Framework‐bound methoxides occur as intermediates in the stepwise mechanism for zeolite‐catalyzed methylation reactions. Herein, the formation of methoxides from methanol or dimethyl ether in H‐ZSM‐5 is investigated by a combination of static and dynamic simulations, with particular focus on the effect of additional water and methanol molecules on the mechanism and kinetics. Metadynamics simulations allow partitioning the reaction path into distinct phases. Proton transfer from the zeolite to the reactants is found to be the rate‐limiting phase in the methoxide formation. Additional methanol molecules only assist the proton transfer in the methoxide formation from methanol, whereas the reaction from dimethyl ether does not benefit from methanol assistance. Once formed, methoxides are found to be as reactive toward alkene methylation as methanol and dimethyl ether.

The methylation of arenes is a key step in the production of hydrocarbons from methanol over acidic zeolites. We performed ab initio static and molecular dynamics free energy simulations of benzene methylation in H-ZSM-5 to determine the factors that influence the reaction kinetics. Special emphasis is given to the effect of the surrounding methanol molecules on the methylation kinetics. It is found that for higher methanol loadings, methylation may also occur from a protonated methanol cluster, indicating that the exact location of the Brønsted acid site is not essential for the zeolite-catalyzed methylation reaction. However, methylations from a protonated methanol cluster exhibit higher free energy barriers than a methylation from a single methanol molecule. Finally, comparison with a pure methanol solvent reaction environment indicates that the main role of the zeolite during the methylation of benzene is to provide the acidic proton and to create a polar environment for the reaction. The metadynamics approach, which is specifically designed to sample rare events, allows exploring new reaction pathways, which take into account the flexibility of the framework and additional guest molecules in the pores and channels of the zeolite framework. This approach goes beyond the often applied static calculations to determine reaction kinetics.

The diffusion of olefins through 8-ring solid acid microporous zeolites is investigated using molecular dynamics simulations techniques and using a newly developed flexible force field. Within the context of the Methanol to Olefin (MTO) process and the observed product distribution, knowledge on the diffusion paths is essential to obtain molecular level control over the process conditions. Eight-ring zeotype materials are favorably used for the MTO process as they give a selective product distribution towards low carbon olefins. To investigate how composition, acidity and flexibility influence the diffusion paths of ethene and propene, a series of isostructural aluminosilicates (zeolites) and silicoaluminophosphates (AlPOs and SAPOs) are investigated with and without randomly distributed acidic sites. Distinct variations in diffusion of ethene are observed in terms of temperature, composition, acidity, and topology (AEI, CHA, AFX). In general, diffusion of ethene is an activated process for which free energy barriers for individual rings may be determined. We observe ring dependent diffusion behavior which can not solely be described in terms of the composition and topology of the rings. A new descriptor had to be introduced namely the accessible window area (AWA), inspired by implicit solvation models of proteins and small molecules. The AWA may be determined throughout the molecular dynamics trajectories and correlates well with the number of ring crossings at the molecular level and the free energy barriers for ring crossings from one cage to the other. The overall observed diffusivity is determined by molecular characteristics of individual rings for which AWA is a proper descriptor. Temperature-induced changes in framework dynamics and diffusivity may be captured by following the new descriptor throughout the simulations.

Green, stable and wide electrochemical window deep eutectic solvents (DESs) are ideal candidates for electrochemical systems. However, despite several studies of their bulk properties, their structure and properties under electrified confinement are barely investigated, which hinders the widespread use of these solvents in electrochemical applications. In this letter, we explore the electrical double layer structure of 1:2 choline chloride-urea (Reline), with a particular focus on the electrosorption of the hydrogen

Realistic representation of protein flexibility in biomolecular simulations remains an unsolved fundamental problem and is an active area of research. The high flexibility of the cytochrome P450 2D6 (CYP2D6) active site represents a challenge for accurate prediction of the preferred binding mode and site of metabolism (SOM) for compounds metabolized by this important enzyme. To account for this flexibility, we generated a large ensemble of unbiased CYP2D6 conformations, to which small molecule substrates were docked to predict their experimentally observed SOM. SOM predictivity was investigated as a function of the number of protein structures, the scoring function, the SOM-heme cutoff distance used to distinguish metabolic sites, and intrinsic reactivity. Good SOM predictions for CYP2D6 require information from the protein. A critical parameter is the distance between the heme iron and the candidate site of metabolism. The best predictions were achieved with cutoff distances consistent with the chemistry relevant to CYP2D6 metabolism. Combination of the new ensemble-based docking method with estimated intrinsic reactivities of substrate sites considerably improved the predictivity of the model. Testing on an independent set of substrates yielded area under curve values as high as 0.93, validating our new approach.

We present a new replica exchange method, designed for optimal native state protein sampling in explicit solvent, called replica exchange with flexible tempering (REFT). The method was built upon the recently introduced replica exchange with solute tempering (REST). The potential function is adapted to direct the conformational search toward interdomain movements and the flexible portions of the protein. We demonstrate the improved sampling efficiency of REFT compared to the original REST for the bacteriophage T4 lysozyme.

a b s t r a c tThis work encompasses a combined experimental and theoretical assessment of how zeolitic acid strength and composition affects acid-catalysed methylation reactions. Overall, higher methylation rates were observed over the material with higher acid strength. Co-reactions of methanol with benzene at 250°C over the two isostructural AFI materials H-SSZ-24 and H-SAPO-5 revealed large differences in selectivity. While the stronger acidic H-SSZ-24 mainly produced toluene and polymethylbenzenes, high yields of C 4+ aliphatics were observed over H-SAPO-5. These results strongly suggest that alkene methylation was preferred over H-SAPO-5 even at very low conversion during methanol/benzene co-reactions. Furthermore, a comparison of benzene and propene methylation at 350-400°C revealed a significantly faster rate of benzene than propene methylation in H-SSZ-24, whereas the rates of benzene and propene methylation were similar in H-SAPO-5. The observed difference in reactivity of the two hydrocarbons in both catalysts could be understood by careful analysis of various molecular dynamics simulations of the co-adsorbed complexes. The probability to form protonated methanol was, as expected, higher in the more acidic material. However, in H-SSZ-24, the probability for methanol protonation was higher when co-adsorbed with benzene than when co-adsorbed with propene, while the same was not observed in H-SAPO-5. Furthermore, it was found that benzene and methanol are more likely to form a reactive co-adsorbed complex in H-SSZ-24 compared to propene and methanol, while the opposite was observed for H-SAPO-5. This work shows that molecular dynamics simulations provide insights into the adsorption behaviour of guest molecules in large pore AFI materials. The obtained insights correlate with the experimentally observed reactivities.

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl3F) and complexing (CH3NO2) solvent models.