Shemesh, D. ; Gerber, B. R. Femtosecond timescale deactivation of electronically excited peroxides at ice surfaces. MOLECULAR PHYSICS 2012, 110, 605-617.Abstract
Peroxides are ubiquitous in the atmosphere and their photochemistry at ice surfaces is important. Here the primary steps following photoexcitation of methyl hydroperoxide (MHP) on ice particles are investigated using the MNDO method that describes semiempirically multiple electronic states and treats non-adiabatic dynamical transitions between them by surface hopping. Results are compared with the isolated MHP. Important findings are as follows. (1) Ice catalyzes the deactivation of MHP from the excited state to the ground state. (2) The deactivation process takes place on a femtosecond timescale and is followed by dissociation into fragments. (3) Recombination of fragments occurs to a small extent on ice, but not for the isolated peroxide.
Pincu, M. ; Gerber, B. R. {{Hydration of cellobiose: Structure and dynamics of cellobiose -(H2O)(n). CHEMICAL PHYSICS LETTERS 2012, 531, 52-58.Abstract
Solvation of beta-cellobiose isomers, cis and trans, in increasingly larger water clusters, is examined here by means of ab initio dynamics. A previously suggested hydration motif, based on a cluster with 2 waters, provides a stable nucleation center for growth of the larger cluster. Key results: (a) the cis form is energetically favored throughout the cluster size range; (b) cis conformer exhibits surfactant properties while (c) trans is better enveloped by water. Water organization at the sugar surface, is significantly different in the two isomers. Rotamer transitions, observed in the isolated sugar at 300 K, are inhibited by the incomplete hydration shell. Published by Elsevier B.V.
Xie, H. -bin; Gerber, B. R. Interaction and reaction of the hydroxyl ion with beta-D-galactose and its hydrated complex: an ab initio molecular dynamics study. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2012, 14, 12086-12089.Abstract
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.
Kalinowski, J. ; Rasanen, M. ; Gerber, R. B. Mechanism and electronic transition in the Cl + O-3 -> ClO + O-2 reaction: On the fly dynamics simulations with multi-reference potentials. CHEMICAL PHYSICS LETTERS 2012, 535, 44-48.Abstract
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.
Jin, L. ; Gerber, B. R. Migration and chemical reaction of H+ in protonated beta-galactose. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2012, 14, 13522-13526.Abstract
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.
Rudic, S. ; Xie, H. -bin; Gerber, B. R. ; Simons, J. P. Protonated sugars: vibrational spectroscopy and conformational structure of protonated O-methyl alpha-D-galactopyranoside. MOLECULAR PHYSICS 2012, 110, 1609-1615.Abstract
`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.
Epstein, S. A. ; Shemesh, D. ; Tran, V. T. ; Nizkorodov, S. A. ; Gerber, B. R. Absorption Spectra and Photolysis of Methyl Peroxide in Liquid and Frozen Water. JOURNAL OF PHYSICAL CHEMISTRY A 2012, 116, 6068-6077.Abstract
Methyl peroxide (CH3OOH) is commonly found in atmospheric waters and ices in significant concentrations. It is the simplest organic peroxide and an important precursor to hydroxyl radical. Many studies have examined the photochemical behavior of gaseous CH3OOH; however, the photochemistry of liquid and frozen water solutions is poorly understood. We present a series of experiments and theoretical calculations designed to elucidate the photochemical behavior of CH3OOH dissolved in liquid water and ice over a range of temperatures. The molar extinction coefficients of aqueous CH3OOH are different from the gas phase, and they do not change upon freezing. Between -12 and 43 degrees C, the quantum yield of CH3OOH photolysis is described by the following equation: Phi(T) = exp((-2175 +/- 448)1/T) + 7.66 +/- 1.56). We use on-the-fly ab initio molecular dynamics simulations to model structures and absorption spectra of a bare CH3OOH molecule and a CH3OOH molecule immersed inside 20 water molecules at 50, 200, and 220 K. The simulations predict large sensitivity in the absorption spectrum of CH3OOH to temperature, with the spectrum narrowing and shifting to the blue under cryogenic conditions because of constrained dihedral motion around the O-O bond. The shift in the absorption spectrum is not observed in the experiment when the CH3OOH solution is frozen suggesting that CH3OOH remains in a liquid layer between the ice grains. Using the extinction coefficients and photolysis quantum yields obtained in this work, we show that under conditions with low temperatures, in the presence of clouds with a high liquid-water content and large solar zenith angles, the loss of CH3OOH by aqueous photolysis is responsible for up to 20% of the total loss of CH3OOH due to photolysis. Gas phase photolysis of CH3OOH dominates under all other conditions.
Gerber, B. R. ; Tsivion, E. ; Khriachtchev, L. ; Rasanen, M. Intrinsic lifetimes and kinetic stability in media of noble-gas hydrides. CHEMICAL PHYSICS LETTERS 2012, 545, 1-8.Abstract
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.
Lignell, H. ; Varner, M. E. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Isomerization and ionization of N2O4 on model ice and silica surfaces. CHEMICAL PHYSICS 2012, 405, 52-59.Abstract
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.
Jin, L. ; Simons, J. P. ; Gerber, B. R. Monosaccharide-Water Complexes: Vibrational Spectroscopy and Anharmonic Potentials. JOURNAL OF PHYSICAL CHEMISTRY A 2012, 116, 11088-11094.Abstract
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.
Hammerich, A. D. ; Finlayson-Pitts, B. J. ; Gerber, B. R. NOx Reactions on Aqueous Surfaces with Gaseous HCl: Formation of a Potential Precursor to Atmospheric Cl Atoms. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2012, 3 3405-3410.Abstract
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.
Dawson, M. L. ; Varner, M. E. ; Perraud, V. ; Ezell, M. J. ; Gerber, B. R. ; Finlayson-Pitts, B. J. Simplified mechanism for new particle formation from methanesulfonic acid, amines, and water via experiments and ab initio calculations. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2012, 109, 18719-18724.Abstract
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.
Pincu, M. ; Xie, H. ; Lin, J. ; Brauer, B. ; Simons, J. P. ; Bar, I. ; Cocinero, E. ; Mayorkas, N. ; Buch, V. ; Gerber, R. B. Computaional studies of saccharide hydration: Spectroscopy, structure and dynamics. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2011, 241.
Shmilovits-Ofir, M. ; Miller, Y. ; Gerber, B. R. Conformational transitions of glycine induced by vibrational excitation of the O-H stretch. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2011, 13, 8715-8722.Abstract
Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. ``On the fly'' simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the v = 1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (v = 1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.
Varner, M. E. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Dynamics of nitrous acid formation in (NO+)(NO3-)-water clusters. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2011, 241.
Simons, J. P. ; Mayorkas, N. ; Cocinero, E. J. ; Rudic, S. ; Gerber, B. R. ; Davis, B. G. Gas phase spectroscopy of hydrated carbohydrates: The anomeric effect laid bare. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2011, 241.
Sebek, J. ; Pele, L. ; Potma, E. O. ; Gerber, B. R. Raman spectra of long chain hydrocarbons: anharmonic calculations, experiment and implications for imaging of biomembranes. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2011, 13, 12724-12733.Abstract
First-principles anharmonic vibrational calculations are carried out for the Raman spectrum of the C-H stretching bands in dodecane, and for the C-D bands in the deuterated molecule. The calculations use the Vibrational Self-Consistent Field (VSCF) algorithm. The results are compared with liquid-state experiments, after smoothing the isolated-molecule sharp-line computed spectra. Very good agreement between the computed and experimental results is found for the two systems. The combined theoretical and experimental results provide insights into the spectrum, elucidating the roles of symmetric and asymmetric CH(3) and CH(2) hydrogenic stretches. This is expected to be very useful for the interpretation of spectra of long-chain hydrocarbons. The results show that anharmonic effects on the spectrum are large. On the other hand, vibrational degeneracy effects seem to be rather modest at the resolution of the experiments. The degeneracy effects may have more pronounced manifestations in higher-resolution experiments. The results show that first-principles anharmonic vibrational calculations for hydrocarbons are feasible, in good agreement with experiment, opening the way for applications to many similar systems. The results may be useful for the analysis of CARS imaging of lipids, for which dodecane is a representative molecule. It is suggested that first-principles vibrational calculations may be useful also for CARS imaging of other systems.
Tsivion, E. ; Gerber, B. R. Stability of noble-gas hydrocarbons in an organic liquid-like environment: HXeCCH in acetylene. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2011, 13, 19601-19606.Abstract
Noble-gas hydrides such as HXeCCH are prepared in cryogenic noble-gas matrices where they are stable. Molecular dynamics simulations reported here predict that HXeCCH is chemically stable in clusters of acetylene, and that stability prevails for temperatures of at least 150 K, at which the clusters are liquid-like. The HXeCCH(C(2)H(2))(n) clusters are studied for sizes up to n = 7. Ab Initio Molecular Dynamics trajectories of 10 ps duration are computed using BLYP-D DFT potential. The liquid-like nature of the system at 150 K is reflected in large amplitude motion of intermolecular distances and orientations. In addition, structures, energetics, NBO charges and bonding analysis at equilibrium are also reported. Complexation is found to be energetically favorable, and to increase the stability of the HXeCCH molecule. The significance of the existence of stable liquid-like complexes of noble-gas hydrides is discussed.
Lignell, H. ; Finlayson-Pitts, B. J. ; Gerber, R. B. Structure, isomerization, and ionization of N2O4 on liquid water, ice, and silica surfaces. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2011, 241.
Varner, M. E. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Effects of water on atmospheric processes studied using ab initio molecular dynamics simulations. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2011, 242.