Theoretical Calculations of the Multistep Reaction Mechanism Involved in Asparagine Pyrolysis Supported by Degree of Rate Control and Thermodynamic Control Analyses

A computational study on the mechanisms of reaction for the pyrolysis of asparagine is presented. A density functional theory (DFT) study at the ωB97XD/6-311G(d,p) level was performed to analyze the differences in two reaction mechanisms: (i) the formation of five-membered cyclic products: maleimide and succinimide, and (ii) the more classical, six-membered cyclic products (diketopiperazine species) which are common in the pyrolysis of many other amino acids. The effect of temperature was included in the calculations at 300 °C or 625 °C, as required. Moreover, a detailed study based on the degree of rate control and thermodynamic control of the proposed mechanism for the formation of maleimide and succinimide is also presented. Results show that, for asparagine, the five-membered ring formation is the preferred process instead of the six-membered cycle (32 kJ/mol of Gibbs free energy difference between them at the first cyclization step); therefore, the polymerization is favored. On the other hand, the rupture of the polymer represents the highest energetic barrier (ΔG‡ = 281 kJ/mol) and the most influential process in the overall rate of the reaction. These results are in good agreement with the experimental evidence.

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Understanding the Lack of Reactivity of 2,4-Dihydroxybenzaldehyde Towards the Biginelli Adduct Using Density Functional Theory Molecular Modeling

Processes ◽

10.3390/pr7080521 ◽

2019 ◽

Vol 7 (8) ◽

pp. 521

Author(s):

Virginia Flores-Morales ◽

Eduardo D. Ayala-Medrano ◽

José García-Elías ◽

Margarita L. Martínez-Fierro ◽

Edgar Marquez ◽

...

Keyword(s):

Density Functional ◽

Natural Bond Orbital ◽

Activation Enthalpy ◽

Computational Study ◽

Theoretical Calculations ◽

Condensation Reaction ◽

Biginelli Reaction ◽

Hydroxyl Group ◽

Functional Theory ◽

Multiple Substitution

The Biginelli reaction is a multicomponent reaction for obtaining dihydropyrimidinthiones quickly, with multiple substitution patterns. The reaction mechanism remains unclear. Three possible pathways proposed for the reaction are the iminium route, an enamine intermediate, and the Knoevenagel pathway. However, when thiourea was used, no theoretical calculations were reported. Thus, based on the literature, the iminium pathway was used to obtain evidence explaining the lack of reactivity of 2,4-dihydroxybenzaldehyde towards the Biginelli adduct, compared with 4-hydroxybenzaldehyde. This computational study, carried out using the B3LYP/6-31++G(d,p) level of theory, showed an increment of 150 kJ/mol in the activation energy of the slowest pathway, due to the presence of a hydroxyl group in position 2 (ortho) of the aromatic aldehyde, decreasing its reactivity. Natural bond orbital (NBO) calculations suggest that the determinant steps are simultaneous, i.e., the polarization of the carbonyl group and its corresponding protonation by the hydrogen of the SH fragment of the thiourea tautomer. The activation enthalpy values suggest that the nucleophile attack takes place later on the compound 2,4-dihydroxybenzaldehyde compared to 4-hydroxybenzaldehyde-TS, confirming that the OH group in position 2 hinders the condensation reaction.

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Distribution of Al and adsorption of NH3 and pyridine in ZSM-12: a computational study

Canadian Journal of Chemistry ◽

10.1139/cjc-2013-0135 ◽

2013 ◽

Vol 91 (10) ◽

pp. 925-934 ◽

Cited By ~ 16

Author(s):

Gang Feng ◽

Ying-Ying Lian ◽

Deqin Yang ◽

Jianwen Liu ◽

Dejin Kong

Keyword(s):

Density Functional Theory ◽

Lewis Acid ◽

Density Functional ◽

Computational Study ◽

Energy Difference ◽

Acid Sites ◽

Main Channel ◽

Lewis Acid Sites ◽

Small Energy ◽

Functional Theory

The distribution of Al and the adsorption of NH3 and pyridine in both Na-form and H-form ZSM-12 were investigated using dispersion-corrected density functional theory. It was found that the energy differences for Al atoms in the different T sites of ZSM-12 (both H form and Na form) were less than 0.3 eV, which indicates that the Al atoms could distribute in all kinds of T sites in ZSM-12. In addition, the small energy difference indicates that both H and Na atoms could stay in either the small cage or the main channel of ZSM-12. The adsorption of NH3 and pyridine on NaZSM-12 is weak, while the adsorption of NH3 and pyridine on HZSM-12 is strong, as they could form NH4+ and NC5H6+ species in the presence of protons. Both NH3 and pyridine could adsorb on the Lewis Al3+ sites in HZSM-12, while the adsorption of NH3 and pyridine on the Lewis acid sites are less stable than on the Brønsted acid sites of ZSM-12.

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Mechanism, kinetics and selectivity of selenocyclization of 5-alkenylhydantoins: an experimental and computational study

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.11.200 ◽

2015 ◽

Vol 11 ◽

pp. 1865-1875 ◽

Cited By ~ 2

Author(s):

Biljana M Šmit ◽

Radoslav Z Pavlović ◽

Dejan A Milenković ◽

Zoran S Marković

Keyword(s):

Density Functional Theory ◽

Double Bond ◽

Density Functional ◽

Computational Study ◽

Theoretical Calculations ◽

Reaction Products ◽

Dft Methods ◽

Functional Theory ◽

H Nmr ◽

Good Agreement

The mechanism and selectivity of a bicyclic hydantoin formation by selenium-induced cyclization are investigated. The proposed mechanism involves the intermediates formed by an electrophilic addition of the selenium reagent on a double bond of the starting 5-alkenylhydantoin prior the cyclization. These intermediates are readily converted into the more stable cyclic seleniranium cations. A key step of the mechanism is an intramolecular cyclization which is realized through an anti-attack of the internal nucleophile, the amidic nitrogen, to the seleniranium cation yielding the intermediate imidazolinium cations. Their deprotonation is followed by the formation of the fused bicyclic reaction products. Important intermediates and key transition states are studied by using density functional theory (DFT) methods. The pathways of the reaction are investigated in detail. There are two regioselective pathways related to 5-exo and 6-endo products. Theoretical calculations and the monitoring of the cyclization reaction using 1H NMR spectroscopy are in a good agreement with the proposed mechanism and are consistent with our experimental results. The preferred pathway for formation of 5-exo products is confirmed.

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Theoretical and Experimental Evaluation of the Effect of Fluorinated Substituent on the Topological Landscape and Thermodynamic Stability of Zeolitic Imidazolate Framework Polymorphs

10.26434/chemrxiv.7072577.v1 ◽

2018 ◽

Author(s):

Mihails Arhangelskis ◽

Athanassis Katsenis ◽

Novendra Novendra ◽

Zamirbek Akimbekov ◽

Dayaker Gandrath ◽

...

Keyword(s):

Density Functional Theory ◽

Mechanochemical Synthesis ◽

Thermodynamic Stability ◽

Experimental Evaluation ◽

Density Functional ◽

Theoretical Calculations ◽

Zeolitic Imidazolate Framework ◽

Functional Theory ◽

Calorimetric Measurements ◽

And Calorimetry

By combining mechanochemical synthesis and calorimetry with theoretical calculations, we demonstrate that dispersion-corrected periodic density functional theory (DFT) can accurately survey the topological landscape and predict relative energies of polymorphs for a previously inaccessible fluorine-substituted zeolitic imidazolate framework (ZIF). Experimental screening confirmed two out of three theoretically anticipated polymorphs, and the calorimetric measurements provided an excellent match to theoretically calculated energetic difference between them.<br>

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Computational Study of the Electron Spectra of Vapor-Phase Indole and Four Azaindoles

Molecules ◽

10.3390/molecules26071947 ◽

2021 ◽

Vol 26 (7) ◽

pp. 1947

Author(s):

Delano P. Chong

Keyword(s):

Density Functional Theory ◽

Vapor Phase ◽

Density Functional ◽

Computational Study ◽

Geometry Optimization ◽

The Other ◽

Functional Theory ◽

Electron Spectra

After geometry optimization, the electron spectra of indole and four azaindoles are calculated by density functional theory. Available experimental photoemission and excitation data for indole and 7-azaindole are used to compare with the theoretical values. The results for the other azaindoles are presented as predictions to help the interpretation of experimental spectra when they become available.

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A computational study for the reaction mechanism of metal-free cyanomethylation of aryl alkynoates with acetonitrile

RSC Advances ◽

10.1039/d1ra01649k ◽

2021 ◽

Vol 11 (30) ◽

pp. 18246-18251

Author(s):

Selçuk Eşsiz

Keyword(s):

Density Functional Theory ◽

Reaction Mechanism ◽

Density Functional ◽

Computational Study ◽

Coupled Cluster ◽

Functional Theory ◽

Metal Free ◽

Coupled Cluster Methods ◽

High Level ◽

Cluster Methods

A computational study of metal-free cyanomethylation and cyclization of aryl alkynoates with acetonitrile is carried out employing density functional theory and high-level coupled-cluster methods, such as [CCSD(T)].

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Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

Journal of Chemical Research ◽

10.1177/174751989902300824 ◽

1999 ◽

Vol 23 (8) ◽

pp. 502-503

Author(s):

Branko S. Jursic

Keyword(s):

Density Functional Theory ◽

Ab Initio ◽

Density Functional ◽

Computational Study ◽

Basis Set ◽

Functional Theory ◽

Complete Basis ◽

Complete Basis Set ◽

High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

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Application of β-Phosphorylated Nitroethenes in [3+2] Cycloaddition Reactions Involving Benzonitrile N-Oxide in the Light of a DFT Computational Study

Organics ◽

10.3390/org2010003 ◽

2021 ◽

Vol 2 (1) ◽

pp. 26-37

Author(s):

Karolina Zawadzińska ◽

Karolina Kula

Keyword(s):

Density Functional ◽

Reaction Path ◽

Computational Study ◽

Cyano Group ◽

Cycloaddition Reactions ◽

Functional Theory ◽

The Density Functional Theory ◽

Reaction Channels ◽

One Step ◽

Step Mechanism

The regiochemistry of [3+2] cycloaddition (32CA) processes between benzonitrile N-oxide 1 and β-phosphorylated analogues of nitroethenes 2a–c has been studied using the Density Functional Theory (DFT) at the M062X/6-31+G(d) theory level. The obtained results of reactivity indices show that benzonitrile N-oxide 1 can be classified both as a moderate electrophile and moderate nucleophile, while β-phosphorylated analogues of nitroethenes 2a–c can be classified as strong electrophiles and marginal nucleophiles. Moreover, the analysis of CDFT shows that for [3+2] cycloadditions with the participation of β-phosphorylatednitroethene 2a and β-phosphorylated α-cyanonitroethene 2b, the more favored reaction path forms 4-nitro-substituted Δ2-isoxazolines 3a–b, while for a reaction with β-phosphorylated β-cyanonitroethene 2c, the more favored path forms 5-nitro-substituted Δ2-isoxazoline 4c. This is due to the presence of a cyano group in the alkene. The CDFT study correlates well with the analysis of the kinetic description of the considered reaction channels. Moreover, DFT calculations have proven the clearly polar nature of all analyzed [3+2] cycloaddition reactions according to the polar one-step mechanism.

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Experimental and Computational Studies on N-alkylation Reaction of N-Benzoyl 5-(Aminomethyl)Tetrazole

Chemistry ◽

10.3390/chemistry3030049 ◽

2021 ◽

Vol 3 (3) ◽

pp. 704-713

Author(s):

Younas Aouine ◽

Aaziz Jmiai ◽

Anouar Alami ◽

Abdallah El Asri ◽

Souad El Issami ◽

...

Keyword(s):

Density Functional Theory ◽

Nmr Spectroscopy ◽

Density Functional ◽

Computational Study ◽

Benzyl Bromide ◽

13C Nmr Spectroscopy ◽

Alkylation Reaction ◽

Computational Studies ◽

Functional Theory ◽

1H And 13C Nmr

The N-alkylation reaction of N-benzoyl 5-(aminomethyl)tetrazole (5-AMT) with benzyl bromide was carried out in the presence of K2CO3 as a base. Two separable regioisomers were obtained, thus their purification led to determine the proportion of each of them, and their structures were attributed essentially based on 1H and 13C NMR spectroscopy in addition to the elemental analysis and MS data. In order to confirm the results obtained at the synthesis level, a computational study was carried out by application of density functional theory (DFT) using the Becke three-parameter hybrid exchange functional and the Lee-Yang-Parr correlation functional (B3LYP).

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