jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Pahweenvaj Ratnatilaka Na Bhuket | Han Wu | Sheri L. Holmen | S. Michael Yu
Source: Biomacromolecules (article, 2025-12-23)
Field: Materials Science — Biomaterials

Modulating Refolding and Collagen Binding of Collagen Hybridizing Peptides through Peptoid Incorporation Collagen hybridizing peptides (CHPs) selectively bind denatured collagens (dColl), offering a powerful platform for diagnostics and targeted drug delivery. However, the rapid self-trimerization of GPO-derived CHPs (O = hydroxyproline) limits their applications. Here, we present peptoid-based strategies to reduce the triple helix stability and refolding speed of (GPO)<sub>9</sub> by introducing derivatives of Nasp (<i>N</i>-carboxymethyl glycine). Systematic substitution studies revealed that N<sup>α</sup>-C<sup>β</sup> branched Nsce (<i>N</i>-(<i>S</i>)-carboxyethyl glycine) destabilized the triple helix primarily through steric hindrance rather than electrostatic repulsion. Triple Nsce substitutions not only drastically reduced the refolding propensity but also compromised dColl binding. In contrast, the nonbranched Nasp residue, under the same conditions, slowed refolding while enhancing gelatin binding compared to (GPO)<sub>9</sub>. The CHP incorporating Nasp stained dColl associated with skin melanoma in histological sections as effective as (GPO)<sub>9</sub>. Our findings demonstrate that CHPs incorporating peptoid residues may enable fine-tuning of CHP folding and binding kinetics for the development of next-generation CHPs. Peptoid ; Triple helix ; Collagen helix ; Steric effects ; Gelatin ; Kinetics ; Helix (gastropod) ; Peptide Collagen: Extraction and Characterization ; Supramolecular Self-Assembly in Materials ; Marine Biology and Environmental Chemistry
Authors: Md Nasir Uddin | Shah Md Tamim Kabir | M. Azizur R. Khan | Muhammad Wajid Ullah | Md. Anamul Hoque | K. M. Anis‐Ul‐Haque | Mansour K. Gatasheh
Source: International Journal of Biological Macromolecules (article, 2025-08-31)
Field: Chemistry — Organic Chemistry

Competitive micellization and host–guest complexation of sodium dodecyl sulfate with <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.svg"> <mml:mi>β</mml:mi> </mml:math> -cyclodextrin: Insights from the Hofmeister series Chemistry ; Sodium dodecyl sulfate ; Medicinal chemistry ; Chromatography ; Analytical Chemistry (journal) Surfactants and Colloidal Systems ; Drug Solubulity and Delivery Systems ; Protein Interaction Studies and Fluorescence Analysis
Authors: Recep Üzek
Source: Hittite Journal of Science & Engineering (article, 2025-09-30)
Field: Materials Science — Materials Chemistry

Tailoring Graphene Quantum Dots through the Pyrolysis of Citric Acid, Phenylalanine, and Tryptophan: Effect of Precursor Ratios on Synthesis Efficiency and Properties Graphene Quantum Dots (GQDs) are gaining significant attention due to their unique optical, electronic, and biocompatible properties, making them ideal candidates for applications in bioimaging, sensing, and drug delivery. This study explores the synthesis of GQDs derived from citric acid (CA), phenylalanine (Phe), and tryptophan (Trp) using a pyrolysis method, where GQDs were synthesized using 2.0 g of CA with varying amounts of Phe (0.75 g, 0.50 g, 0.25 g) and Trp (0.25 g, 0.50 g, 0.75 g), corresponding to GQDs1, GQDs2, and GQDs3, respectively. The influence of precursor composition on the structural, optical, and physicochemical properties of GQDs was analyzed. Particle size measurements showed a hydrodynamic diameter range of 0.89 nm to 1.5 nm, with increasing Trp content leading to larger particles and a broader size distribution, reflected in polydispersity index (PDI) values of 0.221, 0.312, and 0.368 for GQDs1, GQDs2, and GQDs3, respectively. Zeta potential analysis revealed values of -21.4 mV, -12.2 mV, and -7.5 mV for GQDs1, GQDs2, and GQDs3, respectively, indicating reduced surface charge with higher Trp content, which may affect colloidal stability. Optical characterization showed π→π* (~230–270 nm) and n→π* (~300–350 nm) transitions in the UV-Vis spectra, with varying absorbance intensities across samples. Fluorescence spectroscopy confirmed strong emission properties, which were highly dependent on precursor ratios. Quantum yield (QY) values were 32.2%, 95.5%, and 75.6% for GQDs1, GQDs2, and GQDs3, respectively, highlighting the role of nitrogen doping in fluorescence enhancement. These findings demonstrate that controlled precursor composition can fine-tune GQD properties, offering potential for optoelectronic, bioimaging, and sensing applications. Further exploration of functionalization strategies could enhance their practical utility. Quantum dot ; Citric acid ; Zeta potential ; Dispersity ; Quantum yield ; Absorbance ; Particle size ; Fluorescence ; Graphene Carbon and Quantum Dots Applications ; Graphene and Nanomaterials Applications ; Nanocluster Synthesis and Applications
Authors: Yanbo Zhao | Dongnan Tu | Rucheng Dai | Alexander A. Trifonov | Chuanlang Zhan
Source: Chemistry - An Asian Journal (article, 2025-12-09)
Field: Chemistry — Organic Chemistry

Enhancing Circularly Polarized Luminescence of Tb(III) Complexes via Remote Substitutions on Pyridine‐2,6‐Dicarboxamide Chiral trivalent lanthanide complexes are of interest since their parity-allowed magnetic dipole transition generally shows large luminescence dissymmetry (g<sub>lum</sub>) factors. However, the luminescence intensity is normally weak, which is yet another challenge. Herein, we introduce electron-withdrawing and -donating moieties (F and methyl, respectively) at the para-positions of phenyl on N,N'-bis (1-phenylethyl)-2,6-pyridinediamide. We found that this approach, for example, modifying the remote positions of ligands, enables decreasing the triplet state energy levels of ligands from 27060 cm<sup>-1</sup> (H) to 24154 cm<sup>-1</sup> (F) and 24390 cm<sup>-1</sup> (methyl) and enhancing the ligand-to-ion sensitization from 0.35 to 0.41 and 0.47 and photoluminescent quantum yields (PLQYs) from 17% to 23% and 25%. The g<sub>lum</sub>-factors are ±0.1 for the three Tb(III) complexes coordinated with the synthesized ligands in their ethanol solutions, yielding circularly polarized luminescence (CPL) brightness (B) values of 0.017, 0.023, and 0.025, respectively. Single crystal structures reveal the chirality transfer from the chiral ligands to the complex and then to supramolecular chiral packing of complexes and also effective modulations on the supramolecular chiral packing. Collectively, these findings establish remote ligand engineering as a robust and versatile strategy for fine-tuning CPL brightness. Luminescence ; Supramolecular chemistry ; Chirality (physics) ; Lanthanide ; Ligand (biochemistry) ; Photoluminescence ; Magnetic dipole transition ; Supramolecular chirality Synthesis and Properties of Aromatic Compounds ; Lanthanide and Transition Metal Complexes ; Magnetism in coordination complexes
Authors: Xiang Zhuang | Bin Wu | Jiyu Cui | Kehua Feng | Xiaotong Li | Huabin Xing | Keyan Ding | Qiang Zhang | Huajun Chen
Source: ArXiv.org (preprint, 2025-06-29)
Field: Materials Science — Materials Chemistry

Boosting LLM's Molecular Structure Elucidation with Knowledge Enhanced Tree Search Reasoning Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE. Boosting (machine learning) ; GRASP ; Knowledge base ; Construct (python library) ; Tree structure ; Tree (set theory) ; Cheminformatics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Advanced Graph Neural Networks
Authors: Chetan K. Kasar | A. U. Sonawane | Neha Bano
Source: MatSci express. (article, 2025-12-01)
Field: Materials Science — Materials Chemistry

Tailoring the Structural and Optoelectronic Properties of Zinc Oxide Nanofilms through Europium Doping This research comprehensively investigates the synthesis and characterization of zinc oxide (ZnO) nanofilms doped with varying concentrations of europium (Eu) and explores the subsequent effects of post-annealing temperatures. The primary objective was to engineer the properties of ZnO, a pivotal semiconductor, for enhanced optoelectronic applications. Nanofilms with Europium concentrations ranging from 0 to 7 atomic percent were deposited onto glass substrates using a sol-gel spin-coating technique. The structural analysis via X-ray diffraction confirmed that all films retained the hexagonal wurtzite structure of ZnO without the formation of secondary phases, indicating successful incorporation of Eu ions. Interestingly, the crystallite size was observed to increase with higher europium content, a phenomenon attributed to the larger ionic radius of Eu compared to Zn. Optically, the films demonstrated exceptional transparency, exceeding 90% in the visible spectrum. Doping with europium systematically increased the optical bandgap energy from 3.200 eV to 3.262 eV and enhanced absorption in the ultraviolet region. Photoluminescence spectroscopy revealed a characteristic ultraviolet emission peak alongside a weaker visible emission associated with intrinsic defects. The intensity of this emission was modulated by the doping concentration. These findings collectively demonstrate that europium doping is a highly effective strategy for fine-tuning the structural and optical characteristics of ZnO nanofilms, making them promising candidates for advanced light-emitting devices and solar energy applications. Europium ; Wurtzite crystal structure ; Photoluminescence ; Doping ; Band gap ; Crystallite ; Ultraviolet ; Zinc ; Ionic radius ZnO doping and properties ; Polymer Nanocomposite Synthesis and Irradiation ; Optical Coatings and Gratings
Authors: Pavel, Popov
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2025-12-08)
Field: Chemistry — Physical and Theoretical Chemistry

Grid Physics: A Computational Geometric Unification of the Standard Model and Nuclear Binding Energies within Simureality framework Grid Physics: A Geometric Unification of the Standard Model and Nuclear Structure This paper presents the Simureality Framework, a unified theory of fundamental physics derived from the principle of Computational Optimization ($\Sigma K \to \min$). By modeling the physical vacuum as a discrete Face-Centered Cubic (FCC) lattice, we demonstrate that physical laws are emergent protocols of a finite computational system. Key Findings: Voxel Topology: The 12 Gauge Bosons of the Standard Model ($SU(3) \times SU(2) \times U(1)$) are decoded as the geometric degrees of freedom of a single Cubic Voxel (8 Vertices + 3 Axes + 1 Center). Mass Spectrum: We introduce the Node Square Law ($M \propto N^2$), which derives the masses of leptons and quarks from integer lattice excitations with $>99\%$ accuracy. Nuclear Crystallography: The atomic nucleus is redefined not as a liquid drop, but as a crystal of Alpha-particles. The proposed "Alpha-Ladder" model calculates binding energies for alpha-conjugate nuclei (e.g., $^{12}C, ^{16}O, ^{40}Ca$) with $>99.9\%$ precision. Fundamental Constants: The Proton-to-Electron mass ratio ($\mu \approx 6\pi^5$) and the Fine-Structure Constant ($\alpha^{-1} \approx 137.036$) are derived analytically as geometric properties of the lattice interface, matching CODATA values to within $0.002\%$. The framework resolves the fine-tuning problem by replacing arbitrary parameters with rigorous discrete geometry. Binding energy ; Grid ; Lattice (music) ; Degrees of freedom (physics and chemistry) ; Gauge theory ; Standard Model (mathematical formulation) ; Geometric modeling History and advancements in chemistry ; Cold Fusion and Nuclear Reactions ; Computational Physics and Python Applications
Authors: Melda Taspika | Takehiro Yachi | Xu Shi | Daisuke Unabara | Tasuku Hamaguchi | Koji Yonekura | Yusuke Yonamine | Hideyuki Mitomo | Kuniharu Ijiro
Source: Langmuir (article, 2025-10-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Controlled Assembly of Gold Nanodiscs via DNA Hybridization: Tuning Plasmonic Coupling via Interparticle Gap Distance and Multimerization Degree Metal nanoparticle assemblies induce interparticle plasmonic coupling, and precise control of this coupling by arranging the geometrical and spatial conditions is crucial for the application of plasmonic materials. In this study, gold nanodiscs (AuNDs) modified with complementary short DNA ligands (positive-sense DNA, (+)-DNA; negative-sense DNA, (-)-DNA) were assembled into 1D cylindrical structures with various interparticle gap distances and degrees of multimerization, enabling the precise tuning of plasmonic coupling strength. Specifically, AuNDs (90 nm in diameter) functionalized with 11-base (+)-DNA and (-)-DNA ligands were mixed and assembled into multimers through face-to-face interactions, driven by the hybridization of short DNA ligands without linker strands. This assembly induced strong plasmonic coupling owing to the short interparticle gap distance (5.7 nm), which led to significant peak shifts in the extinction spectra. Additionally, the plasmonic coupling strength was fine-tuned by varying the interparticle gap distance using DNA strands of different lengths (8, 11, and 20 base pairs). Furthermore, the assembly and disassembly temperatures of the DNA-AuNDs were tuned by adjusting (i) the salt concentration in the solution and (ii) the length of the DNA ligands. Finally, the degree of multimerization, which has a pronounced effect on the plasmonic coupling strength, was modulated by adjusting (i) the molar ratio of (+)-DNA-AuNDs to (-)-DNA-AuNDs and (ii) the salt concentration in the solution. This paper presents a simple and effective method to tune the plasmonic coupling of AuND assemblies, thereby expanding the potential applications of plasmonic materials. Plasmon ; Coupling (piping) ; DNA origami ; Linker ; Plasmonic nanoparticles ; Nanoparticle ; Colloidal gold ; Nanostructure Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Plasmonic and Surface Plasmon Research
Authors: Wasan Joopor (22820152) | Worawat Wattanathana (11961274) | Chawakorn Chansaenroch (22820155) | Pimpa Hormnirun (1513462)
Source: Figshare (article, 2025-12-10)
Field: Materials Science — Biomaterials

Titanium AlkoxideComplexes of Phenoxy-Azo and Phenoxy-ImineLigands for Cyclic Ester (Co)Polymerization Studies: Tuning PolymerizationActivity through Ligand Design Two series of titanium complexes supported by monoanionic phenoxy-azo (<b>1–7</b>) and phenoxy-imine (<b>8–12</b>) ligands were successfully synthesized and fully characterized. X-ray structure analysis of the bis(phenoxy-azo)titanium complexes <b>1</b> and <b>4</b> revealed that the titanium atom was in a distorted octahedral geometry, with the <i>trans</i>-O, <i>cis</i>-N, <i>cis</i>-O<sup><i>i</i></sup>Pr configuration. All complexes were active for the ring-opening polymerizations of <i>rac</i>-lactide, ε-caprolactone, and ε-decalactone. For <i>rac</i>-LA polymerization, the bis(phenoxy-azo)titanium complex bearing alkyl phenoxy substituents exhibited superior catalytic activity compared to its bis(phenoxy-imine)titanium analogue with identical substituents. In contrast, a reverse trend was observed upon introducing halogenated phenoxy substituents. Kinetic investigations revealed the origin of the diminished catalytic activity of the halogenated bis(phenoxy-azo)titanium complexes. Perfect diblock copolymers, poly(CL-<i>b</i>-<i>rac</i>-LA) and poly(CL-<i>b</i>-l-LA), were successfully synthesized via a sequential-feed copolymerization, while a single-feed copolymerization of <i>rac</i>-LA/l-LA and ε-CL afforded practically random copolymers. This study demonstrated that the catalytic activity of bis(phenoxy-imine)titanium complexes was enhanced by substituting the imine unit with an azo moiety, highlighting that catalytic activity can be fine-tuned through ligand design. Alkoxide ; Catalysis ; Ligand (biochemistry) ; Titanium ; Polymerization ; Octahedron biodegradable polymer synthesis and properties ; Organometallic Complex Synthesis and Catalysis ; Carbon dioxide utilization in catalysis
Authors: Chiara Mariani (20716841) | Alessandro Fracassa (19562353) | Paolo Pastore (1873846) | Sara Bogialli (1598125) | Francesco Paolucci (528046) | Giovanni Valenti (1479859) | Alessandra Zanut (6388544)
Source: Figshare (article, 2025-05-09)
Field: Chemistry — Electrochemistry

Singling Out the ElectrochemiluminescenceProfilein Microelectrode Arrays Among various electrochemical imaging techniques, electrochemiluminescence microscopy (ECLM) stands out as a powerful approach to visualize electrochemical reactions by converting localized reactivity into optical signals. This study investigates ECL light emission spatial distribution in a confined space by using microelectrode arrays (MEAs) fabricated on glassy carbon (GC) and gold (Au) substrates via thermal nanoimprint lithography (TNIL). With the Ru(bpy)<sub>3</sub><sup>2</sup><sup>+</sup>/TPrA system, ECL imaging revealed distinct emission profiles, with Au exhibiting a broader spatial distribution compared to GC under identical geometric conditions. The estimated thickness of the ECL emitting layer (TEL) was significantly larger on Au (∼7 μm) than on GC (∼4 μm), attributed to the interplay between the electrode material and dominant ECL mechanism. Decreasing Ru(bpy)<sub>3</sub><sup>2</sup><sup>+</sup> concentration resulted in minimal perturbation of the GC ECL profile, consistent with a predominant oxidative–reductive mechanism. In contrast, a significant narrowing of the ECL profile was observed on Au, indicative of a transition from a catalytic to an oxidative–reductive pathway. These observations were corroborated and rationalized by finite element simulations. Our findings demonstrate the capacity to fine-tune the Thickness of the Emission Layer (TEL) and modulate ECL emission through electrode material selection and luminophore concentration. Such precise control has significant implications for the development of highly sensitive and spatially resolved bioanalytical assays, particularly those employing bead-based detection methodologies. Electrochemiluminescence ; Luminophore ; Microelectrode ; Electrode ; Glassy carbon ; Microscopy ; Electrochemistry ; Layer (electronics) Electrochemical Analysis and Applications ; Advanced biosensing and bioanalysis techniques ; CO2 Reduction Techniques and Catalysts
Authors: M. Praveen | R. Hari Krishna | E. V. Bhavya | Balamati Choudhury | B.M. Nagabhushana
Source: Ceramics International (article, 2025-07-02)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Magnetic SrFe12O19 and conductive MWCNT/graphene in low-density polyethylene nanocomposite for superior EMI shielding performance: Investigation on the synergistic behavior of fillers Materials science ; Nanocomposite ; Electromagnetic shielding ; EMI ; Composite material ; Graphene ; Electrical conductor ; Low-density polyethylene ; Polyethylene ; Filler (materials) ; Electromagnetic interference ; Nanotechnology ; Electrical engineering Electromagnetic wave absorption materials ; Dielectric materials and actuators ; Advanced Antenna and Metasurface Technologies
Authors: Jialu Yang (11410481) | Ting Chen (15205) | Yuanyuan Li (18671) | Yanmei Zhou (763932)
Source: Figshare (article, 2025-07-03)
Field: Chemistry — Spectroscopy

Rational Design of Organelle-Targeting/Migration FluorescentProbes via Bidirectional Regulatory Strategies and Computational Simulations The establishment of organelle-targeted and inwardly migratable fluorescent probes is important for studying apoptosis mechanisms and understanding the process. By fine-tuning the precise localization of the probes and their migration from the mitochondria to the nucleus, it is possible to image changes in organelle dynamics and the entire apoptotic process. However, existing probes lack a universal design strategy to image the dynamic behavior of organelles at all stages of apoptosis with high specificity, and methods still face significant challenges in resolving the molecular mechanisms of probe migration at the atomic scale. Here, a carbazole backbone platform (<b>Car-X</b>) for fluorescent probes was constructed by organelle-targeting methods and computational simulations. The relevant physical parameters verified the feasibility of the <b>Car-X</b> design. Through the bidirectional regulation strategy of “multivalency principle” and hydrophilic/hydrophobic design, <b>Car-X</b> achieves specific targeting to the cell membrane, mitochondria and nucleus, as well as the shift of mitochondria to nucleus migration when mitochondria are damaged. In addition, the visualization of <b>Car-X</b> on the three organelles facilitates the presentation of different stages of apoptosis in the simulation of intelligent biological processes. This strategy of bidirectional modulation of fluorescent probes by computationally assisted simulations provides new ideas for the design of organelle optical probes, which is expected to advance the research in organelle-related fields. Organelle ; Rational design ; Mitochondrion ; Fluorescence ; Computational model ; Nucleus Molecular Sensors and Ion Detection ; Cell death mechanisms and regulation ; Metal complexes synthesis and properties