jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Shenyan Zhang | Koen Raedschelders | Vidya Venkatraman | Lilith Huang | Ronald J. Holewinski | Qin Fu | Jennifer E. Van Eyk
Source: Journal of Proteome Research (article, 2020-03-16)
Field: Chemistry — Spectroscopy

A Dual Workflow to Improve the Proteomic Coverage in Plasma Using Data-Independent Acquisition-MS Plasma is one of the most important and common matrices for clinical chemistry and proteomic analyses. Data-independent acquisition (DIA) mass spectrometry has enabled the simultaneous quantitative analysis of hundreds of proteins in plasma samples in support population and disease studies. Depletion of the highest abundant proteins is a common tool to increase plasma proteome coverage, but this strategy can result in the nonspecific depletion of protein subsets with which proteins targeted for depletion interact, adversely affecting their analysis. Our work using an antibody-based depletion column revealed significant complementarity not only in the identification of the proteins derived from depleted and undepleted plasma, but importantly also in the extent to which different proteins can be reproducibly quantified in each fraction. We systematically defined four major quantitative parameters of increasing stringency in both the depleted plasma fraction and in undepleted plasma for 757 observed plasma proteins: Linearity cutoff <i>r</i><sup>2</sup> > 0.8; lower limit of quantification (LLOQ); measurement range; limit of detection (LOD). We applied the results of our study to build a web-based tool, PlasmaPilot, that can serve as a protocol decision tree to determine whether the analysis of a specific protein warrants IgY14 mediated depletion. Proteome ; Blood proteins ; Mass spectrometry ; Chemistry ; Proteomics ; Population ; Human plasma ; Tandem mass spectrometry ; Chromatography ; Quantitative proteomics ; Plasma ; Biochemistry ; Physics ; Medicine Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Panangattukara Prabhakaran Praveen Kumar | Atikur Rahman | Tanmay Goswami | Hirendra N. Ghosh | Prakash P. Neelakandan
Source: ChemPlusChem (article, 2020-09-29)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Fine‐Tuning Plasmon‐Molecule Interactions in Gold‐BODIPY Nanocomposites: The Role of Chemical Structure and Noncovalent Interactions Strong coupling between localized surface plasmons and molecular absorptions leads to remarkable changes in the photophysical properties of dye-loaded metal nanoparticles. Here, we report supramolecular nanocomposites consisting of BODIPY, tryptophan, and gold nanoparticles, and investigate the effect of structural variations on their photophysical properties. Our results indicate that the photostability and photosensitization properties of the nanocomposites depend on the chemical composition of the BODIPY molecules. The singlet oxygen quantum yield of the nanocomposites NC1 (BODIPY, B1 bearing a single methyl group) and NC3 (BODIPY, B3 with 5 methyl and 2 iodo groups) were 0.46 and 0.42, respectively, which were significantly higher compared to their individual components. Ultrafast spectroscopy studies revealed that the migration of photoexcited BODIPY electrons to the plasmonic photoexcitation allowed electron transfer into the singlet oxygen states, thereby leading to efficient generation of singlet oxygen. BODIPY ; Singlet oxygen ; Photochemistry ; Photoexcitation ; Plasmon ; Molecule ; Materials science ; Chemistry ; Nanoparticle ; Nanotechnology ; Oxygen ; Fluorescence ; Excited state ; Organic chemistry ; Optoelectronics Gold and Silver Nanoparticles Synthesis and Applications ; Nanoplatforms for cancer theranostics ; Luminescence and Fluorescent Materials
Authors: Voitto Känkänen | Jani Seitsonen | Henri Tuovinen | Janne Ruokolainen | Jouni Hirvonen | Vimalkumar Balasubramanian | Hélder A. Santos
Source: International Journal of Pharmaceutics (article, 2020-09-28)
Field: Chemistry — Organic Chemistry

Evaluation of the effects of nanoprecipitation process parameters on the size and morphology of poly(ethylene oxide)-block-polycaprolactone nanostructures Materials science ; Dispersity ; Polymer ; Polycaprolactone ; Particle size ; Volume fraction ; Ethylene oxide ; Copolymer ; Chemical engineering ; Nanoparticle ; Ethylene glycol ; Polymer blend ; Morphology (biology) ; Nanotechnology ; Polymer chemistry ; Composite material Advanced Polymer Synthesis and Characterization ; Block Copolymer Self-Assembly ; Nanoparticle-Based Drug Delivery
Authors: Huina Lin | Shivani Patel | Frieder Jäkle
Source: Macromolecules (article, 2020-11-25)
Field: Chemistry — Organic Chemistry

Tailored Triarylborane Polymers as Supported Catalysts and Luminescent Materials Two novel luminescent triarylborane polymeric Lewis acids and the corresponding molecular model compounds were prepared, studies on their photophysical properties performed, and applications as supported catalysts in Lewis acid-catalyzed hydrosilylation reactions explored. Variations of the substituents in the ortho-position of a phenylene linker between the Lewis acidic borane and the polystyrene framework lead to steric and electronic fine-tuning while retaining the high Lewis acidity of the boron center. The polymeric Lewis acids serve as effective catalysts in the hydrosilylation of aldehyde, ketone, and imine compounds and because of their distinct solubility characteristics are readily amenable to recycling. In addition, as a result of the twisted biphenyl donor−π-acceptor structure, both the styrene copolymers and model compounds display strong luminescence in solution and the solid state, encompassing prompt fluorescence and in the case of the chlorophenyl-linked derivative also longer-lived room temperature phosphorescence (RTP). Consistent with quantum-chemical calculations, the greater donor strength of the 2,6-dimethylphenyl in comparison to the 2-chlorophenyl linker leads to a red-shifted emission, while the chloro substituent leads to a larger gap between singlet and triplet excited states. In the solid state, distinctly different emission properties are observed for the polymers in comparison to the molecular compounds because of the site isolation of the chromophores embedded in the polymer matrix. Lewis acids and bases ; Chemistry ; Photochemistry ; Frustrated Lewis pair ; Polymer chemistry ; Hydrosilylation ; Singlet state ; Substituent ; Borane ; Polymer ; Luminescence ; Catalysis ; Organic chemistry ; Materials science ; Excited state Organoboron and organosilicon chemistry ; Luminescence and Fluorescent Materials ; Catalytic Cross-Coupling Reactions
Authors: Timothée Stassin | Steve Waitschat | Niclas Heidenreich | Helge Reinsch | Finn Pluschkell | Dmitry E. Kravchenko | João Marreiros | Ivo Stassen | Jonas van Dinter | Rhea Verbeke | Marcel Dickmann | Werner Egger | Ivo F.J. Vankelecom | Dirk De Vos | Rob Ameloot | Norbert Stock
Source: Chemistry - A European Journal (article, 2020-05-31)
Field: Chemistry — Inorganic Chemistry

Aqueous Flow Reactor and Vapour‐Assisted Synthesis of Aluminium Dicarboxylate Metal–Organic Frameworks with Tuneable Water Sorption Properties Energy-efficient indoors temperature and humidity control can be realised by using the reversible adsorption and desorption of water in porous materials. Stable microporous aluminium-based metal-organic frameworks (MOFs) present promising water sorption properties for this goal. The development of synthesis routes that make use of available and affordable building blocks and avoid the use of organic solvents is crucial to advance this field. In this work, two scalable synthesis routes under mild reaction conditions were developed for aluminium-based MOFs: (1) in aqueous solutions using a continuous-flow reactor and (2) through the vapour-assisted conversion of solid precursors. Fumaric acid, its methylated analogue mesaconic acid, as well as mixtures of the two were used as linkers to obtain polymorph materials with tuneable water sorption properties. The synthesis conditions determine the crystal structure and either the MIL-53 or MIL-68 type structure with square-grid or kagome-grid topology, respectively, is formed. Fine-tuning resulted in new MOF materials thus far inaccessible through conventional synthesis routes. Furthermore, by varying the linker ratio, the water sorption properties can be continuously adjusted while retaining the sigmoidal isotherm shape advantageous for heat transformation and room climatisation applications. Sorption ; Materials science ; Microporous material ; Metal-organic framework ; Chemical engineering ; Aqueous solution ; Adsorption ; Aluminium ; Water vapor ; Porosity ; Organic chemistry ; Chemistry ; Composite material Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Membrane Separation and Gas Transport
Authors: Jiali Wu | Lieyin Xia | Shuhui Zhang | Xikui Liu
Source: Materials Today Communications (article, 2020-02-26)
Field: Materials Science — Materials Chemistry

Scalable preparation of individual, uniform hyper-crosslinked polyimide hollow spheres through solid-state powder foaming: The power of network manipulation Materials science ; SPHERES ; Monomer ; Polyimide ; Polymer ; Composite material ; Chemical engineering ; Viscosity ; Solvent ; Organic chemistry Covalent Organic Framework Applications ; Synthesis and properties of polymers ; Membrane Separation and Gas Transport
Authors: Adrián Moreno | Juan C. Ronda | Virgínia Cádiz | Marina Galià | Virgil Percec | Gerard Lligadas
Source: Macromolecules (article, 2020-08-18)
Field: Chemistry — Organic Chemistry

Programming Self-Assembly and Stimuli-Triggered Response of Hydrophilic Telechelic Polymers with Sequence-Encoded Hydrophobic Initiators A recent communication from our laboratory demonstrated that the presence of a small hydrophobic initiator residue (core) in water-soluble telechelic dibromo homopolymers can drive their self-assembly in aqueous solution into micelle-like nano-objects in which polymer chains adopt a folded conformation. Centered on the use of site-selective cleavable difunctional initiators, we demonstrate herein that this approach offers bottom-up and facile access to multistimuli-sensitive nanostructures for effective cargo delivery. Here, we first report the synthesis of homopolymers and copolymers encoding hydrophobicity and cleavable sites in their initiator residue in a precise sequence by single-electron transfer living radical polymerization (SET-LRP) from oligo(ethylene glycol) (macro)monomers. Employing a designed acid pH/UV light dual-cleavable initiator integrating a 2-nitroresorcinol diacetal sequence enabled on-demand middle-chain scission of the polymer chains and hence rapid/slow breakdown of the assemblies upon appropriate stimulation. Additionally, the possibility to interrogate binary co-delivery systems sequence-encoded with complimentary reactivity with combinatorial stimuli not only allows for fine-tuning the guest molecule release kinetics but also provides a mechanism to achieve control of their release behavior when different cargos are loaded. Copolymer ; Monomer ; Ethylene glycol ; Polymerization ; Polymer ; Micelle ; Chemistry ; Polymer chemistry ; Amphiphile ; Sequence (biology) ; Chain transfer ; Aqueous solution ; Self-assembly ; Radical polymerization ; Combinatorial chemistry ; Organic chemistry Advanced Polymer Synthesis and Characterization ; Polymer Surface Interaction Studies ; Dendrimers and Hyperbranched Polymers
Authors: Qin Yang | Marco Fusè | Julien Bloino
Source: Frontiers in Chemistry (article, 2020-09-15)
Field: Materials Science — Materials Chemistry

Theoretical Investigation of the Circularly Polarized Luminescence of a Chiral Boron Dipyrromethene (BODIPY) Dye Over the last decade, molecules capable of emitting circularly polarized light have attracted growing attention for potential technological and biological applications. The efficiency of such devices depend on multiple parameters, in particular the magnitude and wavelength of the peak of emitted light, and also on the dissymmetry factor for chiral applications. In light of these considerations, molecular systems with tunable optical properties, preferably in the visible spectral region, are particularly appealing. This is the case of boron dipyrromethene (BODIPY) dyes, which exhibit large molecular absorption coefficients, have high fluorescence yields, are very stable, both thermally and photochemically, and can be easily functionalized. The latter property has been extensively exploited in the literature to produce chromophores with a wide range of optical properties. Nevertheless, only a few chiral BODIPYs have been synthetized and investigated so far. Using a recently reported axially chiral BODIPY derivative where an axially chiral BINOL unit has been attached to the chromophore unit, we present a comprehensive computational protocol to predict and interpret the one-photon absorption and emission spectra, together with their chiroptical counterparts. From the physico-chemical properties of this molecule, it will be possible to understand the origin of the circularly polarized luminescence better, thus helping to fine-tune the properties of interest. The sensitivity of such processes require accurate results, which can be achieved through a proper account of the vibrational structure in optical spectra. Methodologies to compute vibrationally-resolved electronic spectra can now be applied on relatively large chromophores, such as BODIPYs, but require more extensive computational protocols. For this reason, particular attention is paid in the description of the different steps of the protocol, and the potential pitfalls. Finally, we show how, by means of appropriate tools and approaches, data from intermediate steps of the simulation of the final spectra can be used to obtain further insights into the properties of the molecular system under investigation and the origin of the visible bands. BODIPY ; Chromophore ; Luminescence ; Absorption (acoustics) ; Photochemistry ; Materials science ; Molecule ; Boron ; Emission spectrum ; Chemistry ; Fluorescence ; Spectral line ; Optoelectronics ; Optics ; Physics ; Organic chemistry Luminescence and Fluorescent Materials ; Synthesis and Properties of Aromatic Compounds ; Molecular Sensors and Ion Detection
Authors: Jasmine M. Hershewe | William D. Wiseman | James E. Kath | Chelsea C. Buck | Maneesh K. Gupta | Patrick B. Dennis | Rajesh R. Naik | Michael C. Jewett
Source: ACS Synthetic Biology (article, 2020-11-17)
Field: Materials Science — Biomaterials

Characterizing and Controlling Nanoscale Self-Assembly of Suckerin-12 Structural proteins such as “suckerins” present promising avenues for fabricating functional materials. Suckerins are a family of naturally occurring block copolymer-type proteins that comprise the sucker ring teeth of cephalopods and are known to self-assemble into supramolecular networks of nanoconfined β-sheets. Here, we report the characterization and controllable, nanoscale self-assembly of suckerin-12 (S12). We characterize the impacts of salt, pH, and protein concentration on S12 solubility, secondary structure, and self-assembly. In doing so, we identify conditions for fabricating ∼100 nm nanoassemblies (NAs) with narrow size distributions. Finally, by installing a noncanonical amino acid (ncAA) into S12, we demonstrate the assembly of NAs that are covalently conjugated with a hydrophobic fluorophore and the ability to change self-assembly and β-sheet content by PEGylation. This work presents new insights into the biochemistry of suckerin-12 and demonstrates how ncAAs can be used to expedite and fine-tune the design of protein materials. Self-assembly ; Nanotechnology ; Fluorophore ; Supramolecular chemistry ; Nanoscopic scale ; PEGylation ; Covalent bond ; Chemistry ; Template ; Materials science ; Fluorescence ; Biochemistry ; Molecule ; Organic chemistry ; Physics ; Polyethylene glycol Silk-based biomaterials and applications ; Supramolecular Self-Assembly in Materials ; RNA Interference and Gene Delivery
Authors: Marija Tkalčević | Lovro Basioli | Krešimir Salamon | Iva Šarić | Jordi Sancho Parramon | Matej Bubaš | Iva Bogdanović Radović | Sigrid Bernstorff | Zsolt Fogarassy | Katalin Balázsi | M. Petravić | Maja Mičetić
Source: Solar Energy Materials and Solar Cells (article, 2020-08-24)
Field: Materials Science — Materials Chemistry

Ge quantum dot lattices in alumina prepared by nitrogen assisted deposition: Structure and photoelectric conversion efficiency Germanium ; Quantum dot ; Materials science ; Optoelectronics ; Quantum efficiency ; Sputtering ; Sputter deposition ; Thin film ; Photoelectric effect ; Deposition (geology) ; Annealing (glass) ; Nanotechnology ; Silicon ; Composite material Silicon Nanostructures and Photoluminescence ; Nanowire Synthesis and Applications ; Semiconductor materials and devices
Authors: Yitian Zeng | Steven J. Madsen | Andrew B. Yankovich | Eva Olsson | Robert Sinclair
Source: Nanoscale (article, 2020-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Comparative electron and photon excitation of localized surface plasmon resonance in lithographic gold arrays for enhanced Raman scattering The ability to tune the localized surface plasmon resonance (LSPR) of nanostructures is desirable for surface enhanced Raman spectroscopy (SERS), plasmon-assisted chemistry and other nanophotonic applications. Although historically the LSPR is mainly studied by optical techniques, with the recent advancement in electron monochromators and correctors, it has attracted considerable attention in transmission electron microscopy (TEM). Here, we use electron energy loss spectroscopy (EELS) in a scanning TEM to study individual gold nanodiscs and bowties in lithographic arrays with variable LSPRs by adjusting the size, interspacing, shape and dielectric environment during the nanofabrication process. We observe the strongest Raman signal enhancement when the LSPR frequency is close to the incident laser frequency in Raman spectroscopy. A simplified harmonic oscillator model is used to estimate SERS enhancement factor (EF) from EELS, bridging the connection between electron and photon excitation of plasmonic arrays. This work demonstrates that STEM-EELS shows promise for revealing the contributions of specific LSPR modes to SERS EF. Our results provide guidelines to fine-tune nanoparticle parameters to deliver the maximum signal enhancement in biosensing applications, such as early cancer detection. Raman scattering ; Materials science ; Excitation ; Plasmon ; Surface plasmon resonance ; Raman spectroscopy ; Two-photon excitation microscopy ; X-ray Raman scattering ; Electron-beam lithography ; Resonance (particle physics) ; Lithography ; Photon ; Scattering ; Optoelectronics ; Optics ; Nanotechnology ; Atomic physics ; Nanoparticle ; Physics ; Resist Gold and Silver Nanoparticles Synthesis and Applications ; Plasmonic and Surface Plasmon Research ; Advanced biosensing and bioanalysis techniques
Authors: Maryam Omidi | Nezha Ahmad Agha | Anke Müller | Frank Feyerabend | Heike Helmholz | Regine Willumeit‐Römer | Hartmut Schlüter | Bérengère Luthringer-Feyerabend
Source: Metallomics (article, 2020-04-30)
Field: Materials Science — Biomaterials

Investigation of the impact of magnesium<i>versus</i>titanium implants on protein composition in osteoblast by label free quantification Metallic implant biomaterials predominate in orthopaedic surgery. Compared to titanium-based permanent implants, magnesium-based ones offer new possibilities as they possess mechanical properties closer to the ones of bones and they are biodegradable. Furthermore, magnesium is more and more considered to be "bioactive" i.e., able to elicit a specific tissue response or to strengthen the intimate contact between the implant and the osseous tissue. Indeed, several studies demonstrated the overall beneficial effect of magnesium-based materials on bone tissue (in vivo and in vitro). Here, the direct effects of titanium and magnesium on osteoblasts were measured on proteomes levels in order to highlight metal-specific and relevant proteins. Out of 2100 identified proteins, only 10 and 81 differentially regulated proteins, compare to the control, were isolated for titanium and magnesium samples, respectively. Selected ones according to their relationship to bone tissue were further discussed. Most of them were involved in extracellular matrix maturation and remodelling (two having a negative effect on mineralisation). A fine-tuned balanced between osteoblast maturation, differentiation and viability was observed. Magnesium ; Titanium ; Osteoblast ; Extracellular matrix ; In vivo ; Implant ; Biomedical engineering ; Bone tissue ; Chemistry ; Materials science ; In vitro ; Biophysics ; Biochemistry ; Metallurgy ; Surgery ; Biology ; Biotechnology ; Medicine Magnesium Alloys: Properties and Applications ; Bone Tissue Engineering Materials ; Orthopaedic implants and arthroplasty
Authors: Santosh Kumar | Santu Bera | Sujay Kumar Nandi | Debasish Haldar
Source: Soft Matter (article, 2020-10-20)
Field: Materials Science — Biomaterials

The effect of amide bond orientation and symmetry on the self-assembly and gelation of discotic tripeptides A series of discotic tripeptides containing a rigid aromatic core and l-phenylalanine have been developed. The orientation of the amide bonds yielded variations of the structure and self-assembly properties of the compounds. The aggregation behavior of the discotic tripeptides was studied by various spectroscopic techniques. The morphology of the resulting aggregates was studied by field emission electron microscopy and atomic force microscopy. These studies showed that the orientation of the amide bonds has a strong influence on the intermolecular interactions, resulting in huge differences in the aggregation properties, and morphology of the discotic tripeptides. Only the C<sub>3</sub>-symmetric discotic tripeptides formed organogels. The supramolecular aggregation mechanism of N-centered and C[double bond, length as m-dash]O-centered discotic tripeptides for forming 3-fold intermolecular H-bonded helical column were the same, there was only a smaller enthalpy change due to the occurrence of longer distances for the N-HO[double bond, length as m-dash]C bonds of the N-centered discotic tripeptide. Whereas, the C<sub>2</sub>-symmetric discotic tripeptides 2 and 3 adopted a 6-fold intermolecular H-bonded dimer structure. Thus, this report presents a valuable approach for the fine-tuning of the discotic tripeptide based functional material. Tripeptide ; Amide ; Discotic liquid crystal ; Symmetry (geometry) ; Peptide bond ; Crystallography ; Orientation (vector space) ; Stereochemistry ; Materials science ; Chemistry ; Organic chemistry ; Molecule ; Geometry ; Peptide ; Biochemistry ; Mathematics Supramolecular Self-Assembly in Materials ; Polydiacetylene-based materials and applications ; Luminescence and Fluorescent Materials