jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Paniz Shirmast | Seyed Mohammad Ghafoori | R. M. Irwin | Jan Abendroth | Stephen J. Mayclin | D. Lorimer | Thomas E. Edwards | Jade K. Forwood
Source: Scientific Reports (article, 2021-01-14)
Field: Materials Science — Materials Chemistry

Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNATs) catalyse the acetylation of a diverse range of substrates, thereby orchestrating a variety of biological processes within prokaryotes and eukaryotes. GNAT enzymes can catalyze the transfer of an acetyl group from acetyl coenzyme A to substrates such as aminoglycoside antibiotics, amino acids, polyamines, peptides, vitamins, catecholamines, and large macromolecules including proteins. Although GNATs generally exhibit low to moderate sequence identity, they share a conserved catalytic fold and conserved structural motifs. In this current study we characterize the high-resolution X-ray crystallographic structure of a GNAT enzyme bound with acetyl-CoA from Elizabethkingia anophelis, an important multi-drug resistant bacterium. The tertiary structure is comprised of six α-helices and nine β-strands, and is similar with other GNATs. We identify a new and uncharacterized GNAT dimer interface, which is conserved in at least two other unpublished GNAT structures. This suggests that GNAT enzymes can form at least five different types of dimers, in addition to a range of other oligomers including trimer, tetramer, hexamer, and dodecamer assemblies. The high-resolution structure presented in this study is suitable for future in-silico docking and structure-activity relationship studies. Acetyltransferases ; Biology ; Trimer ; Random hexamer ; Acetyltransferase ; Biochemistry ; Enzyme ; Dimer ; Sequence alignment ; Acetylation ; Stereochemistry ; Peptide sequence ; Chemistry ; Gene Enzyme Structure and Function ; Biochemical and Molecular Research ; Infections and bacterial resistance
Authors: Francesco Sessa | Martina Olsson | Fredrik Söderberg | Fang Wang | Martin Rahm
Source: ChemPhysChem (article, 2021-01-27)
Field: Chemistry — Organic Chemistry

Experimental Quantum Chemistry: A Hammett‐inspired Fingerprinting of Substituent Effects The quantum mechanically calculable Q descriptor is shown to be a potent quantifier of chemical reactivity in complex molecules - it shows a strong correlation to experimentally derived field effects in non-aromatic substrates and Hammett σ<sub>m</sub> and σ<sub>p</sub> parameters. Models for predicting substituent effects from Q are presented and applied, including on the elusive pentazolyl substituent. The presented approach enables fast computational estimation of substituent effects, and, in extension, medium-throughput screening of molecules and compound design. An experimental dataset is suggested as a candidate benchmark for aiding the general development and comparison of electronic structure analyses. It is here used to evaluate the experimental quantum chemistry (EQC) framework for chemical bonding analysis in larger molecules. Substituent ; Chemistry ; Quantum chemistry ; Computational chemistry ; Molecule ; Quantum chemical ; Hammett equation ; Reactivity (psychology) ; Quantum ; Chemical physics ; Stereochemistry ; Organic chemistry ; Quantum mechanics ; Reaction rate constant ; Kinetics ; Physics Organic Chemistry Cycloaddition Reactions ; Computational Drug Discovery Methods ; Free Radicals and Antioxidants
Authors: Bowen Li | Srinivas Rangarajan
Source: Computers & Chemical Engineering (article, 2021-11-22)
Field: Materials Science — Materials Chemistry

A conceptual study of transfer learning with linear models for data-driven property prediction Property (philosophy) ; Transfer of learning ; Context (archaeology) ; Computer science ; Task (project management) ; Artificial intelligence ; Machine learning ; Salient ; Multi-task learning ; Uncorrelated ; Conceptual model ; Mathematics ; Engineering Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Machine Learning and Data Classification
Authors: Masahiko Demura
Source: MATERIALS TRANSACTIONS (article, 2021-10-04)
Field: Materials Science — Materials Chemistry

Materials Integration for Accelerating Research and Development of Structural Materials This paper provides a current research trend for “Materials Integration”, which is a concept to accelerate research and development of structural materials by computationally linking among process, structure, property, and performance. The survey is carried out based on the special issue published in February, 2019 in Materials Transactions (Vol. 60, No. 2) and the overviews published in November, 2020 in Materials Transactions (Vol. 61, No. 11). The concept has been embodied in a computer system named MInt (Materials Integration by Network Technology), on which computational modules and workflows are implemented to predict performance from process through microstructure and property. The research works on the system development and the computational materials analyses are briefly introduced, highlighting the rising trend of data-driven research in structural materials. Workflow ; Process (computing) ; Property (philosophy) ; Systems engineering ; Computer science ; Development (topology) ; Materials science ; Nanotechnology ; Engineering ; Database Machine Learning in Materials Science ; Injection Molding Process and Properties ; Electron and X-Ray Spectroscopy Techniques
Authors: Zhigang Li | Kai Li | Liyuan Dong | Tian‐Meng Guo | Muhammad Azeem | Wei Li | Xian‐He Bu
Source: Research (article, 2021-01-01)
Field: Chemistry — Inorganic Chemistry

Acoustic Properties of Metal-Organic Frameworks Metal-organic frameworks (MOFs) have attracted significant attention in the past two decades due to their diverse physical properties and associated functionalities. Although numerous advances have been made, the acoustic properties of MOFs have attracted very little attention. Here, we systematically investigate the acoustic velocities and impedances of 19 prototypical MOFs <i>via</i> first-principle calculations. Our results demonstrate that these MOFs exhibit a wider range of acoustic velocities, higher anisotropy, and lower acoustic impedances than their inorganic counterparts, which are ascribed to their structural diversity and anisotropy, as well as low densities. In addition, the piezoelectric properties, which are intimately related to the acoustic properties, were calculated for 3 MOFs <i>via</i> density functional perturbation theory, which reveals that MOFs can exhibit significant piezoelectricity due to the ionic contribution. Our work provides a comprehensive study of the fundamental acoustic properties of MOFs, which could stimulate further interest in this new exciting field. Piezoelectricity ; Anisotropy ; Materials science ; Acoustic impedance ; Chemical physics ; Nanotechnology ; Acoustics ; Physics ; Ultrasonic sensor ; Composite material Metal-Organic Frameworks: Synthesis and Applications ; Magnesium Oxide Properties and Applications ; Inorganic Fluorides and Related Compounds
Authors: Ryo Fujiki | Toru Matsui | Yasuteru Shigeta | Haruyuki Nakano | Norio Yoshida
Source: J — Multidisciplinary Scientific Journal (article, 2021-12-10)
Field: Chemistry — Organic Chemistry

Recent Developments of Computational Methods for pKa Prediction Based on Electronic Structure Theory with Solvation Models The protonation/deprotonation reaction is one of the most fundamental processes in solutions and biological systems. Compounds with dissociative functional groups change their charge states by protonation/deprotonation. This change not only significantly alters the physical properties of a compound itself, but also has a profound effect on the surrounding molecules. In this paper, we review our recent developments of the methods for predicting the Ka, the equilibrium constant for protonation reactions or acid dissociation reactions. The pKa, which is a logarithm of Ka, is proportional to the reaction Gibbs energy of the protonation reaction, and the reaction free energy can be determined by electronic structure calculations with solvation models. The charge of the compound changes before and after protonation; therefore, the solvent effect plays an important role in determining the reaction Gibbs energy. Here, we review two solvation models: the continuum model, and the integral equation theory of molecular liquids. Furthermore, the reaction Gibbs energy calculations for the protonation reactions require special attention to the handling of dissociated protons. An efficient method for handling the free energy of dissociated protons will also be reviewed. Protonation ; Solvation ; Deprotonation ; Gibbs free energy ; Chemistry ; Computational chemistry ; Dissociation (chemistry) ; Thermodynamics ; Equilibrium constant ; Molecule ; Implicit solvation ; Physical chemistry ; Organic chemistry ; Physics ; Ion Free Radicals and Antioxidants ; Organic Chemistry Cycloaddition Reactions ; Chemical Reaction Mechanisms
Authors: Rouven Britz | Paul Motzki
Source: Sensors and Actuators A Physical (article, 2021-11-23)
Field: Materials Science — Materials Chemistry

Analysis and evaluation of bundled SMA actuator wires The attractive properties of shape memory alloys (SMA), especially their high energy density, steadily expand the range of applications in which SMA wires represent attractive alternative actuator components. Industrial applications in particular, oftentimes require large forces, which scale with the diameter of SMA actuator wires. The higher the required actuator force, the larger the total effective cross-sectional area of the SMA wires is needed. Increasing the SMA wire diameter results in worse actuator dynamics due to a decreasing surface-to-volume ratio and thus slower convective cooling. Instead of simply increasing the wire diameter, the bundling of several thin wires offers a suitable alternative to generate higher forces. This results in an increased surface-to-volume ratio and thus permits higher dynamic system performance. This paper discusses the mechanical and thermal behavior of SMA wire bundles and shows the influence of contact resistance inside the clamps, which is important to optimize for a long-lasting functionality of SMA bundles. In addition, the experiments show an indirect heating between single SMA wires inside a bundle, which leads to an energy saving capability up to 60%. Two electro-mechanical experiments show the behavior of SMA bundles in a constant force and a constant strain measurement. The experimental results show a maximum stroke of 4–4.5% and a generated maximum force of 1200 N. The results are discussed to provide an understanding of the mechanical characteristics of SMA bundles. In addition, an infrared (IR)-Camera provides an insight into the thermal behavior. SMA* ; Shape-memory alloy ; Actuator ; Materials science ; Bundle ; Thermal ; Mechanical energy ; Mechanical engineering ; Composite material ; Engineering ; Computer science ; Electrical engineering Shape Memory Alloy Transformations
Authors: Haojie Zhao | Beili Yi | Xiaomeng Si | Lei Cao | Longxing Su | Yanli Wang | Lien‐Yang Chou | Jin Xie
Source: ACS Applied Nano Materials (article, 2021-09-16)
Field: Chemistry — Inorganic Chemistry

Solid-State Synthesis of Defect-Rich Zr-UiO-66 Metal–Organic Framework Nanoparticles for the Catalytic Ring Opening of Epoxides with Alcohols Perfect crystals do not exist; however, the introduction of defects can tailor the physical and chemical properties of materials. Defects in metal–organic frameworks (MOFs) have been demonstrated to be important in many applications, including but not limited to catalysis, gas separation, and energy storage. While a few liquid-phase synthesis methods have been reported to prepare defect-rich UiO-66, the heavy use of organic solvents may cause irreversible environmental problems. Here, we present a green, rapid, and facile solid-state synthesis approach to prepare UiO-66. All UiO-66 crystals remain in the nanometer size due to the limited diffusivity of growth species in solid-state synthesis without a large quantity of the solvent. The defect concentrations can be fine-tuned by the content of ethanol addition. Defect-rich UiO-66 shows excellent catalytic activity to the ring opening of epoxides with alcohols. This work provides insights into the large-scale production of defect-rich MOFs. Catalysis ; Materials science ; Metal-organic framework ; Nanoparticle ; Ring (chemistry) ; Solvent ; Nanometre ; Chemical engineering ; Organic synthesis ; Nanotechnology ; Metal ; Organic chemistry ; Chemistry ; Metallurgy ; Composite material Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Reactions ; Carbon dioxide utilization in catalysis
Authors: Tuo Zheng | Fengshun Wu | Huan Fu | Li Zeng | Congxiao Shang | Lihua Zhu | Zhengxiao Guo
Source: Chemistry - An Asian Journal (article, 2021-06-22)
Field: Materials Science — Materials Chemistry

Rational Design of Pt−Pd−Ni Trimetallic Nanocatalysts for Room‐Temperature Benzaldehyde and Styrene Hydrogenation Nanostructures of the multimetallic catalysts offer great scope for fine tuning of heterogeneous catalysis, but clear understanding of the surface chemistry and structures is important to enhance their selectivity and efficiency. Focussing on a typical Pt-Pd-Ni trimetallic system, we comparatively examined the Ni/C, Pt/Ni/C, Pd/Ni/C and Pt-Pd/Ni/C catalysts synthesized by impregnation and galvanic replacement reaction. To clarify surface chemical/structural effect, the Pt-Pd/Ni/C catalyst was thermally treated at X=200, 400 or 600 °C in a H<sub>2</sub> reducing atmosphere, respectively termed as Pt-Pd/Ni/C-X. The as-prepared catalysts were characterized complementarily by XRD, XPS, TEM, HRTEM, HS-LEIS and STEM-EDS elemental mapping and line-scanning. All the catalysts were comparatively evaluated for benzaldehyde and styrene hydrogenation. It is shown that the "PtPd alloy nanoclusters on Ni nanoparticles" (PtPd/Ni) and the synergistic effect of the trimetallic Pt-Pd-Ni, lead to much improved catalytic performance, compared with the mono- or bi- metallic counterparts. However, with the increase of the treatment temperature of the Pt-Pd/Ni/C, the catalytic performance was gradually degraded, which was likely due to that the favourable nanostructure of fine "PtPd/Ni" was gradually transformed to relatively large "PtPdNi alloy on Ni" (PtPdNi/Ni) particles, thus decreasing the number of noble metal (Pt and Pd) active sites on the surface of the catalyst. The optimum trimetallic structure is thus the as synthesised Pt-Pd/Ni/C. This work provides a novel strategy for the design and development of highly efficient and low-cost multimetallic catalysts, e. g. for hydrogenation reactions. Nanomaterial-based catalyst ; Catalysis ; Materials science ; High-resolution transmission electron microscopy ; Palladium ; X-ray photoelectron spectroscopy ; Nanoclusters ; Styrene ; Noble metal ; Benzaldehyde ; Chemical engineering ; Metal ; Nanoparticle ; Inorganic chemistry ; Nanotechnology ; Chemistry ; Metallurgy ; Organic chemistry ; Composite material Catalytic Processes in Materials Science ; Nanomaterials for catalytic reactions ; Catalysis and Hydrodesulfurization Studies
Authors: T. Oku | Hiroki Funashima | Shogo Kawaguchi | Yoshiki Kubota | Atsuko Kosuga
Source: Materials Today Physics (article, 2021-08-12)
Field: Materials Science — Materials Chemistry

Superior room-temperature power factor in GeTe systems via multiple valence band convergence to a narrow energy range GeTe systems are excellent p-type thermoelectric materials at medium temperatures (500–800 K). Recently, their electronic properties were enhanced by band convergence of L and Σ valence bands, which increased the power factor at 500–800 K. However, there are only a few thermoelectric materials suitable for lower-temperature waste-heat recovery applications, and their demand is rapidly increasing. Herein, we demonstrated that the well-known L and Σ bands of GeTe and the additional Δ band converge at a desirable energy level to a very narrow energy range as a result of fine-tuning the crystal symmetry and composition by forming a GeTe-Sb2Te3 alloy. Alloying additionally facilitates a decrease in the bandgap, thereby increasing the near-room-temperature power factor. The GeTe-Sb2Te3 alloy achieved very high room-temperature and maximum power factors of 2.6 mW m−1 K−2 at 300 K and 3.3 mW m−1 K−2 at 423 K, respectively, despite GeTe being a medium-temperature thermoelectric material. Thus, we confirmed the applicability of GeTe as a thermoelectric material at room temperature. This study facilitates the development of high-performance near-room-temperature thermoelectric materials based on existing medium-temperature systems. Materials science ; Thermoelectric effect ; Thermoelectric materials ; Atmospheric temperature range ; Band gap ; Seebeck coefficient ; Power factor ; Alloy ; Optoelectronics ; Condensed matter physics ; Valence (chemistry) ; Engineering physics ; Thermodynamics ; Power (physics) ; Metallurgy ; Composite material ; Thermal conductivity Advanced Thermoelectric Materials and Devices ; Chalcogenide Semiconductor Thin Films ; Perovskite Materials and Applications
Authors: Qi Sheng | Wendy Tian | Colin D. Wood
Source: ACS Applied Materials & Interfaces (article, 2021-08-12)
Field: Materials Science — Surfaces, Coatings and Films

Hyper-Cross-Linked Polymer-Decorated Surfaces with Ultrahigh Efficiency for Oil/Water Emulsion Separation and Recovery A novel superhydrophobic/superoleophilic surface has been developed by direct surface condensation of dichloroxylene that results in a controlled coating of hyper-cross-linked polymers. Specifically, the coating was successfully applied to a melamine formaldehyde sponge and optimized by fine-tuning the reaction variables. The resulting hierarchical porous sorbents stabilized by polydimethylsiloxane exhibited an increased surface area, good physiochemical stability, high selectivity, and adsorption capacities for a variety of oils and solvents. The composite can separate oil in water emulsions with ultrahigh separation efficiency >99% over 10 cycles in liter-scale experiments, wherein the highest separation efficiency was as low as 2 ppm even with a short period of filtration, suggesting strong potential for oil/water separation and recovery. Materials science ; Polydimethylsiloxane ; Emulsion ; Chemical engineering ; Coating ; Polymer ; Melamine ; Filtration (mathematics) ; Adsorption ; Selectivity ; Porosity ; Condensation ; Composite material ; Organic chemistry ; Catalysis Surface Modification and Superhydrophobicity ; Covalent Organic Framework Applications ; Advanced Sensor and Energy Harvesting Materials
Authors: Linyu Yan | Weiwei Jin | Qingwen Zhao | Xuan Cui | Tingyan Shi | Yingjiang Xu | Feiyan Li | Wenfang Jin | Zhe Zhang | Zhao Zhang | Qi‐Qun Tang | Dongning Pan
Source: Advanced Science (article, 2021-06-27)
Field: Materials Science — Electronic, Optical and Magnetic Materials

PWWP2B Fine‐Tunes Adipose Thermogenesis by Stabilizing HDACs in a NuRD Subcomplex Histone deacetylases (HDACs) are widely involved in many biological processes, as well as in control of brown and beige adipose physiology, but the precise molecular mechanisms by which HDACs are assembled into transcriptional machinery to fine-tune thermogenic program remain ill-defined. PWWP domain containing 2b (PWWP2B), which is identified as a component of the nucleosome remodeling and deacetylation complex (NuRD), interacts and stabilizes HDAC1/2 at the thermogenic gene promoters to suppress their expression. Ablation of Pwwp2b promotes adipocyte thermogenesis and ameliorates diet-induced obesity in vivo. Intriguingly, Pwwp2b is not only a brown fat-enriched gene but also dramatically induced by cold and sympathetic stimulation, which may serve as a physiological brake to avoid over-activation of thermogenesis in brown and beige fat cells. Thermogenesis ; Adipose tissue ; Cell biology ; Neuroscience ; Chemistry ; Biology ; Endocrinology Supercapacitor Materials and Fabrication ; Graphene research and applications ; Parallel Computing and Optimization Techniques
Authors: Wei Zhou | Wei Chi | Wanting Shen | Wanying Dou | Junyi Wang | Xuechen Tian | Chris Gehring | Aloysius Wong
Source: Frontiers in Bioinformatics (article, 2021-03-25)
Field: Chemistry — Spectroscopy

Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples In proteins, functional centers consist of the key amino acids required to perform molecular functions such as catalysis, ligand-binding, hormone- and gas-sensing. These centers are often embedded within complex multi-domain proteins and can perform important cellular signaling functions that enable fine-tuning of temporal and spatial regulation of signaling molecules and networks. To discover hidden functional centers, we have developed a protocol that consists of the following sequential steps. The first is the assembly of a search motif based on the key amino acids in the functional center followed by querying proteomes of interest with the assembled motif. The second consists of a structural assessment of proteins that harbor the motif. This approach, that relies on the application of computational tools for the analysis of data in public repositories and the biological interpretation of the search results, has to-date uncovered several novel functional centers in complex proteins. Here, we use recent examples to describe a step-by-step guide that details the workflow of this approach and supplement with notes, recommendations and cautions to make this protocol robust and widely applicable for the discovery of hidden functional centers. Workflow ; Computer science ; Computational biology ; Human proteome project ; Proteome ; Identification (biology) ; Bioinformatics ; Biology ; Proteomics ; Biochemistry ; Database Advanced Proteomics Techniques and Applications ; Protein Structure and Dynamics ; Microbial Natural Products and Biosynthesis
Authors: Jaehoon Ryu | Ha Young Lee | Jeong-Yeon Lee | Hansol Kim | Sung-Hyun Kim | Hyung Soo Ahn | Dong Han Ha | Sam Nyung Yi
Source: Applied Sciences (article, 2021-12-13)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Enhancing SERS Intensity by Coupling PSPR and LSPR in a Crater Structure with Ag Nanowires The sensitive characteristics of surface-enhanced Raman scattering (SERS) can be applied to various fields, and this has been of interest to many researchers. Propagating surface plasmon resonance (PSPR) was initially utilized but, recently, it has been studied coupled with localized surface plasmon resonance that occurs in metal nanostructures. In this study, a new type of metal microstructure, named crater, was used for generating PSPR and Ag nanowires (AgNWs) for the generation of LSPR. A crater structure was fabricated on a GaAs (100) wafer using the wet chemical etching method. Then, a metal film was deposited inside the crater, and AgNWs were uniformly coated inside using the spray coating method. Metal films were used to enhance the electromagnetic field when coupled with AgNWs to obtain a high SERS intensity. The SERS intensity measured inside the crater structure with deposited AgNWs was up to 17.4 times higher than that of the flat structure with a deposited Ag film. These results suggest a new method for enhancing the SERS phenomenon, and it is expected that a larger SERS intensity can be obtained by fine-tuning the crater size and diameter and the length of the AgNWs. Impact crater ; Materials science ; Raman scattering ; Wafer ; Plasmon ; Surface plasmon resonance ; Etching (microfabrication) ; Raman spectroscopy ; Nanotechnology ; Nanowire ; Isotropic etching ; Nanostructure ; Optoelectronics ; Nanoparticle ; Optics ; Layer (electronics) Gold and Silver Nanoparticles Synthesis and Applications ; Plasmonic and Surface Plasmon Research ; Advanced biosensing and bioanalysis techniques