Chemical Approach Research Articles

The potential toxicity of chemically fabricated silver nanomaterials based on accumulation and histological changes in fish (Cyprinus carpio).

The bio-reductive fabrication of nanomaterials is a developing arena of study that seeks to fabricate nanoparticles (NPs) using microorganisms, plants, and animal blood. However, the chemical approach of AgNPs fulfills the need of abundant need of NPs. In contrast, chemically fabricated AgNPs are more toxic than biological AgNPs. Therefore, the current study aimed to assess and evaluate the chemically fabricated silver nanoparticles (AgNPs) for their possible toxicity in Common carp fish (Cyprinus carpio). The chemically synthesized silver nanoparticles were purchased from the market and applied for their possible toxicity. The chemically fabricated AgNPs were used against the Cyprinus carpio for bioaccumulation in different organs and histological alterations in the intestine and muscles. The results revealed that the AgNPs were mostly accumulated in the intestines followed by the gills, liver, and muscles (p < .05). The accumulated AgNPs caused histological alterations in gills and intestines at the highest concentration (0.08 mg/L). However, no alterations were observed by the middle and lowest concentration of AgNPs, particularly, in the intestine. In conclusion, more extensive research is required to establish the hazards related to the use of nanoparticles to disclose their negative effects on fish and the aquatic environment. REASEARCH HIGHLIGHTS: The chemical method fabricates a large amount of AgNPs Additionally, considered more toxic than the bio-reductive method AgNPs have excellent and diverse applications AgNPs deposited in various organs and cause histological changes.

Pretreatment of lignocellulosic biomass for bioethanol production

This review surveys recent progress in pretreatment methods for enhancing bioethanol production from lignocellulosic biomass. Various pretreatment techniques, including physical, chemical, and biological approaches, are evaluated for their efficacy in breaking down biomass structure and improving enzymatic digestibility. Key parameters influencing pretreatment effectiveness and integration with downstream processes are discussed. The review highlights promising strategies and identifies areas for further research to optimize bioethanol production from lignocellulosic feedstocks.

A Chemical Structure and Machine Learning Approach to Assess the Potential Bioactivity of Endogenous Metabolites and Their Association with Early Childhood Systemic Inflammation

Metabolomics has gained much attention due to its potential to reveal molecular disease mechanisms and present viable biomarkers. This work uses a panel of untargeted serum metabolomes from 602 children from the COPSAC2010 mother–child cohort. The annotated part of the metabolome consists of 517 chemical compounds curated using automated procedures. We created a filtering method for the quantified metabolites using predicted quantitative structure–bioactivity relationships for the Tox21 database on nuclear receptors and stress response in cell lines. The metabolites measured in the children’s serums are predicted to affect specific targeted models, known for their significance in inflammation, immune function, and health outcomes. The targets from Tox21 have been used as targets with quantitative structure–activity relationships (QSARs). They were trained for ~7000 structures, saved as models, and then applied to the annotated metabolites to predict their potential bioactivities. The models were selected based on strict accuracy criteria surpassing random effects. After application, 52 metabolites showed potential bioactivity based on structural similarity with known active compounds from the Tox21 set. The filtered compounds were subsequently used and weighted by their bioactive potential to show an association with early childhood hs-CRP levels at six months in a linear model supporting a physiological adverse effect on systemic low-grade inflammation.

Characterization and the physical properties of nano-sized Bi2O3/polymer for energy and high-refractive index applications

The present work focuses on developing nanocomposites for optoelectronics and energy storage devices leveraging the unique physicochemical features of bismuth (III) oxide (Bi2O3) using a polyvinyl pyrrolidone/polyvinyl alcohol matrix (PV(A/P)). Bi2O3 nanofillers (NF) and Bi2O3/PV(A/P) nanocomposite (NC) films were prepared by facile chemical solution approaches. The X-ray (XRD) data and a transmission electron image revealed that the NF exhibits a monoclinic phase, resembling slightly deformed agglomerated spheres. In the FTIR spectrum, different stretching vibrations of Bi-O-Bi bonds were found, along with their complexation and interaction with the reactive groups in the matrix. The SEM revealed a uniform distribution of Bi2O3 NF loading up to 1.5 wt% on the sample’s surface. Thermal analyses (TGA and DSC thermograms) were used to study the thermal stability, melting, and decomposition temperatures of the NC films. The dielectric features were studied under frequencies between 2 × 103 and 8 × 106 Hz and heating from 293 to 393 K. The dielectric constant and energy density were increased with Bi2O3 NF content. This implies that we can utilize the prepared NC for the fabrication of energy storage devices. The influences of the Bi2O3 NF doping level on the transmittance, band gap, Urbach energy, refractive index, conductivity, and other physical parameters were discussed. The modifications induced in the dielectric/optical parameters make the prepared NC films the best candidates for applications requiring a high refractive index, such as optical coatings and integrated photonic devices.

Hybrid Small-Molecule/Protein Fluorescent Probes.

Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.

Strategies to Diversification of the Mechanical Properties of Organic Crystals

AbstractStructurally ordered soft materials that respond to complementary stimuli are susceptible to control over their spatial and temporal morphostructural configurations by intersectional or combined effects such as gating, feedback, shape‐memory, or programming. In the absence of general and robust design and prediction strategies for their mechanical properties, at present, combined chemical and crystal engineering approaches could provide useful guidelines to identify effectors that determine both the magnitude and time of their response. Here, we capitalize on the purported ability of soft intermolecular interactions to instigate mechanical compliance by using halogenation to elicit both mechanical and photochemical activity of organic crystals. Starting from (E)‐1,4‐diphenylbut‐2‐ene‐1,4‐dione, whose crystals are brittle and photoinert, we use double and quadruple halogenation to introduce halogen‐bonded planes that become interfaces for molecular gliding, rendering the material mechanically and photochemically plastic. Fluorination diversifies the mechanical effects further, and crystals of the tetrafluoro derivative are not only elastic but also motile, displaying the rare photosalient effect.

Pharmacological inhibition of α-synuclein aggregation within liquid condensates

Aggregated forms of α-synuclein constitute the major component of Lewy bodies, the proteinaceous aggregates characteristic of Parkinson’s disease. Emerging evidence suggests that α-synuclein aggregation may occur within liquid condensates formed through phase separation. This mechanism of aggregation creates new challenges and opportunities for drug discovery for Parkinson’s disease, which is otherwise still incurable. Here we show that the condensation-driven aggregation pathway of α-synuclein can be inhibited using small molecules. We report that the aminosterol claramine stabilizes α-synuclein condensates and inhibits α-synuclein aggregation within the condensates both in vitro and in a Caenorhabditis elegans model of Parkinson’s disease. By using a chemical kinetics approach, we show that the mechanism of action of claramine is to inhibit primary nucleation within the condensates. These results illustrate a possible therapeutic route based on the inhibition of protein aggregation within condensates, a phenomenon likely to be relevant in other neurodegenerative disorders.

Unlocking the functional potential of Nitraria schoberi extracts using chemical fingerprinting, biological efficiencies, in silico and network pharmacological approaches

The objective of this investigation was to assess the cytotoxic, antioxidant, and enzyme inhibitory properties of the aerial portions of Nitraria schoberi (family Nitrariaceae). Extracts were prepared by sequential maceration in hexane, dichloromethane (DCM), ethyl acetate and methanol (MeOH) and water extract was prepared by infusion. DCM and MeOH extracts accumulated the highest amount of metabolites where the former was characterized by the presence of octadecyl ferulate (16.96 mg/100 mg), methoxyluteolin (8.48 mg/100 mg) and isorhamnetin (5.35 mg/100 mg) and the alkaloids perlolyrine (5.03 mg/100 mg), (+)-5a-hydroxylemannine (2.43 mg/100 mg) and matrine (2.40 mg/100 mg). Results of antioxidant activity showed that the MeOH extract exerted the highest anti-2,2-diphenyl-1-picrylhydrazyl (DPPH) (28.13 mg Trolox equivalent (TE)/g) and Fe+++ (54.38 mg TE/g) reducing capacity. All extracts exerted significant acetylcholinesterase (3.71–4.37 mg galantamine equivalent (GALAE)/g) and tyrosinase (86.40–109.63 mg kojic acid equivalent (KAE)/g) inhibition activity. The best α-amylase and α-glucosidase inhibition was exhibited by the DCM (0.81 mmol ACAE/g) and MeOH (1.34 mmol ACAE/g) extracts respectively. The highest cytotoxic effect was exerted against the breast adenocarcinoma (MDA-MB-231) (IC50: 26.71 μg/mL) and cervix adenocarcinoma (HELA) (IC50: 29.10 μg/mL) cell lines by the MeOH and DCM extracts respectively. In addition, we performed molecular docking analysis to understand the interaction between chemical components and tested enzymes and cellular targets for cancer. Chrysoeriol-3-O-rutinoside bound strongly to AChE. Furthermore, a good interaction between vascular endothelial growth factor receptor 2 (VEGFR2) and isovitexin-2″-O-arabinoside was observed. We employed network pharmacology to understand the role of N. schoberi's compounds in neurological disorder like Alzheimer and multiple sclerosis. Therefore, the results of this study indicate that N. schoberi may serve as a viable starting point for the future creation of phytopharmaceuticals that target particular diseases associated with oxidative stress, such as diabetes and certain neurological disorders.

Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome

BackgroundIn dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties are originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools.ResultsIn this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.ConclusionsOur results provide the first window into the 5-hmU and chromatin accessibility landscapes in dinoflagellates.

40S Ribosomal Protein S6 Kinase Integrates Daylength Perception and Growth Regulation in Arabidopsis thaliana.

Plant growth occurs via the interconnection of cell growth and proliferation in each organ following specific developmental and environmental cues. Therefore, different photoperiods result in distinct growth patterns due to the integration of light and circadian perception with specific Carbon (C) partitioning strategies. In addition, the TARGET OF RAPAMYCIN (TOR) kinase pathway is an ancestral signaling pathway that integrates nutrient information with translational control and growth regulation. Recent findings in Arabidopsis (Arabidopsis thaliana) have shown a mutual connection between the TOR pathway and the circadian clock. However, the mechanistical network underlying this interaction is mostly unknown. Here, we show that the conserved TOR target, the 40S ribosomal protein S6 kinase (S6 K) is under circadian and photoperiod regulation both at the transcriptional and post-translational level. Total S6 K (S6K1 and S6K2) and TOR-dependent phosphorylated-S6 K protein levels were higher during the light period and decreased at dusk especially under short day conditions. Using chemical and genetic approaches we found that the diel pattern of S6 K accumulation results from 26S proteasome-dependent degradation and is altered in mutants lacking the circadian F-box protein ZEITLUPE (ZTL), further strengthening our hypothesis that S6 K could incorporate metabolic signals via TOR, which are also under circadian regulation. Moreover, under short days when C/energy levels are limiting, changes in S6K1 protein levels affected starch, sucrose and glucose accumulation and consequently impacted root and rosette growth responses. In summary, we propose that S6K1 constitutes a missing molecular link where day-length perception, nutrient availability and TOR pathway activity converge to coordinate growth responses with environmental conditions.

Novel pentafluorosulfanyl-containing triclocarban analogs selectively kill Gram-positive bacteria.

The rise of antibiotic resistance among bacterial pathogens poses a significant threat to global health, underscoring the urgent need for novel antimicrobial agents. This study presents research on a promising class of novel compounds with potent antibacterial properties against Gram-positive bacteria, notably Staphylococcus aureus and MRSA. What sets these novel analogs apart is their superior efficacy at substantially lower concentrations compared with commonly used antibiotics like ciprofloxacin and gentamycin. Importantly, these compounds act by disrupting the bacterial cell membrane, offering a unique mechanism that could potentially circumvent existing resistance mechanisms. Preliminary safety assessments also highlight their potential for therapeutic use. This study not only opens new avenues for combating antibiotic-resistant infections but also underscores the importance of innovative chemical approaches in addressing the global antimicrobial resistance crisis.

Electrochemical and quantum chemical approaches to the study of dopamine sensing using bentonite and L-cysteine modified carbon paste electrode

This work presents a significant investigation involving both electrochemical experiments and quantum chemical simulations approaches. The objective was to characterize the electrochemical detection of dopamine (DA). The detection was carried out using a modified carbon paste electrode (CPE) incorporating bentonite (Bent) and L-cysteine (CySH) (named as CySH/Bent/CPE). To understand and explain the oxidation mechanism of DA on the CySH/Bent modified electrode surface, the coupling of the two approaches were exploited. The CySH/Bent/CPE showed excellent electroactivity toward DA such as good sensibility, selectivity, stability, and regenerative ability. The developed sensor shows a dynamic linear range from 0.8 to 80 μM with a limit of detection and quantification of 0.5 μM and 1.5 μM, respectively. During the quantitative analysis of DA in presence of ascorbic acid (AA) and uric acid (UA) the electrochemical oxidation signals of AA, DA, and UA distinctly appear as three separate peaks. The potential differences between the peaks are 190 mv, 150 mv, and 340 mVfor the AA–DA, DA–UA, and AA–UA oxidation pairs, respectively. These observations stem from square wave voltammetry (SWV) studies, along with the corresponding redox peak potential separations. The developed sensor is simple and accurate for measuring DA in human serum samples. On the other hand, CySH acts as an electrocatalyst on the CySH/Bent/CPE surface by increasing its active electron transfer sites, as suggested by the quantum chemical modeling with analytical results of Fukui. Furthermore, the voltammetric results obtained agree well with the theoretical calculations.

Genetic Encoding of Phosphorylated Amino Acids into Proteins.

Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.

Photoelectrochemical Properties of Chemical Bath Deposited CdNiSe Thin Films

The chemical bath deposition approach was used to prepare Cd1−xNixSe thin film photoelectrodes on a substrate made of stainless-steel plate. The constructed cell has the configuration: p-CdNiSe | NaOH (1M)+S (1M)+Na2S (1M) | C (graphite). Studying current-voltage characteristics in the dark, capacitance–voltage in the dark, barrier-height measurements, power output, photo response, and spectral response are all part of characterizing the photoelectrochemical cell of the photoelectrodes. For the composition of Cd0.7Ni0.3Se, the junction ideality factor was determined to be minimal. It was discovered that the flat band potential and barrierheight was 710 mV and 0.181 eV respectively. The power output characteristic reveals that, for composition x = 0.3, the short circuit current, open circuit voltage, conversion efficiency and fill factor are respectively, 161 μA/cm2, 260 mV, 0.64% and 48.11%. The greatest current recorded at 725 nm is displayed in the spectral response.

Cost-effective synthesis of stable CoxC@few-layered graphene nanostructures embedded in a carbon matrix

In this study, a two-step surfactant sol-gel strategy is developed to synthesize Co particles with confined sizes in the nanoscale using organic precursors. This approach does not require the use of vacuum techniques or strong reducing atmospheres, making it a simple approach economically attractive. The strategy involves the generation of few-layered graphene shells to provide chemical stability, prevent oxidation and aggregation tendencies. Additionally, the study investigates the use of precursors based on nitrates and acetates, exploring their structural and magnetic properties in densified samples. Remarkably, magnetic properties are competitive for both approaches, with coercivities reaching up to 300Oe and saturation magnetization of ∼60 and ∼80emu/g for samples based on nitrates and acetates prepared at 650 °C, respectively. However, it is observed that smaller and more uniformly sized nanoparticles (around ∼10nm) are obtained with nitrate-based precursors due to an effective ligand decomposition process. Therefore, this chemical approach offers effective nanoscale confinement with intriguing magnetic properties through a cost-effective and reproducible synthesis.

Behavioral control through the direct, focal silencing of neuronal activity.

The ability to optically stimulate and inhibit neurons has revolutionized neuroscience research. Here, we present a direct, potent, user-friendly chemical approach for optically silencing neurons. We have rendered saxitoxin (STX), a naturally occurring paralytic agent, transiently inert through chemical protection with a previously undisclosed nitrobenzyl-derived photocleavable group. Exposing the caged toxin, STX-bpc, to a brief (5ms) pulse of light effects rapid release of a potent STX derivative and transient, spatially precise blockade of voltage-gated sodium channels (NaVs). We demonstrate the efficacy of STX-bpc for parametrically manipulating action potentials in mammalian neurons and brain slice. Additionally, we show the effectiveness of this reagent for silencing neural activity by dissecting sensory-evoked swimming in larval zebrafish. Photo-uncaging of STX-bpc is a straightforward method for non-invasive, reversible, spatiotemporally precise neural silencing without the need for genetic access, thus removing barriers for comparative research.

Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification.

Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.

Enhancing structural diversity of terpenoids by multisubstrate terpene synthases.

Terpenoids are one of the largest class of natural products with diverse structures and activities. This enormous diversity is embedded in enzymes called terpene synthases (TSs), which generate diverse terpene skeletons via sophisticated cyclization cascades. In addition to the many highly selective TSs, there are many promiscuous TSs that accept multiple prenyl substrates, or even noncanonical ones, with 6, 7, 8, 11, and 16 carbon atoms, synthesized via chemical approaches, C-methyltransferases, or engineered lepidopteran mevalonate pathways. The substrate promiscuity of TSs not only expands the structural diversity of terpenes but also highlights their potential for the discovery of novel terpenoids via combinatorial biosynthesis. In this review, we focus on the current knowledge on multisubstrate terpene synthases (MSTSs) and highlight their potential applications.

Imbalanced Surface Charge Induced Phase Segregation in Mixed Halide Perovskites

AbstractAlloying the metal halide perovskite composition has become a key strategy for engineering the optoelectronic properties for various applications. However, the difference in complexation between ions poses a threat to crystal stability. In particular, the phase segregation in wide‐bandgap perovskites (WBG) with mixed halides is the major challenge in multi‐junction photovoltaic devices. Here, a systematic study is reported on the origin of phase segregation in a prototypical mixed halide perovskite (MHP) MAPbI2Br. It is found that the crystallinity and surface morphology are not associated with the lattice stability. Using highly sensitive external quantum efficiency (s‐EQE) measurement, it is found that the defects in the MHP are mainly associated with the Pb2+ and I−/Br− ions. Consistently, density‐function‐theory (DFT) calculation confirms that the MAPbI2Br surface is dominated by the metal‐halide components, and the imbalanced surface charge is responsible for the lattice instability. The role of physical and chemical passivation approaches in MHP is further investigated. The former limits the ion migration and allows dissociated ions to recover to their corresponding defective sites, whereas the latter lowers the surface energy by neutralizing the charge density on the lattice surface. This work brings insight into the phase segregation and passivation mechanisms in MHP.

Chemical Approach to Control Hydrate in Offshore Gas Production Facilities

- Hydrate formation presents a significant operational challenge in offshore oil and gas production, primarily due to the potential formation of hydrate plugs which obstruct fluid flow, thereby posing serious flow assurance risks. Additionally, these solid, crystalline, icelike structures, composed of low molecular weight gases (such as methane, ethane, and propane) encapsulated in hydrogen-bonded water cages, can aggregate into larger masses capable of damaging or rupturing pipelines. Such formations typically occur under the high-pressure and low-temperature conditions prevalent in subsea flowlines and cold-weather operations. This study employs the Prosper simulation software to model these complex thermodynamic and hydrodynamic conditions and to predict the effective dosages of chemical inhibitors required to prevent hydrate formation. Specifically, our simulations suggest optimal dosages of 35% wt. methanol (MeOH) and 45% wt. monoethylene glycol (MEG) for gas stream 1, and 22% wt. MeOH and 33% wt. MEG for gas stream 2. Based on these findings, we advocate the use of Prosper simulation software as a predictive tool for the strategic administration of hydrate inhibitors in offshore gas production facilities. This research contributes to the ongoing development of chemical strategies for hydrate management, providing a basis for improved safety and efficiency in hydrocarbon extraction processes.