jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Naif Mohammed Al‐Hada | Abbas M. Al-Ghaili | Hairoladenan Kasim | Muneer Aziz Saleh | Elias Saion | Jian Liu | Jihua Wang
Source: IEEE Access (article, 2020-01-01)
Field: Materials Science — Polymers and Plastics

Synthesis and Characterization of Conducting Polyaniline Based on ANI-PVA-MgCl<sub>2</sub>Composites Using Gamma Radiation Technique Conducting polymer composites such as conducting polyaniline composites have numerous attractive physical properties which could be used in several vital applications. In order to give composite materials unique physical and chemical properties that can have broad application potential in various areas, it requires appropriate adding of metal chloride through conductive polymer composites. This study employs the gamma radiation technique to produce conducting polyaniline from an aqueous solution. The solution comprises four materials, including: ANI, PVA, MgCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and distilled H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O, which serve as a binder or film support, precursor, Cl ions provider, and a solvent. To attain the conducting polyaniline composite, a film of ANI-PVA-MgCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> was subjected to gamma radiation under ambient conditions. Conducting polyaniline composite has been formed once the colour began to change from white to green following the doses of radiation. The results have demonstrated that the level of gamma radiation increased to 40 KGy, thereby confirming that the electrical insulation ANI-PVA-MgCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> film was converted into an electrically conductive polyaniline composite film. The production of conducting polyaniline composite has been observed since the colour has been changed from white to green colour alongside radiation doses. Polyaniline ; Conductive polymer ; Materials science ; Composite number ; Composite material ; Aqueous solution ; Polymer ; Chemical engineering ; Polymer chemistry ; Organic chemistry ; Chemistry Conducting polymers and applications ; Polymer Nanocomposite Synthesis and Irradiation ; Advanced Materials and Semiconductor Technologies
Authors: Stefano Nejrotti | Alberto Mannu | Marco Blangetti | Salvatore Baldino | Andréa Fin | Cristina Prandi
Source: Molecules (article, 2020-12-04)
Field: Chemistry — Organic Chemistry

Optimization of Nazarov Cyclization of 2,4-Dimethyl-1,5-diphenylpenta-1,4-dien-3-one in Deep Eutectic Solvents by a Design of Experiments Approach The unprecedented Nazarov cyclization of a model divinyl ketone using phosphonium-based Deep Eutectic Solvents as sustainable non-innocent reaction media is described. A two-level full factorial Design of Experiments was conducted for elucidating the effect of the components of the eutectic mixture and optimizing the reaction conditions in terms of temperature, time, and substrate concentration. In the presence of the Deep Eutectic Solvent (DES) triphenylmethylphosphonium bromide/ethylene glycol, it was possible to convert more than 80% of the 2,4-dimethyl-1,5-diphenylpenta-1,4-dien-3-one, with a specific conversion, into the cyclopentenone Nazarov derivative of 62% (16 h, 60 °C). For the reactions conducted in the DES triphenylmethylphosphonium bromide/acetic acid, quantitative conversions were obtained with percentages of the Nazarov product above 95% even at 25 °C. Surface Responding Analysis of the optimized data furnished a useful tool to determine the best operating conditions leading to quantitative conversion of the starting material, with complete suppression of undesired side-reactions, high yields and selectivity. After optimization, it was possible to convert more than 90% of the model substrate into the desired cyclopentenone with <i>cis</i> percentages up to 77%. Experimental validation of the implemented model confirmed the robustness and the suitability of the procedure, leading to possible further extension to this specific combination of experimental designs to other substrates or even to other synthetic processes of industrial interest. Deep eutectic solvent ; Ethylene glycol ; Eutectic system ; Chemistry ; Bromide ; Selectivity ; Substrate (aquarium) ; Central composite design ; Response surface methodology ; Organic chemistry ; Chromatography ; Catalysis Asymmetric Synthesis and Catalysis ; Chemical Synthesis and Reactions ; Multicomponent Synthesis of Heterocycles
Authors: Michael Schauperl | Sophie Kantonen | Lee‐Ping Wang | Michael K. Gilson
Source: Communications Chemistry (article, 2020-11-13)
Field: Materials Science — Materials Chemistry

Data-driven analysis of the number of Lennard–Jones types needed in a force field Force fields used in molecular simulations contain numerical parameters, such as Lennard-Jones (LJ) parameters, which are assigned to the atoms in a molecule based on a classification of their chemical environments. The number of classes, or types, should be no more than needed to maximize agreement with experiment, as parsimony avoids overfitting and simplifies parameter optimization. However, types have historically been crafted based largely on chemical intuition, so current force fields may contain more types than needed. In this study, we seek the minimum number of LJ parameter types needed to represent key properties of organic liquids. We find that highly competitive force field accuracy is obtained with minimalist sets of LJ types; e.g. two H types and one type apiece for C, O, and N atoms. We also find that the fitness surface has multiple minima, which can lead to local trapping of the optimizer. Maxima and minima ; Force field (fiction) ; Overfitting ; Intuition ; Type (biology) ; Computer science ; Maxima ; Field (mathematics) ; Statistical physics ; Mathematics ; Physics ; Artificial intelligence ; Mathematical analysis Machine Learning in Materials Science ; Protein Structure and Dynamics ; Computational Drug Discovery Methods
Authors: Andy M. Lau | Ruyu Jia | Richard T. Bradshaw | Argyris Politis
Source: Biochemical Society Transactions (article, 2020-06-29)
Field: Chemistry — Spectroscopy

Structural predictions of the functions of membrane proteins from HDX-MS HDX-MS has emerged as a powerful tool to interrogate the structure and dynamics of proteins and their complexes. Recent advances in the methodology and instrumentation have enabled the application of HDX-MS to membrane proteins. Such targets are challenging to investigate with conventional strategies. Developing new tools are therefore pertinent for improving our fundamental knowledge of how membrane proteins function in the cell. Importantly, investigating this central class of biomolecules within their native lipid environment remains a challenge but also a key goal ahead. In this short review, we outline recent progresses in dissecting the conformational mechanisms of membrane proteins using HDX-MS. We further describe how the use of computational strategies can aid the interpretation of experimental data and enable visualisation of otherwise intractable membrane protein states. This unique integration of experiments with computations holds significant potential for future applications. Membrane protein ; Computer science ; Membrane biophysics ; Function (biology) ; Computational biology ; Nanotechnology ; Chemistry ; Membrane ; Biology ; Materials science ; Biochemistry ; Cell biology Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Lipid Membrane Structure and Behavior
Authors: Santiago Ruiz | L.A. Sarabia | M.C. Ortiz | M.S. Sánchez
Source: Chemometrics and Intelligent Laboratory Systems (article, 2020-05-13)
Field: Chemistry — Analytical Chemistry

Residual spaces in latent variables model inversion and their impact in the design space for given quality characteristics Null (SQL) ; Projection (relational algebra) ; Space (punctuation) ; Mathematics ; Latent variable ; Inversion (geology) ; Computer science ; Null hypothesis ; Partial least squares regression ; Algorithm ; Mathematical optimization ; Data mining ; Econometrics ; Statistics Spectroscopy and Chemometric Analyses ; Fault Detection and Control Systems ; Advanced Statistical Methods and Models
Authors: Darshan Bamney | Aaron E. Tallman | Laurent Capolungo | Douglas E. Spearot
Source: Computational Materials Science (article, 2020-01-07)
Field: Materials Science — Materials Chemistry

Virtual diffraction analysis of dislocations and dislocation networks in discrete dislocation dynamics simulations Dislocation ; Diffraction ; Dynamics (music) ; Materials science ; Condensed matter physics ; Statistical physics ; Crystallography ; Physics ; Chemistry ; Optics ; Acoustics Microstructure and mechanical properties ; High Temperature Alloys and Creep ; Aluminum Alloy Microstructure Properties
Authors: Sean A. Tacey | Benjamin W. J. Chen | Tibor Szilvási | Manos Mavrikakis
Source: Computational Materials Science (article, 2020-09-15)
Field: Materials Science — Materials Chemistry

An automated cluster surface scanning method for exploring reaction paths on metal-cluster surfaces Cluster (spacecraft) ; Icosahedral symmetry ; Density functional theory ; Chemistry ; Reactivity (psychology) ; Potential energy surface ; Catalysis ; Atom (system on chip) ; Nanotechnology ; Chemical physics ; Biological system ; Materials science ; Molecule ; Computational chemistry ; Crystallography ; Computer science Machine Learning in Materials Science ; Catalytic Processes in Materials Science ; Quantum Dots Synthesis And Properties
Authors: Chaogeng Lv | Ya-Li He | Chuanzhi Kang | Li Zhou | Tielin Wang | Jian Yang | Lanping Guo
Source: Journal of Analytical Methods in Chemistry (article, 2020-09-12)
Field: Chemistry — Analytical Chemistry

Tracing the Geographical Origins of Dendrobe (<i>Dendrobium</i> spp.) by Near-Infrared Spectroscopy Sensor Combined with Porphyrin and Chemometrics Dendrobe (<i>Dendrobium</i> spp.) is a traditional medicinal and edible food, which is rich in nutrients and contains biologically active metabolites. The quality and price of dendrobe are related to its geographical origins, and high quality dendrobe is often imitated by low quality dendrobe in the market. In this work, near-infrared (NIR) spectroscopy sensor combined with porphyrin and chemometrics was used to distinguish 360 dendrobe samples from twelve different geographical origins. Partial least squares discriminant analysis (PLSDA) was used to study the sensing performance of traditional NIR and tera-(4-methoxyphenyl)-porphyrin (TMPP)-NIR on the identification of dendrobe origin. In the PLSDA model, the recognition rate of the training and prediction set of the TMPP-NIR could reach 100%, which was higher than the 91.85% and 91.34% of traditional NIR. And the accuracy, sensitivity, and specificity of the TMPP-NIR sensor are all 1.00. The mechanism of TMPP improving the specificity of NIR spectroscopy should be related to the <i>π</i>-<i>π</i> conjugated system and the methoxy groups of TMPP interact with the chemical components of dendrobe. This study reflected that NIR spectrum with TMPP sensor was an effective approach for identifying the geographic origin of dendrobe. Chemometrics ; Porphyrin ; Near-infrared spectroscopy ; Partial least squares regression ; Spectroscopy ; Fluorescence spectroscopy ; Chemistry ; Linear discriminant analysis ; Fluorescence ; Analytical Chemistry (journal) ; Chromatography ; Photochemistry ; Computer science ; Artificial intelligence ; Physics ; Optics ; Machine learning Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Biological and pharmacological studies of plants
Authors: Wenrong Chen | Xiaowen Liu
Source: Journal of Proteome Research (article, 2020-11-13)
Field: Chemistry — Spectroscopy

Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry In proteogenomic studies, genomic and transcriptomic variants are incorporated into customized protein databases for the identification of proteoforms, especially proteoforms with sample-specific variants. Most proteogenomic research has been focused on combining genomic or transcriptomic data with bottom-up mass spectrometry data. In the last decade, top-down mass spectrometry has attracted increasing attention because of its capacity to identify various proteoforms with alterations. However, top-down proteogenomics, in which genomic or transcriptomic data are combined with top-down mass spectrometry data, has not been widely adopted, and there is still a lack of software tools for top-down proteogenomic data analysis. In this paper, we introduce TopPG, a proteogenomic tool for generating proteoform sequence databases with genetic alterations and alternative splicing events. Experiments on top-down proteogenomic data of DLD-1 colorectal cancer cells showed that TopPG coupled with database search confidently identified proteoforms with sample-specific alterations. Proteogenomics ; Computational biology ; Identification (biology) ; Proteomics ; Transcriptome ; Computer science ; Genomics ; Biology ; Genome ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Metabolomics and Mass Spectrometry Studies
Authors: Debashis Dhara | Laurence A. Mulard
Source: Chemistry - A European Journal (article, 2020-12-13)
Field: Chemistry — Organic Chemistry

Exploratory N‐Protecting Group Manipulation for the Total Synthesis of Zwitterionic <i>Shigella sonnei</i> Oligosaccharides Shigella sonnei surface polysaccharides are well-established protective antigens against this major cause of diarrhoeal disease. They also qualify as unique zwitterionic polysaccharides (ZPSs) featuring a disaccharide repeating unit made of two 1,2-trans linked rare aminodeoxy sugars, a 2-acetamido-2-deoxy-l-altruronic acid (l-AltpNAcA) and a 2-acetamido-4-amino-2,4,6-trideoxy-d-galactopyranose (AAT). Herein, the stereoselective synthesis of S. sonnei oligosaccharides comprising two, three and four repeating units is reported for the first time. Several sets of up to seven protecting groups were explored, shedding light on the singular conformational behavior of protected altrosamine and altruronic residues. A disaccharide building block equipped with three distinct N-protecting groups and featuring the uronate moiety already in place was designed to accomplish the iterative high yielding glycosylation at the axial 4-OH of the altruronate component and achieve the challenging full deprotection step. Key to the successful route was the use of a diacetyl strategy whereby the N-acetamido group of the l-AltpNAcA is masked in the form of an imide. Disaccharide ; Shigella sonnei ; Moiety ; Protecting group ; Chemistry ; Stereochemistry ; Polysaccharide ; Glycosylation ; Biochemistry ; Shigella ; Escherichia coli ; Organic chemistry Carbohydrate Chemistry and Synthesis ; Glycosylation and Glycoproteins Research ; Polyamine Metabolism and Applications
Authors: Shengbo Zhu | Ran Chen | Wenzhi Zhang | Xiaoling Niu | Weixing Chen | Lingchao Mo | Minggang Hu | Lu Zhang | Jian Li | Xinbing Chen | Zhongwei An
Source: Journal of Molecular Liquids (article, 2020-04-24)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Dissecting terminal fluorinated regulator of liquid crystals for fine-tuning intermolecular interaction and molecular configuration Substituent ; Intermolecular force ; Steric effects ; Dipole ; Chemistry ; Molecule ; Chemical physics ; Chemical polarity ; Twist ; Regulator ; Polar ; Intermolecular interaction ; Liquid crystal ; Computational chemistry ; Crystallography ; Stereochemistry ; Materials science ; Organic chemistry ; Physics ; Geometry Liquid Crystal Research Advancements ; Advanced Materials and Mechanics ; Adhesion, Friction, and Surface Interactions
Authors: Ngoc Linh Nguyen | Thi Thuy Duong | Hien Nguyen | Vũ Quốc Trung
Source: Vietnam Journal of Chemistry (review, 2020-02-01)
Field: Materials Science — Polymers and Plastics

Synthesis of polythiophene containing heterocycle on the side chain: A review Abstract This review highlights some synthesis results of ionic and neutral conjugated polythiophenes containing heterocyclic moieties on side chain using oxidative or cross‐coupling polymerizations. Because of their increasing importance in material science, a lot of methods have recently been developed for their synthesis and modification. The review also reported out that conjugated polythiophenes exhibit special optical and electrical properties with high solubility in water making potential applications of these polymers from aqueous solutions, which can facilitate the preparation of the composites of these polymers. The art of designing side chains with various sizes, electronic properties and polarities was demonstrated to be necessary for fine‐tuning the solubility and other properties of polythiophenes, thereby enhancing their applications as advanced materials. Polythiophene ; Side chain ; Conjugated system ; Polymer ; Solubility ; Materials science ; Ionic bonding ; Polymer chemistry ; Conductive polymer ; Aqueous solution ; Combinatorial chemistry ; Chemical engineering ; Nanotechnology ; Chemistry ; Organic chemistry ; Composite material Conducting polymers and applications ; Organic Electronics and Photovoltaics ; Luminescence and Fluorescent Materials
Authors: Sophia K. Laney | Tao Li | Martyna Michalska | Francisco V. Ramirez-Cuevas | Mark Portnoi | Junho Oh | Manish K. Tiwari | Iain Thayne | Ivan P. Parkin | Ioannis Papakonstantinou
Source: ACS Nano (article, 2020-08-19)
Field: Materials Science — Surfaces, Coatings and Films

Spacer-Defined Intrinsic Multiple Patterning Periodic nanotube arrays render enhanced functional properties through their interaction with light and matter, but to reach optimal performance for technologically prominent applications, such as wettability or photonics, structural fine-tuning is essential. Nonetheless, a universal and scalable method providing independent dimension control, high aspect ratios, and the prospect of further structural complexity remains unachieved. Here, we answer this need through an atomic layer deposition (ALD)-enabled multiple patterning. Unlike previous methods, the ALD-deposited spacer is applied <i>directly</i> on the prepatterned target substrate material, serving as an etching mask to generate a multitude of <i>tailored nanotubes</i>. By concept iteration, we further realize concentric and/or binary nanoarrays in a number of industrially important materials such as silicon, glass, and polymers. To demonstrate the achieved quality and applicability of the structures, we probe how nanotube fine-tuning induces broadband antireflection and present a surface boasting extremely low reflectance of <1% across the wavelength range of 300-1050 nm. Materials science ; Nanotechnology ; Atomic layer deposition ; Photonics ; Etching (microfabrication) ; Substrate (aquarium) ; Wetting ; Nanotube ; Silicon ; Optoelectronics ; Layer (electronics) ; Carbon nanotube Optical Coatings and Gratings ; Nanowire Synthesis and Applications ; GaN-based semiconductor devices and materials
Authors: Anjana K. Othayoth | Billakanti Srinivas | Karuppiah Murugan | Krishnamurthi Muralidharan
Source: Optical Materials (article, 2020-03-30)
Field: Materials Science — Materials Chemistry

Poly(methyl methacrylate)/polyphosphate blends with tunable refractive indices for optical applications Refractive index ; Materials science ; Molar absorptivity ; Polymer ; Ellipsometry ; Optics ; Methyl methacrylate ; Optoelectronics ; Thin film ; Composite material ; Nanotechnology ; Copolymer Silicone and Siloxane Chemistry ; Synthesis and properties of polymers ; Polymer Surface Interaction Studies
Authors: Kyogo Maeda | Yohei Uemura | Wang‐Jae Chun | Shazia Sharmin Satter | Kiyotaka Nakajima | Yuichi Manaka | Ken Motokura
Source: ACS Catalysis (article, 2020-11-25)
Field: Chemistry — Organic Chemistry

Controllable Factors of Supported Ir Complex Catalysis for Aromatic C–H Borylation We have developed a catalyst in which an Ir complex and organic functionalities are coimmobilized on the silica surface. The catalytic activity for aromatic C–H borylation was significantly affected by (i) the linker length of the Ir–bipyridine complex, (ii) the coimmobilized organic functionality, and (iii) the substituents on the aromatic substrate compounds. The fine-tuned supported catalyst showed higher activity than the homogeneous Ir–bipyridine complex when using a specific substrate such as benzonitrile. We elucidated this property by conducting solid-state NMR, FT-IR, XAFS, and in situ FT-IR analysis. Borylation ; Catalysis ; Benzonitrile ; Chemistry ; Substrate (aquarium) ; Heterogeneous catalysis ; Bipyridine ; Homogeneous catalysis ; Linker ; Iridium ; X-ray absorption fine structure ; Combinatorial chemistry ; Organic chemistry ; Spectroscopy Catalytic Cross-Coupling Reactions ; Catalytic C–H Functionalization Methods ; Organoboron and organosilicon chemistry
Authors: Miguel Macias‐Contreras | Lei Zhu
Source: ChemPhotoChem (article, 2020-10-09)
Field: Chemistry — Organic Chemistry

The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging Abstract Genetically encoded protein or peptide tags and bioorthogonal chemistry are two growing classes of tools in cell biological research. A protein or peptide tag could be genetically fused to a protein of interest (POI) in the same manner as fluorescent proteins (FPs). An enzymatic ligation step would then follow to deliver a chemical entity, such as a dye or a probe with properties unattainable from FPs, to the tag, and consequently to the tethered POI. Bioorthogonal chemistry refers to a collection of (mostly) bimolecular conjugation reactions that are fine‐tuned to occur efficiently in a biological environment without the interference to or from the resident (bio)molecules or ions. These two areas of research have been developed independently and more or less concurrently. The combined use of them could expand the utilities of both tools, which is advocated in this Review. The mechanisms and utilities of protein or peptide tags and bioorthogonal chemistry are briefly reviewed separately in the first two sections, while in the third section the examples that utilize both protein or peptide tags and bioorthogonal chemistry are enumerated. Each tool and the strategy of their deployment carry their own advantages and disadvantages, and the selection of a particular tool depends on a given problem. The advances and combined use of the two topical areas are driven by the emerging challenges in illuminating the ever‐finer details of biological structures and actions. Bioorthogonal chemistry ; Chemistry ; Protein tag ; Peptide ; Chemical biology ; Computational biology ; Nanotechnology ; Combinatorial chemistry ; Computer science ; Click chemistry ; Biochemistry ; Biology ; Fusion protein ; Materials science Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Advanced Biosensing Techniques and Applications