Search Results (5)

Statins are important drugs in the regulation of cholesterol levels in the human body that have as a primary target the enzyme β-hydroxy-β-methylglutaryl-CoA reductase (HMGR). This enzyme plays a crucial role in the mevalonate pathway, catalyzing the four-electron reduction of HMG-CoA to mevalonate. A second reduction step of this reaction mechanism has been the subject of much speculation in the literature, with different conflicting theories persisting to the present day. In this study, the different mechanistic hypotheses were evaluated with atomic-level detail through a combination of molecular dynamics simulations (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The obtained Gibbs free activation and Gibbs free reaction energy (15 kcal mol⁻¹ and −40 kcal mol⁻¹) show that this hydride step takes place with the involvement of a cationic His405 and Lys639, and a neutral Glu98, while Asp715 remains in an anionic state. The results provide an atomic-level portrait of this step, clearly demonstrating the nature and protonation state of the amino acid residues involved, the energetics associated, and the structure and charge of the key participating atoms in the several intermediate states, finally elucidating this missing step. Full article

A combination of selective 1D Total Correlation Spectroscopy (TOCSY) and ¹H-¹³C Heteronuclear Multiple Bond Correlation (HMBC) NMR techniques has been employed for the identification of methyl linolenate primary oxidation products without the need for laborious isolation of the individual compounds. Complex hydroperoxides and diastereomeric endo-hydroperoxides were identified and quantified. Strongly deshielded C–O–O–H ¹H-NMR resonances of diastereomeric endo-hydroperoxides in the region of 8.8 to 9.6 ppm were shown to be due to intramolecular hydrogen bonding interactions of the hydroperoxide proton with an oxygen atom of the five-member endo-peroxide ring. These strongly deshielded resonances were utilized as a new method to derive, for the first time, three-dimensional structures with an assignment of pairs of diastereomers in solution with the combined use of ¹H-NMR chemical shifts, Density Functional Theory (DFT), and Our N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) calculations. Full article

In the upgrading of biomass pyrolysis vapors to hydrocarbons, dehydration accomplishes a primary objective of removing oxygen, and acidic zeolites represent promising catalysts for the dehydration reaction. Here, we utilized density functional theory calculations to estimate adsorption energetics and intrinsic kinetics of alcohol dehydration over H-ZSM-5, H-BEA, and H-AEL zeolites. The ONIOM (our Own N-layered Integrated molecular Orbital and molecular Mechanics) calculations of adsorption energies were observed to be inconsistent when benchmarked against QM (Quantum Mechanical)/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, isopropanol (IPA), and tert-amyl alcohol (TAA) over these three zeolites allowed for a detailed examination of how confinement impacts on reaction mechanisms and kinetics. The 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 were significantly overestimated by Knudsen diffusion, which will complicate experimental efforts to develop a kinetic model for catalytic fast pyrolysis. Full article

One of the fundamental issues in catalysis is to identify the catalytic active site. Due to its prominent pore topology and acidity, ferrierite (FER) zeolite has attracted extensive interest in various catalytic reactions such as isomerization of butenes. However knowledge on the active Brönsted acid site is still absent. In the present study, we perform extensive density functional theory calculations to explore the distribution and strength of the Brönsted acid sites and their potential catalytic activity for the double-bond isomerization of 1-butene to 2-butene. We employ a two-layered ONIOM scheme (our Own N-layered Integrated molecular Orbital + molecular Mechanics) to describe the structure and energetic properties of FER zeolite. We find that the hydrogen bond could improve the stability of Brönsted acid sites effectively, and, as a result, Al4-O6-Si2 and Al4-O-(SiO)₂-Al4 are the most stable sites for 1-Al substitution and 2-Al substitution, respectively. We further find that the Brönsted acid strength tends to decrease with the increase of Al contents and increase when the distance between the Al atoms is increased in 2-Al substitution. Finally it is demonstrated that the strength of acid sites determines the catalytic activity for the double bond isomerization of 1-butene to 2-butene. Full article

Isoliquiritigenin (ILTG) possesses many pharmacological properties. However, its poor solubility and stability in water hinders its wide applications. The solubility of bioactive compounds can often be enhanced through preparation and delivery of various cyclodextrin (CD) inclusion complexes. The 6-O-α-D-maltosyl-β-CD (G₂-β-CD), as one of the newest developments of CDs, has high aqueous solubility and low toxicity, especially stable inclusion characteristics with bioactive compounds. In this work, we for the first time construct and characterize the supermolecular structure of ILTG/G₂-β-CD by scanning electron microscopy (SEM), ultraviolet-visible spectroscopy (UV), Fourier transform infrared spectroscopy (FT-IR), and X-ray diffractometry (XRD). The solubility of ILTG in water at 25 °C rises from 0.003 to 0.717 mg/mL by the encapsulation with G₂-β-CD. Our experimental observations on the presence of the ILTG/G₂-β-CD inclusion complex are further supported by the ONIOM(our Own N-layer Integrated Orbital molecular Mechanics)-based QM/MM (Quantum Mechanics/Molecular Mechanics) calculations, typically substantiating these supermolecular characteristics, such as detailed structural assignments, preferred binding orientations, selectivity, solvent effects, interaction energies and forces of the ILTG/G₂-β-CD inclusion complex. Our results have elucidated how ILTG interacts with G₂-β-CD, demonstrating the primary host-guest interactions between ILTG and G₂-β-CD, characterized by hydrogen bonds, hydrophobic interactions, electrostatic forces, and conformational effects, are favored for the formation of the ILTG/G₂-β-CD inclusion. Full article