Search results for "Models"
showing 10 items of 8211 documents
Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity
2011
Two similar enzymes with different biosynthetic function in one species have evolved to catalyze two distinct reactions. X-ray structures of both enzymes help reveal their most important differences. The Rauvolfia alkaloid biosynthetic network harbors two O-glucosidases: raucaffricine glucosidase (RG), which hydrolyses raucaffricine to an intermediate downstream in the ajmaline pathway, and strictosidine glucosidase (SG), which operates upstream. RG converts strictosidine, the substrate of SG, but SG does not accept raucaffricine. Now elucidation of crystal structures of RG, inactive RG-E186Q mutant, and its complexes with ligands dihydro-raucaffricine and secologanin reveals that it is the…
Single-electron self-exchange between cage hydrocarbons and their radical cations in the gas phase.
2010
We show that the radical cations of adamantane (C(10)H(16)(*+), 1H(*+)) and perdeuteroadamantane (C(10)D(16)(*+), 1D(*+)) are stable species in the gas phase. The radical cation of adamantylideneadamantane (C(20)H(28)(*+), 2H(*+)) is also stable (as in solution). By using the natural (13)C abundances of the ions, we determine the rate constants for the reversible isergonic single-electron transfer (SET) processes involving the dyads 1H(*+)/1H, 1D(*+)/1D and 2H(*+)/2H. Rate constants for the reaction 1H(*+)+1D 1H+1D(*+) are also determined and Marcus' cross-term equation is shown to hold in this case. The rate constants for the isergonic processes are extremely high, practically collision-co…
Unveiling the Lewis Acid Catalyzed Diels–Alder Reactions Through the Molecular Electron Density Theory
2020
The effects of metal-based Lewis acid (LA) catalysts on the reaction rate and regioselectivity in polar Diels&ndash
Decarboxylation and alkaline colour fading reactions in presence of humic substances.
2002
Humic substances (HSs) can substantially influence velocity of reactions in the environment as shown on example of decarboxylation and alkaline colour (e.g., malachite green and crystal violet) fading reactions. In colour fading and decarboxylation reactions of 6-nitrobenzisoxazole-3-carboxylic acid HS act as inhibitors, but additions of surfactants change the pattern of reaction. The inhibitory activity of HSs much depends on their origin. The velocity of studied reactions depends also on pH, temperature and concentration of HS used. Possible micellar catalysis mechanism has been suggested.
Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution
2012
We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06-2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substra…
Peptide Bond Formation Mechanism Catalyzed by Ribosome
2015
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708–871…
Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris
2010
In this paper the reaction mechanism for methylation of cytosine at the exocyclic N4 position catalyzed by M.PvuII has been explored by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods. A reaction model was prepared by placing a single cytosine base in the active site of the enzyme. In this model the exocyclic amino group of the base establishes hydrogen bond interactions with the hydroxyl oxygen atom of Ser53 and the carbonyl oxygen atom of Pro54. The reaction mechanism involves a direct methyl transfer from AdoMet to the N4 atom and a proton transfer from this atom to Ser53, which in turn transfers a proton to Asp96. Different timings for the proton transfers and meth…
A phenoxo-bridged dicopper(ii) complex as a model for phosphatase activity: mechanistic insights from a combined experimental and computational study
2017
A μ-phenoxo-bis(μ2-1,3-acetato)-bridged dicopper(II) complex [CuII2(L1)(μ-O2CMe)2][NO3] (1) has been synthesized from the perspective of modeling phosphodiesterase activity. Structural characterization was done initially with 1·3Et2O (vapour diffusion of Et2O into MeOH solution of 1; poor crystal quality) and finally with its perchlorate salt [CuII2(L1)(μ-O2CMe)2][ClO4]·1.375MeCN·0.25H2O, crystallized from vapour diffusion of n-pentane into a MeCN–MeOH mixture (comparatively better crystal quality). An asymmetric unit of such a crystal contains two independent molecules of compositions [CuII2(L1)(μ-O2CMe)2][ClO4] and [CuII2(L1)(μ-O2CMe)2(MeCN)][ClO4] (coordinated MeCN with 0.75 occupancy), …
Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.
2011
We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism. …
Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach
2008
We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6'-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction in aqueous solution and the reaction catalyzed by Chalcone Isomerase. By means of rare event simulations of trajectories started at the transition state, we have computed the transmission coefficients, obtaining 0.76 +/- 0.04 and 0.87 +/- 0.03, in water and in the enzyme, respectively. According to these simulations, the Michael addition can be seen as a formation of a new intramolecular carbon-oxygen bond accompanied by a charge transfer essentially taking place from the nu…