Computational Study Research Articles

Synthesis of β-lactams and transformation to β-amino acid ethyl ester derivatives: Theoretical calculations

Because of the important biological properties of β-amino acids in the present work, two new β-amino acid ethyl ester derivatives were synthesized, and their mechanistic occurrence was investigated. The title compounds were synthesized from related tetralone derivatives containing bromine and methoxy groups. Tetralone derivatives were reduced to their benzyl alcohol derivatives with NaBH4, followed by elimination with p-toluenesulfonic acid (pTSA) to give the desired 1,2-dihydronaphthalene derivatives. The reactions of 1,2-dihydronaphthalenes with chlorosulfonyl isocyanate (CSI) afforded β-lactams. β-Amino acids were obtained from the reaction of β-lactams with EtOH in HCl. Computational studies are concerned with synthesizing four-membered lactams (β-lactam) formed by the reaction between 1,2-dihydronaphthalene derivatives and CSI. The mechanism of the formation of compounds has been elucidated using DFT at M06-2X.

Transition metals tailoring of phosphorus-doped gallium nitride nanotubes as sensors for N-butenyl homoserine lactone (BHL): A computational study

This investigation is focused on the impact of transition metals (Ag, Au, and Cu) encapsulations of phosphorus-doped gallium nitride nanotubes (P@GaNNTs) to achieve precise detection and sensing of N-Butenyl homoserine lactone (BHL), which is a biomarker for urinary tract infection, within the framework of density functional theory (DFT) computation at the B3LYP-D3(BJ)/def2SVP method. Adsorption studies unveil the adsorption energies for BHL detection across the systems, with BHL_Cu_P@GaNNT displaying the most favorable adsorption energy of −1.79247 eV and BSSE correction (−1.7685 eV). Additionally, sensor mechanisms are elucidated through Fermi energy level (EFL) calculations, revealing distinct values of 4.748, 4.242, 5.052, and 3.864 for BHL_Ag_P@GaNNT, BHL_Au_P@GaNNT, BHL_Cu_P@GaNNT, and BHL_P@GaNNT, respectively. These values signify variances in charge transfer dynamics upon BHL interaction. In essence, this study lays the foundation for the development of highly efficient biosensors with exceptional biomarker detection capabilities, particularly in the context of urinary tract infections (UTIs). It opens new avenues in the realm of biosensing technology, promising innovative solutions for healthcare and diagnostics.

Computer Vision Foundation Models in Endoscopy: Proof of Concept in Oropharyngeal Cancer.

To evaluate the performance of vision transformer-derived image embeddings for distinguishing between normal and neoplastic tissues in the oropharynx and to investigate the potential of computer vision (CV) foundation models in medical imaging. Computational study using endoscopic frames with a focus on the application of a self-supervised vision transformer model (DINOv2) for tissue classification. High-definition endoscopic images were used to extract image patches that were then normalized and processed using the DINOv2 model to obtain embeddings. These embeddings served as input for a standard support vector machine (SVM) to classify the tissues as neoplastic or normal. The model's discriminative performance was validated using an 80-20 train-validation split. From 38 endoscopic NBI videos, 327 image patches were analyzed. The classification results in the validation cohort demonstrated high accuracy (92%) and precision (89%), with a perfect recall (100%) and an F1-score of 94%. The receiver operating characteristic (ROC) curve yielded an area under the curve (AUC) of 0.96. The use of large vision model-derived embeddings effectively differentiated between neoplastic and normal oropharyngeal tissues. This study supports the feasibility of employing CV foundation models like DINOv2 in the endoscopic evaluation of mucosal lesions, potentially augmenting diagnostic precision in Otorhinolaryngology. 4 Laryngoscope, 134:4535-4541, 2024.

Computational and experimental investigation on functional monomer selection for a novel molecularly imprinting polymer of remdesivir

Molecularly-imprinted polymers (MIPs) are a sample preparation technique with a functional cavity that can rebind the same or similar analyte to the template. It also can increase the selectivity of the analytical method. Computational approaches are capable of making predictions about the most optimal synthesis conditions, including the most appropriate monomers and solvents. This study used the DFT method, GFN2-xTB, and molecular dynamics simulation to predict MIP synthesis’s best functional monomer, solvent, and stoichiometric ratio. Remdesivir (RMD), used as a template, has also never been developed to be made as MIP. The monomers were acrylic acid (AA), 2-hydroxyethyl methacrylate (HEMA), and acrylamide (AM). Laboratory testing, association constant, and Job plot analysis are carried out to confirm the results of computational tests. The polymer was synthesized using precipitation and characterized using SEM, FTIR, and TGA. The adsorption capacity was evaluated in two different solvents, i.e. acetonitrile (ACN) and water: ACN=9: 1 (v/v). Computational study results identified acrylamide as the most interactive ligand with RMD as a template. The results of molecular dynamics simulations identify that the RMD: AM=1: 1 complex is the most stable in terms of the radial distribution function, hydrogen bond occupancy, and Gibbs bond free energy. The adsorption ability test results show that MIP 1 and MIP 2 have imprinting factor values of 1.36 and 1.15, respectively.

Resonance‐Assisted Self‐Doping in Robust Open‐Shell Ladder‐Type Oligoaniline Analogues

AbstractA novel resonance‐assisted self‐doping mechanism has been demonstrated in ladder‐type oligoaniline‐derived organic conductors. The new class of compounds has a unique structure incorporating acidic phenolic hydroxyl groups into the ladder‐type cyclohexadiene‐1,4‐diimine core, enabling efficient resonance‐assisted proton transfer and electronic doping without the need for external dopants. Mechanistic and computational studies confirm the open‐shell, zwitterionic nature of the self‐doped state and the significant role played by the dielectric environment. This new self‐doping mechanism allows for higher stability and durability in the material‘s electronic performance. The self‐doped form retains durability under harsh conditions and maintains its properties over extended periods of time.

Social Learning in Neural Agent-Based Models

Abstract Agent-based models (ABMs) are widely used to study how individual interactions shape collective behaviors. Critics argue that ABMs are often too simplistic to capture real-world complexities. We address this by integrating artificial neural networks into ABMs, focusing on enhancing the Hegselmann–Krause (HK) model. By using multilayer perceptrons as agents, we create more realistic ABMs that better reflect actual agents. This approach yields multiple models, as core elements of the HK model can be defined in various ways. We conduct two computational studies to compare these models with each other and with traditional individual-learning paradigms.

N-Trifluoroethoxy Benzotriazolium Triflate: A Readily Available Reagent for Direct Radical Trifluoroethoxylation of Alkenes.

Herein, we describe the development and application of a novel benzotriazole-based reagent toward radical trifluoroethoxylation. Various alkene classes, including styrene derivatives, enol carbonates, and allyl silanes, are viable reaction partners in this transformation, yielding diverse trifluoroethoxylated products. Furthermore, this method is readily applicable for the late-stage modification of natural product and drugs molecules. Mechanistic and computational studies suggest the intermediacy of an OCH2CF3 radical generated under photocatalytic conditions.

In Silico, In Vitro, and In Vivo Studies Indicate the Endocrine-Disrupting Effects of Cyproconazole Stereoisomers.

The widespread use of chiral triazole fungicide cyproconazole (CPZ) in agricultural fields has led to frequent detection of CPZ in the environment. The restriction of CPZ in the EU raised wide concerns regarding its potential endocrine-disrupting effects (EDEs). The present study was conducted to evaluate EDEs of CPZ stereoisomers in vitro, in silico, and in vivo. The reporter gene assay indicated that all CPZ stereoisomers were agonists to the human estrogenic receptor α. (2S,3S)-(+)- and (2R,3S)-(-)-CPZ exhibited stronger binding capacities to ERα compared with (2R,3R)-(-)- and (2S,3R)-(+)-CPZ. Our computational studies showed consistent results with reporter gene assay, elucidating the stereoselective binding mode of CPZ to estrogen receptor. In zebrafish embryos, the 96h-lethality of CPZ stereoisomers ordered (2R,3R)-(-)- > (2R,3S)-(-)- > (2S,3S)-(+)- > Rac- > (2S,3R)-(+)-CPZ. Stereoselective developmental toxicity of CPZ was observed while (2R,3S)-(-)-CPZ is the most toxic isomer. The estrogenic hormones were significantly decreased in (2S,3R)-(+)- and (2R,3S)-(-)-CPZ groups and enhanced in (2S,3S)-(+)- and (2R,3R)-(-)-CPZ, along with the gene expression in hypothalamic-pituitary-gonad axis altered. CPZ shows no thyroid hormone activity. These data clarified that CPZ is a new-found endocrine disruptor threatening human health and each stereoisomer of CPZ showed stereoselective EDEs by regulating the nuclear receptor-mediated gene expression.

Structural characterisation of a cyanomesogen by X-ray diffraction and computational methods

The work reports the structural analysis of a cyanomesogen namely, p-cyanobenzylidene p-nonyloxyaniline belonging to the Schiff base class of compounds. It exhibits a partial bilayer/inter-digitated smectic Ad phase and a nematic phase. Polarising Optical Microscopy (POM) and Differential Scanning Calorimetry (DSC) studies have been carried out to study phase sequence and transition temperatures. Micro-structural parameters, like molecular length, spacing, crystallite size, activation energy and micro-strain, have been estimated and pair correlation function (PCF) studies have been done for exhibited mesophases using the X-ray diffraction technique. The study investigated the surface, electronic and optical properties of a compound by computational studies like Density Functional Theory (DFT) and Hirshfeld surface analysis (HSA) methods using the DFT B3LYP/6-311++G(d,p) level basis set. The results reveal that the polarity associated with the polar groups and alkoxy chain lengths, contributes majorly to the mesomorphic characteristics and stability. The Highest Occupied Molecular Orbitals (HOMO) and Lowest Unoccupied Molecular Orbitals (LUMO) analyses of the DFT optimised molecule give electronic and geometrical parameters, atomic charge distribution, polarisability factors which are used to interpret the characteristics of the mesophases and their suitability for electro-optical and non-linear optical applications of the compound in terms of the predicted data.

Redox-Neutral, Iron-Mediated Directed C-H Activation: General Principles and Mechanistic Insights.

Experimental and computational studies have been conducted and established the general principles for enabling redox-neutral C-H activation by iron(II) complexes. The idealized octahedral iron(II) dimethyl complex, (depe)2Fe(CH3)2 (depe = 1,2-bis(diethylphosphino)ethane) promoted the directed, regioselective ortho C(sp2)-H methylation of pivalophenone. The rate of the iron(II)-mediated C(sp2)-H functionalization depended on the lability of L-type phosphine ligands, the spin state of the iron center, and the size of the X-type ligands (halide, hydrocarbyl) in P4FeIIX2 complexes. The C(sp2)-H alkylation reaction proved general among multiple substrates with directing groups including carbonyl, imines and pyridines. Among these, ketones and aldehydes were identified as optimal and were compatible with various steric environments and presence of acidic α-hydrogens. With stronger nitrogen donors, higher barriers for product-forming reductive elimination were observed. The effect of orbital hybridization on the chemoselectivity of C-H activation through a σ-CAM pathway by dn>0 transition metals was also established by studying the stoichiometric reactivity of the differentially substituted (depe)2Fe(Me)R complexes (R = alkyl, aryl), where the Fe-R bond with greater s-character preferentially promoted selective C-H activation. Deuterium labeling and kinetic studies, coupled with computational analysis, supported a pathway involving phosphine dissociation and rate-determining C-H bond activation, leading to the observed products.

Recognition of halide anions by N,N’-bis(4-nitrophenyl)urea in the gas-phase and solution: a computational study

ABSTRACT This study investigates the recognition of halide anions by N,N’-bis(4-nitrophenyl)urea using computational methods in both gas-phase and solution. It examines interaction, stabilization, and deformation energies, revealing a gas-phase selectivity trend of [L⋯F]−>[L⋯Cl]−>[L⋯Br]−>[L⋯I]−. NBO, QTAIM, and EDA-NOCV analyses highlight N-H∙∙∙X hydrogen bonds, with electrostatic forces contributing around 60% to the total interaction. Despite unfavorable solvation energy changes, the intrinsic affinity remains the main factor for selectivity, which aligns with experimental data. The strong correlation between theoretical and experimental formation constants supports the reliability of the computational findings.

Rapid and Environmentally-Friendly Synthesis of Thiazolidinone Analogues in Deep Eutectic Solvent Complemented with Computational Studies.

A greener, safer, and more efficient methodology for the synthesis of (Z)-5-benzylidene-2-thioxothiazolidin-4-ones (3 a-u) and (Z)-5-benzylidenethiazolidine-2,4-diones (4 a-i) has been developed. The deep eutectic solvent (DES) ZnCl2/urea used as a greener solvent as well as a catalyst in this study accelerated the condensation of rhodanine and thiazolidine-2,4-dione with different aldehydes to afford the target scaffolds in excellent yields (88-98 %). The reaction methodology adopted offered significant advantages such as mild reaction conditions, functional group tolerance, quick reaction time, column-free isolation, catalytic recyclability, and applicability to gram-scale production. Moreover, density function theory calculations were carried out to investigate the global reactivity and stability profiles of these compounds. Finally, the green metrics analysis supported the greener nature of the present methodology.

Direct Spectroscopic Confirmation of the Oxygen‐Centered Diradical Character of the Tetraoxidorhenium(VII) Cation [Re(O)4]+

AbstractMononuclear inorganic diradical species are scarce. Here, we confirm, via X‐ray absorption spectroscopy in the gas phase combined with computational studies, the oxygen‐centered diradical character of the tetraoxidorhenium(VII) cation. A dioxido‐superoxido isomer, close in energy to the diradical, is also found, where rhenium appears in its rare oxidation state of +6. Addition of one or two hydrogen atoms to [Re,O4]+ forms hydroxido ligands, and strongly disfavors isomers with any oxygen‐oxygen bond. This adds spectroscopic characterization of the rhenium oxidation state and the nature of ligands to the known ability of [Re,O4]+ to perform two consecutive hydrogen‐atom abstraction reactions from methane, and demonstrates that pentaatomic [Re,O4]+ combines a metal center in its highest oxidation state with two oxygen‐centered radical ligands in a highly reactive species.

Design of Anti-Hund Organic Emitters Based on Heptazine.

Hund's rule, which is powerful in governing the first excited states of closed-shell organic materials, can hardly be violated to get inverted singlet-triplet gap (INVEST) molecules with negative singlet-triplet energy gaps (ΔEST), although INVEST materials have shown extraordinary photophysical properties and promising device performance especially in light-emitting diodes. Here, we propose a facile strategy to construct emissive INVEST molecules by introducing different types of substituents to heptazine in various modes, which can effectively tune the ΔEST to be negative with the enlarged oscillator strength (f) for the high fluorescence rate of the heptazine derivatives. Systematic computational studies show that the double substitution of electron-donating units with another nonconjugated substituent in hybrid substitution mode is the most favorable way in achieving slightly negative ΔEST and large f values; the conjugated substituent will compete with heptazine to make the molecule deviate from the INVEST feature. Especially, a series of high-performance heptazine-based INVEST emitters were constructed, exhibiting ΔEST low to -0.362 eV, f up to 0.0436, as well as a wide range emission color from 339 to 716 nm. Also, the designed molecules were predicted to have fluorescence radiative rates up to 106 s-1, along with efficient reverse intersystem crossing rates reaching 108 s-1. Importantly, the figure of merit (FM) was first proposed as a parameter to wholly evaluate the performance of INVEST emitters, and the highest FM of 0.198 was found in the triazine and double nonconjugated amine-substituted heptazine. These results highlight the great potential of the heptazine chromophore in constructing INVEST emitters, revealing fundamental structure-property understandings for the material design of efficient anti-Hund organic molecules with improved emission properties.

Use of Essential Oils for the Treatment of Fusarium oxysporum f. sp. Albedinis: Chemical Profile, In Vitro Antifungal Activity, and In Silico Investigation by Molecular Docking Study

Background: Fusarium oxysporum f. sp. Albedinis a telluric fungal pathogen commonly found in soils, is the causal agent of fungal vascular wilt of date palms in Moroccan oases. The infection by the pathogen leads to the death of the date palm after six months to two years, which causes enormous economic and environmental damage. Objective: The framework of this paper is to determine the chemical composition of six essential oils using GC-MS and their antifungal activity on the mycelial growth of Fusarium oxysporum f. sp. Albedinis, as well as the molecular docking study to evaluate the inhibitory potential of fungal trypsin. Methods: The essential oils were extracted from different parts of the plants (whole plant, flowers, and leaves) by steam distillation, and were identified using gas chromatography-mass spectrometry (GC/MS). The antifungal assay of the extracted essential oils and their main components was assessed using the direct contact method with the fungus at different concentrations; the obtained results were evaluated by calculating the minimum inhibitory concentration (MIC) of each essential oil, followed by an in-silico study of the major identified compounds for better understanding of the inhibitory potential against fungal trypsin activity. Results: The identification of the different bioactive compounds using GC-MS revealed that Rosmarinus officinalis Eo was characterized by eucalyptol 46.26%, camphor 10.03%, and β-pinene 6.63%; while Lavandula officinalis Eo was endowed by the presence of linalool 14.93%, camphor 14.11%, and linalyl acetate 11.17%. Furthermore, Artemisia herba alba was rich in 1,3,5-cycloheptatriene, 1,6- dimethyl- 36.44%, camphor 22.50%, and α-thujone 7.21%. While Eucalyptus globulus was rich in eucalyptol 74.32%, β-Cymene 11.41%, α-Pinene 6.96%. Finally, Mentha pepirita and Mentha pulegium were both characterized by the presence of D-limonene 20.15%, trans-carveol 19.59%, D-Carvone 14.96%, and pulegone (42.40%), 3-cyclopentene-1-ethanol, 2,2,4-trimethyl- (11.28%), 1,3,4- trimethyl-3-cyclohexenyl-1-carboxaldehyde (9.68%), respectively. Regarding the in vitro, all Eos from different plants exhibited pronounced antifungal effect. The MIC values recorded for E. globulus were MIC= 1.75 mg/L, M. pulegium and L. officinalis (MIC= 1.80 mg/L), and M. piperita (MIC= 1.90 mg/L). The strongest inhibition potential was associated with R. officinalis EO (MIC= 1.15 mg/L) and A. herba alba EO (MIC= 1.60 mg/L). As for the computational study performed camphor one of the bioactive compounds showed its ability to act against trypsin which could be considered a potential candidate against Fusarium oxysporum f. sp. Albedinis. Conclusion: The studied essential oils from different medicinal and aromatic plants showed significant antifungal activity, probably due to the Camphor which could have an inhibitory effect on the Fusarium oxysporum f. sp. Albedinis trypsin. Further research should be conducted in vivo for a better understanding of the mechanism of action of these essential oils.

Computational study on the effect of initial pitch angle on dragonfly hovering performance

Computational study on the effect of initial pitch angle on dragonfly hovering performance

Tridentate N-donor Schiff base metal Complexes: Synthesis, Characterization, computational Studies, and assessment of biomedical applications in cancer Therapy, Helicobacter pylori Eradication, and COVID-19 treatment

A unique Schiff base ligand (BCA), 4-(2-((1E,2E)-1-(2-(p-tolyl)hydrazono)propan-2-ylidene)hydrazinyl)quinazoline, was synthesized and complexed with Mn [II], Co [II], Cu [II, and Cd [II] ions, with 1,10-Phenanthroline (PHN) as an auxiliary ligand. The unique Schiff base ligand BCA and its metal complexes were characterized using multiple analytical techniques, including elemental analysis, UV–visible spectroscopy, FT-IR, mass spectrometry, and conductometric measurements. These methods provided detailed insights into the compounds’ structural and electronic properties. Density Functional Theory (DFT) computations complemented the experimental data, elucidating electronic configuration stability, HOMO-LUMO energy gaps, chemical hardness, and dipole moments. The computational results confirmed the distorted octahedral structure of the complexes. Antimicrobial testing against various bacterial and fungal strains revealed that the Cd (II) complex exhibited the highest activity, with inhibition zones ranging from 19.7 ± 0.6 mm to 35.0 ± 1.0 mm, surpassing the activity of standard antibiotics in some cases. Notably, the compounds displayed significant efficacy against Helicobacter pylori, with the Cd (II) complex showing an inhibition zone of 32.67 ± 0.58 mm and a minimum inhibitory concentration (MIC) of 7.8 μg/ml. Anticancer properties were evaluated against MCF-7 (Breast carcinoma) cells, with the [(BCA)(PHN)Cd(H2O)].2Cl·2H2O complex demonstrating superior activity (IC50 = 29.97 μg/ml) compared to the free ligand (IC50 = 183.96 μg/ml) and other metal complexes. Notably, the Cd(II) complex showed reduced cytotoxicity towards normal VERO cells, suggesting potential selectivity for cancer cells. Molecular docking simulations evaluated the complexes’ binding interactions with protein targets associated with Helicobacter pylori, MCF cancer cells, and the COVID-19 virus. The main objective of this research was to design and synthesize a unique Schiff base ligand and its new corresponding Ternary metal complexes and then investigate their potential medical applications. Specifically, the study aimed to evaluate the compounds’ effectiveness as antibiotics, antitumor agents, and possible treatments for COVID-19.

Synthesis, structural characterization, computational studies, and in silico and in vitro biological activities of cyclodextrin inclusion complex with sulfonamide derived from L-valine as antimicrobial and anti-HIV-1 agents

Synthesis, structural characterization, computational studies, and in silico and in vitro biological activities of cyclodextrin inclusion complex with sulfonamide derived from L-valine as antimicrobial and anti-HIV-1 agents

Enhanced VOCs adsorption with UIO-66–porous carbon nanohybrid from mesquite grain: A combined experimental and computational study

In this study, adsorption of volatile organic compounds (VOCs) (here just gasoline vapor) by activated carbon- modified UIO-66 was investigated. First, activated carbon prepared from mesquite grain (ACPMG) and then UIO/ACPMG nanohybrid was synthesized by the solvothermal method. In following, the effect of main key parameters which effect on the surface and adsorption capacity such as the ratio of ACPMG to UIO-66 was studied. Physiochemical changes of as- synthesized samples were investigated by TGA, HR-TEM, PSD, SEM, EDX/MAP, BET, FT-IR, XRD, and XPS. It was found the UIO/ACPMG20% nanohybrid had the highest adsorption capacity (391.304 mg/g) for VOCs compared with the other samples, while the adsorption capacity of UIO-66, UIO/ACPMG10% nanohybrid, and UIO/ACPMG30% nanohybrid was 298.871, 309.523, and 320 mg/g respectively. UIO/ACPMG20% nanohybrid desorbed 285.71 mg/g of the adsorbed gasoline, which is an excellent result in desorption. So, the sample of UIO/ACPMG20% nanohybrid was selected as the optimum nano-adsorbent. In other hand, all the nano-adsorbent showed a rapid kinetic behavior for gasoline vapor adsorption and the maximum time for reaching a high adsorption capacity approximately was obtained in 20 min. Density functional theory calculations also performed to understand the adsorption characteristics of gasoline vapor on activated carbon-modified UIO-66.

The learnability of natural concepts

According to a recent proposal, natural concepts are represented in an optimally designed similarity space, adhering to principles a skilled engineer would use for creatures with our perceptual and cognitive capacities. One key principle is that natural concepts should be easily learnable. While evidence exists for parts of this optimal design proposal, there has been no direct evidence linking naturalness to learning until now. This article presents results from a computational study on perceptual color space, demonstrating that naturalness indeed facilitates learning.