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Heterogeneous reactions at the surfaces of mineral dusts represent a key process in the formation of atmospheric aerosols. To quantify the rate of aerosol formation in climate modeling as well as combat hazardous aerosols, a deep understanding of the mechanisms of these reactions is essential. In the present work, density functional theory calculations, including a Hubbard-like +U correction, were employed to elucidate the reaction between SO2 and the hematite(0001) surface. Three reaction conditions are considered: dry, wet, and aerobic. In the absence of water and oxygen, adsorption energies of SO2 on the clean Fe–O3–Fe-termination were found to be about −0.8 to −1.0 eV and resulted in the formation of an adsorbed SO3-like species. The addition of water leads to surface hydroxylation and has little effect on promoting the SO2 adsorption. Under such circumstances, an HSO3-like species was formed with a smaller adsorption energy of about −0.5 eV. By contrast, the presence of molecular oxygen enhances the SO2 adsorption significantly as the two species combine to form sulfate SO42−, with adsorption energies of −1.31 to −1.64 eV. The calculated vibrational frequencies of the adsorbate species provide insight into the surface bonding and a useful spectral fingerprinting for experimental measurements. These results elucidate the atomistic mechanism of the reaction between SO2 and hematite and highlight the important role of atmospheric O2 in the formation of sulfates. [ABSTRACT FROM AUTHOR]

The hyperfine (hf) structures of radical cations are calculated using first principles density functional theory. Within the local spin density (LSD) approximation, the isotropic hyperfine coupling constants (Fermi contact terms) are computed for a set of linear (nonbranched) alkane and alkene radical cations with up to four carbon atoms. The results are as a whole in very good agreement with experimental data, obtained from low temperature matrix isolation electron-spin resonance (ESR) measurements, and with results from previous configuration interaction calculations. [ABSTRACT FROM AUTHOR]

Abstract: Exemplars of the state of the art in modeling enzymes are reviewed through a selection of works from leading schools using QM‐only cluster models, QM/MM models and QM/MM/MD models. A computational protocol is proposed, intended to guide neophytes through the myriad of methodological choices that are necessary for the successful study of chemical reactions in the complex enzymatic environment. [ABSTRACT FROM AUTHOR]

Hydrogenation reactions catalyzed by transition-metal-containing nanoparticles represent an important type of reaction in chemical industry. However, the modeling of these reactions in their working conditions requires much longer simulation times than what could usually be achieved with ab initio or first-principle methods. To address this problem, in this work, the density-functional-based tight-binding (DFTB) method was parameterized for hydrogenation reactions on molybdenum carbide catalysts, involving the elements C, H, Mo, O and Si. The overall quality of the DFTB parameters was tested with band structure/molecular orbital energies, molecular/crystal structures, chemisorption bond strengths, hydrogen adsorption energies, hydrogenation reaction energies, molecular vibrational frequencies, energy barriers and the structures of the transition states for systems of interest. The parameterized DFTB method gave errors of <1.45 % for bond distances of hydrocarbons and 4.86 % for non-hydrocarbons. It could reproduce the structure and vibrational frequencies (with errors of about 100 cm−1) of selected hydrocarbon–molybdenum carbide complexes obtained from DFT calculations. Good agreement was reached between DFTB and DFT on the dissociative adsorption of hydrogen on the α-Mo2C (0001) surface. For most of the hydrogenation reactions examined, DFTB showed errors of ~2 kcal/mol compared to DFT/PBE, with a few exceptions of ~5 kcal/mol. It could also describe the reaction energies, the forward and reverse energy barriers and the transition-state structures for the benzene hydrogenation reaction on a Mo38C19 cluster. [ABSTRACT FROM AUTHOR]

Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τdec now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τdec). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases. [ABSTRACT FROM AUTHOR]

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton. [ABSTRACT FROM AUTHOR]