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.

Transition States of Epoxidations: Diradical Character, Spiro Geometries, Transition State Flexibility, and the Origins of Stereoselectivity

Abstract: The transition structures for the epoxidations of ethylene by performic acid, dioxirane, oxaziridine, and peroxynitrous acid have been located with density functional theory methods using the Becke3LYP functional and 6-31G* basis set. All of the epoxidations have spiro transition states; those with performic acid and dioxirane are early and involve synchronous oxygen transfer, while those with oxaziridine and peroxynitrous acid are later with asynchronous oxygen transfer. The results from Becke3LYP/6-31G* theory are compared with MP2/6-31G* literature values. Substitution on ethylene by methoxy, methyl, vinyl, and cyano groups changes the transition state geometries toward asynchronous spiro structures. The activation energies are lowered by all substituents except the cyano group in reactions of performic acid and dioxirane. Experimental stereoselectivities are rationalized by using transition structure models based upon these transition structures.

Activation of C-H and C-C Bonds by an Acidic Zeolite: A Density Functional Study

Abstract: Density functional theory is used to determine transition states and the corresponding energy barriers of the reactions related to C−H bond activation of hydrogen exchange and dehydrogenation of ethane catalyzed by a protonated zeolite as well as hydride transfer between methanol and a methoxide (CH3-zeolite) species. Additionally the C−C bond activation involved in the acid catalyzed cracking reaction of ethane was investigated. The computed activation barriers are 118 for hydrogen exchange, 202 for hydride transfer, 292 for cracking and finally 297 for dehydrogenation, all in kilojoules per mole. For the cracking reaction, two different transition states with the same activation barrier have been obtained, dependent on the approach of the ethane molecule to the zeolite cluster. A study of the relation between acidity and the structure of the zeolite shows that the transition state for the hydrogen exchange reaction is rather covalent and its geometry resembles the well-known carbonium ion, while the oth...

Efficient exploration of reaction paths via a freezing string method.

Abstract: The ability to efficiently locate transition states is critically important to the widespread adoption of theoretical chemistry techniques for their ability to accurately predict kinetic constants. Existing surface walking techniques to locate such transition states typically require an extremely good initial guess that is often beyond human intuition to estimate. To alleviate this problem, automated techniques to locate transition state guesses have been created that take the known reactant and product endpoint structures as inputs. In this work, we present a simple method to build an approximate reaction path through a combination of interpolation and optimization. Starting from the known reactant and product structures, new nodes are interpolated inwards towards the transition state, partially optimized orthogonally to the reaction path, and then frozen before a new pair of nodes is added. The algorithm is stopped once the string ends connect. For the practical user, this method provides a quick and convenient way to generate transition state structure guesses. Tests on three reactions (cyclization of cis,cis-2,4-hexadiene, alanine dipeptide conformation transition, and ethylene dimerization in a Ni-exchanged zeolite) show that this “freezing string” method is an efficient way to identify complex transition states with significant cost savings over existing methods, particularly when high quality linear synchronous transit interpolation is employed.

Toward an alkene hydroamination catalyst: static and dynamic ab initio DFT studies

Abstract: The catalytic hydroamination of alkenes via alkene activation and subsequent nucleophilic attack has been investigated with Car−Parrinello ab initio molecular-dynamics calculations using the projector-augmented wave method. The complete cycle including all intermediates and transition states was studied with d8 transition-metal complexes of the type {MCl(PH3)2}z+ (M = Co, Rh, Ir [z = 0] and Ni, Pd, Pt [z = 1]) as catalysts, comparing the different metals for their suitability. For group 9, nucleophilic attack was identified as the rate-determining step, while the cleavage of the M−C bond is rate-determining for group 10. Overall, group 10 is more favorable than group 9. In particular, nickel complexes were found to be the best-suited potential catalysts with an activation barrier for the rate-determining step of 108 kJ mol-1. β-Hydride elimination as a competing side reaction was found to be kinetically competitive, but thermodynamically disfavored.

Mechanism of Agrobacterium beta-glucosidase: kinetic analysis of the role of noncovalent enzyme/substrate interactions.

Abstract: The role of noncovalent interactions in the catalytic mechanism of the Agrobacterium faecalis beta-glucosidase was investigated by steady-state and pre-steady state kinetic analysis of the hydrolysis of a series of monosubstituted aryl glycosides, in which the hydroxyl groups on the glycone were substituted by hydrogen or fluorine. Contributions of each hydroxyl group to binding of these substrates at the ground state are relatively weak (interaction energies of 3.3 kJ/mol or smaller) but are much greater at the two transition states (glycosylation and deglycosylation). The strongest transition state interactions were at the 2 position (at least 18 and 22 kJ/mol for glycosylation and deglycosylation, respectively) with the interactions at the 3 and 6 positions contributing at least another 9 kJ/mol of binding energy at both transition states. The interaction at the 4 position is less crucial to transition state binding but important for stabilization of the glycosyl-enzyme intermediate. Comparison of observed rates with those for spontaneous hydrolysis of the same substrates provides evidence for oxocarbenium ion character at both transition states, that for deglycosylation apparently having the greater positive charge development at the anomeric center.