Applications of the Conceptual Density Functional Theory Indices to Organic Chemistry Reactivity

Computational analysis of zoanthamine alkaloids from Zoanthus sp. as potential DKK1 and GSK-3β inhibitors for osteoporosis therapy via Wnt signaling

Marine invertebrates are a rich source of structurally diverse secondary metabolites with broad biological activities, making them valuable for drug discovery. The genus Zoanthus is particularly noteworthy, producing numerous bioactive alkaloids, including the zoanthamines, which show promise in treating osteoporosis. Osteoporosis, a debilitating bone disease characterized by reduced bone mineral density and increased fracture risk, is linked to Wnt signaling pathway dysregulation. This highly conserved pathway maintains tissue homeostasis and is crucial for neurogenesis, synapse formation, and bone development. Dickkopf-1 (DKK1) and glycogen synthase kinase-3β (GSK-3β), key Wnt pathway regulators, are established therapeutic targets for osteoporosis. This study employed an integrated computational approach-combining molecular docking, extensive molecular dynamics (MD) simulations, and density functional theory (DFT) calculations-to assess the inhibitory potential of 69 zoanthamine-type alkaloids against DKK1 and GSK-3β. MD simulations, analyzing root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration, and free energy landscape, provided insights into protein-ligand complex stability and key interactions. Binding free energies were calculated using the MM-PBSA method combined with interaction entropy. DFT calculations further elucidated the electronic structure and reactivity of the most promising inhibitors (3α-hydroxyzoanthenamine, epioxyzoanthamine, 7α-hydroxykuroshine E, and norzoanthamine), which exhibited favorable binding interactions with key residues in target proteins. This integrative approach demonstrates the power of computational methods in drug discovery, highlighting the potential of zoanthamine alkaloids as lead compounds for innovative osteoporosis therapies.

Insecticidal Evaluation of New Cyanoacetamide Derivatives Against Spodoptera Littoralis: Molecular Docking and Density Function Theory Approaches

The cotton leafworm Spodoptera littoralis represents a critical agricultural challenge because of its significant crop damage and increasing resistance to conventional insecticides. This study systematically evaluated the synthesized cyanoacetamide derivatives as novel insecticidal agents through comprehensive biochemical and computational analyses. Among the tested compounds, AZ19, AZ20, AZ18, and AZ17 demonstrated remarkable toxicity against third instar larvae, with AZ-19 exhibiting the most promising profile (LC50 = 14.740 mg/L; toxicity index = 81.34%). Biochemical assessments revealed significant modulations in key enzymatic systems, including acetylcholinesterase, aminotransferases, and detoxification enzymes. Molecular docking and density functional theory (DFT) analyses provided critical insights into the binding affinities, electronic properties, and potential modes of action of the compounds. By integrating bioassays, molecular docking, and quantum chemical investigations, this research not only identifies AZ19 as a potent insecticidal candidate but also establishes a robust framework for developing next-generation pest control strategies that address resistance challenges and support sustainable agricultural practices.

A redefinition of global conceptual density functional theory reactivity indexes by means of the cubic expansions of the energy

In the present work, a new definition of the conceptual density functional theory reactivity indexes is proposed, based on a cubic interpolation of the energy as function of number of electrons as well as a generalization of the net electrophilicity index. This new proposal takes into account both the influence of hyperhardness on the reactivity and a weighted average of the electrodonating and electroacepting powers. Thus, the presented redefinition incorporates corrections and additional degrees of freedom to the prior CDFT indexes. Numerical support for global descriptors is presented for 30 benzhydrylium ions (i.e., charged electrophiles) and 15 alkyl and aryl nucleophiles taken as reference cases from the Mayr Database of Reactivity Parameters. In the best-case scenario, the descriptors correlated better with the electrophilicity parameter (r2 = 0.981) than with the nucleophilicity parameter (r2 = 0.827).

Unveiling Hydrogen Bonding and Solvent Effects on Directed Nitrile Oxide [3 + 2] Cycloaddition Reactions: Selectivity of 2,2-Dimethylpropane Nitrile Oxide with Cyclopentenylbenzamide: An MEDT Study

The role of hydrogen bond and solvent effects on the regio- and diastereoselectivity of the [3 + 2] cycloaddition reaction (32CA) between 2,2-dimethylpropanenitrile oxide (NO) and N-(cyclopent-2-en-1-yl)benzamide has been theoretically studied at the B3LYP/6-311++G(d,p) level using the molecular electron density theory (MEDT). Solvent effects of dichloromethane (DCM) and benzene were taken into account. The electron localization function (ELF) classifies NO as a three-atom component with a zwitterionic electronic structure, which participates in zwitterionic-type 32CA reactions. The reactions occur through a one-step mechanism and present high activation Gibbs free energies in DCM and in benzene, with a slight difference favoring the reaction in benzene. Along the intrinsic reaction coordinate reaction pathway, the topological analysis of the ELF shows the asynchronous formation of the C-C bond prior to the C-O bond by coupling the two-carbon pseudoradical centers. The low global electron density transfer indicates that these reactions have a nonpolar character, which accounts for their high Gibbs free activation energies. Analysis of the noncovalent interactions associated with the TSs reveals a hydrogen bond in the favored TS, which confirms its participation in the experimental selectivities.

Valorization of organic fruit peel wastes for Aedes aegypti control: A green chemistry approach integrating in vitro and in silico studies

Vector-borne diseases affect millions of people worldwide, with a significant impact on children below five years. The infections transmitted by mosquitoes cause an estimate of 219 million cases globally, resulting in more than 400,000 deaths every year. As per WHO protocol, spraying of synthetic larvicides over the stagnant drainages and water systems is being one of the most common and effective techniques in the process of disease control. In parallel, the awareness on organic waste pollution had led to the increased practice of sustainable valorization to tackle daily needs. The present study focuses on mixed fruit peel liquid (MFPL) production through anaerobic fermentation of fruit peel wastes and evaluation of its larvicidal efficacy against Aedes aegypti. The in vitro assay revealed that higher concentrations of MFPL and exposure period increased larval mortality, with LC50 values ranging from 1.4% at 6 h to 0.3% at 24 h. Among the twenty bioactive compounds identified through GC-MS analysis of MFPL, n-hexadecanoic acid,2(1H) - quinolinone hydrazone and benzofuran, had significant glide scores of. -12.3 kcal/mol, -7.1 kcal/mol and -5.7 kcal/mol against the target protein 1PZ4 and -11.1 kcal/mol, -7.2 kcal/mol and -5.2 kcal/mol against 1YIY during molecular docking. The stability and interactions of three bioactive compounds were then assessed using DFT and molecular dynamics simulations, in which n-hexadecanoic acid was significantly stable with optimal hydrogen bond interactions. The novel findings of the study confirm MFPL's potential as an effective larvicide which could substitute commercial larvicides that are harmful to the ecosystem.

Integrated deep eutectic system enrichment and AI-assisted high-throughput visual detection for Hg2+ in environmental samples

INTRODUCTION

Mercury ion (Hg2+), a prevalent heavy metal, is commonly found in environmental soils and waters. Its interaction with sulfhydryl groups in proteins and lipids can cause oxidative stress and disruption of calcium homeostasis. These lead to severe health issues, including digestive, nervous, and immune system damage. Conventional Hg2+ detection methods, such as ICP-MS and AAS, require complex procedures and bulky instruments, limiting their applicability for real-time, on-site analysis. Recently, AI-assisted detection methods have emerged as promising solutions, offering portability and rapid detection capabilities. Deep eutectic solvents (DESs), and in particularly hydrophobic DESs (HDESs), provide an environmentally friendly alternative for the enrichment and detection metal ions.

OBJECTIVES

This study aims to develop a portable, cost-effective, and environmentally friendly colorimetric sensing platform based on a silver nanoparticles hydrophobic deep eutectic system (AgNPs-HDES) for Hg2+ enrichment and detection.

METHODS

AgNPs-HDES was synthesized using silver nanoparticle-containing ethylene glycol (AgNPs-EG) as the hydrogen bond donor. Electrostatic potential maps (ESP) and density functional theory (DFT) were employed to elucidate its synthesis and enrichment mechanisms. Smartphone-based image acquisition combined with YOLOv8-based AI software enabled high-throughput colorimetric analysis for Hg2+ detection.

RESULTS

A progressive color change from brownish-yellow to colorless was observed with increasing Hg2+ concentration, thereby eliminating hydrophilic interference and improving sensitivity. The AgNPs-HDES platform demonstrated a linear detection range of 1-40 μmol·L-1 (R2 = 0.9889) and a detection limit of 0.23 μmol·L-1. Recovery rates in real samples, including lake water, soil, seawater and industrial sewage, ranged from 90.3% to 123%.

CONCLUSION

The established platform enables portable, rapid, and highly accurate Hg2+ detection across multiple environmental samples simultaneously. This AI-assisted, high-throughput detection system presents a valuable tool for environmental monitoring and pollutant tracking.

Explainable no-code OECD-compliant machine learning models to predict the mutagenic activity of polycyclic aromatic hydrocarbons and their radical cation metabolites

Polycyclic aromatic hydrocarbons (PAHs) are persistent pollutants with well-known genotoxic and mutagenic effects, posing risks to ecosystems and human health. Their hydrophobic nature promotes accumulation in soils and aquatic environments, increasing exposure risks. Upon metabolic activation, PAHs generate reactive species that form DNA adducts, driving their mutagenic potential. This study presents an OECD-compliant methodology that integrates conceptual density functional theory (CDFT) calculations at the GFN2-xTB level with machine learning models to predict PAH mutagenicity. Using quantum chemical descriptors of procarcinogens and radical cation metabolites alongside Ames test data, key electronic properties linked to mutagenicity were identified. Feature selection consistently highlighted radical cation descriptors as key indicators of metabolic activation pathways. Machine learning models - including SPAARC, Random Tree, and JCHAID - achieved validation accuracies exceeding 89 %, with minimal false-negative rates, ensuring conservative predictions for environmental risk assessment. The PSL and CDP electrophilicity frameworks proved particularly effective in modeling DNA damage-related processes. This no-code, freeware-based methodology provides a scalable and cost-effective tool for assessing mutagenic risks in environmentally relevant conditions. The findings reinforce the importance of metabolic activation, validate the radical cation as a reliable proxy for this process, and demonstrate the predictive value of electronic properties in QSAR modeling. These insights support advances in environmental toxicology and contribute to improved strategies for regulatory risk assessment.

Unveiling Intramolecular [3+2] Cycloaddition Reactions Leading to Functionalized Heterocycles in the Light of Molecular Electron Density Theory

The relative reactivity and cis/trans selectivity of the intramolecular [3+2] cycloaddition (IM32CA) reactions of nitrile oxide (NO), azide (AZ), nitrile sulfide (NS) and nitrile ylide (NY), leading to functionalized heterocycles are studied within the Molecular Electron Density Theory. The kinetically controlled IM32CA reactions are predicted to be cis stereospecific, while the reaction feasibility follows the order NY>NS>NO>AZ with the respective activation Gibbs free energies of 13.7, 17.8, 21.1 and 27.3 kcal ⋅ mol-1 in benzene at 353 K. The decreased activation energy of NY could be correlated with its carbenoid character, relative to the zwitterionic one predicted for the other three species. The AZ reaction showed relatively higher activation parameter, and accordingly higher than that of the NO one, in conformity with the experimental outcomes. Topological analysis of the electronic structure of the transition state structure shows that the formation of the new single bonds has not yet started on any of them according to a non-concerted mechanism. Analysis of the kinetic parameters of the intermolecular [3+2] cycloaddition reactions of NOs and AZs shows that the low activation entropies associated with the intramolecular processes are the factor responsible for the feasibility of these non-polar zw-type IM32CA reactions.

Computational discovery of AKT serine/threonine kinase 1 inhibitors through shape screening for rheumatoid arthritis intervention

Rheumatoid Arthritis (RA) is a chronic, symmetrical inflammatory autoimmune disorder characterized by painful, swollen synovitis and joint erosions, which can cause damage to bone and cartilage and be associated with progressive disability. Despite expanded treatment options, some patients still experience inadequate response or intolerable adverse effects. Consequently, the treatment options for RA remain quite limited. The enzyme AKT1 is crucial in designing drugs for various human diseases, supporting cellular functions like proliferation, survival, metabolism, and angiogenesis in both normal and malignant cells. Therefore, AKT serine/threonine kinase 1 is considered crucial for targeting therapeutic strategies aimed at mitigating RA mechanisms. In this context, directing efforts toward AKT1 represents an innovative approach to developing new anti-arthritis medications. The primary objective of this research is to prioritize AKT1 inhibitors using computational techniques such as molecular modeling and dynamics simulation (MDS) and shape-based virtual screening (SBVS). A combined SBVS approach was employed to predict potent inhibitors against AKT1 by screening a pool of compounds sourced from the ChemDiv and IMPPAT databases. From the SBVS results, only the top three compounds, ChemDiv_7266, ChemDiv_2796, and ChemDiv_9468, were subjected to stability analysis based on their high binding affinity and favorable ADME/Tox properties. The SBVS findings have revealed that critical residues, including Glu17, Gly37, Glu85, and Arg273, significantly contribute to the successful binding of the highest-ranked lead compounds at the active site of AKT1. This insight helps to understand the specific binding mechanism of these leads in inhibiting RA, facilitating the rational design of more effective therapeutic agents.

In silico identification for flavor antioxidant compounds in Chrysanthemi flos uncovers the interactions between saccharides and secondary metabolites

Secondary metabolites and saccharides are responsible for antioxidant activity and flavor of Chrysanthemi flos (CF). However, the flavor antioxidant compounds of CF and their intermolecular interactions remain unclear. Here, we primarily employed in silico methods to identify CF antioxidants. After characterizing by physicochemical properties, FT-NIR and HPLC fingerprint, the "spectrum-effect" fusion correlation was established to select the spectral features of CF antioxidants. Quercetagitrin (QU), chlorogenic acid (CA) and saccharides fragments were clarified based on their characteristic spectrum. The antioxidant efficacy as well as the sweet and bitter taste of these compounds were verified by molecular docking. Quantum chemical calculations demonstrated that non-covalent interactions dominant facilitated the stable existence of CF antioxidants. The most significant binding types between CA, QU and saccharides fragments were hydrogen bonding. These results indicate a novel approach and theoretical support to discovery of new information pertinent to the bioactive compounds related to CF or other tea.

An analysis method including orbital overlap directions for predicting π electron properties and reactivity vectors

An analysis method with the name of the Projection of Orbital Coefficient Vector (POCV) has been proposed for predicting π electronic properties, aromaticity, and the directional reactivity of molecules including reactivity vectors. This approach significantly differs from previous computational methods by explicitly accounting for orbital overlap directions. Using the POCV method, accurate predictions of π electron properties and directional reactivity indices have been successfully demonstrated across various unsaturated molecules. To illustrate the advantages of POCV over conventional methods, we present several case studies involving the computation of π electron properties and reactivity vectors for diverse molecular systems, including non-planar axially chiral molecules, nucleophilic and electrophilic carbenes, and linear conjugated molecules. Here we show, the POCV method enables accurate prediction of chemical reaction sites with multiple orbital overlap directions, and facilitates the calculations of π electron properties.

Computational tools for the prediction of site- and regioselectivity of organic reactions

The regio- and site-selectivity of organic reactions is one of the most important aspects when it comes to synthesis planning. Due to that, massive research efforts were invested into computational models for regio- and site-selectivity prediction, and the introduction of machine learning to the chemical sciences within the past decade has added a whole new dimension to these endeavors. This review article walks through the currently available predictive tools for regio- and site-selectivity with a particular focus on machine learning models while being organized along the individual reaction classes of organic chemistry. Respective featurization techniques and model architectures are described and compared to each other; applications of the tools to critical real-world examples are highlighted. This paper aims to serve as an overview of the field's status quo for both the intended users of the tools, that is synthetic chemists, as well as for developers to find potential new research avenues.

A mechanistic insight into anionic phosphate adsorption on developed chitosan.ZnO@metakaolin biocomposite

Due to their high efficiency, chitosan (Cs)-based materials are increasingly utilized for wastewater treatment applications. In this study, a novel Cs-based biocomposite, Cs.ZnO@Mk was developed by blending Cs with zinc oxide (ZnO) and metakaolin (Mk), and was evaluated for its capability as a biosorbent to remove phosphate (PO43-) ions from water. The biosorbent was characterized using FTIR, XRD, TGA, SEM, and XPS techniques. The determined optimal conditions for PO43- removal were pH 4, initial concentration 100 mg/L, and contact time 120 min, achieving 98.9 % PO43- removal efficiency. The adsorption isotherm and kinetic data were fitted well to Langmuir isotherm and pseudo-second-order kinetic models, while thermodynamic study affirmed that the adsorption process was exothermic. XPS analysis suggested that electrostatic attraction and ligand-exchange were the key mechanisms for PO43- adsorption. Further mechanistic insights were gained through density functional theory (DFT) calculations and non-covalent interaction (NCI) analysis. Regeneration and counter-ions effect studies confirmed the effectiveness and stability of Cs.ZnO@Mk during PO43- adsorption. This demonstrates well its potential as a robust biosorbent for effective PO43- removal from industrial effluents.

How Different Are Nitrile Oxides from Nitrones in zw-type [3 + 2] Cycloaddition Reactions? A Molecular Electron Density Theory Study

Using the molecular electron density theory, the zw-type [3 + 2] cycloaddition (32CA) reactions of three benzonitrile oxides (BNOs) with several ethylenes, exhibiting different nucleophilic/electrophilic activation, have been studied to establish their poor reactivity. ELF topological analysis of the three BNOs reveals that the para substitution on the benzene ring does not affect the electron density distribution on the CNO frameworks. According to a DFT-based reactivity indices analysis, the nonsubstituted BNO is a moderate electrophile and a moderate nucleophile, which accounts for its poor reactivity in polar reactions. The activation energy analysis of the 32CA reactions of the nonsubstituted BNO allows us to establish that it reacts more effectively with strongly nucleophilic ethylenes than strongly electrophilic ones. Additionally, while the 32CA reactions with nucleophilic ethylenes are entirely ortho regioselective, those with electrophilic ethylenes are poor meta regioselective. A relative interacting atomic energy analysis of these 32CA reactions confirms the establishment of participation of these BNOs in zw-type 32CA reactions. The electrophilic BNO framework stabilization in 32CA reactions with supernucleophilic ethylenes is stronger than that of the ethylene framework in reactions with strong electrophilic ethylenes, which explains the higher reactivity of BNOs toward supernucleophilic ethylenes.

Unveiling the Reaction Mechanism of Diels-Alder Cycloadditions between 2,5-Dimethylfuran and Ethylene Derivatives Using Topological Tools

The [4+2] Diels-Alder cycloaddition reaction between 2,5-DMF (1) and ethylene derivatives (2 a-h) activated by electron-withdrawing groups has been studied at the density functional theory level using a panoply of tools to unravel the reaction mechanisms. From the analysis of the reactivity indices, 2 a-h behave as electrophiles while 1 as nucleophile, and the activation of the double bond of ethylene increases its electrophilicity, which is accompanied by an enhancement of the polarity of the reaction. The activation Gibbs free energy decreases linearly as a function of this increase of polarity, as estimated by the electrophilicity difference between the reactants. The difference of electrophilicity drives also the global electron density transfer at the transition state and the asynchronicity of the reaction, as evaluated by the difference of carbon-carbon bond lengths in the transition state. Then, Bonding Evolution Theory shows that the activation of the double bond of ethylene by an electron-withdrawing group changes the reaction mechanism from a one-step synchronous process to a one-step asynchronous process. Generally, the endo pathway is kinetically favored but, thermodynamically, it is the exo pathway. Finally, using the Distortion/Interaction-Activation Strain, it is shown that the endo/exo selectivity is mostly driven by the differences of interaction energies.

Environmental implications of Si2BN nanoflakes in pharmaceutical pollutant detection and removal: insights from first-principle calculations

Pharmaceutical pollutants, such as carbamazepine (CBZ), are emerging contaminants that pose significant environmental and health risks due to their persistence in aquatic ecosystems and incomplete removal by conventional wastewater treatments. This study leverages density functional theory (DFT), a gold-standard computational quantum mechanical modeling method, to evaluate the efficacy of Si2BN nanoflakes-a novel two-dimensional material-for CBZ adsorption and detection. Our first-principles calculations reveal thermodynamically stable interactions between CBZ and Si2BN, with adsorption energies of - 0.83 eV (edge) and - 0.82 eV (surface). The material's responsive optical behavior is quantified through time-dependent DFT, showing a 138 nm blueshift in UV-Vis spectra upon adsorption, a hallmark of its sensing capability. Furthermore, DFT-calculated charge transfer (0.04-0.06 e) and Fermi-level shifts (- 4.52 to - 4.69 eV) underscore Si2BN's enhanced electronic properties, enabling selective pollutant detection. By bridging atomic-scale insights (bond distortions, orbital hybridization) with macroscale environmental applications, this work demonstrates how DFT-guided design unlocks Si2BN's dual functionality as a scalable adsorbent and optical sensor. These findings provide a quantum-mechanical foundation for advancing Si2BN nanoflakes as a scalable, stable, and effective material for addressing pharmaceutical pollutants in water, offering a sustainable alternative to conventional methods plagued by secondary contamination risks.

Synthesis of New Thiazole-Pyrazole Analogues: Molecular Modelling, Antiproliferative/Antiviral Activities, and ADME Studies

Twelve thiazole-pyrazole analogues 4, 6, and 8 were synthesized by introducing various pyrazole systems into the core, 2-((4-acetylphenyl)amino)-4-methylthiazole (2), through many synthetic approaches. The density functional theory (DFT) study of the synthesized analogues revealed coincided configurations of their highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO), except for the nitro derivatives, in which the intramolecular charge-transfer (CT) may be denoted as π → π* and n → π*. In addition, the in vitro antiproliferative efficacy towards some cancer cell lines was examined (Panc-1, HT-29, MCF-7) and the non-cancerous (WI-38), using Dasatinib (Reference). The analogues 4c and 4d demonstrated the most potent anticancer effect, particularly against Panc-1 and MCF-7 cells. Moreover, the antiviral activity against H5N1, using a plaque reduction assay, showed that analogue 6a exhibited the most potent antiviral activity (100% inhibition and TC50 = 61 μg/μL), comparable to the reference drug amantadine (TC50 = 72 μg/μL, 100% inhibition). Furthermore, the molecular docking disclosed that the analogues exhibited a range of interactions, such as H-bonding and π-π stacking, with binding affinities between -4.8558 and - 8.3673 kcal/mol. Additionally, the SwissADME predictions indicated that the synthesized analogues possess promising drug-like characteristics, but analogues 4a-d and 8c demonstrated inadequate solubility and bioavailability, which restricts their use as viable oral medications.

ADME Study, Molecular Docking, Elucidating the Selectivities and the Mechanism of [4 + 2] Cycloaddition Reaction Between (E)-N ((dimethylamino)methylene)benzothioamide and (S)-3-acryloyl-4-phenyloxazolidin-2-one

The molecular electron density theory (MEDT) was employed to examine the [4 + 2] cycloaddition reaction between (E)-N-((dimethylamino)methylene)benzothioamide (1) and (S)-3-acryloyl-4-phenyloxazolidin-2-one (2) at the B3LYP/6-311++G(d,p) design level. Parr functions and energy studies clearly show that this reaction is regio- and stereoselective, in perfect agreement with experimental results. By evaluating the chemical mechanism in terms of bond evolution theory (BET) and electron localization function (ELF), which divulges a variety of variations in the electron density along the reaction path, a single-step mechanism with highly asynchronous transition states structures was revealed. Additionally, we conducted a docking study on compounds P1, P2, P3, and P4 in the SARS-CoV-2 main protease (6LU7) in comparison to Nirmatrelvir. Our findings provide confirmation that product P4 may serve as a potent antiviral drug.

A Multifaceted Computational Approach to Identify PAD4 Inhibitors for the Treatment of Rheumatoid Arthritis (RA)

BACKGROUND/OBJECTIVES

Neutrophil cells' lysis forms the extracellular traps (NETs) to counter the foreign body during insults to the body. Peptidyl arginine deiminase (PAD) participates in this process and is then released into the extracellular fluid with the lysed cell components. In some diseases, patients with abnormal function of PADs, especially PAD 4, tend to form autoantibodies against the abnormal citrullinated proteins that are the result of PAD activity on arginine side chains. Those antibodies, which are highly distinct in RA, are distinctly anti-citrullinated protein antibodies (ACPA). This study used an in-silico drug repurposing approach of FDA-approved medications to identify potential alternative medications that can inhibit this process and address solutions to the current limitations of existing therapies.

METHODS

We utilized Maestro Schrödinger as a computational tool for preparing and docking simulations on the PAD 4 enzyme crystal structure that is retrieved from RCSB Protein Data Bank (PDB ID: 4X8G) while the docked FDA-approved medications are obtained from the Zinc 15 database. The protein was bound to GSK 199-an investigational compound-as a positive control for the docked molecules. Preparation of the protein was performed by Schrödinger Protein Preparation Wizard tool. Binding pocket determination was performed by Glide software (Schrödinger Release 2021-3:Schrödinger, LLC., New York, NY, USA, 2021). and validation of molecular docking was carried out through the redocking of GSK 199 and superimposition. After that, standard and induced fit docking were performed.

RESULTS/CONCLUSIONS

Among the four obtained hits Pemetrexed, Leucovorin, Chlordiazepoxide, and Ioversol, which showed the highest XP scores providing favorable binding interactions. The induced-fit docking (IFD) results displayed the strong binding affinities of Ioversol, Pemetrexed, Leucovorin, Chlordiazepoxide in the order IFD values -11.617, -10.599, -10.521, -9.988, respectively. This research investigates Pemetrexed, Leucovorin, Chlordiazepoxide, and Ioversol as potential repurposing agents in the treatment of rheumatoid arthritis (RA) as they are identified as PAD4 inhibitors.

The Puzzle of the Regioselectivity and Molecular Mechanism of the (3+2) Cycloaddition Reaction Between E-2-(Trimethylsilyl)-1-Nitroethene and Arylonitrile N-Oxides: Molecular Electron Density Theory (MEDT) Quantumchemical Study

The regioselectivity and molecular mechanism of the (3+2) cycloaddition reaction between E-2-(trimethylsilyl)-1-nitroethene and arylonitrile N-oxides were explored on the basis of the ωB97XD/6-311+G(d) (PCM) quantumchemical calculations. It was found that the earlier postulate regarding the regioselectivity of the cycloaddition stage should be undermined. Within our research, several aspects of the title reaction were also examined: interactions between reagents, electronic structures of alkenes and nitrile oxides, the nature of transition states, the influence of the polarity solvent on the reaction selectivity and mechanism, substituent effects, etc. The obtained results offer a general conclusion for all of the important aspects of some groups of cycloaddition processes.

Unveiling the pH-Responsive Mechanisms of the Carbon Dot-Proximicin-A Peptide Conjugate for Targeted Cancer Therapy Using Density Functional Theory

This study investigates the pH-responsive dissociation mechanism of carbon dot (CD) conjugated with the anticancer peptide proximicin-A (PROXI) using density functional theory (DFT) simulations. The CD@PROXI system, designed for targeted cancer therapy, releases the drug in acidic environments typical of cancer sites. DFT simulations, with the B3LYP-D3BJ functional and 6-311G (d, p) basis set, optimized the conjugate's geometry under neutral and acidic conditions. The focus was on the pH-sensitive C=N bond, existing in two protonation states. Key parameters evaluated included the HOMO-LUMO gap, bond length, IR spectroscopy, non-covalent interaction (NCI), electron localization function (ELF), density of states (DOSs), and electrostatic potential (ESP). Under neutral pH, the system showed stability with a HOMO-LUMO gap of 3.22 eV, indicating low reactivity. In acidic pH, this gap decreased to 0.40 eV, suggesting higher reactivity and potential for drug release. IR spectroscopy indicated weakened C=N bonds in acidic conditions, with bond length increasing from 1.288 Å to 1.324 Å. NCI analysis revealed increased van der Waals interactions, supporting bond weakening. ELF analysis showed electron localization at reactive sites, while DOS profiles and ESP maps highlighted distinct electronic states and potential dissociation regions in acidic conditions. These findings confirm the potential of CD@PROXI for targeted cancer therapy, with drug release triggered by the acidic tumor microenvironment.

A new coamorphous ethionamide with enhanced solubility: Preparation, characterization, in silico pharmacokinetics, and controlled release by encapsulation

This study reports the synthesis and the experimental-theoretical characterization of a new coamorphous system consisting of ethionamide (ETH) and mandelic acid (MND) as a coformer. The solid dispersion was synthesized using the slow solvent evaporation method in an ethanolic medium. The structural, vibrational, and thermal properties of the system were characterized. Density functional theory (DFT) calculations were performed to analyze the interactions between ETH and MND in the heterodimer. These results contributed to the suitable assignment of infrared (IR) vibrational modes, to determine the chemical reactivity descriptors and the electronic indices of each component of the molecule. Additionally, Hirshfeld surfaces analysis and calculations of absorption, distribution, metabolism, and excretion (ADME) parameters were performed to examine intermolecular interactions and predict the in silico pharmacokinetic profile of the ETH-MND compound and its forming molecules. Powder X-ray diffraction data confirmed the formation of a coamorphous binary system in the 1:2 and 1:3 ETH and MND ratios. Furthermore, the ETH-MND (1:3) solid dispersion remained amorphous for up to 150 days when stored at 38 °C and 75 % relative humidity. DFT calculations, conducted both in vacuum and in ethanol, indicated that the formation of the coamorphous system is driven by hydrogen bonding between the NH2 groups of ETH and the C=O group of MND. Thermodynamic analysis showed that intermolecular interactions are favored in the gas phase, with Gibbs free energy of -3.20 kcal/mol. The IR spectra showed a correlation between experimental and calculated data. Thermal analyses revealed glass transition temperatures of 59 °C (1:2 ratio) and 61 °C (1:3 ratio), indicating thermal stability of the coamorphous materials. Additionally, dissolution tests showed a 3.58-fold increase in the solubility of ETH compared to its crystalline form. The encapsulation of ETH-MND coamorphous systems in sodium alginate spheres via polyelectrolyte complexation was also investigated, demonstrating significant controlled drug release over 480 min.

Advanced Technologies for Large Scale Supply of Marine Drugs

Marine organisms represent a source of unique chemical entities with valuable biomedical potentialities, broad diversity, and complexity. It is essential to ensure a reliable and sustainable supply of marine natural products (MNPs) for their translation into commercial drugs and other valuable products. From a structural point of view and with few exceptions, MNPs of pharmaceutical importance derive from the so-called secondary metabolism of marine organisms. When production strategies rely on marine macroorganisms, harvesting or culturing coupled with extraction procedures frequently remain the only alternative to producing these compounds on an industrial scale. Their supply can often be implemented with laboratory scale cultures for bacterial, fungal, or microalgal sources. However, a diverse approach, combining traditional methods with modern synthetic biology and biosynthesis strategies, must be considered for invertebrate MNPs, as they are usually naturally accumulated in only very small quantities. This review offers a comprehensive examination of various production strategies for MNPs, addressing the challenges related to supply, synthesis, and scalability. It also underscores recent biotechnological advancements that are likely to transform the current industrial-scale manufacturing methods for pharmaceuticals derived from marine sources.

Defining the Synthetic Scope of ortho-Quinone Methides by Quantifying their Electrophilicity

A series of aryl-substituted ortho-quinone methides (oQMs) was synthesised and structurally characterised. Kinetic studies of the nucleophilic additions of carbanions (reference nucleophiles) to oQMs were used to determine second-order rate constants k2 for the carbon-carbon bond forming reactions (20 °C, DMSO) at the oQMs' exocyclic π-bond. Analysing the kinetic data by the linear free energy relationship lg k2=sN(N+E) revealed the Mayr electrophilicities E of the oQMs. The electrophilicities E of oQMs correlate linearly with Hammett substituent constants and experimentally determined reduction potentials Ep red as well as with quantum-chemically calculated methyl anion affinities (MAAs), which provides valuable tools for prediciting the reactivity of further types of oQMs. Embedding the oQMs in Mayr's reactivity scales enables to predict novel nucleophilic reaction partners for oQMs and can productively be used to prepare simple Michael adducts as well as 4+2 or 4+1 cyclisation products as demonstrated in this work by several novel reactions with neutral or negatively charged C-, N-, and S-nucleophiles.

New Benzothiazole-Thiadiazole-Based Ketones as Potential Antiviral and Anticancer Agents: Synthesis, DFT, and Molecular Docking Studies

Various substituted benzothiazole-thiadiazole-based ketones 4a-i and 6a-c were synthesized and characterized by the IR, NMR, and MS spectral data. The DFT study of the synthesized ketones 4 and 6 displayed matched configurations of their HOMO and LUMO, with the exception of the nitrophenyl derivatives, whose HOMO extended over the entire molecule. Meanwhile, the antiproliferative effectiveness of the produced ketones was evaluated against diverse cell lines and compared with the reference drug Erlotinib. The ketones exhibited variable inhibitory effects, for example, the ketone 6a has the most potent activity versus Panc-1 (IC50 = 9.34 ± 0.18 μM), whereas 4i showed proper effectiveness against HepG2 (IC50 = 10.91 ± 0.23 μM), and ketone 4a exhibited strong activity against MCF-7 cells (IC50 = 5.66 ± 0.16 μM). Moreover, the H5N1 antiviral efficacy was assessed via a plaque reduction assay, using amantadine as a reference drug. Ketones 2a, 4e, and 4g displayed 100% inhibition, while ketone 4e has the lowest toxic concentration (TC50 61 μg/μL). Furthermore, the molecular docking results revealed that ketone 4e had the highest binding score owing to several interactions with amino acids of 1JU6 residues. Finally, SwissADME analysis of the synthesized ketones provides key insights into their pharmacokinetic properties.

Intelligent consensus-based predictions of early life stage toxicity in fish tested in compliance with OECD Test Guideline 210

Early life stage (ELS) toxicity testing in fish is a crucial test procedure used to evaluate the long-term effects of a wide range of chemicals, including pesticides, industrial chemicals, pharmaceuticals, and food additives. This test is particularly important for screening and prioritizing thousands of chemicals under the Registration, Evaluation, Authorization, and Restriction of Chemicals (REACH) regulation. In silico methods can be used to estimate the toxicity of a chemical when no experimental data is available and to reduce the cost, time, and resources involved in the experimentation process. In the present study, we developed predictive Quantitative Structure-Activity Relationship (QSAR) models to assess chronic effects of chemicals on ELS in fish. Toxicity data for ELS in fish was collected from two different sources, i.e. J-CHECK and eChemPortal, which contain robust study summaries of experimental studies performed according to OECD Test Guideline 210. The collected data included two types of endpoints - the No Observed Effect Concentration (NOEC) and the Lowest Observed Effect Concentration (LOEC), which were utilized to develop the QSAR models. Six different partial least squares (PLS) models with various descriptor combinations were created for both endpoints. These models were then employed for intelligent consensus-based prediction to enhance predictability for unknown chemicals. Among these models, the consensus model - 3 (Q2F1 = 0.71, Q2F2 = 0.71) and individual model - 3 (Q2F1 = 0.80, Q2F2 = 0.79) exhibited most promising results for both the NOEC and LOEC endpoints. Furthermore, these models were validated experimentally using experimental data from nine different industrial chemicals provided by Global Product Compliance (Europe) AB. Lastly, the models were used to screen and prioritize chemicals obtained from the Pesticide Properties (PPDB) and DrugBank databases.

Combined Graphene Oxide with 2-Methoxyestradiol for Effective Anticancer Therapy in-vitro Model

Introduction

This article describes the invention of graphene oxide (GO) or reduced graphene oxide (rGO) functionalised with 2-methoxy estradiol. The presence of polar hydroxyl groups enables the binding of 2-ME to GO/rGO through hydrogen bonds with epoxy and hydroxyl groups located on the surface and carbonyl and carboxyl groups located at the edges of graphene flake sheets.

Methods

The patented method of producing the subject of the invention and the research results regarding its anticancer effectiveness via cytotoxicity in an in vivo model (against A375 melanoma and 143B osteosarcoma cells) are described.

Results

It was shown that the inhibition of PTP1B phosphotyrosine phosphatase is one of the mechanisms of action of GO functionalised with 2-ME (GO-2-ME). This is a very important result, considering the fact that 2-ME itself has no inhibitory properties against this phosphatase.

Discussion

Graphene oxide flakes embroidered with 2-methoxyestradiol molecules may be a promising solution, bringing a new and important effect in the form of improving the bioavailability of the therapeutic substance, ie 2-ME. An appropriate dosage of GO-2-ME/rGO-2-ME, in which GO/rGO is a carrier of 2-methoxyestradiol (2-ME), can ensure effective penetration of the active substance through biological boundaries/membranes and controlled modification of cell signalling, ultimately leading to the selective elimination of malignant cells.

DFT Investigation of the Stereoselectivity of the Lewis-Acid-Catalyzed Diels-Alder Reaction between 2,5-Dimethylfuran and Acrolein

Density functional theory (DFT) has been enacted to study the Diels-Alder reaction between 2,5-dimethylfuran (2,5-DMF), a direct product of biomass transformation, and acrolein and to analyze its thermodynamics, kinetics, and mechanism when catalyzed by a Lewis acid (LA), in comparison to the uncatalyzed reaction. The uncatalyzed reaction occurs via a typical one-step asynchronous process, corresponding to a normal electron demand (NED) mechanism, where acrolein is an electrophile whereas 2,5-DMF is a nucleophile. The small endo selectivity in solvents of low dielectric constants is replaced by a small exo selectivity in solvents with larger dielectric constants, such as DMSO. In the catalyzed process, the LA interacts with acrolein, forming a O-LA coordinating bond, that enhances its electron-acceptor character, further favoring the NED mechanism and reducing the activation energy. When AlCl3 and GaCl3 catalyze the reaction, the bond formations of both the endo and exo pathways occur via a two-step asynchronous process. Thus, these processes involve the formation of two transition states and a stable intermediate. The second transition state is the critical one and it dictates the increase of the exo selectivity, in comparison to the uncatalyzed reaction. The DFT calculations have also unraveled that the LA plays additional roles, i.e. it forms stable complexes with the carbonyl group of acrolein while AlCl3 and GaCl3 form dimers, which also impact the different equilibria.

Plasmepsin II inhibitory potential of phytochemicals isolated from African antimalarial plants: a computational approach

Plamepsin II has been identified as a therapeutic target in the Plasmodium falciparum's life cycle and may lead to a drastic reduction in deaths caused by malaria worldwide. Africa flora is rich in medicinal qualities and possesses both simple and complex bioactive phytochemicals. This study utilized computational approaches like molecular docking, molecular dynamics simulation, quantum chemical calculations and ADMET to evaluate the plasmepsin II inhibitory properties of phytochemicals isolated from African antimalarial plants. Molecular docking was carried out to estimate the binding affinity of 229 phytochemicals whereby ekeberin A, dichamanetin, 10-hydroxyusambaresine, chamuvaritin and diuvaretin were selected. Further, RMSD and RMSF plots from the 100 ns simulation results showed that the screened phytochemicals were stable in the enzyme's binding pocket. The quantum chemical calculation revealed that all the phytochemicals are strong electrophiles, while ekeberin A was identified as the most stable and dichamanetin as the most reactive. Also, ADMET studies established the drug candidacy of the phytochemicals. Thus, these phytochemicals could act as good antimalarial agents after extensive in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.

Mechanistic Aspects of [3+2] Cycloaddition Reaction of Trifluoroacetonitrile with Diarylnitrilimines in Light of Molecular Electron Density Theory Quantum Chemical Study

In this study, we investigated the [3+2] cycloaddition reaction of CF3CN (TFAN) with nitrilimine (NI) to produce 1,2,4-triazole and compared the resulting isomers. We determined the preferred reaction pathway by examining the electrophilic and nucleophilic properties of the reaction substrates, performing thermodynamic calculations for the individual pathways, and comparing them with the experimental results.

Gallic Acid: A Potent Metabolite Targeting Shikimate Kinase in Acinetobacter baumannii

Background/Objectives:Acinetobacter baumannii is a highly multidrug-resistant pathogen resistant to almost all classes of antibiotics; new therapeutic strategies against this infectious agent are urgently needed. Shikimate kinase is an enzyme belonging to the shikimate pathway and has become a potential target for drug development. This work describes the search for Food and Drug Administration (FDA)-approved drugs and natural compounds, including gallic acid, that could be repurposed as selective shikimate kinase inhibitors by integrated computational and experimental approaches. Methods: Approaches to drug design using structure-based and ligand-based methodology, in-silico screening, molecular docking, and molecular dynamics for the study of both binding affinity and stability. Experimental Validation Determination of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) on Acinetobacter baumannii and Enterococcus faecalis. Results/Conclusions: Among them, gallic acid, obtained from plants, proved to be the most promising compound that showed sufficient binding with shikimate kinase through computational studies. Gallic acid showed very good activity against Acinetobacter baumannii and Enterococcus faecalis in the MIC and MBC assay, respectively. Gallic acid exhibited better activity against Acinetobacter baumannii due to the overexpression of shikimate kinase. Gallic acid has emerged as a potential therapeutic candidate drug against A. baumannii infection and, therefore, as a strategy against the appearance of multidrug-resistant microorganisms. This study not only identifies a novel repurposing opportunity for gallic acid but also provides a comprehensive computational and experimental framework for accelerating antimicrobial drug discovery against multidrug-resistant pathogens.

DFT study on the mechanism of phosphine-catalyzed ring-opening reaction of cyclopropyl ketones

In the present study, the mechanism, origin of chemoselectivity, and substituent effects of the phosphine-catalyzed ring-opening reaction of cyclopropyl ketone have been investigated using the DFT method. Multiple pathways, including the formation of hydrofluorenone, the Cloke-Wilson product, and cyclopenta-fused product, were studied and compared. The computational results show that the pathway for the formation of hydrofluorenone is the most favorable one, which involves four processes: nucleophilic substitution to open the three-membered ring, an intramolecular Michael addition for the formation of an enolate intermediate, an intramolecular [1,5]-proton transfer to give ylide, and an intramolecular Wittig reaction to deliver the final product. For disclosing the origin of chemoselectivity, structural analysis and local reactivity index analysis were performed. Moreover, substituent effects were also considered using QTAIM analysis. The current study would provide useful insights for understanding phosphine-catalyzed chemoselective reactions.

Gaining molecular insights towards inhibition of foodborne fungi Aspergillus fumigatus by a food colourant violacein via computational approach

Filamentous Fungal Human Pathogens (FFHPs) such as Aspergillus fumigatus, are growing resistant to currently available antifungal drugs. One possible target, the Nucleoside diphosphate kinase (Ndk) is significant for nucleotide biosynthesis and crucial for fungal metabolism. Violacein, a natural food colorant, was examined for its antifungal effects against Aspergillus fumigatus via computational approach against the Ndk protein. Known and predicted interactions of Ndk with proteins was performed using the STRING application. Molecular docking was performed using Schrodinger Maestro software (V.14.1) under enhanced precision docking, with OPLS4 forcefield. MDS was performed for 500ns under OPLS4 forcefield and the TIP3P solvent system. The geometry optimization for DFT was performed using the Becke 3-parameter exchange functional (B3LYP) method. The Molecular Docking Studies revealed significant interactions with good binding energy between Violacein and Ndk. Subsequent MD Simulations confirmed the stability of Violacein-Ndk complex, compared to the reference ligand-complex, indicating a stable interaction between the protein and violacein. The energy band gap of violacein was found to be 0.072567 eV suggesting its softness with lower kinetic stability and higher chemical reactivity. The results suggest Violacein could potentially disrupt nucleotide metabolism by targeting Ndk, thus demonstrating antifungal activity. However, further experimental validation is required to confirm these computational findings and explore the practical use of Violacein in antifungal treatments.

In silico exploration of phytochemicals as inhibitors for acute myeloid leukemia by targeting LIN28A gene: A cheminformatics study

BACKGROUND

Recent discoveries have illustrated that Lin28A is an oncogene in various cancers, particularly acute myeloid leukemia (AML). The upregulation of Lin28A can actively contribute to tumorigenesis and migration processes in multiple organs. Hence, the inhibition of Lin28A can be achieved by applying phytochemical herbals and targeting Lin28A protein using a computer-aided drug design (CAAD) approach.

METHODS

In this study, we comprehensively applied several bioinformatics tools, including gene ontologies, gene enrichment analysis, and protein-protein interactions (PPI), to determine the biological pathways, functional gene ontology, and biological pathway. Furthermore, we investigated a list of phytochemical herbs as a candidate drug by applying a computation technique involving molecular docking, density functional theory (DFT), molecular dynamics simulation (MDs), and pharmacokinetic and physiochemical properties by applying the SwissADME, pkCSM, and Molsoft LLC web-servers.

RESULTS

The Lin28A gene is related to two significant enrichment pathways, including proteoglycans in cancer and the pluripotency of stem cells through interactions with different genes such as MAPK12, MYC, MTOR, and PIK3CA. Interestingly, limonin, 18β Glycyrrhetic Acid, and baicalein have the highest binding energy scores of -8.4, -8.2, and -7.3 kcal/mol, respectively. The DFT study revealed that baicalein has a higher reactivity than limonin and 18β-Glycyrrhetic due to a small energy gap between LUMO and HUMO. Molecular dynamics simulation exhibited that baicalein complex with Lin28A protein is more stable than other complexes during simulation time due to low fluctuation with simulation periods as compared with other complexes, which indicated that baicalein was more fitting to docking and combining in the protein cave because of the largest number of H-bonds available for the docking simulation process. Furthermore, the drug-likeness and ADMET profiles revealed the activity of limonin, baicalein, and 18β-glycyrrhizic Acid, which possess significant inhibiting Lin28A proteins.

CONCLUSION

This study elucidated that baicalein, 18β-glycyrrhizic, and limonin may be applied as potential candidates for targeting Lin28A as an active oncogene for acute myeloid leukemia.

Azocarboxamide-enabled enantioselective regiodivergent unsymmetrical 1,2-diaminations

Enantioenriched unsymmetrical vicinal diamines are important basic structural motifs. While catalytic asymmetric intermolecular 1,2-diamination of carbon-carbon double bonds represents the most straightforward approach for preparing enantioenriched vicinal-diamine-containing heterocycles, these reactions are often limited to the installation of undifferentiated amino functionalities through metal catalysis and/or the use of stoichiometric amounts of oxidants. Here, we report organocatalytic enantioselective unsymmetrical 1,2-diaminations based on the rational design of a bifunctional 1,2-diamination reagent, namely, azocarboxamides (ACAs). Under the catalysis of chiral phosphoric acid, unsymmetrical 1,2-diaminations of ACAs with various electron-rich double bonds readily occur in a regiodivergent manner. Indoles prefer dual hydrogen-bonding mode to give dearomative (4 + 2) products, and 3-vinylindoles and azlactones are inclined to undergo unsymmetrical 1,2-diamination via the (3 + 2) process. DFT calculations are performed to reveal the reaction mechanism and the origin of the regio- and enantioselectivity. Guided by computational design, we are able to reverse the regioselectivity of the dearomative unsymmetrical 1,2-diamination of indoles using Lewis acid catalysis.

Theoretical investigations of some isolated compounds from Calophyllum flavoramulum as potential antioxidant agents and inhibitors of AGEs

In this paper, we have attempted a theoretical calculation of some plant-isolated compounds as potential inhibitors of oxidative stress and Advanced Glycation Endproducts (AGEs). Herein, theoretical reactivity indices based on the CDFT theory were computed to explore the reactivity of five isolated products from Calophyllum flavoramulum. Global reactivity indices based on HOMO and LUMO energy such as electronic chemical potential, hardness, electrophilicity and the local reactivity descriptors Parr function, molecular electrostatic potentials(MEP), electrostatic potential (ESP) and thermodynamic parameters for the studied compounds are computed and discussed using DFT method and two functionals B3LYP and CAM-B3LYP with 6-31 G(d,p) basis set. The free radical scavenging activity mechanisms (HAT, SET-PT, and SPLET) of some of the isolated products with DPPH are also presented in this work. SET-PT mechanism of the antiradical activity is found to be thermodynamically favorable. Furthermore, a molecular docking study with RAGE receptor and AtGSTF2 enzyme was conducted, in which flavonoids 4 and 5 show a low binding affinity with -8.42 and -10.49 kcal/mol for RAGE, -8.67 and -9.00 kcal/mol for AtGSTF2. After the encouraging outcomes from the molecular docking study, the 4-AtGSTF2 and 5-RAGE complex were subjected to 200 ns molecular dynamics simulation using Desmond, where both studied systems exhibited remarkable stability throughout the 200 ns simulations. Also, the MM-GBSA method was measured by calculating the binding free energy using the individual energy components. Finally, the ADMET predictions were assessed to anticipate the behavior of a drug candidate within the human body.

Innovative application of green surfactants as eco-friendly scale inhibitors in industrial water systems

Scale deposition poses significant challenges in various industrial utilities, necessitating the development of eco-friendly scale inhibitors in line with environmental regulations. This study investigates the potential of two natural surfactants, Casein and Rhamnolipid, as innovative inhibitors for calcium carbonate (CaCO3) scale formation, offering an alternative to traditional water treatment chemicals. The anti-scaling characteristics of these two green surfactants were performed using conductivity and electrochemical impedance spectroscopy (EIS) techniques. Additionally, X-ray diffraction (XRD) and scanning electron microscopy (SEM) were utilized to analyze the morphology of CaCO3 crystals and understand the structural changes induced by surfactant interaction. The results revealed that Rhamnolipids significantly outperform Casein in suppressing scale formation, attributed to the adsorption of their multiple functional groups onto scale microcrystals. This adsorption modifies the crystal structure and inhibits further growth. Computational studies were employed to investigate the inhibition mechanism of these surfactants. The spatial and electrical configurations of optimal molecular structures are also analyzed using the Density Functional Theory (DFT) approach. Monte Carlo simulations on the CaCO3 (104) surface demonstrated that Rhamnolipids exhibit superior inhibition compared to Casein, as evidenced by their higher adsorption energy, indicating a more stable binding to the surface. Overall, this research highlights the potential of these natural surfactants as sustainable scale inhibitors, particularly in industries such as food and pharmaceuticals, thereby contributing to environmentally friendly water treatment solutions.

Utilizing MEDT analysis of [3 + 2] cycloaddition reaction: x-ray crystallography of spirooxindole linked with thiophene/furan heterocycles and triazole framework

Hybridization of spirooxindole with different pharmacophores such as triazole and heterocycle such as thiophene and furan moiety was achieved by the [3 + 2] cycloaddition (32CA) reaction approach. Structural investigations of the compounds 4a and 4b were performed using X-ray single crystal structure determinations and Hirshfeld analysis. Both compounds crystallized in monoclinic crystal system. The space group is P21/c for 4a and P21/n for 4b. The crystal parameters are a = 10.2619(3) Å, b = 13.6776(3) Å, c = 10.9318(3), β = 116.640(4)° for the former while a = 13.0012(1) Å, b = 14.9692(1) Å, c = 14.1178(1) Å, β = 97.101(1)° for the latter. In both compounds, the aryl group and the triazole moieties are twisted from one another. The twist angle is 84.75˚for 4a while 86.64˚ for 4b. Based on Hirshfeld calculations, the Cl…H, O…H, N…H and C…H non-covalent interactions in 4a while the O…H interactions in 4b are the most important. The molecular mechanism of the key 32CA reaction between the in situ generated azomethine ylides and the corresponding chalcones has been studied within the Molecular Electron Density Theory (MEDT). The MEDT study reveals that the low activation energies and high experimental selectivity are the result of the supernucleophilic character of the ylides and the strong electrophilicity of the chalcones, which favour the process through a high polar character. This high polar character accounts for the total endo selectivity experimentally found.

DFT investigation of the mechanism and role of N-heterocyclic carbene (NHC) in constructing asymmetric organosilanes using NHC-catalyzed [4+2] cycloaddition reaction

Herein, the mechanism and origin of stereoselectivity for the asymmetric [4+2] cycloaddition between (E)-3-(p-tolyl)acrylaldehyde (R1) and phenyl-3-(trimethylsilyl)prop-2-en-1-one (R2) in the presence of an N-heterocyclic carbene (NHC) were theoretically scrutinized. The desirable catalytic cycle is characterized by five steps: (1) the coupling reaction of the NHC catalyst with R1, the formation of the Breslow and enolate intermediates in the second and third steps, (4) the formal [4+2] cycloaddition reaction to form the stereoselective C-C bond, and (5) the regeneration of NHC to obtain asymmetric organosilanes. In the most energetically favorable pathway, the formation of the enolate intermediate exhibits the highest energy barrier of about 19.48 kcal mol-1 (Re-TS2BA) and is the rate-determining step. The [4+2] cycloaddition reaction is the stereoselectivity-determining step forming the chiral C-C bond with RR, RS, SR and SS configurations, among which RS is the most desirable configuration. The origin of stereoselectivity was investigated using distortion energy analysis. The first and fourth steps helped in investigating the effects of electron-donating (Me) and electron-withdrawing (Cl) groups on cinnamaldehyde. Conceptual DFT (CDFT) analysis was carried out to confirm the critical role of the NHC catalyst as a Lewis base during the reaction processes.

Insights into the mechanism, selectivity, and substituent effects in the Diels-Alder reaction of azatrienes with electron-rich dienophiles: An MEDT study

The reactivity and mechanistic intricacies of azatrienes in Diels-Alder reactions have been relatively unexplored despite their intriguing potential applications. In this study, we employ Molecular Electron Density Theory to theoretically investigate the hetero-Diels-Alder reaction involving azatrienes with ethyl vinyl ether and allenyl methyl ether. Analysis of Conceptual Density Functional Theory, energetic profiles, and the topological characteristics is conducted to elucidate the reactions. The revealed mechanism manifests as a polar one-step two-stages process under kinetic control. We establish a clear relationship of between the periselectivity, regioselectivity, and stereoselectivity on one hand and the characteristics of the reactions mechanism on the other hand. The influence of weak interactions on reaction activation barriers and bonding evolution are discussed in detail. We demonstrate that substituents enhancing the reverse electron density flux facilitate the feasibility of the reactions. The results lay ground for a meticulous control of the reaction of azatriene in similar synthetic scenarios.

An MEDT Study of the Reaction Mechanism and Selectivity of the Hetero-Diels-Alder Reaction Between 3-Methylene-2,4-Chromandione and Methyl Vinyl Ether

The hetero-Diels-Alder (HDA) reaction between the ambident heterodiene 3-methylene-2,4-chromandione (MCDO) and non-symmetric methyl vinyl ether (MVE) is investigated using the molecular electron density theory (MEDT) at the B3LYP/6-311G(d,p) computational level. The aim of this study is to gain insight into its molecular mechanism and to elucidate the factors that control the selectivity found experimentally. DFT-based reactivity indices reveal that MCDO exhibits strong electrophilic characteristics, while MVE displays a strong nucleophilic character. Meanwhile, the Parr function explains the ortho regioselectivity of this HDA reaction. The highly polar nature of this HDA reaction, supported by the high global electron density transfer (GEDT) taking place at the transition state structures (TSs), accounts for the very low activation energy associated with the most favorable TS-4on. The ambident nature of MCDO allows for the formation of two constitutional isomeric cycloadducts. In the case of MVE, pseudocyclic selectivity is attained using a thermodynamic control. This polar HDA reaction displays an endo stereoselectivity and a complete ortho regioselectivity. A comparative relative interacting atomic energy (RIAE) analysis of the two diastereomeric structures TS-4on and TS-6on indicates a high degree of likeness, which explains the low pseudocyclic selectivity under kinetic control.

Unexpected Course of Reaction Between (1E,3E)-1,4-Dinitro-1,3-butadiene and N-Methyl Azomethine Ylide-A Comprehensive Experimental and Quantum-Chemical Study

In recent times, interest in the chemistry of conjugated nitrodienes is still significantly increasing. In particular, the application of these compounds as building blocks to obtain heterocycles is a popular object of research. Therefore, in continuation of our research devoted to the topic of conjugated nitrodienes, experimental and quantum-chemical studies of a cycloaddition reaction between (1E,3E)-1,4-dinitro-1,3-butadiene and N-methyl azomethine ylide have been investigated. The computational results present that the tested reaction is realized through a pdr-type polar mechanism. In turn, the experimental study shows that in a course of this cycloaddition, only one reaction product in the form of 1-methyl-3-(trans-2-nitrovinyl)-Δ3-pyrroline is created. The constitution of this compound has been confirmed via spectroscopic methods. Finally, ADME analysis indicated that the synthesized Δ3-pyrroline exhibits biological potential, and it is a good drug candidate according to Lipinski, Veber and Egan rules. Nevertheless, PASS simulation showed that the compound exhibits weak antimicrobial, inhibitory and antagonist properties. Preliminary in silico research shows that although the obtained Δ3-pyrroline is not a good candidate for a drug, the presence of a nitrovinyl moiety in its structure indicates that the compound is an initial basis for further modifications.

Molecular modelling and antimicrobial activity of newly synthesized benzothiazolo[3,2-a]pyrimidine clubbed thiazole derivatives

A series of benzothiazolopyrimidine-thiazole conjugates 7, 8, and 9 were produced through the reactions of 8-acetylbenzothiazolopyrimidine-thiosemicarbazone compound 6 with chloroacetone, (un)substituted phenacyl chlorides, and ethyl chloroacetate, respectively. Based on DFT study, the synthesized conjugates had a twisted shape, except for the parent benzothiazolopyrimidine 5 and its thiosemicarbazone compound 6, which were flat. The study of FMO's also showed that the substituted thiazole derivatives 7 and 8a-c have equivalent configurations of HOMO and LUMO, as well as exhibiting the least FMO's gap (ΔEH-L). The antimicrobic activeness of the constructed derivatives has been assessed against the two Gram's types of bacteria and fungi using the broth microdilution method. The benzothiazolopyrimidine-thiazole conjugate 8c exhibited the strongest inhibition towards Gram-negative E. coli (MIC <29 μg/mL), while a valuable performance was observed towards S. typhimurium (MIC <132 μg/mL). Also, it displayed broad-spectrum activity with the least MIC versus C. albicans fungi (<207 μg/mL). In contrast, the conjugate 8b demonstrated selective efficacy against Gram + ve S. aureus and B. subtilis bacteria (MIC <40 and < 47 μg/mL, respectively). Besides, molecular docking of these benzothiazolopyrimidine derivatives with the PDB: 2XCT protein carried out to discover their binding types, RMSD, binding scores, and interactions pocket for each derivative, including a drug reference. Furthermore, their physicochemical-pharmacokinetic profile has estimated via the SwissADME prediction. The data indicated that derivative 5 demonstrated constructive pharmacokinetics (M. Wt. 269.28), lipophilicity (Log Po/w = 1.45), and TPSA = 103.47, which foretold high (GI) absorption and good bioavailability = 0.55 without interrupting Lipinski's rules.

Syn-Propanethial S-Oxide as an Available Natural Building Block for the Preparation of Nitro-Functionalized, Sulfur-Containing Five-Membered Heterocycles: An MEDT Study

The regio- and stereoselectivity and the molecular mechanisms of the [3 + 2] cycloaddition reactions between Syn-propanethial S-oxide and selected conjugated nitroalkenes were explored theoretically in the framework of the Molecular Electron Density Theory. It was found that cycloadditions with the participation of nitroethene as well as its methyl- and chloro-substituted analogs can be realized via a single-step mechanism. On the other hand, [3 + 2] cycloaddition reactions between Syn-propanethial S-oxide and 1,1-dinitroethene can proceed according to a stepwise mechanism with a zwitterionic intermediate. Finally, we evaluated the affinity of model reaction products for several target proteins: cytochrome P450 14α-sterol demethylase CYP51 (RSCB Database PDB ID: 1EA1), metalloproteinase gelatinase B (MMP-9; PDB ID: 4XCT), and the inhibitors of cyclooxygenase COX-1 (PDB:3KK6) and COX-2 (PDB:5KIR).

A New Insight into the Molecular Mechanism of the Reaction between 2-Methoxyfuran and Ethyl (Z)-3-phenyl-2-nitroprop-2-enoate: An Molecular Electron Density Theory (MEDT) Computational Study

The molecular mechanism of the reaction between 2-methoxyfuran and ethyl (Z)-3-phenyl-2-nitroprop-2-enoate was investigated using wb97xd/6-311+G(d,p)(PCM) quantum chemical calculations. It was found that the most probable reaction mechanism is fundamentally different from what was previously postulated. In particular, six possible zwitterionic intermediates were detected on the reaction pathway. Their formation is determined by the nature of local nucleophile/electrophile interactions. Additionally, the channel involving the formation of the exo-nitro Diels-Alder cycloadduct was completely ruled out. Finally, the electronic nature of the five- and six-membered nitronates as potential TACs was evaluated.

Synthesis, theoretical analysis, and biological properties of a novel tridentate Schiff base palladium (II) complex

Schiff base complexes play a crucial role in bioinorganic chemistry. A novel curcumin/phenylalanine tridentate Schiff base ligand and its palladium (II) complex were synthesized so that they were stable in aqueous buffer. The structure of the complex was investigated using a variety of methods, including DFT, NBO analysis, FMOs, and MESP. The interaction of the complex with a plasmid (pUC19) and CT-DNA was studied. The anticancer, antibacterial, and antioxidant activities of the complex were examined. The statistical analysis of the MTT assay was compared using the 1-way ANOVA and Tukey test. Results showed that the complexes were stable in aqueous buffer, pH 8. The extrinsic fluorescence emission of the plasmid and CT-DNA was quenched while interacting with the complex. The complex had an IC50 of 72.47 µM against MCF-7 cells. The ANOVA and Tukey analysis of MTT data demonstrated a statistically significant difference between groups (P < 0.0001). The minimum inhibitory concentrations (MIC) of the complex for E. coli and S. aureus were 300 and 200 µg/mL, with 96.3 and 95.2% biofilm growth inhibition at 250 µg/mL, respectively. The sample concentrations contributing to 50% radical inhibition in the 1,1-diphenyl-2-picrylhydrazyl (DPPH) test for curcumin, ligand, and palladium (II) complex were 33.62, 21.27, and 51.26 µM, respectively. The results suggest that the complex interaction with DNA is one of the potential mechanisms for eliminating cancer cells and bacteria in the planktonic and biofilm. On the other hand, while stability in an aqueous buffer at pH 8 increases, the modified curcumin antioxidant effect decreases.

From farm to pharma: Investigation of the therapeutic potential of the dietary plants Apium graveolens L., Coriandrum sativum, and Mentha longifolia, as AhR modulators for Immunotherapy

Autoimmune diseases represent a complex array of conditions where the body's immune system mistakenly attacks its own tissues. These disorders, affecting millions worldwide, encompass a broad spectrum of conditions ranging from rheumatoid arthritis and multiple sclerosis to lupus and type 1 diabetes. The Aryl hydrocarbon receptor (AhR) translocator, expressed across immune and other cell types, plays crucial roles in immune disorders and inflammatory diseases. With a realm towards natural remedies in modern medicine for disease prevention, this study investigates the electronic properties and behaviors of bioactive compounds from dietary sources, including Apium graveolens L. (Celery), Coriandrum sativum seeds (Coriander), and Mentha longifolia, as AhR modulators. Through comprehensive analysis (HOMO-LUMO, ESP, LOL, and ELF), electron-rich and -poor regions, electron localization, and delocalization are identified, contrasting these compounds with the toxic AhR ligand, TCDD. Evaluation of Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties reveals favorable pharmacokinetics without blood-brain barrier penetration, indicating drug-like characteristics. Molecular docking demonstrates stronger interactions of dietary flavonoid ligands with AhR transcription compared to TCDD. Molecular dynamics simulations confirm the stability of complexes and the sustainability of interactions formed. This research underscores the potential of natural compounds as effective AhR modulators for therapeutic interventions in immune-related disorders.

Investigating the electronic properties of edge glycine/biopolymer/graphene quantum dots

This study systematically investigated four types of graphene quantum dots (GQDs) AHEX, ZTRI, ZHEX, and ATRI, and their interactions with glycine to form GQD-glycine complexes. Utilizing density functional theory (DFT) and the PM6 semiempirical method, the study analyzed electronic properties and structure-activity relationships. Global reactivity indices were calculated using Koopmans' theorem, and quantitative structure-activity relationship (QSAR) parameters were assessed via SCIGRESS 0.3. The study further explored interactions using density of states (DOS) and quantum theory of atoms in molecules (QTAIM) analyses. Key findings revealed that glycine interaction significantly increased the total dipole moment (TDM) and decreased the HOMO/LUMO energy gap (ΔE) for the GQD-glycine complexes. Notably, ZTRI/glycine showed a TDM of 4.535 Debye and a reduced ΔE of 0.323 eV, indicating enhanced reactivity. Further interactions with cellulose, chitosan, and sodium alginate identified the ZTRI/glycine/sodium alginate composite as the most reactive, with a TDM of 8.020 Debye and the lowest ΔE of 0.200 eV. This composite also exhibited the highest electrophilicity index (56.421) and lowest chemical hardness (0.145 eV), underscoring its superior reactivity and stability. DOS analysis revealed that biomolecules contributed the most to molecular orbitals, with carbon atoms contributing the least. QTAIM analysis confirmed the greater stability of the ZTRI/glycine/sodium alginate complex compared to other studied composites. These results highlight the enhanced reactivity and stability of GQDs when interacting with glycine and sodium alginate.