scholarly journals Stereoelectronic and Dynamical Effects Dictate Nitrogen Inversion during Valence Isomerism in Benzene Imine

2022 ◽  
Author(s):  
Nilangshu Mandal ◽  
Ankita Das ◽  
Chandralekha Hajra ◽  
Ayan Datta
Keyword(s):  
Quantum Chemical ◽  
Reaction Pathway ◽  
Ring Expansion ◽  
Nitrogen Inversion ◽  
Coupled Reaction

Benzene imine (1) ⇌ 1H-azepine (2) isomerization occurs through sequential valence and endo–exo isomerism. Quantum chemical and quasiclassical trajectory (QCT) simulations reveal the coupled reaction pathway ‒ ring-expansion followed by...

scholarly journals Prebiotic Route to Thymine from Formamide—A Combined Experimental–Theoretical Study

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2248
Author(s):  
Lukáš Petera ◽  
Klaudia Mrazikova ◽  
Lukas Nejdl ◽  
Kristyna Zemankova ◽  
Marketa Vaculovicova ◽  
...  
Keyword(s):  
Formic Acid ◽  
Quantum Chemical ◽  
Prebiotic Chemistry ◽  
Theoretical Study ◽  
Reaction Pathway ◽  
Hydrolysis Product ◽  
Current Paper ◽  
Reaction Conditions ◽  
Chemical Modeling ◽  
Chemistry Research

Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.

scholarly journals Lactamomethylation of alkylphenols: synthesis and quantum-chemical study of the reaction pathway

2021 ◽  
pp. 103424
Author(s):  
Stepan V. Vorobyev ◽  
Olga V. Primerova ◽  
Sergey Yu. Bylikin ◽  
Vladimir N. Koshelev
Keyword(s):  
Quantum Chemical ◽  
Reaction Pathway ◽  
Quantum Chemical Study ◽  
Chemical Study

scholarly journals Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data

2020 ◽  
Author(s):  
Timur Gimadiev ◽  
Ramil Nugmanov ◽  
Dinar Batyrshin ◽  
Timur Madzhidov ◽  
Satoshi Maeda ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Chemical Reaction ◽  
Relational Database ◽  
Quantum Chemical ◽  
Reaction Pathway ◽  
Transition States ◽  
Structural Data ◽  
Database Management System ◽  
Pathway Data ◽  
Machine Learning Applications

Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

scholarly journals Quantum Calculations of VX Ammonolysis and Hydrolysis Pathways via Hydrated Lithium Nitride

2021 ◽  
Vol 22 (16) ◽  
pp. 8653
Author(s):  
Calen J. Leverant ◽  
Chad W. Priest ◽  
Jeffery A. Greathouse ◽  
Mark K. Kinnan ◽  
Susan B. Rempe
Keyword(s):  
Quantum Chemical ◽  
Density Functional ◽  
Reaction Pathway ◽  
Chemical Warfare Agent ◽  
Chemical Warfare ◽  
Quantum Calculations ◽  
Free Energies ◽  
Functional Theory ◽  
Lithium Nitride ◽  
Insight Into

Recently, lithium nitride (Li3N) has been proposed as a chemical warfare agent (CWA) neutralization reagent for its ability to produce nucleophilic ammonia molecules and hydroxide ions in aqueous solution. Quantum chemical calculations can provide insight into the Li3N neutralization process that has been studied experimentally. Here, we calculate reaction-free energies associated with the Li3N-based neutralization of the CWA VX using quantum chemical density functional theory and ab initio methods. We find that alkaline hydrolysis is more favorable to either ammonolysis or neutral hydrolysis for initial P-S and P-O bond cleavages. Reaction-free energies of subsequent reactions are calculated to determine the full reaction pathway. Notably, products predicted from favorable reactions have been identified in previous experiments.

scholarly journals Quantum-chemical study of mechanisms of sulfonation of benzoic and benzenesulfonic acids hydrazides in the gas phase

2020 ◽  
Vol 62 (5) ◽  
pp. 107-115
Author(s):  
Ludmila B. Kochetova ◽  
◽  
Tatyana P. Kustova ◽  
Alyona A. Kruglyakova ◽  
◽  
...  
Keyword(s):  
Transition State ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Potential Energy Surfaces ◽  
Reaction Pathway ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Attack Angle ◽  
Nucleophilic Attack ◽  
Single Transition

Quantum-chemical simulation of the mechanisms of 3-nitrobenzenesulfonyl chloride interaction with benzhydrazide (RHF/6-31G(d)) and benzenesulfohydrazide (DFT//B3LYP/6 311G(d,p)) in the gas phase was carried out. Three-dimensional potential energy surfaces of these processes are calculated in the coordinates of the angle of attack of the nucleophile and the distance between the reacting molecules. It has been established that in the both cases considered, reactions can proceed in the gas phase along a single route, through a single saddle point corresponding to a single transition state; processes begin as an axial attack of nucleophile, which subsequently proceeds with a decrease in the attack angle as the reagents molecules approach each other. It was shown that the both studied processes proceed in accordance with the bimolecular concerted mechanism of nucleophilic substitution SN2, which involves the formation of a single transition state in a reaction pathway and the absence of intermediates on it. Scanning the internal coordinate of benzhydrazide reaction with 3-nitrobenzenesulfonyl chloride made it possible to confirm the reaction route and mechanism of the process pointed out and to clarify the structure of its products and reagents. It was found that the geometric structure of the reaction center in the reactions transition states is medium between the trigonal-bipyramidal and tetragonal-pyramidal, which is due to the change in the nucleophilic attack angle when the reagents molecules approach each other. It was found that in reactions involving hydrazides a “synchronous” transition state is formed in which a new S-N bond is formed simultaneously with the loosening of the old S-Cl bond. The activation energies of the reactions are calculated; they amounted to 173 and 113 kJ/mol, respectively. The high values obtained are explained by the fact that the simulation was carried out for processes occurring in a gas hase. It was shown that the decrease in the activation energy of the reaction involving benzenesulfohydrazide as compared to the benzhydrazide reaction is due to a decrease in steric hindrances during nucleophilic attack created by the lone electron pair of the benzenesulfohydrazide secondary amino group as compared to the benzhydrazide molecule. The calculated values of charges on the nitrogen atoms of the –NH– groups in the hydrazides molecules indicate a weakening of the α-effect upon the transition from benzenesufohydrazide to benzhydrazide.

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