Photochemical Skeletal Editing of Pyridines to Bicyclic Pyrazolines and Pyrazoles.

We present an efficient one-pot photochemical skeletal editing protocol for the transformation of pyridines into diverse bicyclic pyrazolines and pyrazoles under mild conditions. The method requires no metals, photocatalysts, or additives and allows for the selective removal of specific carbon atoms from pyridines, allowing for unprecedented versatility. Our approach offers a convenient and efficient means for the late-stage modification of complex drug molecules by replacing the core pyridine skeleton. Moreover, we have successfully scaled up this procedure in stop-flow and flow-chemistry systems, showcasing its applicability to intricate transformations such as the Diels-Alder reaction, hydrogenation, [3 + 2] cycloaddition, and Heck reaction. Through control experiments and DFT calculations, we provide insights into the mechanistic underpinnings of this skeletal editing protocol.

Iron Heme Enzyme-Catalyzed Cyclopropanations with Diazirines as Carbene Precursors: Computational Explorations of Diazirine Activation and Cyclopropanation Mechanism.

The mechanism of cyclopropanations with diazirines as air-stable and user-friendly alternatives to commonly employed diazo compounds within iron heme enzyme-catalyzed carbene transfer reactions has been studied by means of density functional theory (DFT) calculations of model systems, quantum mechanics/molecular mechanics (QM/MM) calculations, and molecular dynamics (MD) simulations of the iron carbene and the cyclopropanation transition state in the enzyme active site. The reaction is initiated by a direct diazirine-diazo isomerization occurring in the active site of the enzyme. In contrast, an isomerization mechanism proceeding via the formation of a free carbene intermediate in lieu of a direct, one-step isomerization process was observed for model systems. Subsequent reaction with benzyl acrylate takes place through stepwise C-C bond formation via a diradical intermediate, delivering the cyclopropane product. The origin of the observed diastereo- and enantioselectivity in the enzyme was investigated through MD simulations, which indicate a preferred formation of the cis-cyclopropane by steric control.

Comparison of Cyclic and Linear PEG Conjugates.

Bioconjugation of polymers to proteins is a method to impart improved stability and pharmacokinetic properties to biologic systems. However, the precise effects of polymer architecture on the resulting bioconjugates are not well understood. Particularly, cyclic polymers are known to possess unique features such as a decreased hydrodynamic radius when compared to their linear counterparts of the same molecular weight, but have not yet been studied. Here, we report the first bioconjugation of a cyclic polymer, poly(ethylene glycol) (PEG), to a model protein, T4 lysozyme, containing a single engineered cysteine residue (V131C). We compare the stability and activity of this conjugate with those of a linear PEG-T4 lysozyme analogue of similar molecular weight. Furthermore, we used molecular dynamics (MD) simulations to determine the behavior of the polymer-protein conjugates in solution. We introduce cyclic polymer-protein conjugates as potential candidates for the improvement of biologic therapeutics.

A 21st Century View of Allowed and Forbidden Electrocyclic Reactions.

In 1965, Woodward and Hoffmann proposed a theory to predict the stereochemistry of electrocyclic reactions, which, after expansion and generalization, became known as the Woodward-Hoffmann Rules. Subsequently, Longuet-Higgins and Abrahamson used correlation diagrams to propose that the stereoselectivity of electrocyclizations could be explained by the correlation of reactant and product orbitals with the same symmetry. Immediately thereafter, Hoffmann and Woodward applied correlation diagrams to explain the mechanism of cycloadditions. We describe these discoveries and their evolution. We now report an investigation of various electrocyclic reactions using DFT and CASSCF. We track the frontier molecular orbitals along the intrinsic reaction coordinate and modeled trajectories and examine the correlation between HOMO and LUMO for thermally forbidden systems. We also investigate the electrocyclizations of several highly polarized systems for which the Houk group had predicted that donor-acceptor substitution can induce zwitterionic character, thereby providing low-energy pathways for formally forbidden reactions. We conclude with perspectives on the field of pericyclic reactions, including a refinement as the meaning of Woodward and Hoffmann's "Violations. There are none!" Lastly, we comment on the burgeoning influence of computations on all fields of chemistry.

Characterizing Hydroxyl Radical Formation from the Light-Driven Fe(II)-Peracetic Acid Reaction, a Key Process for Aerosol-Cloud Chemistry.

The reaction of peracetic acid (PAA) and Fe(II) has recently gained attention due to its utility in wastewater treatment and its role in cloud chemistry. Aerosol-cloud interactions, partly mediated by aqueous hydroxyl radical (OH) chemistry, represent one of the largest uncertainties in the climate system. Ambiguities remain regarding the sources of OH in the cloud droplets. Our research group recently proposed that the dark and light-driven reaction of Fe(II) with peracids may be a key contributor to OH formation, producing a large burst of OH when aerosol particles take up water as they grow to become cloud droplets, in which reactants are consumed within 2 min. In this work, we quantify the OH production from the reaction of Fe(II) and PAA across a range of physical and chemical conditions. We show a strong dependence of OH formation on ultraviolet (UV) wavelength, with maximum OH formation at λ = 304 ± 5 nm, and demonstrate that the OH burst phenomenon is unique to Fe(II) and peracids. Using kinetics modeling and density functional theory calculations, we suggest the reaction proceeds through the formation of an [Fe(II)-(PAA)2(H2O)2] complex, followed by the formation of a Fe(IV) complex, which can also be photoactivated to produce additional OH. Determining the characteristics of OH production from this reaction advances our knowledge of the sources of OH in cloudwater and provides a framework to optimize this reaction for OH output for wastewater treatment purposes.

Chemiexcitation Acceleration of 1,2-Dioxetanes by Spiro-Fused Six-Member Rings with Electron-Withdrawing Motifs.

The chemiluminescent light-emission pathway of phenoxy-1,2-dioxetane luminophores attracts growing interest within the scientific community. Dioxetane probes undergoing rapid flash-type chemiexcitation exhibit higher detection sensitivity than those with a slow glow-type chemiexcitation rate. We discovered that dioxetanes fused to non-strained six-member rings, with hetero atoms or inductive electron-withdrawing groups, present both accelerated chemiexcitation rates and elevated chemical stability compared to dioxetanes fused to four-member strained rings. DFT computational simulations supported the chemiexcitation acceleration observed by spiro-fused six-member rings with inductive electron-withdrawing groups of dioxetanes. Specifically, a spiro-dioxetane with a six-member sulfone ring exhibited a chemiexcitation rate 293-fold faster than that of spiro-adamantyl-dioxetane. A turn-ON dioxetane probe for the detection of the enzyme ß-galactosidase, containing the six-member sulfone unit, exhibited a S/N value of 108 in LB cell growth media. This probe demonstrated a substantial increase in detection sensitivity towards E. coli bacterial cells expressing ß-galactosidase, with an LOD value that is 44-fold more sensitive than that obtained by the adamantyl counterpart. The accelerated chemiexcitation and the elevated chemical stability presented by dioxetane containing a spiro-fused six-member ring with a sulfone inductive electron-withdrawing group, make it an ideal candidate for designing efficient turn-on chemiluminescent probes with exceptionally high detection sensitivity.

Genome Mining from Agriculturally Relevant Fungi Led to a d-Glucose Esterified Polyketide with a Terpene-like Core Structure.

Comparison of biosynthetic gene clusters (BGCs) found in devastating plant pathogens and biocontrol fungi revealed an uncharacterized and conserved polyketide BGC. Genome mining identified the associated metabolite to be treconorin, which has a terpene-like, trans-fused 5,7-bicyclic core that is proposed to derive from a (4 + 3) cycloaddition. The core is esterified with d-glucose, which derives from the glycosidic cleavage of a trehalose ester precursor. This glycomodification strategy is different from the commonly observed glycosylation of natural products.

Computational Exploration of the Thermal Rearrangement of Basketene: One Forbidden versus Two Allowed Pericyclic Reactions.

The thermal rearrangement of basketene to Nenitzescu's hydrocarbon has been explored using density functional theory (M06-2X and ωB97X-D) and DLPNO-CCSD(T) quantum mechanics. Both the sequential thermally allowed retro Diels-Alder followed by Cope rearrangement and the thermally forbidden retro-[2 + 2] cycloaddition were studied. The controlling role of orbital symmetry rather than reaction thermodynamics is demonstrated.

Computational Study of Iron-Catalyzed Intramolecular [2 + 2] Cycloaddition and Cycloisomerization of Enyne Acetates: Mechanism and Selectivity.

The mechanism of iron-catalyzed intramolecular [2 + 2] cycloaddition and cycloisomerization of enyne acetates has been investigated with DFT computations. Both mechanisms start the catalytic cycle from the stepwise 1,2-acyloxy migration to afford the iron carbene. The [2 + 2] cycloaddition mechanism involves subsequent key steps of [2 + 2] cycloaddition, 1,2-acyloxy migration, and reductive elimination to generate the azabicyclo [3.2.0] heptane product, with the reductive elimination being the rate-determining step. The cycloisomerization mechanism involves subsequent key steps of [2 + 2] cycloaddition, stepwise 1,4-acyloxy migration to produce the allenylpyrrolidine product, with the 1,4-acyloxy migration being the rate-determining step. Reaction potential energy surfaces for two model substrates that have or do not have alkene-terminal substituents have been investigated and the origins of the selectivities have been disclosed. Moreover, energy profiles with three possible spin states (SFe = 0, 1, 2) have been considered. The reaction is suggested to occur mainly on the singlet potential energy surface with a few spin crossovers between singlet and triplet states involved, which indicates that this reaction should have two-state reactivity (TSR).

Experimental and Theoretical Exploration of the Kinetics and Thermodynamics of the Nucleophile-Induced Fragmentation of Ylidenenorbornadiene Carboxylates.

Ylidenenorbornadienes (YNDs), prepared by [4 + 2] cycloadditions between fulvenes and acetylene carboxylates, react with thiol nucleophiles to yield mixtures of four to eight diastereomers depending on the symmetry of the YND substrate. The mixtures of diastereomers fragment via a retro-[4 + 2] cycloaddition with a large variation in rate, with half-lives ranging from 16 to 11,000 min at 80 °C. The diastereomer-enriched samples of propane thiol adducts [YND-propanethiol (PTs)] were isolated and identified by nuclear Overhauser effect spectroscopy (NOESY) correlations. Simulated kinetics were used to extrapolate the rate constants of individual diastereomers from the observed rate data, and it correlated well with rate constants measured directly and from isolated diastereomer-enriched samples. The individual diastereomers of a model system fragment at differing rates with half-lives ranging from 5 to 44 min in CDCl3. Density functional theory calculations were performed to investigate the mechanism of fragmentation and support an asynchronous retro-[4 + 2] cycloaddition transition state. The computations generally correlated well with the observed free energies of activation for four diastereomers of the model system as a whole, within 2.6 kcal/mol. However, the observed order of the fragmentation rates across the set of diastereomers deviated from the computational results. YNDs display wide variability in the rate of fragmentation, dependent on the stereoelectronics of the ylidene substituents. A Hammett study showed that the electron-rich aromatic rings attached to the ylidene bridge increase the fragmentation rate, while electron-deficient systems slow fragmentation rates.

C3-Cyanation of Pyridines: Constraints on Electrophiles and Determinants of Regioselectivity.

Methods for C-H cyanation of pyridines are rare. Here, we report a method for C3-selective cyanation of pyridines by a tandem process with the reaction of an in situ generated dihydropyridine with a cyano electrophile as the key step. The method is suitable for late-stage functionalization of pyridine drugs. The low reduction potential of the electrophile and effective transfer of the nitrile group were found to be essential for the success of this method. We studied the reaction mechanism in detail by means of control experiments and theoretical calculations and found that a combination of electronic and steric factors determined the regioselectivity of reactions involving C2-substituted pyridines.

Enzymatic Benzofuranoindoline Formation in the Biosynthesis of the Strained Bridgehead Bicyclic Dipeptide (+)-Azonazine A.

We uncovered and reconstituted a concise biosynthetic pathway of the strained dipeptide (+)-azonazine A from marine-derived Aspergillus insulicola. Formation of the hexacyclic benzofuranoindoline ring system from cyclo-(l-Trp-N-methyl-l-Tyr) is catalyzed by a P450 enzyme through an oxidative cyclization. Supplementing the producing strain with various indole-substituted tryptophan derivatives resulted in the generation of a series of azonazine A analogs.

Ambimodal Bispericyclic [6 + 4]/[4 + 6] Transition State Competes with Diradical Pathways in the Cycloheptatriene Dimerization: Dynamics and Experimental Characterization of Thermal Dimers.

The thermal dimerization of cycloheptatriene is predicted to occur by a concerted [6 + 4] cycloaddition via an ambimodal [6 + 4]/[4 + 6] transition state (TS) and a competing stepwise diradical (6 + 2) cycloaddition; both dimers subsequently undergo intramolecular [4 + 2] cycloadditions to afford thermally stable tetracyclic products. The ambimodal TS is the 10π-electron version of the prototype bispericyclic dimerization of cyclopentadiene discovered by Caramella et al. in 2002. Quantum mechanical studies using several common DFT functionals and post-HF methods, ωB97X-D, M06-2X, DLPNO-CCSD(T), NEVPT2, and PWPB95-D3(BJ), and quasiclassical molecular dynamics simulations provide details of bond timing and bifurcation pathways. By comparing the ambimodal [6 + 4]/[4 + 6] TS for cycloheptatriene dimerization with the ambimodal [4 + 2]/[2 + 4] TS of cyclopentadiene dimerization, we found that the high distortion energy in cycloheptatriene dimerization is the key to its relatively high energy barrier. The computational investigations were coupled with experimental studies of the cycloheptatriene dimerization, which resulted in the isolation of the two tetracyclic dimers. At lower temperature, the product from the predicted exo-[6 + 4]/[4 + 6] cycloaddition, followed by a subsequent intramolecular [4 + 2] cycloaddition, predominantly forms, while at higher temperature, the diradical (6 + 2) cycloadduct is the major product.

Photooxidation-Driven Purely Organic Room-Temperature Phosphorescent Lysosome-Targeted Imaging.

The construction of host-guest-binding-induced phosphorescent supramolecular assemblies has become one of increasingly significant topics in biomaterial research. Herein, we demonstrate that the cucurbit[8]uril host can induce the anthracene-conjugated bromophenylpyridinium guest to form a linear supramolecular assembly, thus facilitating the enhancement of red fluorescence emission by the host-stabilized charge-transfer interactions. When the anthryl group is photo-oxidized to anthraquinone, the obtained linear nanoconstructs can be readily converted into the homoternary inclusion complex, accompanied by the emergence of strong green phosphorescence in aqueous solution. More intriguingly, dual organelle-targeted imaging abilities have been also distinctively achieved in nuclei and lysosomes after undergoing photochemical reaction upon UV irradiation. This photooxidation-driven purely organic room-temperature phosphorescence provides a convenient and feasible strategy for supramolecular organelle identification to track specific biospecies and physiological events in the living cells.

Lewis-Acid-Promoted Ligand-Controlled Regiodivergent Cycloaddition of Pd-Oxyallyl with 1,3-Dienes: Reaction Development and Origins of Selectivities.

For nearly 30 years, considerable research effort has been focused on the development of methods for catalytic (3 + 2) cycloaddition reactions of palladium-oxyallyl species with alkenes. However, because C-O bond formation is kinetically favored, the (3 + 2) cycloadditions achieved to date have involved C-O reductive elimination. We herein report a method of lithium triflate-promoted (3 + 2) cycloaddition reactions of palladium-oxyallyl species with 1,3-dienes that proceed via a pathway terminated with C-C bond formation to give a five-membered carbocycle. Coordination of the lithium ion with the alkoxide moiety disrupts the C-O reductive elimination and forms a metal-enolate tethered π-allyl-Pd. The π-allyl-Pd moiety then accepts intramolecular allylic attack from the enolate moiety to form carbocyclic products. Furthermore, by tuning the steric properties of the palladium ligand, we could also accomplish the competing (4 + 3) cycloadditions, and thus this method provides regiodivergent access to both cyclopentanones and cycloheptanones. The reaction mechanism was investigated by DFT calculation and the origins of the regioselectivities of the cycloaddition were rationalized.

Ammonia stress on nitrogen metabolism in tolerant aquatic plant-Myriophyllum aquaticum.

Ammonia has been a major reason of macrophyte decline in the water environment, and ammonium ion toxicity should be seen as universal, even in species frequently labeled as "NH4+ specialists". To study the effects of high NH4+-N stress of ammonium ion nitrogen on tolerant submerged macrophytes and investigate the pathways of nitrogen assimilation in different organisms, Myriophyllum aquaticum was selected and treated with various concentrations of ammonium ions at different times. Increasing of ammonium concentration leads to an overall increase in incipient ammonia content in leaves and stems of plants. In middle and later stages, high concentrations of NH4+ ion nitrogen taken up by M. aquaticum decreased, whereas the content of NO3- ion nitrogen increased. Moreover, in M. aquaticum, the activities of the enzymes nitrate reductase, glutamine synthetase and asparagine synthetase changed remarkably in the process of alleviating NH4+ toxicity and deficiency. The results of the present study may support the studies on detoxification of high ammonium ion content in NH4+-tolerant submerged macrophytes and exploration of tissue-specific expression systems.

Bioleaching in batch tests for improving sludge dewaterability and metal removal using Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans after cold acclimation.

Bioleaching is a promising technology for removal of metals from sludge and improvement of its dewaterability. Most of the previous studies of bioleaching were focused on removal of metals; bioleaching in cold environments has not been studied extensively. In this study, Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans were acclimated at 15 °C and co-inoculated to explore the optimal conditions for improvement of sludge dewaterability and removal of metals by the sequencing batch reactors. The data show after 6 days of bioleaching at 15 °C, 89.6% of Zn, 72.8% of Cu and 39.4% of Pb were removed and the specific resistance to filtration (SRF) was reduced to ∼12%. In addition, the best conditions for bioleaching are an initial pH of 6, a 15% (v/v) inoculum concentration, and A. thiooxidans and A. ferrooxidans mixed in a ratio of 4:1. We found that bioleaching of heavy metals is closely related to final pH, while the sludge SRF is dominated by other factors. Bioleaching can be completed in 6 days, and the sludge dewaterability and removal of metals at 15 °C meet the requirements of most sewage treatment plants.

Why •CF2H is nucleophilic but •CF3 is electrophilic in reactions with heterocycles.

Radical substitution is a useful method to functionalize heterocycles, as in the venerable Minisci reaction. Empirically observed regiochemistries indicate that the CF2H radical has a nucleophilic character similar to alkyl radicals, but the CF3 radical is electrophilic. While the difference between •CH3 and •CF3 is well understood, the reason that one and two Fs make little difference but the third has a large effect is puzzling. DFT calculations with M06-2X both reproduce experimental selectivities and also lead to an explanation of this difference. Theoretical methods reveal how the F inductive withdrawal and conjugative donation alter radical properties, but only CF3 becomes decidedly electrophilic toward heterocycles. Here, we show a simple model to explain the radical orbital energy trends and resulting nucleophilicity or electrophilicity of fluorinated radicals.

Evaluation of Retro-Aldol vs Retro-Carbonyl-Ene Mechanistic Pathways in a Complexity-Generating C-C Bond Fragmentation.

We report an experimental and computational investigation of the likely mechanism of a cascade reaction. The reaction involves an intramolecular Diels-Alder reaction, followed by a C-C bond cleavage, to afford a complex bridged bicyclic product. As multiple reaction pathways could be envisioned for the latter step, the mechanism of the C-C bond cleavage step was investigated. Two reasonable reaction pathways were evaluated. Both computations and experiments indicate that the C-C bond cleavage step proceeds by a retro-carbonyl-ene pathway rather than a retro-aldol pathway. This report underscores the synergy between computational and experimental studies and establishes the mechanism of an interesting complexity-generating transformation.