Viable Intermediates Research Articles

Co-Catalyzed Hydrofluorination of Alkenes: Photocatalytic Method Development and Electroanalytical Mechanistic Investigation.

The hydrofluorination of alkenes represents an attractive strategy for the synthesis of aliphatic fluorides. This approach provides a direct means to form C(sp3)-F bonds selectively from readily available alkenes. Nonetheless, conducting hydrofluorination using nucleophilic fluorine sources poses significant challenges due to the low acidity and high toxicity associated with HF and the poor nucleophilicity of fluoride. In this study, we present a new Co(salen)-catalyzed hydrofluorination of simple alkenes utilizing Et3N·3HF as the sole source of both hydrogen and fluorine. This process operates via a photoredox-mediated polar-radical-polar crossover mechanism. We also demonstrated the versatility of this method by effectively converting a diverse array of simple and activated alkenes with varying degrees of substitution into hydrofluorinated products. Furthermore, we successfully applied this methodology to 18F-hydrofluorination reactions, enabling the introduction of 18F into potential radiopharmaceuticals. Our mechanistic investigations, conducted using rotating disk electrode voltammetry and DFT calculations, unveiled the involvement of both carbocation and CoIV-alkyl species as viable intermediates during the fluorination step, and the contribution of each pathway depends on the structure of the starting alkene.

Oxidized Bridged Carbenoids as Viable Intermediates in a Fe(III) Catalyzed C-H Insertion Reaction.

Fe catalyzed carbene insertion reactions present an efficient route for direct C-H functionalization. The use of Fe(III) in place of the widely used Fe(II) presents several benefits. However, the mechanistic understanding of Fe(III) severely lags behind Fe(II) complexes. One of the major unsolved issues relates to the formation of bridged versus terminal metallocarbenes. Even though the oxidized bridged carbenoid complexes have been isolated and found to be thermodynamically more stable, they are generally considered a dead end for the catalytic cycle. In the current report, the formation and the subsequent reactions of the bridged carbenoid complexes for an Fe(TPP)Cl catalyzed C(sp2 )-H insertion are investigated. Using DFT calculations, it is observed that both mono and bis oxidized bridged carbenoid complexes can participate in the catalytic cycle. Importantly, for the first time, a mechanistic pathway showing that these bridged species are not a dead end in Fe catalysis is presented. Their existence in other reactions might be more prevalent than what is currently believed. The current study will have important implications in utilizing Fe(III) complexes for other insertion reactions, especially for heme containing enzymes which necessarily need to be carried out under anaerobic/reducing conditions.

Isolating elusive 'Al(μ-O)M' intermediates in CO2 reduction by bimetallic Al-M complexes (M = Zn, Mg).

The reaction of compounds containing Al-Mg and Al-Zn bonds with N2O enabled isolation of the corresponding Al(μ-O)M complexes. Electronic structure analysis identified largely ionic Al-O and O-M bonds, featuring an anionic μ-oxo centre. Reaction with CO2 confirmed that these species correspond to the proposed intermediates in the formation of μ-carbonate compounds.

DFT Study on the Biosynthesis of Verrucosane Diterpenoids and Mangicol Sesterterpenoids: Involvement of Secondary-Carbocation-Free Reaction Cascades.

Some experimental observations indicate that a sequential formation of secondary (2°) carbocations might be involved in some biosynthetic pathways, including those of verrucosane-type diterpenoids and mangicol-type sesterterpenoids, but it remains controversial whether or not such 2° cations are viable intermediates. Here, we performed comprehensive density functional theory calculations of these biosynthetic pathways. The results do not support previously proposed pathways/mechanisms: in particular, we find that none of the putative 2° carbocation intermediates is involved in either of the biosynthetic pathways. In verrucosane biosynthesis, the proposed 2° carbocations (II and IV) in the early stage are bypassed by the formation of the adjacent 3° carbocations and by unusual skeletal rearrangement reactions, and in the later stage, the putative 2° carbocation intermediates (VI, VII, and VIII) are not present as the proposed forms but as nonclassical structures between homoallyl and cyclopropylcarbinyl cations. In the mangicol biosynthesis, one of the two proposed 2° carbocations (X) is bypassed by a C–C bond-breaking reaction to generate a 3° carbocation with a C=C bond, while the other (XI) is bypassed by a strong hyperconjugative interaction leading to a nonclassical carbocation. We propose new biosynthetic pathways/mechanisms for the verrucosane-type diterpenoids and mangicol-type sesterterpenoids. These pathways are in good agreement with the findings of previous biosynthetic studies, including isotope-labeling experiments and byproducts analysis, and moreover can account for the biosynthesis of related terpenes.

In search of alkene-diazene cross metathesis

Aside from alkene cross metathesis, involving two different alkene units, cross metathesis reactions of two functionally different unsaturated units - heterofunctional cross metathesis - are virtually unknown. We report here on our efforts to realize alkene-diazene cross metathesis to produce imines. The proven alkene-metathesis catalyst (Cy3P)2Cl2Ru = CHPh (1) reacts with aryl diazenes at room temperature to produce imines derived from coupling of the alkylidene unit of 1 with the nitrene fragment of the diazene. Attempts to induce catalytic alkene-diazene cross metathesis by 1 or (NHC)(PCy3)Cl2Ru = CHR (NHC = N-heterocyclic carbene, 2) result only in the transfer of the alkylidene unit from 1 without reaction of the alkene. 1H- and 31P NMR monitoring and other characterizational probes are consistent with the formation of an unreactive imido- or aza-metallacycle intermediate. DFT computational modeling of a potential catalytic pathway for diazene-alkene metathesis with (PMe3)2Cl2RuCH2 (4) has revealed viable intermediates and transition states, involving metal-carbene, metal-nitrene (imido) and derived azametallacyclobutanes. The turnover-limiting steps are calculated to occur during combination of the intermediate imido-complex (PMe3)2Cl2Ru = NMe (4) with alkene via a transition state for retrocyclization of an aza-ruthenacyclobutane (J) with a large energetic span of 47.8 kcal/mol. Modeling of the same reaction step with the experimental complex 1 reacting with PhN = NPh and PhCH = CHPh finds an even larger energetic span, accounting for the experimentally observed stoichiometric production of imine PhCH = NPh. In contrast, the corresponding energy profile for alkene-diazene metathesis promoted by phosphite-carbene complex [(MeO)3P]2Cl2RuCH2 (5) finds a much lower energetic span of 26.4 kcal/mol for conversion of imido complex G′ to imine via the aza-ruthenacyclobutane (J′) and that the turnover-limiting step would involve retrocyclization of the first stage diaza-metallacyclobutane C′ with an energetic span of 29.7 kcal/mol.

Assessing the Structure of Transmembrane Oligomeric Intermediates of an α‑Helical Toxin using Molecular Dynamics Simulations

Pore forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water soluble form (monomers), bind to the target membrane and conformationally transform (protomers), and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. PFTs are broadly classified into or alpha or beta toxins. In contrast to beta-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains have hindered our understanding of alpha-PFT pore formation. We use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial toxin Cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50- 500 ns, we show that transmembrane oligomeric intermediates or ‘arcs’ form stable proteo-lipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the timescale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of 53 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore formation pathway for ClyA.

Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics.

Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of nucleosomes obeys a precise pathway in which tetramers of histones H3 and H4 bind to the DNA first to form tetrasomes, and two dimers of histones H2A and H2B are subsequently incorporated to complete the complex. As viable intermediates, we previously showed that tetrasomes can spontaneously flip between a left-handed and right-handed conformation of DNA-wrapping. To pinpoint the underlying mechanism, here we investigated the role of the H3-H3 interface for tetramer flexibility in the flipping process at the single-molecule level. Using freely orbiting magnetic tweezers, we studied the assembly and structural dynamics of individual tetrasomes modified at the cysteines close to this interaction interface by iodoacetamide (IA) in real time. While such modification did not affect the structural properties of the tetrasomes, it caused a 3-fold change in their flipping kinetics. The results indicate that the IA-modification enhances the conformational plasticity of tetrasomes. Our findings suggest that subnucleosomal dynamics may be employed by chromatin as an intrinsic and adjustable mechanism to regulate DNA supercoiling.

Are Aminomethyl Thioesters Viable Intermediates in Native Chemical Ligation Type Amide Bond Forming Reactions?

The condensation of N-mercaptomethyl amines and thioesters is a potential route to amides, via aminomethyl thioester intermediates, in a native chemical ligation type process followed by self-cleavage of the ‘mercaptomethyl’ auxiliary. This paper describes investigations towards the preparation of aminomethyl thioesters, and subsequent conversion into amides, from a three-component coupling of formaldehyde, a thioacid, and an amine. Our studies suggest that while such intermediates may be formed en route to amides, no advantages are offered over the direct reaction of the amine and thioacid precursors.

Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin.

Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane-assisted protein aggregation to oligomerization and folding. Pore-forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water-soluble form (monomers) bind to the target membrane and conformationally transform (protomers) and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. On the basis of the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins. In contrast to β-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains has hindered our understanding of α-PFT pore formation. In this article, we use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial α-PFT, cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50 to 500 ns, we show that transmembrane oligomeric intermediates or "arcs" form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the time scale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse-grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of -52.9 ± 1.2 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore-formation pathway for ClyA.

Non-isocyanate route to amides and polyamides through reactions of aryl N-phenylcarbamates with carboxylic acids

In pursuit of green processes for synthesizing organic products and polymers, an efficient route of amide formation has been devised by reacting carbamates with carboxylic acids. Aryl N-phenylcarbamates were utilized as alternative reagents to replace aromatic isocyanates in amides and polyamides syntheses. The results showed that the high-yield of amide products can be produced from phospholene oxide-catalyzed reactions. This non-isocyanate route (NIR) resulted in amides with greater than 90 % amide selectivity and little urea or isocyanate by-product contaminants. The polyamides prepared from the subsequent reaction series between aryl N,N′-diphenyl biscarbamates and hexafluoroisopropylidene bis-benzoic acid (HFI-BBA) yielded soluble polyamides with high molecular weight and high thermal stability. Thus, aryl N-phenylcarbamates are considered as the viable intermediates for the green synthesis of amides or polyamides without using the toxic aromatic isocyanates.

Investigating the Handedness Dynamics of Tetrasomes

Nucleosomes formed by DNA wrapping around histone octamers are the basic compaction unit of eukaryotic chromatin. Besides packaging DNA, they also play an essential role in genome regulation by controlling DNA accessibility. Their assembly follows a precise pathway in which first tetramers of H3 and H4 histones bind to DNA, forming tetrasomes, and then two dimers of H2A and H2B histones complete the formation of full nucleosomes. Here, we present our single-molecule studies on the assembly of tetrasomes by directly measuring the length, twist, and torque of single DNA molecules using Freely Orbiting Magnetic Tweezers (FOMT) and electro-Magnetic Torque Tweezers (eMTT). By this means, we have investigated both the replication-coupled histone H3.1 and its replication-independent variant histone H3.3. Our results indicate that tetrasomes exhibit a spontaneous flipping between a preferentially occupied left-handed state (ΔLk = −0.73) and a less populated right-handed state (ΔLk = +1.0), while weak torques convert them from one state into the other. In addition, the stepwise assembly of full nucleosomes suggests that tetrasomes undergoing changes in handedness remain viable intermediates. We further show how studies performed on tetrasomes that are artificially modified at their H3-H3 interface provide more insight into their handedness dynamics. Our findings reveal dynamical rearrangements of the nucleosomal structure that illustrate how chromatin could regulate DNA-supercoiling.

Pyridonate-Supported Titanium(III). Benzylamine as an Easy-To-Use Reductant

The reaction of bis(3-phenyl-2-pyridonate)Ti(NMe2)2 with excess benzylamine leads to an unexpected reduction of the metal center from Ti(IV) to Ti(III). The reduced titanium species was isolated and revealed as tris(3-phenyl-2-pyridonate)Ti(NH2Bn)2. Ammonia and N-benzyl-1-phenylmethanimine are released as byproducts of the reaction, thereby confirming benzylamine as a mild reductant. This new pyridonate-supported titanium(III) complex has been fully characterized, and experimental data and theoretical calculations confirm a d1 metal center with no ligand-based radical character. This Ti(III) complex does not react with aminoalkenes, suggesting that radical species are not viable intermediates for the hydroaminoalkylation or hydroamination reaction.

Are copper(I) carbenes capable intermediates for cyclopropanations? The case for ylide intermediates.

A novel approach is used to synthesize a stable, ligated copper(I) carbene in the gas phase that is capable of typical metal carbenoid chemistry. However, it is shown that copper(I) carbenes generally undergo rapid unimolecular rearrangements including insertions into copper-ligand bonds and Wolff rearrangements. The results indicate that most copper(I) carbenes are inherently unstable and would not be viable intermediates in condensed-phase applications; an alternative intermediate that is less prone to rearrangements is required. Computational data suggest that ylides formed by the complexation of the carbene with solvent or other weak nucleophiles are viable intermediates in the reactions of copper(I) carbenes.

Formation of the Palladium(IV) Complex [(Me3tacn)PdIVMe3]+ through Aerobic Oxidation of (Me3tacn)PdIIMe2 (Me3tacn = N,N′,N″-Trimethyl-1,4,7-triazacyclononane)

The dimethyl PdII complex (Me3tacn)PdIIMe2 (Me3tacn = N,N′,N″-trimethyl-1,4,7-triazacyclononane) undergoes facile aerobic oxidation to yield the stable species [(Me3tacn)PdIVMe3]+. EPR, UV–vis, and ESI-MS studies suggest an inner-sphere mechanism for the oxidation of (Me3tacn)PdMe2 by O2 and formation of PdIV species. In addition, the structurally characterized complex [(Me3tacn)PdIVMe3]I undergoes selective elimination of ethane at elevated temperatures. Overall, this system represents one of the first examples of aerobic oxidation of a PdII organometallic precursor to yield a well-defined PdIV product, supporting the role of PdIV species as viable intermediates in Pd-mediated catalytic or stoichiometric aerobic oxidative transformations.

ChemInform Abstract: Gold‐Catalyzed Intermolecular Reactions of Propiolic Acids with Alkenes: [4 + 2] Annulation and Enyne Cross Metathesis.

A gold-catalyzed intermolecular reaction of propiolic acids with alkenes led to a [4 + 2] annulation or enyne cross metathesis. The [4 + 2] annulation proceeds with net cis-addition with respect to alkenes and provides an expedient route to α,β-unsaturated δ-lactones, for which preliminary asymmetric reactions were also demonstrated. For 1,2-disubstituted alkenes, unprecedented enyne cross metathesis occurred to give 1,3-dienes in a completely stereospecific fashion. DFT calculations and experiments indicated that the cyclobutene derivatives are not viable intermediates and that the steric interactions during concerted σ-bond rearrangements are responsible for the observed unique stereospecificity.

Gold-Catalyzed Intermolecular Reactions of Propiolic Acids with Alkenes: [4 + 2] Annulation and Enyne Cross Metathesis

A gold-catalyzed intermolecular reaction of propiolic acids with alkenes led to a [4 + 2] annulation or enyne cross metathesis. The [4 + 2] annulation proceeds with net cis-addition with respect to alkenes and provides an expedient route to α,β-unsaturated δ-lactones, for which preliminary asymmetric reactions were also demonstrated. For 1,2-disubstituted alkenes, unprecedented enyne cross metathesis occurred to give 1,3-dienes in a completely stereospecific fashion. DFT calculations and experiments indicated that the cyclobutene derivatives are not viable intermediates and that the steric interactions during concerted σ-bond rearrangements are responsible for the observed unique stereospecificity.

The Structure of a Truncated Phosphoribosylanthranilate Isomerase Suggests a Unified Model for Evolution of the (βα)8 Barrel Fold

The (βα)8 barrel is one of the most common protein folds, and enzymes with this architecture display a remarkable range of catalytic activities. Many of these functions are associated with ancient metabolic pathways, and phylogenetic reconstructions suggest that the (βα)8 barrel was one of the very first protein folds to emerge. Consequently, there is considerable interest in understanding the evolutionary processes that gave rise to this fold. In particular, much attention has been focused on the plausibility of (βα)8 barrel evolution from homodimers of half barrels. However, we previously isolated a three-quarter-barrel-sized fragment of a (βα)8 barrel, termed truncated phosphoribosylanthranilate isomerase (trPRAI), that is soluble and almost as thermostable as full-length N-(5′-phosphoribosyl)anthranilate isomerase (PRAI). Here, we report the NMR-derived structure of trPRAI. The subdomain is monomeric, is well ordered and adopts a native-like structure in solution. Side chains from strands β1 (Glu3 and Lys5), β2 (Tyr25) and β6 (Lys122) of trPRAI repack to shield the hydrophobic core from the solvent. This result demonstrates that three-quarter barrels were viable intermediates in the evolution of the (βα)8 barrel fold. We propose a unified model for (βα)8 barrel evolution that combines our data, previously published work and plausible scenarios for the emergence of (initially error-prone) genetic systems. In this model, the earliest proto-cells contained diverse pools of part-barrel subdomains. Combinatorial assembly of these subdomains gave rise to many distinct lineages of (βα)8 barrel proteins, that is, our model excludes the possibility that there was a single (βα)8 barrel from which all present examples are descended.

Perylenequinone Natural Products: Enantioselective Synthesis of the Oxidized Pentacyclic Core

An enantioselective approach to the perylenequinone core found in the mold perylenequinone natural products is outlined. Specifically, the first asymmetric syntheses of helical chiral perylenequinones absent any additional stereogenic centers are described. Key elements of the synthetic venture include a catalytic enantioselective biaryl coupling, a PIFA-induced naphthalene hydroxylation, and a palladium-mediated aromatic decarboxylation. Transfer of the binaphthalene axial stereochemistry to the perylenequinone helical stereochemistry proceeded with good fidelity. Furthermore, the resultant perylenequinones were shown to possess sufficient atropisomeric stability to be viable intermediates in the biogenesis of the perylenequinone natural products. This stability supports the use of the helical axis as a stereochemical relay in synthesis of the natural products containing additional stereochemical centers.

On the XeF+/H2O System: Synthesis and Characterization of the Xenon(II) Oxide Fluoride Cation, FXeOXeFXeF+

The reported synthesis of the H(2)OF(+) cation as a product of the oxidative fluorination of H(2)O by [XeF][PnF(6)] (Pn = As, Sb) in HF solution has been reinvestigated. The system exhibits complex equilibria, producing two new Xe(II) compounds, [Xe(3)OF(3)][PnF(6)] and [H(3)O][PnF(6)] x 2 XeF(2), refuting the original claim for the synthesis of the H(2)OF(+) cation. Both compounds have been isolated and characterized by vibrational spectroscopy and single-crystal X-ray diffraction. The X-ray crystal structures of the [Xe(3)OF(3)][PnF(6)] salts contain the Z-shaped FXeOXeFXeF(+) cation, which represents the first example of an isolated Xe(II) oxide fluoride. The crystal structure of the [H(3)O][AsF(6)] x 2 XeF(2) adduct contains XeF(2) molecules that interact with the H(3)O(+) cations. The vibrational assignments for the Xe(3)OF(3)(+) cation have been made with the aid of quantum-chemical calculations and were confirmed by (18)O-enrichment, and the assignments for [H(3)O][AsF(6)] x 2 XeF(2) were confirmed by (2)D- and (18)O-enrichment. Quantum-chemical calculations have also been carried out for H(3)O(+) x nXeF(2) (n = 1-4) and have been used to interpret the X-ray crystal structure and vibrational spectra of [H(3)O][AsF(6)] x 2 XeF(2). The energy-minimized geometries and vibrational frequencies for HOF and H(2)OF(+) have been calculated, further disproving the original report of the H(2)OF(+) cation. Both FXeOH and FXeOH(2)(+) have also been computed and are viable intermediates in the proposed equilibria between XeF(+) and H(2)O that lead to the Xe(3)OF(3)(+) cation.

Tropoelastin Massively Associates during Coacervation To Form Quantized Protein Spheres

Tropoelastin, the precursor of elastin, undergoes a rapid monomer to multimer association in an inverse temperature transition. This association culminates in the rapid formation of stable, optically distinct droplets of tropoelastin. Light scattering and microscope measurements reveal that these droplets are 2-6 microm in diameter. Scanning electron microscopy confirms that the droplets are spherical. Three-dimensional confocal image stacks based on the autofluorescence of tropoelastin reveal that droplets are loaded with hydrated tropoelastin. Droplets are viable intermediates in synthetic elastin macroassembly. Dense clusters of aggregated droplets and partially formed fibers develop when droplets are incubated in the presence of a lysyl oxidase. Lysine-reacting chemical and enzyme-assisted cross-linking conditions generate cross-linked beads due to interactions between multiple, surface-exposed lysine epsilon-amino groups. Droplets represent an efficient mechanism for the bolus delivery during elastogenesis of quantized packages of preaccreted tropoelastin.