A theoretical study of the mechanism of the isomerization reaction HOC(+) --> HCO(+) is presented. The mechanism was studied in terms of reaction force, chemical potential, reaction electronic flux (REF), and bond orders. It has been found that the evolution of changes in REF along the intrinsic reaction coordinate can be explained in terms of bond orders. The energetic lowering of the hydrogen assisted (catalyzed) reaction has been identified as being due to the stabilization of the H(3)(+) transition state complex and the stepwise bond dissociation and formation of the H-O and H-C bonds, respectively.

Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host–guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with an aromatic or adamantane core and the CB7 host using molecular electron density derived nonbonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the Minimal Basis Iterative Stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound states. The resulting nonbonded force field parameters improve binding affinity prediction, especially for guests with an adamantane core in which repulsive exchange and dispersion interactions to the host dominate.

Methyl transfer reactions play an important role in biology and are catalyzed by various enzymes. Here, the influence of the molecular environment on the reaction mechanism was studied using advanced ab initio methods, implicit solvation models and QM/MM molecular dynamics simulations. Various conceptual DFT and electronic structure descriptors identified different processes along the reaction coordinate e.g. electron transfer. The results show that the polarity of the solvent increases the energy required for the electron transfer and that this spontaneous process is located in the transition state region identified by the (mean) reaction force analysis and takes place through the bonds which are broken and formed. The inclusion of entropic contributions and hydrogen bond interactions in QM/MM molecular dynamics simulations with a validated DFTB3 Hamiltonian yields activation barriers in good agreement with the experimental values in contrast to the values obtained using two implicit solvation models.

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The evaporation of molecules from dust grains is crucial to understanding some key aspects of the star- and the planet-formation processes. During the heating phase, the presence of young protostellar objects induces molecules to evaporate from the dust surface into the gas phase, enhancing its chemical complexity. Similarly, in circumstellar discs, the position of the so-called snow lines is determined by evaporation, with important consequences for the formation of planets. The amount of molecules that are desorbed depends on the interaction between the species and the grain surface, which is controlled by the binding energy. Recent theoretical and experimental works point towards a distribution of values for this parameter instead of the single value often employed in astrochemical models.We present a new “multi-binding energy” framework to assess the effects that a distribution of binding energies has on the amount of species bound to the grains. We find that the efficiency of the surface chemistry is significantly influenced by this process, with crucial consequences on the theoretical estimates of the desorbed species.