ChemInform Abstract: Synthesis Applications of Cationic Aza-Cope Rearrangements. Part 17. Transition-State Geometry of (3,3)-Sigmatropic Rearrangements of Iminium Ions.

ChemInform ◽  
1988 ◽  
Vol 19 (25) ◽  
Author(s):  
R. J. DOEDENS ◽  
G. P. MEIER ◽  
L. E. OVERMAN
Keyword(s):  
Transition State ◽  
Sigmatropic Rearrangements ◽  
Iminium Ions ◽  
Transition State Geometry ◽  
Cope Rearrangements

scholarly journals Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

2017 ◽  
Vol 13 ◽  
pp. 1969-1976 ◽  
Author(s):  
José Enrique Barquera-Lozada ◽  
Gabriel Cuevas
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Density Functional ◽  
Chair Conformation ◽  
High Energy ◽  
Functional Theory ◽  
Sigmatropic Rearrangements ◽  
The Density Functional Theory ◽  
Reaction Proceeds ◽  
Cope Rearrangements

It has been proposed that elemanes are biogenetically formed from germacranes by Cope sigmatropic rearrangements. Normally, this reaction proceeds through a transition state with a chair conformation. However, the transformation of schkuhriolide (germacrane) into elemanschkuhriolide (elemane) may occur through a boat transition state due to the final configuration of the elemanschkuhriolide, but this transition state is questionable due to its high energy. The possible mechanisms of this transformation were studied in the density functional theory frame. The mechanistic differences between the transformation of (Z,E)-germacranes and (E,E)-germacranes were also studied. We found that (Z,E)-germacranolides are significantly more stable than (E,E)-germacranolides and elemanolides. In the specific case of schkuhriolide, even when the boat transition state is not energetically favored, a previous hemiacetalization lowers enough the energetic barrier to allow the formation of a very stable elemanolide that is even more stable than its (Z,E)-germacrane.

scholarly journals Advances in Automated Transition State Theory Calculations: Improvements on the AutoTST Framework

2020 ◽  
Author(s):  
Nathan Harms ◽  
Carl Underkoffler ◽  
Richard West
Keyword(s):  
Transition State ◽  
Kinetic Parameters ◽  
Transition State Theory ◽  
Vibrational Analysis ◽  
Chemical Kinetic ◽  
State Theory ◽  
Combustion Chemistry ◽  
Transition State Geometry ◽  
Substantial Progress ◽  
Symmetry Number

<div>Kinetic modeling of combustion chemistry has made substantial progress in recent years with the development of increasingly detailed models. However, many of the chemical kinetic parameters utilized in detailed models are estimated, often inaccurately. To help replace rate estimates with more accurate calculations, we have developed AutoTST, an automated Transition State Theory rate calculator. This work describes improvements to AutoTST, including: a systematic conformer search to find an ensemble of low energy conformers, vibrational analysis to validate transition state geometries, more accurate symmetry number calculations, and a hindered rotor treatment when deriving kinetics. These improvements resulted in location of transition state geometry for 93% of cases and generation of kinetic parameters for 74% of cases. Newly calculated parameters agree well with benchmark calculations and perform well when used to replace estimated parameters in a detailed kinetic model of methanol combustion.</div>

scholarly journals The interplay of electrostatic fields and binding interactions determining catalytic-site reactivity in actinidin. A possible origin of differences in the behaviour of actinidin and papain

1989 ◽  
Vol 259 (2) ◽  
pp. 443-452 ◽  
Author(s):  
D Kowlessur ◽  
M O'Driscoll ◽  
C M Topham ◽  
W Templeton ◽  
E W Thomas ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Ligand Binding ◽  
Transition State ◽  
Rate Constant ◽  
Ph Dependence ◽  
Order Rate Constant ◽  
Catalytic Site ◽  
Binding Interactions ◽  
Electrostatic Fields ◽  
Transition State Geometry

1. The pH-dependence of the second-order rate constant (k) for the reaction of actinidin (EC 3.4.22.14) with 2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide was determined and the contributions to k of various hydronic states were evaluated. 2. The data were used to assess the consequences for transition-state geometry of providing P2/S2 hydrophobic contacts in addition to hydrogen-bonding opportunities in the S1-S2 intersubsite region. 3. The P2/S2 contacts (a) substantially improve enzyme-ligand binding, (b) greatly enhance the contribution to reactivity of the hydronic state bounded by pKa 3 (the pKa characteristic of the formation of catalytic-site-S-/-ImH+ state) and pKa 5 (a relatively minor contributor in reactions that lack the P2/S2 contacts), such that the major rate optimum occurs at pH 4 instead of at pH 2.8-2.9, and (c) reveal the kinetic influence of a pKa approx. 6.3 not hitherto observed in reactions of actinidin. 4. Possibilities for the interplay of electrostatic effects and binding interactions in both actinidin and papain (EC 3.4.22.2) are discussed.

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