Search results for "Transition state"

The transition state and cognate concepts

2019

Abstract This review aims firstly to clarify the meanings of key terms and concepts associated with the idea of the transition state, as developed by theoreticians and applied by experimentalist, and secondly to provide an update to the meaning and significance of the transition state in an era when computational simulation, in which complexity is being increasingly incorporated, is commonly employed as a means by which to bridge the realms of theory and experiment. The relationship between the transition state and the potential-energy surface for an elementary reaction is explored, with discussion of the following terms: saddle point, minimum-energy reaction path, reaction coordinate, acti…

Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase

2017

Here we report a study of the effect of heavy isotope labeling on the reaction catalyzed by human purine nucleoside phosphorylase (hPNP) to elucidate the origin of its catalytic effect and of the enzymatic kinetic isotope effect (EKIE). Using quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, we study the mechanism of the hPNP enzyme and the dynamic effects by means of the calculation of the recrossing transmission coefficient. A free energy surface (FES), as a function of both a chemical and an environmental coordinate, is obtained to show the role of the environment on the chemical reaction. Analysis of reactive and nonreactive trajectories allows us …

Arene C−H Activation at Aluminium(I): meta Selectivity Driven by the Electronics of S N Ar Chemistry

2020

The reactivity of the electron-rich anionic Al(I) ('aluminyl') compound K 2 [(NON)Al] 2 (NON = 4,5-bis(2,6-diisopropylanilido)-2,7-di- tert -butyl-9,9-dimethylxanthene) towards mono- and disubstituted arenes is reported. C-H activation chemistry with n -butylbenzene gives exclusively the product of activation at the arene meta position. Mechanistically, this transformation proceeds in a single step via a concerted Meisenheimer-type transition state. Selectivity is therefore based on similar electronic factors to classical S N Ar chemistry, which implies the destabilization of transition states featuring electron-donating groups in either the ortho or the para positions. In the cases of tolu…

The photochemistry of mono- and dinuclear cyclometalated bis(tridentate)ruthenium(ii) complexes: dual excited state deactivation and dual emission

2016

The synthesis and characterization of a series of weakly emissive mononuclear cyclometalated [Ru(dpb-R)(tpy)](+) complexes with functional groups R of varying electron-donating characters at the dpb ligand are described (dpbH = 1,3-di(2-pyridyl)benzene, tpy = 2,2';6',2''-terpyridine, 1(+): R = NHCOMe, 2(+): R = NH2, 3(+): R = COOEt, 4(+): R = COOH). Steady-state emission spectroscopy in the temperature range between 298 K and 77 K revealed a previously unrecognized excited state deactivation pathway via low-lying triplet ligand-to-ligand ((3)LL'CT) charge transfer states in addition to the well-known pathway via(3)MC states. Thermal activation barriers for depopulation of the emissive metal…

Theoretical investigation of the spin crossover transition states of the addition of methane to a series of Group 6 metallocenes using minimum energy…

2016

International audience; Density functional calculations are reported on the addition of methane to Group 6 metallocenes, M(η-C5H5)2 (M), M(CH2(η-C5H4)2) (a-M) and M(η-C5Me5)2 (M*) where M = Mo and W. Full geometry optimisations were carried out on the singlet and triplet 16 electron complexes, 1[M] and 3[M], the η2-methane complexes, 1[M(η2-CH4)], and the hydridomethyl adducts, 1[M(CH3)(H)]. The triplet state for [M] was found to be more stable for all six metallocenes, the difference being least in the case of the ansa-bridged system. Formation of the hydridomethyl complexes was exoenergetic for all tungsten systems and for a-Mo, the other two Mo systems being endoenergetic. Minumum energy…

2018

The origin of substrate preference in promiscuous enzymes was investigated by enzyme isotope labelling of the alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH). At physiological temperature, protein dynamic coupling to the reaction coordinate was insignificant. However, the extent of dynamic coupling was highly substrate-dependent at lower temperatures. For benzyl alcohol, an enzyme isotope effect larger than unity was observed, whereas the enzyme isotope effect was close to unity for isopropanol. Frequency motion analysis on the transition states revealed that residues surrounding the active site undergo substantial displacement during catalysis for sterically bulky alcohol…

Diastereoselective synthesis of 6-functionalized 4-aryl-1,3-oxazinan-2-ones and their application in the synthesis of 3-aryl-1,3-aminoalcohols and 6-…

2010

Abstract Halocyclocarbamation of benzyl N -(1-phenyl-3-butenyl)carbamates afforded 6-functionalized 4-aryl-1,3-oxazinan-2-ones with moderate to excellent diastereoselectivity depending on the N -substituent. Importantly, in contrast to reported cyclocarbamations of homoallylic carbamates, which are generally trans -diastereoselective, cyclization of N -unsubstituted Cbz-protected homoallylamines led to cis -1,3-oxazinan-2-ones, predominantly. The use of N -benzylated and in situ prepared N -silylated derivatives resulted however in trans -selectivity. Transition states are proposed to explain the stereochemical influence of the N -substituent on the cyclocarbamations. The functionalized 1,3…

Confined But-2-ene catalytic isomerization inside H-ZSM-5 models: A DFT study

2015

The isomerization of cis-but-2-ene to trans-but-2-ene within a 22T H-ZSM-5 zeolite model, also in the presence of two adsorbed Pd atoms, has been studied by DFT calculations. The results obtained allow us to state that the cis/trans but-2-ene isomerization can easily proceed inside unsupported zeolite cavities. In this case, differently than in the gas phase reaction, the trans-but-2-ene is less stable than the cis-but-2-ene, when adsorbed on the zeolite inner surface. Excluding the adsorption-desorption steps, the isomerization process involves two intermediates and three transition states, whose energy content is always very low with respect to that of reagents and intermediate species. T…

Theozyme for antibody aldolases. Characterization of the transition-state analogueElectronic supplementary information (ESI) available: MP2/6-31G** e…

2003

A theozyme for antibody aldolases has been studied at the MP2/6-31G** computational level. Formation of two cooperative hydrogen-bonds between the acidic hydrogen atoms of the enamine and of a methanol molecule with the oxygen atom of the aldol acceptor markedly favors the C–C bond-formation associated with the aldol reaction. A comparative analysis of the geometry, the charge distribution and the shape of the molecular electrostatic potential of the transition structure (TS) with the covalent adduct, resulting from the reaction of methylamine and the β-diketone used as a hapten allows us to characterize the transition-state analogue (TSA) generated at immunization. This finding allows us t…

Ring splitting of azetidin-2-ones via radical anions

2012

The radical anions of azetidin-2-ones, generated by UV-irradiation in the presence of triethylamine, undergo ring-splitting via N-C4 or C3-C4 bond breaking, leading to open-chain amides. This reactivity diverges from that found for the neutral excited states, which is characterised by alpha-cleavage. The preference for beta-cleavage is supported by DFT theoretical calculations on the energy barriers associated with the involved transition states. Thus, injection of one electron into the azetidin-2-one moiety constitutes a complementary activation strategy which may be exploited to produce new chemistry.