Probing the articaine-human serum albumin interaction and influences of paracetamol and caffeine on the interaction by spectroscopy, voltammetry, and bioinformatics

Interaction between a local anesthetic drug, articaine (ART) and human serum albumin (HSA) was investigated in the absence and presence of paracetamol (PAR) and caffeine (CAF) using spectroscopic, voltammetric, and computational techniques for the first time. The results demonstrated that increasing concentrations of ART in HSA solution led to a decrease in HSA fluorescence signal, indicating the ART-HSA complex formation via the static quenching mechanism. The binding strength of the complex was moderate (binding constant, Ka = 5.87 × 103 M-1 in fluorescence and 6.31 × 103 M-1 in voltammetric at 298 K). Thermodynamic analysis (ΔS = +28.32 J mol-1 K-1; ΔH = -30.17 kJ/mol) of the binding reaction suggested involvement of hydrophobic interactions, van der Waal's forces and hydrogen bonding in stabilizing the ART-HSA complex. Significant microenvironmental alterations near the Trp and Tyr residues of HSA consequent to the ART-HSA complex formation. ART predominantly binds to Sudlow's site I of HSA with more negative binding energy and stronger hydrophobic interactions compared to Site II. The stability of the ART-HSA complex at Site I over a 100 ns timeframe, supported by stable hydrogen bonding and compact HSA structure throughout the molecular dynamics simulations. The effect of PAR and CAF on the binding strength between ART and HSA was also examined, and presence of PAR and CAF in the reaction mixture produced significant reduction in the binding affinity of ART to HSA. These findings underscore the competitive binding between ART, PAR, and CAF, which impacts their pharmacokinetics and efficacy. This study provides valuable insights into the complex interactions between anesthetic drugs and common pharmaceuticals, potentially guiding clinical practices and drug development.

Elucidating the modulatory effects of heteroatoms and substituent groups on ESIPT dynamics and optical properties in HBBX derivants

The benzo furan-extended 2-(2'-hydroxybenzofuranyl) benzazole derivants (HBBX) have attracted widespread attention for their excellent photophysical properties. Some subtle structural alterations have been proven to influence the spectral characteristics significantly. However, a comprehensive understanding of the influence of structural regulation is still lacking. Here, the effects of heteroatoms and substituent groups on the excited state intramolecular proton transfer (ESIPT) process and photophysical properties of HBBX derivants are investigated by the density functional theory/time-dependent density functional theory (DFT/TDDFT). Our simulation results show that heteroatoms and substituent groups significantly change the hydrogen bond strength of HBBX derivants. To the heteroatoms, the HBBX substituted by the N atom (HBBI) has the lowest ESIPT energy barrier in the first excited state, and the substitution of tBu group (HBBO-1) can cause the maximum energy barrier reduction to the substituent groups. Moreover, the absorption, emission spectra and hole-electron analysis are consistent with the experimental results, and the simulation results show that HBBI has the lowest degree of intramolecular charge transfer and highest fluorescence intensity in all HBBX derivants. Our work will provide the comprehensive insight into the effects of heteroatoms and substituent groups on ESIPT processes and photophysical properties for the design of fluorescent materials.

Robust zincophilic-hydrophobic protection layer induces preferential growth of (0 0 2) crystal plane towards ultra-stable Zn anode

The practical deployment of aqueous zinc-ion batteries (AZIBs) in large-scale energy storage applications is hampered by short cycle lifespans and limited zinc utilization due to uncontrollable dendrite growth and water-induced side reactions. Herein, we propose an environmentally friendly electrolyte additive, 2-acrylamido-2-methylpropanesulfonic acid (AMPS), which features dual zincophilic sites and a hydrophobic group, to enhance Zn stability. Theoretical calculations and experimental characterizations demonstrate that AMPS can firmly adsorb onto the Zn (0 0 2) plane through its dual zincophilic sites (SO3H and NHCO), while the CC hydrophobic group orients toward the electrolyte, ultimately forming a stable zincophilic/hydrophobic interface on the Zn electrode in situ. This unique structure not only inhibits water-induced side hydrogen evolution reactions but also induces preferential deposit propagation along the (0 0 2) crystal plane. Benefiting from this synergetic effect, the Zn//Cu asymmetric cell with AMPS electrolyte maintains an ultrahigh average coulombic efficiency of 99.8 % for over 2500 cycles at 2 mA cm-2, achieving 1 mAh cm-2. Furthermore, the Zn//MnO2 full cell shows a high-capacity retention of 67.7 % at 1.8 A g-1 after 1000 cycles, confirming the effectiveness of the AMPS additive in improving the cyclability and performance of AZIBs.

Engineering nitrogen-doped carbon quantum dots: Nitrogen content-controlled dual-phase emission behavior

Nitrogen doping is a widely used method for enhancing the performance of carbon quantum dots (CQD). However, the precise relationship between nitrogen content and emission spectra remains unclear when preparing high-performance nitrogen-doped CQD (N-CQD). This study systematically investigates the effects of nitrogen content on the crystalline structure, optical properties, and electronic band structure of N-CQD. Citric acid was used as the carbon source, and ethylenediamine monohydrate was used as the nitrogen source, with their ratio controlled to hydrothermal synthesized N-CQD with N/C ratios ranging from 0 to 0.4. Notably, when the N/C ratio increases from 0 to 0.2, the N-CQD exhibits redshifted emission with excitation dependence. However, when the N/C ratio rises from 0.2 to 0.4, the N-CQD shows blueshifted emission with excitation-independence. We define it as the dual-phase emission behavior of N-CQD attributed to the transition of doping sites from graphitic nitrogen to pyridine nitrogen with increased nitrogen content. DFT calculations indicate that different doping sites influence electron transfer in N-CQD, resulting in distinct optical behaviors. Importantly, this work comprehensively explains the relationship between nitrogen content and the emission behavior of N-CQD for the first time, providing crucial insights for refining the theoretical framework of N-CQD.

The first example of white-light emission based on pyrimido[4',5':4,5]thieno[2,3-d]pyrimidine moiety: Synthesis, photophysical, and antimicrobial studies

A series of new AIE systems based on the pyrimidothienopyrimidine skeleton were efficiently synthesized and fully characterized. These compounds exhibited weak emission in solution but strong solid-state fluorescence with a red shift. Notably, compound 16 displayed unique white-light emission from a single-component system and tunable emission colors in DMF/water mixtures. This dual emission behavior, arising from AIE and excimer formation, is unprecedented for pyrimidothienopyrimidine derivatives. Although compounds 9a and 9b exhibited AIEE behavior, compounds 15c and 18 demonstrated AIE behavior, with significantly enhanced fluorescence intensity upon water addition. Moreover, most synthesized compounds exhibited moderate to strong antimicrobial activity against various bacterial and fungal strains, suggesting their potential for biological applications.

Theoretical study on acridine-thioxanthene bridged TADF molecules presenting TSCT and TBCT features and the design for full-color emission

We have theoretically studied a series of acridine-thioxanthene bridged thermally activated delayed fluorescence (TADF) molecules, 2PhCzSpiroS, 2PhCzSpiroS-2, SpiroS-2TRZ, TPA-SpiroS-TRZ, BOP-SpiroS-TRZ and QX-SpiroS-TRZ by using DFT/TD-DFT methods, and screened out a series of potential full-color TADF materials. Firstly, we preliminarily predicted the ease of reverse intersystem crossing (RISC) and through-space charge transfer (TSCT) processes for these molecules through singlet-triplet energy gap calculation and weak interaction analysis. Secondly, we detailedly compared the effects of different combinations of TADF functional groups on the intersystem crossing (ISC) channels and radiative/non-radiative processes. In particular, these molecules contain a pair of isomers, whose frontier orbital energy levels are very close, but the electronic structures of the ground state and the excited state are quite different such as frontier orbital distributions. The comparative study reveals the significant influence of the geometrical configuration on the electronic structure and the transition characteristics of TSCT, through-bond charge transfer (TBCT), and local excitation (LE). Finally, we evaluated the TADF properties of these molecules and screened out the target molecules by comprehensively considering the radiative rate, ISC/RISC rate, and the determining parameters of non-radiative process such as the reorganization energy between the excited state and the ground state.

The association between estrogenic activity evolution and the formation of different products during the photochemical transformation of parabens in water

Photochemical transformation is a critical factor influencing the environmental fate of pharmaceutical and personal care products in aquatic ecosystems. However, the relationship between toxicity evolution and the formation of various transformation products has been seldom explored. This study investigates the behavior and changes in estrogenic activity during the photochemical transformation of a series of typical endocrine-disrupting parabens (PBs), focusing on the effects of increasing alkyl-chain length (MPB, EPB, PPB and BPB). Based on MS/MS analysis, four types of transformation products were identified: (1) p-hydroxybenzoic acid (HB), which exhibits no estrogenic activity; (2) hydroxylated products (OH-PBs); (3) dimer products formed between HB and PBs (HB-PBs); and (4) dimer products formed from identical PBs (PBs-PBs), comprising three distinct isomers. In the absence of standard sample, OH-PBs were synthesized and their estrogenic activity was evaluated using a yeast two-hybrid reporter assay. The EC50 values were determined to be <1 × 10-3 M for OH-MPB, 2.05 × 10-4 M for OH-EPB, 5.05 × 10-5 M for OH-PPB, and 1.89 × 10-5 M for OH-BPB. These indicate that the estrogenic activity of OH-PBs is one order of magnitude lower than that of the corresponding PBs. Both HB-PBs and the three isomers of PBs-PBs exhibited significantly higher estrogenic activities than their corresponding parent compounds, increasing 9 - 14 and 32 - 184 times, respectively, based on theoretical calculations. Among the three PBs-PBs isomers, the highest estrogenic activity was observed in the ether dimer, followed by the biphenyl dimers. Consistent with the parent compounds, the estrogenic activities of OH-PBs, HB-PBs, and PBs-PBs increased with the length of the alkyl-chain. The estrogenic activity of MPB and EPB followed an overall downward trend during the photochemical transformation, whereas PPB and BPB remained stable initially before declining rapidly. This behavior was associated with the contributions of toxic transformation products. These findings elucidate the relationship between molecular structure, transformation products, and estrogenic activity, highlighting the importance of understanding estrogenic activity evolution during the photochemical transformation of PBs.

Pore lipid modifications modulate MscS nanopore for enhanced single-molecule sensing

Modifying transmembrane channels is essential for enhancing functionality. Current modification methods often require chemical reactions or protein engineering, which can increase technical complexity and workload. The inner transmembrane region of MscS can bind lipid molecules, referred to as pore lipids, offering an opportunity for fine-tuning channel properties and improving sensing performance. We leveraged lipid-like molecules, specifically detergents, to replace pore lipids, introducing specific chemical groups into the MscS channel. Using Cryo-EM, we determined the structure of MscS from Pseudomonas aeruginosa, demonstrating that DDM bind stably at the entrance of the hydrophobic pathway. Single-channel recordings confirmed that detergent substitution within the pore alters channel conductance and gating behavior. Molecular dynamics simulations further revealed that detergent modifications adjust the tilt of the TM1-TM2 helices, influencing the channel state. By modifying MscS with different detergents, we tailored its properties, enabling selective detection of target molecules at the single-molecule level. This approach capitalizes on the intrinsic characteristics of MscS and lipid-like molecules, providing a convenient and efficient method for nanopore modification without complex chemical reactions or protein recombination.

Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2

Schizophrenia is a severe brain disorder that usually produces a lifetime of disability. Related research shows activating metabotropic glutamate receptors holds therapeutic potential. Agonist-positive allosteric modulations (ago-PAMs) not only activate metabotropic glutamate receptors but also enhance glutamate-induced responses, offering a promising treatment strategy. However, the molecular mechanisms by which ago-PAM enhances glutamate-induced responses remain unclear, as does the potential influence of glutamate on ago-PAM. In this study, Gaussian accelerated molecular dynamics and tau random acceleration molecular dynamics simulations were employed to investigate the molecular mechanism between ago-PAM and glutamate in full-length mGlu2. Results suggest that the ago-PAM JNJ-46281222 enhances the binding affinity and residence time of glutamates in the Venus flytrap (VFT) domains by initiating a variant reverse communication from the heptahelical transmembrane (7TM) domains to VFTs via the cysteine-rich domains. Meanwhile, glutamate facilitates the interaction between Trp676 and Glu701 to further induce the relaxation of TM5, promoting the opening of the PAM-binding pocket. Glutamate can also promote the upward rotation of the cyclopropylmethyl group of the JNJ-46281222 to bring the TM6-TM6 distance closer. Nevertheless, it remains uncertain how the binding between mGlu2 and G protein differs when induced by small molecules binding in allosteric sites, orthosteric sites, or both. In conclusion, this study shed new light on the positive coordination relationship between ago-PAM and glutamate in the full-length mGlu2 receptor, which could help develop novel and more effective ago-PAM to treat schizophrenia.

Solvatochromic fluorophores based on 6-fluoro-2-(aryl)quinoline-4-carboxylic acids: Synthesis, optical studies and evaluation of their antimicrobial and larvicidal properties

6-Fluoro-2-(aryl)quinoline-4-carboxylic acids 1-11 were synthesized via Pfitzinger reactions between 5-fluoroisatin and methyl aryl ketones. The molecules were studied regarding the impact of their substituent patterns (a-e) on their optical and bioactivity properties. All compounds were fluorescent in solution and had significant solvatochromic behavior, measured in tetrahydrofuran, dichloromethane, dimethylsulfoxide, acetonitrile, methanol, and water at different pHs. Compounds emitted in a broad spectral range from ultraviolet to green, with quantum efficiencies, varying from very weak (ex.: <0.5 % for 1a in DMSO and MeOH) to moderate-strong (∼35 % for 11e in dichloromethane). A biomonitoring of the synthetized compounds reveals antimicrobial and larvicidal (Aedes aegypti mosquitoes) profile. Gram-positive bacterial and fungal species showed greater sensitivity to the 11e, that presented both bactericidal and fungicidal nature. This compound with a methylenedioxy substituent showed favourable interactions with Dehydrosqualene synthase (DQS) and Squalene synthase (SQS), well-validated antimicrobial targets, considering key residues in the complex formation. The molecule also presented a good larvicidal profile, ranking second in terms of significant LC50 values. Thus, 11e has demonstrated an advantage scaffold for future biological tests in other organisms or at the cellular level.

Signature of electronically excited states in Raman spectra of azobenzene derivatives. Computational and experimental approaches

Raman spectroscopy can provide highly sensitive and detailed information about the structural fingerprint of molecules, enabling their identification. In this study, our aim is to understand the enhanced intensity observed in experimental Raman measurements. Five azobenzene derivatives were selected, each substituted with different functional groups, for both experimental and theoretical investigations. To reproduce the experimental trend, we employed various levels of theory using the QM-DFT approach. Theoretical results were compared to experimental data through both qualitative and quantitative analyses. A good correlation between theoretical and experimental results was achieved when considering electronic transitions to predict the theoretical Raman spectra and interpret the experimental data. Our theoretical results indicate that even dark (nπ*) transitions, which are forbidden and have an oscillator strength close to zero, can have a signature in the Raman spectra due to the resonance effect with incident energy. Additionally, the vibrational modes stimulated by the presence of ππ* bright states, being at the pre-resonance with the incident energy, was clearly separated from the vibrational frequencies of the dark states, which was evinced in the Raman fingerprint. Theoretical Raman spectra of azobenzene derivatives, substituted with push-pull moieties, revealed contributions from the charge transfer transitions (nπ*CT, ππ*CT) as well as back-donation of electron density, observed for the first time in an azobenzene derivative. Our protocol, proposing a quantitative and qualitative overlap between theoretical and experimental data, confirms the presence of combination modes between vibrational levels and electronically excited states.

A flexible polycyclic chemosensor for simultaneous discernment of Ni2+ and Cd2+ depending on distinct coordination modes

Herein, we present a paradigm of a flexible molecular system for simultaneous discernment of Ni2+ and Cd2+, depending on distinct chemical coordination manners. By incorporating two functional pyridine groups at different positions on the flexible DPAC framework (9,14-diphenyl-9,14-Dihydrodibenzo [a,c]phenazine), two derivatives are prepared as 27Py-DPAC and 36Py-DPAC. The results show that 27Py-DPAC can chemically coordinate with Ni2+ (intermolecular coordination) and Cd2+ (intramolecular coordination), generating fluorescence turn-off and -on behaviors, respectively. The key factors leading to the different coordination ways are the ionic radius and the substituted positions of pyridine groups. Demonstrably, 36Py-DPAC can respond to Ni2+ abiding by the principle of the 27Py-DPAC sensor, but it cannot sense Cd2+ because of the difficulty in forming an effective intramolecular coordination resulted from the large distance between two nitrogen atoms on pyridine and the central heterocyclic ring. Based on the ionic response properties of the two compounds, logic circuits were developed to simulate logical operations and facilitate ion detection. This research expands the applicability of flexible polycyclic conjugated molecules in chemical sensing and underscores the influence of different modification sites of functional groups on ion binding mechanisms.

A ratiometric turn-on fluorescent probe for the detection of BF3 based on imidazole-quinoline

In this study, a novel ratiometric fluorescent sensor SYW for the detection of BF3 was successfully synthesized based on imidazole-quinoline. The sensor showed noticeable fluorescence enhancement after binding to BF3 with remarkable color change observed by naked eye in a short response time (within 30 s). Additionally, the probe had an extremely low detection limit (1.71 nM) and exhibited excellent specificity for BF3. The recognition mechanism of the probe SYW for BF3 was determined by 19F NMR, FTIR, HRMS, and density functional theory (DFT) calculations. Moreover, the probe can also be applied in quantitatively detecting BF3 concentrations as well as gaseous BF3 by test paper strips containing SYW. In addition, the probe SYW was also employed to detect BF3 in living cells. These results suggested that the probe SYW displayed promising applications in environmental monitoring, and industrial production, and biological systems.

Aggregation-induced emission-twisted intramolecular charge transfer-activated fluorescent probe for analyzing mitochondrial viscosity in cells and zebrafish

Mitochondria are crucial energy-supplying organelles that support cellular activities and play vital roles in cell metabolism, aging, autophagy, and apoptosis. Abnormal viscosity can alter the mitochondrial microenvironment, disrupt normal mitochondrial function, and lead to disease. To address this, we designed and developed two aggregation-induced emission-twisted intramolecular charge transfer fluorescent probes, namely, (E)-1,1,3-trimethyl-2-(4-(1,2,2-triphenylvinyl)styryl)-1H-benzo[e]indol-3-ium (HSL-1) and (E)-2-(4-(di-p-tolylamino)styryl)-1,3,3-trimethyl-1H-benzo[e]indol-3-ium (HSL-2). In vitro fluorescence detection revealed that both HSL-1 and HSL-2 were sensitive to viscosity and demonstrated a strong log-linear relationship, with linear coefficients of 0.982 and 0.980, respectively. Notably, the responses of HSL-1 and HSL-2 to viscosity changes were unaffected by pH, polarity, or interfering ions. HSL-1 exhibited stronger resistance to background interference than HSL-2 and significantly enhanced fluorescence intensity; thus, it was selected for cell experiments and animal fluorescence intensity assessments. Furthermore, HSL-1 showed excellent biocompatibility, enabling real-time detection of mitochondrial viscosity changes and identification of viscosity abnormalities triggered by mitophagy in HeLa cells. It could also monitor changes in mitochondrial viscosity in zebrafish. In conclusion, HSL-1 is a valuable tool for studying viscosity and understanding diseases associated with abnormal mitochondrial viscosity.

In silico characterization of the gating and selectivity mechanism of the human TPC2 cation channel

Two-pore channels (TPCs) are twofold symmetric endolysosomal cation channels forming important drug targets, especially for antiviral drugs. They are activated by calcium, ligand binding, and membrane voltage, and to date, they are the only ion channels shown to alter their ion selectivity depending on the type of bound ligand. However, despite their importance, ligand activation of TPCs and the molecular mechanisms underlying their ion selectivity are still poorly understood. Here, we set out to elucidate the mechanistic basis for the ion selectivity of human TPC2 (hTPC2) and the molecular mechanism of ligand-induced channel activation by the lipid PI(3,5)P2. We performed all-atom in silico electrophysiology simulations to study Na+ and Ca2+ permeation across full-length hTPC2 on the timescale of ion conduction and investigated the conformational changes induced by the presence or absence of bound PI(3,5)P2. Our findings reveal that hTPC2 adopts distinct conformations depending on the presence of PI(3,5)P2 and elucidate the allosteric transition pathways between these structures. Additionally, we examined the permeation mechanism, solvation states, and binding sites of ions during ion permeation through the pore. The results of our simulations explain the experimental observation that hTPC2 is more selective for Na+ over Ca2+ ions in the presence of PI(3,5)P2via a multilayer selectivity mechanism. Importantly, mutations in the selectivity filter region of hTPC2 maintain cation conduction but change the ion selectivity of hTPC2 drastically.

A polarity-sensitive fluorescent probe for visualizing lipid droplets in ferroptosis, cuproptosis, and autophagy

Dynamics of lipid droplets (LDs) in various pathological processes provides important information about lipid metabolism during theses biological processes, while only a few reports focused on this field. In this work, a benzothiazine-fused coumarin chromophore BCLD with strong fluorescence in low-polarity environment is described. It is confirmed that cyclization-induced rigidification might be a promising approach to enhance the LDs specificity of phenothiazine-based strucutres.The probe is found to enter cells through a clathrin-mediated endocytosis, and is able to monitor LDs variations in living cells, especially during various pathological processes. It is found that obvious increase in polarity of LDs during ferroptosis and cuproptosis was visualized while a dramatic decrease in the number of LDs was recorded during autophagy, indicating different lipid metabolism manners and LD dynamics in these pathological processes. This work supports the potentials of LDs as markers for drug design targeting ferroptosis, cuproptosis, and autophagy.

Leishmania donovani homoserine dehydrogenase: Biochemical and structural characterization of a novel parasite specific enzyme of aspartate pathway

Visceral leishmaniasis is a neglected tropical disease. Drug resistance and toxicity are the critical issues with the currently available antileishmanial drugs. Therefore, research efforts are underway to identify and validate new drug targets specific to Leishmania parasite. The enzyme homoserine dehydrogenase (HSD) functions in the third step of aspartate pathway. The present study focuses on the biophysical and biochemical characterization of HSD enzyme from Leishmania donovani (LdHSD) which is unique to the parasite with no homologous enzyme in the host. LdHSD gene was cloned in pET28c(+) vector and transformed in E. coli BL21 (DE3) strain. LdHSD recombinant enzyme of molecular weight 46.6 kDa with 6X-His tag at the C-terminal end was expressed, purified by nickel affinity chromatography and confirmed by western blot analysis using anti-His antibody. Effect of pH, temperature, salts, metal ions and amino acids on the recombinant enzyme were evaluated. Kinetic parameters of LdHSD were evaluated for substrates L-homoserine and NADP+. Biophysical analysis revealed that the enzyme is rich in β-sheets. Thermal denaturation study revealed that the protein is stable up to 45 °C. Furthermore, comprehensive comparative sequence analysis and structural modeling revealed the structural and functionally important residues, which are involved in the catalytic mechanisms. The putative binding mode of the natural substrate L-homoserine into the active site of LdHSD was also elucidated. These findings provide a foundation for the development of selective, target-based inhibitors against the HSD enzyme of the parasite.

Fosamprenavir and Tirofiban to combat COPD and cancer: A drug repurposing strategy integrating virtual screening, MD simulation, and DFT studies

Matrix metalloproteinases (MMPs) are involved in different pathophysiological conditions like cancer, COPD, asthma, and inflammatory diseases. Among these MMPs, macrophage metalloelastase is one of the prime targets for COPD, and cancer. Therefore, to combat such diseases, potent novel macrophage metalloelastase inhibitors can be considered. Here, the classification-based molecular modeling was performed on large data of macrophage metalloelastase inhibitors that identified dibenzofuran, and diphenyl ether groups as important substructures contributing towards potent macrophage metalloelastase inhibition. This information was further implicated in repurposing marketed drugs through fragment-based and molecular docking-based virtual screening with molecular dynamics (MD) simulation-based stability validation and DFT calculations. This study identified fosamprenavir and tirofiban as promising hits that can exhibit potent macrophage metalloelastase inhibition which was also validated by the MD simulation and DFT-based calculations. Therefore, this study not only revealed these repurposed drugs as effective macrophage metalloelastase inhibitors but also opened up a horizon in developing novel potent macrophage metalloelastase inhibitors for the management of cancer and COPD in the future.

Structural characterization of Aurora kinase B modulation by Epigallocatechin gallate: Insights from docking and dynamics simulations

Aurora Kinase B (AURKB) is crucial for chromosome alignment, segregation, and cytokinesis, phosphorylating essential proteins for accurate cell division. Mutations and overexpression of AURKB are common in various cancers. Inhibiting AURKB reduces therapy resistance, making it a promising therapeutic target. Synthetic inhibitors like AZD1152 and ZM447439 show selectivity for AURKB but often lack specificity due to high homology within the aurora kinase family. Conversely, natural molecules such as flavonoids offer selectivity, lower toxicity, and potential synergy with existing chemotherapies. Investigating natural AURKB inhibitors could lead to safer and more effective cancer treatments. Epigallocatechin-3-gallate (EGCG), a catechin ester in green tea, inhibits glioma cell line proliferation by inducing spontaneous apoptosis and reduces cancer cell invasiveness by decreasing metalloproteinase, cytokine, and chemokine activities. Additionally, EGCG inhibits several kinases, including PI3K, mTOR, EGFR, and AKT, acting as an effective ATP-competitive inhibitor. Thus, EGCG may enhance the efficacy of anti-cancer therapies as an AURKB inhibitor. This study used in silico tools to predict EGCG's pharmacodynamics and pharmacokinetics, and employed AutoDock for molecular docking with AURKB. The ligand-protein complex and Apo form of AURKB were simulated for 100 ns with GROMACS using the CHARM36 force field. Free energy surface analysis and MMPBSA methods confirmed the stability and spontaneity of EGCG binding to AURKB. The conformational dynamics of the DFG (Asp-Phe-Gly) motif in AURKB upon EGCG binding revealed significant changes crucial for ATP binding and kinase activity. The distance between the phenylalanine residue of the DFG motif and the αC helix in holo AURKB increased from 14.80 Å to 23.62 Å in the lowest free energy structure, indicating a shift from the DFG-in to the DFG-out state, affecting ATP binding. The study also noted transitions in the overall protein secondary structures, such as turn to coil, coil to sheet, and coil to helix, contributing to a stable structure upon EGCG binding. These findings highlight the complex interplay between EGCG and AURKB, providing insights into the conformational dynamics and structural alterations induced by this interaction, which has implications for reducing glioma cell chemosensitivity to therapeutic drugs.

Exploring vacancy defects in s-I clathrate hydrates

This study investigates the role of vacancy defects in s-I clathrate hydrate structures, particularly in the presence of ethylene oxide (EO) molecules, through first-principles calculations. The structural properties, formation energies, and guest-host interactions of these vacancy defects were examined in both periodic systems and finite-size clusters. Our findings demonstrate that EO molecules significantly stabilize vacancy defects via hydrogen bonding, especially when forming double hydrogen bonds with dangling hydrogens (d-Hs) arising from the molecular vacancy defect. The encapsulation of EO in defect-free cages and its interaction with dangling oxygens (d-Os) were also analyzed, highlighting the superior stabilizing effect of double hydrogen bonds. These results provide new insights into the behavior of vacancy defects in hydrate structures and the potential role of polar guest molecules in enhancing defect stability and facilitating hydrate formation processes.

Borophene based quasi planar nanocluster for ethanol, isobutanol, and acetone sensing: A first principle study

In this study, the need for efficient detection of volatile organic compounds (VOCs) in environmental monitoring, industrial safety, is addressed by investigating borophene-based B36 nanoclusters as gas sensors. Density functional theory (DFT) calculations were employed to examine the adsorption behavior of ethanol, isobutanol, and acetone on B36 surfaces, with a focus on vibrational modes, reactivity, and adsorption energies. It was found that acetone exhibits the strongest interaction with pristine B36, indicating its potential for robust sensing applications. To further enhance sensor performance, the effects of doping B36 with nickel (Ni) and iron (Fe) atoms were explored. The electronic structure was significantly modified in Fe@B36, showing strong chemisorption properties, while Ni@B36 showed less impact, serving as a counterexample. Additionally, conductivity, recovery time, and global reactivity parameters were analyzed, providing insights into the sensor's functionality. It is suggested that B36 nanoclusters, particularly Fe-doped systems, offer promising prospects for future gas sensor development and VOC detection.

Exploring the binding mode of BBA protein anchored on defective graphene and evaluating the biocompatibility of two types of graphene with λ-repressor protein

Since defects in nanomaterials are inevitable during experimental manipulation, investigating the interactions between defective materials and active biological proteins is crucial for evaluating the biocompatibility and biosafety of nanomaterials. This study employs molecular dynamics simulation techniques to investigate the interaction mechanisms between two types of graphene (ideal graphene and defective graphene) and two model proteins (BBA protein and λ-repressor protein). The simulation results indicate that both types of graphene exhibit superior biocompatibility with the λ-repressor protein compared to the BBA protein. The difference in binding modes of the BBA protein with the two graphenes arises mainly from its initial orientation. Notably, the positively charged Arg residue forces the BBA protein to "anchor" to the surface of defective graphene, significantly restricting its lateral migration. The λ-repressor protein is "anchored" onto the surface of defective graphene through hydrogen bonding interactions involving its Ser residue. Such hydrogen bonding was never reported in similar systems. The distinctive binding modes of these two model proteins with defective graphene are beneficial for the future development of safer and more efficient nanomedicine technologies.

Glipizide inhibits the glycation of alpha-crystallin: A combined in vitro and in silico approach in retinopathy management

In human eye, structural proteins, known as crystallins, play a crucial role in maintaining the eye's refractive index. These crystallins constitute majority of the total soluble proteins found in the eye lens. Among them, α-crystallins (α-CR) is one of the major components. Under hyperglycaemic conditions, crystallins become susceptible to glycation that ultimately leads to advanced glycation endproducts (AGEs) formation. Glipizide is a well-known oral medication used in controlling levels of blood sugar, this drug stimulates the insulin release from pancreas. However, this drug has not been thoroughly investigated for its impact on α-CR glycation. In this study, we explored glipizide's protective role against glucose-induced α-CR glycation. Remarkably, glipizide effectively inhibited the formation of early glycation products, ultimately reducing AGEs formation. Additionally, glipizide provides protection against modifications of free lysine residues and lowered the carbonyl content. To gain deeper insights into mechanism of inhibition, we turn to binding studies and bioinformatics. Glipizide formed stable complex with α-CR with values of Gibbs energy ranging from -5.848 to -6.695 kcal/mol. Molecular docking revealed the binding energy as -6.5 kcal/mol and lysine residues emerged as a prominent among the key interacting residues. Notably, glipizide appears to mask lysine residues, thereby contributing to the inhibition of α-CR glycation. Furthermore, analysis of molecular simulation data reinforces the stability of this complex. Consequently, the stable α-CR-glipizide complex may prevent glucose from binding to α-CR. Overall, glipizide holds promise as a preventive measure against glycation of eye lens proteins, potentially benefiting in diabetic retinopathy.

Molecular dynamics study of functionalized carbon nanotube loaded with multiple doxorubicin targeted to folate receptor α

Two novel targeted drug delivery systems (DDSs) were designed: folate (FOL) conjugated (9, 9) carbon nanotube (CNT) loaded with 20 doxorubicin (DOX) molecules (FOL-CNT/20DOX) and folate (FOL) conjugated carboxylated (9, 9) CNT (COOH-CNT) loaded with 24 doxorubicin (DOX) molecules (FOL-COOH-CNT/24DOX). The targeted property to folate receptor α (FRα) was calculated using molecular dynamics (MD) calculations. The structures of the FRα/FOL-CNT/20DOX and FRα/FOL-COOH-CNT/24DOX complexes were analyzed in detail. Radial distribution functions were calculated to analyze the distribution of DOX molecules around the CNTs in the complexes. The variation of representative distances and angles between novel DDSs and FRα, number of hydrogen bonds, and secondary structures of FRα during the MD simulations were studied to analyze the dynamic properties of the novel DDSs targeted to FRα. We further analyzed the root mean square displacement and root mean square fluctuation in detail. The results indicate that the two novel DDSs were very stable and well targeted with FRα, and FOL-COOH-CNT/24DOX had better targeting and stability than FOL-CNT/20DOX. This study is expected to provide insights for the design of efficient nano drug delivery systems with good FRα targeting and controllable drug loading dosage.

Thermodynamics of homolytic C-H bond cleavage in proteinogenic α-amino acids: Zwitterions in aqueous solution

This work provides the systematic M06-2X theoretical study of C-H bond dissociation enthalpies (BDE) in aqueous solution for 21 proteinogenic α-amino acids present in eukaryotes. The results reveal that the formation of zwitterions in an aqueous solution significantly affects the thermodynamics of the homolytic C-H bond cleavage for alpha, beta, and gamma carbon atoms. We have found that zwitterions show significantly greater stability against a free radical attack due to considerably higher enthalpies of the hydrogen atom abstraction from the Cα atom. This kind of stabilization can be beneficial during the synthesis of proteins in cells. Compared to the canonical forms, the average increase in BDE is ca. 60 kJ mol-1. For all amino acids, the BDE of the most labile C-H bond was calculated using the ab initio G4 and G4(MP2) composite methods, as well.

Identification of acetylcholinesterase inhibitors and stability analysis of THC@HP-β-CD inclusion complex: A comprehensive computational study

Complexing medications with cyclodextrins can enhance their solubility and stability. In this study, we investigated the host-guest complexation between Tetrahydrocurcumin (THC) and Hydroxypropyl-β-Cyclodextrin (HP-β-CD) using density functional theory (DFT) at the B3LYP-D3/TPZ level of theory in two possible orientations. To determine the reactive sites in both complexes for electrophilic and nucleophilic attacks, we calculated and interpreted the binding energy, HOMO and LUMO orbitals, global chemical reactivity descriptors, natural bond orbital (NBO) analysis, and Fukui indices. The results indicate that Orientation A is energetically more favorable than Orientation B. Non-covalent interactions (NCI) were analyzed using reduced density gradient (RDG) approaches, providing detailed insights into host-guest interactions, including hydrogen bonding and van der Waals forces. To further assess stability, we conducted 1000 ns molecular dynamics (MD) simulations and analyzed the root mean square deviations (RMSD) for systems containing 1, 2, and 10 complexes. The RMSD analysis confirmed the stability of the systems, with average RMSD values of 2.01, 3.21, and 4.29 Å, respectively. In the second part of this study, we examined the interaction between THC and the target protein Acetylcholinesterase (E.C. 3.1.1.7) with PDB ID 1QTI. Molecular docking was performed to identify the binding modes and interaction energies of the THC-protein complex. Subsequently, 1000 ns MD simulations were conducted to assess the stability and dynamic behavior of the THC-protein complex over an extended period. The analysis provided valuable insights into the binding interactions and stability of THC with the target protein, further confirming its potential as a therapeutic agent.

Novel silver(I) complexes with fenamates: Insights into synthesis, spectral characterization, and bioactivity

Six new Ag(I) ions complexes with N-phenylanthranilic, mefenamic, and niflumic acids have been synthesized. Three of them are binary complexes with the [Ag(L)] formula (where L represents N-phenylanthranilate (nfa), mefenamate (mfa), or niflumate (nif) ions), and the other three complexes are ternary with the formula [Ag(L)(phen)2]⋅nH2O (where phen - 1,10-phenanthroline). The complexes were characterized by elemental analysis, differential scanning calorimetry (DSC), X-ray fluorescence, powder X-ray diffraction, and single-crystal X-ray structure analysis. Additionally, techniques such as ESI-MS spectrometry, 1H NMR, UV-Vis, and FTIR spectroscopy were employed. The X-ray crystallography showed that in the solid [Ag(nif)] complex, the cation showed an unusual structure with coordination number 5, i.e. AgO3NC. The silver cation interacts with three niflumate anions, forming a two-dimensional coordination polymer. Complexes have potential antibacterial efficacy with varied minimum inhibitory concentration values (MIC) between 45.96 and 800 μM against multidrug-resistant Pseudomonas aeruginosa. Antibacterial combination therapy of Ag(I) complexes with chloramphenicol (CHL) and kanamycin (KAN) showed a very strong synergistic impact against P. aeruginosa with no cytotoxic effect on normal human fibroblasts. Complexes [Ag(nif)] and [Ag(nfa)] inhibit protein denaturation, bind to BSA via static quenching (kq = 0.65-1.08 × 1013 M-1 s-1). Furthermore, the formation of these complexes enhances the penetration of the drug across human membrane monolayers, which could improve bioavailability and therapeutic potential. The [Ag(nif)] complex demonstrates significant potential for topical dermal application due to its antimicrobial and anti-inflammatory properties. Notably, among all complexes evaluated, it displays the lowest BA/AB ratio (5.41), facilitating the most efficient transdermal permeation.

Effects of the physico-chemical properties of amino acids and chemically functionalized surfaces on DIOS-MS analysis

Desorption ionization on silicon mass spectrometry (DIOS-MS) allows for the detection of low molecular weight species from fluid samples. However, this method remains scarcely used for clinical diagnosis likely because of a lack of knowledge about the desorption/ionization mechanism as well as about the interplay between the surface and analyte properties which are effective in desorption/ionization, impeding the optimization of the DIOS-MS analysis. Herein, the normalized intensity of the DIOS-MS peaks at [M+H]+ of seven amino acids on four different porous silicon modified surfaces are investigated. These amino acids (arginine, phenylalanine, methionine, glutamine, leucine, cysteine and valine) have different isoelectric points, proton affinities, and octanol-water partition coefficients. The four selected surfaces were oxidized porous silicon (SiO2), the same porous silicon modified with a propyl dimethyl ethoxy silane, octadecyl dimethyl ethoxy silane or 3 amino propyl dimethyl ethoxy silane (CH3-short, CH3-long and NH3+, respectively). These surfaces present different electrical charges, alkyl chain lengths, and hydrophilic/hydrophobic properties. For each surface, the intensities of the protonated molecules ([M+H]+) are discussed with respect to the electrical charge and proton affinity of the amino acids, their z-distributions inside the pores (determined by time of flight secondary ion mass spectrometry profiling), their surface interaction energies (calculated by molecular dynamics simulations), the interfacial water content and the proton availability for each surface.

Elucidating the impact of S-adenosylmethionine and histamine binding on N-methyltransferase conformational dynamics: Insights from an in silico study

S-adenosylmethionine (SAM)-dependent histamine N-methyltransferase (HNMT) is a crucial enzyme involved in histamine methylation, playing an important role in the epigenetic modification of biology. It entails the addition of methyl groups to histamine molecules, thereby regulating gene expression, cellular signal transduction, and other biological processes. Therefore, gaining a profound understanding of the detailed mechanism underlying HNMT-mediated methylation reactions is instrumental in elucidating the role of histamine methylation in biology. This study employed molecular dynamics (MD) simulations to assess the mechanism of cooperative catalytic reaction between the substrate-binding domain (S domain) and the cofactor-binding domain (C domain) of HNMT. The results indicated that the interplay between the cofactor (SAM) and the C domain was mostly unaltered by substrate Histamine (HSM) binding. Nevertheless, SAM binding could induce conformational changes in the S domain, thus creating a favorable environment for substrate recognition and catalysis. Additionally, key amino acid residues that significantly contributed to substrate binding were identified based on molecular mechanics-generalized Born surface area (MM/GBSA) calculations. These findings could serve as a theoretical basis for the design of potential inhibitors and modulators targeting HNMT.

Thermodynamic binding properties of a novel umami octapeptide K1ADEDSLA8 and its mutational variants p.A2G, p.D5E, and p.A2G + p.D5E (BMP) in complex with the umami receptor hT1R1/hT1R3

Umami taste properties of a novel octameric peptide K1ADEDSLA8 and its mutants p.A2G, p.D5E, and BMP (KGDEESLA, beef meaty peptide) were assessed by molecular docking, and molecular dynamics (MD) (>1 μsec), MM-PBSA, and Mutational Affinity Prediction (MAP) methods. 3D-structure of the human umami taste receptor (hT1R1/hT1R3) was homology modeled and refined MD. Docking studies yielded three primary binding sites (PBS) for K1ADEDSLA8 and BMP, one on hT1R1 and two on hT1R3. Upto 1200 nsec of MD studies revealed that K1ADEDSLA8 binds only to Venus Flytrap Domains (VFTD) region of hT1R1 at high affinity (ΔGo = -11.94 kcal/mol), while BMP does not exhibit affinity towards hT1R1/hT1R3 in the absence of glutamate. MAP analysis for p.A2G (ΔGo = -7.77 kcal/mol) and p.D5E (ΔGo = -2.88 kcal/mol) strongly suggest that A2 and D5 in KA2DED5SLA increase the affinity and specificity of binding, posing great potential for the development of a novel umami peptide in future studies.

Study of CO2-hydrate formation in contact with bulk nanobubbles: An investigation from experiment and molecular-dynamics simulations

HYPOTHESIS

Nanobubbles (NBs) have been extensively investigated as a sustainable promoter for gas hydrate nucleation, which also contribute to the hydrate memory effect. However, less attention afforded to their effects on the hydrate-growth process, thus lacking a complete perspective of the overall effects from NBs on hydrate formation. We hypothesize that their effect on CO2 hydrate growth may vary depending on the properties of NBs.

EXPERIMENTS AND SIMULATIONS

This study investigates CO2-hydrate nucleation and growth with a dual methodology. Laboratory experiments were conducted using bulk NBs generated either from CO2 hydrate dissociation or electric-field-based electrostriction in virgin water. Simultaneously, molecular dynamics simulations examined hydrate growth in contact with a single NB containing CO2 molecules.

FINDINGS

Experimental results indicate that NBs promote hydrate nucleation, with finer ones from electric fields leading to a slight promotion at the onset of hydrate growth, followed by inhibition. MD simulations reveal that while NBs can serve as a gas source for growth, denser NBs hinder the process due to stronger gas-water interactions and CO2 clustering. These results suggest that optimizing NB size and concentration is critical for maximizing gas-hydrate formation efficiency in industrial applications such as gas storage and carbon capture.

A new polymer with rich carbonyl delocalized π-conjugated structure for high-performance aqueous zinc ion batteries

The development of sustainable and clean energy has become a top priority, driven by global carbon peaking and carbon neutrality targets. Organics are widely used in aqueous zinc ion batteries (AZIBs) due to their environmental friendliness, high structural designability, and safety. However, organic materials often face some challenges, including high solubility, low specific capacity, and unclear mechanism, which hinder its further applications. In this paper, two new conjugated organic polymers were synthesized as cathodes for AZIBs by molecular structure design. Notably, the introduction of new actives (C = O) in (poly-(tetraamino-p-benzoquinone-alt-2,5-dihydroxy-1,4-benzoquinone, DHTA) along with the extension of the π-π conjugated structure to form polymers is conducive to the improvement of the specific capacity and reversibility of AZIBs compared to (poly-(1,2,4,5-tetraaminobenzene-alt-2,5-dihydroxy-1,4-benzoquinone, DHPH). The DHTA cathode delivers high initial specific capacity of 282.5 mAh/g at a current of 0.05 A/g and excellent rate performance (56.8 mAh/g at 5 A/g). The excellent rate performance and long cycle life of the as synthesized DHTA can be attributed to the low solubility, extended π-conjugated structure and enhanced electronic conductivity, which result from the polymerization with the introduction of carbonyl groups into organic skeleton. Moreover, the mechanism of Zn2+ storage in DHTA is also explored by various ex-situ characterization techniques and density-functional theory (DFT) calculations. In each repeating unit, DHTA can store two Zn2+ while transferring four electrons to form a stable O⋯Zn⋯N coordination. This work provides a molecular engineering strategy for organic materials, revealing their potential application in zinc ion batteries.

Strategic control of electron donation in D-A-π-A dyes: Insights from DFT calculations for enhanced DSSC and NLO performance

Dye-sensitized solar cells (DSSCs) are cost-effective and environmentally sustainable alternatives to traditional solar cells. In this study, two groups of novel metal-free organic (MFO) sensitizers (A1 and A2) were designed by modifying the experimentally tested WS-9 dye (E)(E)(E)-2-cyano-3-(3'-hexyl-5'-(7-(4-phenyl-1,2,3,3a,4,8b-hexahydrocyclopenta[b]indol-7-yl)benzo[c][1,2,5]thiadiazol-4-yl)-[2,2'-bithiophen]-5-yl)acrylic acid), which has a D-A-π-A structure and a power conversion efficiency (PCE) of 9.02 %. The designed dyes incorporated two distinct donor cores -indoline (D1) and 2-diphenylaminothiophene (D2)- and a range of electron-donating groups (J to O), resulting in 12 novel dyes with enhanced electron-donating abilities. Their geometrical, optical, electronic, and electrochemical properties were studied using density functional theory (DFT) and time-dependent DFT (TD-DFT) methods, combined with the Conductor-like Polarizable Continuum Model (CPCM) to simulate solvent effects (dichloromethane). Additionally, the adsorption behavior of the dyes on TiO₂ clusters was investigated by calculating adsorption energies and analyzing UV-Vis spectra. The results show significant improvements in the dyes' intramolecular charge transfer (ICT) properties compared to the reference WS-9 dye. A maximum red-shift of 109 nm in the absorption spectrum, an extended excited-state lifetime of 4.95 ns, and lower chemical hardness were observed, accompanied by enhanced electron injection (ΔGinj > 0.2 eV) and dye regeneration (ΔGreg > 0.15 eV) efficiencies. Furthermore, the dyes exhibited large Stokes shifts (231.64-177.62 nm) and superior nonlinear optical (NLO) properties. These findings suggest that the newly designed dyes are highly promising candidates for DSSC applications, offering enhanced light-harvesting capabilities and improved photoelectrical performance.

Exploring the effect of Zr/B ratio on the stability and reactivity of activated ε-caprolactone complexes: A DFT, QTAIM and NCI study

Monomer insertion, leading to the formation of an activated monomer complex, is a critical step in cationic ring-opening polymerization (CROP) of cyclic monomers, such as ε-caprolactone (CL). In this study, Density Functional Theory (DFT) calculations were employed to investigate the structural and electronic properties of four activated complexes at two Zr:B ratios (1:2 and 1:1), where Zr is the cationic zirconocene catalyst, Cp₂ZrMe⁺, and B is the borate cocatalyst, [MeB(C6F5)3]‒ or [B(C6F5)4]‒. Steric hindrance at the reactive site was analyzed using topographic steric maps, while inter- and intramolecular interactions of the complex systems were examined through the Quantum Theory of Atoms in Molecules (QTAIM) and non-covalent interaction (NCI) analyses. The 1:2 ratio exhibited significant steric hindrance above and below the monomer plane, restricting access to the Cp₂ZrMe⁺ catalytic site and potentially limiting monomer insertion. In contrast, the 1:1 ratio displayed reduced steric congestion and stronger localized attractive forces at the catalytic site, facilitating better interactions with monomers and solvents. Conceptual DFT descriptors revealed that 1:1 systems had smaller HOMO-LUMO energy gaps, lower hardness, and higher electrophilicity, with 1:1@[B(C₆F₅)₄]⁻ identified as the most reactive complex. QTAIM identified key hydrogen bonding interactions, and the Zr-OCL bonds, distinguishing stability and reactivity across Zr:B ratios. These findings provide valuable insights into the steric and electronic effects on monomer-activated species, enabling the optimization of Zr:B ratios and cocatalyst conditions for improved polymerization efficiency.

Rational design of alginate lyase ALYI1 for improving the antioxidant activity of the alginate oligosaccharides

To achieve the cost-effective alginate oligosaccharides production, we have developed a novel rational design strategy that optimized capture behavior, orientation movement and hydrogen bond interaction of substrate in alginate lyase ALYI1. This approach led to S56D and G258Q advantageous variants balancing the trade-off challenge, particularly S56D, which exhibited a 1.56-fold increase in specific activity and 23.11 % higher activity at 45 °C for 1 h compared to ALYI1. The variants exhibited reduced binding fluctuation and more favorable binding energy compared to ALYI1, which was ascribed to more favorable dynamic hydrogen bonds and binding energy distribution. Furthermore, we innovatively found that alginate oligosaccharides produced by S56D and G258Q displayed increasing ABTS+ and DPPH• radical scavenging efficiencies than those produced by ALYI1. Especially, S56D degradation product demonstrated 10.80 % higher ABTS+ radical and 29.75 % higher DPPH• radical scavenging activities at 1.0 mg/mL. This was attributed to the improved disaccharides and trisaccharides ratios in the product. Our findings provide critical insights and establish a robust foundation for the development of superior biocatalysts for the industrial production of AOS.

Rational design and construction of a mesoporous silica-supported ratiometric fluorescent probe for the sensitive detection of nicosulfuron

The excessive use of pesticides is an urgent issue facing environmental sustainability and human health. In this study, a uniform dispersion size, good fluorescence performance and mesoporous structure of a ratiometric fluorescent probe were constructed for nicosulfuron detection. A solvent-free in situ solid-phase synthesis method was used to encapsulate biomass carbon dots within mesoporous silica (CDs@mSiO₂), followed by the modification of l-cysteine-modified manganese-doped zinc sulfide quantum dots (ZnS:Mn QDs), to construct a ratiometric fluorescent probe for highly sensitive and selective detection of nicosulfuron. This design effectively prevents the aggregation of CDs and reduces interference between the two fluorescent signals. Nicosulfuron detection had a low detection limit of 0.082 μM. Density functional theory calculations were carried out to uncover the specific interactions between nicosulfuron and ZnS:Mn QDs. The process of fluorescence quenching is ascribed to photoinduced electron transfer. This work offers a special strategy to produce a ratiometric fluorescent probe and illustrate the mechanism, which is crucial for sensing and environmental engineering.

Highly efficient removal of per- and polyfluoroalkyl substances by extrusion-regenerated aminated polyurethane sponges

Per- and polyfluoroalkyl substances (PFAS) are a class of persistent organic compounds widely detected in the environments. Due to their chemical stability, physical adsorption has emerged as one of the most promising techniques for remediating PFAS-containing wastewater, while some newly synthesized functional absorbents in powder form suffer from separation issues. Inspired by mussel biology, we have successfully synthesized a porous spongy absorbent termed aminated polyurethane (PU-PDA-PANI) with over 99.5% removal efficiency for initial 10 mg L-1 perfluorooctanoic acid (PFOA), corresponding to the maximum adsorption capacity of 1.42 g g-1, which was superior to the ion exchange resin (Purolite® PFA694E, 0.764 g g-1). In addition to PFOA, PU-PDA-PANI also showed excellent removal efficiencies for other typical PFAS (i.e. perfluorooctane sulfonates, perfluorobutyric acid, perfluorooctane-1,8-dioic acid, hexafluoropropylene oxide trimer acid, etc), and the adsorption processes resistant to pH changes and co-existing environmental matrixes. Furthermore, PU-PDA-PANI can be readily reused and regenerated by coupling extrusion and elution procedures. The adsorption mechanism of electrostatic, hydrogen bond and hydrophobic synergistic interaction was further proposed with the support of theoretical calculation. In conclusion, this study develops an efficient and recyclable PFAS adsorbent and proposes some new insights for the design of PFAS-selective adsorbents.

Nighttime reactions of a series of unsaturated alcohols with NO3•: Kinetics, products and mechanisms study

Unsaturated alcohols are a class of Biogenic volatile organic compounds (BVOCs) emitted in large quantities by plants when damaged or under adverse environmental conditions, and studies on their atmospheric degradation at night are still lacking. We used chamber experiments to study the gas-phase reactions of three unsaturated alcohols, E-2-penten-1-ol, Z-2-hexen-1-ol and Z-3-hepten-1-ol, with NO3 radicals (NO3•) during the night. The rate constants of these reactions were (11.7 ± 1.76) × 10-13, (8.55 ± 1.33) × 10-13 and (6.08 ± 0.47) × 10-13 cm3/(molecule·s) at 298K and 760 Torr, respectively. In contrast, the reaction rate of similar substances with ozone was about 10-18 cm3/(molecule·s), which indicates that the reaction with NO3• is the main oxidation pathway for unsaturated alcohols at night. Small molecule aldehydes and ketones were the main gas-phase organic products of the reaction of three aldehydes and ketones with NO3•, and the total small molecule aldehydes and ketones yields can reach between 45%-60%. They mainly originate from the breakage of alkoxy radicals, and different breakage sites determine different product distributions. In addition, the SOA yields of the three unsaturated alcohols with NO3• were 7.1% ± 1.0%, 12.5% ± 1.9% and 30.0% ± 4.5%, respectively, which were much higher than those of similarly structured substances with O3 or OH radicals (•OH). The results of high-resolution mass spectrometry shows that the main components of Secondary organic aerosol (SOA) of the three unsaturated alcohols are dimeric compounds containing several nitrate groups, which are formed through the polymerization of oxyalkyl radicals.

Microplate spectrophotometric method for regioselective lipase screening using structured triglycerides with punicic acid as probe

In this study, we propose a continuous assay that provides a high-throughput, efficient method for screening the regioselectivity of lipases at the sn-1,3 and sn-2 positions on triacylglycerols (TAGs). This assay measures the specific hydrolysis rates at the primary and secondary positions of TAGs derivates containing oleic (O) and punicic (P) acids. The method is based on the absorbance ratio of released punicic acid from the hydrolysis of sn-POP (sn-1,3 regiospecific lipases) and sn-OPO (sn-2 regiospecific lipases). The method was validated using pure lipases with known and unknown regioselectivity. Unexpectedly, we found that recombinant Lipase 4 from Candida rugosa (rCRLip4) exhibited significant sn-2 regioselectivity, indicating greater regioselectivity than recombinant lipase A from Candida antarctica (rCALA). In silico analysis and molecular docking studies were conducted to elucidate the main structural differences between CRLip4 and the non-regioselective isoform CRLip1. This continuous regioselective lipase assay on TAGs is versatile and can be used to screen for sn-1,3, sn-2 or non-regioselective lipases. It holds significant potential applications in the biocatalytic production of structured lipids and other industrial processes where regioselectivity is crucial.

Optimized Cerium vanadate catalytic host with simple heterostructure engineering achieving regulated polysulfide deposition for high-performance Lithium-Sulfur batteries under harsh conditions

Meliorating the behavior deposition of lithium polysulfides (LiPS) is crucial for enhancing the electrochemical performance of sulfur cathodes, which could be implemented by the precise modulation on the catalytic host. Herein, heterostructure engineering is employed to tune up the catalytic capability of CeVO4, by introducing CeO2 through a simple adjustment in the addition sequence of reactants. The formed CeVO4/CeO2 heterostructure has been demonstrated to exhibit appropriate interaction strength with LiPS for accelerating the catalytic conversion process, as well as an engineered surface for inducing three dimensional (3D) Li2S deposition, thereby endowing the corresponding sulfur cathodes with excellent electrochemical performance under harsh conditions. The S/CeVO4/CeO2 cathode could deliver a high capacity of 36.5 mAh cm-2 (1278.9 mAh g-1) under high sulfur loading of 28.5 mg cm-2 and lean electrolyte dosage of 6 μL mg-1, and also function well even under a wide temperature range (-30 ∼ 60 °C) or matching with polymer solid electrolyte. This work offers a simple yet practical strategy to modulate the catalysts for sulfur cathodes with heterostructure design, thereby advancing the practical implementation of the lithium-sulfur battery.

Descriptor for electro-oxidation of glycerol with high-efficiency bifunctional Cu-Nx single atom catalyst and coupled with hydrogen evolution/carbon dioxide reduction

Electrochemical glycerol oxidation reaction (GOR) presents a promising approach for converting excess glycerol (GLY) into high-value-added products. However, the complex mechanism and the challenge of achieving selectivity for diverse products make GOR difficult to address in both experimental and theoretical studies. In this work, three nitrogen-doped graphene-supported copper single-atom catalysts (CuNx@Gra SACs, x = 2-4) were selected as the model system due to their simple structure, excellent conductivity and high structural stability. Density functional theory (DFT) calculations were employed to gain deeper insight into the catalytic mechanism. The DFT results revealed that both CuN2@Gra and CuN3@Gra follow the same optimal pathway, leading to the formation of formic acid as a key product. The GOR activity and selectivity of CuNx@Gra catalysts follow the trend CuN3@Gra > CuN2@Gra > CuN4@Gra. Subsequent microkinetic analysis, based co on the DFT-derived energetics, confirmed this predicted activity sequence. The GOR activity determined by the limiting potential (UL) is correlate well with changes in the adsorption free energy (ΔGGLY*), the d-band centers of axial dz2 orbitals (εdz2) and integrated crystal orbital Hamilton population (ICOHP). Notably, the simple descriptor ΔGGLY* exhibits a good linear correlation with the free energies of other adsorbates, clarifying the conversion relationships between reaction intermediates and simplifying the understanding of reaction complexity. Moreover, computational results indicate that CuN2@Gra and CuN3@Gra systems can serve as both anode catalysts (for GOR) and cathode catalysts (CO2 reduction for CuN2@Gra and H2 evolution for CuN3@Gra). This study offers insights for designing efficient electrocatalysts, enhancing GLY utilization.

Understanding the molecular mechanism of fumonisin esterases by kinetic and structural studies

Fumonisins are sphingolipid-like mycotoxins that cause serious damage by contaminating food and feed. The tricarballylic acid (TCA) units of fumonisin B1 (FB1; accounting for 70 % of fumonisin contamination) can be removed by fumonisin B1 esterase (FE, EC 3.1.1.87) providing a biotechnological FB1 detoxification possibility. Here, we report the regioselective cleavage of the TCA ester at C6 in the first step of FB1 hydrolysis and kinetic characterization for two FEs. The low KM values (4.76-44.3 μM) are comparable to concentrations of environmental contaminations, and the high catalytic efficiencies are promising for practical applications. The X-ray structure of one of the FEs enabled the understanding of the FB1 hydrolysis at molecular level and revealed an arginine pocket key for substrate binding, and the catalytic role of the glutamate preceding the catalytic serine. Computations showed that this FE is likely capable of detoxifying any fumonisin indicating its potential applicability in food and feed products.

A simple co-assembly strategy to control the dimensions of nanoparticles for enhanced synergistic therapy

Despite phthalocyanine has excellent photodynamic and photothermal effects as a photosensitizer and photothermal agent, hydrophobicity and aggregation limits its biological application. In this paper, phthalocyanine-cyanine co-assembled nanoparticles were designed to modulate the dimensions and morphology by introducing water-soluble cyanine. The cyanine had the ability to transform the nanomaterials from microrods to nanospheres, thus successfully constructing photoactivated nanomedicines. Their appropriate size effect and improved water solubility conferred the nanoparticles with extended blood circulation time and tumor accumulation capacity. Meanwhile, the fluorescence effect of cyanine enabled the nanoparticles to have the ability of fluorescence imaging. The nanoparticles achieved enhanced PDT/PTT synergistic effect under single laser induction, especially the generation of type I photodynamics.

Isolation, purification and identification of antibacterial peptides from Jinhua ham broth and molecular simulation analyses of their interaction with bacterial porins

The bioactive peptides in Jinhua ham could be released into the broth during cooking. After comparing peptide antibacterial activity from Jinhua ham broth with varying cooking durations, the cooking-2-h broths were selected for further analysis using cation-exchange and reverse-phase-liquid chromatography. The purified peptide sequences were subsequently synthesized and tested for their antibacterial activity. Four peptides (IKKVVKQASEGP, LGRVPRGKKKL, LKGGKKQLQKL, and MDAIKKKMQMLK) were identified with IC50 values for S. typhimurium and S. aureus below 0.4 mg/mL. Molecular docking and dynamics simulations were employed to investigate the interaction between the four antibacterial peptides and the outer membrane protein F (Omp F) of the Salmonella membrane. All four peptides demonstrated binding energies with Omp F lower than -7 kcal/mol. Stability indicators in molecular dynamics showed minimal fluctuations, further confirming the compactness and stability of the peptide-Omp F complexes. Notably, all four peptides altered the conformation of Omp F, thereby enhancing cell membrane permeability.

Design and synthesis of fluorinated polyimides with low thermal expansion and enhanced dielectric properties

Modern microelectronics industries urgently require dielectric materials with low thermal expansion coefficients, low dielectric constants, and minimal dielectric loss. However, the design principles of materials with low dielectric constants and low thermal expansion are contradictory. In this study, a new diamine monomer containing a dibenzocyclooctadiene unit (DBCOD-NH2) was designed and synthesized, which was subsequently polymerized with high fluorine content 4,4'-hexafluoroisopr-opylidene diphthalic anhydride and 4,4'-diamino-2,2'-bis(trifleoromethyl)biphenyl to obtain a series of fluorinated polyimides (PIs). Due to the unique conformational transition of the eight-membered carbon ring, the resulting PI can reach a low averaging thermal expansion coefficient (CTE) of only 12.27 ppm/K over 5-150 ℃ with a size change rate of only 0.16 %. Surprisingly, the synergistic effect of DBCOD-NH2 with the other two monomers enhances the dielectric performance of the PIs. At an electric field frequency of 10 MHz, the dielectric constant (Dk) and the dielectric loss (Df) can be reduced to as low as 2.61 and 0.00194, respectively. The strategy used herein largely tackles the challenge of balancing low Dk with low CTE. Furthermore, these PI films also exhibit good thermal stability (with 5 wt% weight loss temperatures ranging from 453 to 537 ℃ in N2, and glass transition temperatures of 305-337 ℃) and robust mechanical properties (with a tensile modulus of 1.88-2.29 GPa and an elongation at break of 6.36-8.11 %). The combination of low thermal expansion and excellent dielectric properties renders these PIs highly promising for applications in the microelectronics and telecommunications industries.

Insilico molecular characterization of a cyanobacterial lytic polysaccharide monooxygenase

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the oxidative cleavage of β(1-4) glycosidic bonds and have attracted considerable attention because of their potential for enhancing efficiency in degrading recalcitrant polymeric substrates, in synergism with hydrolytic enzymes. Fungal-derived LPMOs are the most prevalent type, while other taxonomic groups have been described as potential alternative sources of these enzymes. In the present study, we aimed to identify and characterize in silico a LPMO of cyanobacterial origin with putative functions in chitin depolymerization. A similarity search of sequences and conservation of domains with characterized LPMOs identified a 289 amino acid protein from the cyanobacterium Mastigocoleus testarum (Order Nostocales), likely belonging to the CAZy-AA10 class. This protein is referred to as MtLPMO10. Phylogenetic analysis revealed that MtLPMO10 is homologous to the protein Tma12 from the fern Tectaria macrodonta, with 52.11 % sequence identity, which was the first LPMO characterized as originating from the plant kingdom. The protein tertiary structure predicted by the AlphaFold server indicates structural features common to LPMOs, such as a histidine brace formed by His31 and His132 and an immunoglobulin-like domain composed of antiparallel beta strands. Molecular dynamics (MD) simulation allowed the assessment of the enzyme-substrate affinity, using an initial pose based on literature data. The MtLPMO10-chitin complex remained stable during 100ns of MD, while the MtLPMO10-cellulose complex dissociated within 30ns of MD. Additionally, there was a shorter Cu(I)-H4 distance in the protein-substrate complex compared to the Cu(I)-H1 distance (averages of 6.0 ± 0.7 Å and 7.9 ± 0.7 Å, respectively), suggesting a C4 regioselectivity. This study highlights the existence of lytic polysaccharide monooxygenases in cyanobacteria and paves the way for further investigations related to this enigmatic class of enzymes and their potential use in biotechnological applications.

A DFT study of pure and Si-decorated boron nitride allotrope Irida monolayer as an effective sensor for hydroxyurea drug

Investigating effective nanomaterials for the detection of hydroxyurea anticancer drugs is essential for promoting human health and safeguarding environmental integrity. This research utilized first-principles estimations for examining the adhesion and electronic characteristics of hydroxyurea (HU) on both pristine and Si-decorated innovative two-dimensional boron nitride allotrope, known as Irida analogous (Ir-BNNS). Analyzing the adsorption energy revealed that the HU molecule has a significant interaction (Ead = -1.27 eV) with the Si@Ir-BNNS, whereas it has weak interaction P-Ir-BN. Moreover, the analysis of the electron density distributions was conducted to investigate the microcosmic interaction mechanism between HU and Ir-BNNS. The Si@Ir-BNNS was highly sensitive to HU due to the observable alterations in the electrical conductance and magnetism. At ambient temperature, the Si@Ir-BNNS had a recovery time of 5.96 ms towards HU molecules. The DFT estimations can be conducive to exploring the applications of Si@Ir-BNNS in effectively sensing HU.

Molecular modelling of 6-oxo-5-Sulfanyl-1H-Pyridine-3-Carboxylic acid and its adsorption with the silver complex: Structural, optical, charge transference, dynamics and docking to nipah virus

This investigation employs DFT to evaluate the structural, molecular, and electronic feature variations of 6-oxo-5-sulfanyl-1H-pyridine-3-carboxylic acid in gas alongside various solvent media. The complex interactions occurring within the molecule are recognised using the Independent gradient model. The application of various electric fields are used to determine the electrical properties of the compound. The topographical inspection shows extreme electron-dense zones to display a good electron reception character of the molecule. The intense covalence nature is maximal between the aromatic zone's C-C and C-N regions. The compound possesses a maximum interaction with the (LP) → π∗ and π → π∗ transitions. The optical and absorbance property shows an upright enhancement in the addition of the solvents. The significant transference of charges inside the compound is signified using the D and H index values and heat maps. The thermal assessment established that the compound is sustainable at varied temperatures with the pressure at 1 atm. The carboxylate ion of 6O5S1HP3CA interacts with the Ag + clusters and its adsorption characteristics are confirmed by the SERS spectrum. The complex's stability is determined by the MD simulations at various speeds. The physiological scrutiny demonstrates that both the compound and complex are benign and the antiviral activities were studied for Nipah virus for the proteins 7pno and 7skt.

Computational modeling of the anti-inflammatory complexes of IL37

Interleukin (IL) 37 is an anti-inflammatory cytokine belonging to the IL1 protein family. Owing to its pivotal role in modulating immune responses, elucidating the IL37 complex structures holds substantial therapeutic promise for various autoimmune disorders and cancers. However, none of the structures of IL37 complexes have been experimentally characterized. This computational study aims to address this gap through molecular modeling and classical molecular dynamics simulations. We modeled all protein-protein complexes of IL37 using a range of methods from homology modeling to AlphaFold2 multimer predictions. Models that successfully recapitulated experimental features underwent further analysis through molecular dynamics simulations. As positive controls, binary and ternary complexes of IL18 from PDB were included for comparison. Several key findings emerged from the comparative analysis of IL37 and IL18 complexes. IL37 complexes exhibited higher mobility than the IL18 complexes. Simulations of the IL37-IL18Rα complex revealed altered receptor conformations capable of accommodating a dimeric IL37, with the N-terminal loop of IL37 contributing significantly to complex mobility. Additionally, the glycosyl chain on N297 of IL18Rα, which contours one edge of the cytokine binding surface, acted as a steric block against the N-terminal loop of IL37. Further, investigations into interactions between IL37 and IL18BP suggested that a binding mode homologous to IL18 was unstable for IL37, indicating an alternative binding mechanism. Altogether, this study accesses to the structure and dynamics of IL37 complexes, revealing the structural underpinnings of the IL37's modulatory effect on the IL18 signaling pathway.

Inhibitory mechanism of lithospermic acid on the fibrillation of type 2 diabetes associated islet amyloid polypeptide

The abnormal fibrillation of a 37-residue peptide hormone human islet amyloid polypeptide (hIAPP) is linked with type 2 diabetes (T2D). Pang et al. depicted a prominent role of lithospermic acid (LA) in blocking hIAPP fibrillation and alleviating the hIAPP aggregates-induced cytotoxicity. LA is a polyphenolic compound present in extra virgin olive oil with therapeutic properties. Despite its notable inhibitory effect on hIAPP fibrillation, the inhibition mechanism remains unclear. Here, molecular dynamics (MD) simulations have been utilized to shed light on the putative binding mechanism and inhibitory mechanism of LA against hIAPP fibrillation. The molecular docking predicted favourable binding (-7.1 kcal/mol) of LA with hIAPP. Interestingly, LA increases the helix content in hIAPP and blocks the conformational transition to the aggregation-competent conformations. The conformational clustering and hydrogen bond analyses depicted that LA formed hydrogen bonds with Asn21 of hIAPP, which play an important role in hIAPP aggregation. LA binds favourably to hIAPP (ΔGbinding = -49.62 ± 3.34 kcal/mol) with a major contribution from the van der Waals interactions. The MD simulations highlighted that LA dramatically interfered with the intrapeptide interactions and inhibited sampling of aggregation-competent β-sheet conformations in hIAPP via hydrogen bonds through its hydroxyl groups, van der Waals interactions with hIAPP residues, thus blocking hIAPP aggregation to β-sheet rich cytotoxic fibrillar aggregates. The MD simulations illuminated specific interactions between hIAPP and LA, which will benefit in developing new chemical entities against hIAPP fibrillation.