Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

Rangelov, Miroslav; Петрова, Г. П.; Yomtova, Vihra M.; Vayssilov, Georgi N.

doi:10.1016/j.jmgm.2010.07.006

Cited by 5 publications

(3 citation statements)

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“… 20 , 21 This role can also be served by a vicinal alcohol. 22 , 23 A second amine molecule can also facilitate the proton transfer via the general base pathway. 24 − 27 Theoretical 19 and experimental 28 studies have shown that 2-pyridinone, acetic acid, 29 and triazabicyclodecene (TBD) 30 can also act as proton conduits.…”

Section: Resultsmentioning

confidence: 99%

“…A proton transfer catalyst, such as water, can promote both reaction pathways (Scheme ). , The water-mediated proton transfer alleviates the strain associated with a four-membered proton transfer. , This role can also be served by a vicinal alcohol. , A second amine molecule can also facilitate the proton transfer via the general base pathway. − Theoretical and experimental studies have shown that 2-pyridinone, acetic acid, and triazabicyclodecene (TBD) can also act as proton conduits. In many systems, the two-step and concerted pathways are nearly isoelectronic; greater differentiation comes from steric and electronic interactions between the reacting partners.…”

Section: Resultsmentioning

confidence: 99%

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Concerted Amidation of Activated Esters: Reaction Path and Origins of Selectivity in the Kinetic Resolution of Cyclic Amines via N-Heterocyclic Carbenes and Hydroxamic Acid Cocatalyzed Acyl Transfer

et al. 2014

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The N-heterocyclic carbene and hydroxamic acid cocatalyzed kinetic resolution of cyclic amines generates enantioenriched amines and amides with selectivity factors up to 127. In this report, a quantum mechanical study of the reaction mechanism indicates that the selectivity-determining aminolysis step occurs via a novel concerted pathway in which the hydroxamic acid plays a key role in directing proton transfer from the incoming amine. This modality was found to be general in amide bond formation from a number of activated esters including those generated from HOBt and HOAt, reagents that are broadly used in peptide coupling. For the kinetic resolution, the proposed model accurately predicts the faster reacting enantiomer. A breakdown of the steric and electronic control elements shows that a gearing effect in the transition state is responsible for the observed selectivity.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Concerted Amidation of Activated Esters: Reaction Path and Origins of Selectivity in the Kinetic Resolution of Cyclic Amines via N-Heterocyclic Carbenes and Hydroxamic Acid Cocatalyzed Acyl Transfer

et al. 2014

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“…For this reason, our investigation included a complete conformational search aiming at finding all lowest energy structures. The applied computational procedure, described in detail in ref 28, is based on the generation of a set of initial structures via stepwise variation of different dihedral angles (N-C-Oe-C1, C-Oe-C1-C2, Oe-C1-C2-Ov, and C1-C2-Ov-Hv) by 10°. Thus, about 46 000 to 160 000 initial structures were generated for each transition state and intermediate, which were further sifted out by elimination of equivalent structures.…”

Section: Jocarticlementioning

confidence: 99%

Catalytic Role of Vicinal OH in Ester Aminolysis: Proton Shuttle versus Hydrogen Bond Stabilization

et al. 2010

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This computational study provoked by the process of peptide bond formation in the ribosome investigates the influence of the vicinal OH group in monoacylated diols on the elementary acts of ester aminolysis. Two alternative approaches for this influence on ester ammonolysis were considered: stabilization of the transition states by hydrogen bonds and participation of the vicinal hydroxyl in proton transfer (proton shuttle). The activation due to hydrogen bonds of the vicinal hydroxyl via tetragonal transition states was rather modest; the free energy of activation was reduced by only 5.2 kcal/mol compared to the noncatalyzed reaction. The catalytic activation via the proton shuttle mechanism with participation of the vicinal OH in the proton transfer via hexagonal transition states resulted in considerable reduction of the free energy of activation to 33.5 kcal/mol, i.e., 16.0 kcal/mol lower than in the referent process. Accounting for the influence of the environment on the reaction center by a continuum model (for ε from 5 to 80) resulted in further stabilization of the rate-determining transition state by 4-5 kcal/mol. The overall reduction of the reaction barrier by about 16 kcal/mol as compared to the noncatalyzed process corresponds to about 10(9)-fold acceleration of the reaction, in agreement with the experimental estimate for acceleration of this process in the ribosome.

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Why p‐Cymene? Conformational Effect in Asymmetric Hydrogenation of Aromatic Ketones with a η⁶‐Arene/Ruthenium(II) Catalyst

Matsuoka¹,

Sandoval²,

Uchiyama³

et al. 2014

Chemistry An Asian Journal

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Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

Cited by 5 publications

References 53 publications

Concerted Amidation of Activated Esters: Reaction Path and Origins of Selectivity in the Kinetic Resolution of Cyclic Amines via N-Heterocyclic Carbenes and Hydroxamic Acid Cocatalyzed Acyl Transfer

Concerted Amidation of Activated Esters: Reaction Path and Origins of Selectivity in the Kinetic Resolution of Cyclic Amines via N-Heterocyclic Carbenes and Hydroxamic Acid Cocatalyzed Acyl Transfer

Catalytic Role of Vicinal OH in Ester Aminolysis: Proton Shuttle versus Hydrogen Bond Stabilization

Why p‐Cymene? Conformational Effect in Asymmetric Hydrogenation of Aromatic Ketones with a η⁶‐Arene/Ruthenium(II) Catalyst

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Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

Cited by 5 publications

References 53 publications

Concerted Amidation of Activated Esters: Reaction Path and Origins of Selectivity in the Kinetic Resolution of Cyclic Amines via N-Heterocyclic Carbenes and Hydroxamic Acid Cocatalyzed Acyl Transfer

Concerted Amidation of Activated Esters: Reaction Path and Origins of Selectivity in the Kinetic Resolution of Cyclic Amines via N-Heterocyclic Carbenes and Hydroxamic Acid Cocatalyzed Acyl Transfer

Catalytic Role of Vicinal OH in Ester Aminolysis: Proton Shuttle versus Hydrogen Bond Stabilization

Why p‐Cymene? Conformational Effect in Asymmetric Hydrogenation of Aromatic Ketones with a η6‐Arene/Ruthenium(II) Catalyst

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Why p‐Cymene? Conformational Effect in Asymmetric Hydrogenation of Aromatic Ketones with a η⁶‐Arene/Ruthenium(II) Catalyst