Search results for "Transition state"
showing 10 items of 85 documents
An ab initio study on the mechanism of the F+O3→FO+O2 reaction: comparative reactivity study along the isoelectronic NH2, OH and F radicals series
2004
Abstract The title reaction has been theoretically studied by using MP2, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. At single-reference MP2 and QCISD levels of theory, the potential energy hypersurface (HPES) shows a two-step reaction mechanism through two transition states (TS1 and TS2) and an intermediate (Int). However, the multiconfigurational CASSCF HPES shows a one-step reaction mechanism, as was previously found for the NH2 + O3 and OH + O3 reactions. The results show that the reactivity of the isoelectronic series of NH2, OH, and F radicals increases from the amino radical to the fluorine atom.
Ab initiostudy of the mechanism of the atmospheric reaction: NO2+ O3→ NO3+ O2
2003
The atmospheric reaction NO2 + O3 --> NO3 + O2 (1) has been investigated theoretically by using the MP2, G2, G2Q, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. The results show that the reaction pathway can be divided in two different parts at the MP2 level of theory. At this level, the mechanism proceeds along two transition states (TS1 and TS2) separated by an intermediate, designated as A. However, when the single-reference higher correlated QCISD methodology has been employed, the minimum A and the transition state TS2 are not found on the hypersurface of potential energy, which confirms a direct reaction mechanism. Single-reference high correlated and mu…
Oxygen Incorporation Reaction into Mixed Conducting Perovskites: a Mechanistic Analysis for (La,Sr)MnO3 Based on DFT Calculations
2009
Based on DFT calculations of intermediates and transition states, several hypothetical mechanisms for oxygen incorporation into mixed conducting La1-xSrxMnO3{plus minus}d perovskites are discussed. In the most probable mechanism, the rate-determining step comprises the encounter of a highly mobile surface oxygen vacancy and a molecular oxygen adsorbate. Starting from these results, the variation of reaction rates for different materials is explored.
Understanding the influence of lewis acids in the regioselectivity of the diels-alder reactions of 2-methoxy-5-methyl-1,4-benzoquinone: a dft study
2009
The mechanisms of the Diels–Alder (DA) reactions of 2-methoxy-5-methyl-1,4-benzoquinone 1 with 2-methyl-1,3-butadiene 2, in the absence and in the presence of LA catalysts, have been studied using the DFT method at the B3LYP/6-31G(d) level of theory. The uncatalyzed DA reactions between 1 and 2 take place via synchronous concerted TSs. The large activation barrier as well as the low stereo and regioselectivity associated with the uncatalyzed process are in clear agreement with the non-polar character of the cycloaddition. Coordination of the LA catalysts, BF3 or SnCl4, to the oxygen atoms of the benzoquinone 1 produces a large acceleration of the reaction, which can be associated with the l…
First Principles Calculations of Oxygen Vacancy Formation and Migration in Ba1−xSrxCo1−yFeyO3−δPerovskites
2011
Based on first principles DFT calculations, we analyze oxygen vacancy formation and migration energies as a function of chemical composition in complex multicomponent (Ba,Sr)(Co,Fe)O3−δ perovskites which are candidate materials for SOFC cathodes and permeation membranes. The atomic relaxation, electronic charge redistribution and energies of the transition states of oxygen migration are compared for several perovskites to elucidate the atomistic reason for the exceptionally low migration barrier in Ba0.5Sr0.5Co0.8Fe0.2O3−δ that was previously determined experimentally. The critical comparison of Ba1−xSrxCo1−yFeyO3−δ perovskites with different cation compositions and arrangements shows that …
Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis.
2006
Glycine N-methyltransferase (GNMT) is an S-adenosyl-l-methionine dependent enzyme that catalyzes glycine transformation to sarcosine. Here, we present a hybrid quantum mechanics/molecular mechanics (QM/MM) computational study of the reaction compared to the counterpart process in water. The process takes place through an SN2 mechanism in both media with a transition state in which the transferring methyl group is placed in between the donor (SAM) and the acceptor (the amine group of glycine). Comparative analysis of structural, electrostatic, and electronic characteristics of the in-solution and enzymatic transition states allows us to get a deeper insight into the origins of the enzyme's c…
Conformationally Locked Pyramidality Explains the Diastereoselectivity in the Methylation of trans-Fused Butyrolactones
2020
A stereoselectivity model inspired by the total synthesis of stemona alkaloids is developed to explain why enolate-derived 3,4-fused butyrolactones are methylated with a preference for syn alkylation. The model shows how conformational locking present in nonplanar enolate structures favors syn over anti methylation, due to less significant structural distortions in the syn pathway. The developed model was also successfully used to rationalize selectivities of previously documented methylation reactions. peerReviewed
Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step.
2015
Highlights • The possible role of enzymatic reaction dynamical effects is examined. • Solution reactions usefully inform the issue of dynamical effects in enzymes. • Division into regions containing and away from the transition state is important. • Motions in passage to/from the transition state need not lead to dynamical effects. • Transition State Theory is usually a reasonable description of enzyme kinetics.
N-Benzyl Residues as the P1′ Substituents in Phosphorus-Containing Extended Transition State Analog Inhibitors of Metalloaminopeptidases
2020
Peptidyl enzyme inhibitors containing an internal aminomethylphosphinic bond system (P(O)(OH)-CH2-NH) can be termed extended transition state analogs by similarity to the corresponding phosphonamidates (P(O)(OH)-NH). Phosphonamidate pseudopeptides are broadly recognized as competitive mechanism-based inhibitors of metalloenzymes, mainly hydrolases. Their practical use is, however, limited by hydrolytic instability, which is particularly restricting for dipeptide analogs. Extension of phosphonamidates by addition of the methylene group produces a P-C-N system fully resistant in water conditions. In the current work, we present a versatile synthetic approach to such modified dipeptides, based…
A DFT Study of the [3+2] Cycloadditions of RCNO (R = H, Me and F) With Carbon Flatland Mimicking Graphene
2012
Graphene is the latest allotrope of carbon to be under the spotlight ever since its discovery by Novoselov and coworkers in 2004. Owing to its fascinating structural, electrical, optical, mechanical and thermal properties, graphene can be regarded as as a rapidly rising star in various fields such as supercapacitors, biosensors and batteries. The organic chemistry of graphene has stimulated a great deal of research and is gaining considerable attention. Among the various experimental studies which have been carried out on graphene, it is found that [3+2] cycloadditions (32CA) can also be achieved on graphene sheets and the resulting functionalized graphenes are dispersible in polar organic …