jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Xavier Just‐Baringo | Igor Larrosa
Source: Chem (article, 2018-06-01)
Field: Chemistry — Organic Chemistry

Ketone C–C Bond Activation Meets the Suzuki-Miyaura Cross-coupling Ketone ; Chemistry ; Bond ; Organic chemistry ; Business ; Finance Synthetic Organic Chemistry Methods ; Catalytic Cross-Coupling Reactions ; Chemical synthesis and alkaloids
Authors: Joseph R. H. Manning | Eleni Routoula | Siddharth V. Patwardhan
Source: Journal of Visualized Experiments (article, 2018-08-01)
Field: Materials Science — Materials Chemistry

Preparation of Functional Silica Using a Bioinspired Method The goal of the protocols described herein is to synthesize bioinspired silica materials, perform enzyme encapsulation therein, and partially or totally purify the same by acid elution. By combining sodium silicate with a polyfunctional bioinspired additive, silica is rapidly formed at ambient conditions upon neutralization. The effect of neutralization rate and biomolecule addition point on silica yield are investigated, and biomolecule immobilization efficiency is reported for varying addition point. In contrast to other porous silica synthesis methods, it is shown that the mild conditions required for bioinspired silica synthesis are fully compatible with the encapsulation of delicate biomolecules. Additionally, mild conditions are used across all synthesis and modification steps, making bioinspired silica a promising target for the scale-up and commercialization as both a bare material and active support medium. The synthesis is shown to be highly sensitive to conditions, i.e., the neutralization rate and final synthesis pH, however tight control over these parameters is demonstrated through the use of auto titration methods, leading to high reproducibility in reaction progression pathway and yield. Therefore, bioinspired silica is an excellent active material support choice, showing versatility towards many current applications, not limited to those demonstrated here, and potency in future applications. Biomolecule ; Sodium silicate ; Titration ; Nanotechnology ; Materials science ; Chemistry ; Chemical engineering ; Combinatorial chemistry ; Organic chemistry Mesoporous Materials and Catalysis ; Diatoms and Algae Research ; Layered Double Hydroxides Synthesis and Applications
Authors: Mark A. Gregory | Bolong Zhang | Andrew J. Tilley | Tamika Scheerlinck | Jonathan M. White | Wallace W. H. Wong
Source: Helvetica Chimica Acta (article, 2018-09-13)
Field: Materials Science — Materials Chemistry

Amine‐Substituted Diazocine Derivatives – Synthesis, Structure, and Photophysical Properties Abstract A series of amine‐substituted diazocines were synthesized in three steps from methyl 2‐aminobenzoate or methyl 3‐aminonaphtholate. The saddle‐shaped diazocine compounds showed similar interplane angle of 75° despite the different steric bulk of the amine substituents. In electrochemical experiments, these diazocines showed irreversible reduction most likely producing indolo[3,2‐ b ]indoles rather than forming the 10‐electron planar aromatic species. The carbazole‐substituted naphthodiazocines showed the most interesting photophysical properties with evidence of transition from the saddle‐shaped ground state to a planar excited state geometry. Chemistry ; Carbazole ; Steric effects ; Amine gas treating ; Excited state ; Aromatic amine ; Photochemistry ; Planar ; Ground state ; Crystallography ; Stereochemistry ; Polymer chemistry ; Organic chemistry Photochromic and Fluorescence Chemistry ; Porphyrin and Phthalocyanine Chemistry ; Organic Electronics and Photovoltaics
Authors: Jacob M. Kirsh | Audra J. Woodside | Brian C. Manor | Patrick J. Carroll | Paul R. Rablen | Christopher R. Graves
Source: Inorganics (article, 2018-05-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Synthesis and Characterization of (pyNO−)2GaCl: A Redox-Active Gallium Complex We report the synthesis of a gallium complex incorporating redox-active pyridyl nitroxide ligands. The (pyNO−)2GaCl complex was prepared in 85% yield via a salt metathesis route and was characterized by 1H and 13C NMR spectroscopies, X-ray diffraction, and theory. UV–Vis absorption spectroscopy and electrochemistry were used to access the optical and electrochemical properties of the complex, respectively. Our discussion focuses primarily on a comparison of the gallium complex to the corresponding aluminum derivative and shows that although the complexes are very similar, small differences in the electronic structure of the complexes can be correlated to the identity of the metal. Gallium ; Redox ; Electrochemistry ; Chemistry ; Metal ; Absorption spectroscopy ; Yield (engineering) ; Inorganic chemistry ; Salt (chemistry) ; Photochemistry ; Materials science ; Organic chemistry ; Physical chemistry ; Optics ; Electrode Magnetism in coordination complexes ; Metal complexes synthesis and properties ; Metal-Organic Frameworks: Synthesis and Applications
Authors: Muhamad Nasir | Rana Ida Sugatri | Putri Putih Puspa Asri | Fitri Dara | Ardeniswan
Source: Epitoanyag-Journal of Silicate Based and Composite Materials (article, 2018-01-01)
Field: Materials Science — Polymers and Plastics

Nanostructure and Surface Characteristic of Electrospun Carbon Black/PVDF Copolymer Nanocomposite Carbon black/PVDF copolymer (CB/PVDF copolymer) nanofiber composite has been synthesized by electrospinning process. Nanostructure and surface property of CB/PVDF copolymer were studied by using Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffraction (XRD) and water contact angle (WCA). Nanofiber composite has smooth surface morphology without bead on nanofiber string. Increase of CB content in nanofiber composite decreased diameter of nanofiber size. Range of average nanofiber diameter was from 405.2 and 421.3 nm where it depended on CB content in nanofiber composite. FTIR and XRD analysis showed that structure of PVDF copolymer in nanofiber composite had a dominant phase crystal structure. The phase was showed and confirmed by vibration band peak at 838.55 cm -1 of IR spectrum and 2 = 20.44 of XRD. Presence of CB in nanofiber composite also influenced WCA and water spreading on nanofiber composite. WCA of pristine PVDF copolymer, CB/PVDF copolymer nanofiber with 1% CB, and CB/PVDF copolymer with 5% CB were 113.8, 105.2, 117.3. From this result showed that nanostructure and surface characteristic can be adjusted and controlled by presence of CB in nanofiber composite. This result has potential application for air filtration to solve air pollution issued. Copolymer ; Nanocomposite ; Materials science ; Nanostructure ; Carbon black ; Electrospinning ; Chemical engineering ; Nanotechnology ; Composite material ; Polymer chemistry ; Polymer ; Natural rubber Conducting polymers and applications ; Electrospun Nanofibers in Biomedical Applications ; Polymer Nanocomposite Synthesis and Irradiation
Authors: Ruiyang Qu | Margherita Macino | Sarwat Iqbal | Xiang Gao | Qian He | Graham J. Hutchings | Meenakshisundaram Sankar
Source: Preprints.org (preprint, 2018-08-05)
Field: Chemistry — Organic Chemistry

Supported Bimetallic AuPd Nanoparticles as Catalyst for the Solvent-Free Selective Hydrogenation of Nitroarenes Selective hydrogenation of nitrobenzene was carried out under solvent-free conditions using supported AuPd nanoparticles catalyst, prepared by modified impregnation method (MIm), as efficient catalyst. &amp;gt;99% yield of aniline (AN) was obtained after 15 hours at 90 &amp;deg;C, 3 bar H2 that can be used without any further purification or separation, therefore reducing cost and energy input. Supported AuPd nanoparticles catalyst, prepared by MIm, was found to be active and stable even after 4 recycle experiments whereas the same catalyst prepared by SIm deactivated during the recycle experiments. The most effective catalyst was tested for the chemoselective hydrogenation of 4-chloronitrobenzene (CNB) to 4-chloroaniline (CAN). The activation energy of CNB to CAN was found to be 25 kJ mol-1, while that of CNB to AN was found to be 31 kJ mol-1. Based on this, the yield of CAN was maximized (92%) by lowering the reaction temperature to 25 &amp;deg;C. Catalysis ; Nitrobenzene ; Aniline ; Bimetallic strip ; Yield (engineering) ; Nanoparticle ; Solvent ; Materials science ; Activation energy ; Nuclear chemistry ; Catalytic hydrogenation ; Chemistry ; Chemical engineering ; Inorganic chemistry ; Organic chemistry ; Nanotechnology ; Metallurgy Nanomaterials for catalytic reactions ; Catalytic Processes in Materials Science ; Ammonia Synthesis and Nitrogen Reduction
Authors: Jinlong Ge | Zhong Wu | Wang Qiuqin | Shanshan Yang
Source: Química Nova (article, 2018-11-28)
Field: Chemistry — Inorganic Chemistry

POSTSYNTHESIS OF TITANIUM INCORPORATED WITH AMINO-FUNCTIONALIZATION UIO-66 FOR ENHANCING CO2 UPTAKE Metal-organic frameworks (MOFs) are promising nanomaterials with unprecedented capacity to store small molecules. Titanium cooperated with NH 2 -UiO-66 were prepared via post synthesis modifications approach and their structures and properties were characterized by X-raydiffraction,Fourier transform infrared spectroscopy, thermogravimetric analysis, nitrogen adsorption isotherms, and scanning electron microscopy. The resultant titanium cooperated with NH 2 -UiO-66 showed excellent performance for CO 2 adsorption via the formation of oxo-bridged hetero-Zr-Ti clusters. This result clearly demonstrates that the smaller Ti ions exchanged with the Zr ions of NH 2 -UiO-66 may decrease the pore sizes within the framework to be closer to the ideal pore sizes for CO 2 adsorption. Surface modification ; Titanium ; Chemistry ; Materials science ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Catalytic Processes in Materials Science ; Carbon dioxide utilization in catalysis
Authors: Xin Zhou | Feng‐Chun Hsia | Yanming Xue | Dai‐Ming Tang | Ovidiu Cretu | Chao Zhang | Masanori Mitome | Yoshio Bando | Takayoshi Sasaki | Dmitri Golberg
Source: physica status solidi (RRL) - Rapid Research Letters (article, 2018-11-30)
Field: Materials Science — Materials Chemistry

Tunable Mechanical and Electrical Properties of Coaxial BN‐C Nanotubes Heterostructures provide a great chance to tune the properties and functions of a nanomaterial, e.g., its mechanical and electrical properties, and thus allowing for the design and realization of novel nanoelectromechanical devices. Boron nitride and carbon nanotubes, with similar structure and mechanical properties but dramatically different electrical properties, are ideal candidates for investigating nanoscale heterostructured materials. In this work, graphitic C‐coated BN nanotubes (BN‐C NTs) were synthesized and their mechanical and electrical properties were simultaneously measured using in situ high‐resolution transmission electron microscopy (TEM). As a function of the coated carbon content, the elastic modulus obtained from second order harmonic resonance of heterostructured nanotubes could be tuned from ∼140 to ∼700 GPa, and their electrical resistivity could be adjusted within three orders of magnitude from ∼0.16 to ∼2.5×10 −4 Ω · m. This work opens the way for making custom‐designed heterostructures for the requirements of specific applications. Materials science ; Carbon nanotube ; Nanoelectromechanical systems ; Boron nitride ; Nanomaterials ; Nanotechnology ; Electrical resistivity and conductivity ; Coaxial ; Mechanical properties of carbon nanotubes ; Nanoscopic scale ; Nanotube ; Composite material ; Optoelectronics ; Nanoparticle Boron and Carbon Nanomaterials Research ; Graphene research and applications ; Carbon Nanotubes in Composites
Authors: Adafih Blackburn | S.H. Partowmah | Haley M. Brennan | Kimberly E. Mestizo | Cristina D. Stivala | Julia Petreczky | Aleida Pérez | Amanda Horn | Seán McSweeney | Alexei S. Soares
Source: Crystals (article, 2018-12-12)
Field: Materials Science — Materials Chemistry

A Simple Technique to Improve Microcrystals Using Gel Exclusion of Nucleation Inducing Elements A technique is described for generating large well diffracting crystals from conditions that yield microcrystals. Crystallization using this technique is both rapid (crystals appear in &lt;1 h) and robust (48 out of 48 co-crystallized with a fragment library, compared with 26 out of 48 using conventional hanging drop). Agarose gel is used to exclude nucleation inducing elements from the remaining crystallization cocktail. The chemicals in the crystallization cocktail are partitioned into high concentration components (presumed to induce aggregation by reducing water activity) and low concentration nucleation agents (presumed to induce nucleation through direct interaction). The nucleation agents are then combined with 2% agarose gel and deposited on the crystallization shelf of a conventional vapor diffusion plate. The remaining components are mixed with the protein and placed in contact with the agarose drop. This technique yielded well diffracting crystals of lysozyme, cubic insulin, proteinase k, and ferritin (ferritin crystals diffracted to 1.43 Å). The crystals grew rapidly, reaching large size in less than one hour (maximum size was achieved in 1–12 h). This technique is not suitable for poorly expressing proteins because small protein volumes diffuse out of the agarose gel too quickly. However, it is a useful technique for situations where crystals must grow rapidly (such as educational applications and preparation of beamline test specimens) and in situations where crystals must grow robustly (such as co-crystallization with a fragment library). Crystallization ; Agarose ; Nucleation ; Protein crystallization ; Materials science ; Crystallography ; Lysozyme ; Chemical engineering ; Crystal (programming language) ; Chromatography ; Chemistry ; Organic chemistry ; Biochemistry ; Computer science Enzyme Structure and Function ; Protein Structure and Dynamics ; Crystallization and Solubility Studies
Authors: Athina Andrea | Jason P. Mansell
Source:  (article, 2018-12-31)
Field: Materials Science — Surfaces, Coatings and Films

A Facile and Sensitive Colorimetric Approach to Confirming the Presence of Polydopamine Thin Films on (Bio)Material Surfaces Mussel foot adhesive proteins are one of nature's remarkable triumphs; they guarantee a secure and robust bond between the mollusc's byssal threads and the surface to which they settle ensuring that they are securely fastened. We now know that some of these adhesive proteins are especially rich in lysine and 3,4-dihydroxy-L-phenylalanine (DOPA) residues. Adhesive ; Materials science ; Nanotechnology ; Surface modification ; Chemistry ; Polymer science ; Layer (electronics) Polymer Surface Interaction Studies ; Marine Biology and Environmental Chemistry ; Diatoms and Algae Research
Authors: Cheryl Suwen Law | Siew Yee Lim | Abel Santos
Source:  (article, 2018-01-02)
Field: Materials Science — Materials Chemistry

Fine tuning of transmission features in nanoporous anodic alumina distributed Bragg reflectors This study introduces an innovative apodisation strategy to tune the filtering features of distributed Bragg reflectors based on nanoporous anodic alumina (NAA-DBRs). The effective medium of NAA-DBRs, which is modulated in a stepwise fashion by a pulse-like anodisation approach, is apodised following a logarithmic negative function to engineer the transmission features of NAA-DBRs. We investigate the effect of various apodisation parameters such as apodisation amplitude difference, anodisation period, current density offset and pore widening time, to tune and optimise the optical properties of NAA-DBRs in terms of central wavelength position, full width at half maximum and quality of photonic stop band. The transmission features of NAA-DBRs are shown to be fully controllable with precision across the spectral regions by means of the apodisation parameters. Our study demonstrates that an apodisation strategy can significantly narrow the width and enhance the quality of the characteristic photonic stop band of NAA-DBRs. This rationally designed anodisation approach based on the combination of apodisation and stepwise pulse anodisation enables the development of optical filters with tuneable filtering features to be integrated into optical technologies acting as essential photonic elements in devices such as optical sensors and biosensors. Nanoporous ; Materials science ; Photonics ; Optical filter ; Optoelectronics ; Offset (computer science) ; Wavelength ; Optics ; Electronic engineering ; Computer science ; Nanotechnology ; Physics ; Engineering Anodic Oxide Films and Nanostructures ; Photonic Crystals and Applications ; Optical Coatings and Gratings
Authors: Joo Hyun Lim | Hyun Ha Hwang | Na Joon Lee | Jae Wook Lee | Eun Gyo Seo | Hye Bin Son | Hye Ji Kim | Yeo Joon Yoon | Je Won Park
Source: Frontiers in Microbiology (article, 2018-09-27)
Field: Materials Science — Materials Chemistry

Enhanced Biosynthesis of 2-Deoxy-scyllo-inosose in Metabolically Engineered Bacillus subtilis Recombinants 2-Deoxy-<i>scyllo</i>-inosose (DOI) has been a valuable starting natural product for the manufacture of pharmaceuticals or chemical engineering resources such as pyranose catechol. DOI synthase, which uses glucose-6-phosphate (Glc6P) as a substrate for DOI biosynthesis, is indispensably involved in the initial stage of the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics including butirosin, gentamicin, kanamycin, and tobramycin. A number of metabolically engineered recombinant strains of <i>Bacillus subtilis</i> were constructed here; either one or both genes <i>pgi</i> and <i>pgcA</i> that encode Glc6p isomerase and phosphoglucomutase, respectively, was (or were) disrupted in the sugar metabolic pathway of the host. After that, three different DOI synthase-encoding genes, which were artificially synthesized according to the codon preference of the <i>B. subtilis</i> host, were separately introduced into the engineered recombinants. The expression of a natural <i>btrC</i> gene, encoding DOI synthase in butirosin-producing <i>B. circulans</i>, in the heterologous host <i>B. subtilis</i> (BSDOI-2) generated approximately 2.3 g/L DOI, whereas expression of an artificially codon-optimized <i>tobC</i> gene, derived from tobramycin-producing <i>Streptomyces tenebrarius</i>, into the recombinant of <i>B. subtilis</i> (BSDOI-15) in which both genes <i>pgi</i> and <i>pgcA</i> are disrupted significantly enhanced the DOI titer: up to 37.2 g/L. Fed-batch fermentation by the BSDOI-15 recombinant using glycerol and glucose as a dual carbon source yielded the highest DOI titer (38.0 g/L). The development of engineered microbial cell factories empowered through convergence of metabolic engineering and synthetic biology should enable mass production of DOI. Thus, strain BSDOI-15 will surely be a useful contributor to the industrial manufacturing of various kinds of DOI-based pharmaceuticals and fine chemicals. Bacillus subtilis ; Biology ; Biochemistry ; Metabolic engineering ; Biosynthesis ; Levansucrase ; Heterologous expression ; Gene ; Microbiology ; Recombinant DNA ; Bacteria ; Genetics Enzyme Structure and Function ; Biochemical and Molecular Research ; Polyamine Metabolism and Applications
Authors: Benjamin W. Parker | Edward Goncz | David T. Krist | Alexander V. Statsyuk | Alexey I. Nesvizhskii | Eric L. Weiss
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2018-07-03)
Field: Chemistry — Spectroscopy

LiF-MS: Mapping unstructured peptide-protein interactions using Ligand-Footprinting Mass Spectrometry Abstract Unstructured peptides, or linear motifs, present a poorly understood molecular language within the context of cellular signaling. These modular regions are often short, unstructured and interact weakly and transiently with folded target proteins. Thus, they are difficult to study with conventional structural biology methods. We present Ligand-Footprinting Mass Spectrometry, or LiF-MS, as a method of mapping the binding sites and dynamic disorder of these peptides on folded protein domains. LiF-MS uses a cleavable crosslinker to mark regions of a protein contacted by a bound linear motif. We demonstrate this method can detect both conformation ensembles and binding orientations of a linear motif in its binding pocket to amino-acid-level detail. Furthermore, marked amino acids can be used as constraints in peptide-protein docking simulations to improve model quality. In conclusion, LiF-MS proves a simple and novel method of elucidating peptide docking structural data not accessible by other methods in the context of a purified system. Footprinting ; Peptide ; Chemistry ; Docking (animal) ; Mass spectrometry ; Amino acid ; Computational biology ; Context (archaeology) ; Biochemistry ; Biology ; Chromatography ; Transcription factor Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; RNA and protein synthesis mechanisms
Authors: Maite Roca | J. Javier Ruiz‐Pernía | Raquel Castillo | Mónica Oliva | Vicent Moliner
Source: Physical Chemistry Chemical Physics (article, 2018-01-01)
Field: Materials Science — Materials Chemistry

Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed light on this debate, has been computed and the results have been compared with previous experimental data. The classical mechanical free energy barrier and the number of recrossing trajectories seem to be temperature-independent while the quantum vibrational corrections and the tunnelling effects are slightly temperature-dependent over the interval of 5-45 °C. The computed primary KIEs are in very good agreement with previous experimental data, being almost temperature-independent within the standard deviations. The modest dependence on the temperature is due to just the quantum vibrational correction contribution. These results, together with the analysis of the evolution of the collective variables such as the electrostatic potential or the electric field created by the protein on the key atoms involved in the reaction, confirm that while the protein is well preorganised, some changes take place along the reaction that favour the hydride transfer and the product release. Coordinates defining these movements are, in fact, part of the real reaction coordinate. Quantum tunnelling ; Kinetic isotope effect ; Kinetic energy ; Formate dehydrogenase ; Formate ; Chemical physics ; Chemical reaction ; Chemistry ; Computational chemistry ; Physical chemistry ; Physics ; Atomic physics ; Condensed matter physics ; Biochemistry ; Deuterium ; Quantum mechanics Enzyme Structure and Function ; Protein Structure and Dynamics ; Biochemical Acid Research Studies