 form on a variety of tropospheric surfaces having dangling -OH bonds should be considered in heterogeneous NOx chemistry. (C) 2012 Elsevier B.V. All rights reserved.

A mechanistic study of the reaction Cl + O-3 -> ClO + O-2 at the high level of multi-reference DET-MRPT2 theory for both the static reaction path and the dynamics is presented. It is found that a spin-flip takes place along the computed dynamical path, a point neglected in previous studies. The time scale of the spin-flip is estimated from the dynamics. The algorithmic improvements that make possible the high-level multi-reference dynamics simulation are briefly discussed. (C) 2012 Elsevier B. V. All rights reserved.

Equilibrium structures for a proton on beta-D-galactose and transition states for proton hopping are computed. Also, Ab Initio Molecular Dynamics (AIMD) simulations are carried out. All calculations used B3LYP potentials with dispersion. At 40 K, proton hopping between sites is of near microsecond timescale. At 300 K, the proton migrates across the sugar on a sub-picosecond timescale. At 500 K, the proton reacts with the sugar to produce H2O. Implications for sugar chemistry are discussed.

Ab initio vibrational self-consistent field (VSCF) calculations are used to predict-the vibrational spectra of an extended series of monosaccharide center dot D2O complexes, including glucose; galactose, mannose, xylose, and fucose in their alpha and beta anomeric; forms, and Compared with recently published experimental data for T their (phenyl-tagged) complexes. Anharmonic VSCF-PT2 frequencies are calculated directly, using ab initio hybrid HF/MP2 potentials, to assess their accuracy in reproducing the vibrational anharmonicities and provide a more rigorous basis for vibrational and structural assignments. The average discrepancies between the calculated and experimental frequencies are similar to 1.0-1.5%, and the first-principles spectroscopic calculations, free of any empirical scaling, yield results: of high accuracy. They encourage confidence in their future application. to the assignment of other carbohydrate systems, both free and complexed, and an improved understanding of their intra- and intermolecular carbohydrate interactions.

Chlorine atoms are highly reactive free radicals known to catalyze ozone depletion in the stratosphere and organic oxidation in the troposphere. They are readily produced photolytically upon irradiation of some stable Cl containing species, for instance, nitrosyl chloride, ClNO. We predict the formation of ClNO using ab initio molecular dynamics (AIMD) simulations of an NO2 dimer on the surface of a thin film of water upon which gaseous HCl impinges. The reactant is chloride ion formed when HCl ionizes on the water film. The same mechanism for ClNO production may occur in humid environments when ONONO2 (the asymmetric NO2 dimer examined here) comes in contact with either HCl or sea salt. The film of water serves to (1) stabilize ONONO2 on the film surface so that it is localized and physically accessible for reaction, (2) provide the medium to ionize HCl, and (3) activate ONONO2 making it more susceptible to nucleophilic attack by chloride. This substitution/elimination mechanism is new for NOx chemistry on thin water films and could not be derived from studies on small clusters.

‘Bridging’ protons provide a common structural motif in biological assemblies such as proton wires and proton-bound dimers. Here we present a ‘proof-of-principle’ computational and vibrational spectroscopic investigation of an ‘intra-molecular proton-bound dimer,’ O-methyl alpha-D-galactopyranoside (alpha MeGal-H+), generated in the gas phase through photo-ionisation of its complex with phenol in a molecular beam. Its vibrational spectrum corresponds well with a classical molecular dynamics simulation conducted ‘on-the-fly’ and also with the lowest-energy structures predicted by DFT and ab initio calculations. They reveal proton-bound structures that bridge neighbouring pairs of oxygen atoms, preferentially O6 and O4, linked together within the carbohydrate scaffold. Motivated by the possibility of an entry into the microscopic mechanism of its acid (or enzyme)-catalysed hydrolysis, we also report the corresponding predictions for its singly hydrated complex.

Airborne particles affect human health and significantly influence visibility and climate. A major fraction of these particles result from the reactions of gaseous precursors to generate low-volatility products such as sulfuric acid and high-molecular weight organics that nucleate to form new particles. Ammonia and, more recently, amines, both of which are ubiquitous in the environment, have also been recognized as important contributors. However, accurately predicting new particle formation in both laboratory systems and in air has been problematic. During the oxidation of organosulfur compounds, gas-phase methanesulfonic acid is formed simultaneously with sulfuric acid, and both are found in particles in coastal regions as well as inland. We show here that: (i) Amines form particles on reaction with methanesulfonic acid, (ii) water vapor is required, and (iii) particle formation can be quantitatively reproduced by a semiempirical kinetics model supported by insights from quantum chemical calculations of likely intermediate clusters. Such an approach may be more broadly applicable in models of outdoor, indoor, and industrial settings where particles are formed, and where accurate modeling is essential for predicting their impact on health, visibility, and climate.

We present an exploration of proton transfer dynamics in a monosaccharide, based upon ab initio molecular dynamic (AIMD) simulations, conducted ‘‘on-the-fly’’, in beta-D-galactose-H+ (beta Gal-H+) and its singly hydrated complex, beta Gal-H+-H2O. Prior structural calculations identify O6 as the preferred protonation site for O-methyl alpha-D-galactopyranoside, but the beta-anomeric configuration favors the inversion of the pyranose ring from the C-4(1) chair configuration, to C-1(4), and the formation of proton bridges to the (axial) O1 and O3 sites. In the hydrated complex, however, the proton bonds to the water molecule inserted between the O6 and Ow sites, and the ring retains its original C-4(1) conformation, supported by a circular network of co-operatively linked hydrogen bonds. Two distinct proton transfer processes, operating over a time scale of 10 ps, have been identified in beta Gal-H+ at 500 K One of them leads to chemical reaction and the formation of an oxacarbenium ion (accompanied by the loss of an H2O molecule). In the hydrated complex, beta Gal-H+-H2O, this reaction is suppressed, and the proton transfer, which involves multiple jumps between the sugar and the H2O creates an H3O+ ion, relevant, perhaps, to the reactivity of protonated sugars both in the gas and condensed phases. Anticipating future spectroscopic investigations, the vibrational spectra of beta Gal-H+ and beta Gal-H+-H2O have also been computed through AIMD simulations conducted at average temperatures of 300 and 40 K and also through vibrational self-consistent field (VSCF) calculations at 0 K

Ab initio molecular dynamics (AIMD) simulations using B3LYP combined with Natural Bond Orbitals (NBO) analysis of partial charges and bond orders along trajectories are used to study the decomposition dynamics of three theoretically known isomers of N-6. The results show that significant changes in bonding and in charge distribution occur in intervals of about 10 fs during the process. The decomposition of one isomer proceeds in two steps through a retro Diels Alder (RDA) mechanism while the other isomers decompose to 3 N-2 directly. It is suggested that this approach may provide useful insights into reactions in general. (C) 2012 Elsevier B.V. All rights reserved.

The conformation and structural dynamics of cellobiose, one of the fundamental building blocks in nature, its C4’ epimer, lactose, and their microhydrated complexes, isolated in the gas phase, have been explored through a combination of experiment and theory. Their structures at low temperature have been determined through double resonance, IR-UV vibrational spectroscopy conducted under molecular beam conditions, substituting D2O for H2O to separate isotopically, the carbohydrate (OH) bands from the hydration (OD) bands. Car-Parrinello (CP2K) simulations, employing dispersion corrected density functional potentials and conducted ‘‘on-the-fly’’ from similar to–’20 to similar to 300 K., have been used to explore the consequences of raising the temperature. Comparisons between the experimental data, an harmonic vibrational self-consistent field calculations based upon ab initio potentials, and the CP2K simulations have established the role of anharmonicity; the reliability of classical molecular dynamics predictions of the vibrational spectra of carbohydrates and the accuracy of the dispersion corrected (BLYP-D) force fields employed; the structural consequences of increasing hydration; and the dynamical consequences of increasing temperature. The isolated and hydrated cellobiose and lactose units both present remarkably rigid structures: their glycosidic linkages adopt a ‘‘cis’’ (anti-phi and syn-psi) conformation bound by inter-ring hydrogen bonds. This conformation is maintained when the temperature is increased to similar to 300 K and it continues to continus to be maintained when the cellobiose(or lactose) unit is hydrated by one or two explicitly bound water molecules. Despite individual-fluctuations in the intra- and intermolecular hydrogen bonding pattern and some local structural motions, the water molecules remain locally bound and the isolated carbohydrates remain trapped within the cis potential well. The Car-Parrinello dynamical simulations do not suggest any accessible pathway to the trans conformations that are formed in aqueous solution and are widespread in nature.

A new algorithm is presented for finding the global minimum, and other low-lying minima, of a potential energy surface (PES) of biological molecules. The algorithm synergetically combines three well-known global optimization methods: the diffusion equation method (DEM), which involves smoothing the PES; a simulated annealing (SA) algorithm; and evolutionary programming (EP), whose population-oriented approach allows for a parallel search over different regions of the PES. Tests on five peptides having between 6 and 9 residues show that the code implementing the new combined algorithm is efficient and is found to outperform the constituent methods, DEM and SA. Results of the algorithm, in the gas phase and with the GBSA implicit solvent model, are compared with crystallographic data for the test peptides; good accord is found in all cases. Also, for all but one of the examples, our hybrid algorithm finds a minimum deeper than those obtained by a very extensive scan. TINKERs implementation of the OPLS-AA force field is employed for the structure prediction. The results show that the new algorithm is a powerful structure predictor, when a reliable potential function is available. Our implementation of the algorithm is time-efficient, and requires only modest computational resources. Work is underway on applications of the new algorithm to structural prediction of proteins and other biological macro-molecules. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 1785-1800, 2011

Proton transfer and dissociation processes following excitation of the OH or NH stretching modes of the proton-bound complex GlyLysH(+) are studied by classical trajectories. ‘‘On the fly’’ simulations with the PM3 semi-empirical electronic structure method for the potential surface are used. Initial conditions are sampled to correspond to the v=1 excited state of the OH or NH stretching modes. Five different conformers of the complex are studied as initial structures. The main findings are (1) Photoinduced proton transfer is on the picosecond time scale. (2) Proton transfer is much faster than the processes of dissociation. (3) Proton transfer involves different sites. Most trajectories show sequences of two proton transfer events. (4) The proton transfer events show high selectivity with regard to the initially excited vibration and the initial structure. (5) Photodissociation of the complex occurs on a typical time scale of 100 ps. (6) Conformational transitions are found to be often faster than proton transfer. These results have implications for the mass spectrometry of complexes, for dynamics of proton wires, and for proton migration in proteins.

Fourier-transform infrared and Raman scattering spectra of solid cellobiose are measured. The monitored spectra are compared to vibrational spectra of isolated cellobiose, computed by the vibrational self-consistent field (VSCF) method and from classical molecular dynamics (MD) simulations. Partial agreement is found between the measured and calculated features, allowing interpretation of parts of the spectra in terms of single-molecule calculations. Deviations between the measured spectra and the calculated ones could be due to environment effects on the molecule, not included in the model, or due to errors in the vibrational methods used. Future investigations of this issue seem desirable. (C) 2011 Elsevier B. V. All rights reserved.

First-principles anharmonic calculations are carried out for the IR and Raman spectra of the C-H stretching bands in butane. The calculations use the Vibrational Self-Consistent Field (VSCF) algorithm. The results are compared with gas-state experiments. Very good agreement between the computed and experimental results is found. Theory is successful also in computing a weak peak which is caused by combination transitions. The B3LYP potential surface is found superior to MP2, though both methods give good accord with experiment. The theoretical results provide an understanding of the role of different modes in the spectra of hydrocarbons. (C) 2011 Elsevier B.V. All rights reserved.

There has been a lot of speculation about the role of water in gas phase reactions involving neutrals, radicals and ions. The reaction of NO and OH has attracted a lot of attention in the past due to its relevance for ozone chemistry in the atmosphere. In the present contribution we report low temperature measurements of the recombination of OH and NO at low temperatures in Laval nozzle expansions between 300 and 60 K. We find an increase of the bimolecular rate constant in the presence of water of up to 40%. This effect has been attributed to water molecules acting either as an efficient collider releasing energy from the intermediate (in collisions) or which is more likely for the present experimental conditions - as a cluster partner of the reaction intermediate HONO that also dissipates energy via cluster dissociation, which can in turn both stabilize the reaction intermediate, decrease back reaction to OH and NO, and enhance finally the overall reaction to the products. The supersaturation of water vapor in the cold Laval nozzle expansion strongly favors the formation of clusters in the nozzle throat; their exact concentration is, however, difficult to estimate due to non-equilibrium conditions. The possible role of clusters in the recombination of OH and NO is investigated using ab initio molecular dynamics calculations. Beyond the reaction intermediate HONO and intramolecular proton transfer events also transient HOON was observed in the theoretical study.

Structure optimization, ab initio molecular dynamics (AIMD) simulation of transitions between structures, vibrational self-consistent field (VSCF) calculations of vibrational spectra and infrared ion dip (IRID) experiments have been used to explore the potential energy landscape of isomeric xylose center dot H2O (and D2O). The VSCF predictions are in close correspondence with the experimental data but the spectra associated with their two low energy isomers are too similar to permit an unequivocal structural assignment. At cryogenic temperatures several low energy isomers could be ‘frozen in’ but at 300 K the AIMD simulations predict rapid transitions between them and in consequence, a highly fluxional system. (C) 2011 Published by Elsevier B.V.