jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Rian L. Griffiths | Klaudia I. Kocurek | Helen J. Cooper
Source: Current Opinion in Chemical Biology (review, 2018-01-16)
Field: Chemistry — Spectroscopy

Ambient surface mass spectrometry–ion mobility spectrometry of intact proteins Ambient surface mass spectrometry encompasses a broad range of sampling and ionization techniques. To date, only a small subset of these, based on liquid microjunction extraction, have proven suitable for intact protein analysis from thin tissue sections. Liquid extraction surface analysis shows particular promise for this application. Recently, a range of ion mobility spectrometry approaches have been coupled with ambient mass spectrometry. Improvements in signal-to-noise ratios, decreased chemical noise and separation of molecular classes have been described for the analysis of various biological substrates. Similar benefits have been described for ambient mass spectrometry imaging studies. In this review, we discuss the application of ambient mass spectrometry and ion mobility spectrometry to the analysis of intact proteins, and discuss opportunities and challenges for the field. Ion-mobility spectrometry ; Mass spectrometry ; Ion-mobility spectrometry–mass spectrometry ; Chemistry ; Analytical Chemistry (journal) ; Extraction (chemistry) ; Mass spectrometry imaging ; Ambient ionization ; Chromatography ; Sample preparation in mass spectrometry ; Ion ; Ionization ; Chemical ionization ; Electrospray ionization ; Organic chemistry Mass Spectrometry Techniques and Applications ; Ion-surface interactions and analysis ; Analytical chemistry methods development
Authors: Tuan‐Anh Nguyen | Marko Cigler | Kathrin Lang
Source: Angewandte Chemie (article, 2018-08-24)
Field: Chemistry — Organic Chemistry

Expanding the Genetic Code to Study Protein–Protein Interactions Abstract Protein–protein interactions are central to many biological processes. A considerable challenge consists however in understanding and deciphering when and how proteins interact, and this can be particularly difficult when interactions are weak and transient. The site‐specific incorporation of unnatural amino acids (UAAs) that crosslink with nearby molecules in response to light provides a powerful tool for mapping transient protein–protein interactions and for defining the structure and topology of protein complexes both in vitro and in vivo. Complementary strategies consist in site‐specific incorporation of UAAs bearing electrophilic moieties that react with natural nucleophilic amino acids in a proximity‐dependent manner, thereby chemically stabilizing low‐affinity interactions and providing additional constraints on distances and geometries in protein complexes. Herein, we review how UAAs bearing fine‐tuned chemical moieties that react with proteins in their vicinity can be utilized to map, study, and characterize weak and transient protein–protein interactions in living systems. Genetic code ; Amino acid ; Chemistry ; Protein–protein interaction ; Computational biology ; Protein engineering ; Electrophile ; Protein structure ; Combinatorial chemistry ; Biology ; Biochemistry ; Enzyme Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Receptor Mechanisms and Signaling
Authors: James F. Brazdil
Source: Catalysts (article, 2018-03-02)
Field: Materials Science — Materials Chemistry

Designing Multifunctionality into Single Phase and Multiphase Metal-Oxide-Selective Propylene Ammoxidation Catalysts Multifunctionality is the hallmark of most modern commercial heterogeneous catalyst systems in use today, including those used for the selective ammoxidation of propylene to acrylonitrile. It is the quintessential principle underlying commercial catalyst design efforts since petrochemical process development is invariably driven by the need to reduce manufacturing costs. This is in large part achieved through new and improved catalysts that increase selectivity and productivity. In addition, the future feedstocks for chemical processes will be invariably more refractory than those currently in use (e.g., replacing alkenes with alkanes or using CO2), thus requiring a disparate combination of chemical functions in order to effect multiple chemical transformations with the fewest separate process steps. This review summarizes the key chemical phenomena behind achieving the successful integration of multiple functions into a mixed-metal-oxide-selective ammoxidation catalyst. An experiential and functional catalyst design model is presented that consists of one or both of the following components: (1) a mixed-metal-oxide–solid solution where the individual metal components serve separate and necessary functions in the reaction mechanism through their atomic level interaction in the context of a single crystallographic structure; (2) the required elemental components and their catalytic function existing in separate phases, where these phases are able to interact for the purposes of electron and lattice oxygen transfer through the formation of a structurally coherent interface (i.e., epitaxy) between the separate crystal structures. Examples are provided from the literature and explained in the context of this catalyst design model. The extension of the model concepts to the design of heterogeneous catalysts in general is also discussed. Ammoxidation ; Catalysis ; Materials science ; Context (archaeology) ; Petrochemical ; Acrylonitrile ; Oxide ; Chemical engineering ; Nanotechnology ; Chemistry ; Organic chemistry ; Engineering ; Metallurgy ; Polymer ; Composite material Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Catalysis and Hydrodesulfurization Studies
Authors: Efrat Resnick | A.R. Bradley | Jinrui Gan | A. Douangamath | T. Krojer | Ritika Sethi | Anthony Aimon | Gabriel Amitai | Dom Belini | James M. Bennett | M. Fairhead | Oleg Fedorov | Paul P. Geurink | Jingxu Guo | A.N. Plotnikov | Nava Reznik | G.F. Ruda | L. Diaz Saez | Volker Straub | Tamás Szommer | Srikannathasan Velupillai | Daniel Zaidman | Alun R. Coker | Christopher G. Dowson | Haim Barr | Killian V.M. Huber | Paul E. Brennan | Huib Ovaa | F. von Delft | Nir London
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2018-10-14)
Field: Chemistry — Organic Chemistry

Rapid covalent-probe discovery by electrophile fragment screening Abstract Covalent probes can display unmatched potency, selectivity and duration of action, however, their discovery is challenging. In principle, fragments that can irreversibly bind their target can overcome the low affinity that limits reversible fragment screening. Such electrophilic fragments were considered non-selective and were rarely screened. We hypothesized that mild electrophiles might overcome the selectivity challenge, and constructed a library of 993 mildly electrophilic fragments. We characterized this library by a new high-throughput thiol-reactivity assay and screened them against ten cysteine-containing proteins. Highly reactive and promiscuous fragments were rare and could be easily eliminated. By contrast, we found selective hits for most targets. Combination with high-throughput crystallography allowed rapid progression to potent and selective probes for two enzymes, the deubiquitinase OTUB2, and the pyrophosphatase NUDT7. No inhibitors were previously known for either. This study highlights the potential of electrophile fragment screening as a practical and efficient tool for covalent ligand discovery. Electrophile ; Chemistry ; Covalent bond ; Combinatorial chemistry ; Ligand efficiency ; Fragment (logic) ; Ligand (biochemistry) ; Drug discovery ; Cysteine ; Selectivity ; Deubiquitinating enzyme ; Stereochemistry ; High-throughput screening ; Enzyme ; Biochemistry ; Organic chemistry ; Gene ; Receptor ; Computer science ; Ubiquitin Click Chemistry and Applications ; Peptidase Inhibition and Analysis ; Ubiquitin and proteasome pathways
Authors: François Loyer | Giuseppe Bengasi | Gilles Frache | Patrick Choquet | Nicolas D. Boscher
Source: Plasma Processes and Polymers (article, 2018-03-09)
Field: Materials Science — Surfaces, Coatings and Films

Insights in the initiation and termination of poly(alkyl acrylates) synthesized by atmospheric pressure plasma‐initiated chemical vapor deposition (AP‐PiCVD) A comprehensive mass‐spectrometry study of a set of poly(alkyl acrylate) layers synthesized by atmospheric pressure plasma‐initiated chemical vapor deposition (AP‐PiCVD) is provided. High‐resolution mass spectrometry investigations demonstrate that exposure of the alkyl acrylate monomers to ultra‐short and low‐frequency plasma pulses produces a defined number of radical and neutral fragments, which can play both the roles of polymerization initiation or termination groups. Further inquiries illustrate the competition between a conventional free‐radical polymerization pathway and plasma‐polymerization. On the basis of the mass‐spectrometry observations and the bond dissociation energies calculated by density functional theory, guidelines are made to select appropriate AP‐PiCVD monomers. Alkyl ; Polymerization ; Monomer ; Mass spectrometry ; Chemistry ; Dissociation (chemistry) ; Acrylate ; Plasma polymerization ; Methyl acrylate ; Polymer chemistry ; Atmospheric pressure ; Atmospheric-pressure plasma ; Trichlorosilane ; Photochemistry ; Chemical engineering ; Analytical Chemistry (journal) ; Polymer ; Plasma ; Organic chemistry ; Chromatography Surface Modification and Superhydrophobicity ; Mass Spectrometry Techniques and Applications ; Ion-surface interactions and analysis
Authors: Michał Krompiec | Sean N. Baxter | Elena L. Klimareva | Dmitry S. Yufit | Daniel G. Congrave | Thomas K. Britten | Igor F. Perepichka
Source: Journal of Materials Chemistry C (article, 2018-01-01)
Field: Materials Science — Polymers and Plastics

3,4-Phenylenedioxythiophenes (PheDOTs) functionalized with electron-withdrawing groups and their analogs for organic electronics A facile one-pot, microwave-assisted synthesis of novel functionalized arylenedioxythiophenes as promising building blocks for conjugated polymers with tuneable electronic properties is presented. Materials science ; Conjugated system ; Electronics ; Polymer ; Organic electronics ; Polar effect ; Combinatorial chemistry ; Nanotechnology ; Microwave ; Organic chemistry ; Transistor ; Physical chemistry ; Chemistry ; Electrical engineering Conducting polymers and applications ; Organic Electronics and Photovoltaics ; Organic Light-Emitting Diodes Research
Authors: Irina Muljajew | Christine Weber | Ivo Nischang | Ulrich S. Schubert
Source: Materials (article, 2018-03-30)
Field: Chemistry — Organic Chemistry

PMMA-g-OEtOx Graft Copolymers: Influence of Grafting Degree and Side Chain Length on the Conformation in Aqueous Solution Depending on the degree of grafting (DG) and the side chain degree of polymerization (DP), graft copolymers may feature properties similar to statistical copolymers or to block copolymers. This issue is approached by studying aqueous solutions of PMMA-<i>g</i>-OEtOx graft copolymers comprising a hydrophobic poly(methyl methacrylate) (PMMA) backbone and hydrophilic oligo(2-ethyl-2-oxazoline) (OEtOx) side chains. The graft copolymers were synthesized via reversible addition-fragmentation chain transfer (RAFT) copolymerization of methyl methacrylate (MMA) and OEtOx-methacrylate macromonomers of varying DP. All aqueous solutions of PMMA-<i>g</i>-OEtOx (9% &le; DG &le; 34%; 5 &le; side chain DP &le; 24) revealed lower critical solution temperature behavior. The graft copolymer architecture significantly influenced the aggregation behavior, the conformation in aqueous solution and the coil to globule transition, as verified by means of turbidimetry, dynamic light scattering, nuclear magnetic resonance spectroscopy, and analytical ultracentrifugation. The aggregation behavior of graft copolymers with a side chain DP of 5 was significantly affected by small variations of the DG, occasionally forming mesoglobules above the cloud point temperature (T<sub>cp</sub>), which was around human body temperature. On the other hand, PMMA-<i>g</i>-OEtOx with elongated side chains assembled into well-defined structures below the T<sub>cp</sub> (apparent aggregation number (N<sub>agg</sub> = 10)) that were able to solubilize Disperse Orange 3. The thermoresponsive behavior of aqueous solutions thus resembled that of micelles comprising a poly(2-ethyl-2-oxazoline) (PEtOx) shell (T<sub>cp</sub> > 60 &deg;C). Copolymer ; Polymer chemistry ; Side chain ; Hydrodynamic radius ; Aqueous solution ; Chain transfer ; Methacrylate ; Materials science ; Degree of polymerization ; Micelle ; Polymerization ; Dynamic light scattering ; Methyl methacrylate ; Chemistry ; Polymer ; Radical polymerization ; Organic chemistry ; Nanoparticle ; Composite material Advanced Polymer Synthesis and Characterization ; Surfactants and Colloidal Systems ; Hydrogels: synthesis, properties, applications
Authors: Tim Leydecker | Matilde Eredia | Fabiola Liscio | Silvia Milita | Georgian Melinte | Ovidiu Ersen | Michael Sommer | Artur Ciesielski | Paolo Samorı́
Source: Carbon (article, 2018-01-11)
Field: Materials Science — Materials Chemistry

Graphene exfoliation in the presence of semiconducting polymers for improved film homogeneity and electrical performances Graphene ; Materials science ; Exfoliation joint ; Polymer ; Electron mobility ; Nanotechnology ; Graphite ; Optoelectronics ; Composite material Graphene research and applications ; Organic Electronics and Photovoltaics ; Conducting polymers and applications
Authors: Camilla Facciotti | Vittorio Saggiomo | Anton Bunschoten | Remco Fokkink | Jan Bart ten Hove | Junyou Wang | Aldrik H. Velders
Source: Soft Matter (article, 2018-01-01)
Field: Chemistry — Organic Chemistry

Cyclodextrin-based complex coacervate core micelles with tuneable supramolecular host–guest, metal-to-ligand and charge interactions Micelles have been recognized as versatile platforms for different biomedical applications, from bioimaging to drug delivery. Complex coacervate core micelles present great advantages compared to traditional micelles, however controlling the number of charges per core-unit and the stability is still a challenge. We here present cyclodextrin-based complex coacervate core micelles where the charge per core-unit can be straightforwardly tuned by cyclodextrin host-guest interactions. By varying the ratio between two adamantane guest molecules, 1-adamantanecarboxylic acid and 1,3-adamantanediacetic acid, the charge of the monomeric core-units can be finely tuned from 6- to 9-. By adding an adamantane bislinker, monomeric core-units can be combined together in dimeric and polymeric structures, increasing the micelles' stability. The orthogonal supramolecular host-guest and coordination-chemistry allows for well-controlled cyclodextrin-based complex coacervate core micelles that offer a versatile platform for designing future, e.g., responsive systems. Coacervate ; Supramolecular chemistry ; Micelle ; Cyclodextrin ; Core (optical fiber) ; Metal ; Host (biology) ; Ligand (biochemistry) ; Chemistry ; Materials science ; Charge (physics) ; Nanotechnology ; Crystallography ; Crystal structure ; Organic chemistry ; Chromatography ; Physics ; Biochemistry Surfactants and Colloidal Systems ; Supramolecular Chemistry and Complexes ; Porphyrin and Phthalocyanine Chemistry
Authors: Alejandro V. Funes | Pablo Alborés
Source: European Journal of Inorganic Chemistry (article, 2018-05-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Recent Developments in Co<sup>III</sup><sub>2</sub>Ln<sup>III</sup><sub>2</sub> Single‐Molecule Magnets In this work we review the Co 2 III Ln 2 III family of compounds reported up to date that shows SMM features. The vast majority of them show a butterfly arrangement with Ln III ions placed at the body positions. The number of Dy III examples constitutes the majority, probably because of the intrinsic properties of this lanthanide ion regarding SMMs characteristics. Butterfly complexes have a SAP geometry around Ln III ions with a variety of distortion degrees. However, when looking at the key U eff parameter trend through this family of complexes, it becomes clear that a pure geometrical consideration is not enough to explain it. Ab initio based calculations provide evidence of highly anisotropic m J ground states for complexes where Ln III = Dy III , pointing to exclusively m J = 15/2 ground Kramers doublets. These calculations also agree with the thermally activated relaxation involving the first excited state and, in some examples where multiple relaxation pathways are observed, higher excited states. A few examples prove that Raman and/or direct mechanisms cannot be discarded a priori. Only two examples of isostructural Ln III families of the same Co 2 III Ln 2 III complex can be found. Chemistry ; Isostructural ; Lanthanide ; Excited state ; Ion ; Crystallography ; Relaxation (psychology) ; Ground state ; Ab initio quantum chemistry methods ; Ab initio ; Molecule ; Atomic physics ; Computational chemistry ; Crystal structure ; Physics Magnetism in coordination complexes ; Lanthanide and Transition Metal Complexes ; Organic and Molecular Conductors Research
Authors: Robert Gray | Ayoub H. Jaafar | E. Verrelli | Neil T. Kemp
Source: Thin Solid Films (article, 2018-07-25)
Field: Materials Science — Materials Chemistry

Method to reduce the formation of crystallites in ZnO nanorod thin-films grown via ultra-fast microwave heating Crystallite ; Nanorod ; Nucleation ; Materials science ; Thin film ; Nanotechnology ; Fabrication ; Microwave ; Optoelectronics ; Recrystallization (geology) ; Dissolution ; Substrate (aquarium) ; Chemical engineering ; Chemistry ; Computer science ; Metallurgy ; Telecommunications ZnO doping and properties ; Advanced Memory and Neural Computing ; Perovskite Materials and Applications
Authors: Lena Decuyper | Sari Deketelaere | Lore Vanparys | Marko Jukič | Izidor Sosič | E. Sauvage | Ana Amoroso | Olivier Verlaine | Bernard Joris | Stanislav Gobec | Matthias D’hooghe
Source: Chemistry - A European Journal (article, 2018-06-08)
Field: Chemistry — Organic Chemistry

In Silico Design and Enantioselective Synthesis of Functionalized Monocyclic 3‐Amino‐1‐carboxymethyl‐β‐lactams as Inhibitors of Penicillin‐Binding Proteins of Resistant Bacteria As a complement to the renowned bicyclic β-lactam antibiotics, monocyclic analogues provide a breath of fresh air in the battle against resistant bacteria. In that framework, the present study discloses the in silico design and unprecedented ten-step synthesis of eleven nocardicin-like enantiomerically pure 2-{3-[2-(2-aminothiazol-4-yl)-2-(methoxyimino)acetamido]-2-oxoazetidin-1-yl}acetic acids starting from serine as a readily accessible precursor. The capability of this novel class of monocyclic 3-amino-β-lactams to inhibit penicillin-binding proteins (PBPs) of various (resistant) bacteria was assessed, revealing the potential of α-benzylidenecarboxylates as interesting leads in the pursuit of novel PBP inhibitors. No deactivation by representative enzymes belonging to the four β-lactamase classes was observed, while weak inhibition of class C β-lactamase P99 was demonstrated. Penicillin binding proteins ; In silico ; Chemistry ; Penicillin ; Stereochemistry ; Bacteria ; Bicyclic molecule ; Lactam ; Enzyme ; Amino acid ; Combinatorial chemistry ; Biochemistry ; Antibiotics ; Microbiology ; Biology Synthesis of β-Lactam Compounds ; Antibiotic Resistance in Bacteria ; Synthesis and Catalytic Reactions
Authors: Ivan Kriuchevskyi | J. P. Wittmer | H. Meyer | Olivier Benzerara | J. Baschnagel
Source: Physical review. E (article, 2018-01-11)
Field: Materials Science — Materials Chemistry

Shear-stress fluctuations and relaxation in polymer glasses We investigate by means of molecular dynamics simulation a coarse-grained polymer glass model focusing on (quasistatic and dynamical) shear-stress fluctuations as a function of temperature T and sampling time Δt. The linear response is characterized using (ensemble-averaged) expectation values of the contributions (time averaged for each shear plane) to the stress-fluctuation relation μ_{sf} for the shear modulus and the shear-stress relaxation modulus G(t). Using 100 independent configurations, we pay attention to the respective standard deviations. While the ensemble-averaged modulus μ_{sf}(T) decreases continuously with increasing T for all Δt sampled, its standard deviation δμ_{sf}(T) is nonmonotonic with a striking peak at the glass transition. The question of whether the shear modulus is continuous or has a jump singularity at the glass transition is thus ill posed. Confirming the effective time-translational invariance of our systems, the Δt dependence of μ_{sf} and related quantities can be understood using a weighted integral over G(t). Shear modulus ; Physics ; Shear stress ; Condensed matter physics ; Thermodynamics ; Bulk modulus ; Mathematical physics ; Materials science Material Dynamics and Properties ; Liquid Crystal Research Advancements ; Polymer crystallization and properties
Authors: Morten H. Christensen | Peter P. Orth | Brian M. Andersen | Rafael M. Fernandes
Source: Physical review. B./Physical review. B (article, 2018-07-30)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Magnetic phase diagram of the iron pnictides in the presence of spin-orbit coupling: Frustration between <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>C</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:math> and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>C</mml:mi><mml:mn>4</mml:mn></mml:msub></mml:math> magnetic phases We investigate the impact of spin anisotropic interactions, promoted by spin-orbit coupling, on the magnetic phase diagram of the iron-based superconductors. Three distinct magnetic phases with Bragg peaks at $(\ensuremath{\pi},0)$ and $(0,\ensuremath{\pi})$ are possible in these systems: one ${C}_{2}$ (i.e., orthorhombic) symmetric stripe magnetic phase and two ${C}_{4}$ (i.e., tetragonal) symmetric magnetic phases. While the spin anisotropic interactions allow the magnetic moments to point in any direction in the ${C}_{2}$ phase, they restrict the possible moment orientations in the ${C}_{4}$ phases. As a result, an interesting scenario arises in which the spin anisotropic interactions favor a ${C}_{2}$ phase, but the other spin isotropic interactions favor a ${C}_{4}$ phase. We study this frustration via both mean-field and renormalization-group approaches. We find that, to lift this frustration, a rich magnetic landscape emerges well below the magnetic transition temperature, with interesting ${C}_{2},{C}_{4}$, and mixed ${C}_{2}$--${C}_{4}$ phases. Near the putative magnetic quantum critical point, spin anisotropies promote a stable Gaussian fixed point in the renormalization-group flow, which is absent in the spin isotropic case, and is associated with a near-degeneracy between ${C}_{2}$ and ${C}_{4}$ phases. We argue that this frustration is the reason why most ${C}_{4}$ phases in the iron pnictides only appear inside the ${C}_{2}$ phase, and discuss additional manifestations of this frustration in the phase diagrams of these materials. Frustration ; Condensed matter physics ; Phase diagram ; Physics ; Magnetic moment ; Anisotropy ; Quantum phase transition ; Phase (matter) ; Phase transition ; Quantum mechanics Iron-based superconductors research