Analysis of volatiles from the thermal decomposition of Amadori rearrangement products in the cysteine-glucose Maillard reaction and density functional theory study.

The Amadori rearrangement products are an important flavor precursor in the Maillard reaction. Its thermal decomposition products usually contribute good flavors in foods. Therefore, investigating the thermal breakdown of Amadori products is significant for understanding the flavor forming mechanism in the Maillard reaction. In this study, volatiles from thermal decomposition of Amadori products in cysteine and glucose Maillard reaction was investigated by a thermal desorption cryo-trapping system combined with gas chromatography-mass spectrometry (GC-MS). A total of 60 volatiles were detected and identified. Meanwhile, the forming mechanism of 2-methylthiophene, a major decomposition product, was also investigated by using density functional theory. Seventeen reactions, 12 transition states, energy barrier and rate constant of each reaction were finally obtained. Results reveal that it is more likely for Amadori products of cysteine and glucose to undergo decomposition under neutral or weakly alkaline conditions.

Evaluation of DFT methods for predicting geometries and NMR spectra of Bi(III) dithiocarbamate complexes with antitumor properties.

CONTEXT: Bismuth complexes with dithiocarbamate ligands have attracted attention because of their biological applications, such as antimicrobial, antileishmanial, and anticancer properties. These complexes have high cytotoxic activity against cancer cells, being more active than the standard drugs cisplatin, doxorubicin, and tamoxifen. In the present study, we investigated the ability of some DFT methods to reproduce the geometries and NMR spectra of the Bi(III) dithiocarbamate complexes, selected based on their proven antitumor activity. Our investigation revealed that the M06-L/def2-TZVP/ECP/CPCM method presented good accuracy in predicting geometries, while the TPSSh/def2-SVP/ECP/CPCM method proved effective in analyzing the 13C NMR spectra of these molecules. In general, all examined methods exhibited comparable performance in predicting 1H NMR signals. METHODS: Calculations were performed with the Gaussian 09 program using the def2-SVP and def2-TZVP basis sets, employing relativistic effective core potential (ECP) for Bi and using the CPCM solvent model. The exchange-correlation functionals BP86, PBE, OLYP, M06-L, B3LYP, B3LYP-D3, M06-2X, TPSSh, CAM-B3LYP, and ωB97XD were used in the study. Geometry optimizations were started from crystallographic structures available at the Cambridge Structural Database. The theoretical results were compared with experimental data using the mean root-mean-square deviation (RMSD), mean absolute deviations (MAD), and linear correlation coefficient (R2).

Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory.

Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood-brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale-yellow organic molecules (copigments). The present work carried out a theoretical study of the copigmentation process between cyanidin and resveratrol (CINRES). We used three levels of density functional theory: M06-2x/6-31g+(d,p) (d3bj); ωB97X-D/6-31+(d,p); APFD/6-31+(d,p), implemented in the Gaussian16W package. In a vacuum, the CINRES was found at a copigmentation distance of 3.54 Å between cyanidin and resveratrol. In water, a binding free energy ∆G was calculated, rendering -3.31, -1.68, and -6.91 kcal/mol, at M06-2x/6-31g+(d,p) (d3bj), ωB97X-D/6-31+(d,p), and APFD/6-31+(d,p) levels of theory, respectively. A time-dependent density functional theory (TD-DFT) was used to calculate the UV spectra of the complexes and then compared to its parent molecules, resulting in a lower energy gap at forming complexes. Excited states' properties were analyzed with the ωB97X-D functional. Finally, Shannon aromaticity indices were calculated and isosurfaces of non-covalent interactions were evaluated.

Reinvestigation of the internal glycan rearrangement of Lewis a and blood group type H1 epitopes.

Protonated ions of fucose-containing oligosaccharides are prone to undergo internal glycan rearrangement which results in chimeric fragments that obfuscate mass-spectrometric analysis. Lack of accessible tools that would facilitate systematic analysis of glycans in the gas phase limits our understanding of this phenomenon. In this work, we use density functional theory modeling to interpret cryogenic IR spectra of Lewis a and blood group type H1 trisaccharides and to establish whether these trisaccharides undergo the rearrangement during gas-phase analysis. Structurally unconstrained search reveals that none of the parent ions constitute a thermodynamic global minimum. In contrast, predicted collision cross sections and anharmonic IR spectra provide a good match to available experimental data which allowed us to conclude that fucose migration does not occur in these antigens. By comparing the predicted structures with those obtained for Lewis x and blood group type H2 epitopes, we demonstrate that the availability of the mobile proton and a large difference in the relative stability of the parent ions and rearrangement products constitute the prerequisites for the rearrangement reaction.

Intermolecular hydrogen bonding behavior of amino acid radical cations.

Amino acid and peptide radicals are of broad interest due to their roles in biochemical oxidative damage, pathogenesis and protein radical catalysis, among others. Using density functional theory (DFT) calculations at the ωB97X-D/def2-QZVPPD//ωB97X-D/def2-TZVPP level of theory, we systematically investigated the hydrogen bonding between water and fourteen α-amino acids (Ala, Asn, Cys, Gln, Gly, His, Met, Phe, Pro, Sel, Ser, Thr, Trp, and Tyr) in both neutral and radical cation forms. For all amino acids surveyed, stronger hydrogen-bonding interactions with water were observed upon single-electron oxidation, with the greatest increases in hydrogen-bonding strength occurring in Gly, Ala and His. We demonstrate that the side chain has a significant impact on the most favorable hydrogen-bonding modes experienced by amino acid radical cations. Our computations also explored the fragmentation of amino acid radical cations through the loss of a COOH radical facilitated by hydrogen bonding. The most favorable pathways provided stabilization of the resulting cationic fragments through hydrogen bonding, resulting in more favorable thermodynamics for the fragmentation process. These results indicate that non-covalent interactions with the environment have a profound impact on the structure and chemical fate of oxidized amino acids.

Binding energies and hydrogen bonds effects on DNA-cisplatin interactions: a DFT-xTB study.

CONTEXT: A systematic study of hydrogen bonds in base pairs and the interaction of cisplatin with DNA fragments was carried out. Structure, binding energies, and electron density were analyzed. xTB has proven to be an accurate method for obtaining structures and binding energies in DNA structures. Our xTB values for DNA base binding energy were in the same order and in some cases better than CAM-B3LYP values compared to experimental values. Double-stranded DNA-cisplatin structures have been calculated and the hydrogen bonds of water molecules are a decisive factor contributing to the preference for the cisplatin-Guanine interaction. Higher values of the water hydrogen bonding energies were obtained in cisplatin-Guanine structures. Furthermore, the electrostatic potential was used to investigate and improve the analysis of DNA-cisplatin structures. METHODS: We applied the xTB method and the CAM-B3LYP functional combined with def2-SVP basis set to perform and analyze of the bonding energies of the cisplatin interaction and the effects of the hydrogen bonds. Results were calculated employing the xTB and the ORCA software.

Migration mechanism of atrazine in the simulated lake icing process at different freezing temperatures based on density function theory.

Atrazine causes concern due to its resistant to biodegradation and could be accumulated in aquatic organisms, causing pollution in lakes. This study measured the concentration of atrazine in ice and the water under ice through a simulated icing experiment and calculated the distribution coefficient K to characterize its migration ability in the freezing process. Furthermore, density functional theory (DFT) calculations were employed to expatiate the migration law of atrazine during icing process. According to the results, it could release more energy into the environment when atrazine staying in water phase (-15.077 kcal/mol) than staying in ice phase (-14.388 kcal/mol), therefore it was beneficial for the migration of atrazine from ice to water. This explains that during the freezing process, the concentration of atrazine in the ice was lower than that in the water. Thermodynamic calculations indicated that when the temperature decreases from 268 to 248 K, the internal energy contribution of the compound of atrazine and ice molecule (water cluster) decreases at the same vibrational frequency, resulting in an increase in the free energy difference of the compound from -167.946 to -165.390 kcal/mol. This demonstrated the diminished migratory capacity of atrazine. This study revealed the environmental behavior of atrazine during lake freezing, which was beneficial for the management of atrazine and other pollutants during freezing and environmental protection.

Decarboxylation Mechanism of iso-Orotate Decarboxylase Revisited.

iso-Orotate decarboxylase (IDCase), which is involved in the thymidine salvage pathway, has attracted considerable interest owing to its chemical similarity to a hypothetical DNA decarboxylase in mammals. Although valuable insights into the active DNA demethylation of 5-methyl-cytosine can be obtained from the decarboxylation mechanism of 5-carboxyl-uracil (5caU) catalyzed by IDCase, this mechanism remains under debate. In this study, the catalytic mechanism of 5caU decarboxylation by IDCase was studied using hybrid quantum mechanics/molecular mechanics (QM/MM) methodologies and density functional theory (DFT) calculations with a truncated model. The calculations supported a mechanism involving three sequential stages: activation of the 5caU substrate via proton transfer from an arginine (R262') to the carboxyl group of 5caU, formation of a tetrahedral intermediate, and decarboxylation of the tetrahedral intermediate to generate uracil as the product. The reaction pathways and structures obtained using the QM/MM and DFT methods coincided with each other. These simulations provided detailed insights into the unique mechanism of IDCase, clarifying various unresolved issues, such as the critical role of R262'. In addition, aspartate D323 was found to act as a general base in the tetrahedral intermediate formation step and a general acid in the later C-C bond cleavage step.

Modulating anti-inflammatory and anticancer properties by designing a family of metal-complexes based on 5-nitropicolinic acid.

A new family of six complexes based on 5-nitropicolinic acid (5-npic) and transition metals has been obtained: [M(5-npic)2]n (MII = Mn (1) and Cd (2)), [Cu(5-npic)2]n (3), and [M(5-npic)2(H2O)2] (MII = Co (4), Ni (5), and Zn (6)), which display 1D, 2D, and mononuclear structures, respectively, thanks to different coordination modes of 5-npic. After their physicochemical characterization by single-crystal X-ray diffraction (SCXRD), elemental analyses (EA), and spectroscopic techniques, quantum chemical calculations using Time-Dependent Density Functional Theory (TD-DFT) were performed to further study the luminescence properties of compounds 2 and 6. The potential anticancer activity of all complexes was tested against three tumor cell lines, B16-F10, HT29, and HepG2, which are models widely used for studying melanoma, colon cancer, and liver cancer, respectively. The best results were found for compounds 2 and 4 against B16-F10 (IC50 = 26.94 and 45.10 µg mL-1, respectively). In addition, anti-inflammatory studies using RAW 264.7 cells exhibited promising activity for 2, 3, and 6 (IC50 NO = 5.38, 24.10, and 17.63 µg mL-1, respectively). This multidisciplinary study points to complex 2, based on CdII, as a promising anticancer and anti-inflammatory material.

Influence of the Pd Oxidation State in PdNi Thin Films on Surface Acoustic Wave Hydrogen Sensing Performance.

PdNi alloy thin films demonstrate exceptional hydrogen sensing performance and exhibit significant potential for application in surface acoustic wave (SAW) hydrogen sensors. However, the long-term stability of SAW H2 sensors utilizing PdNi films as catalysts experiences a substantial decrease during operation. In this paper, X-ray photoelectron spectroscopy (XPS) is employed to investigate the failure mechanisms of PdNi thin films under operational conditions. The XPS analysis reveals that the formation of PdO species on PdNi thin films plays a crucial role in the failure of hydrogen sensing. Additionally, density functional theory (DFT) calculations indicate that hydrogen atoms encounter a diffusion energy barrier during the penetration process from the PdNiOx surface to the subsurface region. The identification of PdNi film failure mechanisms through XPS and DFT offers valuable insights into the development of gas sensors with enhanced long-term stability. Guided by these mechanisms, we propose a method to restore the hydrogen sensing response time and magnitude to a certain extent by reducing the partially oxidized surface of the PdNi alloy under a hydrogen atmosphere at 70 °C, thereby restoring Pd to its metallic state with zero valence.

Harnessing Graphdiyne for Selective Cu2+ Detection: A Promising Tool for Parkinson's Disease Diagnostics and Pathogenesis.

Cu2+ accelerates the viral-like propagation of α-synuclein fibrils and plays a key role in the pathogenesis of Parkinson's disease (PD). Therefore, the accurate detection of Cu2+ is essential for the diagnosis of PD and other neurological diseases. The Cu2+ detection process is impeded by substances that have similar electrochemical properties. In this study, graphdiyne (GDY), a new kind of carbon allotrope with strong electron-donating ability, was utilized for the highly selective detection of Cu2+ by taking advantage of its outstanding adsorption capacity for Cu2+. Density functional theory (DFT) calculations show that Cu atoms are adsorbed in the cavity of GDY, and the absorption energy between Cu and C atoms is higher than that of graphene (GR), indicating that the cavity of GDY is favorable for the adsorption of Cu atoms and electrochemical sensing. The GDY-based electrochemical sensor can effectively avoid the interference of amino acids, metal ions and neurotransmitters and has a high sensitivity of 9.77 µA·µM-1·cm-2, with a minimum detectable concentration of 200 nM. During the investigating pathogenesis and therapeutic process of PD with α-synuclein as the diagnostic standard, the concentration of Cu2+ in cells before and after L-DOPA and GSH treatments were examined, and it was found that Cu2+ exhibits high potential as a biomarker for PD. This study not only harnesses the favorable adsorption of the GDY and Cu2+ to improve the specificity of ion detection but also provide clues for deeper understanding of the role of Cu2+ in neurobiology and neurological diseases.

Shaping the Future of the Neurotransmitter Sensor: Tailored CdS Nanostructures for State-of-the-Art Self-Powered Photoelectrochemical Devices.

Semiconductor-based photoelectrochemical (PEC) test protocols offer a viable solution for developing efficient individual health monitoring by converting light and chemical energy into electrical signals. However, slow reaction kinetics and electron-hole complexation at the interface limit their practical application. Here, we reported a triple-engineered CdS nanohierarchical structures (CdS NHs) modification scheme including morphology, defective states, and heterogeneous structure to achieve precise monitoring of the neurotransmitter dopamine (DA) in plasma and noninvasive body fluids. By precisely manipulating the Cd-S precursor, we achieved precise control over ternary CdS NHs and obtained well-defined layered self-assembled CdS NHs through a surface carbon treatment. The integration of defect states and the thin carbon layer effectively established carrier directional transfer pathways, thereby enhancing interface reaction sites and improving the conversion efficiency. The CdS NHs microelectrode fabricated demonstrated a remarkable negative response toward DA, thereby enabling the development of a miniature self-powered PEC device for precise quantification in human saliva. Additionally, the utilization of density functional theory calculations elucidated the structural characteristics of DA and the defect state of CdS, thus establishing crucial theoretical groundwork for optimizing the polymerization process of DA. The present study offers a potential engineering approach for developing high energy conversion efficiency PEC semiconductors as well as proposing a novel concept for designing sensitive testing strategies.

Significance of Zn2+ in RyR1 for Structural Integrity and Ligand Binding: Insight from Molecular Dynamics.

Ryanodine receptor type 1 (RyR1) is a Ca2+-release channel central to skeletal muscle excitation-contraction (EC) coupling. RyR1's cryo-EM structures reveal a zinc-finger motif positioned within the cytoplasmic C-terminal domain (CTD). Yet, owing to limitations in cryo-EM resolution, RyR1 structures lack precision in detailing the metal coordination structure, prompting the need for an accurate model. In this study, we employed molecular dynamics (MD) simulations and the density functional theory (DFT) method to refine the binding characteristics of Zn2+ in the zinc-finger site of the RyR1 channel. Our findings also highlight substantial conformational changes in simulations conducted in the absence of Zn2+. Notably, we observed a loss of contact at the interface between protein domains proximal to the zinc-finger site, indicating a crucial role of Zn2+ in maintaining structural integrity and interdomain interactions within RyR1. Furthermore, this study provides valuable insights into the modulation of ATP, Ca2+, and caffeine binding, shedding light on the intricate relationship between Zn2+ coordination and the dynamic behavior of RyR1. Our integrative approach combining MD simulations and DFT calculations enhances our understanding of the molecular mechanisms governing ligand binding in RyR1.

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling.

The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.

Light-Responsive Pt(IV) Prodrugs with Controlled Photoactivation and Low Dark Toxicity.

Light-induced release of cisplatin from Pt(IV) prodrugs represents a promising approach for precise control over the antiproliferative activity of Pt-based chemotherapeutic drugs. This method has the potential to overcome crucial drawbacks of conventional cisplatin therapy, such as high general toxicity toward healthy organs and tissues. Herein, we report two Pt(IV) prodrugs with BODIPY-based photoactive ligands Pt-1 and Pt-2, which were designed using carbamate and triazole linkers, respectively. Both prodrugs demonstrated the ability to release cisplatin under blue light irradiation without the requirement of an external reducing agent. Dicarboxylated Pt-2 prodrug turned out to be more stable in the dark and more sensitive to light than its monocarbamate Pt-1 counterpart; these observations were explained using DFT calculations. The investigation of the photoreduction mechanism of Pt-1 and Pt-2 prodrugs using DFT modeling and ΔG0 PET estimation suggests that the photoinduced electron transfer from the singlet excited state of the BODIPY axial ligand to the Pt(IV) center is the key step in the light-induced release of cisplatin from the complexes. Cytotoxicity studies demonstrated that both prodrugs were nontoxic in the dark and toxic to MCF-7 cells under low-dose irradiation with blue light, and the observed effect was solely due to the cisplatin release from the Pt(IV) prodrugs. Our research presents an elegant synthetic approach to light-activated Pt(IV) prodrugs and presents findings that may contribute to the future rational design of photoactivatable Pt(IV) prodrugs.

Multifunctional in vitro, in silico and DFT analyses on antimicrobial BagremycinA biosynthesized by Micromonospora chokoriensis CR3 from Hieracium canadense.

Among the actinomycetes in the rare genera, Micromonospora is of great interest since it has been shown to produce novel therapeutic compounds. Particular emphasis is now on its isolation from plants since its population from soil has been extensively explored. The strain CR3 was isolated as an endophyte from the roots of Hieracium canadense, and it was identified as Micromonospora chokoriensis through 16S gene sequencing and phylogenetic analysis. The in-vitro analysis of its extract revealed it to be active against the clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Candida tropicalis (15 mm). No bioactivity was observed against Gram-negative bacteria, Escherichia coli ATCC 25922, and Klebsiella pneumoniae ATCC 706003. The Micromonospora chokoriensis CR3 extract was also analyzed through the HPLC-DAD-UV-VIS resident database, and it gave a maximum match factor of 997.334 with the specialized metabolite BagremycinA (BagA). The in-silico analysis indicated that BagA strongly interacted with the active site residues of the sterol 14-α demethylase and thymidylate kinase enzymes, with the lowest binding energies of - 9.7 and - 8.3 kcal/mol, respectively. Furthermore, the normal mode analysis indicated that the interaction between these proteins and BagA was stable. The DFT quantum chemical properties depicted BagA to be reasonably reactive with a HOMO-LUMO gap of (ΔE) of 4.390 eV. BagA also passed the drug-likeness test with a synthetic accessibility score of 2.06, whereas Protox-II classified it as a class V toxicity compound with high LD50 of 2644 mg/kg. The current study reports an endophytic actinomycete, M. chokoriensis, associated with H. canadense producing the bioactive metabolite BagA with promising antimicrobial activity, which can be further modified and developed into a safe antimicrobial drug.

Electron transfer mediated photo-Fenton-like synergistic catalysis of Fe,Cu-doped MIL-101 coupled with Ag3PO4: Quantitative evaluation and DFT calculations.

Widespread use of tetracycline (TC) results in its persistent residue and bioaccumulation in aquatic environments, posing a high toxicity to non-target organisms. In this study, a bimetal-doped composite material Ag3PO4/MIL-101(Fe,Cu) has been designed for the treatment of TC in aqueous solutions. As the molar ratio of Fe/Cu in composite is 1:1, the obtained material AP/MFe1Cu1 is placed in an aqueous environment under visible light irradiation in the presence of 3 mM peroxydisulfate (PDS), which forms a photo-Fenton-like catalytic system that can completely degrade TC (10 mg/L) within 60 min. Further, the degradation rate constant (0.0668 min-1) is 5.66 and 7.34 times higher than that of AP/MFe and AP/MCu, respectively, demonstrating a significant advantage over single metal-doped catalysts. DFT calculations confirm the strong adsorption capacity and activation advantage of PDS on the composite surface. Therefore, the continuous photogenerated electrons (e-) accelerate the activation of PDS and the production of SO4•-, resulting in the stripping of abundant photogenerated h + for TC oxidation. Meanwhile, the internal circulation of FeⅢ/FeⅡ and CuⅡ/CuⅢ in composite also greatly enhances the photo-Fenton-like catalytic stability. According to the competitive dynamic experiments, SO4•- have the greatest contribution to TC degradation (58.93%), followed by 1O2 (23.80%). The degradation intermediates (products) identified by high-performance liquid chromatography-mass spectrometry (HPLC/MS) technique indicate the involvement of various processes in TC degradation, such as dehydroxylation, deamination, N-demethylation, and ring opening. Furthermore, as the reaction proceeds, the toxicity of the intermediates produced during TC degradation gradually decreases, which can ensure the safety of the aquatic ecosystem. Overall, this work reveals the synergy mechanism of PDS catalysis and photocatalysis, as well as provides technical support for removal of TC-contaminated wastewater.

Exploring enzyme inhibition and comprehensive mechanisms of antioxidant/prooxidative activity of natural furanocoumarin derivatives: A comparative kinetic DFT study.

This study aimed to explore the antioxidant and prooxidative activity of two natural furanocoumarin derivatives, Bergaptol (4-Hydroxy-7H-furo [3,2-g] [1]benzopyran-7-one, BER) and Xanthotoxol (9-Hydroxy-7H-furo [3,2-g] [1]benzopyran-7-one, XAN). The collected thermodynamic and kinetic data demonstrate that both compounds possess substantial antiradical activity against HO• and CCl3OO• radicals in physiological conditions. BER exhibited better antiradical activity in comparison to XAN, which can be attributed to the enhanced deprotonation caused by the positioning of the -OH group on the psoralen ring. In contrast to highly reactive radical species, newly formed radical species BER• and XAN• exhibited negligible reactivity towards the chosen constitutive elements of macromolecules (fatty acids, amino acids, nucleobases). Furthermore, in the presence of O2•─, the ability to regenerate newly formed radicals BER• and XAN• was observed. Conversely, in physiological conditions in the presence of Cu(II) ions, both compounds exhibit prooxidative activity. Nevertheless, the prooxidative activity of both compounds is less prominent than their antioxidant activity. Furthermore, it has been demonstrated that anionic species can engage in the creation of a chelate complex, which restricts the reduction of metal ions when reducing agents are present (O2•─ and Asc─). Moreover, studies have demonstrated that these chelating complexes can be coupled with other radical species, hence enhancing their ability to inactivate radicals. Both compounds exhibited substantial inhibitory effects against enzymes involved in the direct or indirect generation of ROS: Xanthine Oxidase (XOD), Lipoxygenase (LOX), Myeloperoxidase (MPO), NADPH oxidase (NOX).

A novel fluorescent indicator-based fluorene derivative for rapid and visual trace water sensing.

Fluorene nucleus derivatives show great potential for building outstanding fluorescence probes. In this paper, a novel fluorescent probe was developed by reacting with fluorene core with azacyclobutane, which exhibits typical solvation chromogenic effect in solvent. The fluorescence of the probe quenched in highly polar solvent. Based on this phenomenon, a novel fluorescence system for trace water was constructed. The response of this probe was fast (30 s) and sensitive for the detection of trace water in organic solvents, and the detection limit of water content in DMSO reached 0.13%. In addition, the probe can also be made as a test strip combined with homemade portable device and a smartphone for rapid detection of trace water. The luminescence mechanism of the probe is theoretically calculated based on time-contained density functional theory (TDDFT). To showcase its practicality, it has been applied for the detection of trace water in honey and alcohol by dipstick. This method provides a new idea for designing efficient fluorescent probes based on dipstick and mobile phone rapid detection.

Exploring Antiviral Drugs on Monolayer Black Phosphorene: Atomistic Theory and Explainable Machine Learning-Assisted Platform.

Favipiravir (FP) and ebselen (EB) belong to a diverse class of antiviral drugs known for their significant efficacy in treating various viral infections. Utilizing molecular dynamics (MD) simulations, machine learning, and van der Waals density functional theory, we accurately elucidate the binding properties of these antiviral drugs on a phosphorene single-layer. To further investigate these characteristics, this study employs four distinct machine learning models-Random Forest, Gradient Boosting, XGBoost, and CatBoost. The Hamiltonian of antiviral molecules within a monolayer of phosphorene is appropriately trained. The key aspect of utilizing machine learning (ML) in drug design revolves around training models that are efficient and precise in approximating density functional theory (DFT). Furthermore, the study employs SHAP (SHapley Additive exPlanations) to elucidate model predictions, providing insights into the contribution of each feature. To explore the interaction characteristics and thermodynamic properties of the hybrid drug, we employ molecular dynamics and DFT calculations in a vacuum interface. Our findings suggest that this functionalized 2D complex exhibits robust thermostability, indicating its potential as an effective and enabled entity. The observed variations in free energy at different surface charges and temperatures suggest the adsorption potential of FP and EB molecules from the surrounding environment.