Cohen, A. ; Gerber, R. B. A Noble-Gas Hydride in a Nitrogen Medium: Structure, Spectroscopy, and Intermolecular Vibrations of HXeBr@(N2)22. Journal of Physical Chemistry A 2016, 120, 3372-3379. Publisher's Version
Shemesh, D. ; Nizkorodov, S. A. ; Gerber, R. B. Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics. Journal of Physical Chemistry A 2016, 120, 7112-7120. Publisher's Version
Chen, H. ; Varner, M. E. ; Gerber, R. B. ; Finlayson-Pitts, B. J. Reactions of Methanesulfonic Acid with Amines and Ammonia as a Source of New Particles in Air. Journal of Physical Chemistry B 2016, 120, 1526-1536. Publisher's Version
Roy, T. K. ; Sharma, R. ; Gerber, B. R. First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2016, 18, 1607-1614.Abstract
First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data. Using hybrid HF/MP2 potentials, the Vibrational Self-Consistent Field with Second-Order Perturbation Correction (VSCF-PT2) algorithm is used to compute the spectra without any ad hoc scaling or fitting. All of the vibrational modes (135 for the largest system) are treated quantum mechanically and anharmonically using full pair-wise coupling potentials to represent the interaction between different modes. In the hybrid potential scheme the MP2 method is used for the harmonic part of the potential and a modified HF method is used for the anharmonic part. The overall agreement between computed spectra and experiment is very good and reveals different signatures for different conformers. This study shows that first-principles spectroscopic calculations of good accuracy are possible for dipeptides hence it opens possibilities for determination of dipeptide conformer structures by comparison of spectroscopic calculations with experiment.
Knaanie, R. ; Sebek, J. ; Tsuge, M. ; Myyllys, N. ; Khriachtchev, L. ; Rasanen, M. ; Albee, B. ; Potma, E. O. ; Gerber, B. R. Infrared Spectrum of Toluene: Comparison of Anharmonic Isolated-Molecule Calculations and Experiments in Liquid Phase and in a Ne Matrix. JOURNAL OF PHYSICAL CHEMISTRY A 2016, 120, 3380-3389.Abstract
First-principles anharmonic calculations are carried out for the CH stretching vibrations of isolated toluene and compared with the experimental infrared spectra of isotopologues of toluene in a Ne matrix at 3 K and of liquid toluene at room temperature. The calculations use the vibrational self-consistent field method and the B3LYP potential surface. In general, good agreement is found between the calculations and experiments. However, the spectrum of toluene in a Ne matrix is more complicated than that predicted theoretically. This distinction is discussed in terms of matrix-site and resonance effects. Interestingly, the strongest peak in the CH stretching spectrum has similar widths in the liquid phase and in a Ne matrix, despite the very different temperatures. Implications of this observation to the broadening mechanism are discussed. Finally, our results show that the B3LYP potential offers a good description of the anharmonic CH stretching band in toluene, but a proper description of matrix-site and resonance effects remains a challenge.
Cohen, A. ; Gerber, R. B. A Noble-Gas Hydride in a Nitrogen Medium: Structure, Spectroscopy, and Intermolecular Vibrations of HXeBr@(N-2)(22). JOURNAL OF PHYSICAL CHEMISTRY A 2016, 120, 3372-3379.Abstract
Noble-gas hydrides have been extensively studied in noble gas matrices. However, little is known on their stability and properties in molecular hosts. Here, HXeBr in the N-2 environment is modeled at the B3LYP-D level of theory in a complete single shell of 22 N-2 molecules. The system is compared to similar models of HXeBr in CO2 and Xe clusters. The optimized structure of (HXeBr)@(N-2)(22) is of low symmetry and is highly anisotropic. None of the N-2 molecules are freely rotating, and the host molecules are not symmetrically positioned with respect to the HXeBr axis. The axes of the N-2 molecules are nonuniformly distributed. The computed anharmonic H-Xe stretching frequency of HXeBr in the N-2 cluster is in good accord with the experimental value. The soft mode frequencies of the cluster including both intermolecular vibrations and librations, have a broad distribution that ranges from 8.7 to 107 cm(-1). It is expected that these findings and specifically, the single-shell model, may shed light also on the local structure and vibrations of other impurities in a molecular media.
Chen, H. ; Varner, M. E. ; Gerber, B. R. ; Finlayson-Pitts, B. J. Reactions of Methanesulfonic Acid with Amines and Ammonia as a Source of New Particles in Air. JOURNAL OF PHYSICAL CHEMISTRY B 2016, 120, 1526-1536.Abstract
New particle formation (NPF) from gaseous precursors as a significant source of aerosol needs to be better understood to accurately predict the impacts on visibility, climate change, and human health. While ternary nucleation of sulfuric acid, amines/NH3, and water is recognized as a significant driver for NPF, increasing evidence suggests a contribution from methanesulfonic acid (MSA) and amines under certain conditions. Here we report the formation of particles 2.5-10 nm in diameter from the reactions of MSA with methylamine (MA), dimethylamine (DMA), and NH3 at reaction times of 2.3-7.8 s in a flow reactor and compare these particles with those previously reported to be formed from reaction with trimethylamine (TMA). The effects of water vapor and concentrations of gaseous precursors on the particle number concentration and particle size were studied. The presence of water significantly enhances particle formation and growth. Under similar experimental conditions, particle number concentrations decrease in the order MA >> TMA approximate to DMA >> NH3, where NH3 is 2-3 orders of magnitude less efficient than DMA. Quantum chemical calculations of likely intermediate clusters were carried out to provide insights into the role of water and the different capacities of amines/NH3 in particle formation. Both gas-phase basicity and hydrogen-bonding capacity of amines/NH3 contribute to the potential for particles to form and grow. Our results indicate that, although amines typically have concentrations 1-3 orders of magnitude lower than that of NH3 in the atmosphere, they still play an important role in driving NPF.
Partanen, L. ; Murdachaew, G. ; Gerber, B. R. ; Halonen, L. Temperature and collision energy effects on dissociation of hydrochloric acid on water surfaces. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2016, 18, 13432-13442.Abstract
Collisions of HCl at the air-water interface modelled by a 72 molecule water slab are studied for a range of various impact energies and temperatures using ab initio molecular dynamics with density functional theory. A range of short-timescale events can follow the collision, from direct scattering to nondissociative trapping on the surface. In most cases, HCl dissociation occurs within a few picoseconds, followed by the formation of a solvent-separated ion pair, or rarely, the reformation of HCl. With increasing impact energy and/or system temperature, dissociation occurs more rapidly, with Cl tending to diffuse deeper into the slab. At temperatures corresponding to the frozen water regime, dissociation is seen only once out of the five thermal collisions, but with the addition of a total of 4kT or more of kinetic energy to HCl, it occurs in all our trajectories within a few ps.
Kalinowski, J. ; Foreman, E. S. ; Kapnas, K. M. ; Murray, C. ; Rasanen, M. ; Gerber, B. R. Dynamics and spectroscopy of CH2OO excited electronic states. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2016, 18, 10941-10946.Abstract

The excited states of the Criegee intermediate CH2OO are studied in molecular dynamics simulations using directly potentials from multi-reference perturbation theory (MR-PT2). The photoexcitation of the species is simulated, and trajectories are propagated in time on the excited state. Some of the photoexcitation events lead to direct fragmentation of the molecule, but other trajectories describe at least several vibrations in the excited state, that may terminate by relaxation to the ground electronic state. Limits on the role of non-adiabatic contributions to the process are estimated by two different simulations, one that forces surface-hopping at potential crossings, and another that ignores surface hopping altogether. The effect of non-adiabatic transitions is found to be small. Spectroscopic implications and consequences for the interpretation of experimental results are discussed.

Gerber, B. R. ; Varner, M. E. ; Hammerich, A. D. ; Riikonen, S. ; Murdachaew, G. ; Shemesh, D. ; Finlayson-Pitts, B. J. Computational Studies of Atmospherically-Relevant Chemical Reactions in Water Clusters and on Liquid Water and Ice Surfaces. ACCOUNTS OF CHEMICAL RESEARCH 2015, 48, 399-406.Abstract
Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed. The main computational approaches employed are classical trajectory simulations using interaction potentials derived from quantum chemical methods. This comprises both ab initio molecular dynamics (AIMD) and semiempirical molecular dynamics (SEMD), the latter referring to semiempirical quantum chemical methods. Presented examples are as follows: (i) Reaction of the (NO+)(NO3-) ion pair with a water cluster to produce the atmospherically important HONO and HNO3. The simulations show that a cluster with four water molecules describes the reaction. This provides a hydrogen-bonding network supporting the transition state. The reaction is triggered by thermal structural fluctuations, and ultrafast changes in atomic partial charges play a key role. This is an example where a reaction in a small cluster can provide a model for a corresponding bulk process. The results support the proposed mechanism for production of HONO by hydrolysis of NO2 (N2O4). (ii) The reactions of gaseous HCl with N2O4 and N2O5 on liquid water surfaces. Ionization of HCl at the water/air interface is followed by nucleophilic attack of Cl on N2O4 or N2O5. Both reactions proceed by an SN2 mechanism. The products are ClNO and ClNO2, precursors of atmospheric atomic chlorine. Because this mechanism cannot result from a cluster too small for HCl ionization, an extended water film model was simulated. The results explain ClNO formation experiments. Predicted ClNO2 formation is less efficient. (iii) Ionization of acids at ice surfaces. No ionization is found on ideal crystalline surfaces, but the process is efficient on isolated defects where it involves formation of H3O+-acid anion contact ion pairs. This behavior is found in simulations of a model of the ice quasi-liquid layer corresponding to large defect concentrations in crystalline ice. The results are in accord with experiments. (iv) Ionization of acids on wet quartz. A monolayer of water on hydroxylated silica is ordered even at room temperature, but the surface lattice constant differs significantly from that of crystalline ice. The ionization processes of HCl and H2SO4 are of high yield and occur in a few picoseconds. The results are in accord with experimental spectroscopy. (v) Photochemical reactions on water and ice. These simulations require excited state quantum chemical methods. The electronic absorption spectrum of methyl hydroperoxide adsorbed on a large ice cluster is strongly blue-shifted relative to the isolated molecule. The measured and calculated adsorption band low-frequency tails are in agreement. A simple model of photodynamics assumes prompt electronic relaxation of the excited peroxide due to the ice surface. SEMD simulations support this, with the important finding that the photochemistry takes place mainly on the ground state. In conclusion, dynamics simulations using quantum chemical potentials are a useful tool in atmospheric chemistry of water media, capable of comparison with experiment.
Foreman, E. S. ; Kapnas, K. M. ; Jou, Y. T. ; Kalinowski, J. ; Feng, D. ; Gerber, B. R. ; Murray, C. High resolution absolute absorption cross sections of the (B)over-tilde(1)A `-(X)over-tilde(1)A ` transition of the CH2OO biradical. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2015, 17, 32539-32546.Abstract
Carbonyl oxides, or Criegee intermediates, are formed from the gas phase ozonolysis of alkenes and play a pivotal role in night-time and urban area atmospheric chemistry. Significant discrepancies exist among measurements of the strong (B) over tilde (1)A'-(X) over tilde (1)A' electronic transition of the simplest Criegee intermediate, CH2OO in the visible/near-UV. We report room temperature spectra of the (B) over tilde (1)A'-(X) over tilde (1)A' electronic absorption band of CH2OO acquired at higher resolution using both single-pass broadband absorption and cavity ring-down spectroscopy. The new absorption spectra confirm the vibrational structure on the red edge of the band that is absent from ionization depletion measurements. The absolute absorption cross sections over the 362-470 nm range are in good agreement with those reported by Ting et al. Broad-band absorption spectra recorded over the temperature range of 276-357 K were identical within their mutual uncertainties, confirming that the vibrational structure is not due to hot bands.
Tsuge, M. ; Kalinowski, J. ; Gerber, B. R. ; Lee, Y. - P. Infrared Identification of Proton-Bound Rare-Gas Dimers (XeHXe)(+), (KrHKr)(+), and (KrHXe)(+) and Their Deuterated Species in Solid Hydrogen. JOURNAL OF PHYSICAL CHEMISTRY A 2015, 119, 2651-2660.Abstract
Proton-bound rare-gas dimer (RgHRg)(+), in which Rg represents a rare-gas atom, serves as a prototypical system for proton solvation by inert-gas atoms. Until now, only centrosymmetric species with Rg = Ar, Kr, or Xe have been identified with infrared spectra. We employed electron bombardment during deposition of a mixture of Xe (or Kr) in p-H-2 at 3.2 K to prepare (RgHRg)(+). Lines at 847.0 and 972.1 cm(-1) are assigned as the Rg-H-Rg antisymmetric stretching (nu(3)) mode and its combination with the RgHRg symmetric stretching (nu(1) + nu(3)) mode of (XeHXe)(+) in solid p-H-2, respectively. Lines at 871.1 and 974.0 cm(-1) are assigned as the nu(3) and nu(1) + nu(3) modes of (KrHKr)(+) in solid p-H-2, respectively. Slightly shifted and broadened lines were observed for these species in solid n-H-2. These results agree satisfactorily with reported experimental values of (XeHXe)(+) and (KrHKr)(+) in solid Xe, Kr, and Ar, and with the quantum-chemically predicted anharmonic vibrational wavenumbers of these species in the gaseous phase; the significant spectral shifts in various matrixes are rationalized with the proton affinities of the hosts. When a mixture of Xe and Kr in p-H-2 was used, an additional broad feature at 1284 cm(-1) was observed and assigned as the nu(3) mode of (KrHXe)(+) in solid p-H-2. This line shifted to 1280 cm(-1) in solid n-H-2 and the corresponding line of (KrDXe)(+) was observed at 954 cm(-1) in n-D-2. The observations of these lines are new; the wavenumbers significantly blue shifted from those of the centrosymmetric (RgHRg)(+) agree with the quantum-chemically predicted anharmonic vibrational wavenumbers of 1279 cm(-1) for (KrHXe)(+) and 916 cm(-1) for (KrDXe)(+). Analysis of the computational results shows that electronic correlation effects play a much greater role for the asymmetric than for the symmetric species. An interpretation for this is provided.
Hammerich, A. D. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Mechanism for formation of atmospheric Cl atom precursors in the reaction of dinitrogen oxides with HCl/Cl- on aqueous films. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2015, 17, 19360-19370.Abstract
Nitryl chloride (ClNO2) and nitrosyl chloride (ClNO) are potential sources of highly reactive atmospheric chlorine atoms, hence of much interest, but their formation pathways are unknown. This work predicts production of these nitrogen oxychlorides from ab initio molecular dynamics (AIMD) simulations of N2O5 or an NO2 dimer on the surface of a thin film of water which is struck by gaseous HCl. Both of these heterogeneous reactions proceed at the liquid/vapor interface by an S(N)2 mechanism where the nucleophile is chloride ion formed from the ionization of HCl on the aqueous surface. The film of water enhances the otherwise very slow gas phase reaction to occur by (1) stabilizing and localizing the adsorbed N2O5 or NO2 dimer so it is physically accessible for reaction, (2) ionizing the impinging HCl, and (3) activating the adsorbed oxide for nucleophilic attack by chloride. Though both nitrogen oxychloride products are produced by S(N)2 reactions, the N2O5 mechanism is unusual in that the electrophilic N atom to be attacked oscillates between the two normally equivalent NO2 groups. Chloride ion is found to react with N2O5 less efficiently than with N2O4. The simulations provide an explanation for this. These substitution/elimination mechanisms are new for NOx/y chemistry on thin water films and cannot be derived from small cluster models.
Chen, H. ; Ezell, M. J. ; Arquero, K. D. ; Varner, M. E. ; Dawson, M. L. ; Gerber, B. R. ; Finlayson-Pitts, B. J. New particle formation and growth from methanesulfonic acid, trimethylamine and water. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2015, 17, 13699-13709.Abstract
New particle formation from gas-to-particle conversion represents a dominant source of atmospheric particles and affects radiative forcing, climate and human health. The species involved in new particle formation and the underlying mechanisms remain uncertain. Although sulfuric acid is commonly recognized as driving new particle formation, increasing evidence suggests the involvement of other species. Here we study particle formation and growth from methanesulfonic acid, trimethylamine and water at reaction times from 2.3 to 32 s where particles are 2-10 nm in diameter using a newly designed and tested flow system. The flow system has multiple inlets to facilitate changing the mixing sequence of gaseous precursors. The relative humidity and precursor concentrations, as well as the mixing sequence, are varied to explore their effects on particle formation and growth in order to provide insight into the important mechanistic steps. We show that water is involved in the formation of initial clusters, greatly enhancing their formation as well as growth into detectable size ranges. A kinetics box model is developed that quantitatively reproduces the experimental data under various conditions. Although the proposed scheme is not definitive, it suggests that incorporating such mechanisms into atmospheric models may be feasible in the near future.
Kalinowski, J. ; Heinonen, P. ; Kilpelainen, I. ; Rasanen, M. ; Gerber, B. R. Stability of Criegee Intermediates Formed by Ozonolysis of Different Double Bonds. JOURNAL OF PHYSICAL CHEMISTRY A 2015, 119, 2318-2325.Abstract
{{The formation of Criegee intermediates by ozonolysis of different species containing C=N and C=P bonds is studied computationally. Electronic structure calculations are carried out for the energetics of ozonolysis, and the lifetime of the Criegee intermediate formed is computed by transition state theory. All calculations are carried out for formation of CH2OO, the simplest Criegee intermediate. Extremely large differences are found for the lifetime of CH2OO depending on the specific C=N
Khriachtchev, L. ; Pettersson, M. ; Gerber, B. R. Tribute to Markku O. Rasanen. JOURNAL OF PHYSICAL CHEMISTRY A 2015, 119, 2187-2190.
Romonosky, D. E. ; Nguyen, L. Q. ; Shemesh, D. ; Nguyen, T. B. ; Epstein, S. A. ; Martin, D. B. C. ; Vanderwal, C. D. ; Gerber, B. R. ; Nizkorodov, S. A. Absorption spectra and aqueous photochemistry of beta-hydroxyalkyl nitrates of atmospheric interest. MOLECULAR PHYSICS 2015, 113, 2179-2190.Abstract
Molar absorption coefficients were measured for select alkyl nitrates and beta-hydroxyalkyl nitrates in methanol. The presence of the beta-hydroxyl group has a relatively minor effect on the absorption spectrum in the vicinity of the weak n -> pi* transition, which is responsible for photolysis of organic nitrates in the atmosphere. For both alkyl nitrates and beta-hydroxyalkyl nitrates, there is an enhancement in the absorption coefficients in solution compared to the gas-phase values. The effect of the beta-hydroxyl group on the spectra was modelled with molecular dynamics simulations using an OM2/GUGA-CI Hamiltonian for ethyl nitrate and beta-hydroxyethyl nitrate. The simulation provided a qualitatively correct shape of the low energy tail of the absorption spectrum, which is important for atmospheric photochemistry. The role of direct aqueous photolysis in removal of beta-hydroxyalkyl nitrates in cloud and fog water was modelled using a relative rate approach, and shown to be insignificant relative to gas-phase photochemical processes and aqueous OH oxidation under typical atmospheric conditions.
Roy, T. K. ; Kopysov, V. ; Nagornova, N. S. ; Rizzo, T. R. ; Boyarkin, O. V. ; Gerber, B. R. Conformational Structures of a Decapeptide Validated by First Principles Calculations and Cold Ion Spectroscopy. CHEMPHYSCHEM 2015, 16, 1374-1378.Abstract
Calculated structures of the two most stable conformers of a protonated decapeptide gramicidin S in the gas phase have been validated by comparing the vibrational spectra, calculated from first- principles and measured in a wide spectral range using infrared (IR)-UV double resonance cold ion spectroscopy. All the 522 vibrational modes of each conformer were calculated quantum mechanically and compared with the experiment without any recourse to an empirical scaling. The study demonstrates that first-principles calculations, when accounting for vibrational anharmonicity, can reproduce high-resolution experimental spectra well enough for validating structures of molecules as large as of 200 atoms. The validated accurate structures of the peptide may serve as templates for in silico drug design and absolute calibration of ion mobility measurements.
Perraud, V. ; Horne, J. R. ; Martinez, A. S. ; Kalinowski, J. ; Meinardi, S. ; Dawson, M. L. ; Wingen, L. M. ; Dabdub, D. ; Blake, D. R. ; Gerber, B. R. ; et al. The future of airborne sulfur-containing particles in the absence of fossil fuel sulfur dioxide emissions. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2015, 112, 13514-13519.Abstract
Sulfuric acid (H2SO4), formed from oxidation of sulfur dioxide (SO2) emitted during fossil fuel combustion, is a major precursor of new airborne particles, which have well-documented detrimental effects on health, air quality, and climate. Another precursor is methanesulfonic acid (MSA), produced simultaneously with SO2 during the atmospheric oxidation of organosulfur compounds (OSCs), such as dimethyl sulfide. In the present work, a multidisciplinary approach is used to examine how contributions of H2SO4 and MSA to particle formation will change in a large coastal urban area as anthropogenic fossil fuel emissions of SO2 decline. The 3-dimensional University of California Irvine-California Institute of Technology airshed model is used to compare atmospheric concentrations of gas phase MSA, H2SO4, and SO2 under current emissions of fossil fuel-associated SO2 and a best-case futuristic scenario with zero fossil fuel sulfur emissions. Model additions include results from (i) quantum chemical calculations that clarify the previously uncertain gas phase mechanism of formation of MSA and (ii) a combination of published and experimental estimates of OSC emissions, such as those from marine, agricultural, and urban processes, which include pet waste and human breath. Results show that in the zero anthropogenic SO2 emissions case, particle formation potential from H2SO4 will drop by about two orders of magnitude compared with the current situation. However, particles will continue to be generated from the oxidation of natural and anthropogenic sources of OSCs, with contributions from MSA and H2SO4 of a similar order of magnitude. This could be particularly important in agricultural areas where there are significant sources of OSCs.
Chandra, K. ; Naoum, J. N. ; Roy, T. K. ; Gilon, C. ; Gerber, B. R. ; Friedler, A. Mechanistic Studies of Malonic Acid-Mediated In Situ Acylation. BIOPOLYMERS 2015, 104, 495-505.Abstract
We have previously introduced an easy to perform, cost-effective and highly efficient acetylation technique for solid phase synthesis (SPPS). Malonic acid is used as a precursor and the reaction proceeds via a reactive ketene that acetylates the target amine. Here we present a detailed mechanistic study of the malonic acid-mediated acylation. The influence of reaction conditions, peptide sequence and reagents was systematically studied. Our results show that the methodology can be successfully applied to different types of peptides and nonpeptidic molecules irrespective of their structure, sequence, or conformation. Using alkyl, phenyl, and benzyl malonic acid, we synthesized various acyl peptides with almost quantitative yields. The ketenes obtained from the different malonic acid derived precursors were characterized by in situ 1 H-NMR. The reaction proceeded in short reaction times and resulted in excellent yields when using uronium-based coupling agents, DIPEA as a base, DMF/DMSO/ NMP as solvents, Rink amide/Wang/Merrifield resins, temperature of 20 degrees C, pH 8-12 and 5 min preactivation at inert atmosphere. The reaction was unaffected by Lewis acids, transition metal ions, surfactants, or salt. DFT studies support the kinetically favorable concerted mechanism for CO2 and ketene formation that leads to the thermodynamically stable acylated products. We conclude that the malonic acid-mediated acylation is a general method applicable to various target molecules. (C) 2015 Wiley Periodicals, Inc.