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.

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.

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.

S_N2-type halide substitution and hydrolysis are two of the most ubiquitous reactions in chemistry. The interplay between these processes is fundamental in atmospheric chemistry through reactions of N₂O₅ and seawater. N₂O₅ plays a major role in regulating levels of O₃, OH, NO _x , and CH₄. While the reactions of N₂O₅ and seawater are of central importance, little is known about their mechanisms. Of interest is the activation of Cl in seawater by the formation of gaseous ClNO₂, which occurs despite the fact that hydrolysis (to HNO₃) is energetically more favorable. We determine key features of the reaction landscape that account for this behavior in a theoretical study of the cluster N₂O₅/Cl^-/H₂O. This was carried out using ab initio molecular dynamics to determine reaction pathways, structures, and time scales. While hydrolysis of N₂O₅ occurs in the absence of Cl^-, results here reveal that a low-lying pathway featuring halide substitution intermediates enhances hydrolysis.

We present an ab initio molecular dynamics study of deprotonation of sulfuric acid 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 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.

Mechanisms of particle formation and growth in the atmosphere are of great interest due to their impacts on climate, health and visibility. However, the microscopic structures and related properties of the smallest nanoparticles are not known. In this paper we pursue computationally a microscopic description for the formation and growth of methanesulfonic acid (MSA) and methylamine (MA) particles under dry conditions. Energetic and dynamics simulations were used to assess the stabilities of proposed model structures for these particles. Density functional theory (DFT) and semi-empirical (PM3) calculations suggest that (MSA-MA)4 is a major intermediate in the growth process, with the dissociation energies, enthalpies and free energies indicating considerable stability for this cluster. Dynamics simulations show that this species is stable for at least 100 ps at temperatures up to 500 K, well above atmospheric temperatures. In order to reach experimentally detectable sizes (>1.4 nm), continuing growth is suggested to occur via clustering of (MSA-MA)4. The dimer (MSA-MA)4(MSA-MA)4 may be one of the smaller experimentally measured particles. Step by step addition of MSA to (MSA-MA)4, is also a likely potential growth mechanism when MSA is excess. In addition, an MSA-MA crystal is predicted to exist. These studies demonstrate that computations of particle structure and dynamics in the nano-size range can be useful for molecular level understanding of processes that grow clusters into detectable particles.

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.

Ionization of N(2)O(4) in and on thin water films on surfaces is believed to be a key step in the hydrolysis of NO(2) which generates HONO, a significant precursor to the OH free radical in the lower atmosphere. Molecular dynamics simulations using "on the fly" high-level MP2 potentials are carried out for ONONO(2) x (H(2)O)(n) clusters, n < or = 8, used to mimic the surface reaction, in order to investigate the ionization process and determine its time-scale and mechanism around room temperature. The results are (i) the isolated molecule does not convert to the NO(+)NO(3)(-) ion pair, even for long times; (ii) for ONONO(2) x (H(2)O)(n) with n = 1 and 2, ionization takes place in several picoseconds; (iii) for n > or = 3, ionization is essentially immediate, implying that the neutral species does not have sufficient lifetime to be considered a significant intermediate in the reaction; and (iv) even at ice temperatures, T < or = 250 K, ionization for n > or = 3 is immediate. The implications for hydrolysis of oxides of nitrogen on surfaces in the atmosphere are discussed.

Atmospheric particles are notorious for their effects on human health and visibility and are known to influence climate. Though sulfuric acid and ammonia/amines are recognized as main contributors to new particle formation (NPF), models and observations have indicated that other species may be involved. It has been shown that nucleation from methanesulfonic acid (MSA) and amines, which is enhanced with added water, can also contribute to NPF. While organics are ubiquitous in air and likely to be involved in NPF by stabilizing small clusters for further growth, their effects on the MSA-amine system are not known. This work investigates the effect of oxalic acid (OxA) on NPF from the reaction of MSA and methylamine (MA) at 1 atm and 294 K in the presence and absence of water vapor using an aerosol flow reactor. OxA and MA do not efficiently form particles even in the presence of water, but NPF is enhanced when adding MSA to OxA-MA with and without water. The addition of OxA to MSA-MA mixtures yields a modest NPF enhancement, whereas the addition of OxA to MSA-MA-H₂O has no effect. Possible reasons for these effects are discussed.