jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Limashree Sahoo | Yi Zhang | Amrit Das | Sam de Visser | Chivukula V. Sastri
Source: Dalton Transactions (article, 2025-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Role of heteroatom substitution on the stability and reactivity of mononuclear Cu(<scp>ii</scp>)–alkylperoxo complexes Motivated by copper's essential role in biology and its wide range of applications in catalytic and synthetic chemistry, this work aims to understand the effect of heteroatom substitution on the overall stability and reactivity of biomimetic Cu(II)-alkylperoxo complexes. In particular, we designed a series of tetracoordinated ligand frameworks based on iso-BPMEN = (<i>N</i>,<i>N</i>-bis(2-pyridylmethyl)-<i>N</i>',<i>N</i>'-dimethylethane-1,2-diamine) with varying the primary coordination sphere using different donor atoms (N, O, or S) bound to Cu(II). The copper(II) complexes bearing iso-BPMEN and their modified heteroatom-substituted ligands were synthesized and structurally characterized. These novel complexes are manifested as biomimetic models of enzymatic copper(II) complexes that typically bind the metal through some neutral and anionic amino acid side chains. The <i>in situ</i> generated Cu(II)-alkylperoxo intermediates were spectroscopically characterized and evaluated for their stability and reactivity. The stability and reactivity of copper(II)-alkylperoxo intermediates exhibited diverse behaviors depending on the ligand. Interestingly, the reactivity for the S- and O-coordinated Cu(II)-alkylperoxo intermediates exhibited significantly higher (200-300 fold) electrophilic heteroatom oxidation efficiency compared to the N-bound Cu(II)-alkylperoxo species. Computational studies further support a mechanism involving O-O bond homolysis, followed by efficient oxygen atom transfer. These findings suggest that heteroatom substitution plays a crucial role in fine-tuning the oxidation chemistry of copper(II) complexes, enhancing their potential as biomimetic models for copper-based oxidation reactions. Heteroatom ; Substitution (logic) ; Reactivity (psychology) ; Chemistry ; Substitution reaction ; Stereochemistry ; Medicinal chemistry ; Organic chemistry ; Ring (chemistry) ; Philosophy ; Medicine Magnetism in coordination complexes ; Polyoxometalates: Synthesis and Applications ; Metal complexes synthesis and properties
Authors: Giulia Capitoli | Kirsten C. J. van Abeelen | Isabella Piga | Vincenzo L’Imperio | Marco S. Nobile | Daniela Besozzi | Stefania Galimberti
Source: Stats (article, 2025-07-10)
Field: Chemistry — Spectroscopy

Well Begun Is Half Done: The Impact of Pre-Processing in MALDI Mass Spectrometry Imaging Analysis Applied to a Case Study of Thyroid Nodules The discovery of proteomic biomarkers in cancer research can be effectively performed in situ by exploiting Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry Imaging (MSI). However, due to experimental limitations, the spectra extracted by MALDI-MSI can be noisy, so pre-processing steps are generally needed to reduce the instrumental and analytical variability. Thus far, the importance and the effect of standard pre-processing methods, as well as their combinations and parameter settings, have not been extensively investigated in proteomics applications. In this work, we present a systematic study of 15 combinations of pre-processing steps—including baseline, smoothing, normalization, and peak alignment—for a real-data classification task on MALDI-MSI data measured from fine-needle aspirates biopsies of thyroid nodules. The influence of each combination was assessed by analyzing the feature extraction, pixel-by-pixel classification probabilities, and LASSO classification performance. Our results highlight the necessity of fine-tuning a pre-processing pipeline, especially for the reliable transfer of molecular diagnostic signatures in clinical practice. We outline some recommendations on the selection of pre-processing steps, together with filter levels and alignment methods, according to the mass-to-charge range and heterogeneity of data. Mass spectrometry ; Mass spectrometry imaging ; Thyroid nodules ; MALDI imaging ; Thyroid ; Chemistry ; Medicine ; Matrix-assisted laser desorption/ionization ; Chromatography ; Internal medicine Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Nuclear Physics and Applications
Authors: Sameena | Shabbir Muhammad | Abdullah G. Al‐Sehemi | Aijaz Rasool Chaudhry | A. Alexandar | Saifeldin M. Siddeeg
Source: Journal of Nonlinear Optical Physics & Materials (article, 2025-07-18)
Field: Chemistry — Physical and Theoretical Chemistry

Quantum chemical prediction of nonlinear optical properties in Benzoxazine derivatives with symmetrical double acceptors: Insights from gas-phase, implicit solvent, and dynamics frequency studies The benzoxazine class of molecules offers promising potential for optical and nonlinear optical (NLO) properties, as their conjugated structures and electron-donating/withdrawing groups can be fine-tuned to enhance optical properties. The symmetrical double acceptor groups are introduced into central double donor benzoxazine core, and their NLO responses are thoroughly investigated using DFT. Among the designed compounds, DBB4 shows the highest performance with linear isotropic ([Formula: see text] and anisotropic ([Formula: see text] polarizabilities of [Formula: see text][Formula: see text]esu and [Formula: see text][Formula: see text]esu, respectively. The third-order NLO polarizability [Formula: see text] for DBB4 was found to be [Formula: see text][Formula: see text]esu, [Formula: see text] times greater than para-nitroaniline. To assess the solvent effects, polar and nonpolar implicit solvation models were applied to DPB4 and DBB4 for comparative study, revealing that the PCM model tends to overestimate NLO properties compared to gas phase calculations. TD-DFT analysis for DBB4 indicates the lowest transition energy of 2.81[Formula: see text]eV and the smallest HOMO–LUMO energy gap of 3.61[Formula: see text]eV for DBB4. The UV–Visible absorption spectra exhibit a red-shift at 440[Formula: see text]nm, while IR bands at 1708[Formula: see text]cm[Formula: see text] and 1532[Formula: see text]cm[Formula: see text] confirm presence of nitro group. The charge transfer properties are supported by molecular electrostatic and electron density difference maps. The topological analysis further reveals efficient electronic charge delocalization consolidating the role of DBB4 as a high-performance NLO candidate. Our findings underscore the strong potential of our designated derivatives as a next-generation NLO material for photonic and optoelectronic device applications. Quantum chemical ; Nonlinear system ; Solvent ; Quantum ; Gas phase ; Nonlinear optical ; Phase (matter) ; Materials science ; Chemical physics ; Physical chemistry ; Thermodynamics ; Quantum mechanics ; Physics ; Molecule ; Chemistry ; Organic chemistry Photochemistry and Electron Transfer Studies ; Nonlinear Optical Materials Research ; Protein Interaction Studies and Fluorescence Analysis
Authors: Elsa Susan Zachariah | Raji Mary Mathew | Jasmine Jose | Josmi John | G. Vinitha | Vinoy Thomas | I. Rejeena
Source: Materials Science and Engineering B (article, 2025-02-14)
Field: Materials Science — Materials Chemistry

Defect induced third order optical nonlinearities of nitrogen doped graphene quantum dots Graphene ; Quantum dot ; Doping ; Order (exchange) ; Materials science ; Nitrogen ; Condensed matter physics ; Nanotechnology ; Optoelectronics ; Physics ; Quantum mechanics ; Business Carbon and Quantum Dots Applications ; Graphene and Nanomaterials Applications ; Graphene research and applications
Authors: Jialu Yang | Ting Chen | Yuanyuan Li | Yanmei Zhou
Source: Analytical Chemistry (article, 2025-07-03)
Field: Materials Science — Biomaterials

Rational Design of Organelle-Targeting/Migration Fluorescent Probes 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. Chemistry ; Organelle ; Fluorescence ; Rational design ; Nanotechnology ; Biophysics ; Computational biology ; Biological system ; Cell biology ; Biochemistry Supramolecular Self-Assembly in Materials ; Click Chemistry and Applications ; Molecular Sensors and Ion Detection
Authors: Cecil Cherian Lukose | Guillaume Zoppi | Martin Birkett
Source: Applied Surface Science (article, 2025-01-09)
Field: Materials Science — Materials Chemistry

Emergence of near-zero temperature coefficient of resistance in the Mn3CuN antiperovskite thin film structure • Growth of Mn 3 CuN thin films with near-zero temperature coefficient of resistance (TCR). • Decreasing deposition pressure improves film density and resistance stability. • Heat treatment forms protective MnO layer to fine tune electrical properties. • Mn 3 CuN films grown at 0.2 Pa have TCR < 6 ppm/°C and resistance stability < 0.6 %. Thin film material systems with extremely low temperature coefficient of resistance (TCR) are highly sought for the fabrication of high precision electronic devices to replace existing nichrome and tantalum nitride technologies. Using reactive magnetron sputtering in a mixed argon/nitrogen atmosphere we produced Mn 3 CuN antiperovskite thin film structures and by careful control of the deposition parameters, reveal the emergence of near-zero TCR values. Optimum properties were obtained for films deposited at 0.2–0.3 Pa in a 17 % partial nitrogen plasma environment and following heat treatment (nitrogen at 325 °C) and stabilisation (air at 260 °C), with average TCR values reaching −6 ppm/°C and resistance stability as low as 0.57 % for unprotected films. We present full compositional, morphological and structural characterisation of the films and demonstrate that dense and stable Mn 3 CuN antiperovskite structures can be successfully grown by reactive magnetron sputtering for the future development of high precision thin film resistive components. Antiperovskite ; Materials science ; Temperature coefficient ; Thin film ; Condensed matter physics ; Zero (linguistics) ; Composite material ; Nanotechnology ; Physics ; Layer (electronics) ; Nitride Thermal Expansion and Ionic Conductivity ; Advanced Battery Materials and Technologies ; Ferroelectric and Piezoelectric Materials
Authors: Nirmala JP | M. Kanchana | R. R. Ambríz R.
Source: Food Biophysics (article, 2025-06-30)
Field: Materials Science — Biomaterials

Optimization of CMC/ɩ-Carrageenan Films for Packaging of Indian Cottage Cheese (Paneer) Using Response Surface Methodology Carrageenan ; Response surface methodology ; Materials science ; Food science ; Composite material ; Chemistry ; Chromatography Nanocomposite Films for Food Packaging ; Postharvest Quality and Shelf Life Management ; Polysaccharides Composition and Applications
Authors: J. Wang
Source: Journal of Physics Conference Series (article, 2025-05-01)
Field: Materials Science — Materials Chemistry

Density Functional Theory Study of Photocatalytic Applications of Metalloporphyrins: Structural, Electronic, and Photophysical Insights into Tetraphenylporphyrin Derivatives Abstract Metalloporphyrins, particularly tetraphenylporphyrin (TPP) derivatives, have established themselves as promising photocatalysts for environmental remediation, owing to their robust macrocyclic structures, extensive π-conjugated systems, and tunable photophysical properties through metal substitutions. This study employs density functional theory (DFT) to investigate the structural, electronic, and photophysical properties of mono-, bis-, and tetra-TPP configurations with Fe(II), Co(II), and Mg(II) as central metal ions. Detailed analyses of bond lengths, bond angles, and dihedral angles reveal the influence of metal substitution on molecular geometry, π-conjugation, and charge transfer efficiency. Evaluation of frontier molecular orbitals demonstrates that all studied porphyrins exhibit LUMO energy levels substantially below -0.33 V, enabling effective electron donation to reduce O 2 to •O 2 − . The HOMO-LUMO energy gaps and UV-vis absorption spectra reveal distinct differences in photophysical behavior among the derivatives, with MgTPP exhibiting the most redshifted absorption and narrowest energy gaps, thus enhancing its suitability for visible-light-driven photocatalytic applications. This investigation provides critical insights into the design and optimization of metalloporphyrin-based photocatalysts, demonstrating their potential as sustainable solutions for water pollution. The capability to fine-tune their electronic and photophysical properties through metal substitution offers a pathway toward developing efficient, cost-effective technologies for addressing the growing global challenge of water contamination. Tetraphenylporphyrin ; Photocatalysis ; Density functional theory ; Photochemistry ; Porphyrin ; Chemistry ; Materials science ; Computational chemistry ; Nanotechnology ; Catalysis ; Organic chemistry Porphyrin and Phthalocyanine Chemistry ; Photochemistry and Electron Transfer Studies ; Surface Chemistry and Catalysis
Authors: Michel Sassi | Tom Autrey
Source: ChemRxiv (preprint, 2025-02-18)
Field: Materials Science — Materials Chemistry

First principles study of molecular hydrogen activation by defects in boron nitride We used density functional theory simulations in combination with ab initio thermodynamics to determine the H2 partial pressure (p_("H" _"2" )) dependent energetics associated with H2 activation and recovery at various defect sites in hexagonal boron nitride (h-BN). We found that some defects are very reactive with hydrogen thereby definitely trapping hydrogen in defective h-BN. However, depending on hydrogen partial pressure, less reactive defect sites can be populated. Because of the lower binding capability of these sites, they would allow for hydrogen to be recycled and recovered. For small defect sizes, we found that hydrogen preferentially bind to nitrogen sites by forming N—H bonds, and if no N sites are available then boron sites would be the next to bind hydrogen. Hydrogen dissociation via Frustrated Lewis Pair (FLP) is found to be more favorable than forming only N—H bonds but only if the defect size is large enough to accommodate steric effects. For specific conditions such as T= 400 K, p_("H" _"2" )=1 bar, and only considering one molecular H2 per defect, three defects, namely the N monovacancy, 3V(1B2N), and hexagonal 6V(3B3N) could play a role in both the activation and recycling of H2, as they would be reacting enough to allow a favorable splitting of H2 while not binding too strongly to allow its recovery. More broadly, a range of p_("H" _"2" ) and hydrogen loading conditions were investigated for different types of defects and the finding suggests that p_("H" _"2" ) could be used to fine tune the Gibbs free energy of hydrogenation, thereby allowing several types of defects at different hydrogen loading content to play a role in the activation/recovery process of H2 in defective h-BN. Boron nitride ; Boron ; Hydrogen ; Materials science ; Nitride ; Chemistry ; Nanotechnology ; Organic chemistry Boron and Carbon Nanomaterials Research ; Metal and Thin Film Mechanics ; Semiconductor materials and devices
Authors: Bo Zhuang | Guangliu Ran | Wenkai Zhang | Feng Gai
Source: Chemical Science (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Mechanism and dynamics of photoswitchable flavoprotein charge-transfer complexes Because of their diverse uses in biological science and engineering, continued effort has been made to expand the pool of photoswitchable protein systems. A recent study demonstrated that in monomeric sarcosine oxidase (MSOX), photoexcitation of a charge-transfer (CT) complex formed by a flavin cofactor and a nonreactive ligand (<i>e.g.</i>, methylthioacetate) induces the ligand to reversibly change conformation, with implications for the development of flavin-dependent fast photochromic proteins. However, the factors that control the underlying switching mechanism and dynamics remain largely unexplored. Herein, combining extensive protein mutagenesis, ultrafast laser spectroscopic measurements and classical and quantum computational approaches, we assess those factors in a range of protein variants, including those of MSOX and another flavoenzyme, <i>N</i>-methyltryptophan oxidase (MTOX), where we find that a similar photoswitching cycle can occur. We demonstrate that (1) the kinetic behaviors of the photoswitching cycle are protein- and ligand-dependent; (2) the photoswitching and backward thermal recovery rates can be tuned by mutation of a specific active-site residue (Met245 and Thr239 in MSOX and MTOX, respectively), with recovery rates spanning over an order of magnitude, and (3) modifications of the protein environment alter the conformational energy landscape of the ligand-flavin complex, consequently regulating the photocycle. Taken together, these findings highlight the versatility of such photoswitchable systems, providing a molecular basis for fine-tuning their photophysical properties. Mechanism (biology) ; Flavoprotein ; Dynamics (music) ; Charge (physics) ; Chemical physics ; Chemistry ; Nanotechnology ; Materials science ; Physics ; Biochemistry ; Particle physics ; Quantum mechanics Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Light effects on plants
Authors: Renan S. Nunes | Victor Dal Posolo Cinel | Joana Claudio Pieretti | Kelli Cristina Freitas Mariano | Roberta Albino dos Reis | Morgana Halfeld | Amedea B. Seabra
Source: Nanoscale (article, 2025-01-01)
Field: Materials Science — Biomaterials

Multivariate chemometric design of nitric oxide-releasing chitosan nanoparticles for skin-related biomedical applications Nitric oxide (NO) is a critical signaling molecule with significant therapeutic potential for biomedical applications, particularly in wound healing, antimicrobial activity, and tissue repair. However, its clinical translation is hindered by its instability and rapid degradation in biological environments. In this study, we employed chemometric techniques to optimize the synthesis of glutathione-loaded chitosan nanoparticles (GSH-CSNPs) produced <i>via</i> ionotropic gelation. GSH serves as a precursor molecule for <i>S</i>-nitrosoglutathione (GSNO), a key NO donor. A multivariate experimental design was applied to systematically investigate eight synthesis parameters, optimizing particle size, polydispersity index (PDI), zeta potential (ZP), stability, storage conditions, and NO release kinetics. The optimized nanoparticles exhibited a hydrodynamic diameter of 77.1 ± 1.5 nm, a PDI of 0.209 ± 0.010, and a ZP of +15.3 ± 2.1 mV, ensuring considerable colloidal stability for at least 60 days at room temperature. NO release kinetics demonstrated a sustained and controlled release profile from GSNO-CSNPs compared to free GSNO, enhancing NO availability. Franz permeation cell assays revealed efficient GSNO permeation through synthetic skin membranes, and <i>in vitro</i> cytotoxicity assays using human fibroblast cells confirmed the biocompatibility of GSNO-CSNPs up to a NO donor concentration of 250 μmol L<sup>-1</sup>. Additionally, <i>S</i>-nitrosylated protein quantification in FN1 cells showed that GSNO-CSNPs at 500 μM induced a significant increase in <i>S</i>-nitrosylation levels, approximately 3 fold-higher than free GSNO at the same concentration, without a corresponding increase in cytotoxicity. This suggests that CSNPs enhance intracellular GSNO delivery, facilitating protein <i>S</i>-nitrosylation while maintaining cell viability. These findings highlight the pivotal role of Design of Experiments (DoE)-driven optimization in fine-tuning nanoparticle properties, providing a deeper understanding of how synthesis parameters influence their characteristics, and ultimately enhancing NO delivery systems for biomedical applications, particularly in skin-related therapies. Chitosan ; Multivariate statistics ; Nitric oxide ; Nanoparticle ; Nanotechnology ; Multivariate analysis ; Materials science ; Chemistry ; Computer science ; Organic chemistry ; Machine learning Nanocomposite Films for Food Packaging ; Polydiacetylene-based materials and applications ; Analytical Chemistry and Sensors
Authors: Murat Aydemir | Gülçin Haykır | Seda Demir | Esra Aydemir | Elif Arslan | Harun Selvi̇topi̇ | Mehmet Enes Arslan | Abdurrahim Kadı | Andrew P. Monkman | Figen Türksoy
Source: Journal of Photochemistry and Photobiology A Chemistry (article, 2025-08-06)
Field: Chemistry — Spectroscopy

Anthracene–pyridine derivatives as fluorescent probes: The role of nitrogen positioning in bioimaging performance Chemistry ; Anthracene ; Fluorescence ; Pyridine ; Nitrogen ; Photochemistry ; Organic chemistry Molecular Sensors and Ion Detection ; Luminescence and Fluorescent Materials ; Analytical Chemistry and Sensors