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.

The ultraviolet photodissociation dynamics of d1‐vinyl chloride

Abstract: We have used partially deuterated vinyl chloride to elucidate the photodissociation mechanism of this molecule. We have found that 75% of the HCl fragments are produced by three‐center α,α elimination. Surprisingly, the rotational energy distributions of HCl are the same for both elimination pathways. One possible explanation is that H atom migration in the parent molecule results in similar transition states for the two pathways. Alternatively, dissociation and fragment isomerization may be strongly coupled so that the product angular momentum distribution is determined late in the reaction coordinate. Very different rotational state distributions were observed for v‘=0 and v‘≳0. We speculate that this dichotomy is caused by formation of a hydrogen‐bonded π complex between HCl(v‘≳0) and acetylene. We have also determined that HCl+ ions are produced primarily by an α,β mechanism. This mechanism consists of electronic excitation of vinyl chloride, followed by photoelimination and photoionization of electronically excited HCl*. Finally, we determined that H atoms are preferentially produced by detachment from the β carbon, as predicted from the relative stabilities of the α‐ and β‐chlorovinyl radicals.

Ab initio study of the SN2 reactions of hydroxide and hydroperoxide with chloromethane

Abstract: Ab initio molecular orbital calculations have been used to determine energy profiles for the S/sub N/2 reactions of hydroxide and hydroperoxide anions with methyl chloride. Geometry optimizations were carried out at the Hartree-Fock level with the 6-31 +G(d) basis set. These calculations were supplemented by computations of the correlation energy with second and third-order Moeller-Plesset theory. Though the reactions are exothermic by 40-50 kcal/mol, both are found to have the double-well energy surfaces characteristic of gas-phase S/sub N/2 reactions. At the Hartree-Fock level the central barrier heights are 2.9 and 4.1 kcal/mol for OH/sup -/ and OOH/sup -/, and the transition states are 12.4 and 9.7 kcal/mol lower in energy than the reactants. Electron correlation raises the barrier by 2.1 kcal/mol for OH/sup -/, but it has much larger effects on the overall exothermicities. Vibrational energy changes are found to be less than 1.5 kcal/mol up to the transition state. The geometrical results for the ion-molecule complexes and transition states are discussed and show a somewhat later transition state for the reaction with hydroperoxide ion. The results are consistent with experimental observations including the lower reactivity of OOH/sup -/ than OH/sup -/ in the gas phase. Experimental and theoretical datamore » are also combined to consider energy profiles for S/sub N/2 reactions in aqueous solution.« less

Phosphate ester hydrolysis: calculation of gas-phase reaction paths and solvation effects

Abstract: Quantum-mechanical and solvation-effect calculations of the hydrolysis mechanism of dimethyl and ethylene phosphate, which are model compounds for the hydrolysis of DNA and RNA, respectively, are reported and used to explain the fact that in solution, five-membered-ring cyclic phosphates hydrolyse 106–108 times faster than acyclic esters. Ab initio energy profiles for the base-catalysed hydrolysis (i.e. attack by OH–) of dimethyl and ethylene phosphate are determined at the Hartree–Fock level and with MP2 correlation corrections. The reaction proceeds through the formation of a pentacovalent phosphorane transition state with attack by the hydroxide ion as the rate-determining step; stable phosphorane intermediates are not observed in the gas phase. A detailed analysis is made of the ring strain in the cyclic phosphate reactant, which had been proposed as the origin of the observed rate effect and the results for the reactants are compared with those for the transition state. Although there is strain in the ground state of the cyclic reactant, it does not contribute to the rate acceleration because of dihedral angle constraints present in the cyclic transition state. An estimate of solvation effects indicates that most of the rate acceleration observed in solution arises from differential solvation of the transition states.

Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.

Abstract: The inhibition mechanism of matrix metalloproteinase 2 (MMP2) by the selective inhibitor (4-phenoxyphenylsulfonyl)methylthiirane (SB-3CT) and its oxirane analogue is investigated computation- ally. The inhibition mechanism involves C-H deprotonation with concomitant opening of the three- membered heterocycle. SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part and the AMBER force field for the MM part were used to examine the reaction of these two inhibitors in the active site of MMP2. The calculationsshowthatthereactionbarrierfortransformationofSB-3CTis1.6kcal/mollowerthanitsoxirane analogue, and the ring-opening reaction energy of SB-3CT is 8.0 kcal/mol more exothermic than that of its oxirane analogue. Calculations also show that protonation of the ring-opened product by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane than for the thiolate obtained from the thiirane. A six-step partial charge fitting procedure is introduced for the QM/MM calculations to update atomic partial charges of the quantum mechanics region and to ensure consistent electrostatic energies for reactants, transition states, and products.