Hirshberg, B. ; Gerber, B. R. ; Krylov, A. I. Calculations predict a stable molecular crystal of N-8. NATURE CHEMISTRY 2014, 6 52-56.Abstract
Nitrogen, one of the most abundant elements in nature, forms the highly stable N-2 molecule in its elemental state. In contrast, polynitrogen compounds comprising only nitrogen atoms are rare, and no molecular crystal made of these compounds has been prepared. Here, we predict the existence of such a molecular solid, consisting of N-8 molecules, that is metastable even at ambient pressure. In the solid state, the N-8 monomers retain the same structure and bonding pattern as those they adopt in the gas phase. The interactions that bind N-8 molecules together are weak van der Waals and electrostatic forces. The solid is, according to calculations, more stable than a previously reported polymeric nitrogen solid, including at low pressure (below 20 GPa). The structure and properties of the N-8 molecular crystal are discussed and a possible preparation strategy is suggested.
Chandra, K. ; Roy, T. K. ; Naoum, J. N. ; Gilon, C. ; Gerber, B. R. ; Friedler, A. A highly efficient in situ N-acetylation approach for solid phase synthesis. ORGANIC & BIOMOLECULAR CHEMISTRY 2014, 12, 1879-1884.Abstract
We describe a new general N-acetylation method for solid phase synthesis. Malonic acid is used as a precursor and the reaction proceeds by in situ formation of a reactive ketene intermediate at room temperature. We have successfully applied this methodology to peptides and non-peptidic molecules containing a variety of functional groups. The reaction gave high yields compared to known acetylation methods, irrespective of the structure, conformation and sequence of the acetylated molecule. Computational studies revealed that the concerted mechanism via the ketene intermediate is kinetically favorable and leads to a thermodynamically stable acetylated product. In conclusion, our method can be easily applied to acetylation in a wide variety of chemical reactions performed on the solid phase.
Varner, M. E. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Reaction of a charge-separated ONONO2 species with water in the formation of HONO: an MP2 Molecular Dynamics study. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2014, 16, 4483-4487.Abstract
The reaction of (NO+)(NO3-) with water is modelled in ONONO2. (H2O)(4) clusters. Molecular Dynamics simulations using second-order Moller-Plesset perturbation (MP2) theory support the feasibility of the reaction of a charge-separated species to produce HONO and nitric acid.
Gerber, R. B. ; Shemesh, D. ; Varner, M. E. ; Kalinowski, J. ; Hirshberg, B. Ab initio and semi-empirical Molecular Dynamics simulations of chemical reactions in isolated molecules and in clusters. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2014, 16, 9760-9775.Abstract
Recent progress in ``on-the-fly'' trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available. New developments in the use of both ab initio and semi-empirical electronic structure algorithms are described. The emphasis is on: (i) calculations of electronic properties along the reactive trajectories and the unique insights this can contribute to the processes; (ii) electronic structure methods recently introduced to this topic to improve accuracy, extend applicability or enhance computational efficiency. The methods are presented with examples, including new results, of reactions of both isolated molecules and of molecules in media, mostly clusters. Possible future directions for this fast growing field are suggested.
Kalinowski, J. ; Rasanen, M. ; Gerber, B. R. Chemically-bound xenon in fibrous silica. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2014, 16, 11658-11661.Abstract
High-level quantum chemical calculations reported here predict the existence and remarkable stability, of chemically-bound xenon atoms in fibrous silica. The results may support the suggestion of Sanloup and coworkers that chemically-bound xenon and silica account for the problem of ``missing xenon'' (by a factor of 20!) from the atmospheres of Earth and Mars. So far, the host silica was assumed to be quartz, which is in contradiction with theory. The xenon-fibrous silica molecule is computed to be stable well beyond room temperature. The calculated Raman spectra of the species agree well with the main features of the experiments by Sanloup et al. The results predict computationally the existence of a new family of noble-gas containing materials. The fibrous silica species are finite molecules, their laboratory preparation should be feasible, and potential applications are possible.
Knaanie, R. ; Sebek, J. ; Kalinowski, J. ; Gerber, B. R. Hybrid MP2/MP4 potential surfaces in VSCF calculations of IR spectra: Applications for organic molecules. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014, 119, 2-11.Abstract
This study introduces an improved hybrid MP2/MP4 ab initio potential for vibrational spectroscopy calculations which is very accurate, yet without high computational demands. The method uses harmonic vibrational calculations with the MP4(SDQ) potential to construct an improved MP2 potential by coordinate scaling. This improved MP2 potential is used for the anharmonic VSCF calculation. The method was tested spectroscopically for four molecules: butane, acetone, ethylene and glycine. Very good agreement with experiment was found. For most of the systems, the more accurate harmonic treatment considerably improved the MP2 anharmonic results. (C) 2013 Elsevier B.V. All rights reserved.
Kalinowski, J. ; Rasanen, M. ; Heinonen, P. ; Kilpelainen, I. ; Gerber, B. R. Isomerization and Decomposition of a Criegee Intermediate in the Ozonolysis of Alkenes: Dynamics Using a Multireference Potential. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2014, 53, 265-268.Abstract
The isomerization and decomposition dynamics of the simplest Criegee intermediate CH2OO have been studied by classical trajectory simulations using the multireference abinitio MR-PT2 potential on the fly. A new, accelerated algorithm for dynamics with MR-PT2 was used. For an initial temperature of 300K, starting from the transition state from CH2OOCH2O2, the system reaches the dioxirane structure in around 50fs, then isomerizes to formic acid (in ca.2800fs), and decomposes into CO+H2O at around 2900fs. The contributions of different configurations to the multiconfigurational total electronic wave function vary dramatically along the trajectory, with diradical contributions being important for transition states corresponding to H-atom transfers, while being only moderately significant for CH2OO. The implications for reactions of Criegee intermediates are discussed.
Kalinowski, J. ; Gerber, B. R. ; Rasanen, M. ; Lignell, A. ; Khriachtchev, L. Matrix effect on vibrational frequencies: Experiments and simulations for HCl and HNgCl (Ng = Kr and Xe). JOURNAL OF CHEMICAL PHYSICS 2014, 140.Abstract
We study the environmental effect on molecules embedded in noble-gas (Ng) matrices. The experimental data on HXeCl and HKrCl in Ng matrices is enriched. As a result, the H-Xe stretching bands of HXeCl are now known in four Ng matrices (Ne, Ar, Kr, and Xe), and HKrCl is now known in Ar and Kr matrices. The order of the H-Xe stretching frequencies of HXeCl in different matrices is nu(Ne) < nu(Xe) < nu(Kr) < nu(Ar), which is a non-monotonous function of the dielectric constant, in contrast to the ``classical'' order observed for HCl: nu(Xe) < nu(Kr) < nu(Ar) < nu(Ne). The order of the H-Kr stretching frequencies of HKrCl is consistently nu(Kr) < nu(Ar). These matrix effects are analyzed theoretically by using a number of quantum chemical methods. The calculations on these molecules (HCl, HXeCl, and HKrCl) embedded in single Ng' layer cages lead to very satisfactory results with respect to the relative matrix shifts in the case of the MP4(SDQ) method whereas the B3LYP-D and MP2 methods fail to fully reproduce these experimental results. The obtained order of frequencies is discussed in terms of the size available for the Ng hydrides in the cages, probably leading to different stresses on the embedded molecule. Taking into account vibrational anharmonicity produces a good agreement of the MP4(SDQ) frequencies of HCl and HXeCl with the experimental values in different matrices. This work also highlights a number of open questions in the field. (C) 2014 AIP Publishing LLC.
Cohen, A. ; Tsuge, M. ; Khriachtchev, L. ; Rasanen, M. ; Gerber, B. R. Modeling of HXeBr in CO2 and Xe environments: Structure, energetics and vibrational spectra. CHEMICAL PHYSICS LETTERS 2014, 594, 18-22.Abstract
HXeBr in CO2 and Xe environments is modeled at the B3LYP-D level of theory, using a full single shell of CO2 molecules and Xe atoms around the HXeBr molecule. For the CO2 environment, the optimized structure indicates a double substitutional site in the otherwise approximately preserved structure of solid CO2. The calculated vibrational spectra and energetic properties indicate strong interactions of HXeBr with the CO2 environment, which is significantly stronger than in the case of the Xe environment. The H-Xe stretching frequency obtained by a variant of the anharmonic VSCF method is in good accord with the available experimental data. (C) 2014 Elsevier B.V. All rights reserved.
Shemesh, D. ; Blair, S. L. ; Nizkorodov, S. A. ; Gerber, B. R. Photochemistry of aldehyde clusters: cross-molecular versus unimolecular reaction dynamics. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2014, 16, 23861-23868.Abstract
The unimolecular photochemistry of aldehydes has been extensively studied, both experimentally and computationally. However, less is known about the role of cross-molecular photochemical processes in the condensed-phase photolysis of aldehydes. The triplet-state photochemistry of pentanal in its pentameric (n = 5) cluster was investigated as a model for photochemical reactions of aliphatic aldehydes in atmospheric aerosols. This study employs ``on the fly'' dynamics simulations using a semi-empirical MRCI electronic code for the singlet and triplet states involved. Previous studies have shown that the triplet-state photochemistry of an isolated pentanal molecule is dominated by Norrish I and II reactions. The main findings for the cluster are: (1) 55% of the trajectories lead to a unimolecular or cross-molecular reaction within a timescale of 100 ps; (2) cross-molecular reactions occur in over 70% of the reactive trajectories; (3) the main cross-molecular processes involve an H-atom transfer from the CHO group of the excited pentanal to an O atom of a nearby pentanal; and (4) the unimolecular Norrish II reaction is suppressed by the cluster environment. The predictions are qualitatively supported by experimental results on the condensed-phase photolysis of an aliphatic aldehyde, undecanal. The computational approach should be useful for predicting the mechanisms of other condensed-phase organic photochemical reactions. These results demonstrate a major role of cross-molecular processes in the condensed-phase photolysis of carbonyls. The cross-molecular reactions discussed in this work are relevant to photolysis-driven processes in atmospheric organic aerosols. It is expected that the condensed-phase environment of an organic aerosol particle should support a multitude of similar cross-molecular photochemical processes.
Roy, T. K. ; Carrington, Jr., T. ; Gerber, B. R. Approximate First-Principles Anharmonic Calculations of Polyatomic Spectra Using MP2 and B3LYP Potentials: Comparisons with Experiment. JOURNAL OF PHYSICAL CHEMISTRY A 2014, 118, 6730-6739.Abstract
Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations have been performed for the molecules HNO3, C2H4, C2H4O, H2SO4, CH3COOH, glycine, and alanine. Both MP2 and B3LYP give results in good accord with experimental frequencies, though, on the whole, MP2 gives very slightly better agreement. A statistical analysis of deviations in frequencies from experiment is carried out that gives interesting insights. The most probable percentage deviation from experimental frequencies is about -2% (to the red of the experiment) for B3LYP and +2% (to the blue of the experiment) for MP2. There is a higher probability for relatively large percentage deviations when B3LYP is used. The calculated intensities are also found to be in good accord with experiment, but the percentage deviations are much larger than those for frequencies. The results show that both MP2 and B3LYP potentials, used in VSCF-PT2 calculations, account well for anharmonic effects in the spectroscopy of molecules of the types considered.
Goldstein, M. ; Zmiri, L. ; Segev, E. ; Wyttenbach, T. ; Gerber, B. R. An atomistic structure of ubiquitin+13 relevant in mass spectrometry: Theoretical prediction and comparison with experimental cross sections. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014, 367, 10-15.Abstract
The 3D structure of protein ions in the gas phase is presently not obtainable from experiment in atomic detail. Here we use a theoretical approach to determine the 3D structure of ubiquitin +13 (UBQ +13) in the absence of solvent. Global minimization of the UBQ +13 force field within the recently developed DEEPSAM algorithm yields a nearly linear overall geometry. Four helical segments are found in this full atomistic structure - three of them are 3(10)-helices and one is an a-helix. The protein cross section computed for the predicted structure is in excellent accord with ion mobility experimental results of UBQ +13. This suggests that computational structure predictions together with (theoretical and experimental) cross section values can serve as a useful tool for determining the atomistic structures of charged proteins in the gas phase. (c) 2014 Elsevier B.V. All rights reserved.
Riikonen, S. ; Parkkinen, P. ; Halonen, L. ; Gerber, R. B. Ionization of Acids on the Quasi-Liquid Layer of Ice. JOURNAL OF PHYSICAL CHEMISTRY A 2014, 118, 5029-5037.Abstract
The ice quasi-liquid layer (QLL) forms on ice surfaces below the bulk ice melting temperature. It is abundant in the atmosphere, and its importance for atmospheric chemistry is recognized. In the present work, we have studied the microscopic mechanisms of acid ionization on the QLL using ab initio molecular dynamics. The model system QLL is established by nanosecond time scale simulations with empirical force fields, while the reactivity of the QLL is studied using ab initio molecular dynamics. Our ab initio simulations reveal that QLL is reactive, exhibiting stable crystalline point defects, which contribute to efficient acid solvation, ionization, and proton transfer. We study in detail deuterated hydrogen iodide (DI) and nitric acid (DNO3). Ionization in both cases benefits from the abundance of weakly bonded hydrogen-bond single-acceptor double-donor water molecular species available on the QLL in high relative concentration. Picosecond time scale ionization is demonstrated for both molecular species. Our results suggest efficient reactivity of acid ionization and proton transfer at temperature ranges appropriate for the upper troposphere and lower stratosphere.
Murdachaew, G. ; Varner, M. E. ; van der Veer, W. E. ; Gerber, B. R. ; Phillips, L. F. Raman spectroscopy of solutions and interfaces containing nitrogen dioxide, water, and 1,4 dioxane: Evidence for repulsion of surface water by NO2 gas. JOURNAL OF CHEMICAL PHYSICS 2014, 140.Abstract
The interaction of water, 1,4 dioxane, and gaseous nitrogen dioxide, has been studied as a function of distance measured through the liquid-vapour interface by Raman spectroscopy with a narrow (<0.1 mm) laser beam directed parallel to the interface. The Raman spectra show that water is present at the surface of a dioxane-water mixture when gaseous NO2 is absent, but is virtually absent from the surface of a dioxane-water mixture when gaseous NO2 is present. This is consistent with recent theoretical calculations that show NO2 to be mildly hydrophobic. (C) 2014 AIP Publishing LLC.
Dawson, M. L. ; Varner, M. E. ; Perraud, V. ; Ezell, M. J. ; Wilson, J. ; Zelenyuk, A. ; Gerber, B. R. ; Finlayson-Pitts, B. J. Amine-Amine Exchange in Aminium-Methanesulfonate Aerosols. JOURNAL OF PHYSICAL CHEMISTRY C 2014, 118, 29431-29440.Abstract
Aerosol particles are ubiquitous in the atmosphere and have been shown to impact the Earths climate, reduce visibility, and adversely affect human health. Modeling the evolution of aerosol systems requires an understanding of the species and mechanisms involved in particle growth, including the complex interactions between particle- and gas-phase species. Here we report studies of displacement of amines (methylamine, dimethylamine, or trimethylamine) in methanesulfonate salt particles by exposure to a different gas-phase amine, using a single particle mass spectrometer, SPLAT II. The variation of the displacement with the nature of the amine suggests that behavior is dependent on water in or on the particles. Small clusters of methanesulfonic acid with amines are used as a model in quantum chemical calculations to identify key structural elements that are expected to influence water uptake, and hence the efficiency of displacement by gas-phase molecules in the aminium salts. Such molecular-level understanding of the processes affecting the ability of gas-phase amines to displace particle-phase aminium species is important for modeling the growth of particles and their impacts in the atmosphere.
Murdachaew, G. ; Gaigeot, M. - P. ; Halonen, L. ; Gerber, B. R. First and second deprotonation of H2SO4 on wet hydroxylated (0001) alpha-quartz. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2014, 16, 22287-22298.Abstract
We present an ab initio molecular dynamics study of deprotonation of sulfuric add on wet quartz, a topic of atmospheric interest. The process is preferred, with 65% of our trajectories at 250 K showing deprotonation. The time distribution of the deprotonation events shows an exponential behavior and predicts an average deprotonation time of a few picoseconds. The process is exoergic, with most of the temperature increase being due to formation of hydrogen bonds prior to deprotonation. In agreement with existing studies of H2SO4 in water clusters, in liquid water, and at the air-water interface, the main determinant of deprotonation is the degree of solvation of H2SO4 by neighboring water molecules. However, we find that if both hydrogens of H2SO4 are simultaneously donated to water oxygens, deprotonation is disfavored. Predicted spectroscopic signatures showing the presence of solvated hydronium and bisulfate are presented. Increasing the temperature up to 330 K accelerates the process but does not change the main features of the deprotonation mechanisms or the spectroscopic signatures. The second deprotonation of H2SO4, studied only at 250 K, occurs provided there is sufficient solvation of the bisulfate by additional water molecules. In comparison to HCl deprotonation on the identical surface examined in our previous work, the first deprotonation of H2SO4 occurs more readily and releases more energy.
Chandra, K. ; Roy, T. K. ; Shalev, D. E. ; Loyter, A. ; Gilon, C. ; Gerber, B. R. ; Friedler, A. A Tandem In Situ Peptide Cyclization through Trifluoroacetic Acid Cleavage. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2014, 53, 9450-9455.Abstract
We present a new approach for peptide cyclization during solid phase synthesis under highly acidic conditions. Our approach involves simultaneous in situ deprotection, cyclization and trifluoroacetic acid (TFA) cleavage of the peptide, which is achieved by forming an amide bond between a lysine side chain and a succinic acid linker at the peptide N-terminus. The reaction proceeds via a highly active succinimide intermediate, which was isolated and characterized. The structure of a model cyclic peptide was solved by NMR spectroscopy. Theoretical calculations support the proposed mechanism of cyclization. Our new methodology is applicable for the formation of macrocycles in solid-phase synthesis of peptides and organic molecules.
Blair, S. L. ; Gerber, B. R. ; Epstein, S. A. ; Hinks, M. L. ; Lignell, H. ; Nizkorodov, S. A. ; Romonosky, D. E. ; Shemesh, D. Combined experimental and theoretical studies of photolysis of atmospherically relevant organic compounds in various phases. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 247.
Varner, M. E. ; Chen, H. ; Arquero, K. D. ; Ezell, M. J. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Complexes leading to particle formation from methanesulfonic acid, amines, and water. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 248.
Varner, M. E. ; Raff, J. D. ; Gerber, B. R. Computational studies of the role of water in the formation and reaction of NOx species. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 248.