jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Enrique Escorihuela | Mauricio Regalado Aguilar | Biswajit Mondal | Sara Cuscó | Pilar Romero | Ross J. Davidson | Pilar Cea | Jordi Benet-Buchholz | Eliseo Ruiz | Albert C. Aragonès | Santiago Martín
Source: Cell Reports Physical Science (article, 2025-12-19)
Field: Chemistry — Organic Chemistry

Enhancement of molecular conductance through a supramolecular five-molecule assembly Achieving a comprehensive understanding and precise control of non-covalent interactions is crucial in molecular design and the development of functional molecular electronic devices, where supramolecular interactions enable the control of the local environment in molecular assemblies. Here, intermolecular interactions are used to create a complex supramolecular assembly by π stacking of 1,1′-bis(4-(methylthio)-phenyl)-[4,4′-bipyridine]-1,1′-diium chloride (1[Cl]2) and tetracyanoquinodimethane radical anion (TCNQ·−), whose crystal structure is determined by an electron diffraction technique, showing the presence of stacked 12+-2(TCNQ·−) units. This solid dissolves in aqueous solutions of cucurbit[8]uril (CB[8]), which acts as the host, to form a supramolecular five-molecule {12+-2(TCNQ·−)@2CB[8]} assembly. Its transport properties result in a significant enhancement of conductance. Theoretical studies confirm the stability of the supramolecular assembly and corroborate the enhancement in conductance. These results present a simple and effective method for stabilizing and enhancing charge transport efficiency through a combination of non-covalent and supramolecular interactions, with significant implications for the development of future (opto)electronic devices. Supramolecular chemistry ; Stacking ; Intermolecular force ; Supramolecular assembly ; Tetracyanoquinodimethane ; Crystal engineering ; Conductance ; Molecule Supramolecular Chemistry and Complexes ; Crystallography and molecular interactions ; Synthesis and Properties of Aromatic Compounds
Authors: Sara Tanovic | Ewa Wieczorek | Fernanda Duarte
Source: ChemRxiv (preprint, 2025-07-30)
Field: Materials Science — Materials Chemistry

An exploration of dataset bias in single-step retrosynthesis prediction Single-step retrosynthesis models are integral to the development of computer-aided synthesis planning (CASP) tools, leveraging past reaction data to generate new synthetic pathways. However, it remains unclear how the diversity of reactions within a training set impacts model performance. Here, we assess how dataset size and diversity, as defined using automatically extracted reaction templates, affect accuracy and reaction feasibility of three state-of-the-art architectures – template-based LocalRetro and template-free MEGAN and RootAligned. We show that increasing the diversity of the training set (from 1k to 10k templates) significantly increases top-5 round-trip accuracy while reducing top-10 accuracy, impacting prediction feasibility and recall, respectively. In contrast, increasing dataset size without increasing template diversity yields minimal performance gains for LocalRetro and MEGAN, showing that these architectures are robust even with smaller datasets. Moreover, reaction templates that are less common in the training dataset have significantly lower top-k accuracy than more common ones, regardless of the model architecture. Finally, we use an external data source to validate the drastic difference between top-k accuracies on seen and unseen templates, showing that there is limited capability for generalisation to novel disconnections. Our findings suggest that reaction templates can be used to describe the underlying diversity of reaction datasets and the scope of trained models, and that the task of single-step retrosynthesis suffers from a class imbalance problem. Retrosynthetic analysis ; Artificial intelligence ; Computer science ; Machine learning ; Data mining Machine Learning in Materials Science ; Chemical Synthesis and Analysis ; Computational Drug Discovery Methods
Authors: Sofia Apergi | Sreejith Pallikkara Chandrasekharan | Charles Cornet | Laurent Pédesseau
Source: ArXiv.org (preprint, 2025-05-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Computational assessment of non-polar and polar GaP terminations for photoelectrochemical water splitting With photoelectrochemical water splitting being one of the most promising approaches for clean energy production and storage, the search for efficient photoelectrode materials is greater than ever. Gallium phosphide (GaP) is a well-established semiconductor with suitable band edge positions that has already been successfully employed in photoelectrochemical solar cells. However, to utilize it as efficiently as possible, a proper understanding of its properties when interfaced with water is required, and this is currently lacking. In this work we use ab initio molecular dynamics simulations to study the properties of the aqueous interfaces of various GaP non-polar (110) and polar (001) terminations. We calculate their band alignment with respect to the standard hydrogen electrode potential and investigate their interfacial structural properties. Based on these properties we assess the capability of the various terminations to catalyze the reactions associated with water splitting and propose approaches for improving the performance of GaP for application in PECs. Water splitting ; Gallium phosphide ; Band gap ; Semiconductor ; Photoelectrochemical cell ; Hydrogen ; Polar ; Ab initio ; Work (physics) ; Photoelectrochemistry Ga2O3 and related materials ; Electron and X-Ray Spectroscopy Techniques ; Semiconductor materials and devices
Authors: Kardo Khalid Abdullah | Kolos Molnár
Source: Macromolecular Materials and Engineering (article, 2025-10-30)
Field: Materials Science — Biomaterials

Enhancing Crystallinity of Electrospun Polylactic Acid Fibers: Insights into Formation Mechanisms and Property Modulation–A Review ABSTRACT Polylactic acid (PLA) electrospun fibers often lack sufficient crystallinity, which limits their mechanical strength, thermal stability, and functional performance. Tailoring a specific degree of crystallinity is therefore required for expanding the use of PLA fibers in various fields, where durability, degradation, and processability depend on controlled polymorphic phases. This review highlights recent studies on optimizing crystallinity by tuning electrospinning parameters to control fiber alignment and enhance molecular ordering. It also covers adding nucleating agents or fillers to lower crystallization barriers and using thermal or solvent annealing post‐treatments to stabilize phases. Various additives have been demonstrated to modify the crystallinity of PLA electrospun fiber mats, influencing the balance between β‐phase piezoelectricity, α′ (metastable) and α (stable) phases, and α′→α phase transition during solvent evaporation. Scalable hybrid techniques and green processing approaches are emphasized to address sustainability concerns, while advances in real‐time monitoring are highlighted as promising tools for achieving precise control over crystallization. This review synthesizes current knowledge to guide the design of PLA electrospun fibers with tailored crystallinity, balancing mechanical integrity, functional versatility, and environmental impact. Crystallinity ; Polylactic acid ; Electrospinning ; Crystallization ; Fiber ; Crystallization of polymers ; Thermal stability Electrospun Nanofibers in Biomedical Applications ; biodegradable polymer synthesis and properties ; Nanocomposite Films for Food Packaging
Authors: Emre Görgün | Mehtap Erşan
Source: Black Sea Journal of Engineering and Science (article, 2025-07-09)
Field: Materials Science — Materials Chemistry

Enhanced Corrosion Resistance of X120Mn12 Steel in Acidic Media by a Novel Nanolignin-Based Protective Coating This study investigated the corrosion inhibition of X120Mn12 steel in a 1 mol/L hydrochloric acid solution using a novel biomass-derived inhibitor, Modified Lignin-Based Corrosion Protector (MLCP). Scanning electron microscopy (SEM) analyses revealed a significant reduction in surface corrosion with increasing MLCP concentration. At 15 mg/L, the surface exhibited almost no signs of corrosion, indicating the formation of an effective protective film by MLCP. These findings strongly demonstrated that MLCP could be used as a high-performance and environmentally friendly corrosion inhibitor for X120Mn12 steel, effectively preventing corrosion in acidic environments. This research investigated the potential applications and mechanisms of environmentally friendly inhibitors to prevent the corrosion of X120Mn12 steel under acidic conditions. In this study, the inhibitory effect of MLCP on X120Mn12 steel was investigated. SEM analyses showed a significant reduction in corrosion damage with increasing MLCP concentration. Corrosion ; Coating ; Materials science ; Metallurgy ; Composite material Corrosion Behavior and Inhibition ; Metal and Thin Film Mechanics ; Anodic Oxide Films and Nanostructures
Authors: Ariadna Llop‐Peiró | Salvador Vega y León | Gerard Pujadas | Santiago Garcı́a-Vallvé | Aleix Gimeno
Source: Protein Science (article, 2025-11-12)
Field: Materials Science — Materials Chemistry

<scp>PDB</scp> ‐ <scp>CAT</scp> : A user‐friendly tool to classify and analyze <scp>PDB</scp> protein–ligand complexes The Protein Data Bank (PDB) contains more than 235,000 three-dimensional biostructures and is growing at a rate of nearly 10% per year. The PDB is essential to gain knowledge on how proteins and ligands interact and how these interactions are correlated with the quantitative activity of each ligand/target pair. Unfortunately, the lack of a tool that can classify structures as apo or holo, that is by no means straightforward, and differentiate between covalent and non-covalent ligand-protein complexes makes it difficult to obtain the structures that belong to each set. To address this issue, we present PDB-CAT, a user-friendly tool that facilitates the categorization and extraction of key information from PDBx/mmCIF files through an efficient parallelized implementation. PDB-CAT uses a blacklist-based approach to automatically identify the ligand in a complex. It then classifies the PDB files based on ligand presence: structures without a ligand are classified as apo, whereas those with a ligand are classified as covalently or non-covalently bound, depending on the type of binding. As well as making this classification, the program can verify if there are any mutations in the protein sequence by comparing it to a reference sequence. An example is included to illustrate two different uses: the classification of SARS-CoV-2 Main Protease complexes depending on their variant, and the complete screening of the PDBbindv2020, achieved in <10 min. PDB-CAT is now available on GitHub (https://github.com/URV-cheminformatics/PDB-CAT) and the corresponding tutorial on GitBook (https://ariadnallopps-organization.gitbook.io/pdb-cat). Protein Data Bank (RCSB PDB) ; Protein Data Bank ; Categorization ; Ligand (biochemistry) ; Sequence (biology) ; Protein structure ; Key (lock) ; Covalent bond Enzyme Structure and Function ; Protein Structure and Dynamics ; Computational Drug Discovery Methods
Authors: Carlos Henrique Barbosa Queiroz | Davi Alves Marques | Otílio B. F. Diógenes | Daniel de Castro Girão | Roberta B. Vasques | Adolfo Kalergis do Nascimento Viana | Gemma Fargas | Mauro Andrés Cerra Flórez | Walney Silva Araújo
Source: Metals (article, 2025-08-07)
Field: Materials Science — Metals and Alloys

Electrochemical Behavior of Thermomechanically Processed UNS S41003 Steel in Acidic Chloride Media: Assessing Martensitic Transformation Effects UNS S41003 is a low-cost, low-carbon ferritic stainless steel that exhibits moderate corrosion resistance but limited mechanical performance. This study evaluates the electrochemical behavior of untreated and thermomechanically treated UNS S41003 samples. Corrosion tests were conducted in acidic electrolytes with varying pH to simulate aggressive environments relevant to industrial and structural applications where exposure to acidic media and corrosive pollutants occurs. Potentiodynamic polarization curves for all samples displayed passive regions typically associated with protective oxide film formation; however, localized pitting corrosion was detected post-test. Electrochemical impedance spectroscopy indicated a marked decrease in corrosion resistance as pH decreased. The corrosion resistance of the treated alloy remained comparable to that of the untreated condition, indicating that thermomechanical processing did not detrimentally affect passivity or corrosion performance under the tested conditions. The literature suggests that the applied treatment enhances mechanical properties, supporting the potential use of this alloy in structural components subjected to acidic environments requiring a balance of mechanical strength and corrosion resistance. Corrosion ; Materials science ; Dielectric spectroscopy ; Metallurgy ; Electrochemistry ; Pitting corrosion ; Chloride ; Alloy ; Polarization (electrochemistry) ; Oxide ; Martensite ; Carbon steel ; Electrolyte ; Microstructure ; Electrode ; Chemistry Hydrogen embrittlement and corrosion behaviors in metals ; Corrosion Behavior and Inhibition ; Concrete Corrosion and Durability
Authors: E. Ayedun
Source: World Journal of Applied Science & Technology (article, 2025-06-17)
Field: Materials Science — Materials Chemistry

Seebeck coefficient, figure of merit, power factor, and electronic fitness function as vital tools for assessing thermoelectric behaviour of MnNip compound by first principle approach This work engaged Perdew-Burke-Ernzehof for solid (PBEsol) within the framework of Generalised Gradient Approximation based on Density Functional Theory as its exchange correlation functional as found in Quantum Espresso pseudopotential library to examine structural and electronic qualities of ternary semiconductor half-Heusler MnNiP compound. Structural evaluation indicates optimised lattice constant of 5.29Å, volume of 250.488a.u3 , bulk modulus 500 Kbar and pressure derivative of 4.99. A direct energy gap of 0.3 eV from W→W, k-vector path was observed. Electronic transport properties were explored using Semi-Classical Boltzmann Transport Theory as expressed in the Boltz Trap code. High values of Seebeck coefficient (1292.85 µV/K) as it varied with chemical potential and electronic fitness function (10.85 W5/3ms-1/3K-2 ) as a function of hole were reported at 800 K. This material is a future prospect for a sustainable thermoelectric generation. Seebeck coefficient ; Thermoelectric effect ; Figure of merit ; Function (biology) ; Power factor ; Power (physics) ; Thermoelectric materials ; Fitness function ; Materials science ; Engineering physics ; Engineering ; Mathematics ; Physics ; Thermodynamics ; Optoelectronics ; Mathematical optimization Advanced Thermoelectric Materials and Devices
Authors: Mohamed Gamal El‐Din | Ibrahim Ashour | Nehal A. Erfan
Source: Research Square (preprint, 2025-09-02)
Field: Chemistry — Organic Chemistry

Pilot Plant for Ethanol Amines Production from Chlorohydrin Process with AI Validation Production (economics) ; Process validation ; Process (computing) ; Ethanol ; Process engineering ; Biochemical engineering ; Chemistry ; Computer science ; Organic chemistry ; Engineering ; Operations management ; Economics ; Programming language ; Verification and validation Nanomaterials for catalytic reactions ; Innovative Microfluidic and Catalytic Techniques Innovation ; Process Optimization and Integration
Authors: Mohammad Hajjar | Victoria A. Maola | J. Lee | Manuel J. Holguin | Riley N. Quijano | K. Nguyen | K. Ho | J. Medina | Elionel Botello-Cornejo | Bhawna Barpuzary | Nicholas Chim | John C. Chaput
Source: Nature Communications (article, 2025-12-19)
Field: Materials Science — Materials Chemistry

Directed evolution of a TNA polymerase identifies independent paths to fidelity and catalysis Directed evolution facilitates functional adaptations through stepwise changes in sequence that alter protein structure. While most campaigns yield solutions that maintain the framework of a rigid protein architecture, a few have produced enzymes with more notable structural differences. One example is a polymerase that was evolved to synthesize threose nucleic acid (TNA) with near-natural activity. Understanding how this enzyme arose provides a model for studying pathways that guide enzymes toward more productive regions of the fitness landscape. Here, we trace the evolutionary trajectory of an unnatural polymerase by solving crystal structures of key intermediates along the pathway and evaluating their biochemical activity. Contrary to the view that fidelity is a product of increased catalytic efficiency, we find that accuracy and catalysis are decoupled activities guided by separate ground-state and transition-state discrimination events. Together, these results offer a glimpse into the forces responsible for shaping the emergence of new enzyme functions. Directed evolution ; Polymerase ; Directed Molecular Evolution ; Enzyme ; Fidelity ; Sequence (biology) ; Nucleic acid ; Yield (engineering) ; DNA Enzyme Structure and Function ; Protein Structure and Dynamics ; Biochemical and Molecular Research
Authors: Jie Pan
Source: Advances in Engineering Technology Research (article, 2025-07-26)
Field: Materials Science — Materials Chemistry

Quantum Dots in Bioimaging: Advances, Challenges, and Future Perspectives Quantum dots (QDs) are size-dependent semiconductor crystal fluorescent markers at the nanoscale, which have revolutionized biomedical imaging through enhanced photostability, multiplexing, and emission-spectrum tunability. QDs, in the last two decades, have proved their utility across several types of imaging applications, ranging from in vitro labeling to deep-tissue visualization and tracking living cells. But their clinical use is limited because of their toxicity, long-term biocompatibility, and complicated surface modification. This is a narrative overview of the synthesis and structural engineering of QDs, including bottom-up chemical approaches, core–shell engineering, and biomedical compatibility surface modifications. The article also addresses the significant characterization methods—like TEM, DLS, PL spectroscopy, and zeta potential analysis—that are critical for evaluating their morphology, optical, and surface characteristics. Biomedical applications are classified as in vitro, in vivo, and molecular targeting imaging, each with specific requirements and challenges for performance. QDs hold promise, but they suffer from important hurdles, including toxic effects of heavy metals, photoxicity, and inefficient clearance from biological systems, as well as restricted regulatory endorsement. Future directions, including metal-free QDs, AI-based fluorescence analysis, and compatibility with multimodal imaging platforms, are discussed in this review as well. They seek to bypass the hurdles and propel QDs toward clinic readiness. In conclusion, quantum dots represent a powerful yet evolving imaging technology. Their future lies in balancing performance with safety through interdisciplinary research, material innovation, and ethical oversight. Quantum dot ; Nanotechnology ; Data science ; Engineering ethics ; Computer science ; Materials science ; Engineering Quantum Dots Synthesis And Properties ; Advanced biosensing and bioanalysis techniques ; Carbon and Quantum Dots Applications
Authors: Si Liu | Peiji Deng | Qianfan Chen | Qijun Sun | Yanhan Wang | Hongyu Shi | Kang Liang
Source: Advanced Science (review, 2025-12-12)
Field: Materials Science — Materials Chemistry

Reticular Chemistry: A Versatile Platform for Engineering Heterogenous Biocatalysts Reticular materials, including metal-organic frameworks (MOFs), covalent organic frameworks (COFs), and hydrogen-bonded organic frameworks (HOFs), have emerged as a promising platform for enzyme immobilization due to their large surface area, tunable porosity, and diverse functional sites. However, the performance of enzymes encapsulated within these frameworks is frequently compromised, which primarily arises from spatial confinement, unfavorable interactions, and altered microenvironments that impair the native structure and dynamics of enzymes. A comprehensive understanding of the molecular events underlying enzyme encapsulation within frameworks is pivotal for the development of effective strategies to boost biocatalyst activity, thus unlocking its full potential in practical applications. Based on cutting-edge examples, this review summarizes these approaches from the multiscale aspect, encompassing material tuning at the nano/macro level, interface design at the molecular interface level, and protein surface engineering at the molecular level. Meanwhile, the differences in improving the enzyme activity among MOFs-, COFs-, and HOFs-based biocomposites are highlighted. Additionally, the regulations derived from the nano-bio effect can achieve the nanobiohybrids with customized, non-native biocatalytic functions, which are systematically discussed. Finally, the current challenges and opportunities in heterogeneous biocatalysts based on reticular chemistry are underscored, charting a path toward advanced designs and their translation into impactful real-world applications. Reticular connective tissue ; Biocatalysis ; Covalent bond ; Interface (matter) ; Immobilized enzyme ; Protein engineering Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Advanced Nanomaterials in Catalysis
Authors: Michelle Ernst | Rostislav Fedorov | Alessandro Calzolari | Catherine Mollart | Fabian F. Grieser | Sophia Ber | Ganna Gryn’ova
Source: Materials Chemistry Frontiers (article, 2025-11-26)
Field: Materials Science — Materials Chemistry

Fragment to framework: automatic fragmentation of covalent organic frameworks into building blocks for band gap analysis Understanding structure-property relationships in ordered functional materials is essential for their rational design and optimisation. Fragment-based approaches relating materials' properties to those of their building blocks (fragments) are intuitive to chemistry and have been successfully applied in the design of metal-organic frameworks (MOFs). However, covalent organic frameworks (COFs) are resistant to such <i>in silico</i> fragmentation due to their covalent bonds and ambiguous definitions of nodes and linkers. Here we introduce a new algorithm, <i>deCOFpose</i>, designed to systematically fragment COFs into building blocks according to chemically intuitive rules, enabling fragment-based structure-property analysis, and exemplify the latter for COF band gaps. Our results reveal that the electronic features (<i>e.g.</i>, energies of the frontier molecular orbitals) of the building blocks alone are insufficient to fully represent these materials, and the inclusion of their topological characteristics is required to engineer bespoke COFs with desired band structures. Covalent bond ; Bespoke ; Band gap ; Fragment (logic) ; Bridging (networking) ; Fragmentation (computing) ; Electronic structure Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Supramolecular Chemistry and Complexes
Authors: Mengjie Zheng | Qingfeng Guo | Yizhi Yue | Chaoyang Lu | Jianhua Ran | Shuguang Bi
Source: Research Square (preprint, 2025-06-17)
Field: Chemistry — Inorganic Chemistry

Study on the preparation and performance of functional cotton fabrics based on zeolite-like imidazole organic frameworks (ZIFs) Imidazole ; Zeolite ; Business ; Materials science ; Nanotechnology ; Chemical engineering ; Chemistry ; Organic chemistry ; Engineering ; Catalysis Metal-Organic Frameworks: Synthesis and Applications ; Advanced Nanomaterials in Catalysis ; Conducting polymers and applications