Murdachaew, G. ; Gaigeot, M. - P. ; Halonen, L. ; Gerber, B. R. Dissociation of HCl into ions on wet hydroxylated (0001) alpha-quartz. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 247.
Shemesh, D. ; Nizkorodov, S. A. ; Gerber, B. R. Dynamics of triplet state photochemistry of aldehydes. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 247.
Varner, M. E. ; Kebede, M. A. ; Scharko, N. K. ; Raff, J. D. ; Gerber, B. R. Intermediates in the photooxidation of ammonia. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 247.
Kalinowski, J. ; Rasanen, M. ; Gerber, B. R. Nature, isomerization, and decomposition of a Criegee intermediate: Dynamics using a multireference potential. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 247.
Gerber, B. R. ; Goldstein, M. ; Segev, E. ; Zmiri, L. ; Shahar, A. ; Gantman, T. Structure and structural transitions of charged proteins in mass spectrometry. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 247.
Hirshberg, B. ; Krylov, A. I. ; Gerber, B. R. Theoretical prediction of crystalline N-8. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 247.
Tsivion, E. ; Rasanen, M. ; Gerber, B. R. Destabilization of noble-gas hydrides by a water environment: calculations for HXeOH@(H2O)(n), HXeOXeH@(H2O)(n), HXeBr@(H2O)(n), HXeCCH@(H2O)(n). PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2013, 15, 12610-12616.Abstract
HNgY molecules are chemically-bound compounds of a noble-gas atom (Ng) with a hydrogen and with an electronegative group Y. There is considerable current interest in the stability of these species in different types of media. The kinetic stability of several compounds, HXeOH, HXeOXeH, HXeBr and HXeCCH, in water clusters is explored by ab initio calculations. It is found that the kinetic stability of the compounds is reduced by the water environment, generally falling off with the number of H2O molecules. For a relatively modest number of water molecules, the compounds decompose spontaneously. Implications of the results for storage of HNgY in molecular media are discussed.
Murdachaew, G. ; Varner, M. E. ; Phillips, L. F. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Nitrogen dioxide at the air-water interface: trapping, absorption, and solvation in the bulk and at the surface. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2013, 15, 204-212.Abstract
The interaction of NO2 with water surfaces in the troposphere is of major interest in atmospheric chemistry. We examined an initial step in this process, the uptake of NO2 by water through the use of molecular dynamics simulations. An NO2-H2O intermolecular potential was obtained by fitting to high-level ab initio calculations. We determined the binding of NO2-H2O to be about two times stronger than that previously calculated. From scattering simulations of an NO2 molecule interacting with a water slab we observed that the majority of the scattering events resulted in outcomes in which the NO2 molecule became trapped at the surface or in the interior of the water slab. Typical surface-trapped/adsorbed and bulk-solvated/absorbed trajectories were analyzed to obtain radial distribution functions and the orientational propensity of NO2 with respect to the water surface. We observed an affinity of the nitrogen atom for the oxygen in water, rather than hydrogen-bonding which was rare. The water solvation shell was less tight for the bulk-absorbed NO2 than for the surface-adsorbed NO2. Adsorbed NO2 demonstrated a marked orientational preference, with the oxygens pointing into the vacuum. Such behavior is expected for a mildly hydrophobic and surfactant molecule like NO2. Estimates based on our results suggest that at high NO2 concentrations encountered, for example, in some sampling systems, adsorption and reaction of NO2 at the surface may contribute to the formation of gas-phase HONO.
Roy, T. K. ; Gerber, B. R. Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2013, 15, 9468-9492.Abstract
This review describes the vibrational self-consistent field (VSCF) method and its other variants for computing anharmonic vibrational spectroscopy of biological molecules. The superiority and limitations of this algorithm are discussed with examples. The spectroscopic accuracy of the VSCF method is compared with experimental results and other available state-of-the-art algorithms for various biologically important systems. For large biological molecules with many vibrational modes, the scaling of computational effort is investigated. The accuracy of the vibrational spectra of biological molecules using the VSCF approach for different electronic structure methods is also assessed. Finally, a few open problems and challenges in this field are discussed.
Pincu, M. ; Brauer, B. ; Gerber, B. R. When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2013, 15, 15382-15391.Abstract
Investigations of reaction pathways between a proton and cellobiose (CB), a glucose disaccharide of importance, were carried out in cis and trans CB using Ab Initio Molecular Dynamics (AIMD) simulations starting from optimized configurations where the proton is initially placed near groups with affinity for it. Near and above 300 K, protonated CB (H+CB) undergoes several transient reactions including charge transfer to the sugar backbone, water formation and dehydration, ring breaking and glycosidic bond breaking events as well as mutarotation and ring puckering events, all on a 10 ps timescale. cis H+CB is energetically favoured over trans H+CB in vacuo, with an energy gap larger than for the neutral CB.
Goldtzvik, Y. ; Goldstein, M. ; Gerber, B. R. On the crystallographic accuracy of structure prediction by implicit water models: Tests for cyclic peptides. CHEMICAL PHYSICS 2013, 415, 168-172.Abstract
Five small cyclic peptides and four implicit water models, were selected for this study. DEEPSAM, a structure prediction algorithm built upon TINKER, was used. Structures predicted using implicit water models were compared with experimental data, and with predictions calculated in the gas phase. The existence of very accurate X-ray crystallographic data allowed firm and conclusive comparisons between predictions and experiment. The introduction of implicit water models into the calculations improved the RMSD from experiment by about 13% compared with computations neglecting the presence of water. GBSA is shown to be consistently the best implicit water model. (C) 2013 Elsevier B.V. All rights reserved.
Murdachaew, G. ; Gaigeot, M. - P. ; Halonen, L. ; Gerber, B. R. Dissociation of HCl into Ions on Wet Hydroxylated (0001) alpha-Quartz. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2013, 4 3500-3507.Abstract
The acidification of surfaces in the natural and built environments is important to atmospheric science because the process can enhance chemistry at surfaces and increase the release of highly reactive products into the gas phase. We present the results of an ab initio molecular dynamics study using density functional theory of HCl ionic dissociation on the hydroxylated (0001) alpha-quartz surface. We observed that at temperatures in the range of 250-300 K, HCl ionizes rapidly on a surface wetted with a water monolayer. It seems that ionization is enhanced by lattice mismatch between the silica and water layer. The first proton transfer to a neighboring water molecule initiates proton migration within the water adlayer via the Grotthuss mechanism. Spectroscopic signatures for the ionization are calculated and are in fair agreement with experiment.
Shemesh, D. ; Lan, Z. ; Gerber, B. R. Dynamics of Triplet-State Photochemistry of Pentanal: Mechanisms of Norrish I, Norrish II, and H Abstraction Reactions. JOURNAL OF PHYSICAL CHEMISTRY A 2013, 117, 11711-11724.Abstract
The photochemistry of aldehydes in the gas phase has been the topic of extensive studies over the years. However, for all but the smallest aldehydes the dynamics of the processes is largely unknown, and key issues of the mechanisms are open. In this article, the photochemistry of pentanal is studied by dynamics simulation using a semiempirical MRCI code for the singlet and triplet potential energy surfaces involved. The simulations explore the processes on the triplet state following intersystem crossing from the initially excited singlet. Test simulations show that the photochemistry takes place on the adiabatic triplet surface only and that no nonadiabatic transitions occur to the other triplets. The main findings include the following: (1) Norrish type I and type II reactions and H detachment have been observed. (2) The time scales of Norrish type I and Norrish type II reactions are determined: Norrish type I reaction tends to occur in the time scale below 10 ps, whereas the Norrish type II reaction is mostly pronounced after 20 ps. The factors affecting the time scales are analyzed. (3) The relative yield for Norrish type I and type II reactions is 34% and 66%, which is close to the experimental observed ones. Bond orders and Mulliken partial charges are computed along the trajectories and provide mechanistic insights. The results throw light on the time scales and mechanisms and competition between different channels in aldehyde photochemistry. It is suggested that direct dynamics simulations using semiempirical potentials can be a very useful tool for exploring the photochemistry of large aldehydes, ketones, and related species.
Lignell, H. ; Epstein, S. A. ; Marvin, M. R. ; Shemesh, D. ; Gerber, R. B. ; Nizkorodov, S. Experimental and Theoretical Study of Aqueous cis-Pinonic Acid Photolysis. JOURNAL OF PHYSICAL CHEMISTRY A 2013, 117, 12930-12945.Abstract
Direct aqueous photolysis of cis-pinonic acid (PA; 2-(3-acetyl-2,2-dimethylcyclobutyl)acetic acid; CAS Registry No. 473-72-3) by 280-400 nm radiation was investigated. The photolysis resulted in Norrish type II isomerization of PA leading to 3-isopropenyl-6-oxoheptanoic acid (CAS Registry No. 4436-82-2), also known as limononic acid, as the major product, confirmed by H-1 and C-13 NMR analysis, chemical ionization mass spectrometry, and electrospray ionization mass spectrometry. Several minor products resulting from Norrish type I splitting of PA were also detected. The molar extinction coefficients of aqueous PA were measured and used to calculate the photolysis quantum yield of aqueous PA as 0.5 +/- 0.3 (effective average value over the 280-400 nm range). The gas-phase photolysis quantum yield of 0.53 +/- 0.06 for PA methyl ester (PAMe; CAS Registry No. 16978-11-3) was also measured for comparison. These results indicate that photolysis of PA is not significantly suppressed by the presence of water. This fact was confirmed by photodissociation dynamics simulations of bare PA and of PAMe hydrated with one or five water molecules using on-the-fly dynamics simulations on a semiempirical potential energy surface. The calculations correctly predicted the occurrence of both Norrish type I and Norrish type II photolysis pathways, both driven by the dynamics on the lowest triplet excited state of PA and PAMe. The rate of removal of PA by direct aqueous photolysis in cloudwater and in aerosol water was calculated for a range of solar zenith angles and compared with rates of other removal processes such as gas-phase oxidation by OH, aqueous-phase oxidation by OH, and gas-phase photolysis. Although the direct photolysis mechanism was not the most significant sink for PA in cloud and fog droplets, direct photolysis can be expected to contribute to removal of PA and more soluble/less volatile biogenic oxidation products in wet particulate matter.
Riikonen, S. ; Parkkinen, P. ; Halonen, L. ; Gerber, R. B. Ionization of Nitric Acid on Crystalline Ice: The Role of Defects and Collective Proton Movement. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2013, 4 1850-1855.Abstract
Ionization of nitric acid (HNO3) on a model ice surface is studied using ab initio molecular dynamics at temperatures of 200 and 40 K with a surface slab model that consists of the ideal ice basal plane with locally optimized and annealed defects. Pico- and subpicosecond ionization of nitric acid can be achieved in the defect sites. Key features of the rapid ionization are (a) the efficient solvation of the polyatomic nitrate anion, by stealing hydrogen bonds from the weakened hydrogen bonds at defect sites, (b) formation of contact ion pairs to stable ``presolvated'' molecular species that are present at the defects, (c) rapid formation of the ``solvent-separated'' ion pair, which is facilitated by collective proton migration that is typical to ice, and (d) the facile formation of Eigen ions on the ice basal plane.
Kebede, M. A. ; Varner, M. E. ; Scharko, N. K. ; Gerber, B. R. ; Raff, J. D. Photooxidation of Ammonia on TiO2 as a Source of NO and NO2 under Atmospheric Conditions. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2013, 135, 8606-8615.Abstract
Ammonia is the most abundant reduced nitrogen species in the atmosphere and an important precursor in the industrial-scale production of nitric acid. A coated-wall flow tube coupled to a chemiluminescence NOx analyzer was used to study the kinetics of NH3 uptake and NOx formation from photochemistry initiated on irradiated (lambda > 290 tun) TiO2 surfaces under atmospherically relevant conditions. The speciation of NH3 on TiO2 surfaces in the presence of surface adsorbed water was determined using diffuse reflection infrared Fourier transform spectroscopy. The uptake kinetics exhibit an inverse dependence on NH3 concentration as expected for reactions proceeding via a Langmuir-Hinshelwood mechanism. The mechanism of NOx formation is shown to be humidity dependent: Water catalyzed reactions promote NOx formation up to a relative humidity of 50%. Less NOx is formed above 50%, where increasing amounts of adsorbed water may hinder access to reactive sites, promote formation of unreactive NH4+, and reduce oxidant levels due to higher OH radical recombination rates. A theoretical study of the reaction between the NH2 photoproduct and O-2 in the presence of H2O supports the experimental conclusion that NOx formation is catalyzed by water. Calculations at the MP2 and CCSD(T) level on the bare NH2 + O-2 reaction and the reaction of NH2 + O-2 in small water clusters were carried out Solvation of NH2OO and NHOOH intermediates likely facilitates isomerization via proton transfer along water wires, such that the steps leading ultimately to NO are exothermic. These results show that photooxidation of low levels of NH3 on TiO2 surfaces represents a source of atmospheric NOx, which is a precursor to ozone. The proposed mechanism may be broadly applicable to dissociative chemisorption of NH3 on other metal oxide surfaces encountered in rural and urban environments and employed in pollution control applications (selective catalytic oxidation/reduction) and during some industrial processes.
Sebek, J. ; Knaanie, R. ; Albee, B. ; Potma, E. O. ; Gerber, B. R. Spectroscopy of the C-H Stretching Vibrational Band in Selected Organic Molecules. JOURNAL OF PHYSICAL CHEMISTRY A 2013, 117, 7442-7452.Abstract
The vibrational spectroscopy of C-H stretches in organic molecules is of considerable importance for the characterization of these systems and for exploration of their properties. These stretches are strongly anharmonic, and thus methods including anharmonicity have to be used. The vibrational self-consistent field (VSCF) is applied to the following organic compounds: acetone, dimethylacetylene, neopentane, toluene, ethylene, and cyclopropane. The computed spectra are compared to new experimental data, including Raman measurements of all molecules except cyclopropane and IR of acetone, neopentane, and ethylene. A high level of agreement is found for all of the molecules. The characteristic features of CH3 and CH2 groups are studied and analyzed in detail. A reliable, unambiguous assignment of vibrational modes to spectral peaks is provided. Several characteristic features of CH3 and CH2 vibrations in polyatomic molecules are clarified, providing easier assignments for different types of organic molecules.
Dawson, M. L. ; Varner, M. E. ; Perraud, V. ; Ezell, M. J. ; Wingen, L. M. ; Gerber, R. B. ; Finlayson-Pitts, B. J. Atmospheric particle formation and growth from methanesulfonic acid and amines. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2012, 243.
Xie, H. -bin; Jin, L. ; Rudic, S. ; Simons, J. P. ; Gerber, B. R. Computational Studies of Protonated beta-D-Galactose and Its Hydrated Complex: Structures, Interactions, Proton Transfer Dynamics, and Spectroscopy. JOURNAL OF PHYSICAL CHEMISTRY B 2012, 116, 4851-4859.Abstract
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
Hirshberg, B. ; Gerber, B. R. Decomposition mechanisms and dynamics of N-6: Bond orders and partial charges along classical trajectories. CHEMICAL PHYSICS LETTERS 2012, 531, 46-51.Abstract
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.