jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ganna Gryn’ova | Clémence Corminbœuf
Source: Beilstein Journal of Organic Chemistry (article, 2018-06-19)
Field: Chemistry — Physical and Theoretical Chemistry

Steric “attraction”: not by dispersion alone Non-covalent interactions between neutral, sterically hindered organic molecules generally involve a strong stabilizing contribution from dispersion forces that in many systems turns the 'steric repulsion' into a 'steric attraction'. In addition to London dispersion, such systems benefit from electrostatic stabilization, which arises from a short-range effect of charge penetration and gets bigger with increasing steric bulk. In the present work, we quantify this contribution for a diverse set of molecular cores, ranging from unsubstituted benzene and cyclohexane to their derivatives carrying <i>tert</i>-butyl, phenyl, cyclohexyl and adamantyl substituents. While the importance of electrostatic interactions in the dimers of sp<sup>2</sup>-rich (e.g., π-conjugated) cores is well appreciated, less polarizable assemblies of sp<sup>3</sup>-rich systems with multiple short-range CH···HC contacts between the bulky cyclohexyl and adamantyl moieties are also significantly influenced by electrostatics. Charge penetration is drastically larger in absolute terms for the sp<sup>2</sup>-rich cores, but still has a non-negligible effect on the sp<sup>3</sup>-rich dimers, investigated herein, both in terms of their energetics and equilibrium interaction distances. These results emphasize the importance of this electrostatic effect, which has so far been less recognized in aliphatic systems compared to London dispersion, and are therefore likely to have implications for the development of force fields and methods for crystal structure prediction. Steric effects ; Chemistry ; Electrostatics ; Chemical physics ; London dispersion force ; van der Waals force ; Cyclohexane ; Polarizability ; Dispersion (optics) ; Attraction ; Non-covalent interactions ; Molecule ; Computational chemistry ; Stereochemistry ; Organic chemistry ; Hydrogen bond ; Physical chemistry Crystallography and molecular interactions ; Supramolecular Chemistry and Complexes ; Luminescence and Fluorescent Materials
Authors: Yuxiao Qin | Li Sun | Qingsong Hua | Ping Liu
Source: Sustainability (article, 2018-07-12)
Field: Materials Science — Materials Chemistry

A Fuzzy Adaptive PID Controller Design for Fuel Cell Power Plant Solid oxide fuel cells (SOFCs) are promising electrochemical devices which translate chemical energy directly into electric energy with high efficiency and low pollution. However, the control of the output voltage of SOFCs is quite challenging because of the strong nonlinearity, limited fuel flow, and rapid variation of the load disturbance. Nowadays, proportional-integral-derivative (PID) controllers are commonly utilized in industrial control systems for their high reliability and simplicity. However, it will lead to overshoot and windup issues when used in the wide-range operation of SOFCs. This paper aims to improve the PID controller performance based on fuzzy logic by (1) identifying a linear model based on the least squares method; (2) optimizing the PID parameters based on the generated linear model; and (3) designing a fuzzy adaptive PID controller based on the optimized parameters. The simulation results of the conventional PID controller and the fuzzy adaptive PID controller are compared, demonstrating that the proposed controller can achieve satisfactory control performance for SOFCs in terms of anti-windup, overshoot reduction, and tracking acceleration. The main contribution of this paper can be summarized as: (1) this paper identifies the SOFC model and uses the identified model as a control object to optimize conventional PID controllers; (2) this paper combines a fuzzy logic control scheme and PID control scheme to design our proposed fuzzy adaptive PID controller; and (3) this paper develops an anti-windup structure based on a back-calculation method to reduce saturation time and overshoot. PID controller ; Control theory (sociology) ; Overshoot (microwave communication) ; Fuzzy logic ; Control engineering ; Controller (irrigation) ; Engineering ; Computer science ; Temperature control ; Control (management) Advancements in Solid Oxide Fuel Cells ; Fuel Cells and Related Materials ; Advanced battery technologies research
Authors: Brendan Sullivan | Richard Archibald | Patricia S. Langan | Holger Dobbek | Martin Bommer | Robert L. McFeeters | Leighton Coates | Xiaoping Wang | Franz X. Gallmeier | J.M. Carpenter | V. E. Lynch | Paul Langan
Source: Acta Crystallographica Section D Structural Biology (article, 2018-10-29)
Field: Materials Science — Materials Chemistry

Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space Neutron crystallography is a powerful technique for directly visualizing the locations of H atoms in biological macromolecules. This information has provided key new insights into enzyme mechanisms, ligand binding and hydration. However, despite the importance of this information, the application of neutron crystallography in biology has been limited by the relatively low flux of available neutron beams and the large incoherent neutron scattering from hydrogen, both of which contribute to weak diffraction data with relatively low signal-to-background ratios. A method has been developed to fit weak data based on three-dimensional profile fitting of Bragg peaks in reciprocal space by an Ikeda-Carpenter function with a bivariate Gaussian. When applied to data collected from three different proteins, three-dimensional profile fitting yields intensities with higher correlation coefficients (CC<sub>1/2</sub>) at high resolutions, decreased R<sub>free</sub> factors, extended resolutions and improved nuclear density maps. Importantly, additional features are revealed in nuclear density maps that may provide additional scientific information. These results suggest that three-dimensional profile fitting will help to extend the capabilities of neutron macromolecular crystallography. Reciprocal lattice ; Neutron ; Neutron diffraction ; Neutron scattering ; Resolution (logic) ; Neutron reflectometry ; Computational physics ; Physics ; Crystallography ; Materials science ; Diffraction ; Small-angle neutron scattering ; Optics ; Chemistry ; Nuclear physics ; Computer science Enzyme Structure and Function ; Protein Structure and Dynamics ; Heat shock proteins research
Authors: Dandan Xu | Omar Abdelrahman | Sang Hyun Ahn | Yasmine Guefrachi | Anatoliy Kuznetsov | Limin Ren | Son‐Jong Hwang | Maryam Khaleel | Saeed Al Hassan | Dongxia Liu | Suk Bong Hong | Paul J. Dauenhauer | Michael Tsapatsis
Source: AIChE Journal (article, 2018-12-19)
Field: Chemistry — Inorganic Chemistry

A quantitative study of the structure–activity relationship in hierarchical zeolites using liquid‐phase reactions Micro/meso/macroporous (hierarchical) zeolites show remarkable catalytic performance for reactions involving bulky reactants. However, quantitative assessment of the microstructural characteristics contributing to the observed performance remains elusive. Here, structure–activity relationships are established for a set of micro/mesoporous self‐pillared pentasil (SPP) zeolites using two parallel liquid‐phase reactions (benzyl alcohol alkylation and self‐etherification) based on analysis of mass transport and reaction kinetics. A reaction–diffusion mathematical model is developed that quantitatively assigns the catalytic contributions of the external surface and micropores of SPP zeolites for these reactions. In addition, the effect of the zeolite external surface structure on the corresponding catalytic activity is quantitatively assessed by comparing SPP zeolites (with MFI structure) with MCM‐22 (with MWW structure). This work demonstrates that reaction–diffusion modeling allows quantitative description of the catalytic performance of hierarchical zeolites and provides a model reaction to assess nm‐sized characteristic diffusion lengths in MFI. © 2018 American Institute of Chemical Engineers AIChE J , 65: 1067–1075, 2019 Zeolite ; Catalysis ; Mesoporous material ; Benzyl alcohol ; Alkylation ; Diffusion ; Chemistry ; Chemical engineering ; Phase (matter) ; Liquid phase ; Mass transport ; Chemical kinetics ; Kinetics ; Materials science ; Thermodynamics ; Organic chemistry Zeolite Catalysis and Synthesis ; Mesoporous Materials and Catalysis ; Catalysis for Biomass Conversion
Authors: Matthew The | Lukas Käll
Source: Molecular & Cellular Proteomics (article, 2018-11-27)
Field: Chemistry — Spectroscopy

Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics Protein quantification by label-free shotgun proteomics experiments is plagued by a multitude of error sources. Typical pipelines for identifying differential proteins use intermediate filters to control the error rate. However, they often ignore certain error sources and, moreover, regard filtered lists as completely correct in subsequent steps. These two indiscretions can easily lead to a loss of control of the false discovery rate (FDR). We propose a probabilistic graphical model, <i>Triqler</i>, that propagates error information through all steps, employing distributions in favor of point estimates, most notably for missing value imputation. The model outputs posterior probabilities for fold changes between treatment groups, highlighting uncertainty rather than hiding it. We analyzed 3 engineered data sets and achieved FDR control and high sensitivity, even for truly absent proteins. In a bladder cancer clinical data set we discovered 35 proteins at 5% FDR, whereas the original study discovered 1 and MaxQuant/Perseus 4 proteins at this threshold. Compellingly, these 35 proteins showed enrichment for functional annotation terms, whereas the top ranked proteins reported by MaxQuant/Perseus showed no enrichment. The model executes in minutes and is freely available at https://pypi.org/project/triqler/. Shotgun proteomics ; Shotgun ; Identification (biology) ; Computer science ; Computational biology ; Proteomics ; Chemistry ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Advanced Biosensing Techniques and Applications
Authors: Xiupei Yang | Mingxian Liu | Yanru Yin | Fenglin Tang | Hua Xu | Xiangjun Liao
Source: Sensors (article, 2018-03-24)
Field: Materials Science — Materials Chemistry

Green, Hydrothermal Synthesis of Fluorescent Carbon Nanodots from Gardenia, Enabling the Detection of Metronidazole in Pharmaceuticals and Rabbit Plasma Strong fluorescent carbon nanodots (FCNs) were synthesized with a green approach using gardenia as a carbon source through a one-step hydrothermal method. FCNs were characterized by their UV-vis absorption spectra, photoluminescence (PL), Fourier transform infrared spectroscopy (FTIR) as well as X-ray photoelectron spectroscopy (XPS). We further explored the use of as-synthesized FCNs as an effective probe for the detection of metronidazole (MNZ), which is based on MNZ-induced fluorescence quenching of FCNs. The proposed method displayed a wide linear range from 0.8 to 225.0 µM with a correlation coefficient of 0.9992 and a limit of detection as low as 279 nM. It was successfully applied to the determination of MNZ in commercial tablets and rabbit plasma with excellent sensitivity and selectivity, which indicates its potential applications in clinical analysis and biologically related studies. Detection limit ; X-ray photoelectron spectroscopy ; Fourier transform infrared spectroscopy ; Fluorescence ; Quenching (fluorescence) ; Materials science ; Hydrothermal circulation ; Nanodot ; Carbon fibers ; Analytical Chemistry (journal) ; Nuclear chemistry ; Spectroscopy ; Fluorescence spectroscopy ; Photoluminescence ; Chemistry ; Nanotechnology ; Chemical engineering ; Chromatography ; Optoelectronics ; Optics Carbon and Quantum Dots Applications ; Heavy Metal Exposure and Toxicity ; Nanocluster Synthesis and Applications
Authors: Sylvester M. Greer | Simone Sidoli | Mariel Coradin | Malena Schack Jespersen | Veit Schwämmle | Ole N. Jensen | Benjamin A. García | Jennifer S. Brodbelt
Source: Analytical Chemistry (article, 2018-07-31)
Field: Chemistry — Spectroscopy

Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle–Down Strategy The ability to map combinatorial patterns of post-translational modifications (PTMs) of proteins remains challenging for traditional bottom-up mass spectrometry workflows. There are also hurdles associated with top-down approaches related to limited data analysis options for heavily modified proteoforms. These shortcomings have accelerated interest in middle-down MS methods that focus on analysis of large peptides generated by specific proteases in conjunction with validated bioinformatics strategies to allow quantification of isomeric histoforms. Mapping multiple PTMs simultaneously requires the ability to obtain high sequence coverage to allow confident localization of the modifications, and 193 nm ultraviolet photodissociation (UVPD) has been shown to cause extensive fragmentation for large peptides and proteins. Histones are an ideal system to test the ability of UVPD to characterize multiple modifications, as the combinations of PTMs are the underpinning of the biological significance of histones and at the same time create an imposing challenge for characterization. The present study focuses on applying 193 nm UVPD to the identification and localization of PTMs on histones by UVPD and comparison to a popular alternative, electron-transfer dissociation (ETD), via a high-throughput middle-down LC/MS/MS strategy. Histone Coder and IsoScale, bioinformatics tools for verification of PTM assignments and quantification of histone peptides, were adapted for UVPD data and applied in the present study. In total, over 300 modified forms were identified, and the distributions of PTMs were quantified between UVPD and ETD. Significant differences in patterns of PTMs were found for histones from HeLa cells prior to and after treatment with a deacetylase inhibitor. Additional fragment ion types generated by UVPD proved essential for extensive characterization of the most heavily modified forms (>5 PTMs). Chemistry ; Photodissociation ; Mass spectrometry ; Ultraviolet ; Characterization (materials science) ; Analytical Chemistry (journal) ; Photochemistry ; Chromatography ; Nanotechnology ; Optoelectronics Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Genomics and Chromatin Dynamics
Authors: Jose F. Gómez‐Cortés | M.L. Nó | I. Ruiz‐Larrea | T. Bręczewski | A. López‐Echarri | Christopher A. Schuh | J. San Juán
Source: Acta Materialia (article, 2018-12-28)
Field: Materials Science — Materials Chemistry

Ultrahigh superelastic damping at the nano-scale: A robust phenomenon to improve smart MEMS devices Micro and nano pillars of Copper-based shape memory alloys (SMAs) with feature sizes between about 2 μm and 250 nm are known to exhibit ultra-high mechanical damping due to the nucleation and motion of stress-induced martensite interfaces during superelastic straining. While this behavior could be extremely useful to protect micro electro-mechanical systems (MEMS) against vibrations in aggressive environments, a fundamental question must yet be answered in order to envisage further applications, namely, whether this damping is reproducible and stable over long times and many cycles, or whether the damping is a signal of accumulating damage that could compromise long-term usage. In the present paper this crucial question is answered; we show that micropillar arrays of Cu-Al-Ni SMAs exhibit a completely recoverable and reproducible superelastic response, with an ultra-high damping loss factor η > 0.1, or even higher for sub-micrometer pillars, η > 0.2, even after thousands of cycles (>5000) and after long times spanning more than four years. Furthermore, the first high-frequency tests on such nanoscale SMAs show that their superelastic response is very fast and relevant to ultra-high damping even at frequencies as high as 1000 Hz. This paves the way for the design of micro/nano dampers, based on SMAs, to improve the reliability of MEMS in noisy environments. Materials science ; Microelectromechanical systems ; Shape-memory alloy ; Nano- ; Thermoelastic damping ; Nanoscopic scale ; Smart material ; Micrometer ; Vibration ; Damper ; Nucleation ; Martensite ; Nanotechnology ; Structural engineering ; Composite material ; Mechanical engineering ; Acoustics ; Microstructure Shape Memory Alloy Transformations ; Nonlocal and gradient elasticity in micro/nano structures ; Ferroelectric and Piezoelectric Materials
Authors: Sophie L. Mader | Alois Bräuer | M. Groll | Ville R. I. Kaila
Source: Nature Communications (article, 2018-03-15)
Field: Chemistry — Inorganic Chemistry

Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ The recently discovered Fe<sup>II</sup>/α-ketoglutarate-dependent dioxygenase AsqJ from Aspergillus nidulans stereoselectively catalyzes a multistep synthesis of quinolone alkaloids, natural products with significant biomedical applications. To probe molecular mechanisms of this elusive catalytic process, we combine here multi-scale quantum and classical molecular simulations with X-ray crystallography, and in vitro biochemical activity studies. We discover that methylation of the substrate is essential for the activity of AsqJ, establishing molecular strain that fine-tunes π-stacking interactions within the active site. To rationally engineer AsqJ for modified substrates, we amplify dispersive interactions within the active site. We demonstrate that the engineered enzyme has a drastically enhanced catalytic activity for non-methylated surrogates, confirming our computational data and resolved high-resolution X-ray structures at 1.55 Å resolution. Our combined findings provide crucial mechanistic understanding of the function of AsqJ and showcase how combination of computational and experimental data enables to rationally engineer enzymes. Dioxygenase ; Active site ; Substrate (aquarium) ; Function (biology) ; Chemistry ; Enzyme ; Quinolone ; Biosynthesis ; Stacking ; Catalysis ; Combinatorial chemistry ; Computational biology ; Stereochemistry ; Biochemistry ; Biology ; Genetics Metal-Catalyzed Oxygenation Mechanisms ; Microbial metabolism and enzyme function ; Synthesis and Biological Evaluation
Authors: Joan Papavasiliou | Αλεξάνδρα Παξινού | Grzegorz Słowik | Stylianos G. Neophytides | George Avgouropoulos
Source: Catalysts (article, 2018-11-15)
Field: Materials Science — Materials Chemistry

Steam Reforming of Methanol over Nanostructured Pt/TiO2 and Pt/CeO2 Catalysts for Fuel Cell Applications A research and technological challenge for fuel processors integrated with High Temperature Polymer Electrolyte Membrane Fuel Cells (HT-PEMFCs), also known as Internal Reforming Methanol Fuel Cells (IRMFCs), operating at 200–220 °C, is the development of highly efficient catalysts, which will be able to selectively (low CO and other by-products formation) produce the required quantity of hydrogen at these temperatures. In this work, various amounts of platinum were dispersed via deposition-precipitation (DP) and impregnation (I) methods onto the surface of hydrothermally prepared ceria nanorods (CNRs) and titania nanotubes (TNTs). These nanostructured catalysts were evaluated in steam reforming of methanol process targeting the operation level of IRMFCs. The (DP) method resulted in highly (atomically) dispersed platinum-based catalysts, as confirmed with Scanning Transmission Electron Microscopy (STEM) analysis, with a mean particle size of less than 1 nm in the case of 0.35 wt.% Pt/CNRs catalyst. Ultra-fine dispersion of platinum species correlated with the presence of oxygen vacancies, together with the enrichment of CNRs surface with active metallic phase resulted in a highly active catalyst achieving at 220 °C a hydrogen production rate of 5500 cm3 min−1 per g of loaded platinum. Steam reforming ; Catalysis ; Platinum ; Materials science ; Chemical engineering ; Hydrogen production ; Methanol ; Hydrogen ; Platinum nanoparticles ; Chemistry ; Organic chemistry Catalytic Processes in Materials Science ; Electrocatalysts for Energy Conversion ; Catalysis and Hydrodesulfurization Studies
Authors: Yan Lyu | Jingqi Tian | Jing Li | Peng Chen | Kanyi Pu
Source: Angewandte Chemie International Edition (article, 2018-08-15)
Field: Materials Science — Materials Chemistry

Semiconducting Polymer Nanobiocatalysts for Photoactivation of Intracellular Redox Reactions An organic semiconducting polymer nanobiocatalyst (SPNB) composed of a semiconducting polymer core conjugated with microsomal cytochrome P450 (CYP) has been developed for photoactivation of intracellular redox. The core serves as the light-harvesting unit to initiate photoinduced electron transfer (PET) and facilitate the regeneration of dihydronicotinamide adenine dinucleotide phosphate (NADPH), while CYP is the catalytic center for intracellular redox. Under light irradiation, the semiconducting core can efficiently catalyze the generation of NADPH with a turnover frequency (TOF) 75 times higher than the reported nanosystems, ensuring the supply of the cofactor for intracellular redox. SPNB-mediated intracellular redox thus can be efficiently activated by light in living cells to convert the model substrate and also to trigger the bioactivation of anticancer drugs. This study provides an organic nanobiocatalytic system that allows light to remotely control intracellular redox in living systems. Intracellular ; Redox ; Chemistry ; Photochemistry ; Biophysics ; Conjugated system ; Cofactor ; Electron transfer ; Electron transport chain ; Polymer ; Enzyme ; Biochemistry ; Organic chemistry ; Biology Photochromic and Fluorescence Chemistry ; Advanced biosensing and bioanalysis techniques ; Nanoplatforms for cancer theranostics
Authors: Emad Yousif
Source: Archives of Organic and Inorganic Chemical Sciences (review, 2018-07-17)
Field: Chemistry — Organic Chemistry

A Review of Organotin Compounds: Chemistry and Applications The field of organotin chemistry has a long history that started since 1849, when Frankland isolated a specimen of diethyltin diiodide [1]. In 1852, Lowich reported on the reaction of alkyl halides with a tin-sodium alloy giving alkyltin compounds [2]. This last publication is usually considered to represent the beginning of organotin chemistry. By 1935, about hundreds of publications concerning organotin chemistry had appeared in the literature. At that time, important names had played a role in the development of organotin chemistry were Krause in Germany, Kraus in the United States, and Kozeshkov in Russia. The discovery of organotin compounds industrial applications as polyvinyl chloride (PVC) stabilizers, as agrochemicals, biocides, and wood preservatives produced a revival of organotin chemistry. Particularly van der Kerk and his co-workers in Netherlands played a major role in this development [3,4]. In early of 1960s it was found that the tin atom Chemistry ; Tin ; Pyridine ; Electrophile ; Medicinal chemistry ; Alkyl ; Coordination complex ; Organic chemistry ; Divalent ; Halide ; Crystal chemistry ; Polymer chemistry ; Crystal structure ; Catalysis Organometallic Compounds Synthesis and Characterization ; Marine Biology and Environmental Chemistry ; Organometallic Complex Synthesis and Catalysis