Search results for "Transition state"
showing 10 items of 85 documents
Reaction coordinates and transition states in enzymatic catalysis
2017
Enzymatic reactions are complex chemical processes taking place in complex dynamic environments. Theoretical characterization of these reactions requires the determination of the reaction coordinate and the transition state ensemble. This is not an easy task because many degrees of freedom may be involved in principle. We present recent efforts to find good enzymatic reaction coordinates and the implications of these findings in the interpretation of enzymatic efficiency. In particular, we analyze different strategies based on the use of minimum free energy paths and direct localization of the dividing surface on multidimensional free energy surfaces. Another strategy is based on the genera…
Quantifying the limits of transition state theory in enzymatic catalysis
2017
Significance Transition state theory (TST) is the most popular theory to calculate the rates of enzymatic reactions. However, in some cases TST could fail due to the violation of the nonrecrossing hypothesis at the transition state. In the present work we show that even for one of the most controversial enzymatic reactions—the hydride transfer catalyzed by dihydrofolate reductase—the error associated to TST represents only a minor correction to the reaction rate. Moreover, this error is actually larger for the reaction in solution than in the enzymatic active site. Based on this finding and on previous studies we propose an “enzymatic shielding” hypothesis which encompasses various aspects …
Influence of Remote Substituents on the Equatorial/Axial Selectivity in the Monooxygenation of Methylene C−H Bonds of Substituted Cyclohexanes
2001
The reactivity of individual C--H bonds in the methyl(trifluoromethyl)dioxirane TFDO oxygenation of stereogenic methylene groups in conformationally homogeneous monosubstituted cyclohexanes (2) has been determined. The unexpectedly high occurrence of O-atom insertion into C--H(ax) bonds suggests an in plane trajectory attack in the oxygenation while the diastereoselectivity of the reaction is qualitatively interpreted on the basis of the distinct hyperconjugative stabilization by the substituent of diastereomeric transition states due to long-range through bond interactions.
Theoretical study of the regio- and stereoselectivity of the intramolecular Povarov reactions yielding 5H-chromeno[2,3-c] acridine derivatives
2016
The intramolecular Povarov (IMP) reactions involved in the synthesis of 5H-chromeno[2,3-c] acridine derivatives [Tetrahedron Lett., 2010, 51, 3071–3074] have been studied using density functional theory (DFT) methods. The studied IMP reaction is a domino process that comprises two consecutive reactions: (i) a BF3 Lewis acid catalysed intramolecular aza-Diels–Alder (IMADA) reaction of an alkene tethered chromene imine (ATCI) giving a formal [4 + 2] cycloadduct, and (ii) a 1,3-hydrogen shift yielding the final chromeno product. The possible regio-(fused/bridged) and stereo-(cis/trans) isomeric channels associated with the IMADA reaction were thoroughly investigated and analysed. The activatio…
A three-component Mannich-type condensation leading to phosphinic dipeptides—extended transition state analogue inhibitors of aminopeptidases
2011
Abstract N-Protected α-aminoalkylphosphinic acids bearing a P–H function were found to be novel practical building blocks in three-component condensations with formaldehyde and secondary amines (amino acids). Such Mannich-type N -phosphonomethylation is a common approach for phosphorus acid derived substrates and leads to multifunctional (phosphonic/amino/carboxylic) compounds of diverse relevance. The utility of this reaction was examined for construction, in a single synthetic step, of advanced phosphinic pseudodipeptides designed to act as extended transition state analogue inhibitors of selected aminopeptidases. Phosphinomethylation of primary amino acids was less efficient and yielded …
The skeletal isomerization of but-1-ene catalyzed by theta-1 zeolite
2001
The complete mechanism for the skeletal isomerization of but-1-ene catalyzed by theta-1 zeolite was investigated theoretically by means of DFT calculations, and the influence of the local geometry of the active site and of electrostatic effects on the geometries of the species involved and on activation and reaction energies were analyzed. It was found that whereas the geometry and stability of alkoxide intermediates are strongly influenced by the local geometry of the active site, the ionic transition states are mainly stabilized by electrostatic effects. Both aspects result in a lowering of the activation energies of the elementary steps that form the mechanism and therefore in enhanced r…
Mukaiyama–Michael Reactions with trans-2,5-Diarylpyrrolidine Catalysts: Enantioselectivity Arises from Attractive Noncovalent Interactions, Not from …
2013
The scope of the enantioselective Mukaiyama-Michael reactions catalyzed by trans-2,5-diphenylpyrrolidine has been expanded to include both α- and β-substituted enals. However, the rationalization of the observed enantioselectivity is far from obvious since the catalyst is not very sterically hindered. DFT calculations were carried out to rationalize the observed stereoselectivities. Transition states of the C-C bond formation between iminium intermediates and silyloxyfurans were located and their relative energies were used to estimate the stereoselectivity data. We find excellent agreement between the predicted and observed stereoselectivities. The analysis of intermolecular forces reveals…
Designing a Transition State Analogue for the Disfavored Intramolecular Michael Addition of 2-(2-Hydroxyethyl)acrylate Esters
1999
The rate-determining steps for the intramolecular 1,2 and 1,4 addition reactions in basic medium of methyl 2-(2-hydroxyethyl)acrylate to give the corresponding γ-lactone and tetrahydrofuran, respec...
Diastereoselectivity in Organometallic Additions to the Carbonyl Group of Protected Erythrulose Derivatives
1998
We have investigated a number of nucleophillic additions to L-erythrulose derivatives (4-12) bearing protective O-silyl, O-benzyl, and O-trityl groups in various relative positions. The results are discussed in the frame of chelated vs nonchelated transition states with additional support of previously published theoretical calculations. Sound evidence appears to exist for the formation of alpha-chelates as the key intermediates in nucleophillic additions to these alpha,beta-dioxygenated ketones. Since such evidence is still lacking in the case of beta-chelates, proposals of their intermediacy have been relegated in favor of the more solid Felkin-Anh model, which predicts the same stereoche…
ChemInform Abstract: Diastereoselectivity in Organometallic Additions to the Carbonyl Group of Protected Erythrulose Derivatives.
2010
We have investigated a number of nucleophillic additions to l-erythrulose derivatives (4−12) bearing protective O-silyl, O-benzyl, and O-trityl groups in various relative positions. The results are discussed in the frame of chelated vs nonchelated transition states with additional support of previously published theoretical calculations. Sound evidence appears to exist for the formation of α-chelates as the key intermediates in nucleophillic additions to these α,β-dioxygenated ketones. Since such evidence is still lacking in the case of β-chelates, proposals of their intermediacy have been relegated in favor of the more solid Felkin−Anh model, which predicts the same stereochemical result. …