jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Arun Gopalan | Benjamin J. Bucior | N. Scott Bobbitt | Randall Q. Snurr
Source: Molecular Physics (article, 2019-08-28)
Field: Chemistry — Inorganic Chemistry

Prediction of hydrogen adsorption in nanoporous materials from the energy distribution of adsorption sites We present a fast and accurate, semi-analytical method for predicting hydrogen adsorption in nanoporous materials. For any temperature and pressure, the adsorbed amount is calculated as an integral over the energy density of adsorption sites (guest-host interactions) plus an average guest-guest term. The guest-host interaction energy is calculated using a classical force field with hydrogen modelled as a single-site probe. The guest-guest interaction energy is approximated using an average coordination number, which is regressed using Gaussian Process Regression (GPR). Local adsorption at each site is then modelled using a Langmuir isotherm, which when weighted with its probability density gives an accurate description of hydrogen adsorption. The method is tested on 933 metal-organic frameworks (MOFs) from the Computation-Ready Experimental (CoRE) MOF database at 77 K from 10−5 to 100 bar, and the results are compared against GCMC predictions. To demonstrate the utility of the method, we calculated hydrogen adsorption isotherms for 12,914 existing MOF structures, at two different temperatures at a speed about 100 times that of GCMC simulations and analyzed the results. We found 13 MOFs with predicted deliverable capacities exceeding the DOE target of 50 g/L for adsorption at 100 bar, 77 K and desorption at 5 bar, 160 K. Adsorption ; Nanoporous ; Hydrogen ; Bar (unit) ; Interaction energy ; Langmuir adsorption model ; Thermodynamics ; Desorption ; Hydrogen bond ; Hydrogen storage ; Chemistry ; Materials science ; Metal-organic framework ; Physical chemistry ; Chemical physics ; Molecule ; Nanotechnology ; Physics ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Machine Learning in Materials Science ; Crystallography and molecular interactions
Authors: Bo Liu | Ru Li | Haidong Li | Guangyong You | Shouguang Yan | Qingxi Tong
Source: Sensors (article, 2019-11-25)
Field: Chemistry — Analytical Chemistry

Crop/Weed Discrimination Using a Field Imaging Spectrometer System Nowadays, sensors begin to play an essential role in smart-agriculture practices. Spectroscopy and the ground-based sensors have inspired widespread interest in the field of weed detection. Most studies focused on detection under ideal conditions, such as indoor or under artificial lighting, and more studies in the actual field environment are needed to test the applicability of this sensor technology. Meanwhile, hyperspectral image data collected by imaging spectrometer often has hundreds of channels and, thus, are large in size and highly redundant in information. Therefore, a key element in this application is to perform dimensionality reduction and feature extraction. However, the processing of highly dimensional spectral imaging data has not been given due attention in recent studies. In this study, a field imaging spectrometer system (FISS; 380-870 nm and 344 bands) was designed and used to discriminate carrot and three weed species (purslane, humifuse, and goosegrass) in the crop field. Dimensionality reduction was performed on the spectral data based on wavelet transform; the wavelet coefficients were extracted and used as the classification features in the weed detection model, and the results were compared with those obtained by using spectral bands as the classification feature. The classification features were selected using Wilks' statistic-based stepwise selection, and the results of Fisher linear discriminant analysis (LDA) and the highly dimensional data processing-oriented support vector machine (SVM) were compared. The results indicated that multiclass discrimination among weeds or between crops and weeds can be achieved using a limited number of spectral bands (8 bands) with an overall classification accuracy of greater than 85%. When the number of spectral bands increased to 15, the classification accuracy was improved to greater than 90%; further increasing the number of bands did not significantly improve the accuracy. Bands in the red edge region of plant spectra had strong discriminant capability. In terms of classification features, wavelet coefficients outperformed raw spectral bands when there were a limited number of variables. However, the difference between the two was minimal when the number of variables increased to a certain level. Among different discrimination methods, SVM, which is capable of nonlinear classification, performed better. Hyperspectral imaging ; Dimensionality reduction ; Artificial intelligence ; Pattern recognition (psychology) ; Spectrometer ; Computer science ; Linear discriminant analysis ; Feature extraction ; Weed ; Wavelet ; Support vector machine ; Multispectral image ; Wavelet transform ; Imaging spectrometer ; Remote sensing ; Physics ; Optics ; Agronomy Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Remote Sensing in Agriculture
Authors: Vishma Pratap Sur | Markéta Komínková | Žaneta Buchtová | Kristyna Dolezelikova | Ondřej Zítka | Amitava Moulick
Source: Nanomaterials (article, 2019-10-16)
Field: Materials Science — Materials Chemistry

CdSe QD Biosynthesis in Yeast Using Tryptone-Enriched Media and Their Conjugation with a Peptide Hecate for Bacterial Detection and Killing The physical and chemical synthesis methods of quantum dots (QDs) are generally unfavorable for biological applications. To overcome this limitation, the development of a novel "green" route to produce highly-fluorescent CdSe QDs constitutes a promising substitute approach. In the present work, CdSe QDs were biosynthesized in yeast <i>Saccharomyces cerevisiae</i> using a novel method, where we showed for the first time that the concentration of tryptone highly affects the synthesis process. The optimum concentration of tryptone was found to be 25 g/L for the highest yield. Different methods were used to optimize the QD extraction from yeast, and the best method was found to be by denaturation at 80 °C along with an ultrasound needle. Multiple physical characterizations including transmission electron microscopy (TEM), dynamic light scattering (DLS), energy-dispersive X-ray spectroscopy (EDX), and spectrophotometry confirmed the optical features size and shape distribution of the QDs. We showed that the novel conjugate of the CdSe QDs and a cell-penetrating peptide (hecate) can detect bacterial cells very efficiently under a fluorescent microscope. The conjugate also showed strong antibacterial activity against vancomycin-resistant <i>Staphylococcus aureus</i> (VRSA), methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), and <i>Escherichia coli</i>, which may help us to cope with the problem of rising antibiotic resistance. Biosynthesis ; Yeast ; Peptide ; Yeast extract ; Chemistry ; Biochemistry ; Microbiology ; Fermentation ; Biology ; Enzyme Quantum Dots Synthesis And Properties ; Advanced biosensing and bioanalysis techniques ; Advanced Nanomaterials in Catalysis
Authors: Feliks Nüske | Lorenzo Boninsegna | Cecilia Clementi
Source: The Journal of Chemical Physics (article, 2019-07-28)
Field: Materials Science — Materials Chemistry

Coarse-graining molecular systems by spectral matching Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale systems become computationally tractable. While significant progress has been made in tuning thermodynamic properties of reduced models, it remains a key challenge to ensure that relevant kinetic properties are retained by coarse-grained dynamical systems. In this study, we focus on data-driven methods to preserve the rare-event kinetics of the original system and make use of their close connection to the low-lying spectrum of the system's generator. Building on work by Crommelin and Vanden-Eijnden [Multiscale Model. Simul. 9, 1588 (2011)], we present a general framework, called spectral matching, which directly targets the generator's leading eigenvalue equations when learning parameters for coarse-grained models. We discuss different parametric models for effective dynamics and derive the resulting data-based regression problems. We show that spectral matching can be used to learn effective potentials which retain the slow dynamics but also to correct the dynamics induced by existing techniques, such as force matching. Parametric statistics ; Matching (statistics) ; Focus (optics) ; Key (lock) ; Work (physics) ; Spectrum (functional analysis) ; Eigenvalues and eigenvectors ; Dynamical systems theory ; Spectral properties Machine Learning in Materials Science ; Protein Structure and Dynamics ; Block Copolymer Self-Assembly
Authors: Laura M. Agosto | Matthew R. Gazzara | Caleb M. Radens | Simone Sidoli | Josue Baeza | Benjamin A. García | Kristen W. Lynch
Source: Genome Research (article, 2019-11-14)
Field: Chemistry — Spectroscopy

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing Alternative pre-mRNA splicing has long been proposed to contribute greatly to proteome complexity. However, the extent to which mature mRNA isoforms are successfully translated into protein remains controversial. Here, we used high-throughput RNA sequencing and mass spectrometry (MS)-based proteomics to better evaluate the translation of alternatively spliced mRNAs. To increase proteome coverage and improve protein quantitation, we optimized cell fractionation and sample processing steps at both the protein and peptide level. Furthermore, we generated a custom peptide database trained on analysis of RNA-seq data with MAJIQ, an algorithm optimized to detect and quantify differential and unannotated splice junction usage. We matched tandem mass spectra acquired by data-dependent acquisition (DDA) against our custom RNA-seq based database, as well as SWISS-PROT and RefSeq databases to improve identification of splicing-derived proteoforms by 28% compared with use of the SWISS-PROT database alone. Altogether, we identified peptide evidence for 554 alternate proteoforms corresponding to 274 genes. Our increased depth and detection of proteins also allowed us to track changes in the transcriptome and proteome induced by T-cell stimulation, as well as fluctuations in protein subcellular localization. In sum, our data here confirm that use of generic databases in proteomic studies underestimates the number of spliced mRNA isoforms that are translated into protein and provides a workflow that improves isoform detection in large-scale proteomic experiments. Protein isoform ; Proteome ; Biology ; Alternative splicing ; Proteomics ; Database ; RNA splicing ; Computational biology ; RefSeq ; RNA-Seq ; Sequence database ; Transcriptome ; RNA ; Gene isoform ; Bioinformatics ; Gene ; Genetics ; Gene expression ; Genome ; Computer science Advanced Proteomics Techniques and Applications ; RNA Research and Splicing ; RNA and protein synthesis mechanisms
Authors: Andrey G. Lvov | Yasushi Yokoyama | Валерий З. Ширинян
Source: The Chemical Record (review, 2019-05-07)
Field: Materials Science — Materials Chemistry

Post‐Modification of the Ethene Bridge in the Rational Design of Photochromic Diarylethenes Fine-tuning of the molecular structure of organic bistable compounds to improve their photochromic performance or to introduce additional functions remains an important issue in the development of photoresponsive materials. Diarylethenes bearing heterocyclic moieties belong to the most intensively studied class of organic photochromes due to their excellent photochemical properties. A huge number of diarylethenes have been synthesized so far. Analysis of the literature data shows that there are very worthy examples of diarylethenes developed by the Irie and Feringa groups, which can be the common starting material for a number of diarylethenes functionalized in hetaryl moieties. We refer to these structures as photochromic diarylethene precursors. These diarylethenes have proved to be very useful in the construction of functional molecules with desired properties. On the other hand, in our groups, we have elaborated on diarylethene precursors with modifiable ethene bridges. In this review, we have collected examples of such structures and their chemical modifications, leading to the improvement or fine-tuning of photochromic switching. Photochromism ; Diarylethene ; Bistability ; Molecular switch ; Molecule ; Materials science ; Rational design ; Photochemistry ; Chemistry ; Nanotechnology ; Combinatorial chemistry ; Organic chemistry ; Optoelectronics Photochromic and Fluorescence Chemistry ; Synthesis of Indole Derivatives ; Photoreceptor and optogenetics research
Authors: Yu Shao | Shuguang Yang | Wenbin Zhang
Source: Chemistry - A European Journal (article, 2019-11-14)
Field: Chemistry — Organic Chemistry

Macromolecular Isomerism in Giant Molecules Macromolecular isomerism has been an important yet largely understudied subject. Giant molecules based on molecular nanoparticles exhibit properties highly dependent on the primary structures, providing a platform for such studies. Various isomers have been designed, synthesized and characterized, including sequence-, regio-, and topo-isomers. The self-assembly of these isomers is influenced by the distinct symmetry and collective interaction of each building block in a subtle and delicate way. The results suggest that isomerism may be exploited as a new way for fine-tuning the structures and properties of macromolecules, which should be of great interest in both fundamental research and technical innovation. Macromolecule ; Molecule ; Structural isomer ; Sequence (biology) ; Chemistry ; Nanotechnology ; Materials science ; Stereochemistry ; Organic chemistry Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials ; Crystallography and molecular interactions
Authors: Ke Dong | Qi Sun | Yongquan Tang | Chuan Shan | Briana Aguila | Sai Wang | Xiangju Meng | Shengqian Ma | Feng‐Shou Xiao
Source: Nature Communications (article, 2019-07-11)
Field: Materials Science — Materials Chemistry

Bio-inspired creation of heterogeneous reaction vessels via polymerization of supramolecular ion pair Precise control of the outer-sphere environment around the active sites of heterogeneous catalysts to modulate the catalytic outcomes has long been a challenge. Here, we demonstrate how this can be fulfilled by encapsulating catalytic components into supramolecular capsules, used as building blocks for materials synthesis, whereby the microenvironment of each active site is tuned by the assembled wall. Specifically, using a cationic template equipped with a polymerizable functionality, anionic ligands can be encapsulated by ion pair-directed supramolecular assembly, followed by construction into porous frameworks. The hydrophilic ionic wall enables reactions to be achieved in water that usually requires organic solvents and also facilitates the enrichment of the substrate into the hydrophobic pocket, leading to superior catalytic performances as demonstrated by the industrially relevant hydroformylation. Remarkably, the formation of the supramolecular assembly and catalyst encapsulation further engenders reaction selectivity, which reaches an even greater extent after construction of the porous framework. Supramolecular chemistry ; Catalysis ; Cationic polymerization ; Polymerization ; Ionic bonding ; Nanotechnology ; Hydroformylation ; Materials science ; Chemistry ; Supramolecular assembly ; Chemical engineering ; Combinatorial chemistry ; Ion ; Polymer chemistry ; Polymer ; Organic chemistry ; Molecule ; Rhodium Covalent Organic Framework Applications ; Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials
Authors: Anja S. Goldmann | Nathan R. B. Boase | Lukas Michalek | James P. Blinco | Alexander Welle | Christopher Barner‐Kowollik
Source: Advanced Materials (review, 2019-08-15)
Field: Materials Science — Biomaterials

Adaptable and Reprogrammable Surfaces Establishing control over chemical reactions on interfaces is a key challenge in contemporary surface and materials science, in particular when introducing well-defined functionalities in a reversible fashion. Reprogrammable, adaptable and functional interfaces require sophisticated chemistries to precisely equip them with specific functionalities having tailored properties. In the last decade, reversible chemistries-both covalent and noncovalent-have paved the way to precision functionalize 2 or 3D structures that provide both spatial and temporal control. A critical literature assessment reveals that methodologies for writing and erasing substrates exist, yet are still far from reaching their full potential. It is thus critical to assess the current status and to identify avenues to overcome the existing limitations. Herein, the current state-of-the-art in the field of reversible chemistry on surfaces is surveyed, while concomitantly identifying the challenges-not only synthetic but also in current surface characterization methods. The potential within reversible chemistry on surfaces to function as true writeable memories devices is identified, and the latest developments in readout technologies are discussed. Finally, we explore how spatial and temporal control over reversible, light-induced chemistries has the potential to drive the future of functional interface design, especially when combined with powerful laser lithographic applications. Nanotechnology ; Characterization (materials science) ; Materials science ; Interface (matter) ; Function (biology) ; Surface modification ; Computer science ; Current (fluid) ; Engineering ; Mechanical engineering ; Electrical engineering Supramolecular Self-Assembly in Materials ; Luminescence and Fluorescent Materials ; Surface Chemistry and Catalysis
Authors: Evi R. M. Habraken | Andrew R. Jupp | Maria B. Brands | Martin Nieger | Andreas W. Ehlers | J. Chris Slootweg
Source: European Journal of Inorganic Chemistry (article, 2019-04-17)
Field: Chemistry — Organic Chemistry

Parallels between Metal‐Ligand Cooperativity and Frustrated Lewis Pairs Metal ligand cooperativity (MLC) and frustrated Lewis pair (FLP) chemistry both feature the cooperative action of a Lewis acidic and a Lewis basic site on a substrate. A lot of work has been carried out in the field of FLPs to prevent Lewis adduct formation, which often reduces the FLP reactivity. Parallels are drawn between the two systems by looking at their reactivity with CO<sub>2</sub>, and we explore the role of steric bulk in preventing dimer formation in MLC systems. Frustrated Lewis pair ; Chemistry ; Cooperativity ; Steric effects ; Lewis acids and bases ; Reactivity (psychology) ; Adduct ; Parallels ; Ligand (biochemistry) ; Stereochemistry ; Computational chemistry ; Organic chemistry ; Catalysis ; Receptor Organoboron and organosilicon chemistry ; Catalytic Cross-Coupling Reactions ; Coordination Chemistry and Organometallics
Authors: Inbal Weisbord | Neta Shomrat | Hen Moshe | Alejandro Sosnik | Tamar Segal‐Peretz
Source: Advanced Functional Materials (article, 2019-03-13)
Field: Materials Science — Materials Chemistry

Nano Spray‐Dried Block Copolymer Nanoparticles and Their Transformation into Hybrid and Inorganic Nanoparticles Abstract A novel combination of block copolymer (BCP) nano spray‐drying (NSD), solvent annealing, and selective metal oxide growth is utilized to create functional polymer nanoparticles, polymer‐metal‐oxide hybrid nanoparticles, and templated metal oxide nanoparticles with tunable composition, internal morphology, and porosity. NSD of BCPs from chloroform and toluene solutions results in porous and nonporous nanoparticles, respectively, with various degrees of phase separation. Further tuning of the nanoparticle internal morphology is performed by solvent annealing the spray‐dried particles with judicious choice of the nonsolvent dispersion medium and the surfactant, yielding assembly of both blocks at the surface of the nanoparticles. Finally, ZnO and Al 2 O 3 are grown inside the polar blocks of phase‐ordered nanoparticles using a sequential infiltration synthesis method, in a post‐assembly process, resulting in hybrid BCP‐ZnO particles and BCP‐templated Al 2 O 3 nanoparticles, as demonstrated by scanning transmission electron microscopy tomography. These structure engineering methods open new ways to direct and template functional nanoparticles. Materials science ; Nanoparticle ; Chemical engineering ; Polymer ; Copolymer ; Annealing (glass) ; Nanotechnology ; Porosity ; Scanning electron microscope ; Composite material Block Copolymer Self-Assembly ; Advanced Polymer Synthesis and Characterization ; Nanoparticle-Based Drug Delivery
Authors: Mia Sterby | Rikard Emanuelsson | Fikret Mamedov | Maria Strømme | Martin Sjödin
Source: Electrochimica Acta (article, 2019-04-02)
Field: Materials Science — Polymers and Plastics

Investigating electron transport in a PEDOT/Quinone conducting redox polymer with in situ methods A conducting redox polymer is investigated in acidic electrolyte using various in situ methods, including electron paramagnetic resonance (EPR), UV–vis spectroscopy, and conductance measurements. The quinone redox active pendant group has a formal potential of 0.67 V (vs. standard hydrogen electrode) where a 2e2H process occurs. By analyzing the rate constant at different temperatures, the rate-limiting step in the redox reaction was found to be a thermally activated process with an activation energy of 0.3 eV. The electron transport through the conducting polymer was found to be non-thermally activated and, hence, not redox rate-limiting. This is also the first time a negative temperature dependence has been reported for a conducting redox polymer in the same potential region where the redox active pendant group has its formal potential. EPR and conductance data indicated that the conductivity is governed by both polarons and bipolarons but their ratio is shifting during oxidation and reduction of the polymer. Redox ; Half-reaction ; Polaron ; Chemistry ; Electron paramagnetic resonance ; Quinone ; Conductive polymer ; Polymer ; PEDOT:PSS ; Activation energy ; Electrode potential ; Electrochromism ; Electrolyte ; Photochemistry ; Inorganic chemistry ; Electrode ; Physical chemistry ; Electron ; Nuclear magnetic resonance ; Organic chemistry Conducting polymers and applications ; Analytical Chemistry and Sensors ; Electrochemical sensors and biosensors