Mechanistic Dichotomy Research Articles

Dearomative (3 + 2) Cycloaddition of Indoles for the Stereoselective Assembly of Fully Functionalized Cyclopentanoids.

The gold(I)-catalyzed dearomative cyclopentannulation of various indoles with 2-ethynyl-1,3-dithiolane is reported. The method generates three new stereocenters with excellent control of relative stereochemistry and is tolerant of diverse functionalization and substitution patterns on the indoles. The obtained cyclopentane-fused indolines allow for interesting subsequent synthetic manipulations, giving rise to fully substituted cyclopentanes with control of the relative stereochemistry of all five stereocenters. The reported reaction illustrates and elucidates a mechanistic dichotomy underlying gold(I)-catalyzed reactions of 2-ethynyl-1,3-dithiolane.

Stereodivergent Zweifel Olefination and its Mechanistic Dichotomy

AbstractStereoselective Zweifel olefination using boronate complexes carrying two different reactive π‐systems was achieved to synthesize vinyl heteroarenes and conjugated 1,3‐dienes in good yield and up to 100 % stereoselectivity, which remains unexplored until now. Most importantly, we report the unprecedented formation of E vs. Z‐vinyl heteroarenes for different heteroarenes under identical conditions. Density functional theory (DFT) investigations unveil the mechanistic dichotomy between olefin and heteroarene activation followed by 1,2‐migration, leading to E or Z‐vinyl heteroarenes respectively. We also report a previously unknown reversal of stereoselectivity by using 2,3‐Dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ) as an electrophile. The Zweifel olefination using a boronate complex that carries two different olefins was previously unexplored due to significant challenges associated with the site‐selective activation of olefins. We have solved this problem and reported the site‐selective activation of olefins for the stereoselective synthesis of 1,3‐dienes.

Stereodivergent Zweifel Olefination and its Mechanistic Dichotomy.

Stereoselective Zweifel olefination using boronate complexes carrying two different reactive π-systems was achieved to synthesize vinyl heteroarenes and conjugated 1,3-dienes in good yield and up to 100% stereoselectivity, which remains unexplored until now. Most importantly, we report the unprecedented formation of E vs. Z-vinyl heteroarenes for different heteroarenes under identical conditions. Density functional theory (DFT) investigations unveil the mechanistic dichotomy between olefin and heteroarene activation followed by 1,2-migration, leading to E or Z-vinyl heteroarenes respectively. We also report a previously unknown reversal of stereoselectivity by using 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electrophile. The Zweifel olefination using a boronate complex that carries two different olefins was previously unexplored due to significant challenges associated with the site-selective activation of olefins. We have solved this problem and reported the site-selective activation of olefins for the stereoselective synthesis of 1,3-dienes.

Mechanistic dichotomy in the solvent dependent access to E vs. Z-allylic amines via decarboxylative vinylation of amino acids.

The solvent plays an important role in the photophysical properties of donor–acceptor based photocatalysts. The solvent-dependent access to E vs. Z-allylic amines was achieved via decarboxylative vinylation of amino acids with vinyl sulfones. Detailed experimental studies have been conducted to understand the role of the solvent in the reactivity and stereoselectivity of the vinylation reactions.

The surprising structural and mechanistic dichotomy of membrane-associated phosphoglycosyl transferases.

Phosphoglycosyl transferases (PGTs) play a pivotal role at the inception of complex glycoconjugate biosynthesis pathways across all domains of life. PGTs promote the first membrane-committed step in the en bloc biosynthetic strategy by catalyzing the transfer of a phospho-sugar from a nucleoside diphospho-sugar to a membrane-resident polyprenol phosphate. Studies on the PGTs have been hampered because they are integral membrane proteins, and often prove to be recalcitrant to expression, purification and analysis. However, in recent years exciting new information has been derived on the structures and the mechanisms of PGTs, revealing the existence of two unique superfamilies of PGT enzymes that enact catalysis at the membrane interface. Genome neighborhood analysis shows that these superfamilies, the polytopic PGT (polyPGT) and monotopic PGT (monoPGT), may initiate different pathways within the same organism. Moreover, the same fundamental two-substrate reaction is enacted through two different chemical mechanisms with distinct modes of catalysis. This review highlights the structural and mechanistic divergence between the PGT enzyme superfamilies and how this is reflected in differences in regulation in their varied glycoconjugate biosynthesis pathways.

Mechanistic Dichotomy in the Activation of SAM by Radical SAM Enzymes: QM/MM Modeling Deciphers the Determinant

Activation of S-adenosyl methionine (SAM) is an initiating step in hundreds of thousands of radical SAM enzymes that catalyze over 80 diverse types of reactions. The fundamental mechanisms, however...

Cover Feature: A Mechanistic Dichotomy in Two‐Electron Reduction of Dioxygen Catalyzed by N,N’‐Dimethylated Porphyrin Isomers (Chem. Eur. J. 46/2020)

Selective two-electron reduction of O2 to H2O2 has been achieved by nonplanar N,N’-dimethylated porphyrin isomers as organocatalysts, showing the highest TON among homogeneous metal-free catalysts. Hydrogen bonding between pyrrolic protons of reduced porphyrinoids and O2 plays an important role to control the reaction mechanism in catalytic O2 reduction. The cover art describes different mechanisms of the O2 reduction by the two isomers on the background showing shining Mt. Tsukuba in the sunset. More information can be found in the Full Paper by T. Kojima et al. on page 10480.

A Mechanistic Dichotomy in Two‐Electron Reduction of Dioxygen Catalyzed by N,N’‐Dimethylated Porphyrin Isomers

Selective two-electron reduction of dioxygen (O2 ) to hydrogen peroxide (H2 O2 ) has been achieved by two saddle-distorted N,N'-dimethylated porphyrin isomers, an N21,N'22-dimethylated porphyrin (anti-Me2 P) and an N21,N'23-dimethylated porphyrin (syn-Me2 P) as catalysts and ferrocene derivatives as electron donors in the presence of protic acids in acetonitrile. The higher catalytic performance in an oxygen reduction reaction (ORR) was achieved by anti-Me2 P with higher turnover number (TON=250 for 30 min) than that by syn-Me2 P (TON=218 for 60 min). The reactive intermediates in the catalytic ORR were confirmed to be the corresponding isophlorins (anti-Me2 Iph or syn-Me2 Iph) by spectroscopic measurements. The rate-determining step in the catalytic ORRs was concluded to be proton-coupled electron-transfer reduction of O2 with isophlorins based on kinetic analysis. The ORR rate by anti-Me2 Iph was accelerated by external protons, judging from the dependence of the observed initial rates on acid concentrations. In contrast, no acceleration of the ORR rate with syn-Me2 Iph by external protons was observed. The different mechanisms in the O2 reduction by the two isomers should be derived from that of the arrangement of hydrogen bonding of a O2 with inner NH protons of the isophlorins.

The Dichotomy of Gold‐catalyzed Interplay between Cyanamides and Ynamides: Controllable Switch from [2+2+2] to [4+2] Cycloaddition

AbstractThe gold‐catalyzed interplay between cyanamides and ynamides demonstrates condition‐dependent mechanistic dichotomy. [2+2+2] Cycloaddition proceeds under kinetically controlled conditions to give 2,4,6‐triaminopyrimidines (19 examples, up to 99%). Under thermodynamically controlled conditions, the reactivity switches from [2+2+2]‐ to [4+2] cycloaddition; the latter [4+2] reaction accomplishes 1,3‐diaminoisoquinolines (19 examples, up to 97%). The advantages of both methods include regioselectivity, mild reaction conditions (even for the thermodynamically controlled [4+2] reaction) and the possibility of introducing a variety of dialkyl, diaryl, and heterocyclic amino substituents into the target pyrimidine and isoquinoline cores. The reactions were conducted on gram scales and the versatility of the obtained products was demonstrated by post‐functionalizations.magnified image

Quantitative Analysis on Two-Point Ligand Modulation of Iridium Catalysts for Chemodivergent C-H Amidation.

The transition-metal-catalyzed nitrenoid transfer reaction is one of the most attractive methods for installing a new C-N bond into diverse reactive units. While numerous selective aminations are known, understanding complex structural effects of the key intermediates on the observed chemoselectivity is still elusive in most cases. Herein, we report a designing approach to enable selective nitrenoid transfer leading to sp2 spirocyclization and sp3 C-H insertion by cooperative two-point modulation of ligands in the CpXIr(III)(κ2-chelate) catalyst system. Computational analysis led us to interrogate structural motifs that can be attributed to the desired mechanistic dichotomy. Multivariate linear regression analysis on the perturbation on the η5-cyclopentadienyl ancillary (CpX) and LX coligand, wherein we prepared over than 40 new catalysts for screening, allowed for construction of an intuitive yet robust statistical model that predicts a large set of chemoselective outcomes, implying that the catalysts' structural effects play a critical role on the chemoselective nitrenoid transfer. On the basis of this quantitative analysis, a new catalytic platform is now established for the unique lactam formation, leading to the unprecedented chemoselective reactivity (up to >20:1) toward a diverse array of competing sites, such as tertiary, secondary, benzylic, allylic C-H bonds, and aromatic π system.

Mechanistic dichotomies in redox reactions of mononuclear metal-oxygen intermediates.

There are mechanistic dichotomies with regard to the formation, electronic structures and reaction mechanisms of metal-oxygen intermediates, since these metal-oxygen species could be composed of different resonance structures or canonical structures of the oxidation states of metals and ligands, which may undergo different reaction pathways. Even the same metal-oxygen intermediates, such as metal-oxo species, may undergo an electron-transfer pathway or a direct hydrogen or oxygen atom transfer pathway depending on the one-electron redox potentials of metal-oxo species and substrates. Electron-transfer pathways are also classified into two mechanisms, such as outer-sphere and inner-sphere pathways. The one-electron redox potentials of metal-oxygen species and substrates are also shifted because of the binding of acids, which can result from either hydrogen bonding or protonation. There are a rebound pathway and a non-rebound pathway following the initial electron transfer or hydrogen atom transfer step to produce hydroxylated products, depending on the one-electron redox potentials of metal-oxo species and substrates. Nucleophilic reactions can be switched to electrophilic pathways, depending on reaction conditions such as reaction temperature. Spin states of metal-oxygen intermediates are also an important factor that controls the redox reactivity of oxidants in oxidation reactions. Here, we review such various mechanistic dichotomies in redox reactions of metal-oxygen intermediates with the emphasis on understanding and controlling the redox reactivity of metal-oxygen intermediates from experimental and theoretical points of view.

Meisenheimer complexes as hidden intermediates in the aza-SNAr mechanism.

In this work we report a computational study about the aza-SNAr mechanism in fluorine- and chlorine-containing azines with the aim to unravel the physical factors that determine the reactivity patterns in these heterocycles towards propylamine. The nature of the reaction intermediate was analyzed in terms of its electronic structure based on a topological analysis framework in some non-stationary points along the reaction coordinate. The mechanistic dichotomy of a concerted or a stepwise pathway is interpreted in terms of the qualitative Diabatic Model of Intermediate Stabilization (DMIS) approach, providing a general mechanistic picture for the SNAr process involving both activated benzenes and nitrogen-containing heterocycles. With the information collected, a unified vision of the Meisenheimer complexes as transition state, hidden intermediate or real intermediate was proposed.

Scope and Limitations of TBA[Fe]‐Catalyzed Carbene Transfer to X−H‐bonds – Indication of a Mechanistic Dichotomy

AbstractAn in‐depth study of carbene transfer reactions into polar X−H‐bonds catalyzed by the nucleophilic Fe‐complex Bu4N[Fe(CO)3(NO)] (TBA[Fe]) is presented. Whereas alcohols are unreactive, thiols and secondary amines are reactive, silanes showed modest activities. Hammett correlations indicate the presence of an X−H‐acidity dependent mechanistic dichotomy.

Mechanistic Dichotomy of Magnesium- and Zinc-Based Germanium Nucleophiles in the C(sp3 )-Ge Cross-Coupling with Alkyl Electrophiles.

Robust procedures for two mechanistically distinct C(sp3 )-Ge bond formations from alkyl electrophiles and germanium nucleophiles are reported. The germanium reagents were made available as bench-stable solutions by lithium-to-magnesium and lithium-to-zinc transmetalation, respectively. The germanium Grignard reagent reacts with various primary and secondary alkyl electrophiles by an ionic nucleophilic displacement. Conversely, the coupling of the corresponding zinc reagent requires a nickel catalyst, which then engages in radical bond formations with primary, secondary, and even tertiary alkyl bromides. Both methods avoid the regioselectivity issue of alkene hydrogermylation and enable the synthesis of a wide range of functionalized alkyl-substituted germanes.

Establishing cell painting in a smaller chemical biology lab - A report from the frontier.

In this paper we will outline the efforts we have made recently to establish the profiling platform known as cell painting in our laboratory. This platform, which is based on fluorescence microscopy, allows rapid and cheap access to bioactivity fingerprints for small molecules and thereby can contribute with important information in many experimental situations that is faced in laboratories involved in molecular probe design, mode-of-action studies or that perform focused phenotypic screens. We have tried to achieve the following two objectives: (1) provide a detailed description of the hurdles that we had to overcome during establishment and describe our final protocol; (2) provide a more pedagogical description of the different methods used to analyse and represent data from this experiment. Finally, we provide an example of how the method can be used to clarify mechanistic dichotomies.

Mechanistic Dichotomy in Proton-Coupled Electron-Transfer Reactions of Phenols with a Copper Superoxide Complex.

The kinetics and mechanism(s) of the reactions of [K(Krypt)][LCuO2] (Krypt = 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane, L = a bis(arylcarboxamido)pyridine ligand) with 2,2,6,6-tetramethylpiperdine- N-hydroxide (TEMPOH) and the para-substituted phenols XArOH (X = para substituent NO2, CF3, Cl, H, Me, tBu, OMe, or NMe2) at low temperatures were studied. The reaction with TEMPOH occurs rapidly ( k = 35.4 ± 0.3 M-1 s-1) by second-order kinetics to yield TEMPO• and [LCuOOH]- on the basis of electron paramagnetic resonance spectroscopy, the production of H2O2 upon treatment with protic acid, and independent preparation from reaction of [NBu4][LCuOH] with H2O2 ( Keq = 0.022 ± 0.007 for the reverse reaction). The reactions with XArOH also follow second-order kinetics, and analysis of the variation of the k values as a function of phenol properties (Hammett σ parameter, O-H bond dissociation free energy, p Ka, E1/2) revealed a change in mechanism across the series, from proton transfer/electron transfer for X = NO2, CF3, Cl to concerted-proton/electron transfer (or hydrogen-atom transfer) for X = OMe, NMe2 (data for X = H, Me, tBu are intermediate between the extremes). Thermodynamic analysis and comparisons to previous results for LCuOH, a different copper-oxygen intermediate with the same supporting ligand, and literature for other [CuO2]+ complexes reveal significant differences in proton-coupled electron-transfer mechanisms that have implications for understanding oxidation catalysis by copper-containing enzymes and abiological catalysts.

Mechanistic Dichotomy in Bacterial Trichloroethene Dechlorination Revealed by Carbon and Chlorine Isotope Effects.

Tetrachloroethene (PCE) and trichloroethene (TCE) are significant groundwater contaminants. Microbial reductive dehalogenation at contaminated sites can produce nontoxic ethene but often stops at toxic cis-1,2-dichloroethene ( cis-DCE) or vinyl chloride (VC). The magnitude of carbon relative to chlorine isotope effects (as expressed by ΛC/Cl, the slope of δ13C versus δ37Cl regressions) was recently recognized to reveal different reduction mechanisms with vitamin B12 as a model reactant for reductive dehalogenase activity. Large ΛC/Cl values for cis-DCE reflected cob(I)alamin addition followed by protonation, whereas smaller ΛC/Cl values for PCE evidenced cob(I)alamin addition followed by Cl- elimination. This study addressed dehalogenation in actual microorganisms and observed identical large ΛC/Cl values for cis-DCE (ΛC/Cl = 10.0 to 17.8) that contrasted with identical smaller ΛC/Cl for TCE and PCE (ΛC/Cl = 2.3 to 3.8). For TCE, the trend of small ΛC/Cl could even be reversed when mixed cultures were precultivated on VC or DCEs and subsequently confronted with TCE (ΛC/Cl = 9.0 to 18.2). This observation provides explicit evidence that substrate adaptation must have selected for reductive dehalogenases with different mechanistic motifs. The patterns of ΛC/Cl are consistent with practically all studies published to date, while the difference in reaction mechanisms offers a potential answer to the long-standing question of why bioremediation frequently stalls at cis-DCE.

Soluble matrix protein is a potent modulator of mesenchymal stem cell performance

We challenge the conventional designation of structural matrix proteins primarily as supporting scaffolds for resident cells. The extracellular matrix protein tropoelastin is classically regarded as a structural component that confers mechanical strength and resilience to tissues subject to repetitive elastic deformation. Here we describe how tropoelastin inherently induces a range of biological responses, even in cells not typically associated with elastic tissues and in a manner unexpected of typical substrate-dependent matrix proteins. We show that tropoelastin alone drives mesenchymal stem cell (MSC) proliferation and phenotypic maintenance, akin to the synergistic effects of potent growth factors such as insulin-like growth factor 1 and basic fibroblast growth factor. In addition, tropoelastin functionally surpasses these growth factors, as well as fibronectin, in allowing substantial media serum reduction without loss of proliferative potential. We further demonstrate that tropoelastin elicits strong mitogenic and cell-attractive responses, both as an immobilized substrate and as a soluble additive, via direct interactions with cell surface integrins αvβ3 and αvβ5. This duality of action converges the long-held mechanistic dichotomy between adhesive matrix proteins and soluble growth factors and uncovers the powerful, untapped potential of tropoelastin for clinical MSC expansion and therapeutic MSC recruitment. We propose that the potent, growth factor-like mitogenic and motogenic abilities of tropoelastin are biologically rooted in the need for rapid stem cell homing and proliferation during early development and/or wound repair.

Theoretical insights into the E1cB/E2 mechanistic dichotomy of elimination reactions.

E1cB and E2 eliminations have been described as competing mechanisms that can even share a common pathway when the E1cB/E2 borderline mechanism operates. A suitable case study evincing such a mechanistic dichotomy corresponds to the elimination reaction of β-phenylmercaptoethyl phenolate, since its mechanism has been thought to be an E2 elimination. Nonetheless, according to the computational assessment of the substituents on the leaving group, we demonstrate that the reaction proceeds via a borderline E1cB mechanism. Stabilization of the carbanion was provided not only by substituent effects tuning the nucleofugality of the leaving group, but also by a base, since distortion/interaction-activation strain and Natural Bond Order (NBO) analyses suggest a stabilizing interaction between the base and Cβ of the E1cB intermediate. In order to gain insights into these results in a more general context, we have rationalized them with a qualitative picture of the E1cB/E2 mechanistic dichotomy using simple relationships between diabatic parabolas modeling the potential wells of reactants, intermediates, and products. In this Diabatic Model of Intermediate Stabilization (DMIS), the borderline E1cB mechanism for the elimination reaction of β-phenylmercaptoethyl phenolate was discussed in terms of bonding and dynamic stepwise processes. The conceptual model presented herein should be useful for the analysis of any reaction comprising competing one- and two-step mechanisms.

Hydrogen Atom Transfer Reactions of Mononuclear Nonheme Metal-Oxygen Intermediates.

Molecular oxygen (O2), the greenest oxidant, is kinetically stable in the oxidation of organic substrates due to its triplet ground state. In nature, O2 is reduced by two electrons with two protons to produce hydrogen peroxide (H2O2) and by four electrons with four protons to produce water (H2O) by oxidase and oxygenase metalloenzymes. In the process of the two-electron/two-proton and four-electron/four-proton reduction of O2 by metalloenzymes and their model compounds, metal-oxygen intermediates, such as metal-superoxido, -peroxido, -hydroperoxido, and -oxido species, are generated depending on the numbers of electrons and protons involved in the O2 activation reactions. The one-electron reduction of metal-oxygen intermediates is coupled with the binding of one proton. Such a hydrogen atom transfer (HAT) is defined as proton-coupled electron transfer (PCET), and there is a mechanistic dichotomy whether HAT occurs via a concerted PCET pathway or stepwise pathways [i.e., electron transfer followed by proton transfer (ET/PT) or proton transfer followed by electron transfer (PT/ET)]. The metal-oxygen intermediates formed are oxidants that can abstract a hydrogen atom (H-atom) from substrate C-H bonds. The H-atom abstraction from substrate C-H bonds by the metal-oxygen intermediates can also occur via a concerted PCET or stepwise PCET pathways. In the PCET reactions, a proton can be provided not only by the substrate itself but also by an acid that is added to a reaction solution. This Account describes the reactivities of metal-oxygen intermediates, such as metal-superoxido, -peroxido, -hydroperoxido, and -oxido complexes, in HAT reactions, focusing on the mechanisms of PCET reactions of metal-oxygen intermediates and on the mechanistic dichotomy of concerted versus stepwise pathways. Recent developments in the reactivity studies of Cr-, Fe-, and Cu-superoxido complexes in H-atom and hydride transfer reactions are discussed. Reactivities of an iron(III)-hydroperoxido complex and an iron(III)-peroxido complex binding redox-inactive metal ions are also summarized briefly. Mononuclear nonheme iron(IV)- and manganese(IV)-oxido complexes have shown high reactivities in HAT reactions, and their chemistry in PCET reactions is discussed intensively. Acid-catalyzed HAT reactions of metal-oxygen intermediates are also discussed to demonstrate a unified driving force dependence of logarithm of the rate constants of acid-catalyzed oxidation of various substrates by an iron(IV)-oxido complex and that of PCET from one-electron donors to the iron(IV)-oxido complex. PCET reactions of metal-oxygen intermediates are shown to proceed via a concerted pathway (one-step HAT) or a stepwise ET/PT pathway depending on the ET and PCET driving forces (-Δ G). The boundary conditions between concerted versus stepwise PCET pathways are clarified to demonstrate a switchover of the mechanisms only by changing the reaction temperature in the boundary conditions. This Account summarizes recent developments in the HAT reactions by synthetic mononuclear nonheme metal-oxygen intermediates over the past 10 years.