jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yike Huang | Zuxin Jin | Linfeng Zhang | Mohan Chen | Rui Chen | Ling Li
Source: arXiv (Cornell University) (article, 2026-03-14)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Systematically Improvable Numerical Atomic Orbital Basis Using Contracted Truncated Spherical Waves To solve the Kohn-Sham equation within the framework of density functional theory, we develop a scheme to construct numerical atomic orbital (NAO) basis sets by contracting truncated spherical waves (TSWs). The contraction minimizes the trace of the kinetic operator in the residual space, generalizing the spillage minimizing scheme [M. Chen et al., J. Phys. Condens. Matter 22, 445501 (2010); P. Lin et al., Phys. Rev. B 103, 235131 (2021)]. In addition to the systematic improvability inherited from previous schemes, the use of TSW instead of plane waves as the expansion basis bridges reference states and NAOs more effectively, and eliminates spurious interactions between periodic images, thereby enabling better transferability through the inclusion of extensive reference states. Benchmarks demonstrate that the constructed NAO achieves satisfactory precision for various properties of both molecules and bulk systems, including total energy, bond length, atomization energy, lattice constant, cohesive energy, band gap, and energy-level alignment. By incorporating unoccupied states, the improved transferability in describing the conduction band is demonstrated to be effective and substantial. Spurious relationship ; Residual ; Basis (linear algebra) ; Basis function ; Transferability ; Operator (biology) ; Wannier function ; Lattice (music) ; TRACE (psycholinguistics) Magnetism in coordination complexes ; Advanced Chemical Physics Studies ; Machine Learning in Materials Science
Authors: Ayunda Pratiwi Kusumaningrum | Endang Astuti | Harno Dwi Pranowo
Source: Journal of Applied Pharmaceutical Science (article, 2026-01-01)
Field: Chemistry — Organic Chemistry

Molecular docking study and molecular dynamics simulation of quinazoline derivatives targeting p53 and EGFR proteins as anti gastric cancer Gastric cancer is closely associated with mutations in p53 and Epidermal Growth Factor Receptor (EGFR), disrupting key cellular regulatory functions. Quinazoline derivatives have demonstrated anticancer activity, yet their molecular interactions with p53 and EGFR remain unexplored. This study investigates these interactions through molecular docking, followed by structural optimization to enhance binding affinity. Stability was further assessed using molecular dynamics (MD) simulations, and pharmacokinetic properties were evaluated via ADMET analysis. The optimized derivatives Q-2, Q-4, and Q-9 showed strong binding affinities to p53 (Val147) with energies of −8.3120, −8.1330, and −8.1240 kcal/mol, and to EGFR (Asp831) with energies of −8.7090, −8.7800, and −9.1060 kcal/mol. MD simulations revealed that Q-2–p53 and Q-9–EGFR complexes maintained high structural stability, while ADMET predictions confirmed favorable pharmacokinetics. These findings indicate that Q-2 and Q-9, as optimized forms of known quinazoline scaffolds, have strong potential as lead compounds for targeted gastric cancer therapy. Molecular dynamics ; Quinazoline ; Epidermal growth factor receptor ; Docking (animal) ; EGFR inhibitors ; Cancer ; Molecular model Quinazolinone synthesis and applications ; Cancer-related Molecular Pathways ; HER2/EGFR in Cancer Research
Authors: Vasant Madanrao Dhumal | Kalimoddin I. Momin | Vishwas G. Mane | P.A. Jagtap | Sharad P. Panchgalle | Vijaykumar S. More
Source: Asian Journal of Chemistry (article, 2026-03-06)
Field: Chemistry — Organic Chemistry

Synthesis, Structural Characterisation and Biological Evaluation of Novel Pyrimido[1,6-a]pyrimidine Derivatives Bearing Phenoxy, Phenylamino and Pyrazolyl Moieties as Potent Antimicrobial and Cytotoxic Agents A new series of pyrimido[1,6-a]pyrimidine-based heterocycles (HP1-HP10) was synthesised and structurally characterised using FTIR, 1H/13C NMR, HRMS and elemental analysis. The key intermediate, 6-((4-chlorophenyl)amino)-8-hydroxy-2-(methylthio)-4-oxo-4H-pyrimido[1,6-a]pyrimidine-3-carbonitrile (HP1), was synthesised via base-catalysed cyclisation of ethyl 2-cyano-3,3-bis(methylthio)-acrylate with 6-amino-2-((4-chlorophenyl)amino)pyrimidin-4-ol. Subsequent nucleophilic substitutions of HP1 afforded phenoxy (HP2-4), phenylamino (HP5-7) and pyrazolo-fused (HP8-10) derivatives. The biological evaluations revealed that the compounds HP3 and HP6 exhibited significant antibacterial activity, particularly against Staphylococcus aureus and Escherichia coli, outperforming the standard drug streptomycin. HP3 also demonstrated the strongest antifungal efficacy against Candida albicans (26 mm), exceeding fluconazole. Cytotoxicity assessed via brine shrimp lethality bioassay showed that HP1 and HP5 possessed the lowest LD50 values (35 µM), suggesting promising bioactivity. Structure-activity relationship (SAR) analysis highlighted the importance of electron-donating and halogenated substituents in modulating antimicrobial potency. These findings suggest that the HP1-HP10 scaffold offers a viable platform for further medicinal chemistry development. Molecular docking with AutoDock Vina revealed strong interactions of the tested ligands with the C. albicans protein target. Fluconazole, used as the reference, showed a binding affinity of -7.3 kcal/mol via hydrogen bonds with Thr411 and Glu70, while HP9 demonstrated the highest affinity (-9.3 kcal/mol) through hydrophobic contacts with Phe52, Trp54 and Glu70, followed by HP8 (-9.2 kcal/mol) and HP4 (-9.0 kcal/mol). Several ligands, including HP5, HP10 and HP2, formed multiple hydrogen bonds with active-site residues, while HP6 and HP7 exhibited strong nonpolar interactions. Low RMSD values (0.678 Å) confirmed reliable binding poses. Candida albicans ; Antimicrobial ; Hydrogen bond ; Cytotoxicity ; Escherichia coli ; Brine shrimp ; Docking (animal) ; Lipophilicity ; Antibacterial activity Synthesis and biological activity ; Synthesis and Reactivity of Sulfur-Containing Compounds ; Multicomponent Synthesis of Heterocycles
Authors: Christos P. Constantinides | Jin-Seok Yi | Haidar Dakdouk | Simona Marincean
Source: Crystals (article, 2026-03-18)
Field: Chemistry — Organic Chemistry

Positional Methyl Effects in Benzo[e][1,2,4]triazines—Synthesis and Crystal Structure Analysis of 5-Methyl-3-phenylbenzo[e][1,2,4]triazine and Its Precursor, N′-(3-Methyl-2-nitrophenyl)benzohydrazide We report the synthesis, spectroscopic characterization, and single-crystal X-ray structures of 5-methyl-3-phenylbenzo[e][1,2,4]triazine (I) and its precursor N′-(3-methyl-2-nitrophenyl)benzohydrazide (IV). Compound IV was obtained by nucleophilic aromatic substitution of 1-fluoro-3-methyl-2-nitrobenzene with benzohydrazide and was converted to I through a reductive cyclodehydration/oxidative aromatization sequence. The present study provides a concise route to the 5-methyl regioisomer together with full structural characterization and examines how methyl substitution at the 5-position influences molecular geometry and crystal packing relative to the previously reported 6- and 8-methyl analogs. X-ray analysis shows that IV adopts a conjugated hydrazide framework with a twisted N–N linkage and an out-of-plane nitro group. In the crystal, it forms one-dimensional N–H⋯O hydrogen-bonded chains further assembled by weaker intermolecular contacts. By contrast, I displays an essentially planar benzo[e][1,2,4]triazine core with an almost coplanar phenyl substituent and packs into slipped π-stacked columns reinforced by secondary C–H⋯N contacts. Comparison with the previously reported methyl regioisomers shows that relocation of the methyl group to the 5-position has little effect on the intrinsic molecular geometry of the benzo[e][1,2,4]triazine scaffold, while subtly modulating the stacking arrangement and secondary packing interactions in the solid state. These results further define the role of methyl-substituent position in shaping the supramolecular organization of 3-phenylbenzo[e][1,2,4]triazines. Structural isomer ; Crystal structure ; Stacking ; Substituent ; Supramolecular chemistry ; Intermolecular force ; Nucleophilic substitution ; Molecular geometry Synthesis and Characterization of Heterocyclic Compounds ; Energetic Materials and Combustion ; Luminescence and Fluorescent Materials
Authors: Xinning Kang
Source: Exploring Science Academic Conference Series (article, 2026-03-24)
Field: Chemistry — Organic Chemistry

Chemical Biology Approaches in Drug Target Discovery: From Affinity Probes to Thermal Stability Analysis Drug target discovery is a critical step in new drug research and development, and chemical biology techniques and theories provide powerful tools to advance this process. This review summarizes two major categories of drug target discovery methods—affinity probes and thermal stability analysis—and their recent research progress, highlighting the role of chemical biology approaches. It also aims to deepen the author’s understanding of future directions for advanced study in chemical biology. The review focuses on activity-based protein profiling (ABPP) and affinity-based protein profiling (AfBPP) as representative affinity probe technologies, as well as label-free thermal stability techniques including DARTS, CETSA, and TPP, with extensions to related developments. Both categories of drug target discovery technologies have distinct advantages, and their combined use enables a complete workflow from theory to practice and from discovery to validation. Chemical biology methods play a positive role in drug target identification. Chemical biology ; Drug discovery ; Profiling (computer programming) ; Drug target ; Workflow ; Systems biology ; Drug ; Chemical stability Click Chemistry and Applications ; Advanced Biosensing Techniques and Applications ; Biochemical and Structural Characterization
Authors: María Elena Sánchez Vergara | Ricardo Ballinas-Indilí | Naomi Itzel Medina Morales | Emilio Iván Sandoval Plata | Ruben A. Toscano | Cecilio Álvarez Toledano
Source: Crystals (article, 2026-02-13)
Field: Materials Science — Materials Chemistry

Study of 2-Benzylidene-1-indanone Derivatives as Electrodes In this work, indanone derivatives with a triphenylamine core structure (IND-1, IND-2, and IND-3) were studied as prospective electrodes. The indanones were synthesized and characterized for optimal deposition as charge-modulating electrodes. The structural arrangement of compound IND-3 was established, and the structure crystallized in a P21/c monoclinic space group. The electrodes were evaluated for reflectance and band gaps of direct and indirect transitions. Indanones show optical band gap values in the range of 2.46 and 2.86 eV. These values were compared with those obtained theoretically by means of DFT, from which the HOMO and LUMO molecular orbitals were also calculated. To evaluate the indanone response, photoactive devices with indanone-derivative electrodes and copper phthalocyanine as a photoactive electrode were fabricated. Cyclic voltammetry (CV) was conducted using a two-electrode arrangement, within a potential range of −0.1 to 1 V, a step of 10 mV, and a scan rate of 0.1 V/s. The transported current is around 10−1–104 µA, and CV revealed distinct behaviors related to each kind of indanone. Finally, the electrodes were removed from each device and analyzed by IR spectroscopy, demonstrating that they did not undergo degradation during operation and can continue to be used for the manufacture of other devices. Electrode ; Triphenylamine ; Cyclic voltammetry ; Band gap ; Phthalocyanine ; HOMO/LUMO ; Monoclinic crystal system ; Deposition (geology) Photochromic and Fluorescence Chemistry ; Organic Light-Emitting Diodes Research ; Organic Electronics and Photovoltaics
Authors: Suresh S Honnalli | Girish A. Hampannavar | Iranna S. Gatibyali
Source: Asian Journal of Chemistry (article, 2026-04-08)
Field: Chemistry — Organic Chemistry

A New Class of 1,2,4-Triazolo-Benzothiazole Hybrids as Promising Antibacterial Agents A novel series of 1,2,4‑triazolo‑benzothiazole derivatives (6a-l) were designed, synthesised and evaluated for antimicrobial activity. The synthesis proceeded through multistep construction of the triazolo‑benzothiazole core from m‑chloroaniline, followed by functionalisation with substituted aromatic and heterocyclic amines. Structures were confirmed by IR, NMR and mass spectrometry. Antibacterial screening against Gram‑positive (S. aureus, B. subtilis) and Gram‑negative (E. coli, P. aeruginosa) strains employed cup‑plate and serial‑dilution assays. Compounds 6a, 6e and especially 6h displayed broad‑spectrum potency, with 6h active at low concentrations. Molecular docking showed strong binding where, 6e scored -10.8 kcal/mol against S. aureus (PDB 5CPQ) and 6d scored -10.5 kcal/mol against E. coli (PDB 5TZ1), surpassing ciprofloxacin (-8.0 and -8.5 kcal/mol, respectively). Interactions involved multiple hydrogen bonds and extensive hydrophobic contacts. ADMET profiling indicated compliance with Lipinski’s rule of five, high gastrointestinal absorption, low toxicity risk and no blood‑brain barrier penetration, supporting their potential as orally active antimicrobial agents. Antimicrobial ; Ciprofloxacin ; Docking (animal) ; Antibacterial activity ; Hydrogen bond ; Escherichia coli ; Proton NMR ; Active site Click Chemistry and Applications ; Synthesis and biological activity ; Quinazolinone synthesis and applications
Authors: Tímea Kaszás | Bence Szakács | Tekla Blága | Kyle Doherty | Rachel Keenan-Dillon | Shauna Reynolds | Kevin Kavanagh | Trinidad Velasco-Torrijos | László Somsák | Marietta Tóth
Source: Frontiers in Chemistry (article, 2026-04-09)
Field: Chemistry — Organic Chemistry

Synthesis of mono- and di-(C-glycopyranosyl-isoxazol(in)yl) derivatives on aromatic scaffolds and their evaluation as anti-adherence agents of Candida albicans The yeast Candida albicans is one of the most prevalent fungal pathogens. It induces superficial and systemic infections in immunocompromised patients. The high pathogenicity of Candida species may be related to their adherence to the host tissues. Cell surface glycans are important receptors for C. albicans and warrant the development of anti-adherence ligands that can mimic them and disrupt C. albicans –epithelial cell interactions. A divalent galactoside glycomimetic containing 1,2,3-triazole units was found to be one of the most potent inhibitors of C. albicans adhesion to exfoliated buccal epithelial cells. Based on this lead molecule, herein we report on the synthesis and evaluation of a new series of mono- and divalent glycosides, featuring isophthalamide and benzene scaffolds with C -glycosyl isoxazoline and isoxazole, as well as N -glycosyl 1,2,3-triazole units. The new compounds were obtained by 1,3-dipolar cycloaddition reactions between the above scaffolds functionalized with one or two alkenyl or alkynyl moieties and glycosyl nitrile oxides and glycosyl azides, respectively. The tested deprotected compounds were non-toxic to the C. albicans cells and exhibited significant inhibition of C. albicans adhesion, showing good and moderate inhibition in exclusion and competitive assays, respectively. This study demonstrated the utility of isoxazole/isoxazoline heterocycles to replace 1,2,3-triazoles in aromatic-core glycoconjugates to furnish anti-adhesion molecules equipotent with the lead and also showed that the simple benzene core can serve well in potential anti-adhesives against C. albicans . Candida albicans ; Glycoconjugate ; Glycan ; Glycosyl ; Divalent ; Yeast ; Cycloaddition ; Glycosylation Carbohydrate Chemistry and Synthesis ; Click Chemistry and Applications ; Antifungal resistance and susceptibility
Authors: Jingjin Hu | Xiaoyu Tang | Qian He | Xinying Fan | Haodong Su | Hang Luo | Dan Ma
Source: International Journal of Nanomedicine (article, 2026-01-01)
Field: Materials Science — Materials Chemistry

Nanozymes in Therapeutic Prospects and Challenges for Autoimmune Diseases Nanozymes are a class of nanomaterial-based catalysts with enzyme-like functionalities. They exhibit excellent physicochemical properties and stable catalytic activity in both in vivo and in vitro environments, demonstrating immense potential for biomedical applications. Autoimmune diseases arise from the immune system's erroneous attack on self-tissues or cells, affecting individuals across all age groups. Current therapies primarily rely on immunosuppressive drugs, which may control disease progression or alleviate symptoms but often fail to achieve a cure. Long-term use of these drugs is associated with significant side effects, imposing substantial health burdens on patients. Oxidative stress, driven by excessive reactive oxygen species (ROS) production or dysfunctional antioxidant defense systems, is a key mechanism underlying many autoimmune diseases. Excessive ROS accumulation exacerbates cellular damage and inflammatory responses, accelerating disease progression. Nanozymes, with their enzyme-mimicking catalytic capabilities, are ideal tools for modulating ROS levels, offering promising applications in the prevention and treatment of autoimmune diseases. Furthermore, by regulating the ROS microenvironment, nanozymes may enhance the proliferation, differentiation, and regenerative capacity of stem cells, further amplifying their therapeutic potential. This review comprehensively explores recent advancements in nanozymes for biomedical applications, focusing on their roles in oxidative stress modulation and mesenchymal stem cell (MSC)-based therapies. It aims to provide innovative insights and solutions for future clinical strategies. Mesenchymal stem cell ; Reactive oxygen species ; Oxidative stress ; Autoimmune disease ; Immune system ; Regenerative medicine ; Disease ; Immune modulation Advanced Nanomaterials in Catalysis ; Nanoplatforms for cancer theranostics ; Nanocluster Synthesis and Applications
Authors: D. Ravi Sankara Reddy | T. Srinivasarao
Source: Asian Journal of Chemistry (article, 2026-01-31)
Field: Chemistry — Organic Chemistry

Therapeutic Potential of Disubstituted [{[5-(2-Chloro phenyl)-1,3,4-thiadiazole-2-yl]imino}-methyl]phenyl Derivatives as α-Amylase Antagonists: Synthesis, In silico and In vitro Screening During the last few decades medicinal chemist focus turns to the novel heterocyclic moiety thiadiazole having similar stereotype with thiazole ring with hypoglycemic activity. Henceforth, this study aims to synthesise the designed novel 2,5-diarylsubstituted 1,3,4 thiadiazole derivatives (TDZ) by two step process using microwave irradiation method. The title compounds with electron withdrawing groups (nitro), electron donating groups (hydroxy, dimethyl amine) were synthesized from condensation of thiosemicarbazide with o-chlorobenzoic acid in presence of acidic catalyst followed by the condensation of the intermediate with substituted benzaldehydes under microwave irradiation. Molecular docking studies against α-amylase using Autodock and Schrödinger, molecular dynamic simulation studies using Growmacs and in vitro antidiabetic activity by α-amylase inhibition assay was performed to all the 2,5-diarylsubstituted 1,3,4-thiadiazole derivatives. There is a correlation of in silico and in vitro results, derivatives TDZ7 and TDZ2 (61% and 59%) showed significant α-amylase inhibition than the miglitol (81%) at 1000 µg/mL concentration. Molecular modelling studies demonstrates that derivatives TDZ2 and TDZ7 against 7taa (-8.67 and -7.82 kcal/mol), 1b2y (-4.8 and -4.5 kcal/mol), respectively, possess least binding energies than that of the standard drugs miglitol (-5.05 kcal/mol) and metformin (-8.19 kcal/mol) against 7taa with enzyme inhibition constant 442.33 nM, 1.85, 197.74 µM and 998 nM, respectively. All the ligands and standard drugs showed hydrophilic interactions with active site amino acids, with varying distances. Further research is needed to get the active derivatives with hypoglycemic potential. In silico ; AutoDock ; Thiazole ; Moiety ; Docking (animal) ; In vitro ; Polar effect ; Enzyme Synthesis and biological activity ; Enzyme function and inhibition ; Natural Antidiabetic Agents Studies
Authors: Heba M. Karam | Mai H. Mekkawy | Amira Abd-ElRaouf | Aiten M. Soliman | Mostafa M. Ghorab
Source: Naunyn-Schmiedeberg s Archives of Pharmacology (article, 2026-04-09)
Field: Chemistry — Organic Chemistry

Radiomodulatory and antioxidant properties of a novel pyrazine-linked quinazolinone sulfonamide derivative: Insights into renal apoptosis Quinazolinone derivatives possess a privileged scaffold with variable pharmacological activities. This study conducted an in vitro evaluation of the pyrazine-linked quinazolinone sulfonamide derivative (PQS) to assess its anticancer activity, following confirmation of its safety in a normal cell line. Results revealed that PQS has a noteworthy cytotoxic effect on HepG-2 and HeLa cells, indicating its potential anticancer activity. Additionally, PQS is quite safe on normal Vero cells. Furthermore, in vivo biological activity of PQS was evaluated for its radioprotective properties in (5 Gy) irradiated mice. PQS showed mitigation of gamma radiation-induced oxidative stress, verified by the decline in MDA, ROS and NO levels, while GSH levels and GST activities were improved in kidney tissues. The apoptotic pathway was also assessed, where weak expression of caspase-3 and Bcl2-associated X protein (Bax) was noticed paired with higher expression of B-cell lymphoma 2 (Bcl2) after PQS treatment in irradiated mice. These results were confirmed by histopathological examination of kidney tissues. Besides, in-silico ADME studies revealed that compound PQS showed drug-like properties, confirmed by its physicochemical and pharmacokinetic properties. In conclusion, the results of the present study demonstrated that PQS has dual activity as a potential anticancer on HepG-2 and HeLa cancer cell lines and radio-protective activity through its anti-apoptotic and antioxidant action in the in vivo study. HeLa ; Quinazolinone ; Apoptosis ; Nephrotoxicity ; Cytotoxicity ; Antioxidant ; Sulfonamide ; Cytotoxic T cell ; Cell culture Quinazolinone synthesis and applications ; Effects of Radiation Exposure ; Genomics, phytochemicals, and oxidative stress
Authors: Amir Ali | Zia-ur-Rehman Mashwani | Ashfaq Ahmad | Juan Pedro Luna-Arias | Gabriela Medina-Pérez | Ajaz Ahmad
Source: PLoS ONE (article, 2026-04-03)
Field: Materials Science — Biomaterials

Elucidating the binding mechanism of Caralluma tuberculata metabolites with type 2 diabetes targets through molecular docking and dynamics simulations This study provides a comprehensive computational evaluation of luteolin derived from Caralluma tuberculata, offering detailed insights into its enzyme-specific interactions with key carbohydrate hydrolyzing enzymes relevant to type 2 diabetes. Although the results are promising, experimental and clinical validation is essential to confirm luteolin's therapeutic efficacy for managing type 2 diabetes. Luteolin ; In silico ; Metabolite ; Molecular dynamics ; Metabolomics ; Docking (animal) ; Sucrase Phytochemistry and Bioactive Compounds ; Computational Drug Discovery Methods ; Seaweed-derived Bioactive Compounds
Authors: Hengfu Yang | Guoming Zhao | Xing Fan | Chunxiao Qiao | Bingfei Li | Xiang Bai | Qingxin Wu
Source: Research Square (preprint, 2026-02-18)
Field: Chemistry — Inorganic Chemistry

The qualitative correlation between activation energy and acid strength: the influence of crystal structure regulation on the acidity of H 2 SO 4 /ZrO 2 -WO 3 in low-temperature dealkylation Sulfuric acid ; Catalysis ; Activation energy ; Arrhenius equation ; Alkylation ; Aqueous solution ; Monoclinic crystal system ; Selectivity ; Ammonia Zeolite Catalysis and Synthesis ; Polyoxometalates: Synthesis and Applications ; Mesoporous Materials and Catalysis