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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.