Search results for " Catalysis"
showing 10 items of 585 documents
Theoretical insights in enzyme catalysis
2004
In this tutorial review we show how the methods and techniques of computational chemistry have been applied to the understanding of the physical basis of the rate enhancement of chemical reactions by enzymes. This is to answer the question: Why is the activation free energy in enzyme catalysed reactions smaller than the activation free energy observed in solution? Two important points of view are presented: Transition State (TS) theories and Michaelis Complex (MC) theories. After reviewing some of the most popular computational methods employed, we analyse two particular enzymatic reactions: the conversion of chorismate to prephenate catalysed by Bacillus subtilis chorismate mutase, and a m…
Unraveling the role of protein dynamics in dihydrofolate reductase catalysis
2013
Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy ((15)N, (13)C, (2)H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy e…
Cooperative Assistance in Bifunctional Organocatalysis: Enantioselective Mannich Reactions with Aliphatic and Aromatic Imines
2012
both of which contain a thiourea moiety (Scheme 1).The catalysts are capable of deprotonating suitable nucleo-philes, such as activated carbonyl compounds. This proton-transfer reaction generates an ion pair, which is composed ofthe protonated catalyst and the anionic nucleophile interact-ing through hydrogen bonds. At least one of the NH moietiesin the protonated catalyst is involved in activating theelectrophilic reaction partner.
On the Catalytic Effect of Water in the Intramolecular Diels–Alder Reaction of Quinone Systems: A Theoretical Study
2012
The mechanism of the intramolecular Diels#8211;Alder (IMDA) reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT) methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES). The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition stat…
Modification of Nanocrystalline WO3 with a Dicationic Perylene Bisimide: Applications to Molecular Level Solar Water Splitting
2015
[(N,N?-Bis(2-(trimethylammonium)ethylene) perylene 3,4,9,10-tetracarboxylic acid bisimide)(PF6)2] (1) was observed to spontaneously adsorb on nanocrystalline WO3 surfaces via aggregation/hydrophobic forces. Under visible irradiation (? > 435 nm), the excited state of 1 underwent oxidative quenching by electron injection (kinj > 108 s-1) to WO3, leaving a strongly positive hole (Eox ? 1.7 V vs SCE), which allows to drive demanding photo-oxidation reactions in photoelectrochemical cells (PECs). The casting of IrO2 nanoparticles (NPs), acting as water oxidation catalysts (WOCs) on the sensitized electrodes, led to a 4-fold enhancement in photoanodic current, consistent with hole transfer from …
Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase
2008
Molecular simulations based on the use of hybrid quantum mechanics/molecular mechanics methods are able to provide detailed information about the complex enzymatic reactions and the consequences of specific mutations on the activity of the enzyme. In this work, the reduction of pyruvate to lactate catalysed by wild-type and Asp168Ala mutant lactate dehydrogenase (LDH) has been studied by means of simulations using a very flexible molecular model consisting of the full tetramer of the enzyme, together with the cofactor NADH, the substrate and solvent water molecules. Our results indicate that the Asp168Ala mutation provokes a shift in the p K a value of Glu199 that becomes unprotonated at n…
Role of Protein Flexibility in Enzymatic Catalysis: Quantum Mechanical−Molecular Mechanical Study of the Deacylation Reaction in Class A β-Lactamases
2002
We present a theoretical study of a mechanism for the hydrolysis of the acyl-enzyme complex formed by a class A beta-lactamase (TEM1) and an antibiotic (penicillanate), as a part of the process of antibiotic's inactivation by this type of enzymes. In the presented mechanism the carboxylate group of a particular residue (Glu166) activates a water molecule, accepting one of its protons, and afterward transfers this proton directly to the acylated serine residue (Ser70). In our study we employed a quantum mechanics (AM1)-molecular mechanics partition scheme (QM/MM) where all the atoms of the system were allowed to relax. For this purpose we used the GRACE procedure in which part of the system …
Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase.
2015
Abstract Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N‐terminal segment containing heavy isotopes (2H, 13C, 15N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C‐terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N‐terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C‐terminal segment. QM/MM studies support th…
Controlling the molecular diffusion in MOFs with the acidity of monocarboxylate modulators.
2021
The catalytic performance of metal-organic frameworks (MOFs) is related to their physicochemical properties, such as particle size, defect-chemistry and porosity, which synthetic control can be potentially achieved by coordination modulation. By combining PXRD, 1HNMR, FT-IR, N2 uptake measurements we have found insights that the different types of defects (missing linker or missing clusters consequence of the spatial distribution of missing linkers, and the combination of both) could be controlled by the type of modulator employed. We show that the molar percent of defects, either as missing linkers or as part of missing cluster defects, is related to the modulator’s acidity and subse…
Silver-Catalyzed C-C Bond Formation between Methane and Ethyl Diazoacetate in Supercritical CO2
2011
Even in the context of hydrocarbons’ general resistance to selective functionalization, methane’s volatility and strong bonds pose a particular challenge. We report here that silver complexes bearing perfluorinated indazolylborate ligands catalyze the reaction of methane (CH4) with ethyl diazoacetate (N2CHCO2Et) to yield ethyl propionate (CH3CH2CO2Et). The use of supercritical carbon dioxide (scCO2) as the solvent is key to the reaction’s success. Although the catalyst is only sparingly soluble in CH4/CO2 mixtures, optimized conditions presently result in a 19% yield of ethyl propionate (based on starting quantity of the diazoester) at 40°C over 14 hours.