The 9-barbaralyl and related C9H9+ carbocations — A QTAIM-DI-VISAB computational study

2010 ◽  
Vol 88 (11) ◽  
pp. 1195-1204 ◽  
Author(s):  
Nick H. Werstiuk
Keyword(s):  
Quantum Theory ◽  
Computational Study ◽  
Transition States ◽  
Molecular Graphs

QTAIM-DI-VISAB analyses were used to characterize the bonding of the 9-barbaralyl cation, related C9H9+ cations, and rearrangement transition states. These analyses involved obtaining quantum theory of an atom in a molecule (QTAIM) molecular graphs and delocalization indexes (DIs) that were correlated with visualization of the proximities of atomic basins (VISAB). This study provides new insights into the bonding of these species and cements the QTAIM-DI-VISAB analysis as a method of choice for establishing the nature of the bonding in so-called nonclassical carbocations, while obviating the need for dashed-line representations of bonding.

Do aromatic transition states lower barriers to silatropic shifts? A synthetic, NMR spectroscopic, and computational study

1996 ◽  
Vol 251 (1-2) ◽  
pp. 355-364 ◽  
Author(s):  
Suzie S. Rigby ◽  
Hari K. Gupta ◽  
Nick H. Werstiuk ◽  
Alex D. Bain ◽  
Michael J. McGlinchey
Keyword(s):  
Computational Study ◽  
Transition States

QTAIM–DI–VISAB computational study on the Diels–Alder reaction of cyclopentadiene — On the nature of the so-called secondary orbital interactions

2008 ◽  
Vol 86 (7) ◽  
pp. 737-744 ◽  
Author(s):  
Nick Henry Werstiuk ◽  
Wojciech Sokol
Keyword(s):  
Computational Study ◽  
Transition States ◽  
Alder Reaction ◽  
Diels Alder ◽  
Physical Organic Chemistry ◽  
Hydrogen Atoms ◽  
Endo Isomer ◽  
Orbital Interactions ◽  
Physical Organic ◽  
Diels Alder Reaction

We have undertaken a QTAIM–DI–VISAB computational study of the dimerization of cyclopentadiene (1), the archetypal example of a Diels–Alder reaction that has been studied experimentally and computationally. Secondary orbital interactions (SOIs) that have gained acceptance in the interpretation of stereoselectivities seen in many cycloaddition reactions have been used to account for the fact that the endo isomer was the kinetic product of the reaction. To this point, “classical” MO analyses along with a variety of arbitrarily assigned solid and dashed lines (solid lines and bold dashes for “primary” interactions and dashed and dotted lines to differentiate between different SOI schemes) have been used in an attempt to describe the bonding of the transition states. Yet, the existence of SOIs has been challenged. Our interest in applying QTAIM to fundamental chemical problems in physical organic chemistry, with the goal of refining our knowledge of the bonding in transition-states and ground-state molecules while obviating the need to use a variety of confusing arbitrarily assigned dashed and dotted lines, led us to a QTAIM–DI–VISAB computational study of the endo and exo dimerizations of 1 at the DFT B3PW91 and MPW1PW91 levels. We have characterized the bonding interactions between cyclopentadiene rings in the various transition states and show that “normal” bonds are present where SOIs have been considered to exist. There is no need to use different types of dashed and dotted lines. An analysis of the changes in atom energies revealed that the significant destabilization of the carbon atoms in achieving the TSs (potentially leading to a very high barrier) is ameliorated by a stabilization of the hydrogen atoms leading to the relatively low barrier for the D–A reaction.Key words: cyclopentadiene dimerization, bispericyclic transition states, DFT calculations, QTAIM–DI–VISAB analysis, bonding, atom energy analysis.

Computational study of transition states for reaction path of energetic material TKX-50

2019 ◽  
Vol 37 (2) ◽  
pp. 240-250 ◽  
Author(s):  
Miao Li ◽  
Houyang Chen ◽  
Xingqing Xiao ◽  
Li Yang ◽  
Changjun Peng ◽  
...  
Keyword(s):  
Reaction Path ◽  
Computational Study ◽  
Energetic Material ◽  
Transition States

Reversal of π-face selectivity in the Evans aldol reaction with fluoral: A computational study on the transition states using semiempirical calculations

1995 ◽  
Vol 36 (36) ◽  
pp. 6527-6530 ◽  
Author(s):  
Yukihiro Makino ◽  
Katsuhiko Iseki ◽  
Kazuhisa Fujii ◽  
Satoshi Oishi ◽  
Tohru Hirano ◽  
...  
Keyword(s):  
Computational Study ◽  
Aldol Reaction ◽  
Transition States ◽  
Semiempirical Calculations ◽  
Face Selectivity

scholarly journals Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

2020 ◽  
Author(s):  
Klaudia Szeler ◽  
Nicholas Williams ◽  
Alvan C. Hengge ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Alkaline Hydrolysis ◽  
Computational Study ◽  
Transition States ◽  
Building Blocks ◽  
Ester Hydrolysis ◽  
Mechanistic Study ◽  
Phosphate Ester ◽  
Sulfate Ester ◽  
The Impact ◽  
Hydrolysis Of

<div> <div> <div> <p>Phosphate and sulfate esters have important roles as biological building blocks and in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less (in particular computational) work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals and both pure implicit solvation as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider both the impact of how the system is modeled on computed linear free energy relationships (LFER) and the nature of the transition states. Although our calculations consistently underestimate the absolute activation free energies, we obtain good agreement with experimental LFER data when using pure implicit solvent, and excellent agreement with experimental kinetic isotope effects for all models used. Our calculations suggest that the hydrolysis of sulfate diesters proceeds through loose transition states, with minimal bond formation to the nucleophile and with bond cleavage to the leaving group already initiated. Comparison to prior work indicates that these transition states are similar in nature to those of analogous reactions such as the alkaline hydrolysis of neutral arylsulfonate monoesters or charged phosphate diesters and fluorophosphates. Obtaining more detailed insight into the transition states involved assists in understanding the selectivity of enzymes that hydrolyze these reactions; however, this work also highlights the methodological challenges involved in reliably modeling sulfate ester hydrolysis. </p> </div> </div> </div>

scholarly journals Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

2020 ◽  
Author(s):  
Klaudia Szeler ◽  
Nicholas Williams ◽  
Alvan C. Hengge ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Alkaline Hydrolysis ◽  
Computational Study ◽  
Transition States ◽  
Building Blocks ◽  
Ester Hydrolysis ◽  
Mechanistic Study ◽  
Phosphate Ester ◽  
Sulfate Ester ◽  
The Impact ◽  
Hydrolysis Of

<div> <div> <div> <p>Phosphate and sulfate esters have important roles as biological building blocks and in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less (in particular computational) work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals and both pure implicit solvation as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider both the impact of how the system is modeled on computed linear free energy relationships (LFER) and the nature of the transition states. Although our calculations consistently underestimate the absolute activation free energies, we obtain good agreement with experimental LFER data when using pure implicit solvent, and excellent agreement with experimental kinetic isotope effects for all models used. Our calculations suggest that the hydrolysis of sulfate diesters proceeds through loose transition states, with minimal bond formation to the nucleophile and with bond cleavage to the leaving group already initiated. Comparison to prior work indicates that these transition states are similar in nature to those of analogous reactions such as the alkaline hydrolysis of neutral arylsulfonate monoesters or charged phosphate diesters and fluorophosphates. Obtaining more detailed insight into the transition states involved assists in understanding the selectivity of enzymes that hydrolyze these reactions; however, this work also highlights the methodological challenges involved in reliably modeling sulfate ester hydrolysis. </p> </div> </div> </div>

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