scholarly journals New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents

2020 ◽  
Vol 2 ◽  
pp. e4
Author(s):  
Pedro J. Silva
Keyword(s):  
Hydrogen Bonding ◽  
Transition State ◽  
Aromatic Amines ◽  
Density Functional ◽  
Large Scale ◽  
Reaction Pathway ◽  
Reaction Rates ◽  
Functional Study ◽  
Computational Studies ◽  
Charge Delocalization

Extensive computational studies of the imine synthesis from amines and aldehydes in water have shown that the large-scale structure of water is needed to afford appropriate charge delocalization and enable sufficient transition state stabilization. These insights cannot, however, be applied to the understanding of the reaction pathway in apolar solvents due their inability to form extensive hydrogen-bonding networks. In this work, we perform the first computational studies of this reaction in nonpolar conditions. This density-functional study of the reaction of benzaldehyde with four closely related aromatic amines (aniline, o-toluidine, m-toluidine and p-toluidine) shows that, although an additional molecule of amine may provide some stabilization of the first transition state even in the absence of a hydrogen bonding network, this is insufficient to achieve high reaction rates. Our computations also show that when an extra proton is added to the spectator amine, the activation energies become so low that even picomolar amounts of protonated base are enough to achieve realistic rates. Additional computations show that those minute amounts of protonated base may be obtained under reaction conditions without the addition of extraneous acid through the auto-protolysis of the amines themselves. To our knowledge, this is the first report of a role for the auto-protolysis of anilines in their extensive reactional repertoire.

scholarly journals New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents

2019 ◽  
Author(s):  
Pedro J Silva
Keyword(s):  
Transition State ◽  
Aromatic Amines ◽  
Density Functional ◽  
Large Scale ◽  
Reaction Pathway ◽  
Acid Catalyst ◽  
Functional Study ◽  
Computational Studies ◽  
Reaction Conditions ◽  
Polar Solvents

Extensive computational studies of the imine synthesis from amines and aldehydes in water have shown that the large-scale structure of water is needed to afford appropriate charge delocalisation and enable sufficient transition state stabilisation. These insights cannot, however, be applied to the understanding of the reaction pathway in apolar solvents due their inability to form extensive hidrogen-bonding networks. In this work, we perform the first computational studies of this reaction in apolar conditions. This density-functional study of the reaction of benzaldehyde with four closely related aromatic amines (aniline, o-toluidine, m-toluidine and p-toluidine) shows that an additional molecule of amine may provide enough stabilization of the first transition state even in the absence of a hydrogen bonding network. Our computations also show that the second reaction step cannot take place unless an extra proton is added to the system but, crucially, that reaction rate is so high that even picomolar amounts of protonated base are enough to achieve realistic rates. Additional computations show that those minute amounts of protonated base may be obtained under reaction conditions without the addition of extraneous acid through the auto-protolysis of the amines themselves. To our knowledge, this is the first report of a role for the auto-protolysis of anilines in their extensive reactional repertoire.

scholarly journals New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents

2019 ◽  
Author(s):  
Pedro J Silva
Keyword(s):  
Transition State ◽  
Aromatic Amines ◽  
Density Functional ◽  
Large Scale ◽  
Reaction Pathway ◽  
Acid Catalyst ◽  
Functional Study ◽  
Computational Studies ◽  
Reaction Conditions ◽  
Polar Solvents

Extensive computational studies of the imine synthesis from amines and aldehydes in water have shown that the large-scale structure of water is needed to afford appropriate charge delocalisation and enable sufficient transition state stabilisation. These insights cannot, however, be applied to the understanding of the reaction pathway in apolar solvents due their inability to form extensive hidrogen-bonding networks. In this work, we perform the first computational studies of this reaction in apolar conditions. This density-functional study of the reaction of benzaldehyde with four closely related aromatic amines (aniline, o-toluidine, m-toluidine and p-toluidine) shows that an additional molecule of amine may provide enough stabilization of the first transition state even in the absence of a hydrogen bonding network. Our computations also show that the second reaction step cannot take place unless an extra proton is added to the system but, crucially, that reaction rate is so high that even picomolar amounts of protonated base are enough to achieve realistic rates. Additional computations show that those minute amounts of protonated base may be obtained under reaction conditions without the addition of extraneous acid through the auto-protolysis of the amines themselves. To our knowledge, this is the first report of a role for the auto-protolysis of anilines in their extensive reactional repertoire.

scholarly journals Photolysis-induced scrambling of PAHs as a mechanism for deuterium storage

2020 ◽  
Vol 635 ◽  
pp. A9 ◽  
Author(s):  
Sandra D. Wiersma ◽  
Alessandra Candian ◽  
Joost M. Bakker ◽  
Jonathan Martens ◽  
Giel Berden ◽  
...  
Keyword(s):  
Transition State ◽  
Ir Spectra ◽  
Density Functional ◽  
Zero Point ◽  
Reaction Rates ◽  
Ion Cyclotron Resonance ◽  
Point Energy ◽  
Polycyclic Aromatic ◽  
Atom Loss ◽  
Ground State Structures

Aims. We investigate the possible role of polycyclic aromatic hydrocarbons (PAHs) as a sink for deuterium in the interstellar medium (ISM) and study UV photolysis as a potential underlying chemical process in the variations of the deuterium fractionation in the ISM. Methods. The UV photo-induced fragmentation of various isotopologs of deuterium-enriched, protonated anthracene and phenanthrene ions (both C14H10 isomers) was recorded in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Infrared multiple photon dissociation spectroscopy using the Free-Electron Laser for Infrared eXperiments was applied to provide IR spectra. Infrared spectra calculated using density functional theory were compared to the experimental data to identify the isomers present in the experiment. Transition-state energies and reaction rates were also calculated and related to the experimentally observed fragmentation product abundances. Results. The photofragmentation mass spectra for both UV and IRMPD photolysis only show the loss of atomic hydrogen from [D − C14H10]+, whereas [H − C14D10]+ shows a strong preference for the elimination of deuterium. Transition state calculations reveal facile 1,2-H and -D shift reactions, with associated energy barriers lower than the energy supplied by the photo-excitation process. Together with confirmation of the ground-state structures via the IR spectra, we determined that the photolytic processes of the two different PAHs are largely governed by scrambling where the H and the D atoms relocate between different peripheral C atoms. The ∼0.1 eV difference in zero-point energy between C–H and C–D bonds ultimately leads to faster H scrambling than D scrambling, and increased H atom loss compared to D atom loss. Conclusions. We conclude that scrambling is common in PAH cations under UV radiation. Upon photoexcitation of deuterium-enriched PAHs, the scrambling results in a higher probability for the aliphatic D atom to migrate to a strongly bound aromatic site, protecting it from elimination. We speculate that this could lead to increased deuteration as a PAH moves towards more exposed interstellar environments. Also, large, compact PAHs with an aliphatic C–HD group on solo sites might be responsible for the majority of aliphatic C–D stretching bands seen in astronomical spectra. An accurate photochemical model of PAHs that considers deuterium scrambling is needed to study this further.

scholarly journals Large-Scale Density Functional Theory Transition State Searching in Enzymes

2014 ◽  
Vol 5 (21) ◽  
pp. 3614-3619 ◽  
Author(s):  
Greg Lever ◽  
Daniel J. Cole ◽  
Richard Lonsdale ◽  
Kara E. Ranaghan ◽  
David J. Wales ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Density Functional ◽  
Large Scale ◽  
Functional Theory

Density functional study of the hydrogen bonding: H2O·HO

1999 ◽  
Vol 303 (1-2) ◽  
pp. 96-100 ◽  
Author(s):  
Baoshan Wang ◽  
Hua Hou ◽  
Yueshu Gu
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Functional Study ◽  
Density Functional Study

scholarly journals The effect of magnesium ions on triphosphate hydrolysis

2017 ◽  
Vol 89 (6) ◽  
pp. 715-727 ◽  
Author(s):  
Alexandre Barrozo ◽  
David Blaha-Nelson ◽  
Nicholas H. Williams ◽  
Shina C. L. Kamerlin
Keyword(s):  
Transition State ◽  
Metal Ions ◽  
Density Functional ◽  
Reaction Pathway ◽  
Enzymatic Reaction ◽  
Phosphate Ester ◽  
Mechanistic Pathway ◽  
Phosphate Hydrolysis ◽  
The Impact

AbstractThe role of metal ions in catalyzing phosphate ester hydrolysis has been the subject of much debate, both in terms of whether they change the transition state structure or mechanistic pathway. Understanding the impact of metal ions on these biologically critical reactions is central to improving our understanding of the role of metal ions in the numerous enzymes that facilitate them. In the present study, we have performed density functional theory studies of the mechanisms of methyl triphosphate and acetyl phosphate hydrolysis in aqueous solution to explore the competition between solvent- and substrate-assisted pathways, and examined the impact of Mg2+ on the energetics and transition state geometries. In both cases, we observe a clear preference for a more dissociative solvent-assisted transition state, which is not significantly changed by coordination of Mg2+. The effect of Mg2+ on the transition state geometries for the two pathways is minimal. While our calculations cannot rule out a substrate-assisted pathway as a possible solution for biological phosphate hydrolysis, they demonstrate that a significantly higher energy barrier needs to be overcome in the enzymatic reaction for this to be an energetically viable reaction pathway.

Mechanism of the addition of alkynes to silenes and germenes: A density functional study

2015 ◽  
Vol 93 (1) ◽  
pp. 134-142 ◽  
Author(s):  
Laura C. Pavelka ◽  
Margaret A. Hanson ◽  
Viktor N. Staroverov ◽  
Kim M. Baines
Keyword(s):  
Experimental Data ◽  
Density Functional Theory ◽  
Density Functional ◽  
Reaction Pathway ◽  
Cluster Method ◽  
Functional Study ◽  
Coupled Cluster ◽  
Computational Results ◽  
Coupled Cluster Method ◽  
Functional Theory

Density functional theory (DFT) and the coupled cluster method have been used to study the mechanism of the cycloaddition of acetylene to silene, H2Si=CH2, and germene, H2Ge=CH2, at the B3LYP/6-311++G(d,p) and CCSD/6-311++G(d,p) levels of theory. Diradical, zwitterionic, and concerted pathways were located for both metallenes. The computational results were compared to experimental data to propose the most likely reaction pathway for each metallene.

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