Transition state

About: Transition state is a research topic. Over the lifetime, 4978 publications have been published within this topic receiving 117965 citations. The topic is also known as: transition state of elementary reaction.

A Novel Addition Mechanism for the Reaction of Frustrated Lewis Pairs with Olefins

Abstract: Density functional theory calculations have been carried out to investigate the addition mechanism for the reactions of “frustrated Lewis pairs” with olefins. Several reactions are studied in this work, which include a three-component reaction between a sterically demanding phosphane [P(tBu)3], borane [B(C6F5)3], and ethylene, and a two-component reaction between an olefin derivative of phosphane [CH2=CH–(CH2)3P(tBu)2] and B(C6F5)3. For the two-component reaction, we find a concerted addition mechanism, in which the formation of the B–C and P–C bonds takes place simultaneously. For the three-component reaction, our calculations show that the reaction may be initiated by the weak association of B(C6F5)3 with ethylene (to form a transient species) and then proceeds in a concerted transition state similar to that in the two-component reaction under study. The natural population analyses for the corresponding transition states indicate that the CH2=CH group (in the two-component reaction) and C2H4 (in the three-component reaction) seem to act as a bridge for electron transfer from the Lewis base center P to the Lewis acid center B. We also investigate the reaction between P(tBu)3, propylene, and B(C6F5)3. The results account well for the experimentally observed regioselectivity. In addition, our calculations also indicate that the presence of fluorine atoms in the borane is essential for stabilizing the addition product.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Structural consequences of the addition of lithium halides in enolization and aldol reactions

Abstract: Aggregates consisting of lithium halides with either lithium amides or lithium enolates have been characterized by X-ray crystallography. Two structural types, solvated heterodimers and heterotrimers, have been found for halide/amide combinations. Two compounds containing both lithium halide and lithium enolate have also been identified as heterodimers. Using this information, we propose a reaction sequence for enolization and subsequent aldol addition reaction involving halide-containing aggregates. An ab initio and PM3 theoretical study of model systems shows that solvated heterodimers between LiBr and either LiNH2 or LiOC(H)=CH2 are favored over the respective homodimers. Calculations reveal a stable eight-membered ring transition state for the enolization step between LiCl·LiNH2 and acetaldehyde. Two independent transition states, a 4,8 and a 4,4,6 ring system, were calculated for the model reaction between the heterotrimer [(LiNH2)2·LiCl] and acetaldehyde. Dissociation of donor solvent was computed t...

Computational study of the aminolysis of esters. The reaction of methylformate with ammonia.

Abstract: The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.

Mechanistic Insights into the Decomposition of Fructose to Hydroxy Methyl Furfural in Neutral and Acidic Environments Using High-Level Quantum Chemical Methods

Abstract: Efficient catalytic chemical transformation of fructose to hydroxy methyl furfural (HMF) is one of the key steps for attaining industrial level conversion of biomass to useful chemicals. We report an investigation of the reaction mechanisms for the decomposition of fructose to HMF in both neutral and acidic environments at the Gaussian-4 level of theory including calculation of enthalpies, free energies, and effective solvation interactions. In neutral water solvent, the transformation of fructose to HMF involves a four step reaction sequence with four transition states. The effective activation energy relative to fructose in neutral water at 298 K is very large, about 74 kcal/mol, so that transformation in neutral media around this temperature is unlikely. In contrast, the computed potential energy surface is much more favorable for the transformation in acidic media at 498 K, as the effective activation barrier is about 39 kcal/mol. The transformation in acidic media is a much more complex mechanism involving dehydration and hydrogen transfer steps, which are more favorable when protonated intermediates are involved.

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

Abstract: We describe a method for the systematic improvement of reaction coordinates in quantum mechanical/molecular mechanical (QM/MM) calculations of reaction free-energy profiles. In umbrella-sampling free-energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (approximately 10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations.