A Closure Study of the Reaction between Sulfur Dioxide and the Sulfate Radical Ion from First-Principles Molecular Dynamics Simulations.

In a previous study, we applied quantum chemical methods to study the reaction between sulfur dioxide (SO2) and the sulfate radical ion (SO4(-)) at atmospheric relevant conditions and found that the most likely reaction product is SO3SO3(-). In the current study, we investigate the chemical fate of SO3SO3(-) by reaction with ozone (O3) using first-principles molecular dynamics collision simulations. This method assesses both dynamic and steric effects in the reactions and therefore provides the most likely reaction pathways. We find that the majority of the collisions between SO3SO3(-) and O3 are nonsticking and that the most frequent reactive collisions regenerate sulfate radical ions and produce sulfur trioxide (SO3) while ejecting an oxygen molecule (O2). The rate of this reaction is determined to be 2.5 × 10(-10) cm(3) s(-1). We then conclude that SO4(-) is a highly efficient catalyst in the oxidation of SO2 by O3 to SO3.

Correction: Resolving the anomalous infrared spectrum of the MeCN-HCl molecular cluster using ab Initio molecular dynamics.

Correction for 'Resolving the anomalous infrared spectrum of the MeCN-HCl molecular cluster using ab Initio molecular dynamics' by Nicolai Bork et al., Phys. Chem. Chem. Phys., 2014, 16, 24685-24690.

Structures, Hydration, and Electrical Mobilities of Bisulfate Ion-Sulfuric Acid-Ammonia/Dimethylamine Clusters: A Computational Study.

Despite the well-established role of small molecular clusters in the very first steps of atmospheric particle formation, their thermochemical data are still not completely available due to limitation of the experimental techniques to treat such small clusters. We have investigated the structures and the thermochemistry of stepwise hydration of clusters containing one bisulfate ion, sulfuric acid, base (ammonia or dimethylamine), and water molecules using quantum chemical methods. We found that water facilitates proton transfer from sulfuric acid or the bisulfate ion to the base or water molecules, and depending on the hydration level, the sulfate ion was formed in most of the base-containing clusters. The calculated hydration energies indicate that water binds more strongly to ammonia-containing clusters than to dimethylamine-containing and base-free clusters, which results in a wider hydrate distribution for ammonia-containing clusters. The electrical mobilities of all clusters were calculated using a particle dynamics model. The results indicate that the effect of humidity is negligible on the electrical mobilities of molecular clusters formed in the very first steps of atmospheric particle formation. The combination of the results of this study with those previously published on the hydration of neutral clusters by our group provides a comprehensive set of thermochemical data on neutral and negatively charged clusters containing sulfuric acid, ammonia, or dimethylamine.

Resolving the anomalous infrared spectrum of the MeCN-HCl molecular cluster using ab initio molecular dynamics.

We present a molecular dynamics (MD) based study of the acetonitrile-hydrogen chloride molecular cluster in the gas phase, aimed at resolving the anomalous features often seen in infrared spectra of hydrogen bonded complexes. We find that the infrared spectrum obtained from the Fourier transform of the electric dipole moment autocorrelation function converges very slowly due to the floppy nature of the complex. Even after 55 picoseconds of simulation, significant differences in the modelled and experimental spectrum are seen, likely due to insufficient configurational sampling. Instead, we utilize the MD trajectory for a structural based analysis. We find that the most populated values of the N-H-Cl angle are around 162°. The global minimum energy conformation at 180.0° is essentially unpopulated. We re-model the spectrum by combining population data from the MD simulations with optimizations constraining the N-H-Cl angle. This re-modelled spectrum is in excellent accordance with the experimental spectrum and we conclude that the observed spectral anomaly is due to the dynamics of the N-H-Cl angle.

Benchmarking ab initio binding energies of hydrogen-bonded molecular clusters based on FTIR spectroscopy.

Models of formation and growth of atmospheric aerosols are highly dependent on accurate cluster binding energies. These are most often calculated by ab initio electronic structure methods but remain associated with significant uncertainties. We present a computational benchmarking study of the Gibbs free binding energies in molecular complexes and clusters based on gas phase FTIR spectroscopy. The acetonitrile-HCl molecular complex is identified via its redshifted H-Cl stretching vibrational mode. We determine the Gibbs free binding energy, ΔG°295 K, to between 4.8 and 7.9 kJ mol(-1) and compare this range to predictions from several widely used electronic structure methods, including five density functionals, Møller-Plesset perturbation theory, and five coupled cluster methods up to CCSDT quality, considering also the D3 dispersion correctional scheme. With some exceptions, we find that most electronic structure methods overestimate ΔG°295 K. The effects of vibrational anharmonicity is approximated using scaling factors, reducing ΔG°295 K by ca. 1.8 kJ mol(-1), whereby ΔG°295 K predictions well within the experimental range can be obtained.

Mechanistic insight into benzenethiol catalyzed amide bond formations from thioesters and primary amines.

The influence of arylthiols on cysteine-free ligation, i.e. the reaction between an alkyl thioester and a primary amine forming an amide bond, was studied in a polar aprotic solvent. We reacted the ethylthioester of hippuric acid with cyclohexylamine in the absence or presence of various quantities of thiophenol (PhSH) in a slurry of disodium hydrogen phosphate in dry DMF. Quantitative conversions into the resulting amide were observed within a few hours in the presence of equimolar amounts of thiophenol. Ab initio calculations showed that the reaction mechanism in DMF is similar to the well-known aqueous reaction mechanism. The energy barrier of the catalyzed amidation reaction is approximately 40 kJ mol(-1) lower than the non-catalyzed amidation reaction. At least partially this can be explained by a hydrogen bond from the amine to the π-electrons of the thiophenol, stabilizing the transition state in the aromatic thioester amidation reaction. Under similar conditions, cysteine-free ligation was achieved by coupling a fully side-chain protected 15 amino acid phosphopeptide thioester to the free N-terminal of a side-chain protected 9 amino acid peptide producing the corresponding 24 amino acid phosphopeptide.

On the gas-phase reaction between SO2 and O2(-)(H2O)(0-3) clusters--an ab initio study.

We present an ab initio investigation of the gas-phase reaction between SO2 and a O2(-)(H2O)n molecular cluster, n = 0-3. The associative product cluster, O2SO2(-)(H2O)n, is formed with high energy gain although the binding energies decrease with increasing hydration. About 54 kcal mol(-1) may be gained by isomerization of O2SO2(-)(H2O)n to the sulfate radical, SO4(-)(H2O)n, but a high energy barrier separates the two states. Although the isomerization is catalysed by the presence of a second SO2 molecule, the formation of SO4(-)(H2O)nvia O2(-)(H2O)n and SO2 is found to be negligible under atmospheric conditions. At thermal equilibration at 298.15 K and 50% relative humidity the end products are mainly O2SO2(-) and O2SO2(-)(H2O)1.

Identification and characterization of the HCl-DMS gas phase molecular complex via infrared spectroscopy and electronic structure calculations.

Models of atmospheric aerosol formation are dependent on accurate Gibbs free binding energies (ΔG°) of gaseous acids and bases, but for most acid­base pairs, only ab initio data are available. We report a combined experimental and theoretical study of the gaseous molecular complex of dimethylsulfide (DMS) and HCl. On the basis of infrared spectroscopy and anharmonic local mode calculations, we determine ΔG(295K)° to be between 6.2 and 11.1 kJ mol(­1). We test the performance of MP2 and five often used DFT functionals with respect to this result. M06-2X performs the best, but also the MP2 prediction is within the experimental range. We find that coupled cluster corrections to the electronic energy improves ΔG° estimates if and only if triple excitations are included. These estimates may be further improved by applying vibrational scaling factors to account for anharmonicity. Hereby, all but the PW91 based predictions are within the experimental range.

Reactions and reaction rate of atmospheric SO2 and O3(-) (H2O)n collisions via molecular dynamics simulations.

We present an ab initio study of gaseous SO(2) and O(3)(­)(H(2)O)(n) collisions. Opposed to the usual approach to determine reaction rates via structural optimizations and transition state theory, we successfully approach this problem using ab initio molecular dynamics. We demonstrate the advantages of this approach, being the automatic and unbiased inclusion of dynamic and steric effects as well as the simultaneous assessment of all possible reactions. For this particular system, we find that only one reaction will be of atmospheric significance. Further, we identify the main geometrical parameters governing and limiting the observed reaction and suggest a new measure of the reaction rate being ca. 3/4 of the collision rate.

Thermodynamic and kinetic properties of hydrogen defect pairs in SrTiO3 from density functional theory.

A density functional theory investigation of the thermodynamic and kinetic properties of hydrogen-hydrogen defect interactions in the cubic SrTiO(3) perovskite is presented. We find a net attraction between two hydrogen atoms with an optimal separation of ∼2.3 Å. The energy gain is ca. 0.33 eV compared to two non-interacting H defects. The main cause of the net attractive potential is elastic defect interactions through lattice deformation. Two possible diffusion paths for the hydrogen defect pair are investigated and are both determined to be faster than the corresponding diffusion path for single hydrogen atoms. Finally, we set up a simple model to determine the contribution from the double hydrogen defect to the total hydrogen flux, and find the double defect to be the main diffusing species at temperatures below ca. 400 °C. Post submission infrared absorption experiments show excellent agreement with the proposed properties of the double hydrogen defect.

Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1.

Recently, we described the first small-molecule inhibitor, (E)-ethyl 2-cyano-3-(3,4-dichlorophenyl)acryloylcarbamate (1), of the PDZ domain of protein interacting with Calpha-kinase 1 (PICK1), a potential drug target against brain ischemia, pain and cocaine addiction. Herein, we explore structure-activity relationships of 1 by introducing subtle modifications of the acryloylcarbamate scaffold and variations of the substituents on this scaffold. The configuration around the double bond of 1 and analogues was settled by a combination of X-ray crystallography, NMR and density functional theory calculations. Thereby, docking studies were used to correlate biological affinities with structural considerations for ligand-protein interactions. The most potent analogue obtained in this study showed an improvement in affinity compared to 1 and is currently a lead in further studies of PICK1 inhibition.