jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Beáta Lemli | Szilárd Pál | Ala’ Salem | Aleksandar Széchenyi
Source: International Journal of Molecular Sciences (review, 2024-11-09)
Field: Chemistry — Physical and Theoretical Chemistry

Prioritizing Computational Cocrystal Prediction Methods for Experimental Researchers: A Review to Find Efficient, Cost-Effective, and User-Friendly Approaches Pharmaceutical cocrystals offer a versatile approach to enhancing the properties of drug compounds, making them an important tool in drug formulation and development by improving the therapeutic performance and patient experience of pharmaceutical products. The prediction of cocrystals involves using computational and theoretical methods to identify potential cocrystal formers and understand the interactions between the active pharmaceutical ingredient and coformers. This process aims to predict whether two or more molecules can form a stable cocrystal structure before performing experimental synthesis, thus saving time and resources. In this review, the commonly used cocrystal prediction methods are first overviewed and then evaluated based on three criteria: efficiency, cost-effectiveness, and user-friendliness. Based on these considerations, we suggest to experimental researchers without strong computational experiences which methods and tools should be tested as a first step in the workflow of rational design of cocrystals. However, the optimal choice depends on specific needs and resources, and combining methods from different categories can be a more powerful approach. Cocrystal ; Workflow ; Computer science ; Process (computing) ; Biochemical engineering ; Rational design ; Management science ; Data science ; Nanotechnology ; Chemistry ; Engineering ; Materials science ; Molecule ; Database Crystallography and molecular interactions ; Crystallization and Solubility Studies ; Enzyme Structure and Function
Authors: Di Yang | Chang-Hwa Chiang | Taveechai Wititsuwannakul | Charles L. Brooks | Paul M. Zimmerman | Alison R. H. Narayan
Source: Journal of the American Chemical Society (article, 2024-12-06)
Field: Chemistry — Inorganic Chemistry

Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction Non-heme iron (Fe<sup>II</sup>), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of Fe<sup>II</sup>/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others. Herein, we showcase a novel ancestral sequence reconstruction (ASR)-guided strategy in which evolutionary information is used to pinpoint the residues critical for controlling different reaction pathways. Following this, a combinatorial site-directed mutagenesis approach was used to quickly evaluate the importance of each residue. These results were validated using a DNA shuffling strategy and through quantum mechanical/molecular mechanical (QM/MM) simulations. Using this approach, we identified a set of active site residues together with a key hydrogen bond between the substrate and an active site residue, which are crucial for dictating the dominant reaction pathway. Ultimately, we successfully converted both extant and ancestral enzymes that perform benzylic hydroxylation into variants that can catalyze an oxidative ring-expansion reaction, showcasing the potential of utilizing ASR to accelerate the reaction pathway engineering within enzyme families that share common structural and mechanistic features. DNA shuffling ; Chemistry ; Saturated mutagenesis ; Mutagenesis ; Active site ; Protein engineering ; Heme ; Directed evolution ; Hydroxylation ; Site-directed mutagenesis ; Enzyme ; DNA ; Stereochemistry ; Shuffling ; Residue (chemistry) ; Computational biology ; Combinatorial chemistry ; Biochemistry ; Mutation ; Gene ; Biology Metal-Catalyzed Oxygenation Mechanisms ; Metalloenzymes and iron-sulfur proteins ; Electrocatalysts for Energy Conversion
Authors: Zahid Ali | Wajid Rehman | Liaqat Rasheed | Abdullah Yahya Abdullah Alzahrani | Nawab Ali | Rafaqat Hussain | Abdul‐Hamid Emwas | Mariusz Jaremko | Magda H. Abdellattif
Source: ACS Omega (article, 2024-02-05)
Field: Chemistry — Organic Chemistry

New 1,3,4-Thiadiazole Derivatives as α-Glucosidase Inhibitors: Design, Synthesis, DFT, ADME, and In Vitro Enzymatic Studies Diabetes is an emerging disorder in the world and is caused due to the imbalance of insulin production as well as serious effects on the body. In search of a better treatment for diabetes, we designed a novel class of 1,3,4-thiadiazole-bearing Schiff base analogues and assessed them for the α-glucosidase enzyme. In the series (<b>1</b>-<b>12</b>), compounds are synthesized and <b>3</b> analogues showed excellent inhibitory activity against α-glucosidase enzymes in the range of IC<sub>50</sub> values of 18.10 ± 0.20 to 1.10 ± 0.10 μM. In this series, analogues <b>4</b>, <b>8</b>, and <b>9</b> show remarkable inhibition profile IC<sub>50</sub> 2.20 ± 0.10, 1.10 ± 0.10, and 1.30 ± 0.10 μM by using acarbose as a standard, whose IC<sub>50</sub> is 11.50 ± 0.30 μM. The structure of the synthesized compounds was confirmed through various spectroscopic techniques, such as NMR and HREI-MS. Additionally, molecular docking, pharmacokinetics, cytotoxic evaluation, and density functional theory study were performed to investigate their behavior. Acarbose ; ADME ; Chemistry ; Enzyme ; Stereochemistry ; IC50 ; In vitro ; Lead compound ; Combinatorial chemistry ; Biochemistry Synthesis and biological activity ; Natural Antidiabetic Agents Studies ; Synthesis and Characterization of Heterocyclic Compounds
Authors: P. Anees | Lorenzo Bastonero | Nicola Marzari | Michele Simoncelli
Source: Physical Review Applied (article, 2024-08-26)
Field: Materials Science — Materials Chemistry

First-principles characterization of thermal conductivity in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"><mml:msub><mml:mrow><mml:mi>La</mml:mi><mml:mi>PO</mml:mi></mml:mrow><mml:mn>4</mml:mn></mml:msub></mml:math>-based alloys Alloys based on lanthanum phosphate (<a:math xmlns:a="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"><a:msub><a:mrow><a:mi>La</a:mi><a:mi>PO</a:mi></a:mrow><a:mn>4</a:mn></a:msub></a:math>) are often employed as thermal barrier coatings, due to their low thermal conductivity and structural stability over a wide temperature range. To enhance the thermal-insulation performance of these alloys, it is essential to comprehensively understand the fundamental physics governing their heat conduction. Here, we employ the Wigner formulation of thermal transport in conjunction with first-principles calculations to elucidate how the interplay between anharmonicity and compositional disorder determines the thermal properties of <d:math xmlns:d="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"><d:msub><d:mi>La</d:mi><d:mrow><d:mn>1</d:mn><d:mo>−</d:mo><d:mi>x</d:mi></d:mrow></d:msub><d:msub><d:mi>Gd</d:mi><d:mi>x</d:mi></d:msub><d:msub><d:mi>PO</d:mi><d:mn>4</d:mn></d:msub></d:math> alloys, and discuss the fundamental physics underlying the emergence and coexistence of particlelike and wavelike heat-transport mechanisms. We also show how the Wigner transport equation correctly describes the thermodynamic limit of a compositionally disordered crystal, while the Boltzmann transport equation does not. Our predictions for microscopic vibrational properties (temperature-dependent Raman spectrum) and for macroscopic thermal conductivity are validated against experiments. Finally, we leverage these findings to devise strategies to optimize the performance of thermal barrier coatings. Published by the American Physical Society 2024 Scroll ; Computer science ; Physics ; Algorithm ; Philosophy ; Theology Thermal and Kinetic Analysis ; Nuclear materials and radiation effects ; Luminescence Properties of Advanced Materials
Authors: Hamza Moussa | Sarah Hamid | Amal Mameri | Sabrina Lekmine | Hichem Tahraoui | Mohammed Kebir | Nabil Touzout | Farid Dahmoune | Mohammad Shamsul Ola | Jie Zhang | Abdeltif Amrane
Source: Bioengineering (article, 2024-11-28)
Field: Materials Science — Materials Chemistry

From Green Chemistry to Healthy Environments: Silver Nanoparticles as a Dual Antioxidant and Antibacterial Agents for Advancing Biomedicine and Sustainable Wastewater Treatment The green synthesis of silver nanoparticles (AgNPs) using plant extracts is an eco-friendly method with potential for biomedical and environmental applications. This study aims to synthesize silver nanoparticles (SO-AgNPs) using <i>Salvia officinalis</i> L. extract and evaluate their antioxidant and antibacterial properties, positioning them as candidates for applications in sustainable biomedicine and wastewater treatment. <i>S. officinalis</i> L. extract was used to synthesize AgNPs under optimized conditions, with a 10% extract/AgNO₃ ratio and a reaction time of 180 min. The SO-AgNPs were characterized using ATR-FTIR, XRD, SEM, DLS, and Zeta potential analysis. The antioxidant activity of the extract and SO-AgNPs was evaluated using ABTS<sup>+•</sup> and DPPH<sup>•</sup> radical scavenging assays. Antibacterial activity was tested against 11 bacterial strains and bacteria isolated from industrial effluent, with minimal inhibitory concentrations (MIC) determined for both the extract and SO-AgNPs. The SO-AgNPs demonstrated potent antioxidant activity, with IC₅₀ values of 0.233 mg/mL and 0.305 mg/mL in the ABTS<sup>+•</sup> assay, and 0.173 mg/mL and 0.185 mg/mL in the DPPH<sup>•</sup> assay for the extract and SO-AgNPs, respectively. Antibacterial testing showed MIC values of 0.25 mg/mL for SO-AgNPs and between 3.12 and 6.25 mg/mL for <i>S. officinalis</i> L. extract against <i>E. coli</i>, <i>P. aeruginosa</i>, <i>A. baumannii</i>, <i>MRSA</i>, <i>B. cereus</i>, and <i>S. epidermidis</i>. For bacteria isolated from industrial effluent, the MIC values were 0.125 mg/mL for SO-AgNPs and 0.5 mg/mL for the extract. This study highlights the dual antioxidant and antibacterial capabilities of <i>S. officinalis</i> L. extract and SO-AgNPs, demonstrating their potential for use in both biomedical and environmental applications, including wastewater treatment. DPPH ; ABTS ; Silver nanoparticle ; Chemistry ; Antibacterial activity ; Antioxidant ; Nuclear chemistry ; Salvia officinalis ; Minimum inhibitory concentration ; Zeta potential ; Chromatography ; Antimicrobial ; Traditional medicine ; Bacteria ; Nanoparticle ; Organic chemistry ; Officinalis ; Nanotechnology ; Materials science ; Biology ; Medicine Nanoparticles: synthesis and applications ; Healthcare and Environmental Waste Management
Authors: Rajiv Borah | Julia O’Sullivan | Meenakshi Suku | Dahnan Spurling | Daniel Clarke | Valeria Nicolosi | Maeve A. Caldwell | Michael G. Monaghan
Source: Journal of Biomedical Materials Research Part A (article, 2024-12-24)
Field: Materials Science — Biomaterials

Electrically Conductive Injectable Silk/<scp>PEDOT</scp>: <scp>PSS</scp> Hydrogel for Enhanced Neural Network Formation With no effective treatments for functional recovery after injury, spinal cord injury (SCI) remains one of the unresolved healthcare challenges. Human induced pluripotent stem cell (hiPSC) transplantation is a versatile patient-specific regenerative approach for functional recovery after SCI. Injectable electroconductive hydrogel (ECH) can further enhance the cell transplantation efficacy through a minimally invasive manner as well as recapitulate the native bioelectrical microenvironment of neural tissue. Given these considerations, we report a novel ECH prepared through self-assembly facilitated in situ gelation of natural silk fibroin (SF) derived from mulberry Bombyx mori silk and electrically conductive PEDOT:PSS. PEDOT:PSS was pre-stabilized to prevent the potential delamination of its hydrophilic PSS chain under aqueous environment using 3% (v/v) (3-glycidyloxypropyl)trimethoxysilane (GoPS) and 3% (w/v) poly(ethylene glycol)diglycidyl ether (PeGDE). The resultant ECH formulations are easily injectable with standard hand force with flow point below 100 Pa and good shear-thinning properties. The ECH formulations with unmodified and GoPS-modified PEDOT:PSS, that is, SF/PEDOT and SF/PEDOTGoP maintain comparable elastic modulus to spinal cord (~10-60 kPa) under physiological condition, indicating their flexibility. The GoPS-modified ECHs also display improved structural recoverability (~70%-90%) as compared to the unmodified versions of the ECHs (~30%-80%), as indicated by the three interval time thixotropy (3ITT) test. Additionally, these ECHs possess electrical conductivity in the range of ~0.2-1.2 S/m comparable to spinal cord (1-10 S/m), indicating their ability to mimic native bioelectrical environment. Approximately 80% or more cell survival was observed when hiPSC-derived cortical neurons and astrocytes were encapsulated within these ECHs. These ECHs support the maturation of cortical neurons when embedded for 7 days, fostering the development of a complex, interconnected network of long axonal processes and promoting synaptogenesis. These results underline the potential of silk ECHs in cell transplantation therapy for spinal cord regeneration. Materials science ; PEDOT:PSS ; Fibroin ; Thixotropy ; Biomedical engineering ; Ethylene glycol ; Chemical engineering ; SILK ; Composite material ; Polymer ; Medicine Silk-based biomaterials and applications ; Conducting polymers and applications ; Advanced Sensor and Energy Harvesting Materials
Authors: In-Sik Jo | Sung-Kyu Chung | Kyungwho Choi
Source: International Journal of Precision Engineering and Manufacturing-Smart Technology (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Recent Progress in Self-Powered Sensors for Structural and Human Monitoring Systems Using Thermoelectric Energy Harvesters With the evolution of Internet of Things (IoT), it has become essential to build systems that enable real-time monitoring of structures, the environment, and the human body. Among them, various studies have identified self-powering of real-time monitoring systems as one of the most important technologies . Thermoelectric generators are reported to be one of the most suitable power sources for real-time monitoring systems because they have the advantage of converting thermal energy into electrical energy through temperature gradients without using additional power sources. In this review, we will discuss structural/environmental and human health monitoring systems utilizing thermoelectric generators (TEGs). First, we will introduce the type of thermoelectric generators. Then, we will provide an overview of the thermoelectric generators utilized in structural/environmental monitoring and biomonitoring systems. The latest applications of thermoelectric generator-based systems will also be introduced to showcase their potential in industrial applications. Thermoelectric generator ; Thermoelectric effect ; Computer science ; Internet of Things ; Systems engineering ; Thermoelectric cooling ; Thermoelectric materials ; Energy harvesting ; Energy (signal processing) ; Embedded system ; Engineering ; Physics Advanced Thermoelectric Materials and Devices ; Gas Sensing Nanomaterials and Sensors ; Advanced Chemical Sensor Technologies
Authors: Andreas Furchner | Tetiana Parker | Vincent Mauchamp | Simon Hurand | Julian Plaickner | Jörg Rappich | Aline Alencar Emerenciano | Karsten Hinrichs | Yury Gogotsi | Tristan Petit
Source: The Journal of Physical Chemistry C (article, 2024-12-27)
Field: Materials Science — Materials Chemistry

Ti <sub>3</sub> C <sub>2</sub> T <sub> <i>x</i> </sub> MXene Thin Films and Intercalated Species Characterized by IR-to-UV Broadband Ellipsometry MXenes are two-dimensional (2D) materials with versatile applications in optoelectronics, batteries, and catalysis. To unlock their full potential, it is crucial to characterize MXene interfaces and intercalated species in more detail than is currently possible with conventional optical spectroscopies. Here, we combine ultra-broadband ellipsometry and transmission spectroscopy from the mid-infrared (IR) to the deep-ultraviolet (UV) to probe quantitatively the composition, structure, transport, and optical properties of spray-coated Ti<sub>3</sub>C<sub>2</sub>T <sub><i>x</i></sub> MXene thin films with varying material properties. We find film thickness heterogeneity and surface roughness in the low-nanometer range as well as depth-dependent conductivity properties, which we quantify with a graded Drude model. The optically determined sheet resistance is confirmed by four-point probe measurements. Furthermore, we employ density-functional-theory calculations to assign the observed absorption bands in the MXene dielectric function to various interband transitions from mixed MXene surface terminations. The prominent 1.48 eV (833 nm) spectral feature is found to be related to oxygen termination. Additional plasmonic effects are also suggested. Finally, we leverage the chemical sensitivity of state-of-the-art IR ellipsometry to separate the fingerprints of intercalated species within the MXene from the dominant Drude contributions, presenting for the first time a set of infrared optical constants of intercalated water. This work lays the foundation for optical metrology for interface engineering of MXene and other 2D materials. Materials science ; Ellipsometry ; MXenes ; Drude model ; Thin film ; Optoelectronics ; Infrared ; Refractive index ; Nanotechnology ; Optics MXene and MAX Phase Materials ; 2D Materials and Applications ; Advanced Memory and Neural Computing
Authors: Zaid H. Mahmoud | Uday Abdul‐Reda Hussein | Aya Mohammed Dhiaa | Ali Fawzi Al‐Hussainy | Najwa Aljbory | Mahmood Hasen Shuhata | Mohammed Jawad Alnajar | Ali Saeed Owayez Khawaf Aljaberi | Debarshi Kar Mahapatra | Ehsan Kianfar | Tomy Muringayil Joseph | Sabu Thomas
Source: Trends in Sciences (article, 2024-11-20)
Field: Materials Science — Biomaterials

Nano-Based Drug Delivery in Cancer: Tumor Tissue Characteristics and Targeting Cell mutations are the root cause of cancer. Mutated cells outgrow healthy ones, starving them of oxygen and nutrients as they proliferate. This condition is managed using a variety of approaches, including surgery, chemotherapy, radiation treatment, or a mix of these. Common treatment approaches are costly and do huge damage due to their energy-intensive and labor-intensive treatment cycles and their destruction of both healthy and sick cells. Cancer is one of the most difficult illnesses to treat. Much progress in the management of this illness has coincided with the growth of our understanding of it. Still, one of the therapeutic issues is the toxic effects of chemotherapy medications, which are typically seen as a result of their non-specific action. Inventions in drug delivery methods within the last 20 years have helped alleviate some of the chemotherapy-related issues. Nanoparticles comprising both organic and inorganic substances are part of these systems. While many of these systems are still in the pre-clinical phase, a few have broken into the pharmaceutical industry. Modern nanoparticles have solved the problem of drug-resistant cells and opened up a new area of cancer therapy; this articleexplores medication delivery to tumor tissue, a method that is more successful than traditional methods of drug delivery. HIGHLIGHTS Investigating Passive Targeting Using Leaky Tumor Capillary Networks. Investigating Passive targeting using tumor tissue environment. Investigating Targeting based on environmental acidity. GRAPHICAL ABSTRACT Drug delivery ; Drug ; Cancer ; Cancer drugs ; Nano- ; Medicine ; Targeted drug delivery ; Cancer research ; Nanotechnology ; Pharmacology ; Materials science ; Internal medicine Nanoparticle-Based Drug Delivery ; RNA Interference and Gene Delivery ; Nanoplatforms for cancer theranostics
Authors: Avinash Sharma | K. Akash | Swati Kumari | Kartik Chauhan | Abija James | Riya Goel | Jay Singh | Rupak Nagraik | Deepak Kumar
Source: ECS Journal of Solid State Science and Technology (article, 2024-04-01)
Field: Materials Science — Materials Chemistry

Biogenic Zinc Oxide Nanoparticles: An Insight into the Advancements in Antimicrobial Resistance Multidrug resistance (MDR) is a significant global challenge requiring strategic solutions to address bacterial infections. Recent advancements in nanotechnology, particularly in the synthesis of zinc oxide nanoparticles (ZnO NPs) using natural agents as stabilizers and reducing agents, have shown promising results in combating MDR. These nanoparticles possess strong antimicrobial properties against different strains of Gram-positive and Gram-negative, making them suitable for various industries, including food, pharmaceuticals, coatings, and medical devices. ZnO-NPs work by generating reactive oxygen species, releasing zinc ions (Zn2+), disrupting the bacterial cell membrane, interfering with metabolic processes and genetic material, and inducing oxidative stress and apoptosis. However, more research is needed to refine synthesis techniques, control size and morphology, and increase antibacterial efficacy. To fully understand their potential, interactions with proteins, DNA, and bacterial cell walls must also be examined. Investigating the synergistic potential of biogenic ZnO NPs with conventional antibacterial treatments could enhance therapeutic effectiveness while minimizing the risk of resistance emergence. Here we provide insight into the advancements in biogenic synthesis of nanoparticles using bio extracts and their applications in antimicrobial resistance as well as various factors affecting the synthesis process and characterization techniques for ZnO NPs. Recent studies on the antimicrobial activity of biogenic ZnO NPs against different pathogens and their mechanisms of action are discussed. Furthermore, potential applications of biogenic ZnO NPs as antimicrobial agents are highlighted. Antimicrobial ; Nanotechnology ; Zinc ; Nanoparticle ; Multiple drug resistance ; Materials science ; Chemistry ; Biology ; Antibiotics ; Microbiology ; Biochemistry Nanoparticles: synthesis and applications ; Advanced Nanomaterials in Catalysis ; Bacterial biofilms and quorum sensing