In the upgrading of biomass pyrolysis vapors to hydrocarbons, dehydration accomplishes a primary objective of removing oxygen and acidic zeolites represent promising catalysts for dehydration reaction. Here, we utilize density functional theory calculations to estimate adsorption energetics and intrinsic kinetics of alcohol dehydration over H-ZSM-5, H-BEA, and H-AEL zeolites. ONIOM calculations of adsorption energies were observed to be inconsistent when benchmarked against QM/Hartree-Fock and periodic boundary condition calculations. However, reaction coordinate calculations of adsorbed species and transition states were consistent across all levels considered. Comparison of ethanol, iso-propanol (IPA), and tert-amyl alcohol (TAA) over these three zeolites allowed for a detailed examination of how confinement impacts reaction mechanisms and kinetics. TAA, seen to proceed via a carbocationic mechanism, was found to have the lowest activation barrier, followed by IPA and then ethanol, both of which dehydrate via a concerted mechanism. Barriers in H-BEA were consistently found to be lower than in H-ZSM-5 and H-AEL, attributed to late transition states and either elevated strain or inaccurately estimating long-range electrostatic interactions in H-AEL, respectively. Molecular dynamics simulations revealed that the diffusivity of these three alcohols in H-ZSM-5 are significantly overestimated by Knudsen diffusion, which will complicate experimental efforts to develop a kinetic model for catalytic fast pyrolysis.

Heme is located in the active site of proteins and has diverse and important biological functions, such as electron transfer and oxygen transport and/or storage. The distortion of heme porphyrin is considered an important factor for the diverse functions of heme because it correlates with the physical properties of heme, such as oxygen affinity and redox potential. Therefore, clarification of the relationship between heme distortion and the protein environment is crucial in protein science. Here, we analyzed the fluctuation in heme distortion in the protein environment for hemoglobin and myoglobin using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations. We also investigated the protein structures of hemoglobin and myoglobin stored in Protein Data Bank and found that heme is distorted along the doming mode, which correlates with its oxygen affinity, more prominently in the protein environment than in the isolated state, and the magnitude of distortion is different between hemoglobin and myoglobin. This tendency was also observed in the results of MD simulations and QM calculations. These results suggest that heme distortion is affected by its protein environment and fluctuates around its fitted conformation, leading to physical properties that are appropriate for protein functions.