Thermodynamic H-Abstraction Abilities of Nitrogen Centered Radical Cations as Potential Hydrogen Atom Transfer Catalysts in Y-H Bond Functionalization

Y-H bond functionalization has always been the focus of research interest in the area of organic synthesis. Direct hydrogen atom transfer (HAT) from the Y-H bond is one of the most efficient and practical methods to activate the Y-H bond. Recently, nitrogen centered radical cations were broadly utilized as H-abstraction catalysts to activate Y-H bonds via the HAT process. As a type of HAT catalyst, the H-affinity of nitrogen centered radical cations is a significant thermodynamic parameter to quantitatively evaluate the thermodynamic H-abstraction potentials of nitrogen centered radical cations. In this work, the pK a values of 120 protonated N-containing compounds in acetonitrile (AN) are predicted, and the H-affinities of 120 nitrogen centered radical cations in AN are derived from the reduction potentials of nitrogen centered radical cations and pK a of protonated N-containing compounds using Hess' law. This work focuses on the H-abstraction abilities of 120 nitrogen centered radical cations in AN to enrich the molecule library of novel HAT catalysts or H-abstractors and provides valuable thermodynamic guidelines for the application of nitrogen centered radical cations in Y-H bond functionalization.

Transition Metal-Free Catalytic C-H Zincation and Alumination

C-H metalation is the most efficient method to prepare aryl-zinc and -aluminium complexes that are ubiquitous nucleophiles. Virtually all C-H metalation routes to form Al/Zn organometallics require stoichiometric, strong Brønsted bases with no base-catalyzed reactions reported. Herein we present a catalytic in amine/ammonium salt (Et3N/[(Et3N)H]+) C-H metalation process to form aryl-zinc and aryl-aluminium complexes. Key to this approach is coupling an endergonic C-H metalation step with a sufficiently exergonic dehydrocoupling step between the ammonium salt by-product of C-H metalation ([(Et3N)H]+) and a Zn-H or Al-Me containing complex. This step, forming H2/MeH, makes the overall cycle exergonic while generating more of the reactive metal electrophile. Mechanistic studies supported by DFT calculations revealed metal-specific dehydrocoupling pathways, with the divergent reactivity due to the different metal valency (which impacts the accessibility of amine-free cationic metal complexes) and steric environment. Notably, dehydrocoupling in the zinc system proceeds through a ligand-mediated pathway involving protonation of the β-diketiminate Cγ position. Given this process is applicable to two disparate metals (Zn and Al), other main group metals and ligand sets are expected to be amenable to this transition metal-free, catalytic C-H metalation.

Accurate Protein pKa Prediction with Physical Organic Chemistry Guided 3D Protein Representation

Protein pKa is a fundamental physicochemical parameter that dictates protein structure and function. However, accurately determining protein site-pKa values remains a substantial challenge, both experimentally and theoretically. In this study, we introduce a physical organic approach, leveraging a protein structural and physical-organic-parameter-based representation (P-SPOC), to develop a rapid and intuitive model for protein pKa prediction. Our P-SPOC model achieves state-of-the-art predictive accuracy, with a mean absolute error (MAE) of 0.33 pKa units. Furthermore, we have incorporated advanced protein structure prediction models, like AlphaFold2, to approximate structures for proteins lacking three-dimensional representations, which enhances the applicability of our model in the context of structure-undetermined protein research. To promote broader accessibility within the research community, an online prediction interface was also established at isyn.luoszgroup.com.

Catalytic Asymmetric Construction of α,α-Diaryl Aldehydes via Oxo-Hydroarylation of Terminal Alkynes

Chiral aldehydes containing a tertiary stereogenic center are versatile building blocks in organic chemistry. In particular, such structural motifs bearing an α,α-diaryl moiety are very challenging scaffolds and their efficient asymmetric synthesis is not reported. In this work, a phosphoric acid-catalyzed enantioselective synthesis of α,α-diaryl aldehydes from simple terminal alkynes is presented. This approach yields a wide range of highly enolizable α,α-diaryl aldehydes in good yields with excellent enantioselectivities. Facile transformations of the products, as well as an efficient synthesis of bioactive molecules, including an effective anti-smallpox agent and an FDA-approved antidepressant drug (+)-sertraline, are demonstrated.

Asymmetric C-H Dehydrogenative Alkenylation via a Photo-induced Chiral α‑Imino Radical Intermediate

The direct alkenylation with simple alkenes stands out as the most ideal yet challenging strategy for obtaining high-valued desaturated alkanes. Here we present a direct asymmetric dehydrogenative α-C(sp3)-H alkenylation of carbonyls based on synergistic photoredox-cobalt-chiral primary amine catalysis under visible light. The ternary catalytic system enables the direct coupling of β-keto-carbonyls and alkenes through a cooperative radical addition-dehydrogenation process involving a chiral α-imino radical and Co(II)-metalloradical intermediate. A catalytic H-transfer process involving nitrobenzene is engaged to quench in situ generated cobalt hydride species, ensuring a chemoselective alkenylation in good yields and high enantioselectivities.

Intramolecular chaperone-assisted dual-anchoring activation (ICDA): a suitable preorganization for electrophilic halocyclization

The halocyclization reaction represents one of the most common methodologies for the synthesis of heterocyclic molecules. Many efforts have been made to balance the relationship between structure, reactivity and selectivity, including the design of new electrophilic halogenation reagents and the utilization of activating strategies. However, discovering universal reagents or activating strategies for electrophilic halocyclization remains challenging due to the case-by-case practice for different substrates or different cyclization models. Here we report an intramolecular chaperone-assisted dual-anchoring activation (ICDA) model for electrophilic halocyclization, taking advantage of the non-covalent dual-anchoring orientation as the driving force. This protocol allows a practical, catalyst-free and rapid approach to access seven types of small-sized, medium-sized, and large-sized heterocyclic units and to realize polyene-like domino halocyclizations, as exemplified by nearly 90 examples, including a risk-reducing flow protocol for gram-scale synthesis. DFT studies verify the crucial role of ICDA in affording a suitable preorganization for transition state stabilization and X+ transfer acceleration. The utilization of the ICDA model allows a spatiotemporal adjustment to straightforwardly obtain fast, selective and high-yielding synthetic transformations.

Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C-H Acids

The pKa of C-H acids is an important parameter in the fields of organic synthesis, drug discovery, and materials science. However, the prediction of pKa is still a great challenge due to the limit of experimental data and the lack of chemical insight. Here, a new model for predicting the pKa values of C-H acids is proposed on the basis of graph neural networks (GNNs) and data augmentation. A message passing unit (MPU) was used to extract the topological and target-related information from the molecular graph data, and a readout layer was utilized to retrieve the information on the ionization site C atom. The retrieved information then was adopted to predict pKa by a fully connected network. Furthermore, to increase the diversity of the training data, a knowledge-infused data augmentation technique was established by replacing the H atoms in a molecule with substituents exhibiting different electronic effects. The MPU was pretrained with the augmented data. The efficacy of data augmentation was confirmed by visualizing the distribution of compounds with different substituents and by classifying compounds. The explainability of the model was studied by examining the change of pKa values when a specific atom was masked. This explainability was used to identify the key substituents for pKa. The model was evaluated on two data sets from the iBonD database. Dataset1 includes the experimental pKa values of C-H acids measured in DMSO, while dataset2 comprises the pKa values measured in water. The results show that the knowledge-infused data augmentation technique greatly improves the predictive accuracy of the model, especially when the number of samples is small.

Cross-coupling of organic fluorides with allenes: a silyl-radical-relay pathway for the construction of α-alkynyl-substituted all-carbon quaternary centres

Controlling the transformation of versatile and reactive allenes is a considerable challenge. Herein, we report an efficient silylboronate-mediated cross-coupling reaction of organic fluorides with allenes to construct a series of sterically demanding α-ethynyl-containing all-carbon quaternary centers (ACQCs), using catalyst-free silyl-radical-relay reactions to selectively functionalize highly inert C-F bonds in organic fluorides. The key to the success of this transformation lies in the radical rearrangement of an in situ-generated allenyl radical to form a bulky tertiary propargyl radical; however, the transformation does not show efficiency when using the propargyl isomer directly. This unique reaction enables the cross-coupling of a tertiary carbon radical center with a C(sp2)-F bond or a benzylic C(sp3)-F bond. α-Ethynyl-containing ACQCs with (hetero)aromatic substituents and benzyl were efficiently synthesized in a single step using electronically and sterically diverse organic fluorides and allenes. The practical utility of this protocol is showcased by the late-stage functionalization of bioactive molecules and the modification of a liquid crystalline material.

Caltrop-like Small-Molecule Antidotes That Neutralize Unfractionated Heparin and Low-Molecular-Weight Heparin In Vivo

Unfractionated heparin (UFH) and low-molecular-weight heparins (LMWHs) are widely applied for surgical procedures and extracorporeal therapies, which, however, suffer bleeding risk. Protamine, the only clinically approved antidote, can completely neutralize UFH, but only partially neutralizes LMWHs, and also has a number of safety drawbacks. Here, we show that caltrop-like multicationic small molecules can completely neutralize both UFH and LMWHs. In vitro and ex vivo assays with plasma and whole blood and in vivo assays with mice and rats support that the lead compound is not only superior to protamine by displaying higher neutralization activity and broader therapeutic windows but also biocompatible. The effective neutralization dose and the maximum tolerated dose of the lead compound are determined to be 0.4 and 25 mg/kg in mice, respectively, suggesting good promise for further preclinical studies.

Aqueous alkaline phosphate facilitates the non-exchangeable deuteration of peptides and proteins

The incorporation of deuterium into peptides and proteins holds broad applications across various fields, such as drug development and structural characterization. Nevertheless, current methods for peptide/protein deuteration often target exchangeable labile sites or require harsh conditions for stable modification. In this study, we present a late-stage approach utilizing an alkaline phosphate solution to achieve deuteration of non-exchangeable backbone sites of peptides and proteins. The specific deuteration regions are identified through ultraviolet photodissociation (UVPD) and mass spectrometry analysis. This deuteration strategy demonstrates site and structure selectivity, with a notable affinity for labeling the α-helix regions of myoglobin. The deuterium method is particularly suitable for peptides and proteins that remain stable under high pH conditions.

Current-Controlled Electrochemical Approach Toward Mono- and Trifluorinated Isoindolin-1-one Derivatives

An electrochemical intramolecular 5-exo-dig aza-cyclization of 2-alkynylbenzamides and subsequent nucleophilic fluorination have been developed to afford the highly selective synthesis of mono- and trifluorinated isoindolin-1-one derivatives. This work demonstrates the unique capability of synthetic electrochemistry in controlling reaction selectivity through the applied electrolytic parameters. In addition, the obtained monofluorinated 3-methyleneisoindolin-1-one (19) displays interesting photophysical properties that are not observed in its nonfluorinated analog.

Substrate binding and catalytic mechanism of the Se-glycosyltransferase SenB in the biosynthesis of selenoneine

Selenium is an essential multifunctional trace element in diverse organisms. The only Se-glycosyltransferase identified that catalyzes the incorporation of selenium in selenoneine biosynthesis is SenB from Variovorax paradoxus. Although the biochemical function of SenB has been investigated, its substrate specificity, structure, and catalytic mechanism have not been elucidated. Here, we reveal that SenB exhibits sugar donor promiscuity and can utilize six UDP-sugars to generate selenosugars. We report crystal structures of SenB complexed with different UDP-sugars. The key elements N20/T23/E231 contribute to the sugar donor selectivity of SenB. A proposed catalytic mechanism is tested by structure-guided mutagenesis, revealing that SenB yields selenosugars by forming C-Se glycosidic bonds via spontaneous deprotonation and disrupting Se-P bonds by nucleophilic water attack, which is initiated by the critical residue K158. Furthermore, we functionally and structurally characterize two other Se-glycosyltransferases, CbSenB from Comamonadaceae bacterium and RsSenB from Ramlibacter sp., which also exhibit sugar donor promiscuity.

Accurate Electronic and Optical Properties of Organic Doublet Radicals Using Machine Learned Range-Separated Functionals

Luminescent organic semiconducting doublet-spin radicals are unique and emergent optical materials because their fluorescent quantum yields (Φfl) are not compromised by the spin-flipping intersystem crossing (ISC) into a dark high-spin state. The multiconfigurational nature of these radicals challenges their electronic structure calculations in the framework of single-reference density functional theory (DFT) and introduces room for method improvement. In the present study, we extended our earlier development of ML-ωPBE [J. Phys. Chem. Lett., 2021, 12, 9516-9524], a range-separated hybrid (RSH) exchange-correlation (XC) functional constructed using the stacked ensemble machine learning (SEML) algorithm, from closed-shell organic semiconducting molecules to doublet-spin organic semiconducting radicals. We assessed its performance for a new test set of 64 doublet-spin radicals from five categories while placing all previously compiled 3926 closed-shell molecules in the new training set. Interestingly, ML-ωPBE agrees with the nonempirical OT-ωPBE functional regarding the prediction of the molecule-dependent range-separation parameter (ω), with a small mean absolute error (MAE) of 0.0197 a0-1, but saves the computational cost by 2.46 orders of magnitude. This result demonstrates an outstanding domain adaptation capacity of ML-ωPBE for diverse organic semiconducting species. To further assess the predictive power of ML-ωPBE in experimental observables, we also applied it to evaluate absorption and fluorescence energies (Eabs and Efl) using linear-response time-dependent DFT (TDDFT), and we compared its behavior with nine popular XC functionals. For most radicals, ML-ωPBE reproduces experimental measurements of Eabs and Efl with small MAEs of 0.299 and 0.254 eV, only marginally different from those of OT-ωPBE. Our work illustrates a successful extension of the SEML framework from closed-shell molecules to doublet-spin radicals and will open the venue for calculating optical properties for organic semiconductors using single-reference TDDFT.

NacNac-zinc-pyridonate mediated ε-caprolactone ROP

Herein we report the synthesis, isolation and polymerisation activity of two new zinc compounds based on a 2,6-diisopropylphenyl (Dipp) β-diiminate (NacNac) ligand framework with zinc also ligated by an amidate (2-pyridonate or 6-methyl-2-pyridonate) unit. The compounds crystallised as either monomeric (6-Me-2-pyridonate derivative) or dimeric (2-pyridonate) species, although both were found to be monomeric in solution via1H DOSY NMR spectroscopy, which was supported by DFT calculations. These observations suggest that both complexes initiate ring-opening polymerisation (ROP) through a single-site monometallic mechanism. High molecular weight poly ε-caprolactone (PCL) was achieved via exogenous initiator-free ROP conditions with both catalysts. An increase in the 2-pyridonate initiator steric bulk (6-Me- vs. 6-H-) resulted in an improved catalytic activity, facilitating complete monomer conversion within 1 h at 60 °C. Pyridonate end-groups were observed by MALDI-ToF mass spectrometry, contrasting with previous observations for DippNacNac-Zn acetate complexes (where no acetate end groups are observed), instead this more closely resembles the reactivity of DippNacNac-Zn alkoxide complexes in ROP (where RO end groups are observed). Additional major signals in the MALDI-ToF spectra were consistent with cyclic PCL species, which are attributed to back-biting ring-closing termination steps occuring in a process facilitated by the pyridonate unit being an effective leaving group. To the best of our knowledge, these complexes represent the first examples of pyridonate, and indeed amidate, initated ROP.

Organocatalytic Asymmetric Vinylogous Michael Addition of Electron-Deficient Aryl Alkane Nucleophiles to Enals

We report herein a protocol for an organocatalyzed asymmetric vinylogous Michael addition of aryl alkane nucleophiles with enals under base- and additive-free conditions. A series of allylic building blocks were obtained in 60%-93% yield and 88-99% ee with 20 mol % diphenylprolinol silyl ether as catalyst. This protocol has advantages such as excellent chemoselectivity and regioselectivity, good tolerance of functionalities, and simple reaction conditions.

Enantioselective De Novo Synthesis of α,α-Diaryl Ketones from Alkynes

Chiral α,α-diaryl ketones are structural motifs commonly present in bioactive molecules, and they are also valuable building blocks in synthetic organic chemistry. However, catalytic asymmetric synthesis of α,α-diaryl ketones bearing a tertiary stereogenic center remains largely unsolved. Herein, we report a catalytic de novo enantioselective synthesis of α,α-diaryl ketones from simple alkynes via chiral phosphoric acid (CPA) catalysis. A broad range of enolizable α,α-diaryl ketones are prepared in good yields and with excellent enantioselectivities. The described protocol also serves as an efficient deuteration method for the preparation of enantiomerically enriched deuterated α,α-diaryl ketones. Using the methodology reported, bioactive molecules, including one of the best-selling anti-breast cancer drugs, tamoxifen, are readily synthesized.

Metal ion assistant transformation strategy to synthesize catechol-based metal-organic frameworks from Ti3C2Tx precursors

Chemical transformation strategy is capable of fabricating nanomaterials with well-defined structures and fascinating performance via controllable crystallization kinetics in the phase transformation. V2CTx MXene has been used as precursors to fabricate vanadium porphyrin metal-organic frameworks (V-PMOFs) via the coordination of deprotonated carboxylic acid ligands. However, the rational and in-depth exploration of synthesis mechanism with the aim of enriching the variety of MXene (i.e., Ti3C2Tx) and organic ligands (i.e., catechol-based) to design new MOFs is rarely reported. Herein, we have first developed a metal ion assistant transformation strategy to synthesize three-dimensional catechol-based TiCu-HHTP (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene) MOFs with a non-interpenetrating SrSi2 (srs) framework using two-dimensional Ti3C2Tx as precursors. The unique synergetic transformation mechanism involves the electron transfer from Ti3C2Tx to electrostatically adsorbed Cu2+ ion for redox reaction, the subsequent Ti-C bond rupture for Ti4+ ion release, and the continuous chelation coordination between Ti4+/Cu2+ and HHTP. Ti3C2Tx precursors and auxiliary metal ion could be rationally substituted by V2CTx and Mn+ (e.g., Ni2+, Co2+, Mn2+, and Zn2+), respectively. This strategy lays the foundation for the design and synthesis of innovative and multifarious MOFs derived from MXene or other unconventional metal precursors.

Thermodynamic Evaluations of Amines as Hydrides or Two Hydrogen Ions Reductants and Imines as Protons or Two Hydrogen Ions Acceptors, as Well as Their Application in Hydrogenation Reactions

Since the hydrogenation of imines (X) and the dehydrogenation of amines (XH2) generally involve the two hydrogen ions (H- + H+) transfer, the thermodynamic abilities of various amines releasing hydrides or two hydrogen ions as well as various imines accepting protons or two hydrogen ions are important and characteristic physical parameters. In this work, the pKa values of 84 protonated imines (XH+) in acetonitrile were predicted. Combining Gibbs free energy changes of amines releasing hydrides in acetonitrile from our previous work with the pKa(XH+) values, the Gibbs free energy changes of amines releasing two hydrogen ions and imines accepting two hydrogen ions were derived using Hess's law by constructing thermochemical cycles, and the thermodynamic evaluations of amines as hydrides or two hydrogen ions reductants and imines as protons or two hydrogen ions acceptors are well compared and discussed. Eventually, the practical application of thermodynamic data for amines and imines on hydrogenation feasibility, mechanism, and possible elementary steps was shown and discussed in this paper from the point of thermodynamics.

Optimized synthesis of anti-COVID-19 drugs aided by retrosynthesis software

Considering the millions of COVID-19 patients worldwide, a global critical challenge of low-cost and efficient anti-COVID-19 drug production has emerged. Favipiravir is one of the potential anti-COVID-19 drugs, but its original synthetic route with 7 harsh steps gives a low product yield (0.8%) and has a high cost ($68 per g). Herein, we demonstrated a low-cost and efficient synthesis route for favipiravir designed using improved retrosynthesis software, which involves only 3 steps under safe and near-ambient air conditions. A yield of 32% and cost of $1.54 per g were achieved by this synthetic route. We also used the same strategy to optimize the synthesis of sabizabulin. We anticipate that these synthetic routes will contribute to the prevention and treatment of COVID-19.

Calculating the Aqueous pKa of Phenols: Predictions for Antioxidants and Cannabinoids

We aim to develop a theoretical methodology for the accurate aqueous pK_a prediction of structurally complex phenolic antioxidants and cannabinoids. In this study, five functionals (M06-2X, B3LYP, BHandHLYP, PBE0, and TPSS) and two solvent models (SMD and PCM) were combined with the 6-311++G(d,p) basis set to predict pK_a values for twenty structurally simple phenols. None of the direct calculations produced good results. However, the correlations between the calculated Gibbs energy difference of each acid and its conjugate base, ΔGaq(BA)°=ΔGaqA-°-ΔGaq(HA)°, and the experimental aqueous pK_a values had superior predictive accuracy, which was also tested relative to an independent set of ten molecules of which six were structurally complex phenols. New correlations were built with twenty-seven phenols (including the phenols with experimental pK_a values from the test set), which were used to make predictions. The best correlation equations used the PCM method and produced mean absolute errors of 0.26-0.27 pK_a units and R² values of 0.957-0.960. The average range of predictions for the potential antioxidants (cannabinoids) was 0.15 (0.25) pK_a units, which indicates good agreement between our methodologies. The new correlation equations could be used to make pK_a predictions for other phenols in water and potentially in other solvents where they might be more soluble.

Hydroxylation of some emerging disinfection byproducts (DBPs) in water environment: Halogenation induced strong pH-dependency

In this work, the hydroxylation mechanisms and kinetics of some emerging disinfection byproducts (DBPs) have been systematically investigated through theoretical calculation methods. Five chlorophenols and eleven halogenated pyridinols were chosen as the model compounds to study their pH-dependent reaction laws in UV/H₂O₂ system. For the reactions of HO^• with 37 different dissociation forms, radical adduct formation (RAF) was the main reaction pathway, and the reactivity decreased with the increase of halogenation degree. The k_app values (at 298 K) increased with the increase of pH from 0 to 10, and decreased with the increase of pH from 10 to 14. Compared with phenol, the larger the chlorination degree in chlorophenols was, the stronger the pH sensitivity of the k_app values; compared with chlorophenols, the pH sensitivity in halogenated pyridinols was further enhanced. As the pH increased from 2 to 10.5, the degradation efficiency increased at first and then decreased. With the increase of halogenation degree, the degradation efficiency range increased, the pH sensitivity increased, the optimal degradation efficiency slightly increased, and the optimal degradation pH value decreased. The ecotoxicity and bioaccumulation of most hydroxylated products were lower than their parental compounds. These findings provided meaningful insights into the strong pH-dependent hydroxylation of emerging DBPs on molecular level.

Incorporating Domain Knowledge and Structure-Based Descriptors for Machine Learning: A Case Study of Pd-Catalyzed Sonogashira Reactions

Machine learning has revolutionized information processing for large datasets across various fields. However, its limited interpretability poses a significant challenge when applied to chemistry. In this study, we developed a set of simple molecular representations to capture the structural information of ligands in palladium-catalyzed Sonogashira coupling reactions of aryl bromides. Drawing inspiration from human understanding of catalytic cycles, we used a graph neural network to extract structural details of the phosphine ligand, a major contributor to the overall activation energy. We combined these simple molecular representations with an electronic descriptor of aryl bromide as inputs for a fully connected neural network unit. The results allowed us to predict rate constants and gain mechanistic insights into the rate-limiting oxidative addition process using a relatively small dataset. This study highlights the importance of incorporating domain knowledge in machine learning and presents an alternative approach to data analysis.

The calcium channel modulator 2-APB hydrolyzes in physiological buffers and acts as an effective radical scavenger and inhibitor of the NADPH oxidase 2

2-aminoethoxydiphenyl borate (2-APB) is commonly used as a tool to modulate calcium signaling in physiological studies. 2-APB has a complex pharmacology and acts as activator or inhibitor of a variety of Ca²⁺ channels and transporters. While unspecific, 2-APB is one of the most-used agents to modulate store-operated calcium entry (SOCE) mediated by the STIM-gated Orai channels. Due to its boron core structure, 2-APB tends to readily hydrolyze in aqueous environment, a property that results in a complex physicochemical behavior. Here, we quantified the degree of hydrolysis in physiological conditions and identified the hydrolysis products diphenylborinic acid and 2-aminoethanol by NMR. Notably, we detected a high sensitivity of 2-APB/diphenylborinic acid towards decomposition by hydrogen peroxide to compounds such as phenylboronic acid, phenol, and boric acid, which were, in contrast to 2-APB itself and diphenylborinic acid, insufficient to affect SOCE in physiological experiments. Consequently, the efficacy of 2-APB as a Ca²⁺ signal modulator strongly depends on the reactive oxygen species (ROS) production within the experimental system. The antioxidant behavior of 2-APB towards ROS and its resulting decomposition are inversely correlated to its potency to modulate Ca²⁺ signaling as shown by electron spin resonance spectroscopy (ESR) and Ca²⁺ imaging. Finally, we observed a strong inhibitory effect of 2-APB, i.e., its hydrolysis product diphenylborinic acid, on NADPH oxidase (NOX2) activity in human monocytes. These new 2-APB properties are highly relevant for Ca²⁺ and redox signaling studies and for pharmacological application of 2-APB and related boron compounds.

Transition-metal-free silylboronate-mediated cross-couplings of organic fluorides with amines

C-N bond cross-couplings are fundamental in the field of organic chemistry. Herein, silylboronate-mediated selective defluorinative cross-coupling of organic fluorides with secondary amines via a transition-metal-free strategy is disclosed. The cooperation of silylboronate and potassium tert-butoxide enables the room-temperature cross-coupling of C-F and N-H bonds, effectively avoiding the high barriers associated with thermally induced S_N2 or S_N1 amination. The significant advantage of this transformation is the selective activation of the C-F bond of the organic fluoride by silylboronate without affecting potentially cleavable C-O, C-Cl, heteroaryl C-H, or C-N bonds and CF₃ groups. Tertiary amines with aromatic, heteroaromatic, and/or aliphatic groups were efficiently synthesized in a single step using electronically and sterically varying organic fluorides and N-alkylanilines or secondary amines. The protocol is extended to the late-stage syntheses of drug candidates, including their deuterium-labeled analogs.

Electrocatalytic Upcycling of Biomass and Plastic Wastes to Biodegradable Polymer Monomers and Hydrogen Fuel at High Current Densities

Transformation of biomass and plastic wastes to value-added chemicals and fuels is considered an upcycling process that is beneficial to resource utilization. Electrocatalysis offers a sustainable approach; however, it remains a huge challenge to increase the current density and deliver market-demanded chemicals with high selectivity. Herein, we demonstrate an electrocatalytic strategy for upcycling glycerol (from biodiesel byproduct) to lactic acid and ethylene glycol (from polyethylene terephthalate waste) to glycolic acid, with both products being as valuable monomers for biodegradable polymer production. By using a nickel hydroxide-supported gold electrocatalyst (Au/Ni(OH)₂), we achieve high selectivities of lactic acid and glycolic acid (77 and 91%, respectively) with high current densities at moderate potentials (317.7 mA/cm² at 0.95 V vs RHE and 326.2 mA/cm² at 1.15 V vs RHE, respectively). We reveal that glycerol and ethylene glycol can be enriched at the Au/Ni(OH)₂ interface through their adjacent hydroxyl groups, substantially increasing local concentrations and thus high current densities. As a proof of concept, we employed a membrane-free flow electrolyzer for upcycling triglyceride and PET bottles, attaining 11.2 g of lactic acid coupled with 9.3 L of H₂ and 13.7 g of glycolic acid coupled with 9.4 L of H₂, respectively, revealing the potential of coproduction of valuable chemicals and H₂ fuel from wastes in a sustainable fashion.

Tandem Reaction of Azide with Isonitrile and TMSCnFm(H): Access to N-Functionalized C-Fluoroalkyl Amidine

N-Functionalized C-fluoroalkyl amidines are attracting great attention due to their potential in pharmaceuticals. Herein, we report a Pd-catalyzed tandem reaction of azide with isonitrile and fluoroalkylsilane via a carbodiimide intermediate, providing facile access to N-functionalized C-fluoroalkyl amidines. This protocol offers an approach toward not only N-sulphonyl, N-phosphoryl, N-acyl, and N-aryl but also C-CF₃, C₂F₅, and CF₂H amidines with a broad substrate scope. The accomplishment of further transformations and Celebrex derivatization in gram scale and biological evaluation reveals the important utility of this strategy.

Crystallographic Deciphering of Spontaneous Self-Assembly of Achiral Calciphores to Chiral Complexes

Thiapyricins (TPC-A/B, 1 and 2), which are new metallophore scaffolds exhibiting selective divalent cation binding property, were produced in response to metal-deprived conditions by Saccharothrix sp. TRM_47004 isolated from the Lop Nor Salt Lake. TPCs represent a thiazolyl-pyridine skeleton of a calcium-binding natural product, calciphore, owing to the selectivity to calcium ions among diverse metal ions. The thiapyricins exhibited notable co-crystalline characteristics of the apo- and holo-forms with racemic enantiomers comprising a pair of space isomers in a Δ/Λ-form. Therefore, we postulated a mechanism for the four-hierarchical self-assembly of achiral natural products into chiral complexes. Furthermore, their metal-chelating trait aided the adaptation of the host during metal starvation by increasing the production of TPCs. This study presents a structural paradigm of a new calciphore, provides insight into the mechanism of natural product assembly, and highlights the causality between the production of the metallophore and metallic habitats.

Predict Ionization Energy of Molecules Using Conventional and Graph-Based Machine Learning Models

Ionization energy (IE) is an important property of molecules. It is highly desirable to predict IE efficiently based on, for example, machine learning (ML)-powered quantitative structure-property relationships (QSPR). In this study, we systematically compare the performance of different machine learning models in predicting the IE of molecules with distinct functional groups obtained from the NIST webbook. Mordred and PaDEL are used to generate informative and computationally inexpensive descriptors for conventional ML models. Using a descriptor to indicate if the molecule is a radical can significantly improve the performance of these ML models. Support vector regression (SVR) is the best conventional ML model for IE prediction. In graph-based models, the AttentiveFP gives an even better performance compared to SVR. The difference between these two types of models mainly comes from their predictions for radical molecules, where the local environment around an unpaired electron is better described by graph-based models. These results provide not only high-performance models for IE prediction but also useful information in choosing models to obtain reliable QSPR.

Ozone mechanism, kinetics, and toxicity studies of halophenols: Theoretical calculation combined with toxicity experiment

Aromatic disinfection by-products (DBPs), which are generally more toxic than aliphatic DBPs, have attracted increasing attention. The toxicity of 13 typical halophenols on Scenedesmus obliquus was experimentally investigated, and the ozonation mechanism and kinetics of representative halophenols were further studied by quantum chemical calculations. The results showed that the EC₅₀ values of halophenols ranged from 2.74 to 60.23 mg/L, and their toxicity ranked as follows: di-halogenated phenols > mono-halogenated phenols, mixed halogen-substituted phenols > single halogen-substituted phenols, and iodophenols > bromophenols > chlorophenols. The toxicity of halophenols was well described by the electronegativity index (ω) as lg(EC₅₀)^-1 = 6.228ω - 3.869, indicating halophenols capturing electrons as their potential toxicity mechanism. The reactions of O₃ with halophenolate anions were dominated by three mechanisms: 1,3-dipolar cycloaddition, oxygen addition, and single electron transfer. The kinetic calculation indicated that O₃ oxidized aqueous halophenols by reacting with halophenolate anions with the reaction rate constants as high as (0.91-3.47) × 10¹⁰ M^-1 s^-1. The number of halogen substituents affected the k_{O3, cal} values of halophenolate anions, which are in the order of 2,4-dihalophenolate anions >4-halophenolate anions > 2,4,6-trihalophenolate anions. During the ozonation of 2,4,6-tribromophenol (246TBP), the toxic products (dimers and brominated benzoquinones) could be synergistically degraded by O₃ and HO^•. Thus, ozonation is feasible as a strategy to degrade aromatic DBPs.

Understanding and Expanding Zinc Cation/Amine Frustrated Lewis Pair Catalyzed C-H Borylation

[(NacNac)Zn(DMT)][B(C₆F₅)₄], 1, (NacNac = {(2,6- ⁱ Pr₂H₃C₆)N(CH₃)C}₂CH), DMT = N,N-dimethyl-4-toluidine), was synthesized via two routes starting from either (NacNac)ZnEt or (NacNac)ZnH. Complex 1 is an effective (pre)catalyst for the C-H borylation of (hetero)arenes using catecholborane (CatBH) with H₂ the only byproduct. The scope included weakly activated substrates such as 2-bromothiophene and benzothiophene. Computational studies elucidated a plausible reaction mechanism that has an overall free energy span of 22.4 kcal/mol (for N-methylindole borylation), consistent with experimental observations. The calculated mechanism starting from 1 proceeds via the displacement of DMT by CatBH to form [(NacNac)Zn(CatBH)]⁺, D, in which CatBH binds via an oxygen to zinc which makes the boron center much more electrophilic based on the energy of the CatB-based LUMO. Combinations of D and DMT act as a frustrated Lewis pair (FLP) to effect C-H borylation in a stepwise process via an arenium cation that is deprotonated by DMT. Subsequent B-H/[H-DMT]⁺ dehydrocoupling and displacement from the coordination sphere of zinc of CatBAr by CatBH closes the cycle. The calculations also revealed a possible catalyst decomposition pathway involving hydride transfer from boron to zinc to form (NacNac)ZnH which reacts with CatBH to ultimately form Zn(0). In addition, the key rate-limiting transition states all involve the base, thus fine-tuning of the steric and electronic parameters of the base enabled a further minor enhancement in the C-H borylation activity of the system. Outlining the mechanism for all steps of this FLP-mediated process will facilitate the development of other main group FLP catalysts for C-H borylation and other transformations.

Quantitative evaluation of the actual hydrogen atom donating activities of O-H bonds in phenols: structure-activity relationship

The H-donating activity of phenol and the H-abstraction activity of phenol radicals have been extensively studied. In this article, the second-order rate constants of 25 hydrogen atom transfer (HAT) reactions between phenols and PINO and DPPH radicals in acetonitrile at 298 K were studied. Thermo-kinetic parameters ΔG ^≠o(XH) were obtained using a kinetic equation [ΔG ^≠ _XH/Y = ΔG ^≠o(XH) + ΔG ^≠o(Y)]. Bond dissociation free energies ΔG ^o(XH) were calculated by the iBonD HM method, whose details are available at https://pka.luoszgroup.com/bde_prediction. Intrinsic resistance energies ΔG ^≠ _XH/X and ΔG ^≠o(X) were determined as ΔG ^≠o(XH) and ΔG ^o(XH) were available. ΔG ^o(XH), ΔG ^≠ _XH/X, ΔG ^≠o(XH) and ΔG ^≠o(X) were used to assess the H-donating abilities of the studied phenols and the H-abstraction abilities of phenol radicals in thermodynamics, kinetics and actual HAT reactions. The effect of structures on these four parameters was discussed. The reliabilities of ΔG ^≠o(XH) and ΔG ^≠o(X) were examined. The difference between the method of determining ΔG ^≠ _XH/X mentioned in this study and the dynamic nuclear magnetic method mentioned in the literature was studied. Via this study, not only ΔG ^o(XH), ΔG ^≠ _XH/X, ΔG ^≠o(XH) and ΔG ^≠o(X) of phenols could be quantitatively evaluated, but also the structure-activity relationship of phenols is clearly demonstrated. Moreover, it lays the foundation for designing and synthesizing more antioxidants and radicals.

The fecal arsenic excretion, tissue arsenic accumulation, and metabolomics analysis in sub-chronic arsenic-exposed mice after in situ arsenic-induced fecal microbiota transplantation

Arsenic can be specifically enriched by rice, and the health hazards caused by high arsenic rice are gradually attracting attention. This study aimed to explore the potential of microbial detoxification via gut microbiome in the treatment of sub-chronic arsenic poisoning. We first exposed mice to high-dose arsenic feed (30 mg/kg, rice arsenic composition) for 60 days to promote arsenic-induced microbes in situ in the gastrointestinal tract, then transplanted their fecal microbiota (FMT) into another batch of healthy recipient mice, and dynamically monitored the microbial colonization by 16S rRNA sequencing and ITS sequencing. The results showed that in situ arsenic-induced fecal microbiome can stably colonized and interact with indigenous microbes in the recipient mice in two weeks, and established a more stable network of gut microbiome. Then, the recipient mice continued to receive high-dose arsenic exposure for 52 days. After above sub-chronic arsenic exposure, compared with the non-FMT group, fecal arsenic excretion, liver and plasma arsenic accumulation were significantly lower (P < 0.05), and that in kidney, hair, and thighbone present no significant differences. Metabolomics of feces- plasma-brain axis were also disturbed, some up-regulated metabolites in feces, plasma, and cerebral cortex may play positive roles for the host. Therefore, microbial detoxification has potential in the treatment of sub-chronic arsenic poisoning. However, gut flora is an extremely complex community with different microorganisms have different arsenic metabolizing abilities, and various microbial metabolites. Coupled with the matrix effects, these factors will have various effects on the efflux and accumulation of arsenic. The definite effects (detoxification or non-detoxification) could be not assured based on the current study, and more systematic and rigorous studies are needed in the future.

OSCAR: an extensive repository of chemically and functionally diverse organocatalysts

The automated construction of datasets has become increasingly relevant in computational chemistry. While transition-metal catalysis has greatly benefitted from bottom-up or top-down strategies for the curation of organometallic complexes libraries, the field of organocatalysis is mostly dominated by case-by-case studies, with a lack of transferable data-driven tools that facilitate both the exploration of a wider range of catalyst space and the optimization of reaction properties. For these reasons, we introduce OSCAR, a repository of 4000 experimentally derived organocatalysts along with their corresponding building blocks and combinatorially enriched structures. We outline the fragment-based approach used for database generation and showcase the chemical diversity, in terms of functions and molecular properties, covered in OSCAR. The structures and corresponding stereoelectronic properties are publicly available (https://archive.materialscloud.org/record/2022.106) and constitute the starting point to build generative and predictive models for organocatalyst performance.

Potentiometric Determination of Acid Dissociation Constants (pK a) for an Anticancer Pyrrole-Imidazole Polyamide

To optimize the pharmacological properties of an anticancer pyrrole-imidazole (Py-Im) polyamide (PIP-1), we characterized the acid dissociation constants of PIP-1, three other structurally related hairpin-shaped polyamides, and a cyclic polyamide bearing the same core sequence as PIP-1 via potentiometric titration. The acidities of the carboxylic acid at the C-terminus and the tertiary amine in the triamine linker remained very similar among the polyamides tested, whereas the pK a of the N-methylimidazole (Im) moieties varied with the peptide sequence and molecular architecture. A nearly 0.2 pH unit pK a shift of terminal Im toward the neutral state compared to internal Im was observed. Furthermore, according to the dissociation constants, a speciation diagram of PIP-1 as a function of pH is presented, which allows an assessment of the net charge and distribution of protonated species in the range of physiological pH.

Machine learning methods for pKa prediction of small molecules: Advances and challenges

The acid-base dissociation constant (pK_a) is a fundamental property influencing many ADMET properties of small molecules. However, rapid and accurate pK_a prediction remains a great challenge. In this review, we outline the current advances in machine-learning-based QSAR models for pK_a prediction, including descriptor-based and graph-based approaches, and summarize their pros and cons. Moreover, we highlight the current challenges and future directions regarding experimental data, crucial factors influencing pK_a and in silico prediction tools. We hope that this review can provide a practical guidance for the follow-up studies.

A Mild Silica Gel Promoted Synthesis and Initial Functional Study of Tetrapyridyl Tetrahydropyrrolopyrrolones

A one-pot strategy with yields up to 82% was reported to generate 2-(pyridin-2-yl)-2-(3,3a,6-tris(5-pyridin-2-yl)-5-oxohexahydropyrrolo[3,2-b] pyrrol-2(1H)-ylidene)acetonitrile 1a and its derivatives 1b-d. Silica gel promoted quantitative conversion from stable intermediate to 1a within 30 min at room temperature. Finally, four chemical σ bonds and two chiral carbons with high diastereoselectivity were achieved. Compound 1a can act as a novel high selective UV-vis and fluorescence "turn-on" probe for Zn²⁺ and Cd²⁺, respond to proton, and show dual-state emission (DSE) characteristics.

Equilibration for Electrospray Ionization Mass Spectrometry in Quantitative Analysis

Electrospray ionization mass spectrometry (ESI-MS) is widely used in drug development, therapeutic drug monitoring, and other fields. However, unstable mass spectral signals, especially during the initial stages of instrument operation, plague analysts. Generally, in quantitative experiments, the stability of response can be achieved by running the analytical system for some time. However, the equilibration time required for the responses of different compounds to stabilize has been elusive. To investigate the response stability of the ESI-MS system, 72 compounds with different physicochemical properties were employed on three systems, and flow injection analysis was performed in positive ion mode. With the use of 5.00% (response stable factor, RSF) as the stability limit, about 80% of the compounds were stable within 60 min. Under a 2.00% criterion, the stabilization time was significantly longer. The stabilization time varies with different instruments and physicochemical properties of the compounds. When positive ion detection is performed in an acidic mobile phase, the octanol-water partition coefficient (Log P), molecular weight, and molar volume can all affect the time required to stabilize the response. In general, it is necessary to balance the ESI-MS system for an appropriate time before sample detection, especially for the analysis of compounds with strong hydrophilicity, small molecular weight, or small molar volume under the conditions above.

Discovering and Evaluating the Reducing Abilities of Polar Alkanes and Related Family Members as Organic Reductants Using Thermodynamics

In this work, the pK_a values of 69 polar alkanes (YH₂) in acetonitrile were computed using the method developed by Luo and Zhang in 2020, and representative 69 thermodynamic network cards on 22 elementary steps of YH₂ and related polar alkenes (Y) releasing or accepting H₂ were naturally established. Potential electron reductants (YH^-), hydride reductants (YH^-), antioxidants (YH₂ and YH^-), and hydrogen molecule reductants (YH₂) are unexpectedly discovered according to thermodynamic network cards. It is also found that there are great differences between YH₂ and common hydrogen molecule reductants (XH₂), such as Hantzsch ester (HEH₂), benzothiazoline (BTH₂), and dihydro-phenanthridine (PH₂), releasing two hydrogen ions to unsaturated compounds. During the hydrogenation process, XH₂ release hydrides first, then the oxidation state XH⁺ release protons. However, in the case of YH₂, YH₂ release protons first, then YH^- release hydrides. It is the differences on acidic properties of YH₂ and XH₂ that result in the behavioral and thermodynamic differences on YH₂ and XH₂ releasing two hydrogen ions (H^--H⁺). The redox mechanisms and behaviors of Y, YH^-, and YH₂ as electron, hydrogen atom, hydride, and hydrogen molecule donors or acceptors in the chemical reaction are reasonably investigated and discussed in this paper using thermodynamics.

Advancing Rare-Earth Separation by Machine Learning

Constituting the bulk of rare-earth elements, lanthanides need to be separated to fully realize their potential as critical materials in many important technologies. The discovery of new ligands for improving rare-earth separations by solvent extraction, the most practical rare-earth separation process, is still largely based on trial and error, a low-throughput and inefficient approach. A predictive model that allows high-throughput screening of ligands is needed to identify suitable ligands to achieve enhanced separation performance. Here, we show that deep neural networks, trained on the available experimental data, can be used to predict accurate distribution coefficients for solvent extraction of lanthanide ions, thereby opening the door to high-throughput screening of ligands for rare-earth separations. One innovative approach that we employed is a combined representation of ligands with both molecular physicochemical descriptors and atomic extended-connectivity fingerprints, which greatly boosts the accuracy of the trained model. More importantly, we synthesized four new ligands and found that the predicted distribution coefficients from our trained machine-learning model match well with the measured values. Therefore, our machine-learning approach paves the way for accelerating the discovery of new ligands for rare-earth separations.

Asymmetric C-H Dehydrogenative Allylic Alkylation by Ternary Photoredox-Cobalt-Chiral Primary Amine Catalysis under Visible Light

We report herein an asymmetric C-H dehydrogenative allylic alkylation by a synergistic catalytic system involving a chiral primary amine, a photoredox catalyst, and a cobaloxime cocatalyst. The ternary catalytic system enables the coupling of β-ketocarbonyls and olefins with good yields and high enantioselectivities. Mechanism studies disclosed a cooperative radical addition process with a chiral α-imino radical and Co(II)-metalloradical wherein the chiral primary aminocatalyst and the cobaloxime catalyst work in concert to control the stereoinduction.