Aromatic Ring Research Articles

Accurate carbon structure for prediction of reaction pathway during bio-coal production using torrefaction

The structural parameters of carbon were accurately determined through correction by employing a linear correlation method. Further, the nuclear Overhauser effect (NOE) was reduced in solid 13C-nuclear magnetic resonance spectra using a solid cross-polarization/magic angle spinning (CP/MAS) probe and the total suppression of sidebands sequence (TOSS). The reaction pathway during torrefaction was inferred from analysis of the accurate bond behavior and product distribution. The results show that torrefaction has a significant influence on the structural evolution of biomass. After correction, the relative deviations in the H/C ratio and aromaticity of the carbon structure decreased below 20 %. During torrefaction, the aliphatic carbon bonds were cleaved and aromatic carbon bonds were formed by dehydration, deoxygenation, oligomerization, aromatization, and Diels-Alder reaction. Torrefaction of biomass is divided into three stages. The first stage occurs below 220 °C, with disruption of the hydrogen bonds, a decrease in the number of Cal-O bonds, and the release of some CO2, CO, and furaldehyde. The second stage proceeds in the 220–260 °C range, where β-O-α bonds and glycoside bonds are broken, with the generation of ketones, furan, phenols, CO, and CO2. In the third stage between 260 and 300 °C, Cal-O and Cal-Cal bonds are broken. Bio-coal is composed of monomers of C20H14O3 with two aromatic rings linked by one aromatic ring. This significant, fundamental study enables accurate calculation and simulations for optimizing the industrial utilization of biomass.

One-step synthesis of [15]paracyclophane and [16]paracyclophane via Pd-catalyzed C(sp2)–C(sp3) coupling and the cyclohexane-encapsulating crystal structure of [16]paracyclophane

Abstract Macrocycles consisting of methylene-bridged aromatic rings had been synthesized by aromatic electrophilic substitution reactions, thus limiting the substrates to electron-rich aromatic compounds. In this work, we developed a novel method for 1-step synthesis of [15]paracyclophane (PCP) and [16]PCP by the self-condensation of 4-bromobenzyl bromide via a Pd-catalyzed desulfinative coupling reaction between C(sp2) and C(sp3) carbon atoms. In the crystal structure, [16]PCP encapsulated cyclohexane and formed a 1D columnar structure

Photocatalytic furan-to-pyrrole conversion.

The identity of a heteroatom within an aromatic ring influences the chemical properties of that heterocyclic compound. Systematically evaluating the effect of a single atom, however, poses synthetic challenges, primarily as a result of thermodynamic mismatches in atomic exchange processes. We present a photocatalytic strategy that swaps an oxygen atom of furan with a nitrogen group, directly converting the furan into a pyrrole analog in a single intermolecular reaction. High compatibility was observed with various furan derivatives and nitrogen nucleophiles commonly used in drug discovery, and the late-stage functionalization furnished otherwise difficult-to-access pyrroles from naturally occurring furans of high molecular complexity. Mechanistic analysis suggested that polarity inversion through single electron transfer initiates the redox-neutral atom exchange processes at room temperature.

ReaxFF molecular dynamics study of N-containing PAHs formation in the pyrolysis of C2H4/NH3 mixtures

The reactive force field molecular dynamics (ReaxFF MD) simulations are performed to depict the whole process including fuel pyrolysis, the formation and growth of PAHs/NPAHs and soot formation in the pyrolysis of C2H4 and C2H4/NH3 mixtures. NH3 doping increases the concentration of H radicals through the decomposition of NH3. These H radicals then promote the consumption of C2H4 by participating in H-abstraction reactions. The formation of C-N species (mainly HCN, H2CN, C2N, CH3CN, NCCN, and HC3N) removes the C atoms participating in the formation of PAHs and soot, thus inhibiting the formation of soot. And such inhibitory effect is strengthened with increasing temperature due to the promoted formation of C-N species. Most importantly, the structure, formation and evolution paths of N-containing PAHs (NPAHs) are identified based on the experimental and simulation results for the first time, revealing that N atoms in the NPAHs are almost always present in the carbon chains attached to the aromatic rings while barely enter the rings to form heterocyclic structure. The simulations further reveal that when the temperature is less than 2500 K, the first N-containing aromatic ring is formed through the reaction of phenyl with small C-N species (such as HCN and CN radicals), followed by the increase of new rings primarily via the HACA mechanism. At temperatures greater than 2500 K, the formation and growth of NPAHs are dominated by the continuous attachment of N-containing carbon chains and cyclic polycondensation-cyclization reactions. The identification of new C-N species especially NPAHs would help improve the kinetic mechanisms for ammonia blending combustion.

Mild Catalyst- and Additive-Free Three-Component Synthesis of 3-Thioisoindolinones and Tricyclic γ-Lactams Accelerated by Microdroplet Chemistry.

Isoindolinones, bearing both γ-lactam and aromatic rings, draw extensive interest in organic, pharmaceutical, and medicinal communities as they are important structural motifs in many natural products, bioactive compounds, and pharmaceuticals. As the main contributor to isoindolinone synthesis, metal catalysis is associated with many drawbacks including essential use of toxic/precious metals and excessive additives, high reaction temperatures, specially predesigned starting materials, and long reaction times (typically 8-30 h). In this study, we developed a catalyst- and additive-free, minute-scale, and high-yield microdroplet method for tricomponent isoindolinone synthesis at mild temperatures. By taking advantage of the astonishing reaction acceleration (1.9 × 102-9.4 × 103 acceleration factor range with a typical rate acceleration factor of 1.51 × 103 for the prototype reaction as the ratio of rate constants by microdroplet and bulk phase), 12 3-thioisoindolinones and two tricyclic γ-lactams were synthesized using various 2-acylbenzaldehydes, amines, and thiols with satisfactory yields ranging from 85% to 97% as well as a scale-up rate of 3.49 g h-1. Because of the advantages (no use of any catalysts or additives, mild temperature, rapid and satisfactory conversion, broad substrate scope, and gram scalability), the microdroplet method represents an attractive alternative to metal catalysis for laboratory synthesis of isoindolinones and their derivatives.

Metal-Cation-Induced Tiny Ripple on Graphene.

Ripples on graphene play a crucial role in manipulating its physical and chemical properties. However, producing ripples, especially at the nanoscale, remains challenging with current experimental methods. In this study, we report that tiny ripples in graphene can be generated by the adsorption of a single metal cation (Na+, K+, Mg2+, Ca2+, Cu2+, Fe3+) onto a graphene sheet, based on the density functional theory calculations. We attribute this to the cation-π interaction between the metal cation and the aromatic rings on the graphene surface, which makes the carbon atoms closer to metal ions, causing deformation of the graphene sheet, especially in the out-of-plane direction, thereby creating ripples. The equivalent pressures applied to graphene sheets in out-of-plane direction, generated by metal cation-π interactions, reach magnitudes on the order of gigapascals (GPa). More importantly, the electronic and mechanical properties of graphene sheets are modified by the adsorption of various metal cations, resulting in opened bandgaps and enhanced rigidity characterized by a higher elastic modulus. These findings show great potential for applications for producing ripples at the nanoscale in graphene through the regulation of metal cation adsorption.

Effects of Cosolvent on the Intermolecular Interactions between an Analyte and a Gold Nanostar Surface Studied Using SERS.

For surface-enhanced Raman scattering (SERS), reproducible solution-phase results are typically obtained using nanoparticles functionalized with surface-stabilizing molecules that can prevent the adsorption of analyte molecules with surface affinities lower than those of the stabilizing agent. Herein, we investigate the effects of intermolecular interactions between a nonthiolated analyte and cosolvent to facilitate and modulate analyte adsorption to gold nanostars. SERS, extinction spectroscopy, transmission electron microscopy (TEM), and density functional theory (DFT) calculations are employed in this regard. Tetrahydrofuran (THF) is utilized as a cosolvent in water to facilitate the detection of acetylsalicylic acid (aspirin) on anisotropic gold nanoparticles. Intermolecular interactions between the analyte, solvent, and surface are modulated by changing the solution composition to understand how THF facilitates the SERS detection of aspirin in THF-water cosolvents. SERS signals for 5 mM aspirin arise only in the presence of THF at and above 60 mM, while no signal with or without THF below 60 mM is observed. SERS detection of aspirin is hypothesized to depend on THF forming a hydrogen-bonded complex with aspirin that reduces aspirin hydrophobicity, thus stabilizing the acid form of the molecule and allowing it to weakly interact with the gold nanoparticles. The aspirin-THF complex adsorbs to the gold surface through π-orbital overlap between the aromatic ring and gold, where additional THF weakens orbital overlap. Understanding the mechanism by which organic cosolvents facilitate the SERS detection of nonthiolated analytes such as aspirin, in aqueous media, allows other cosolvents, nonthiolated analytes, and other surfaces to obtain a SERS signal in a variety of systems.

Molecular characteristics of dissolved organic matter regulate the binding and migration of tungsten in porous media

Tungsten (W) is an emerging contaminant that poses potential risks to both the environment and human health. While dissolved organic matter (DOM) can significantly influence the W's environmental behavior in natural aquifers, the mechanisms by which DOM's molecular structure and functional group diversity impact W binding and migration remain unclear. Using molecular weight-fractionated soil and sediment DOM (<1 kDa, 1–100 kDa, and 100 kDa–0.45 μm), this study systematically investigated the relationship between DOM molecular characteristics and tungstate (WO42−) binding properties using multiple spectroscopic methods, including FTIR, fluorescence spectroscopy and XPS. The migration behavior of WO42− in porous media was also investigated through quartz sand column experiments. Results revealed that approximately 75 % of W was controlled by DOM, with over 50 % binding to low molecular weight DOM (<1 kDa). Tungsten bound to medium-high molecular weight DOM (1–100 kDa, >100 kDa) showed a greater propensity for retention, with the >100 kDa fractions demonstrating stronger selective binding to W, exhibiting distribution coefficients (Kmd) of 6.11 L/g and 10.69 L/g, respectively. Further analysis indicated that W primarily binds with aromatic rings, phenolic hydroxyls, polysaccharides, and carboxyl groups in DOM, potentially affecting DOM structural stability and consequently influencing W migration characteristics. Free W migration in quartz sand was primarily controlled by Langmuir monolayer adsorption, leading to local enrichment (Da = 6.83, Rd = 86.98). When bound to DOM, W's migration ability significantly increased (Rd = 8–10), with adsorption shifting to a Freundlich multilayer model, primarily controlled by convective transport (Npe = 27–62> > 1.96), while adsorption effects weakened (Da ≈ 1). This study, for the first time, systematically reveals the regulatory mechanisms of DOM molecular characteristics on tungsten's environmental behavior. It offers crucial parameter support for constructing tungsten migration models and provides important guidance for tungsten pollution risk assessment and remediation strategies.

Insight into evolution characteristics of pyrolysis products of HLH and HL coal with Py-VUVPI-MS and DFT

To achieve a comprehensive understanding of the influence of chemical structure on the evolution characteristics of coal pyrolysis products, pyrolysis reaction of two kinds of low rank coal (Huolinhe and Huangling coal) were investigated with pyrolysis-vacuum ultraviolet photoionization mass spectrometry (Py-VUVPI-MS). The soft ionized mass spectral detection can provide evolved information of original pyrolysis product. The chemical structure of coal samples was characterized by solid-state 13C-NMR, indicating HLH coal with more branched chain and longer aliphatic chain structure. The bond dissociation enthalpies (BDE) of β-Cal-Cal and β-Cal-O within model compounds were obtained with density functional theory. The difference of peak temperature with maximum evolution was collected to investigate the effect of the chemical environment on evolution behavior of pyrolysis products. The results reveal that branched and long aliphatic side-chains can reduces BDE of β-Cal-Cal and β-Cal-O, resulting in the lower peak temperature of pyrolysis products derived from HLH coal. Substituent groups (such as alkyl and hydroxyl groups) attached on the aromatic rings can reduce peak temperatures. Moreover, the effects of the different substituted position on the aromatic ring of the methyl group presented on differences of the BDE. An increase in aromatic ring size correlates with a certain degree of reduction in BDE for β-Cal-Cal; consequently, peak temperature of pyrolysis products with larger aromatic rings is lower. The pyrolysis behavior of coal were discussed based on the experimental observations and theoretical calculation, which are beneficial to understand the reaction route and mechanism of coal pyrolysis.

Understanding of the bond dissociation energy of C-NO2 in five- and six-membered N-heteroaromatic derivatives

A clear structure-sensitivity relationship in energetic molecules is beneficial for designing energetic materials. At the molecular level, sensitivity is closely related to the bond dissociation energy (BDE) of trigger linkages like C/N/O-NO2 in the widely used nitro compounds. Herein, the BDE of C-NO2 in a series of designed five- and six-membered N-heteroaromatic derivatives, including pyrrole, pyrazole, imidazole, triazole, tetrazole, pyridine, pyridazine, pyrimidine, pyrazine, triazine, tetrazine, and pentazine, are investigated to quantify the impact of substituent groups and N atoms on aromatic rings on it. We find that introducing pyridine-type N atoms decreases the BDE and increasing their number further reduces it. Additionally, increasing vicinal pyridine-type N atoms and C-NO2 also lowers the BDE. Conspicuously, the intramolecular hydrogen bonding between vicinal C-NO2 and C-NH2 facilitates high BDE.

Adsorption and removal of herbicide paraquat from aqueous solutions via novel bimetal organic framework: Kinetics, equilibrium and statistical surface modeling

This study examines the adsorption and removal of the herbicide paraquat in relation to a bimetal organic framework known as the Terbium/Palladium Metal-Organic Framework (Tb/Pd-MOF). Analysis of N2 adsorption/desorption isotherms, which were used to assess the properties of the Tb/Pd-MOF, revealed that the absorption of paraquat on Tb/Pd-MOF resulted in a reduction in pore volume, pore size, and surface area. Specifically, the pore volume decreased from 8.25 to 5.68 cm3/g, the pore size decreased from 11.34 nm to 8.92 nm, and the surface area decreased from 1456.61 to 1262.82 m2/g. The pore radius also decreased from 0.96 nm to 0.58 nm. Tb/Pd-MOF’s functional groups were identified through FT-IR, and the structure of the compound was confirmed using XPS. Various adsorption parameters including temperature, adsorbent dosage, pH, paraquat concentration, and contact time were studied. Density functional theory (DFT) was used to understand the electrical properties, reactivity, and morphology of paraquat. Results from the DFT analysis revealed that the electrophilic and nucleophilic attack sites aligned with the molecular orbitals (HOMO and LUMO) and MEP outcomes. The study found that Tb/Pd-MOF demonstrated a significant absorption capacity for paraquat, with adsorption data consistent with the Langmuir isotherm and pseudo-second-order kinetic models. The paraquat adsorption capability of Tb/Pd-MOF was determined to be 574.8 mg/g. Furthermore, chemisorption was identified as the primary form of adsorption, as indicated by the adsorption energy of 26.98 kJ·mol−1. The optimal conditions for achieving a high adsorption capacity were identified as pH 8 and 0.02 g of Tb/Pd-MOF. The temperature-dependent changes in the thermodynamic parameters ΔG°, ΔH°, and ΔS° indicated that the paraquat absorption onto Tb/Pd-MOF occurred spontaneously, was endothermic, and involved random processes. To optimize the absorption process, Response Surface Methodology and Box-Behnken design (RSM, BBD) were employed. These techniques enabled effective removal of paraquat from the Tb/Pd-MOF material. During chemisorption, the adsorbate and adsorbent form chemical bonds, while aromatic rings are involved in π-π bonding. Additionally, pore-filling occurs when the adsorbate fills the pores of the adsorbent, and electrostatic interactions result from the attraction or repulsion of charges between the adsorbate and adsorbent. As a means of eliminating paraquat from wastewater, Tb/Pd-MOF demonstrates significant potential due to its diverse absorption processes and high capacity for adsorption.

Development of deep learning software to improve HPLC and GC predictions using a new crown-ether based mesogenic stationary phase and beyond

The application of AI to analytical and separative sciences is a recent challenge that offers new perspectives in terms of data prediction. In this work, we report an AI-based software, named Chrompredict 1.0, which based on chromatographic data of a novel mesogenic crown ether stationary phase (CESP). Its molecular design represents a significant advancement due to the unique combination of properties and binding capabilities, including the formation of a cavity, mesogenic behavior via mobile chains, and a range of polar and non-polar interactions (aromatic rings, N=N and O=O double bonds, alkyl chains, π–π interactions, and hydrogen bonding). The mesogenic phase is effective in both normal and reversed-phase chromatography, enhancing the software's adaptability across diverse datasets.Here we introduce for the first time an unprecedented scientific approach, integrating deep learning techniques with the novel CESP, which demonstrates exceptional thermal and analytical performance in both liquid chromatography modes, especially in the separation of complex hydrocarbon isomers. This ability enables the results obtained with CESP to extend across various types of stationary phases.Leveraging these insights, a comprehensive chromatographic dataset on a series of aromatic and polyaromatic molecules interacting with our CESP was used to train a Deep Learning Model (DLM). This model is embedded within a user-friendly software, Chrompredict 1.0, designed for predicting chromatographic parameters (MAE = 0.042, R² = 0.95) by selecting chemical descriptors directly from SMILES notation. It offers a deeper understanding of molecular structure and interactions through exploratory data analysis, identifying key factors affecting model accuracy and chromatographic behavior.Users can configure hyperparameters, choose from six machine learning models, and compare their performance with DLM. Chrompredict 1.0 excels in retention behavior prediction for compounds with known structures, and it accurately predicts chromatographic retention and thermal characteristics for different temperatures in HPLC and GC. The model has been successfully tested with METLIN database of 1,023 small molecules of diverse structures and polarities (R² > 0.75, error range ±7.8 s). Overall, the CESP, combined with Chrompredict 1.0, offers a robust tool for intelligent chromatographic analysis, encompassing chemo-informatics, statistical analysis, and graphical capabilities across a broad range of compounds and stationary phases.

Efficient biodecolorization of direct black 22 Azo Dye by Aspergillus tamarii Kita UCP1279 isolated from caatinga soil

The textile industry is a major consumer of water, generating large volumes of wastewater contaminated with harmful substances, particularly azo dyes, which contain aromatic rings, amines, and sulfonic groups that contribute to their environmental toxicity. The use of microbial agents for wastewater treatment offers a cost-effective and sustainable solution, minimizing sludge production. Fungi from the Caatinga biome have demonstrated potential for bioremediation, especially under extreme environmental conditions. This study explores the ability of Aspergillus tamarii Kita to decolorize the azo dye Direct Black 22 (DB22) under varying conditions, including the use of both active and inactive fungal biomass, in static and agitated systems (120 rpm), at a controlled temperature of 30°C. Dye concentrations of 50, 125, and 250 mg/L were evaluated over time intervals of 75, 180, and 180 minutes, respectively. The influence of dissolved oxygen concentration and redox potential on the decolorization process was also investigated to identify optimal treatment conditions. Decolorization efficiency was quantified via spectrophotometric analysis. Results revealed decolorization rates of 100%, 97%, and 63% for the respective dye concentrations, with active biomass in agitated conditions achieving the highest removal rates. The study further demonstrated that dissolved oxygen levels and redox potential are critical factors in enhancing dye decolorization. These findings underscore the bioremediation potential of Aspergillus tamarii Kita in treating textile dye effluents, offering a promising approach to sustainable industrial wastewater management.

Hydrogen bonds between the oxygen-containing functional groups of biochar and organic contaminants significantly enhance sorption affinity

Sorption affinity is an essential parameter to immobilize contaminants, but the controlling structures of biochar with strong sorption affinity to organic compounds are unidentified, hindering targeted biochar modification. In the face of multiple types and structures of organic contaminants in the aquatic environment, it is urgent to prepare biochar which can remove a large number of contaminants by targeted biochar modification. This study compared the sorption and desorption of five different type organic contaminants on biochar and graphite to understand sorption affinity and to inform the structural regulation of biochar. The sorption capacity of organics on biochar was 3–7 times higher than graphite, and the desorption ratios of organics on biochar were approximately one-fourth of those on graphite. Hydrophobic areas and aromatic rings were confirmed to be low-energy sorption sites, and most pores were inaccessible. The stronger sorption affinity was thus attributed to the hydrogen bonds between biochar surface functional groups and organics. Furthermore, sorption capacity and desorption ratios correlated positively with calculated sorption thermodynamics and binding energies, aligning with theoretical models based on oxygen- and nitrogen-containing groups. Further verification experiments revealed that functionalized graphite with hydroxyl and carboxyl groups showed the most significantly increased sorption capacity and rate, and decreased desorption ratios, enhancing sorption affinity through hydrogen bonds. These findings offer valuable insights into biochar sorption affinity to organics and guide its structural regulation for organic pollution control in the aquatic environment

An innovative guanidinium-based ionic covalent organic frameworks with abundant aromatic rings for high-efficiency naproxen removal: Adsorption behavior, mechanisms, and density functional theory calculations

In recent years, naproxen (NPX) has raised significant environmental concerns requiring urgent attention. This study presents an innovative guanidinium-based ionic covalent organic framework (TFPB-TgCl), containing abundant aromatic rings, which was successfully synthesized via Schiff base reaction for the efficient and selective removal of NPX. Remarkably, TFPB-TgCl manifested a maximal NPX adsorption capacity of 308 mg/g at pH = 5. The adsorption on the active site (AOAS) model highlighted the simultaneous occurrence of both physical and chemical adsorption during the NPX uptake. The coefficients of the physical adsorption rates (5.6479, 1.9224, and 1.9224 min−1 for NPX concentrations of 20, 50, and 100 mg/L, respectively) were significantly higher than those of the chemical adsorption rates (0.1759, 0.0681, and 0.0567 g·mg−1·min−1 for the same concentrations), indicating the predominance of physical adsorption. Furthermore, the multilayer adsorption (MLA) model suggested that an adsorption site can interact with more NPX molecules, benefiting from various electrostatic and π-π interactions. The negative values of enthalpy change (ΔH° = −11.956 kJ/mol) and Gibbs free energy (ΔG < 0) confirmed the exothermic and spontaneous nature of the adsorption process. Additionally, in the optimal adsorption configuration (−131.57 kcal/mol), the Independent Gradient Model based on Hirshfeld partition (IGMH) was utilized to identify interaction sites between the guanidinium group of TFPB-TgCl and the carboxyl group of NPX, with subsequent electrostatic potential (ESP) analysis emphasizing their crucial role in electrostatic adsorption. Overall, the adsorption mechanism of electrostatic and π-π interactions in TFPB-TgCl highlights the significant contribution of its guanidinium and aromatic rings in facilitating NPX adsorption.

Comparative study of MMO and BDD anodes for electrochemical degradation of diuron in methanol medium

Treating emerging pollutants at low concentrations presents significant challenges in terms of degradation efficiency. Anodic oxidation using active and non-active electrodes shows great potential for wastewater treatment. Thus, this study compared the efficiency of a commercial mixed metal oxide anode (MMO: Ti/Ti0.7Ru0.3O2) and a boron-doped diamond anode (BDD) for the electrochemical oxidation of diuron in methanol, in chloride and sulfate media. The MMO anode achieved diuron removal rates of 94.9% and 92.8% in chloride and sulfate media, respectively, with pseudo-first-order kinetic constants of 0.0177 and 0.0143 min−1. The BDD anode demonstrated slightly higher removal rates, achieving 96.2% in sulfate medium and 96.9% in chloride medium, with respective kinetic constants of 0.0193 min⁻1 and 0.0177 min⁻1. Increasing the current density enhanced diuron removal by up to 15% for both electrodes; however, excessively high current densities led to increased energy consumption due to side reactions. The present of water had antagonistic effects, resulting in removal rates of 91.1% for chloride media using the BDD anode; and 87.4% and 90.4% in sulfate media with MMO and BDD anodes, respectively. The MMO anode in chloride medium did not show significant difference in the degradation percentage, reaching 96% of diuron removals. The degradation mechanism was proposed based on the detection of various by-products. The primary reactions observed during the oxidation of diuron in methanol involved chlorine substitution in the aromatic ring and dealkylation. These processes generated several intermediates and by-products at low concentrations, ultimately leading to high diuron removal.

Introduction of the Trifluoropropionate Moiety into Aromatic Rings via Rhodium-Catalyzed Coupling of Arylboronic Acids with Diazoesters.

A catalytic method for the introduction of pharmaceutically meaningful fluorinated propionic acid side chains into aromatic compounds is presented. In the presence of rhodium catalyst [RhCp*Cl2]2, various arylboronic acids are efficiently coupled with an easy-to-access diazoester reagent to give perfluorinated derivatives of phenylpropionic acids, including top-selling profen drugs. The key advantage of this approach is that the pharmacophore is introduced as a whole and is compatible with various functionalities and drug discovery.

Development of a carbohydrate-binding protein prediction algorithm using structural features of stacking aromatic rings

Carbohydrate-protein interactions play fundamental roles in numerous aspects of biological activities, and the search for new carbohydrate (CHO)-binding proteins (CBPs) has long been a research focus. In this study, through the analysis of CBP structures, we identified significant enrichment of aromatic residues in CHO-binding regions. We further summarized the structural features of these aromatic rings within the CHO-stacking region, namely “exposing” and “proximity” features, and developed a screening algorithm that can identify CHO-stacking Trp (tryptophan) residues based on these two features. Our Trp screening algorithm can achieve high accuracy in both CBP (specificity score 0.93) and CBS (Carbohydrate binding site, precision score 0.77) prediction using experimentally determined protein structures. We also applied our screening algorithm on AlphaGO pan-species predicted models and observed significant enrichment of carbohydrate-related functions in predicted CBP candidates across different species. Moreover, through carbohydrate arrays, we experimentally verified the CHO-binding ability of four candidate proteins, which further confirms the robustness of the algorithm. This study provides another perspective on proteome-wide CBP and CBS prediction. Our results not only help to reveal the structural mechanism of CHO-binding, but also provide a pan-species CBP dataset for future CHO-protein interaction exploration.

Herbidomicins, two pairs of polyketide tautomers produced by an actinomycete of the genus Herbidospora.

Herbidospora is one of the underexplored actinomycete genera from which only a limited number of secondary metabolites are reported. In our continuing investigation on less explored actinomycetes, a liquid culture of Herbidospora sp. RD 11066 was found to contain unknown metabolites that had no match in our in-house UV database. Chromatographic separation and following structural analysis using NMR and MS identified these metabolites to be chromanone and chromene derivatives, which were respectively composed of an inseparable mixture of two isomeric forms. The former polyketides, designated to be herbidomicins A1 (1) and A2 (2), are positional isomers in terms of a methyl substituent on an aromatic ring that mutually interconvert by acetal exchange by two phenolic hydroxy groups. The latter pair, herbidomicins B1 (3) and B2 (4), is Z/E-isomers regarding an enol ether double bond. Herbidomicins 1-4 were weakly antifungal against a dermatophytic fungus Trichophyton rubrum and were moderately cytotoxic against murine leukemia P388 cells.

Captodative Versus Push‐Pull Aromatic Cyclopentadienyl Derivatives

ABSTRACTThe problem of whether and how the captodative aromatic systems with the donor and acceptor substituents at the same carbon atom of the C=C bond can be more stable than the π‐conjugated push‐pull counterparts with the two substituents in the vicinal position is analyzed for cyclopentadienyl derivatives possessing an aromatic cyclopentadienyl ring. The analysis of electronic, magnetic, and structural criteria of aromaticity showed that among typical organic donors, such as amines NR3, ethers R2O, guanidine (NH2)2C=NH, siloxane O(SiH3)2, silatrane, the captodative isomers [cyclopentadienylium]−C(X+) = CH2 can be more stable than their push‐pull isomeric counterparts [cyclopentadienylium]−—CH=CH—X+. The largest energy difference in favor of the former was found to be ca. 13 kcal/mol for X = NH=C(NH2)2.