Concerted Reaction Pathway Research Articles

Mimicking Ozonolysis via Mechanochemistry: Internal Alkynes to 1,2-Diketones using H5IO6.

Utilizing periodic acid as an environmentally benign oxidizing agent, this study introduces a novel mechanochemical method that mimics ozonolysis to convert internal alkynes into 1,2-diketones, showcasing effective emulation of ozone's reactivity. Notably, this oxidation occurs at room temperature in aerobic conditions, eliminating the need for toxic transition metals, hazardous oxidants, or expensive solvents. Through control experiments validating the mechanism, substantial evidence supports a concerted reaction pathway. This progress marks a significant stride toward cleaner and more efficient chemical synthesis, mitigating the environmental impact of conventional processes. Assessing the green chemistry metrics in both solvent-free and previously reported solvent-based methods, our eco-friendly protocol demonstrates an E-factor of 7.40, a 51.7 % atom economy, a 45.5 % atom efficiency, 100 % carbon efficiency, and 11.9 % reaction mass efficiency when solvents are not used.

Cu-electrodeposited gold electrode for the sensitive electrokinetic investigations of nitrate reduction and detection of the nitrate ion in acidic medium

The electro-catalytic reduction of nitrate ion in acidic media was observed at the Cu-electrodeposited Au surface. The voltammetric analysis represented that the Cu/Au electrode has an enhanced catalytic activity towards nitrate reduction in acidic medium through by eight electrons transfer process. Ammonia (NH3) was produced from the reduction of nitrate (NO3–) which followed a concerted reaction pathway as the value of transfer coefficient was 0.45 at Cu/Au electrode in the acidic medium. The value of standard rate constant and open circuit potential was evaluated as 2.48 × 10−4 cms−1 and 0.10 V respectively. This Cu/Au electrode displayed a good sensitivity (5.9378 μAµM−1cm−2) and lower detection limit (LOD: 0.52 µM) towards the reduction of nitrate ion and exhibited excellent performance in real sample analysis.

Prediction of High-Yielding Single-Step or Cascade Pericyclic Reactions for the Synthesis of Complex Synthetic Targets.

Pericyclic reactions, which involve cyclic concerted transition states without ionic or radical intermediates, have been extensively studied since their definition in the 1960s, and the famous Woodward-Hoffmann rules predict their stereoselectivity and chemoselectivity. Here, we describe the application of a fully automated reaction-path search method, that is, the artificial force induced reaction (AFIR), to trace an input compound back to reasonable starting materials through thermally allowed pericyclic reactions via product-based quantum-chemistry-aided retrosynthetic analysis (QCaRA) without using any a priori experimental knowledge. All categories of pericyclic reactions, including cycloadditions, ene reactions, group-transfer, cheletropic, electrocyclic, and sigmatropic reactions, were successfully traced back via concerted reaction pathways, and starting materials were computationally obtained with the correct stereochemistry. Furthermore, AFIR was used to predict whether the identified reaction pathway can be expected to occur in good yield relative to other possible reactions of the identified starting material. In order to showcase its practical utility, this state-of-the-art technology was also applied to the retrosynthetic analysis of a natural product with a relatively high number of atoms (52 atoms: endiandric acid C methyl ester), which was first synthesized by Nicolaou in 1982 and provided the corresponding starting polyenes with the correct stereospecificity via three pericyclic reaction cascades (one Diels-Alder reaction as well as 6π and 8π electrocyclic reactions). Moreover, not only systems that obey the Woodward-Hoffmann rules but also systems that violate these rules, such as those recently calculated by Houk, can be retrosynthesized accurately.

Insights into syngas to methanol conversion on Cr2O3 oxide from first-principles-based microkinetic simulations

Cr2O3 has been recognized as a key oxide component in bifunctional catalysts to produce bridging intermediate, e.g., methanol, from syngas. By combining density functional theory calculations and microkinetic modeling, we computationally studied the surface structures and catalytic activities of bare Cr2O3 (001) and (012) surfaces, and two reduced (012) surfaces covered with dissociative hydrogens or oxygen vacancies. The reduction of (001) surface is much more difficult than that of (012) surface. The stepwise or the concerted reaction pathways were explored for the syngas to methanol conversion, and the hydrogenation of CO or CHO is identified as rate-determining step. Microkinetic modeling reveals that (001) surface is inactive for the reaction, and the rates of both reduced (012) surfaces (25−28 s−1) are about five times higher than bare (012) surface (4.3 s−1) at 673 K. These theoretical results highlight the importance of surface reducibility on the reaction and may provide some implications on the design of individual component in bifunctional catalysis.

Quantifying Effects of Active Site Proximity on Rates of Methanol Dehydration to Dimethyl Ether over Chabazite Zeolites through Microkinetic Modeling.

Control of the spatial proximity of Brønsted acid sites within the zeolite framework can result in materials with properties that are distinct from materials synthesized through conventional crystallization methods or available from commercial sources. Recent experimental evidence has shown that turnover rates of different acid-catalyzed reactions increase with the fraction of proximal sites in chabazite (CHA) zeolites. The catalytic conversion of oxygenates is an important research area, and the dehydration of methanol to dimethyl ether (DME) is a well-studied reaction as part of methanol-to-olefin chemistry catalyzed by solid acids. Published experimental data have shown that DME formation rates (per acid site) increase systematically with the fraction of proximal acid sites in the six-membered ring of CHA. Here, we probe the effect of acid site proximity in CHA on methanol dehydration rates using electronic structure calculations and microkinetic modeling to identify the primary causes of this chemistry and their relationship to the local structure of the catalyst at the nanoscale. We report a density functional theory-parametrized microkinetic model of methanol dehydration to DME, catalyzed by acidic CHA zeolite with direct comparison to experimental data. Effects of proximal acid sites on reaction rates were captured quantitatively for a range of operating conditions and catalyst compositions, with a focus on total paired acid site concentration and reactant clustering to form higher nuclearity complexes. Next-nearest neighbor paired acid sites were identified as promoting the formation of methanol trimer clusters rather than the inhibiting tetramer or pentamer clusters, resulting in large increases in the rate for DME production due to the lower energy barriers present in the concerted methanol trimer reaction pathway. The model framework developed in this study can be extended to other zeolite materials and reaction chemistries toward the goal of rational design and development of next-generation catalytic materials and chemical processes.

Conformer-specific polar cycloaddition of dibromobutadiene with trapped propene ions

Diels–Alder cycloadditions are efficient routes for the synthesis of cyclic organic compounds. There has been a long-standing discussion whether these reactions proceed via stepwise or concerted mechanisms. Here, we adopt an experimental approach to explore the mechanism of the model polar cycloaddition of 2,3-dibromo-1,3-butadiene with propene ions by probing its conformational specificities in the entrance channel under single-collision conditions in the gas phase. Combining a conformationally controlled molecular beam with trapped ions, we find that both conformers of the diene, gauche and s-trans, are reactive with capture-limited reaction rates. Aided by quantum-chemical and quantum-capture calculations, this finding is rationalised by a simultaneous competition of concerted and stepwise reaction pathways, revealing an interesting mechanistic borderline case.

(Me6TREN)MgOCHPh2][B(C6F5)4]: A Model Complex to Explore the Catalytic Activity of Magnesium Alkoxides in Ketone Hydroboration

AbstractThe sterically hindered monomeric alkoxomagnesium compound [(Me6TREN)MgOCHPh2][B(C6F5)4] (1) has been used to explore the role of magnesium alkoxides in ketone hydroboration. Experiments and DFT calculations are suggestive of a concerted reaction pathway traversing through a six‐membered transition state involving Mg−OCHPh2, B−H, and C=O bonds. Prompted by this hypothesis, we investigated the activity of [Mg(OCHPh2)2] (3), which exhibits turn‐over frequency reaching up to 59,400 h−1 under solvent‐free conditions and stability towards C=C, −OH, −NH2 and −NO2. Due to the non‐existence of a metal hydride intermediate, such catalytic reactions will not get hindered in the presence of additional reactive functional groups.

Phosphinylation of Non‐activated Aryl Fluorides through Nucleophilic Aromatic Substitution at the Boundary of Concerted and Stepwise Mechanisms

AbstractNon‐activated aryl fluorides reacted with potassium diorganophosphinites through a nucleophilic aromatic substitution (SNAr) reaction. Remarkably, both electron‐neutral and electron‐rich aryl fluorides participated in the reaction with substantially stabilized anionic P nucleophiles to form the corresponding tertiary phosphine oxides. Quantum chemical calculations suggested a nucleophile‐dependent mechanism that involves both concerted and stepwise SNAr reaction pathways.

Phosphinylation of Non-activated Aryl Fluorides through Nucleophilic Aromatic Substitution at the Boundary of Concerted and Stepwise Mechanisms.

Non-activated aryl fluorides reacted with potassium diorganophosphinites through a nucleophilic aromatic substitution (SN Ar) reaction. Remarkably, both electron-neutral and electron-rich aryl fluorides participated in the reaction with substantially stabilized anionic P nucleophiles to form the corresponding tertiary phosphine oxides. Quantum chemical calculations suggested a nucleophile-dependent mechanism that involves both concerted and stepwise SN Ar reaction pathways.

Reactive atomistic simulations of Diels-Alder-type reactions: conformational and dynamic effects in the polar cycloaddition of 2,3-dibromobutadiene radical ions with maleic anhydride

The kinetics, dynamics and conformational specificities for the ionic Diels-Alder reaction (polar cycloaddition) of maleic anhydride with 2,3-dibromobutadiene radical ions have been studied theoretically using multisurface adiabatic reactive molecular dynamics. A competition of concerted and stepwise reaction pathways was found and both the s-cis and s-trans conformers of the diene are reactive. The analysis of the minimum dynamic path of the reaction indicates that both, rotations and vibrations of the reactant molecules are important for driving the system towards the transition state. The rates were computed as s for the s-cis and s for the s-trans conformer of 2,3-dibromobutadiene at an internal temperature of 300 K. The present results are to be contrasted with the neutral variant of the title system in which only the gauche conformer of the diene was found to undergo a considerably slower, concerted and mostly synchronous reaction driven by the excitation of rotations. The results presented here inform detailed experimental studies of the dynamics of polar cycloadditions under single-collision conditions in the gas phase.

Degradation mechanism for Zearalenone ring-cleavage by Zearalenone hydrolase RmZHD: A QM/MM study

The danger of zearalenone (ZEN) as an endocrine disruptor to humans and the environment has aroused increasing attention. In this study, we implemented the quantum mechanics/molecular mechanics (QM/MM) method to investigate the degradation mechanism of ZEN hydrolase (RmZHD) toward ZEN at the atomic level. The degradation process involves two concerted reaction pathways, where the active site contains a Ser-His-Glu triplet as a proton donor. With the Boltzmann-weighted average potential barriers of 18.1 and 21.5 kcal/mol, the process undergoes proton transfer and nucleophilic-substituted ring opening to form a hydroxyl product. Non-covalent interaction analyses elucidated hydrogen bonding between key amino acids with ZEN. The electrostatic influence analysis of 16 amino acids proposes residues Asp34 and His128 as the possible mutation target for future mutation design of enzyme RmZHD. An in-depth investigation of the protein environment of RmZHD can improve the bioremediation efficiency of endocrine disrupting chemicals.

A reaction force perspective of a model amide bond formation reaction

A reaction force approach of amide bond formation between ammonia and formic acid is demonstrated along with each atom’s contribution to structural changes and electronic reordering of the chemical reaction. The B3LYP/6-31G(d,p) level of density functional theory based calculations were carried out to explore transition states (TSs) of stepwise and concerted amide bond formation reaction pathways. Various stages that characterize structural and electronic properties in the progress of reaction are identified from reaction force calculations on energetics of geometries obtained from intrinsic reaction coordinate (IRC) pathways. The reaction works in preparative region of the pathway are less than that in relaxation stage, reflecting favorable formation of product geometries (Formamide and water). More than 80% of the activation energy comes from structural changes in preparative region. A comparison of reaction force profiles and reaction works in preparative region of TS1 and TS2 of stepwise path and TS3 of concerted path discloses that both the stepwise and concerted mechanisms are equally competent in terms of kinetic feasibility. The atomic resolution of pathways unveils that, hydrogen and oxygen forming the water molecule contribute significantly to the negative reaction energy of product geometries. The preferential contribution of the atoms comes from enhanced negative charge of the oxygen and positive charge on hydrogen in the progress of reaction.

A novel ring-shaped reaction pathway with interconvertible intermediates in chitinase A as revealed by QM/MM simulation combined with a one-dimensional projection technique.

Substrate-assisted catalysis (SAC), a mechanism of chitin hydrolysis by chitinases belonging to the glycoside hydrolase family 18 (GH18), has been studied experimentally and theoretically for several decades. However, the detailed reaction mechanism in chitinase A (ChiA) remains unclear at the atomic level. In this study, we investigated glycosylation, the first step of SAC, of ChiA obtained from Serratia marcescens (SmChiA), using QM/MM simulations combined with a one-dimensional projection (ODP) technique, which enabled us to explore the multi-dimensional free energy surface efficiently. The results showed that the reaction proceeds via a novel ring-shaped concerted reaction pathway with interconvertible intermediates, viz. oxazolinium ion and oxazoline, which have not been fully identified in previous studies. We also compared this chitin hydrolysis mechanism in SmChiA with that in SmChiB reported previously. The computational protocol developed in this study could also be applicable for elucidating complicated reaction mechanisms in other enzymes.

Benzyne-Mediated Nonconcerted Pathway toward Synthesis of Sterically Crowded [5]- and [7]Oxahelicenoids, Stereochemical and Theoretical Studies, and Optical Resolution of Helicenoids.

Synthesis of [5]- and [7]oxahelicenoids via Diels-Alder reaction of sterically crowded bichromenes with benzyne is presented. Studies carried out on Diels-Alder addition product establish the unusual preference for a stepwise mechanism over the concerted reaction pathway. This high yielding general synthetic protocol affords unexpected anti cycloadducts [5]- and [7]oxahelicenoids, as confirmed by crystallographic analysis. To rationalize these intriguing antiaddition products, the reaction mechanism was elucidated by means of DFT analysis. Additionally, hydroxy-functionalized [7]oxahelicenoid has been resolved in its optically pure forms.

A new imidazoline-containing Bunte salt: synthesis, molecular and electronic structure

Abstract S-[(4,5-dihydro-1H-imidazol-2-yl)methyl]sulfothioate, a new imidazoline-containing Bunte salt 4 was prepared by reacting 2-chloromethylimidazoline 3 with sodium thiosulfate in aqueous solution at room temperature. The mechanism of the concerted SN2 reaction pathway was studied by means of quantum chemical calculations at the B3LYP/6-31G** level of theory. The molecular structure of compound 4 incorporating a formal amidine moiety was confirmed by single crystal X-ray diffraction analysis, while its electronic structure was studied using quantum chemical calculations at the MP2/6-311++G** level of theory.

Substrate Pre‐Folding and Water Molecule Organization Matters for Terpene Cyclase Catalyzed Conversion of Unnatural Substrates

AbstractTerpene cyclase enzymes have recently been challenged with terpene substrate derivatives to generate additional chemical complexity beyond to what is currently found in nature. Herein, molecular dynamics and biocatalysis are used to shed light on the flexibility and inherent limitation of a triterpene cyclase in converting unnatural substrates. Our studies suggest that populating binding modes which allows for concerted reaction pathways is a key element towards an expanded substrate scope and new chemistries displayed by terpene cyclases. Additionally, we show that the spatial organization of water, which is influenced by both the substrate architecture as well as the active site geometry, controls the product selectivity. This highlights that activity and selectivity displayed by terpene cyclases acting on unnatural substrates is particularly difficult to predict, since they depend on various parameters.

A Model Study on the Carbon‐Halogen Activation in Perhalonated Arenes with Isonitrile Under Photoirradiation

AbstractThe mechanisms of the photochemical carbon‐halogen bond activation reactions were investigated theoretically using a model system of hexahalobenzene C6X6 (X=F, Cl, and Br) and phenyl isonitrile (PhN=C:), with the M06‐2X method and the 6–311G(d) basis set. The theoretical findings suggest the photoactivation mechanism should proceed as follows: Rea‐X‐S0 + hν → FC‐X‐T1 → PhNC‐T1 + C6X6 → Int‐X‐T1 → TS‐X‐T1 → T1/S0‐X → Pro‐X‐S0. The present theoretical evidence confirms the reported results by Studer and co‐workers that using UV irradiation, a simple and efficient transition‐metal‐free C‐F activation in various perfluoroarenes with aryl and alkyl isonitriles obtain imidoyl fluorides. Nevertheless, due to the highly vertical Frank‐Condon excitation energy, our theoretical study demonstrates N‐heterocyclic carbene cannot undergo the C‐F bond activation reaction with hexafluorobenzene under photoirradiation, which closely agrees with the available experimental observations. The present theoretical research reveals the spin crossover processes, which lead to a concerted reaction pathway, play a key role in the regioselecitivities of the final photoinsertion products.

Nitrone Cycloadditions of 1,2-Cyclohexadiene.

We report the first 1,3-dipolar cycloadditions of 1,2-cyclohexadiene, a rarely exploited strained allene. 1,2-Cyclohexadiene is generated in situ under mild conditions and trapped with nitrones to give isoxazolidine products in synthetically useful yields. The reactions occur regioselectively and exhibit a notable endo preference, thus resulting in the controlled formation of two new bonds and two stereogenic centers. DFT calculations of stepwise and concerted reaction pathways are used to rationalize the observed selectivities. Moreover, the strategic manipulation of nitrone cycloadducts demonstrates the utility of this methodology for the assembly of compounds bearing multiple heterocyclic units. These studies showcase the exploitation of a traditionally avoided reactive intermediate in chemical synthesis.

Theoretic studies on decomposition mechanism of o-methoxy phenethyl phenyl ether: Primary and secondary reactions

In order to understand the pyrolysis mechanism of lignin and identify the chemical pathways for the formation of main products during pyrolysis, the primary and secondary reactions of o-methoxy phenethyl phenyl (o-CH3O-PPE) pyrolysis are investigated by DFT method at (M06-2X)/6-31G+ (d,p) level. It is found that the o-methoxy group reduces the bond dissociation energies (BDEs) of CβO and C(aromatic)O bonds of the β-O-4 linkage. Kinetic analysis results support the concerted reaction pathway 12 as the major primary reaction channel which leads to the formation of guaiacol and styrene. Salicylaldehyde is arisen from the secondary pyrolysis of guaiacol via bimolecular reaction at higher temperature.

Regio‐ and Enantioselective Aza‐Diels–Alder Reactions of 3‐Vinylindoles: A Concise Synthesis of the Antimalarial Spiroindolone NITD609

AbstractAn asymmetric aza‐Diels–Alder reaction of 3‐vinylindoles with isatin‐derived ketimines has been developed. A series of spiroindolone derivatives were thus obtained in good to excellent yields with excellent enantioselectivity (up to 96 % yield and 99 % ee). Furthermore, the antimalarial compound NITD609 could be obtained in three steps with an overall yield of 40.6 %. Control experiments and operando IR experiments imply a concerted reaction pathway. The regioselectivity and exo selectivity result from π–π interactions between the two indoline rings of the two reactants.