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.

Carboxylic Acid Catalyzed Hydration of Acetaldehyde

Abstract: Electronic structure calculations of the pertinent stationary points on the potential energy surface show that carboxylic acids can act effectively as catalysts in the hydration of acetaldehyde. Barriers to this catalyzed process correlate strongly with the pKa of the acid, providing the potential to provide the predictive capacity of the effectiveness of carboxylic acid catalysts. Transition states for the acid-catalyzed systems take the form of pseudo-six-membered rings through the linear nature of their hydrogen bonds, which accounts for their relative stability compared to the more strained direct and water-catalyzed systems. When considered as a stepwise reaction of a dimerization followed by reaction/complexation, it is likely that collisional stabilization of the prereactive complex is more likely than reaction in the free gas phase, although the catalyzed hydration does retain the potential to proceed on water surfaces or in droplets. Lastly, it is observed that postreactive diol-acid complexes are significantly stable (∼12-17 kcal/mol) relative to isolated products, suggesting the possibility of long-lived hygroscopic species that could act as a seed molecule for condensation of secondary organic aerosols.

Exploring the role of large conformational changes in the fidelity of DNA polymerase β

Abstract: The relationships between the conformational landscape, nucleotide insertion catalysis and fidelity of DNA polymerase β are explored by means of computational simulations. The simulations indicate that the transition states for incorporation of right (R) and wrong (W) nucleotides reside in substantially different protein conformations. The protein conformational changes that reproduce the experimentally observed fidelity are significantly larger than the small rearrangements that usually accompany motions from the reactant state to the transition state in common enzymatic reactions. Once substrate binding has occurred, different constraints imposed on the transition states for insertion of R and W nucleotides render it highly unlikely that both transition states can occur in the same closed structure, because the predicted fidelity would then be many orders of magnitude too large. Since the conformational changes reduce the transition state energy of W incorporation drastically they decrease fidelity rather than increase it. Overall, a better agreement with experimental data is attained when the R is incorporated through a transition state in a closed conformation and W is incorporated through a transition state in one or perhaps several partially open conformations. The generation of free energy surfaces for R and W also allow us to analyze proposals about the relationship between induced fit and fidelity.

Convenient, enantioselective hydrosilylation of imines in protic media catalyzed by a Zn-trianglamine complex

Abstract: Chiral hexamine macrocycle derived from trans-1,2-diaminocyclohexane (DACH) in a complex with diethylzinc efficiently catalyzes the asymmetric hydrosilylation of N-phosphorylated aryl-alkyl or aryl-aryl ketimines in protic media with enantiomeric excess of the product approaching 100%. The cyclic structure of the trianglamine ligand increases the enantioselectivity and/or the yield of the reaction, in comparison to the catalysis by acyclic N,N′-dibenzyl-DACH ligands. Density functional theory (DFT) computations on the structure of the model ligand-zinc complex and on the structures of the pre-organized reactants together with the calculations of possible transition states allow rationalization of the direction of the asymmetric induction of the hydrosilylation reaction. This is the first example of asymmetric catalysis of the hydrosilylation reaction of ketimines with the use of a readily available and inexpensive macrocyclic trianglamine ligand.

The azulene-to-naphthalene rearrangement revisited: a DFT study of intramolecular and radical-promoted mechanisms.

Abstract: Intramolecular and radical-promoted mechanisms for the rearrangement of azulene to naphthalene are assessed with the aid of density functional calculations. All intramolecular mechanisms have very high activation energies (≥350 kJ mol-1 from azulene) and so can only be competitive at temperatures above 1000 °C. Two radical-promoted mechanisms, the methylene walk and spiran pathways, dominate the reaction below this temperature. The activation energy for an orbital symmetry-allowed mechanism via a bicyclobutane intermediate is 382 kJ mol-1. The norcaradiene−vinylidene mechanism that has been proposed in order to explain the formation of small amounts of 1-phenyl-1-buten-3-ynes from flash thermolysis of azulene has an activation energy of 360 kJ mol-1; subtle features of the B3LYP/6-31G(d) energy surface for this mechanism are discussed. All intermediates and transition states on the spiran and methylene walk radical-promoted pathways have been located at the B3LYP/6-31G(d) level. Interconversion of all n-H...

Intermetallic NaAu2 as a heterogeneous catalyst for low-temperature CO oxidation.

Abstract: The enhanced stability and modified electronic structure of intermetallic compounds provide discovery of superior catalysts for chemical conversions with high activity, selectivity, and stability We find that the intermetallic NaAu2 is an active catalyst for CO oxidation at low temperatures From density functional theory calculations, a reaction mechanism is suggested to explain the observed low reaction barrier of CO oxidation by NaAu2, in which a CO molecule reacts directly with an adsorbed O2 to form an OOCO* intermediate The presence of surface Na increases the binding energy of O2 and decreases the energy barrier of the transition states