jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tendy Oktriawan | Bina Agustin Aulia | Timur Setyawan | Tri Joko Raharjo | Winarto Haryadi | Laurent Commeiras | Muhammad Idham Darussalam Mardjan
Source: Trends in Sciences (article, 2025-10-15)
Field: Chemistry — Organic Chemistry

Quinazolinone Derivatives as Targeting pfDHFR and pfDHODH Inhibitor: In Silico Studies Using Molecular Docking, Molecular Dynamics Simulations, MM-PBSA, and ADMET Analysis Malaria remains a significant global health concern, with rising resistance to current antimalarial drugs. pfDHFR (Plasmodium falciparum Dihydrofolate Reductase) and pfDHODH (Plasmodium falciparum Dihydroorotate Dehydrogenase) are critical enzymes for parasite survival and have emerged as promising targets for drug development. Quinazolinones have shown potential as antimalarial agents due to their diverse pharmacological activities. This study aims to evaluate quinazolinones as potential inhibitors of pfDHFR and pfDHODH using molecular docking, molecular dynamics simulations, and ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) profiling to identify optimal candidates with improved efficacy and pharmacokinetics. Thirty quinazolinone derivatives were subjected to molecular docking against pfDHFR and pfDHODH to assess binding affinity and interaction modes. Promising compounds were further analyzed through molecular dynamics simulations to evaluate complex stability. Additionally, ADMET profiling was conducted to predict pharmacokinetic properties and toxicity. Molecular docking identified compounds 3, 5, and 12 as promising pfDHFR inhibitors, with compound 3 exhibiting the most favorable binding energy. For pfDHODH, compounds 2, 11, and 20 showed strong interactions. Molecular dynamics simulations confirmed the stability of these complexes, with compounds 3 and 5 being stable against pfDHFR and compounds 20 and 11 against pfDHODH. ADMET analysis revealed favorable drug-like properties for these compounds, although some toxicity concerns were noted. This study demonstrates the potential of quinazolinone derivatives as next-generation antimalarial agents targeting pfDHFR and pfDHODH. Compounds 3, 5, 11, and 12 are identified as promising candidates due to their strong binding affinities and stable pharmacokinetic profiles. Further optimization and experimental validation are necessary to develop these compounds into effective therapeutic agents against malaria. HIGHLIGHTS Thirty quinazolinone derivatives were designed and examined as potential inhibitors of pfDHFR and pfDHODH through molecular docking and dynamic simulations. C-Arylquinazolinones bearing hydroxyl groups were the most potential candidates. The ADMET results showed that the quinazolinones exhibited no potential toxicity. GRAPHICAL ABSTRACT Quinazolinone ; Molecular dynamics ; In silico ; Binding affinities ; Lipinski's rule of five ; Molecular model ; Drug ; Drug discovery Quinazolinone synthesis and applications ; Malaria Research and Control ; Computational Drug Discovery Methods
Authors: Catriona H. E. Rooney | Justin Y. C. Lau | Esben Søvsø Szocska Hansen | Nichlas Vous Christensen | Duy Dang | Kristoffer Petersson | Iain D. C. Tullis | Borivoj Vojnovic | Sean Smart | William K. Myers | Zoe Richardson | Jarrod Lewis | Brett W. C. Kennedy | Alice M. Bowen | Lotte Bonde Bertelsen | Christoffer Laustsen | Damian J. Tyler | Jack J. Miller
Source: Science Advances (preprint, 2025-11-21)
Field: Chemistry — Spectroscopy

Stable electron-irradiated [1- <sup>13</sup> C]alanine radicals for metabolic imaging with dynamic nuclear polarization Dissolution dynamic nuclear polarization (dDNP) increases the sensitivity of magnetic resonance experiments by >10<sup>4</sup>-fold, permitting isotopically labeled molecules to be transiently visible in magnetic resonance imaging scans. dDNP mechanistically takes place at ~1 K and requires unpaired electrons and microwaves. These electrons are usually chemical radicals, requiring removal by filtration prior to injection into humans. Alternative sources, such as ultraviolet irradiation, generate lower polarization and require cryogenic transport. We present ultrahigh-dose rate electron irradiation as an alternative for generating nonpersistent radicals in alanine/glycerol mixtures. These are stable for months at room temperature, quench spontaneously upon dissolution, are present in dose-dependent concentrations, and generate comparable nuclear polarization (17%) to trityl radicals used clinically (19%) through a previously unknown mechanism we believe to involve partial ordering and electron-electron interactions. Owing to the large radiation doses required, this process is sterilizing, permits imaging of alanine metabolism in vivo in the rat kidney, and may aid clinically translating dDNP. Radical ; Polarization (electrochemistry) ; Unpaired electron ; Electron ; Magnetic resonance imaging ; In vivo ; Molecule ; Irradiation Advanced NMR Techniques and Applications ; Electron Spin Resonance Studies ; Advanced MRI Techniques and Applications
Authors: Muhammad Irfan | Bill D. Aparicio-Huacarpuma | Carlos M. O. Bastos | Maurício J. Piotrowski | Celso R. C. Rêgo | Diego Guedes‐Sobrinho | Rafael Besse | A. M. Silva | Alexandre C. Dias | Luiz Antônio Ribeiro
Source: ArXiv.org (preprint, 2025-06-18)
Field: Materials Science — Materials Chemistry

Towards High-Efficiency Solar Cells: Insights into AsNCa 3 Antiperovskite as Active Layer Advances in photovoltaic technology are a viable route to contribute to cleaner and more sustainable energy solutions, placing perovskite-based materials among the best candidates for solar energy conversion. However, some challenges must be addressed to enhance their performance and stability. Herein, we report an investigation of the AsNCa3 antiperovskite system for its potential in photovoltaic devices. We consider eight distinct crystalline phases, their structural parameters, dynamical stability, and electronic and optical properties. Furthermore, we consider each structural phase's contributions to solar harvesting efficiency by calculating the power conversion efficiency (PCE) using the spectroscopiclimited maximum efficiency (SLME) formalism, which in this case reaches a maximum of 31.2%. All dynamically stable phases exhibit a band gap around 1.3 eV, which lies within the optimal range for single-junction solar cells and yields PCE values comparable to the theoretical maximum PCE for silicon. These results place AsNCa3 antiperovskites as promising candidates for high-efficiency photovoltaic applications. Notably, the PCE is only slightly changed by structural phase modification, suggesting that phase transitions induced by environmental conditions during device operation might not compromise device performance. Antiperovskite ; Photovoltaic system ; Energy conversion efficiency ; Solar energy ; Band gap ; Photovoltaics ; Sustainable energy ; Active layer Thermal Expansion and Ionic Conductivity ; Perovskite Materials and Applications ; Advanced Battery Materials and Technologies
Authors: X. L. Wang
Source: Theory and Practice of Science and Technology (article, 2025-07-01)
Field: Materials Science — Materials Chemistry

EIS response characteristics and Randles modeling analysis of typical solid electrolytes at low temperatures Solid-state batteries, due to their high safety and high energy density, have gradually become a key technology to promote the development of new energy vehicles, aerospace and renewable energy storage systems. However, its capacity decay and rate performance decline are common problems at low temperatures, which are mainly limited by the decrease of ionic conductivity and the increase of interface impedance of solid electrolyte materials. In order to further understand the electrochemical characteristics of different electrolyte materials at low temperatures, three representative solid electrolytes - polymer PEO, sulfide LPS and oxide LLZO - were selected in this paper, and equivalent circuits based on simplified Randles model were constructed to carry out impedance frequency domain simulation analysis. The transport resistance and interface behavior of the three materials at -20 °C were compared by using the simulated Nyquist diagram. The simulation results show that LPS exhibits the lowest interfacial impedance and excellent ion conductivity, LLZO achieves a good balance between conductivity and stability. At the same time, PEO has the highest interfacial reaction resistance, limiting its cryogenic application potential. This study provides the theoretical basis and technical support for material selection and structure optimization of solid-state batteries in cold environment. Electrolyte ; Materials science ; Analytical Chemistry (journal) ; Chemistry ; Chromatography ; Physical chemistry Solid-state spectroscopy and crystallography
Authors: Harsh P. Chavda | Kevin J. Liang | Tanner J. Megna | Olivia R. Taylor | Grace Kim | Angie López | Ana Bahamonde
Source: ChemRxiv (preprint, 2025-04-04)
Field: Chemistry — Organic Chemistry

Indole Photocatalysts and Secondary Amine Ligands Enable Nickel-Photoredox C(sp2)–Heteroatom Couplings Nickel-photochemical C(sp²)–heteroatom coupling reactions have emerged as a powerful tool for constructing diverse molecular architectures. However, most existing methods rely on expensive photocatalysts or specialized ligands, limiting their practicality and scalability. Here, we introduce a photocatalytic initiation strategy driven by inexpensive indoles, eliminating the need for designer photocatalysts. Additionally, we demonstrate the effectiveness of highly tunable secondary amine ligands in facilitating coupling while suppressing side reactions that sequester the Ni catalyst off-cycle. Our approach enables a broad range of amination and etherification reactions with excellent yields and functional group tolerance, providing a scalable platform for C–N and C–O couplings that relies on a readily available photocatalyst and cost-effective, modular ligands. Finally, mechanistic investigations suggest that the reaction operates via an unconventional aryl radical-initiated Ni(I/III) catalytic cycle, distinguishing it from traditional Ni-photoredox processes. This new initiation mode, in which aryl radicals are generated under mild conditions compatible with organometallic catalysis, is expected to serve as a generalizable platform for other synthetic transformations beyond Ni-catalyzed processes. Heteroatom ; Nickel ; Amine gas treating ; Indole test ; Chemistry ; Photochemistry ; Combinatorial chemistry ; Organic chemistry ; Ring (chemistry) Radical Photochemical Reactions ; Catalytic C–H Functionalization Methods ; Polyoxometalates: Synthesis and Applications
Authors: Elif Şahin | Ahmet Gürses
Source: DergiPark (Istanbul University) (article, 2025-06-24)
Field: Chemistry — Spectroscopy

Preparation and characterization of melamine formaldehyde organo clay nanocomposite foams (MFCNCF) Melamine formaldehyde resins are one of the well-known thermosetting resins. It has been observed that melamine formaldehyde foam composites prepared with various nanoparticle reinforcements exhibit better mechanical, thermal and sound insulation properties. In this study, it was aimed to synthesize melamine formaldehyde organoclay nanocomposite foams and investigate their thermal insulation and mechanical stability by using microwave irradiation and heating technique together, which can offer advantages such as faster reaction, high yield and purity, reduced curing time. Pure melamine formaldehyde foam, MFF and melamine formaldehyde organoclay nanocomposite foams, MAFCNFs prepared with various organoclay contents were characterized by HRTEM, FTIR, SEM and XRD techniques. From spectroscopic and microscopic analyses, it was observed that organoclay platelets could be exfoliated with increasing clay content without undergoing much change in the resin matrix. The highest compressive strength was obtained in the MFCNCF3 foam with high organo clay content (0.68MPaN/mm2) and the bulk density was determined to be quite low (0.20g/cm3). On the other hand, in the nanocomposite with 0.15% organo clay content (MFCNCF2), a compressive strength of 0.32 N/mm2 and a thermal conductivity coefficient of 0.065 were measured. Nanocomposite ; Characterization (materials science) ; Formaldehyde ; Melamine ; Fourier transform infrared spectroscopy Aerogels and thermal insulation ; Mesoporous Materials and Catalysis ; Polymer Nanocomposites and Properties
Authors: Rebecca Olanrewaju | Yunlong Jiang | Thao D. Nguyen | David O. Kazmer
Source: Polymers (article, 2025-10-08)
Field: Materials Science — Polymers and Plastics

Influence of Shape-Forming Elements on Microstructure and Mechanical Properties in Coextruded Thermoplastic Composites The immiscibility of most polymers leads to poor interfacial adhesion in blends, a critical challenge that often limits the mechanical performance of polymer composites. This research introduces shape-forming elements (SFEs), a novel class of coextrusion dies designed to create additional geometric complexity and control over interfacial architecture. Specifically inspired by Julia Set and T-Square fractals, SFEs were simulated, prototyped, and found to be effective in coextrusion of different-colored polymer clays. The SFEs were employed to coextrude architected composites consisting of a liquid crystalline polymer (Vectra A950) and a cycloaliphatic polyamide (Trogamid CX7323). Mechanical testing revealed a strong positive correlation between the draw ratio and both the tensile modulus (adjusted R<sup>2</sup> = 0.94) and tensile stress at break (adjusted R<sup>2</sup> = 0.84). However, experimental cross-sections significantly differed from simulation results. These discrepancies were attributed to interfacial instabilities caused by material incompatibility between the two polymers and potential moisture-induced defects. This finding highlights critical challenges that arise during practical processing, emphasizing the importance of addressing polymer compatibility and moisture management to realize the full potential of SFEs in designing advanced polymer composites with targeted properties. Polymer ; Ultimate tensile strength ; Compatibility (geochemistry) ; Polyamide ; Microstructure ; Modulus ; Tensile testing ; Adhesion Polymer crystallization and properties ; Rheology and Fluid Dynamics Studies ; Polymer Nanocomposites and Properties
Authors: Alejandro Martínez León | L.B. Andersen | Jochen S. Hub
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-09-27)
Field: Chemistry — Spectroscopy

BindFlow: a free, user-friendly pipeline for absolute binding free energy calculations using free energy perturbation or MM(PB/GB)SA Abstract We present BindFlow, a Python-based software for automated absolute binding free energy (ABFE) calculations at the free energy perturbation (FEP) or at the molecular mechanics Poisson-Boltzmann/generalized Born surface area [MM(PB/GB)SA] level of theory. BindFlow is free, open-source, user-friendly, easily customizable, runs on work-stations or distributed computing platforms, and provides extensive documentation and tutorials. BindFlow uses GROMACS as molecular dynamics engine and provides built-in support for the small-molecule force fields GAFF, OpenFF, and Espaloma. We test BindFlow by computing affinities for 139 ligand/target pairs, involving eight different targets including six soluble proteins, one membrane protein and one non-protein host– guest system. Quantified by Pearson, Kendall, and Spearman correlations coefficients, we find that the agreement of BindFlow predictions with experiments are overall similar to gold standards in the field. Interestingly, we find that MM(PB/GB)SA achieves correlations that, for some systems and force fields, approach those obtained with FEP, while requiring only a fraction of the computational cost. This study establishes BindFlow as a validated and accessible tool for ABFE calculations. Free energy perturbation ; Molecular dynamics ; Thermodynamic integration ; Software ; Pipeline (software) ; Perturbation (astronomy) ; Total energy ; Energy (signal processing) Advanced NMR Techniques and Applications ; Advanced Chemical Physics Studies ; Protein Structure and Dynamics
Authors: Meshkat Dolat | Andrew D. Wright | Soudabeh Bahrami Gharamaleki | Loukia-Pantzechroula Merkouri | Melis S. Duyar | Michael Short
Source: ArXiv.org (preprint, 2025-10-14)
Field: Materials Science — Materials Chemistry

Kinetic modelling of the CO2 capture and utilisation on NiRu-Ca/Al dual function material via parameter estimation This study presents a detailed, open-source kinetic modelling computational framework for CO2 capture and utilisation using a newly formulated dual-function material (DFM) comprising 15 wt% Ni, 1 wt% Ru, and 10 wt% CaO supported on spherical alumina. A finite difference reactor model was developed to simulate the cyclic adsorption, purge, and hydrogenation stages. The model incorporates experimentally-derived rate expressions, accounts for system delay via a second-order response function, and was fitted to time-resolved concentration laboratory data using Bayesian optimisation. A combined parameter estimation strategy was employed to ensure mass continuity across stages and improve the robustness of purge kinetics. The kinetic parameters extracted reveal that carbonate decomposition, not methanation, is the rate-limiting step during hydrogenation. Temperature-dependent simulations confirm a trade-off between reaction kinetics and CO2 storage capacity, with methane yield maximised at 300C when compared with the other temperature sets. By offering transparent methodology and reproducible code, this work provides a robust platform for researchers and practitioners to study, validate, and optimise DFM systems. Robustness (evolution) ; Design for manufacturability ; Estimation theory ; Kinetic energy ; Work (physics) ; Methane ; Model parameter ; Yield (engineering) Catalytic Processes in Materials Science ; Intermetallics and Advanced Alloy Properties ; Metallurgical and Alloy Processes
Authors: Jiajing Sun
Source: Highlights in Science Engineering and Technology (article, 2025-07-02)
Field: Materials Science — Materials Chemistry

Development of TiNi Alloy Superelastic Guidewire Needle for New Type of Medical Arthroscopic Surgery This research focuses on the development of TiNi alloy super elastic guide needles for new medical arthroscopic surgery. With the development of sports medicine and the increasing demand for minimally invasive arthroscopic surgeries, the limitations of traditional surgical needles have become more prominent. TiNi shape - memory alloy (SMA) has unique super elasticity, shape - memory effect, and excellent mechanical properties, making it suitable for manufacturing super elastic suture needles. The project aimed to develop high - performance nickel - rich Ti - 50.8Ni - 0.4V SMA. The preparation process included designing alloys, melting into ingots, hot forging, rolling, and heat treatment. Various experimental methods were used, such as SEM, OM, DSC, TEM, and tensile testing, to analyze the phase transformation temperature, phase composition, microstructure, and super elastic properties of the alloys under different processing conditions. The results showed that for NiTi alloy wires, when annealed at 400 - 600 °C, as the heat - treatment temperature increased, the critical stress for stress - induced martensitic transformation decreased, the residual strain after tensile testing increased, and the super elasticity decreased significantly. When aged at 500 °C, with the prolongation of aging time, similar changes occurred. In the cyclic stress - strain curves, as the heat - treatment temperature increased, the residual strain of the wire increased, indicating a greater loss of super elasticity. However, wires annealed at 400 - 450 °C showed good continuous super elasticity. Also, the fatigue performance test of the alloy showed a fatigue life of more than 88,800 cycles under a stress of 200 MPa, with low energy loss and little impact on accuracy during use. In conclusion, low - temperature and short - time heat treatment is beneficial for obtaining good superelasticity of the alloy. The research provides a theoretical basis and experimental support for the actual production and application of superelastic guide needles with high strength and superelasticity for low - temperature use in arthroscopic surgeries. Pseudoelasticity ; Medicine ; Alloy ; Materials science ; Surgery ; Metallurgy ; Microstructure Shape Memory Alloy Transformations ; Titanium Alloys Microstructure and Properties ; Welding Techniques and Residual Stresses
Authors: Ling Meng | Samad Razzaq | Diwakar Singh | Francesc Viñes | Francesc Illas | Kai S. Exner
Source: Research Square (preprint, 2025-07-14)
Field: Materials Science — Materials Chemistry

Nitrogen Embedding Enhances Stability and Activity of Single-Atom Motifs of MXenes under Anodic Polarization MXenes ; Nitrogen ; Embedding ; Anode ; Nitrogen atom ; Polarization (electrochemistry) ; Atom (system on chip) ; Chemical physics ; Materials science ; Chemistry ; Nanotechnology ; Computer science ; Physical chemistry ; Electrode ; Artificial intelligence ; Organic chemistry MXene and MAX Phase Materials ; Ferroelectric and Negative Capacitance Devices ; Advanced Memory and Neural Computing
Authors: Lidia Santiago‐Silva | H. Cruz‐Martínez | H. Rojas‐Chávez | L. López‐Sosa | Patrizia Calaminici
Source: Journal of Molecular Modeling (article, 2025-02-10)
Field: Materials Science — Materials Chemistry

Structural transformation in Pd nanoclusters induced by Cu doping: an ADFT study Ground state structures and properties of Pd<sub>19</sub>, Pd<sub>18</sub>Cu, and Pd<sub>17</sub>Cu<sub>2</sub> nanoclusters were studied using the auxiliary density functional theory (ADFT), as implemented in the deMon2k code. For obtaining the ground state structures of Pd<sub>19</sub>, Pd<sub>18</sub>Cu, and Pd<sub>17</sub>Cu<sub>2</sub> nanoclusters, several dozen initial structures were taken along Born-Oppenheimer molecular dynamics (BOMD) trajectories and subsequently optimized without symmetry restrictions. The optimizations were performed with the revised PBE functional in combination with TZVP-GGA for the Cu atoms and using an 18-electron QECP|SD basis set for the Pd atoms. Different energetic and electronic properties were calculated for the most stable structures of Pd<sub>19</sub>, Pd<sub>18</sub>Cu, and Pd<sub>17</sub>Cu<sub>2</sub> nanoclusters. Interestingly, when the Pd nanocluster is doped with two Cu atoms (Pd<sub>17</sub>Cu<sub>2</sub>), there is a structural transition, because the most stable structures for Pd<sub>19</sub> and Pd<sub>18</sub>Cu are icosahedral. While the Pd<sub>17</sub>Cu nanocluster is characterized for a double-icosahedral-base structure. The binding energy per atom increases when the Cu concentration in the nanoclusters increases. According to the HOMO-LUMO gap, the chemical reactivity of the nanoclusters tends to increase as the Cu content in the nanoclusters increases. Nanoclusters ; Doping ; Materials science ; Density functional theory ; Nanoparticle ; Context (archaeology) ; Nanotechnology ; Chemical physics ; Nanomaterials ; Octahedron ; Transition metal ; Ground state ; Crystallography ; Molecular dynamics ; Crystal structure ; Computational chemistry ; Chemistry ; Physics ; Atomic physics ; Catalysis ; Optoelectronics ; Organic chemistry Nanocluster Synthesis and Applications ; nanoparticles nucleation surface interactions ; Advanced Chemical Physics Studies