A DFT-based mechanistic study on the formation of oximes

Kırmızıaltın, Serdal; Yildiz, Banu Sizirici; Yildiz, İbrahim

doi:10.1002/poc.3711

Cited by 7 publications

(4 citation statements)

References 36 publications

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“…Truncated electrophiles and α-nucleophiles, acetaldehyde, and methoxyamine, respectively, were used in all other reaction steps (Figures 5a and 6a). The DFT results reported here for aniline closely match the results reported for the same model compounds at nearly the same level of theory by Kirmizialtin et al 29 Our inclusion of the D3 empirical dispersion correction 30 to B3LYP may account for the small discrepancies at some points in the reaction free energy profile.…”

Section: ■ Results and Discussionsupporting

confidence: 89%

Glycoconjugate Oxime Formation Catalyzed at Neutral pH: Mechanistic Insights and Applications of 1,4-Diaminobenzene as a Superior Catalyst for Complex Carbohydrates

et al. 2018

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The reaction of unprotected carbohydrates with aminooxy reagents to provide oximes is a key method for the construction of glycoconjugates. Aniline and derivatives serve as organocatalysts for the formation of oximes from simple aldehydes, and we have previously reported that aniline also catalyzes the formation of oximes from the more complex aldehydes, carbohydrates. Here, we present a comprehensive study of the effect of aniline analogues on the formation of carbohydrate oximes and related glycoconjugates depending on organocatalyst structure, pH, nucleophile, and carbohydrate, covering more than 150 different reaction conditions. The observed superiority of the 1,4-diaminobenzene (PDA) catalyst at neutral pH is rationalized by NMR analyses and DFT studies of reaction intermediates. Carbohydrate oxime formation at pH 7 is demonstrated by the formation of a bioactive glycoconjugate from a labile, decorated octasaccharide originating from exopolysaccharides of the soil bacterium Mesorhizobium loti. This study of glycoconjugate formation includes the first direct comparison of aniline-catalyzed reaction rates and equilibrium constants for different classes of nucleophiles, including primary oxyamines, secondary N-alkyl oxyamines, as well as aryl and arylsulfonyl hydrazides. We identified 1,4-diaminobenzene as a superior catalyst for the construction of oxime-linked glycoconjugates under mild conditions.

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Section: ■ Results and Discussionsupporting

confidence: 89%

Glycoconjugate Oxime Formation Catalyzed at Neutral pH: Mechanistic Insights and Applications of 1,4-Diaminobenzene as a Superior Catalyst for Complex Carbohydrates

et al. 2018

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“…Using a carboxylic acid group as proton shuttle further reduces the barrier to 15.8 kcal/mol (in acetonitrile or toluene, at 298 K). Kirmizialtin and co‐workers [77] have shown that the calculated cost of condensation of oximes in water can be reduced from 31.4 kcal/mol to 12.9 kcal/mol by adding two explicit water molecules. These promising studies enticed us to investigate the role of proton shuttles for the hitherto not‐studied case of metal‐stabilized pincer molecules.…”

Section: Resultsmentioning

confidence: 99%

“…To bypass the high-energy barriers resulting from the 4membered ring TS route, we investigated proton transfers facilitated by proton shuttles, as is known to work in experimental setting [74][75][76] and has been calculated recently for metal-free dynamic exchanges. [64][65]77] According to Rufino and Pliego, [65] using two water molecules as shuttle decreases the energy barrier for condensation of acetaldehyde with methylamine from 47.7 to 26.4 kcal/mol (in toluene at 298 K). Using a carboxylic acid group as proton shuttle further reduces the barrier to 15.8 kcal/mol (in acetonitrile or toluene, at 298 K).…”

Section: Condensation Reaction With Proton-shuttling Aminesmentioning

confidence: 99%

DFT Study of Imine‐Exchange Reactions in Iron(II)‐Coordinated Pincers

van Dam,

van Schendel,

Gangarapu

et al. 2023

Chemistry A European J

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The imine bond is among the most applied motifs in dynamic covalent chemistry. Although its uses are varied and often involve coordination to a transition metal for stability, mechanistic studies on imine exchange reactions so far have not included metal coordination. Herein, we investigated the condensation and transimination reactions of an Fe2+‐coordinated diimine pyridine pincer, employing wB97XD/6‐311G(2d,2p) DFT calculations in acetonitrile. We first experimentally confirmed that Fe2+ is strongly coordinated by these pincers, and is thus a justified model ion. When considering a four‐membered ring‐shaped transition state for proton transfers, the required activation energies for condensation and transimination reaction exceeded values expected for reactions known to be spontaneous at room temperature. The nature of the incoming and exiting amines and the substituents on the para‐position of the pincer had no effect on this. Replacing Fe2+ with Zn2+ or removing it altogether did not reduce it either. However, addition of two ethylamine molecules lowered the energy barriers to be compatible with experiment (19.4 and 23.2 kcal/mol for condensation and transimination, respectively). Lastly, the energy barrier of condensation of a non‐coordinated pincer was significantly higher than found for Fe2+‐coordinating pincers, underlined the catalyzing effect of metal coordination on imine exchange reactions.

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“…Elimination of the protonated hydroxyl group results in the formation of hydrochloride salts of ( E )- and ( Z )-stereoisomers (fast reaction step). In acidic conditions, the protonation of the nitrogen atom follows with the transfer of the proton via an explicit water molecule to the hydroxyl group [ 26 , 27 ].…”

Section: Resultsmentioning

confidence: 99%

Polytopal Rearrangement Governing Stereochemistry of Bicyclic Oxime Ether Synthesis

Spahić¹,

Hrenar²,

Primožič³

2022

IJMS

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In the present study, four O-substituted oximes of quinuclidin-3-one were synthesized using appropriate O-substituted hydroxylamine hydrochlorides. In order to perform these reactions in a solvent, a mixture of (E) and (Z) products was yielded. Using mechanochemical and microwave synthesis, we then obtained pure (E) oximes. In almost all cases, the conversion to oxime ethers was completed. Reactions were monitored by ATR spectroscopy and the ratios of (E) and (Z) oxime ethers were deduced from 1H NMR data. Several reactions were very rapid (1 min) with 100% conversion and stereospecificity. To investigate the reaction mechanisms, full conformational analyses of the reaction intermediates were performed and the lowest energy conformers were determined. These conformers differed in spatial arrangement around the nitrogen atom of the amino group and were in the correct orientation for reactions to occur. Calculated standard Gibbs energies of the formation were in agreement with the experimentally obtained ratios of (E) and (Z) isomers. This work shows alternatives to the classical synthesis of O-substituted oxime ether precursors and highlights the fast reaction rate and stereoselectivity of microwave synthesis as well as the “green” aspects of mechanochemistry.

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A DFT-based mechanistic study on the formation of oximes

Cited by 7 publications

References 36 publications

Glycoconjugate Oxime Formation Catalyzed at Neutral pH: Mechanistic Insights and Applications of 1,4-Diaminobenzene as a Superior Catalyst for Complex Carbohydrates

Glycoconjugate Oxime Formation Catalyzed at Neutral pH: Mechanistic Insights and Applications of 1,4-Diaminobenzene as a Superior Catalyst for Complex Carbohydrates

DFT Study of Imine‐Exchange Reactions in Iron(II)‐Coordinated Pincers

Polytopal Rearrangement Governing Stereochemistry of Bicyclic Oxime Ether Synthesis

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