jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mengbo Li | Gordon K. Smyth
Source: Bioinformatics (article, 2023-04-17)
Field: Chemistry — Spectroscopy

Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics Data and code to reproduce the results shown in this article are available from https://mengbo-li.github.io/protDP/. Missing data ; Imputation (statistics) ; Statistical power ; Statistics ; Computer science ; Censoring (clinical trials) ; False discovery rate ; Mathematics ; Data mining Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Pharmacological Effects and Assays
Authors: Daniel Flam-Shepherd | Alán Aspuru‐Guzik
Source: arXiv (Cornell University) (preprint, 2023-05-09)
Field: Materials Science — Materials Chemistry

Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files Language models are powerful tools for molecular design. Currently, the dominant paradigm is to parse molecular graphs into linear string representations that can easily be trained on. This approach has been very successful, however, it is limited to chemical structures that can be completely represented by a graph -- like organic molecules -- while materials and biomolecular structures like protein binding sites require a more complete representation that includes the relative positioning of their atoms in space. In this work, we show how language models, without any architecture modifications, trained using next-token prediction -- can generate novel and valid structures in three dimensions from various substantially different distributions of chemical structures. In particular, we demonstrate that language models trained directly on sequences derived directly from chemical file formats like XYZ files, Crystallographic Information files (CIFs), or Protein Data Bank files (PDBs) can directly generate molecules, crystals, and protein binding sites in three dimensions. Furthermore, despite being trained on chemical file sequences -- language models still achieve performance comparable to state-of-the-art models that use graph and graph-derived string representations, as well as other domain-specific 3D generative models. In doing so, we demonstrate that it is not necessary to use simplified molecular representations to train chemical language models -- that they are powerful generative models capable of directly exploring chemical space in three dimensions for very different structures. Computer science ; Chemical space ; String (physics) ; Parsing ; Graph ; Theoretical computer science ; Protein Data Bank (RCSB PDB) ; Representation (politics) ; Generative model ; Molecular graph ; Protein Data Bank ; File format ; Generative grammar ; Artificial intelligence ; Natural language processing ; Programming language ; Protein structure ; Drug discovery ; Bioinformatics ; Chemistry ; Mathematics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Yiwen Cao | You Wang | Yuli Fu | Fa Zhou | Jianhan Huang
Source: Separation and Purification Technology (article, 2023-06-08)
Field: Materials Science — Materials Chemistry

Fabrication of the hyper-crosslinked polymers chemically functionalized by 8-hydroxyquinoline and their efficient adsorptive removal of 2-naphthol from water Adsorption ; Heteroatom ; Polymer ; Chemistry ; Alkylation ; Pyridine ; Chemical engineering ; Monomer ; Friedel–Crafts reaction ; Porosity ; Polymer chemistry ; Organic chemistry ; Catalysis ; Ring (chemistry) Covalent Organic Framework Applications ; Membrane Separation and Gas Transport ; Adsorption and biosorption for pollutant removal
Authors: Jacquelyn N. Bracco | Gabriela Camacho Meneses | Omar Colón | Ke Yuan | Joanne E. Stubbs | Peter J. Eng | Anna K. Wanhala | Jeffrey D. Einkauf | Matthew G. Boebinger | Andrew G. Stack | Juliane Weber
Source: ACS Applied Materials & Interfaces (article, 2023-12-29)
Field: Materials Science — Materials Chemistry

Reaction Layer Formation on MgO in the Presence of Humidity Mineralization by MgO is an attractive potential strategy for direct air capture (DAC) of CO<sub>2</sub> due to its tendency to form carbonate phases upon exposure to water and CO<sub>2</sub>. Hydration of MgO during this process is typically assumed to not be rate limiting, even at ambient temperatures. However, surface passivation by hydrated phases likely reduces the CO<sub>2</sub> capture capacity. Here, we examine the initial hydration reactions that occur on MgO(100) surfaces to determine whether they could potentially impact CO<sub>2</sub> uptake. We first used atomic force microscopy (AFM) to explore changes in reaction layers in water (pH = 6 and 12) and MgO-saturated solution (pH = 11) and found the reaction layers on MgO are heterogeneous and nonuniform. To determine how relative humidity (R.H.) affects reactivity, we reacted samples at room temperature in nominally dry N<sub>2</sub> (∼11-12% R.H.) for up to 12 h, in humid (>95% R.H.) N<sub>2</sub> for 5, 10, and 15 min, and in air at 33 and 75% R.H. for 8 days. X-ray reflectivity and electron microscopy analysis of the samples reveal that hydrated phases form rapidly upon exposure to humid air, but the growth of the hydrated reaction layer slows after its initial formation. Reaction layer thickness is strongly correlated with R.H., with denser reaction layers forming in 75% R.H. compared with 33% R.H. or nominally dry N<sub>2</sub>. The reaction layers are likely amorphous or poorly crystalline based on grazing incidence X-ray diffraction measurements. After exposure to 75% R.H. in air for 8 days, the reaction layer increases in density as compared to the sample reacted in humid N<sub>2</sub> for 5-15 min. This may represent an initial step toward the crystallization of the reaction layer. Overall, high R.H. favors the formation of a hydrated, disordered layer on MgO. Based on our results, DAC in a location with a higher R.H. will be favorable, but growth may slow significantly from initial rates even on short timescales, presumably due to surface passivation. Materials science ; Layer (electronics) ; Humidity ; Chemical engineering ; Nanotechnology ; Meteorology Magnesium Oxide Properties and Applications ; High-pressure geophysics and materials ; Magnetic and transport properties of perovskites and related materials
Authors: Min Wang | Wei Wu | Yingqian Lin | Wei Tang | Guanhui Gao | Haixia Li | Frederick F. Stewart | Lu‐Cun Wang | Yingchao Yang | Dong Ding
Source: ACS Applied Energy Materials (article, 2023-07-25)
Field: Materials Science — Materials Chemistry

Improved Solid-State Reaction Method for Scaled-Up Synthesis of Ceramic Proton-Conducting Electrolyte Materials Protonic ceramic electrochemical cells (PCECs) represent promising technologies in the production of clean electricity, decarbonized hydrogen, chemicals, and fuels at intermediate temperatures. One of the challenges in commercializing PCECs is to produce the electrolyte materials on a large scale. The conventional solid-state reaction (SSR) method suffers from tedious synthesis procedures and low phase purity of the products due to the formation of unwanted secondary phases. Herein, we report an improved SSR (i-SSR) method for kilogram-scale production of high phase-purity electrolyte material BaZr0.4Ce0.4Y0.1Yb0.1O3−δ (BZCYYb4411). In this method, the ball-milled precursor powders are pelletized prior to calcination, which effectively reduces the length of the diffusion paths between the components during perovskite phase formation. The synthesis procedure and calcination temperature are carefully optimized for efficient and repeatable production based on the powder crystallization behavior. A combined technoeconomic analysis and life cycle assessment modeling suggest that the i-SSR method could reduce the total production cost and greenhouse gas emissions by up to 19% and 39%, respectively, compared to the conventional SSR method. The high quality of the synthesized electrolyte material is corroborated by the excellent electrical conductivity and electrochemical performance of the fabricated PCEC cells. Calcination ; Electrolyte ; Materials science ; Ceramic ; Chemical engineering ; Crystallization ; Electrochemistry ; Conductivity ; Process engineering ; Catalysis ; Metallurgy ; Electrode ; Chemistry ; Organic chemistry Advancements in Solid Oxide Fuel Cells ; Thermal Expansion and Ionic Conductivity ; Perovskite Materials and Applications
Authors: Zahra Sasan Narkesabad | Reza Rafiee | Elham Jalilnejad
Source: Scientific Reports (article, 2023-03-04)
Field: Materials Science — Polymers and Plastics

Experimental study on evaluation and optimization of heavy metals adsorption on a novel amidoximated silane functionalized Luffa cylindrica This study aimed to synthesize an amidoximated Luffa cylindrica (AO-LC) bioadsorbent, and evaluate its efficiency in the adsorption of heavy metals from the aqueous solutions. For this purpose, NaOH solution was used to alkaline treatment of Luffa cylindrica (LC) fibers. The silane modification of LC was performed using 3-(trimethoxysilyl)propyl methacrylate (MPS). Polyacrylonitrile (PAN)/LC biocomposite (PAN-LC) was synthesized by PAN grafting onto the MPS-modified LC (MPS-LC). Finally, the AO-LC was obtained by the amidoximation of PAN-LC. The chemical structures, morphology, and thermal properties of biocomposites were characterized by the infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, and field emission scanning electron microscopy. The results showed a successful grafting of MPS and PAN on the surface of LC. The order of heavy metals adsorption on AO-LC was: Pb<sup>2+</sup> > Ag<sup>+</sup> > Cu<sup>2+</sup> > Cd<sup>2+</sup> > Co<sup>2+</sup> > Ni<sup>2+</sup>. The effects of operational parameters on the Pb<sup>2+</sup> adsorption were studied using Taguchi experimental design method. Statistical analysis of the results showed that the initial Pb<sup>2+</sup> concentration and the bioadsorbent dosage significantly affect the adsorption efficiency. The adsorption capacity and removal percentage of Pb<sup>2+</sup> ions were obtained as 18.88 mg/g and 99.07%, respectively. The Langmuir isotherm and Pseudo-second order kinetics models were found to be better compatible with experimental data as a consequence of the isotherm and kinetics analysis. Polyacrylonitrile ; Adsorption ; Thermogravimetric analysis ; Langmuir adsorption model ; Nuclear chemistry ; Silane ; Grafting ; Aqueous solution ; Chemistry ; Surface modification ; Materials science ; Chemical engineering ; Polymer ; Organic chemistry ; Physical chemistry Natural Fiber Reinforced Composites ; Advanced Cellulose Research Studies ; biodegradable polymer synthesis and properties
Authors: Katherine J. Levey | Martin A. Edwards | Henry S. White | Julie V. Macpherson
Source: Physical Chemistry Chemical Physics (article, 2023-01-01)
Field: Chemistry — Electrochemistry

Simulation of the cyclic voltammetric response of an outer-sphere redox species with inclusion of electrical double layer structure and ohmic potential drop A finite-element model has been developed to simulate the cyclic voltammetric (CV) response of a planar electrode for a 1e outer-sphere redox process, which fully accounts for cell electrostatics, including ohmic potential drop, ion migration, and the structure of the potential-dependent electric double layer. Both reversible and quasi-reversible redox reactions are treated. The simulations compute the time-dependent electric potential and ion distributions across the entire cell during a voltammetric scan. In this way, it is possible to obtain the interdependent faradaic and non-faradaic contributions to a CV and rigorously include all effects of the electric potential distribution on the rate of electron transfer and the local concentrations of the redox species O<sup><i>z</i></sup> and R<sup><i>z</i>-1</sup>. Importantly, we demonstrate that the driving force for electron transfer can be different to the applied potential when electrostatic interactions are included. We also show that the concentrations of O<sup><i>z</i></sup> and R<sup><i>z</i>-1</sup> at the plane of electron transfer (PET) significantly depart from those predicted by the Nernst equation, even when the system is characterised by fast electron transfer/diffusion control. A mechanistic rationalisation is also presented as to why the electric double layer has a negligible effect on the CV response of such reversible systems. In contrast, for quasi-reversible electron transfer the concentrations of redox species at the PET are shown to play an important role in determining CV wave shape, an effect also dependant on the charge of the redox species and the formal electrode potential of the redox couple. Failure to consider electrostatic effects could lead to incorrect interpretation of electron-transfer kinetics from the CV response. Simulated CVs at scan rates between 0.1 and 1000 V s<sup>-1</sup> are found to be in good agreement with experimental data for the reduction of 1.0 mM Ru(NH<sub>3</sub>)<sub>6</sub><sup>3+</sup> at a 2 mm diameter gold disk electrode in 1.0 M potassium nitrate. Ohmic contact ; Redox ; Drop (telecommunication) ; Inclusion (mineral) ; Cyclic voltammetry ; Chemistry ; Electrochemistry ; Voltage drop ; Materials science ; Layer (electronics) ; Chemical physics ; Chemical engineering ; Nanotechnology ; Analytical Chemistry (journal) ; Inorganic chemistry ; Thermodynamics ; Mineralogy ; Electrode ; Chromatography ; Physical chemistry ; Current (fluid) ; Physics ; Electrical engineering Electrochemical Analysis and Applications ; Analytical Chemistry and Sensors ; Conducting polymers and applications
Authors: Sihan Yu | Zhou Ye | Rajdip Roy | Ravi R. Sonani | Irawan Pramudya | Sijie Xian | Yuanhui Xiang | Guoqiang Liu | Belen Flores | Einat Nativ‐Roth | Ronit Bitton | Edward H. Egelman | Matthew J. Webber
Source: Advanced Materials (article, 2023-12-14)
Field: Materials Science — Biomaterials

Glucose‐Triggered Gelation of Supramolecular Peptide Nanocoils with Glucose‐Binding Motifs Peptide self-assembly is a powerful tool to prepare functional materials at the nanoscale. Often, the resulting materials have high aspect-ratio, with intermolecular β-sheet formation underlying 1D fibrillar structures. Inspired by dynamic structures in nature, peptide self-assembly is increasingly moving toward stimuli-responsive designs wherein assembled structures are formed, altered, or dissipated in response to a specific cue. Here, a peptide bearing a prosthetic glucose-binding phenylboronic acid (PBA) is demonstrated to self-assemble into an uncommon nanocoil morphology. These nanocoils arise from antiparallel β-sheets, with molecules aligned parallel to the long axis of the coil. The binding of glucose to the PBA motif stabilizes and elongates the nanocoil, driving entanglement and gelation at physiological glucose levels. The glucose-dependent gelation of these materials is then explored for the encapsulation and release of a therapeutic agent, glucagon, that corrects low blood glucose levels. Accordingly, the release of glucagon from the nanocoil hydrogels is inversely related to glucose level. When evaluated in a mouse model of severe acute hypoglycemia, glucagon delivered from glucose-stabilized nanocoil hydrogels demonstrates increased protection compared to delivery of the agent alone or within a control nanocoil hydrogel that is not stabilized by glucose. Antiparallel (mathematics) ; Self-healing hydrogels ; Peptide ; Supramolecular chemistry ; Phenylboronic acid ; Glucose oxidase ; Materials science ; Biophysics ; Coiled coil ; Nanotechnology ; Biosensor ; Molecule ; Biochemistry ; Chemistry ; Polymer chemistry ; Catalysis ; Biology ; Organic chemistry Supramolecular Self-Assembly in Materials ; Glycosylation and Glycoproteins Research ; Chemical Synthesis and Analysis
Authors: Baher I. Salman
Source: Journal of Fluorescence (article, 2023-03-03)
Field: Materials Science — Materials Chemistry

A Novel Design Eco-friendly Microwave-assisted Cu–N@CQDs Sensor for the Quantification of Eravacycline via Spectrofluorimetric Method; Application to Greenness Assessments, Dosage Form and Biological Samples Community-acquired pneumonia is one of the most common infectious diseases and a substantial cause of mortality and morbidity worldwide. Therefore eravacycline (ERV) was approved by the FDA in 2018 for the treatment of acute bacterial skin infections, GIT infections, and community-acquired bacterial pneumonia caused by susceptible bacteria. Hence, a green highly sensitive, cost-effective, fast, and selective fluorimetric approach was developed for the estimation of ERV in milk, dosage form, content uniformity, and human plasma. The selective method is based on the utilization of plum juice and copper sulphate for the synthesis of green copper and nitrogen carbon dots (Cu-N@CDs) with high quantum yield. The quantum dots' fluorescence was enhanced after the addition of ERV. The calibration range was found to be in the range 1.0 - 80.0 ng mL<sup>-1</sup> with LOQ equal to 0.14 ng mL<sup>-1</sup> and LOD was found to be 0.05 ng mL<sup>-1</sup>. The creative method is simple to deploy in clinical labs and therapeutic drug health monitoring system. The current approach has been bioanalytically validated using US-FDA and validated ICH criteria. High-resolution transmission electron microscopy (HR-TEM), X-ray photon spectroscopy (XPS), Zeta potential measurements, fluorescence, UV-VIS, and FTIR spectroscopy have all been used to fully characterize the Cu-N@CQDs. The Cu-N@CQDs were effectively applied in human plasma and milk samples with a high percentage of recovery ranging from 97.00 to 98.80%. Chemistry ; Environmentally friendly ; Microwave ; Chromatography ; Environmental chemistry ; Nanotechnology ; Process engineering ; Analytical Chemistry (journal) ; Telecommunications ; Ecology Carbon and Quantum Dots Applications ; Advanced biosensing and bioanalysis techniques ; Pregnancy and Medication Impact
Authors: Kumar Vikrant | Myoung Won Chung | Danil W. Boukhvalov | Philippe M. Heynderickx | Ki‐Hyun Kim | Seunghyun Weon
Source: Chemical Engineering Journal (article, 2023-09-11)
Field: Materials Science — Materials Chemistry

A platinum ensemble catalyst for room-temperature removal of formaldehyde in the air Catalysis ; Platinum ; Chemistry ; Formaldehyde ; Adsorption ; Dissociation (chemistry) ; Oxygen ; Redox ; Platinum nanoparticles ; Titanium dioxide ; Space velocity ; Inorganic chemistry ; Photochemistry ; Chemical engineering ; Physical chemistry ; Organic chemistry ; Selectivity Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Electrocatalysts for Energy Conversion
Authors: Dan He | Jianfu Wu | Chenglong Yu | Bichun Huang | Xiang Tu | Danping Li | Xuehui Jia | Junhui Dan | Zheng Fang | Zhenhua Dai | Rong Liu | Qian Zhou
Source: Journal of Chemical Technology & Biotechnology (article, 2023-05-10)
Field: Materials Science — Materials Chemistry

Synthesis of corncob biochar with high surface area by <scp>KOH</scp> activation for <scp>VOC</scp> adsorption: effect of <scp>KOH</scp> addition method Abstract BACKGROUND Carbon materials have been regarded as valuable adsorbents for removal of volatile organic compounds (VOCs) owing to their high specific surface area and abundant pore structure. However, the complexity and high cost of the process used to treat the feedstock to produce commercial activated carbon has limited its application. In this reported study, a series of biochar materials was prepared using the KOH modification method employing corn cob as the raw material. The effects of different potassium hydroxide dosages, various activation temperatures and the activator addition method on the structure, physicochemical properties and VOC adsorption performance of the resulting biochars and their structure–activity relationship were systematically studied. RESULTS Adsorption performance tests and a series of characterization results showed that the CC‐3‐700 (corn cob/KOH = 1:3, T = 700 °C, two‐step dry mixing pyrolysis method) sample had highest toluene dynamic adsorption capacity (up to 573.5 mg g −1 ) compared to the other prepared samples. This result was attributed to the maximum specific surface area (2349 m 2 g −1 ) and pore volume (1.22 cm 3 g −1 ) of this sample. Moreover, the result suggested that the high specific surface area, abundant pore structure and highly disordered non‐graphitizable carbon in sample CC‐3‐700 were the major reasons for its excellent adsorption performance. The results of a multi‐component adsorption performance test showed that corn cob biochar had a strong adsorption capacity for toluene when simultaneously exposed to benzene and toluene. CONCLUSION The results of this study revealed that the corn cob biochar prepared using a two‐step roasting method offers good potential prospects for application in the field of VOC pollution control. © 2023 Society of Chemical Industry (SCI). Adsorption ; Biochar ; Specific surface area ; Corncob ; Toluene ; Pyrolysis ; Activated carbon ; Potassium hydroxide ; Chemistry ; Raw material ; Benzene ; Chemical engineering ; Carbon fibers ; Nuclear chemistry ; Organic chemistry ; Materials science ; Catalysis ; Composite material Catalytic Processes in Materials Science ; Adsorption and biosorption for pollutant removal ; Graphene research and applications
Authors: Sara Elsayed | Ahmed S. Abdelkhalek | Samar Rezq | Mansour E. Abu Kull | Damián G. Romero | Hend Kothayer
Source: European Journal of Medicinal Chemistry (article, 2023-08-15)
Field: Chemistry — Organic Chemistry

Magic shotgun approach to anti-inflammatory pharmacotherapy: Synthesis of novel thienopyrimidine monomers/heterodimer as dual COX-2 and 15-LOX inhibitors endowed with potent antioxidant activity Chemistry ; Stereochemistry ; Pharmacology Synthesis and biological activity ; Inflammatory mediators and NSAID effects ; Synthesis and Biological Evaluation