Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase

The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed li…

Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase.

A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD + ), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The analysis of free downhill molecular dynamic trajectories, performed in the enzyme and compared with the reaction in aqueous solution, has allowed the study of the dynamic coupling between the reacting fragments and the protein or the solvent water molecules, as well as an estimation of the dynamic effect contribution to the catalytic effect from calculation of the transmission coefficient in the enzyme and in solution. The obtained transmission coefficients for the enzyme…

A Theoretical Study of the Favorskii Rearrangement. Calculation of Gas-Phase Reaction Paths and Solvation Effects on the Molecular Mechanism for the Transposition of the α-Chlorocyclobutanone

The molecular mechanism of the α-chlorocyclobutanone transposition to yield cyclopropanecarboxylic acid, as a model of the Favorskii rearrangement, has been theoretically characterized in vacuo by means of ab initio molecular orbital procedures at the Hartree−Fock (HF) level of theory with the 6-31G* and 6-31+G* basis sets. The electron correlation has been estimated at the MP2/6-31G* level and calculations based on density functional theory, BLYP/6-31G*. The solvent effects are included at HF/6-31G* level by means of a polarizable continuum model. The questions related to the two accepted molecular mechanisms, the semibenzilic acid and the cyclopropanone transpositions, as well as the comp…

An AM1 theoretical study on the effect of Zn2+ Lewis acid catalysis on the mechanism of the cycloaddition between 3-phenyl-1-(2-pyridyl)-2-propen-1-one and cyclopentadiene

Abstract The mechanism of the Diels–Alder reaction between 3-phenyl-1-(2-pyridyl)-2-propen-1-one and cyclopentadiene has been investigated with the AM1 semiempirical method. Stationary points for two reactive channels, endo - cis and exo - cis , have been characterized. The role of the Lewis acid catalyst has been modeled taking into account the formation of a complex between Zn 2+ and the carbonyl oxygen atom and the pyridyl nitrogen atom of the 3-phenyl-1-(2-pyridyl)-2-propen-1-one system with and without the presence of two molecules of water around the cation. The mechanism of the uncatalyzed reaction corresponds to a concerted process, but in the presence of Lewis acid catalyst the mec…

Theoretical Study on the Molecular Mechanism of the Domino Cycloadditions between Dimethyl Acetylenedicarboxylate and Naphthaleno- and Anthracenofuranophane

AM1, B3LYP/6-31G//AM1, and B3LYP/6-31G computational studies were performed to select the reaction pathway controlling the reactions between dimethyl acetylenedicarboxylate (DMAD) and two furanophanes, naphthalenofuranophane and anthracenofuranophane. For these domino reactions, several pathways have been characterized on the potential energy surface corresponding to two consecutive cycloadditions. The first step corresponds to a [4 + 2] intermolecular cycloaddition of DMAD with the furan ring or with the naphthalene or anthracene ring of both furanophane systems to yield an oxabicyclo[2.2.1]heptadiene or a bicyclo[2.2.2]octadiene intermediate, respectively. The second step corresponds to […

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

We have studied the dependence of the chemical reaction mechanism of L-lactate dehydrogenase (LDH) on the protonation state of titratable residues and on the level of the quantum mechanical (QM) description by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods; this methodology has allowed clarification of the timing of the hydride transfer and proton transfer components that hitherto had not been possible to state definitively. Ferrer Castillo, Silvia, Silvia.Ferrer@uv.es, Silla Santos, Estanislao, Estanislao.Silla@uv.es ; Tuñon Garcia de Vicuña, Ignacio Nilo, Ignacio.Tunon@uv.es

Experimental and theoretical study of the energetic, morphological, and photoluminescence properties of CaZrO3:Eu3+

In this study, we present a combined experimental and theoretical study of the geometry, electronic structure, morphology, and photoluminescence properties of CaZrO3:Eu3+ materials. The polymeric precursor method was employed to synthesize CaZrO3:Eu3+ crystals, while density functional theory calculations were performed to determine the geometrical and electronic properties of CaZrO3:Eu3+ in its ground and excited electronic states (singlet and triplet). The results were combined with X-ray diffraction (XRD) measurements to elucidate the local structural changes induced by the introduction of Eu3+ in the crystal lattice. This process results in the formation of intermediate levels in the ba…

Theoretical study of the molecular mechanism of the domino pathways for squarate ester sequential reactions

A Theoretical Study of the Reaction between Cyclopentadiene and Protonated Imine Derivatives:  A Shift from a Concerted to a Stepwise Molecular Mechanism

The reaction between cyclopentadiene and protonated pyridine-2-carboxaldehyde imine derivatives has been studied by using Hartree-Fock (HF) and B3LYP methods together with the 6-31G basis set. The molecular mechanism is stepwise along an inverted energy profile. This results from the protonation on both nitrogen atoms of the imine group and the pyridine framework. The first step corresponds to the nucleophilic attack of cyclopentadiene on the electron-poor carbon atom of the iminium cation group to give an acyclic cation intermediate, and the second step is associated with the ring closure of this intermediate via the formation of a C-N single bond yielding the final cycloadduct. Two reacti…

A PM3 study of the molecular mechanism for the cycloaddition between cyclopentadiene and protonated pyridine-imine derivatives

Abstract The molecular mechanism of the cycloaddition reaction between cyclopentadiene (CP) and three pyridine-imine derivatives has been studied by means of PM3 semiempirical method. The role of the protonation, endo/exo and π-facial stereoselectivity are analyzed and discussed. In neutral conditions the cycloaddition between CP and the pyridine-imine takes place along a concerted mechanism. Protonation on both nitrogen atoms brings out that the reaction pathway takes with a very low barrier along a stepwise mechanism. PM3 results are capable to find the key factors governing this chemical reaction and to explain the experimental outcome.

A theoretical study of the addition of CH3MgCl to chiral α-alkoxy carbonyl compounds

Abstract A theoretical characterisation of the addition of CH 3 MgCl to the carbonyl group of 2-hydroxypropanal and 3,4-di- O -methyl-1- O -trimethylsilyl- l -erythrulose has been carried out. The PM3 semiempirical procedure and the ab initio method at HF level of theory with the 3–21G and 6–31G ∗ basis sets have been applied to identify the stationary points on the potential energy surface. The correlation effects have been included by using the MP2/6–31G ∗ method, as well as by means of MP3/6–31G ∗ // MP2/6–31G ∗ and MP4/6–31G ∗ //MP2/6–31G ∗ single point calculations. The geometry, harmonic vibrational frequencies, transition vector and electronic structure of the transition structures h…