Computational Analysis of Cyclophane-Based Bisthiourea-Catalyzed Henry Reactions

The Henry reaction between benzaldehyde and nitromethane catalyzed by a cyclophane-based bisthiourea has been studied with density functional theory [M06-2X-D3/def2-TZVPP/IEFPCM//TPSS-D2/6-31G­(d)/IEFPCM]. The results of our study reveal that the transformation involves the reaction of a thiourea–nitronate complex with the uncoordinated aldehyde. On the basis of our calculations, the formation of the major stereoisomer is kinetically preferred. Employing smaller model systems, we show that the observed stereoselectivity arises primarily from differences in hydrogen bonding in diastereomeric transition states

Formation of Breslow Intermediates from N-Heterocyclic Carbenes and Aldehydes Involves Autocatalysis by the Breslow Intermediate, and a Hemiacetal

Under aprotic conditions, the stoichiometric reaction of N-heterocyclic carbenes (NHCs) such as imidazolidin-2-ylidenes with aldehydes affords Breslow Intermediates (BIs), involving a formal 1,2-C-to-O proton shift. We herein report kinetic studies (NMR), complemented by DFT calculations, on the mechanism of this kinetically disfavored H-translocation. Variable time normalization analysis (VTNA) revealed that the kinetic orders of the reactants vary for different NHC-to-aldehyde ratios, indicating different and ratio-dependent mechanistic regimes. We propose that for high NHC-to-aldehyde ratios, the H-shift takes place in the primary, zwitterionic NHC-aldehyde adduct. With excess aldehyde, the zwitterion is in equilibrium with a hemiacetal, in which the H-shift occurs. In both regimes, the critical H-shift is auto-catalyzed by the BI. Kinetic isotope effects observed for R-CDO are in line with our proposal. Furthermore, we detected an H-bonded complex of the BI with excess NHC (NMR)

Synergistic Effects between Lewis and Brønsted Acids: Application to the Prins Cyclization

Brønsted and Lewis acids can catalyze the Prins cyclization, an efficient method for the synthesis of tetrahydropyrans from homoallylic alcohols and carbonyl compounds. Synergistic effects between weak Brønsted and Lewis acids in these reactions have been analyzed by density functional theory [M06-L/def2-QZVP/IEFPCM­(CH₂Cl₂)//M06-L/6-311+G­(2df,2p)]. In order to characterize the reactivities of the employed Lewis acids, methyl anion and hydroxide affinities were determined. On the basis of our calculations, we found that the coordination of Lewis acids to carboxylic and sulfonic acids results in a significant increase in the Brønsted acidities of the latter

Theoretical Exploration of the Mechanism of Riboflavin Formation from 6,7-Dimethyl-8-ribityl­lumazine: Nucleophilic Catalysis, Hydride Transfer, Hydrogen Atom Transfer, or Nucleophilic Addition?

The cofactor riboflavin is biochemically synthesized by a constitutionally intricate process in which two molecules of 6,7-dimethyl-8-ribityl­lumazine react with each other to form one molecule of the cofactor and one molecule of 5-amino-6-(ribitylamino)­uracil. Remarkably, this complex molecular transformation also proceeds non-enzymatically in boiling aqueous solution at pH 7.3. Four different mechanistic pathways for this transformation (nucleophilic catalysis, hydride transfer, hydrogen atom transfer, and a nucleophilic addition mechanism) have now been analyzed by density functional theory [M06-2X/def2-TZVPP/CPCM//­M06-2X/6-31+G­(d,p)/IEFPCM]. On the basis of these computational results, a so far unpublished nucleophilic addition mechanism is the lowest energy pathway yielding riboflavin. The previously proposed mechanism involving nucleophilic catalysis is higher in energy but is still a viable alternative for an enzyme-catalyzed process assisted by suitably positioned catalytic groups. Pathways involving the transfer of a hydride ion or of a hydrogen atom are predicted to proceed through higher energy transition states and intermediates

Zwitterions and Unobserved Intermediates in Organocatalytic Diels–Alder Reactions of Linear and Cross-Conjugated Trienamines

The Diels–Alder reactions of cyclic linear and cross-conjugated trienamines with oxindoles have been studied with density functional theory [M06-2X/def2-TZVPP/IEFPCM//B97D/6-31+G­(d,p)/IEFPCM]. These reactions are found to proceed in a stepwise fashion. Computations revealed that these transformations involve complex mechanisms including zwitterionic intermediates and several unstable alternate cycloadducts arising from (2 + 2) cycloadditions and hetero-Diels–Alder reactions. The observed regio- and stereochemistry can be rationalized by a combination of kinetic and thermodynamic control

δ‑Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions

Molecular Iodine-Catalyzed Carbonyl-Olefin Metathesis

The carbonyl-olefin metathesis reaction is a synthetically valuable transformation that could facilitate rapid functional group interconversion and construction of new organic structures. Herein we demonstrate that elemental iodine, a very simple and mild catalyst, can efficiently promote this chemical transformation under mild reaction conditions with excellent outcomes. Our mechanistic studies revealed intriguing aspects of iodine activation mode that could change the previously established perception of catalyst and substrate design for the carbonyl-olefin metathesis reaction

Redox-Neutral α-Oxygenation of Amines: Reaction Development and Elucidation of the Mechanism

Cyclic secondary amines and 2-hydroxybenzaldehydes or related ketones react to furnish benzo[e][1,3]oxazine structures in generally good yields. This overall redox-neutral amine α-C–H functionalization features a combined reductive N-alkylation/oxidative α-functionalization and is catalyzed by acetic acid. In contrast to previous reports, no external oxidants or metal catalysts are required. Reactions performed under modified conditions lead to an apparent reductive amination and the formation of o-hydroxybenzylamines in a process that involves the oxidation of a second equivalent of amine. A detailed computational study employing density functional theory compares different mechanistic pathways and is used to explain the observed experimental findings. Furthermore, these results also reveal the origin of the catalytic efficiency of acetic acid in these transformations