Finlayson-Pitts, B. J. ; Perraud, V. ; Ezell, M. J. ; Dawson, M. L. ; Varner, M. E. ; Gerber, B. R. Formation and growth of particles in air: New insights from laboratory studies. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2011, 242.
Pincu, M. ; Cocinero, E. J. ; Mayorkas, N. ; Brauer, B. ; Davis, B. G. ; Gerber, B. R. ; Simons, J. P. Isotopic Hydration of Cellobiose: Vibrational Spectroscopy and Dynamical Simulations. JOURNAL OF PHYSICAL CHEMISTRY A 2011, 115, 9498-9509.Abstract
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.
Goldstein, M. ; Fredj, E. ; Gerber, B. R. A New Hybrid Algorithm for Finding the Lowest Minima of Potential Surfaces: Approach and Application to Peptides. JOURNAL OF COMPUTATIONAL CHEMISTRY 2011, 32, 1785-1800.Abstract
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
Shmilovits-Ofir, M. ; Gerber, B. R. Proton Transfer and Dissociation of GlyLysH(+) following O-H and N-H Stretching Mode Excitations: Dynamics Simulations. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2011, 133, 16510-16517.Abstract
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.
Xie, H. -bin; Pincu, M. ; Brauer, B. ; Gerber, B. R. ; Bar, I. Raman and infrared spectra of cellobiose in the solid state: What can be learned from single-molecule calculations?. CHEMICAL PHYSICS LETTERS 2011, 514, 284-290.Abstract
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.
Pele, L. ; Sebek, J. ; Potma, E. O. ; Gerber, B. R. Raman and IR spectra of butane: Anharmonic calculations and interpretation of room temperature spectra. CHEMICAL PHYSICS LETTERS 2011, 515, 7-12.Abstract
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.
Liessmann, M. ; Miller, Y. ; Gerber, B. R. ; Abel, B. Reaction of OH and NO at Low Temperatures in the Presence of Water: the Role of Clusters. ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS 2011, 225, 1129-1144.Abstract
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.
Gerber, B. R. Tributes to Victoria Buch. JOURNAL OF PHYSICAL CHEMISTRY A 2011, 115, 5709-5714.
Brauer, B. ; Pincu, M. ; Buch, V. ; Bar, I. ; Simons, J. P. ; Gerber, B. R. Vibrational Spectra of alpha-Glucose, beta-Glucose, and Sucrose: Anharmonic Calculations and Experiment. JOURNAL OF PHYSICAL CHEMISTRY A 2011, 115, 5859-5872.Abstract
The anharmonic vibrational spectra of alpha-D-glucose, beta-D-glucose, and sucrose are computed by the vibrational self-consistent field (VSCF) method, using potential energy surfaces from electronic structure theory, for the lowest energy conformers that correspond to the gas phase and to the crystalline phase, respectively. The results are compared with ultraviolet-infrared (UV-IR) spectra of phenyl beta-D-glucopyranoside in a molecular beam, with literature results for sugars in matrices and with new experimental data for the crystalline state. Car-Parrinello dynamics simulations are also used to study temperature effects on the spectra of alpha-D-glucose and beta-D-glucose and to predict their vibrational spectra at 50, 150, and 300 K The effects of temperature on the spectral features are analyzed and compared with results of the VSCF calculations conducted at OK. The main results include: (i) new potential surfaces, constructed from Hartree-Fock, adjusted to fit harmonic frequencies from Moller-Plesset (MP2) calculations, that give very good agreement with gas phase, matrix, and solid state spectra; (ii) computed infrared spectra of the crystalline solid of alpha-glucose, which are substantially improved by including mimic groups that represent the effect of the solid environment on the sugar; and (iii) identification of a small number of combination-mode transitions, which are predicted to be strong enough for experimental observation. The results are used to assess the role of anharmonic effects in the spectra of the sugars in isolation and in the solid state and to discuss the spectroscopic accuracy of potentials from different electronic structure methods.
Jin, L. ; Simons, J. P. ; Gerber, B. R. Structures of the xylose-water complex: Energetics, transitions between conformers and spectroscopy. CHEMICAL PHYSICS LETTERS 2011, 518, 49-54.Abstract
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.
Njegic, B. ; Raff, J. D. ; Finlayson-Pitts, B. J. ; Gordon, M. S. ; Gerber, B. R. Catalytic Role for Water in the Atmospheric Production of ClNO. JOURNAL OF PHYSICAL CHEMISTRY A 2010, 114, 4609-4618.Abstract
High level ab initio calculations of clusters comprised of water, HCl, and ON-ONO2 are used to study nitrosyl chloride (ClNO) formation in gas phase water clusters, which are also mimics for thin water films present at environmental interfaces. Two pathways are considered, direct formation from the reaction of gaseous HCl with ON-ONO2 and an indirect pathway involving the hydrolysis of ON-ONO2 to form HONO, followed by the reaction of HONO with HCl to form ClNO. Surprisingly, direct formation of ClNO is found to be the dominant channel in the presence of water despite the possibility of a competing hydrolysis of ON-ONO2 to form HONO. A single water molecule effectively catalyzes the ON-ONO2 + HCl reaction, and in the presence of two or more water molecules the reaction to form ClNO becomes spontaneous. Direct formation of ClNO is fast at room and ice temperatures, indicating the possible significance of this pathway for chlorine activation chemistry in both the polar and midlatitude troposphere, in volcanic plumes and indoors. The reaction enthalpies, activation energies, and rate constants for all studied reactions are reported. The results are discussed in light of recent experiments.
Harmon, C. W. ; Grimm, R. L. ; McIntire, T. M. ; Peterson, M. D. ; Njegic, B. ; Angel, V. M. ; Alshawa, A. ; Underwood, J. S. ; Tobias, D. J. ; Gerber, B. R. ; et al. Hygroscopic Growth and Deliquescence of NaCl Nanoparticles Mixed with Surfactant SDS. JOURNAL OF PHYSICAL CHEMISTRY B 2010, 114, 2435-2449.Abstract
Several complementary experimental and theoretical methodologies were used to explore water uptake on sodium chloride (NaCl) particles containing varying amounts of sodium dodecyl sulfate (SDS) to elucidate the interaction of water with well-defined, environmentally relevant surfaces. Experiments probed the hygroscopic growth of mixed SDS/NaCl nanoparticles that were generated by electrospraying aqueous 2 g/L solutions containing SDS and NaCl with relative NaCl/SDS weight fractions of 0, 5, 11, 23, or 50 wt/wt %. Particles with mobility-equivalent diameters of 14.0(+/- 0.2) nm were size selected and their hygroscopic growth was monitored by a tandem nano-differential mobility analyzer as a function of relative humidity (RH). Nanoparticles generated from 0 and 5 wt/wt % Solutions deliquesced abruptly at 79.1 (+/- 1.0)% RH. Both of these nanoparticle compositions had 3.1(+/- 0.5) monolayers of adsorbed surface water prior to deliquescing and showed good agreement with the Brunauer-Emmett-Teller and the Frenkel-Halsey-Hill isotherms. Above the deliquescence point, the growth curves could be qualitatively described by Kohler theory after appropriately accounting for the effect of the particle shape on mobility. The SDS/NaCl nanoparticles with larger SDS fractions displayed gradual deliquescence at a RH that was significantly lower than 79.1%. All compositions of SDS/NaCl nanoparticles had monotonically Suppressed mobility growth factors (GF(m)) with increasing fractions of SDS in the electrosprayed solutions. The Zdanovskii-Stokes-Robinson model was used to estimate the actual fractions of SDS and NaCl in the nanoparticles; it suggested the nanoparticles were enhanced in SDS relative to their electrospray solution concentrations. X-ray photoelectron spectroscopy (XPS), FTIR, and AFM were consistent with SDS forming first a monolayer and then a crystalline phase around the NaCl core. Molecular dynamics simulations of water vapor interacting with SDS/NaCl slabs showed that SDS kinetically hinders the initial water uptake. Large binding energies of sodium methyl sulfate (SMS)-(NaCl)(4), H(2)O-(NaCl)(4), and SMS-H(2)O-(NaCl)(4) calculated at the MP2/cc-pVDZ level suggested that placing H(2)O in between NaCl and surfactant headgroup is energetically favorable. These results provide a comprehensive description of SDS/NaCl nanoparticles and their properties.
Tsivion, E. ; Gerber, B. R. Predicted compounds of radon with acetylene and water. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2010, 12, 11791-11794.Abstract
It is found that HRnCCH and HRnOH are metastable, chemically bound compounds of radon. These molecules are studied by multi-reference ab initio methods. Equilibrium geometry, NBO partial charges and bond orders, harmonic frequencies, are calculated. Intrinsic life-times are obtained by calculating the dissociation barriers and related partition functions, and by applying transition state theory. HRnCCH and HRnOH are found to be protected by an energy barrier of 2.1 and 0.79 eV, respectively. Using transition state theory, HRnOH is predicted to have a half-life of 1 h at about 230 K. HRnCCH is found to be kinetically stable at room temperature with its lifetime limited by the lifetime of the radioactive Rn atom. The significance of compound formation of radon with acetylene and water is discussed.
Pincu, M. ; Brauer, B. ; Gerber, R. B. ; Buch, V. Sugar-salt and sugar-salt-water complexes: structure and dynamics of glucose-KNO3-(H2O)(n). PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2010, 12, 3550-3558.Abstract
Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO3 and for complexes of the type glucose-KNO3-(H2O)(n), for n <= 11. Structure and dynamic properties of the systems are explored. The MD simulations are carried out using primarily the DL\_POLY/OPLS force field, and global and local minimum energy structures of some of the systems are compared with ab initio calculations. The main findings include: (1) complexation with KNO3 leads to an ``inverse anomeric effect'', with the beta-glucose complex more stable than the alpha-glucose by B1.74 kcal mol(-1); (2) as temperature is increased to 600 K, the KNO3 remains undissociated in the 1 : 1 complex, with the K+ hooked to the equilibrium site, and the NO3- bound to it, undergoing large-amplitude bending/torsional motions; (3) for n >= 3 water molecules added to the system, charge separation into K+ and NO3- ions takes place; (4) for the sugar-water system with n = 11 water molecules all hydroxyl groups are hydrated with the glucose adopting a surface position, indicative of a surfactant property of the sugar; and (5) comparison of DL\_POLY with MP2/TZP structure predictions indicates that the empirical force field predicts global and local minimum structures reasonably well, but errs in giving the energy rankings of the different minima. The implications of the results on the effects of salts on saccharides are discussed.
Pele, L. ; Gerber, B. R. On the Mean Accuracy of the Separable VSCF Approximation for Large Molecules. JOURNAL OF PHYSICAL CHEMISTRY C 2010, 114, 20603-20608.Abstract
The separable VSCF approximation and the VSCF-PT2 method are extensively used for anharmonic vibrational spectroscopy calculations of large molecules. VSCF-PT2 uses second-order perturbation theory to correct the VSCF level, and is thus more accurate. It is shown by test calculations for a series of amino acids and peptides that the mean deviation of VSCF from VSCF-PT2 frequencies decreases for an increasing number of modes N, the decrease scaling roughly with log N. It is conjectured that the result is a manifestation of improved mean accuracy of VSCF as a mean-field approximation, a consequence of increased averaging with increasing numbers of modes. There is no systematic increase in VSCF accuracy with N for individual vibrational transitions. Increased accuracy of VSCF with N is found for certain groups of transitions, e.g., N-H stretches. The results are expected to be useful in choosing methods for spectroscopy calculations of extended systems such as large peptides, proteins, and nucleic acids.
Kamboures, M. A. ; Nizkorodov, S. A. ; Gerber, R. B. Ultrafast photochemistry of methyl hydroperoxide on ice particles. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2010, 107, 6600-6604.Abstract
Simulations show that photodissociation of methyl hydroperoxide, CH(3)OOH, on water clusters produces a surprisingly wide range of products on a subpicosecond time scale, pointing to the possibility of complex photodegradation pathways for organic peroxides on aerosols and water droplets. Dynamics are computed at several excitation energies at 50 K using a semiempirical PM3 potential surface. CH(3)OOH is found to prefer the exterior of the cluster, with the CH(3)O group sticking out and the OH group immersed within the cluster. At atmospherically relevant photodissociation wavelengths the OH and CH(3)O photofragments remain at the surface of the cluster or embedded within it. However, none of the 25 completed trajectories carried out at the atmospherically relevant photodissociation energies led to recombination of OH and CH(3)O to form CH(3)OOH. Within the limited statistics of the available trajectories the predicted yield for the recombination is zero. Instead, various reactions involving the initial fragments and water promptly form a wide range of stable molecular products such as CH(2)O, H(2)O, H(2), CO, CH(3)OH, and H(2)O(2).
Suwan, I. ; Gerber, R. B. VSCF in internal coordinates and the calculation of anharmonic torsional mode transitions. CHEMICAL PHYSICS 2010, 373, 267-273.Abstract
The vibrational self-consistent field (VSCF) method assumes separability in normal modes in its usual version. However, the method fails in cases such as soft torsional modes which are better treated by angular variables. We develop VSCF equations based on the assumption of wave function separability in internal coordinates. To test the method, simple illustrative applications to small systems are provided: trans-HONO, cis-HONO, H2S2, and H2O2. The code directly uses points from ab initio calculations, and the method proves to be accurate for all types of transitions. For typical torsional transitions, the error in the computed frequency is smaller than that of VSCF in normal coordinates. The wave functions for the torsional mode are compared with the corresponding normal mode wave functions. The differences are substantial. The results are encouraging for extension of the model for large polyatomic systems. Work along these lines is in progress. (C) 2010 Elsevier B. V. All rights reserved.
Adesokan, A. A. ; Gerber, R. B. Anharmonic Vibrational Spectroscopy Calculations for Proton-Bound Amino Acid Dimers. JOURNAL OF PHYSICAL CHEMISTRY A 2009, 113, 1905-1912.Abstract
Results of anharmonic frequency calculations carried out for GlysLysH(+) and GlyGlyH(+) are presented and compared to gas phase electrospray ionization (ESI) spectroscopy experiments. Anharmonic frequencies are obtained via correlation-corrected vibrational self-consistent field (CC-VSCF) calculations. The potential used is based on the PM3 semiempirical electronic structure method, but improved by fitting to ab initio MP2 calculations at the harmonic level. The key results are as follows: (1) Hydrogens acting as intermolecular bridges have very anharmonic stretches whose frequencies cannot be reliably predicted by the harmonic approximation. An example is the carboxylate bound NH3+ stretch. (2) The computed anharmonic vibrational frequencies are in good agreement with experiment and provides a very large improvement over harmonic frequencies especially for OH and NH stretches. For example the calculated CC-VSCF frequencies of GlysLysH(+) and GlyGlyH(+) have overall average deviations of 1.35% and 1.48% only, respectively, from experiment. (3) The harmonic OH bond stretching frequency deviates by 6.64% from experiments. The CC-VSCF calculations reduce this deviation by more than an order of magnitude to 0.56%. The anharmonicity of the OH stretch is intrinsic, rather than due to coupling with other modes. (4) Anharmonic coupling between the NH3+ stretch and several other normal modes is strong, and provide the main contribution for the anharmonicity of this mode. Properties of the potential energy surfaces of the proton-bound complexes are briefly discussed in light of the results.
Gerber, R. B. Autobiography of Robert Benny Gerber. JOURNAL OF PHYSICAL CHEMISTRY A 2009, 113, 7163+.
Raff, J. D. ; Njegic, B. ; Chang, W. L. ; Gordon, M. S. ; Dabdub, D. ; Gerber, B. R. ; Finlayson-Pitts, B. J. Chlorine activation indoors and outdoors via surface-mediated reactions of nitrogen oxides with hydrogen chloride. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2009, 106, 13647-13654.Abstract
Gaseous HCl generated from a variety of sources is ubiquitous in both outdoor and indoor air. Oxides of nitrogen (NOy) are also globally distributed, because NO formed in combustion processes is oxidized to NO2, HNO3, N2O5 and a variety of other nitrogen oxides during transport. Deposition of HCl and NOy onto surfaces is commonly regarded as providing permanent removal mechanisms. However, we show here a new surface-mediated coupling of nitrogen oxide and halogen activation cycles in which uptake of gaseous NO2 or N2O5 on solid substrates generates adsorbed intermediates that react with HCl to generate gaseous nitrosyl chloride (ClNO) and nitryl chloride (ClNO2), respectively. These are potentially harmful gases that photolyze to form highly reactive chlorine atoms. The reactions are shown both experimentally and theoretically to be enhanced by water, a surprising result given the availability of competing hydrolysis reaction pathways. Airshed modeling incorporating HCl generated from sea salt shows that in coastal urban regions, this heterogeneous chemistry increases surface-level ozone, a criteria air pollutant, greenhouse gas and source of atmospheric oxidants. In addition, it may contribute to recently measured high levels of ClNO2 in the polluted coastal marine boundary layer. This work also suggests the potential for chlorine atom chemistry to occur indoors where significant concentrations of oxides of nitrogen and HCl coexist.