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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Methyl peroxide (CH3OOH) is commonly found in atmospheric waters and ices in significant concentrations. It is the simplest organic peroxide and an important precursor to hydroxyl radical. Many studies have examined the photochemical behavior of gaseous CH3OOH; however, the photochemistry of liquid and frozen water solutions is poorly understood. We present a series of experiments and theoretical calculations designed to elucidate the photochemical behavior of CH3OOH dissolved in liquid water and ice over a range of temperatures. The molar extinction coefficients of aqueous CH3OOH are different from the gas phase, and they do not change upon freezing. Between -12 and 43 degrees C, the quantum yield of CH3OOH photolysis is described by the following equation: Phi(T) = exp((-2175 +/- 448)1/T) + 7.66 +/- 1.56). We use on-the-fly ab initio molecular dynamics simulations to model structures and absorption spectra of a bare CH3OOH molecule and a CH3OOH molecule immersed inside 20 water molecules at 50, 200, and 220 K. The simulations predict large sensitivity in the absorption spectrum of CH3OOH to temperature, with the spectrum narrowing and shifting to the blue under cryogenic conditions because of constrained dihedral motion around the O-O bond. The shift in the absorption spectrum is not observed in the experiment when the CH3OOH solution is frozen suggesting that CH3OOH remains in a liquid layer between the ice grains. Using the extinction coefficients and photolysis quantum yields obtained in this work, we show that under conditions with low temperatures, in the presence of clouds with a high liquid-water content and large solar zenith angles, the loss of CH3OOH by aqueous photolysis is responsible for up to 20% of the total loss of CH3OOH due to photolysis. Gas phase photolysis of CH3OOH dominates under all other conditions.

Peroxides are ubiquitous in the atmosphere and their photochemistry at ice surfaces is important. Here the primary steps following photoexcitation of methyl hydroperoxide (MHP) on ice particles are investigated using the MNDO method that describes semiempirically multiple electronic states and treats non-adiabatic dynamical transitions between them by surface hopping. Results are compared with the isolated MHP. Important findings are as follows. (1) Ice catalyzes the deactivation of MHP from the excited state to the ground state. (2) The deactivation process takes place on a femtosecond timescale and is followed by dissociation into fragments. (3) Recombination of fragments occurs to a small extent on ice, but not for the isolated peroxide.

Solvation of beta-cellobiose isomers, cis and trans, in increasingly larger water clusters, is examined here by means of ab initio dynamics. A previously suggested hydration motif, based on a cluster with 2 waters, provides a stable nucleation center for growth of the larger cluster. Key results: (a) the cis form is energetically favored throughout the cluster size range; (b) cis conformer exhibits surfactant properties while (c) trans is better enveloped by water. Water organization at the sugar surface, is significantly different in the two isomers. Rotamer transitions, observed in the isolated sugar at 300 K, are inhibited by the incomplete hydration shell. Published by Elsevier B.V.