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.

Will water act as a photocatalyst for cluster phase chemical reactions? Vibrational overtone-induced dehydration reaction of methanediol.

Abstract: The possibility of water catalysis in the vibrational overtone-induced dehydration reaction of methanediol is investigated using ab initio dynamical simulations of small methanediol-water clusters. Quantum chemistry calculations employing clusters with one or two water molecules reveal that the barrier to dehydration is lowered by over 20 kcal/mol because of hydrogen-bonding at the transition state. Nevertheless, the simulations of the reaction dynamics following OH-stretch excitation show little catalytic effect of water and, in some cases, even show an anticatalytic effect. The quantum yield for the dehydration reaction exhibits a delayed threshold effect where reaction does not occur until the photon energy is far above the barrier energy. Unlike thermally induced reactions, it is argued that competition between reaction and the irreversible dissipation of photon energy may be expected to raise the dynamical threshold for the reaction above the transition state energy. It is concluded that quantum chemistry calculations showing barrier lowering are not sufficient to infer water catalysis in photochemical reactions, which instead require dynamical modeling.

The energy gap as a universal reaction coordinate for the simulation of chemical reactions.

Abstract: The selection of a proper reaction coordinate is a major bottleneck in simulations of chemical reactions in complex systems. Increasing the number of variables that are used to bias the reaction largely affects the convergence and leads to an unbearable increase in computational price. This problem can be overcome by employing a complex reaction coordinate that depends on many geometrical variables of the system, such as the energy gap (EGAP) in the empirical valence bond (EVB) method. EGAP depends on all of the coordinates of the system, and its robustness has been demonstrated for a variety of enzymatic reactions. In this work, we demonstrate that EGAP, derived from a classical representation, can be used as a reaction coordinate in systems described with any quantum chemistry Hamiltonian. Benefits of using EGAP as a reaction coordinate as compared to a traditional geometrical variable are illustrated in the case of a symmetric nucleophilic substitution reaction in water solution. EGAP is shown to provide a significantly more efficient sampling and allows a better localization of the transition state as compared to a geometrical reaction coordinate.

Retro-Diels-Alder reaction of 4H-1,2-benzoxazines to generate o-quinone methides: involvement of highly polarized transition states.

Abstract: Here, we describe mechanistic studies of the retro-Diels−Alder reaction of 4H-1,2-benzoxazines bearing various substituents on the benzene ring. 4H-1,2-Benzoxazines are very simple, but quite new, heterocyclic compounds that afford substituted o-quinone methides (o-QMs) through retro-Diels−Alder reaction under mild thermal conditions. The resultant o-QMs undergo Diels−Alder reaction in situ with dienophiles to give phenol and chroman derivatives. The mechanism of the generation of o-QMs has been little studied. Our experimental and density functional theory (DFT) studies have yielded the following results. (1) The generation of o-QMs, i.e., the retro-hetero-Diels−Alder reaction of 4H-1,2-benzoxazines, is rate determining, rather than the subsequent Diels−Alder reaction of the resultant o-QM with dienophiles. (2) The reaction rate is strongly influenced by the electronic features of substituents and the polarity of the solvent. The reaction proceeds faster in a polar solvent such as dimethyl sulfoxide, pro...

Basic questions in mass spectrometry

Abstract: The unimolecular dissociation of ionized molecules seldom consists in a direct bond cleavage where the reaction coordinate can be adequately represented by a simple bond stretch. The coordinate which controls the progress of the reaction is not always the reaction coordinate (defined as the degree of freedom whose extension leads to spatial separation of the molecular fragments). The specificity of a dissociation mechanism in a polyatomic species is due to its inherently multidimensional character, i.e. it requires participation of several degrees of freedom. It often consists of a sequence of elementary steps and is therefore controlled by several bottlenecks. The complicated and multistep nature of the reaction mechanism results in a natural tendency towards energy randomization. Radiationless transition from the initial upper electronic states to the ground state of the ion is not always very fast with respect to dissociation. A unimolecular reaction should be seen as a flux in phase space through a critical surface. A transition state corresponds to a surface of least flux, i.e. to a bottleneck of the reaction. For a given elementary step, several may exist, whose positions may vary with energy. The nature of these transition states is not immediately obvious. For instance, they do not necessarily coincide with saddle points or with rotational barriers.