α‐Alkylene‐β‐lactone is an important skeleton in a variety of biologically active molecules. It is of great significance to study the mechanism of regioselective cyclocarbonylation of tertiary alkynols catalyzed by palladium, which is applied to the synthesis of α‐alkylene‐β‐lactone. We employed density functional theory (DFT) calculations at the M06‐2X level to investigate the valence state of Pd participating in the catalytic cycle, the reaction pathways, and the mechanism of ligand‐controlled regioselectivity. Our results reveal that palladium participates in the reaction with the Pd(II) oxidation state. Distortion/interaction–activation strain(D/I‐AS) analyses indicate that the regioselectivity of the reaction with ligand L1 is predominantly governed by hydrogen–bond interaction in alkyne migration insertion, while the regioselectivity of the reaction with ligand L2 is mainly governed by kinetically suppressing byproduct formation.

Allenes and alkynes are versatile functional groups in total synthesis, medicinal chemistry, and bioorthogonal conjugation. The biosynthetic logic of how Nature installs allene or alkyne in natural products, especially that of allenes, is not well understood. Here we uncovered allenes and alkynes can be formed enzymatically through oxidative C(sp 2)-demethylation of the common five-carbon prenyl group. Two fungal cytochrome P450 monooxygenases, PpnB and NseB, from the penipratynolene and sinuxylamide biosynthetic pathways, respectively, were shown to catalyze oxidative removal of a C(sp 2)-methyl group in O-prenyl-l-tyrosine to afford O-homoallenyl-l-tyrosine and O-but-2-ynyl-l-tyrosine, respectively. Combining density functional theory calculations, heterologous expression, biotransformation and enzymatic assays with isotopically labeled substrates, a mechanism involving selective C-C bond cleavage followed by product-determining hydrogen atom abstraction is presented. An additional P450 enzyme from the penipratynolene pathway, PpnD, acts as an oxidative isomerase that converts the four-carbon terminal allene into a terminal alkyne. This unprecedented enzymatic editing strategy to install allene and alkyne expands the catalytic repertoire of P450 enzymes.

ABSTRACT Bioorthogonal reactions have revolutionized our way of performing chemistry in a highly complex biological environment. In particular, strain‐promoted 1,3‐dipolar cycloadditions, employing cyclooctyne probes in conjunction with azido‐reporters (strain‐promoted alkyne‐azide cycloaddition, SPAAC), have permitted the labeling and visualization of bio‐macromolecules in vitro, in living cells, as well as in animals. However, SPAAC's slow kinetics (< 1 M −1 s −1 ), in combination with the necessity to eliminate the excess of the used fluorescent probes, have hampered its widespread application, especially for the real‐time imaging of low concentration targets. Here we describe two novel thiophene‐based cycloalkynes that not only exhibit very high kinetics toward a variety of 1,3‐dipoles (up to 1528 M −1 s −1 ), but are also efficiently turned‐on (up to 150‐fold increase in brightness) upon reaction with their target. We demonstrated their fast and fluorogenic capabilities by monitoring the labeling overtime of a glycoprotein in physiological and no‐wash conditions, using as little as 5 µM of the probes and reaching full labeling in less than 15 min. These fluorogenic cycloalkynes significantly expand our chemical biology toolbox, and we anticipate them to open new avenues for the fast and real‐time imaging of biomolecules in complex environments.

The ring opening of cyclopropenes provides a compelling platform for the rapid synthesis of various polysubstituted acyclic alkenes. However, radical-mediated reactions of this type remain underexplored, and none of the existing methods have successfully produced tetrasubstituted olefins with high stereoselectivity. We present here an aminative ring-opening of cyclopropenes with iron-aminyl radical to afford tetrasubstituted alkenyl nitriles in a highly stereoselective manner. Computational studies indicate that both the substrate-directed radical addition and the following stereospecific ring-opening of cyclopropyl radical contribute to the extraordinary stereocontrol observed in the reaction. In addition, trisubstituted alkenyl nitriles could also be obtained using this method or via a base-promoted isomerization of the tetrasubstituted alkenyl nitriles, both with consistently high stereoselectivity.

Manipulation of polar functional groups to extend the druggability and developability space is an important approach in the current field of drug discovery. Here, we report an editing method that enables the direct insertion of anthranilyl units into inert amides to form versatile oligoamides and cyclic peptides under exceptionally mild reaction conditions. We showcase a diverse array of pharmaceuticals, natural products, and bioactive molecules involving the mentioned scaffold insertion. The synthesis of the secondary metabolites from marine-derived fungi, the expedited construction of bioactive molecules, and the assembly of functionalized peptide macrocycles through iterative insertions highlight the synthetic utility of this method. Computational tools and experimental measurements indicate that a hydrogen bond network formed by reacting and catalytic amide enables the insertion of the anthranilyl unit into a C─N bond.

A kinetic, product, and computational study on the reactions of the cumyloxyl radical (CumO(center dot)) with 1,4-dimethyl- and 1,4-diphenylcyclohexanes is reported. The rate constants for hydrogen atom transfer (HAT) from the C-H bonds of these substrates to CumO(center dot), together with the corresponding oxygenation product distributions reveal the role of strain release on reaction site selectivity. Transition structures and activation barriers obtained by DFT calculations are in excellent agreement with the experimental results. Tertiary/secondary ratios of oxygenation products of 0.6, 1.0, and 3.3 were observed, for trans-1,4-dimethyl-, cis-1,4-dimethyl-, and trans-1,4-di- phenylcyclohexane, respectively. With cis-1,4-diphenylcyclohexane, exclusive formation of the diastereomeric tertiary alcohol products was observed. Within the two diastereomeric couples, the tertiary equatorial C-H bond in the cis- isomer is ca. 6 and 27 times more reactive, respectively, than the tertiary axial ones, a behavior that reflects the release of 1,3-diaxial strain in the HAT transition state. The tertiary axial C-H bonds of the four substrates show remarkably similar reactivities in spite of the much greater stabilization of the benzyl radicals resulting from HAT from the 1,4-diphenylcyclohexanes. The lack of benzylic acceleration is discussed in the framework of Bernasconi's'principle of nonperfect synchronization'.

Berberine bridge enzyme (BBE)-like enzymes catalyze various oxidative cyclization and dehydrogenation reactions in natural product biosynthesis, but the molecular mechanism underlying the selectivity remains unknown. Here, we elucidated the catalytic mechanism of BBE-like oxidases from Morus alba involved in the oxidative cyclization and dehydrogenation of moracin C. X-ray crystal structures of a functionally promiscuous flavin adenine dinucleotide (FAD)-bound oxidase, MaDS1, with and without an oxidative dehydrogenation product were determined at 2.03 Å and 2.21 Å resolution, respectively. Structure-guided mutagenesis and sequence analysis have identified a conserved aspartic acid that directs the reaction toward the oxidative dehydrogenation pathway. A combination of density functional theory (DFT) calculations and molecular dynamics (MD) simulations has revealed that aspartic acid acts as the catalytic base to deprotonate the carbon-cation intermediate to generate the dehydrogenated product, which otherwise undergoes a spontaneous 6π electrocyclization in the oxidative cyclization pathway to furnish the 2H-benzopyran product.

N-Aryl ketenimines have been established as highly reactive aza-dienophiles. Intermolecular cycloadditions are achieved upon heating in the presence of 2,5-bis(silyloxy)furans and proceed with high levels of peri-, regio-, chemo- and diastereo-selectivity. Spontaneous C-O cleavage yields oxygenated pyridone derivatives in a highly convergent and redox-neutral manner. Combined experimental and computational studies demonstrate N-aryl ketenimines to be significantly more reactive than imino dienophiles, as a consequence of less distorted transition states. Derivatization studies include the development of isocyanate and cyclic ketenimine equivalents as aza-dienophiles, while extension to a one-pot aza-Diels-Alder/oxa-Diels-Alder sequence provides a three-component approach to complex fused pyridone/pyran systems.

We report the enantioselective hydrodifluoroalkylation of alkenes proceeding via an asymmetric hydrogen atom transfer (HAT) event catalyzed by thiol-containing tetrapeptides. Photocatalytic generation of a difluoroacetyl radical followed by carbon-carbon bond formation results in a prochiral carbon-centered radical that engages with the chiral catalyst. A trialkylamine reductant is proposed to turn over the catalyst in this net-reductive transformation. Notably, incorporating an (S)-β-methyl-substituted cysteine as the N-terminal residue improved selectivity relative to that of the native N-terminal cysteine (Cys) residue, and X-ray crystallographic analysis supports the conformational underpinning of this effect. A range of enantioenriched γ-substituted amides were synthesized in up to a 96:4 enantiomeric ratio, demonstrating the broad functional group tolerance of this method. Models accounting for asymmetric induction are proposed with supporting DFT calculations.

Computational methods for predicting product ratios in dynamically controlled reactions with shallow intermediates or bifurcating pathways after an ambimodal transition state are reviewed and benchmarked. The range of methods includes molecular dynamics simulations, machine learning-based models and recent advancements in correlational methods, all of which rely on quantum mechanical computations. Together, these approaches form a computational toolbox that enhances the efficiency and effectiveness of exploring reaction selectivity influenced by dynamic effects.

Advancements in molecular electronics focus on single molecules as key components to create stable and functional devices that meet the requirements of device miniaturization and molecular function exploration. However, as the pioneering concept of a molecular diode, all single-molecule rectifiers reported previously are limited by their modest rectification ratios, owing to electron transmission in the off-state, highlighting the imperative for performance enhancements. Here, we demonstrate a unique method capable of realizing a stable and reproducible high-performance single-molecule rectifier through the strategic application of an electric-field-catalyzed Fries rearrangement. This flexible reaction enables the exquisite control of reversible conductance switching between a structure with constructive quantum interference and a structure with destructive quantum interference, therefore leading to an exceptional rectification ratio of up to 5000 at a bias of 1.0 V, which ranks the highest among the rectifiers constructed by only one individual molecule. The stable operation of nearly 100 devices at high temperatures demonstrates reproducibility. Moreover, on-chip integration of different single-molecule rectifiers succeeds in achieving half-wave and bridge rectifications, thus facilitating efficient alternating current-to-direct current conversions. This convenient strategy of electric-field-catalyzed quantum interference switching potentially revolutionizes device efficiency and miniaturization in nanotechnology, laying an actual step toward future practical integrated molecular-scale electronic nanocircuits.

Cysteine residues play key roles in protein structure and function and can serve as targets for chemical probes and even drugs. Chemoproteomic studies have revealed that heightened cysteine reactivity toward electrophilic probes, such as iodoacetamide alkyne (IAA), is indicative of likely residue functionality. However, while the cysteine coverage of chemoproteomic studies has increased substantially, these methods still provide only a partial assessment of proteome-wide cysteine reactivity, with cysteines from low-abundance proteins and tough-to-detect peptides still largely refractory to chemoproteomic analysis. Here, we integrate cysteine chemoproteomic reactivity data sets with structure-guided computational analysis to delineate key structural features of proteins that favor elevated cysteine reactivity toward IAA. We first generated and aggregated multiple descriptors of cysteine microenvironment, including amino acid content, solvent accessibility, residue proximity, secondary structure, and predicted pKa. We find that no single feature is sufficient to accurately predict the reactivity. Therefore, we developed the CIAA (Cysteine reactivity toward IodoAcetamide Alkyne) method, which utilizes a Random Forest model to assess cysteine reactivity by incorporating descriptors that characterize the three-dimensional (3D) structural properties of thiol microenvironments. We trained the CIAA model on existing and newly generated cysteine chemoproteomic reactivity data paired with high-resolution crystal structures from the Protein Data Bank (PDB), with cross-validation against an external data set. CIAA analysis reveals key features driving cysteine reactivity, such as backbone hydrogen bond donor atoms, and reveals still underserved needs in the area of computational predictions of cysteine reactivity, including challenges surrounding protein structure selection data set curation. Thus, our work provides a strong foundation for deploying artificial intelligence (AI) on cysteine chemoproteomic data sets.

Due to the diverse chemical and physical properties of functional groups, mild and controllable ligation methods are often required to construct complex drugs and functional materials. To make diverse sets of products with tunable physicochemical properties, it is also useful to employ complimentary ligation methods that adopt the same starting materials. Here, we disclose the efficient and modular synthesis of amides or thioamides through the chemical ligation of acylsilanes with amines, simply by turning a light on or off. This method is fast, mild, high-yielding and displays excellent functional-group tolerance. The versatility of these reactions is highlighted by their ability to perform post-synthetic modifications on a variety of marketed medications, peptides, natural substances, and compounds with biological activity. In-depth computational and experimental studies clarified the photo-dependent umpolung of reactivity of acylsilanes, namely: photoexcitation leads to nucleophilic O-silyl carbenes that react with S8 to form O-silyl thionoesters and eventually amides. In contrast, acylsilanes react as electrophiles with amines thermally in the dark, with C→O silyl transfer, prior to reacting with S8 to form thioamides. These mechanistic details are expected to guide the development of similar coupling reactions.

Carbon-hydrogen (C-H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp3)-H bond1, 2-3. In recent years, metalloenzymes have been found to perform C(sp3)-H bond functionalization4,5. Despite substantial progresses in the past two decades6,7, enzymatic halogenation and pseudohalogenation of unactivated C(sp3)-H-providing a functional handle for further modification-have been achieved with only non-haem iron/alpha-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes8. Here we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp3)-H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp3)-H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs-one interchain and two intrachain-of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp3)-H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.

Metal-mediated cysteine S-arylation is an emerging bioconjugation technique due to its high chemoselectivity, rapid kinetics, and aqueous compatibility. We have previously demonstrated that by altering the sterics of the ligand and aryl groups of an Au(III) oxidative addition complex, one can modulate the kinetics of the bimolecular coordination and induce rate constants up to 16,600 M^−1s^−1. To further enhance the rate of coordination, density functional theory (DFT) calculations were performed to investigate the steric properties of the P,N-ligated Au(III) oxidative addition complex as well as the thermodynamics of the S-arylation reaction. This allowed for the accelerated screening of 13 new Au(III) oxidative addition complexes. Three of the more sterically available, synthetically accessible P,N-ligands were synthesized, incorporated into Au(I) and Au(III) complexes, and their rates determined experimentally. The comprehensive mechanistic insights from the DFT calculations led to the development of new reagents with bimolecular coordination rate constants as fast as 20,200 M^−1s^−1. Further experimental characterization of these reagents’ efficacy as S-arylation reagents led to a proposed switch in selectivity-determining step for the fastest reagent, which was further confirmed by profiling the reductive elimination kinetics. This work provides a concise workflow for the screening of metal-mediated cysteine S-arylation reagents and new fundamental insights into the coordination chemistry behavior of Au(III) systems.

Group 13 aminoxy complexes of the form (L)E(TEMPO)3 (TEMPO = 2,2,6,6-tetramethylpiperidine 1-oxyl; L = THF (tetrahydrofuran) or Py (pyridine); E = Al, Ga, In) were prepared and structurally characterized. The complexes (THF)Ga(TEMPO)3 (1·THF) and (Py)In(TEMPO)3 (2·Py) are shown to heterolytically cleave H2 under mild conditions (3 atm, 20 °C, t ≤ 1 h). 1·THF reacts reversibly with H2 to form a formal H2-adduct that bears a Ga(iii) hydride site and a protonated TEMPO ligand with concomitant loss of THF, consistent with Ga(iii) and TEMPO functioning as Lewis acid and base, respectively. Conversely, 2·Py is reduced by H2 to form an intermediate dimer complex of monovalent {In(TEMPO)}2, which undergoes further reactivity with H2 to form elemental indium as determined by powder X-ray diffraction. Treatment of 2·Py with H2 and Ph3PSe forms binary InSe, in addition to Ph3P and TEMPOH, demonstrating that 2·Py functions as a molecular source of zero-valent indium under mildly reducing conditions. Computational studies support an intramolecular metal-ligand cooperativity pathway in the heterolytic cleavage of H2.

Reaction mechanism studies typically involve the characterization of products, and intermediates are often characterized by (sub)millisecond techniques, such as nuclear magnetic resonance, while femto/attosecond spectroscopies are used to elucidate the evolution of transition states and electron dynamics. However, due to the lack of detection techniques in the microsecond to nanosecond range, as well as the emergent complexity with increasing scale, most of the proposed intermediates have not yet been detected, which significantly hinders reaction optimization. Here, we present such a nanosecond-scale real-time single-molecule electrical monitoring technique. Using this technique, a series of hidden intermediates in an example Morita-Baylis-Hillman reaction were directly observed, allowing the visualization of the reaction pathways, clarification of the two proposed proton transfer pathways, and quantitative description of their contributions to the turnover. Moreover, the emergent complexity of the catalysis, including the catalysis oscillation effect and the proton quantum tunneling effect, is further unveiled. Finally, this useful yet low-yield reaction was successfully catalyzed by the application of an electric field, leading to a high turnover frequency (similar to 5000 s-1 at a 1 V bias voltage). This new paradigm of mechanistic study and reaction optimization shows potential application in scalable synthesis by integrated single-molecule electronic devices on chip. Real-time single-molecule electrical monitoring at the nanosecond scale reveals hidden reaction steps in catalytic processes, enabling efficient on-chip chemical synthesis through electrostatic catalysis.

While enantioenriched alcohols are highly significant in medicinal chemistry, total synthesis, and materials science, the stereoselective synthesis of tertiary alcohols with two adjacent stereocenters remains a formidable challenge. In this study, we present a dual catalysis approach utilizing photoredox and nickel catalysts to enable the unprecedented chemoselective functionalization of tertiary allylic C‐H bonds in allyl ethers instead of cleaving the C‐O bond. The resulting allyl‐Ni intermediates can undergo coupling with various aldehydes, facilitating a novel enantioconvergent approach to access extensively functionalized homoallylic sec,tert‐vicinal diols frameworks. This protocol exhibits nice tolerance towards functional groups, a broad scope of substrates, excellent diastereo‐ and enantioselectivity (up to 20:1 dr, 99% ee). Mechanistic studies suggested that allyl‐NiII acts as the nucleophilic species in the coupling reaction with carbonyls.

Conformational isomerism determines the performance of materials and the activity of biomolecules. However, a complete dynamic study of conformational isomerization is still a formidable challenge at the single-molecule level. In this work, we present real-time in situ electrical monitoring of the full rotation dynamics of a single aromatic chain covalently embedded in graphene electrodes with single-event resolution. We reveal that the dynamic process of phenyl ring rotations at low temperature is dominated by quantum rotation tunneling rather than the quasi-free rotation process. The emergent complexity of different intramolecular rotations in a single aromatic molecule is demonstrated, including the alternating unidirectional rotation with multi-, single-, and half-circle delays driven by inelastic electron tunneling, which has not been previously adequately considered at the macroscopic level. This work builds a bridge between macroscopic and microscopic worlds and improves our understanding of structure-activity relationships, potentially bringing different functions to ordinary materials.