jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Enrico Riccardi | Andreas Krämer | Titus S. van Erp | An Ghysels
Source: Duo Research Archive (University of Oslo) (article, 2020-01-01)
Field: Chemistry — Spectroscopy

Permeation Rates of Oxygen through a Lipid Bilayer Using Replica Exchange Transition Interface Sampling Several simulations strategies have emerged to predict the permeability of solutes across membranes, which is important for many biological or industrial processes such as drug design. The widespread inhomogeneous solubility-diffusion (ISD) model is based on the Smoluchowski equation and describes permeation as purely diffusive. The counting method, which counts membrane transitions in a long molecular dynamics (MD) trajectory, is free of this diffusive assumption, but it lacks sufficient statistics when the permeation involves high free energy barriers. Metadynamics and variations thereof can overcome such barriers, but they generally lack the kinetics information. The milestoning framework has been used to describe permeation as a rare event, but it still relies on the Markovian assumption between the milestones. Replica Exchange Transition Interface Sampling (RETIS) has been shown to be an effective method for sampling rare events while simultaneously describing the kinetics without assumptions. This paper is the first permeation application of RETIS on an all-atom lipid bilayer consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) to compute the entrance, escape and complete transition of molecular oxygen. Conventional MD was performed as a benchmark, and the MD rates from counting were converted to rate constants, giving good agreement with the RETIS values. Moreover, a correction factor was derived to convert the collective order parameter in RETIS, which was aimed to improve efficiency, to a single-particle order parameter. With this work, we showed how the exact kinetics of drug molecules permeation can be assessed with RETIS even if the permeation is truly a rare event or if the permeation is non-Markovian. RETIS will therefore be a valuable tool for future permeation studies. Permeation ; Chemistry ; Metadynamics ; Smoluchowski coagulation equation ; Molecular dynamics ; Umbrella sampling ; Kinetics ; Chemical physics ; Bilayer ; Lipid bilayer ; Diffusion ; Membrane ; Statistical physics ; Thermodynamics ; Computational chemistry ; Physics Analytical Chemistry and Chromatography ; Spectroscopy and Quantum Chemical Studies ; Drug Transport and Resistance Mechanisms
Authors: Allen C. Robinson | Andrew Porwitzky
Source: Physics of Plasmas (article, 2020-10-01)
Field: Materials Science — Materials Chemistry

Pulsed power accelerator surface Joule heating models Understanding the effects of contaminant plasmas generated within the Z machine at Sandia is critical to understanding current loss mechanisms. The plasmas are generated at the accelerator electrode surfaces and include desorbed species found in the surface and substrate of the walls. These desorbed species can become ionized. The timing and location of contaminant species desorbed from the wall surface depend non-linearly on the local surface temperature. For accurate modeling, it is necessary to utilize wall heating models to estimate the amount and timing of material desorption. One of these heating mechanisms is Joule heating. We propose several extended semi-analytic magnetic diffusion heating models for computing surface Joule heating and demonstrate their effects for several representative current histories. We quantitatively assess under what circumstances these extensions to classical formulas may provide a validatable improvement to the understanding of contaminant desorption timing. Joule heating ; Plasma ; Physics ; Electric heating ; Desorption ; Current (fluid) ; Diffusion ; Electromigration ; Ionization ; Joule effect ; Electrode ; Computational physics ; Joule (programming language) ; Surface (topology) ; Nuclear engineering ; Atomic physics ; Mechanics ; Power (physics) ; Thermodynamics ; Ion ; Materials science ; Nuclear physics ; Chemistry ; Composite material Fusion materials and technologies ; Laser-Plasma Interactions and Diagnostics ; Plasma Diagnostics and Applications
Authors: Alexandre Poloni | A. Oudriss | J. Creus | S. Cohendoz | J. Bouhattate | Simon Frappart | Thierry Millot | Aude Mathis | X. Feaugas
Source: MATEC Web of Conferences (article, 2020-01-01)
Field: Materials Science — Metals and Alloys

Influence of hydrogen on mechanical properties of pure titanium T40 (grade 2) and TA6V ELI (grade 23): a local approach of fracture The effect of hydrogen charging by cathodic polarization on T40 (grade 2) and TA6V ELI (grade 23) in artificial seawater appeared to be dependent on the metallurgical structure of the alloys. Mechanical tensile tests were performed on smooth samples and with different notches without and with hydrogen charging. Evolution of the fracture mode has been studied and the impact of hydrides was questioned. FEM calculation offers the opportunity to associate the local hydrostatic stress σ m and equivalent plastic strain ε peq leading to the fracture and to illustrate the evolution of these conditions with hydrogen absorption and hydrides formation. Hydrogen charged by cathodic polarization appeared to have a small impact on grade 2 reducing its A%, whereas it leads to a strong embrittlement of grade 23 when the solubility limit of β-phase is exceeded and hydrides formed. Hydrogen embrittlement ; Materials science ; Hydrogen ; Cathodic protection ; Ultimate tensile strength ; Hydrostatic stress ; Embrittlement ; Titanium ; Metallurgy ; Fracture (geology) ; Polarization (electrochemistry) ; Composite material ; Finite element method ; Electrochemistry ; Corrosion ; Chemistry ; Thermodynamics Hydrogen embrittlement and corrosion behaviors in metals ; Titanium Alloys Microstructure and Properties ; Corrosion Behavior and Inhibition
Authors: Emad A. S. Al-Hyali | Ra rsquo ed Al-Abady | Fedaa Marie Altaie
Source: Egyptian Journal of Chemistry (article, 2020-08-27)
Field: Chemistry — Organic Chemistry

Correlation Study for The Determination of pKa of A Number of Schiff Bases Derived from N-Formyl Pyridine using Quantum Mechanical Methods Statistical analysis employing multiparametric regression analysis was used to correlate the pKa values of 16 substituted Schiff bases (imines) derived from heterogeneous carbonyl compounds with various descriptors as parameters. These parameters are based on quantum mechanical methods. Four sets of parameters are used for these treatments. Two of them were derived depending on the semiempirical calculation represented by Austin method1 (AM1) and parameterized method3 (PM3) .. The other two sets were chosen as Ab initio models, expressed by Hartree fock (HF) and MP2 calculation models performed at 6.311G (d,p) level of theory. The descriptors employed to test their impact on the variation of the experimental pKa(s) are of two kinds, electronic and geometrical including atomic charges (Muliken and lowding), length of the imine (C=N) and connected bonds. Other molecular characteristic are also used such as energies of the HOMO and LUMO orbitals, total energies (TE), kinetic energy (KE), torsion, Vender Waals interactions of the 1,4 type (VDW 1,4) and non 1,4 type (Non 1,4 VDW). The correlation between the pKa values of the studied compounds and the selected parameters are investigated. Depending on the obtained results, several sets of parameters were constructed. The best set is indicated by the values of correlation coefficient (R‌‌‌‌‌2) and standard error (SE). Comparison are carried out between the experimental and calculated pKa obtained from AM1, PM3, MP2, and HF methods. Models of HF showed better consistency among the experimental and the calculated pKa(s) of the studied compounds. Hypothetical compounds of similar structures but with different substituents not included in the regression analysis are used to test the success of the derived equations. Good results are obtained. Pyridine ; Schiff base ; Quantum ; Correlation ; Chemistry ; Mathematics ; Polymer chemistry ; Medicinal chemistry ; Physics ; Quantum mechanics ; Geometry Free Radicals and Antioxidants ; Inorganic and Organometallic Chemistry ; Chemistry and Chemical Engineering
Authors: Nabaweya Sharafeldin
Source: Egyptian Journal of Chemistry (article, 2020-04-03)
Field: Chemistry — Organic Chemistry

Indoline-based heterocyclic scaffold: Synthetic methods, chemical reactions and biological prospect Inolines have be significant compounds because of their diversity of applications in synthetic organic chemistry, pharmaceutical, industrial chemistry as well as they are present in several biologically active compounds in both natural and synthetic origins. In recent years there are high expectations that they exhibit interesting applications in selective potentiate the activity of β-lactam antibiotics in MRSA as well as other pharmacological arena, such as anticancer, anti-inflammatory, antioxidant, anticoagulant agents, etc. Furthermore, they are considered as substantial compounds due to their widespread use as building blocks and as chiral support in asymmetric synthesis. As a result, the existing events of the indoline-based nucleus in medicinal chemistry studies require to be collected and recognized especially many reports have been suggested that the indoline-based compounds have a very high therapeutic value (in MRSA) and needs to be explored for further studies. So, this review deals with the main innovations regarding indoline-based heterocycle scaffold stressing on their synthesis, reactions and their pharmacological activities. Indoline ; Chemistry ; Combinatorial chemistry ; Scaffold ; Biochemical engineering ; Organic chemistry ; Computer science ; Engineering Synthesis of β-Lactam Compounds ; Synthesis and Biological Evaluation ; Synthesis and Catalytic Reactions
Authors: Denise Böck | Andreas Beuchel | Richard Goddard | Peter Imming | Rüdiger W. Seidel
Source: Journal of Chemical Crystallography (article, 2020-10-01)
Field: Chemistry — Organic Chemistry

Structural Characterization of Two Polymorphs of 1-(4-Methylpyridin-2-yl)thiourea and Two Derived 2-Aminothiazoles Abstract Two polymorphic forms of 1-(4-methylpyridin-2-yl)thiourea ( 1 ) and the crystal and molecular structures of the 2-aminothiazoles N -(4-methylpyridin-2-yl)-4-(pyridin-2-yl)thiazol-2-amine ( 2 ) and N -(4-methylpyridin-2-yl)-4-(pyrazin-2-yl)thiazol-2-amine ( 3 ), derived from 1 and the respective α-bromoketone via the Hantzsch reaction, are described. Both polymorphic forms 1α (space group P 2 1 / c , Z = 4) and 1β (space group P 2 1 / n , Z = 8) crystallize in the monoclinic system but exhibit distinctly different intermolecular hydrogen bonding patterns. Compound 2 (orthorhombic, space group Pca 2 1 , Z = 8) forms polymeric N–H⋯N hydrogen-bonded zigzag tapes in the polar crystal structure, with a significant twisting between the thiazole and pyridine rings. In contrast, the crystal structure of 3 (monoclinic, space group P 2 1 / c , Z = 4) features nearly planar centrosymmetric N–H⋯N hydrogen-bonded dimers, which are laterally joined through long C–H⋯N contacts, affording a π⋯π stacked layered structure. Graphic Abstract Two polymorphs of 1-(4-methylpyridin-2-yl)thiourea and the crystal and molecular structures of two 2-aminothiazoles, derived from 1-(4-methylpyridin-2-yl)thiourea and α-bromoketones via Hantzsch reaction, are reported. Monoclinic crystal system ; Chemistry ; Crystallography ; Thiourea ; Crystal structure ; Orthorhombic crystal system ; Hydrogen bond ; Thiazole ; Pyridine ; Stereochemistry ; Amine gas treating ; Molecule ; Medicinal chemistry ; Organic chemistry Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity ; Phenothiazines and Benzothiazines Synthesis and Activities
Authors: Patrick Erickson | James Fulcher | Michael S. Kay
Source: ChemRxiv (preprint, 2020-07-13)
Field: Chemistry — Organic Chemistry

Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I) Chemoselective ligation reactions, such as native chemical ligation (NCL), enable the assembly of synthetic peptides into proteins. However, the scope of proteins accessible to total chemical synthesis is limited by ligation efficiency. Sterically hindered thioesters and poorly soluble peptides can undergo incomplete ligations, leading to challenging purifications with low yields. This work describes a new method, ClickAssisted NCL (CAN), which overcomes these barriers. In CAN, peptides are modified with traceless “helping hand” lysine linkers that enable addition of dibenzocyclooctyne (DBCO) and azide handles for strain-promoted alkyne-azide cycloaddition (SPAAC) reactions. This cycloaddition templates the peptides to increase their effective concentration and greatly accelerate ligation kinetics. After ligation, mild hydroxylamine treatment tracelessly removes the linkers to afford the native ligated peptide. Although DBCO is incompatible with standard Fmoc solid-phase peptide synthesis (SPPS) due to an acid-mediated rearrangement that occurs during peptide cleavage, we demonstrate that copper(I) protects DBCO from this side reaction, enabling direct production of DBCO-containing synthetic peptides. Excitingly, low concentrations of triazole-linked model peptides reacted ~1,200-fold faster than predicted for non-templated control ligations, which also accumulated many side products due to the long reaction time. Using the E. coli ribosomal subunit L32 as a model protein, we further demonstrate that the SPAAC, ligation, desulfurization, and linker cleavage steps can be performed in a one-pot fashion. CAN will be useful for overcoming ligation challenges to expand the reach of chemical protein synthesis. Native chemical ligation ; Chemical ligation ; Chemistry ; Combinatorial chemistry ; Click chemistry ; Cycloaddition ; Peptide ; Azide ; Ligation ; Linker ; Chemical biology ; Chemical synthesis ; Organic chemistry ; Biochemistry ; Biology Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Peptidase Inhibition and Analysis
Authors: Sibel Avunduk | R Wu | Z Le | Z Wang | S Tian | Y Xue | H Hyperjaponol | J Gershenzon | N Dudareva | F Makkar | K Chakraborty | T Kuzuyama | X Luo | C Chen | K Li | X Lin | C Gao | I Parshikov | A Netrusov | J Sutherland | T Liebgott | M Miollan | Y Berchadsky | K Drieu | M Culcasi | S Ebada | W Lin | P Proksch | R Geris | T Simpson | H Li | W Sun | M Deng | C Qi | H Chen | H Kikuchi | K Kawai | Y Nakashiro | T Yonezawa | K Kawaji | E Zubia | Ortega | J Salva | M Menna | A Aiello | Fd' Aniello | C Imperatore | P Luciano | Y Matsuda | I Abe | R Morton | E Fernholz | J Moncrief | W Lipscomb | L Kaysser | P Bernhardt | S Nam | S Loesgen | J Ruby | T Awakawa | L Zhang | T Wakimoto | S Hoshino | T Mori | X Yin | T Feng | Z-H Li | Z-J Dong | Y Li | J Liu | De Los Reyes | H Zbakh | V Motilva | E Zuba | T Mamemura | N Tanaka | A Shibazaki | T Gonoi | J Kobayashi | Q Luo | L Di | W Dai | Q Lu | Y Yan | H Choi | H Hwang | J Chin | E Kim | J Lee | D Tran | N Cramer | X Qin | H Yan | W Ni
Source:  (review, 2020-08-17)
Field: Chemistry — Organic Chemistry

Cytotoxic Meroterpenes: A Review Meroterpenes are mixed natural products. They consist of one terpene and one polyketide skeletons. Due to their structural varieties, meroterpenoids display diverse bioactivities, like anticancer, anti-inflammatory, anti-biotic, and antifibrotic activities. Our aim is to highlight the importance of the meroterpenes which have been the most studied on and reported among the bioactive natural products last years. According to our literature survey, the three most effective meroterpene groups have been determined. One group is the meroterpenes isolated from the brown alga Sargassum siliquastrum: Sargachromanol E, D, and P have exerted strong cytotoxicity against AGS (gastric cancer cells), HT-29 (colorectal adenocarcinoma cancer cell), and HT-1080 (human fibrosarcoma cells) cell lines, with IC 50 values varying from 0.5 to 5.7 g/mL [100]. The other most effective meroterpene is Eucalypglobulusal F, which is isolated from E. globulus fruit, has shown cytotoxicity against the human acute lymphoblastic cell line (CCRF-CEM) with an IC 50 value of 3.3 M Also, the last one is 11-dehydroxy epoxyphomalin A (4), from the endophytic fungus Peyronellaea coffeae-arabicae FT238, which was obtained from the native Hawaiian plant Pritchardia lowreyana showed a strong antiproliferative effect with an IC 50 of 0.5 M against OVCAR3 (Ovarian carsinoma cells) [102]. Conclusively, meroterpenes have potential nominees as an anticancer drug. Moreover, the structure of naturally isolated meroterpenes has a moderate anticancer activity that can easliy be modified by semi-synthetic ways due to their simple structures comparing to other natural compounds such as triterpenes or phenolic compounds. Cytotoxic T cell ; Biology ; Genetics ; In vitro Organophosphorus compounds synthesis
Authors: Isabel Karkossa | Anne Bannuscher | Bryan Hellack | Wendel Wohlleben | Julie Laloy | Miruna S. Stan | Anca Dinischiotu | Martin Wiemann | Andreas Luch | Andrea Haase | Martin von Bergen� | Kristin Schubert
Source: Research Square (preprint, 2020-08-12)
Field: Materials Science — Materials Chemistry

Nanomaterials induce different levels of oxidative stress, depending on the used model system: Comparison of in vitro and in vivo effects Abstract Background The immense variety and constant development of nanomaterials (NMs) raise the demand for a facilitated risk assessment, for which knowledge on NMs mode of actions (MoAs) is required. For this purpose, a comprehensive data basis is of paramountcy that can be obtained using omics. Furthermore, the establishment of suitable in vitro test systems is indispensable to follow the 3R concept and to master the high number of NMs. In the present study, we aimed at comparing NM effects in vitro and in vivo using a multi-omics approach. We applied an integrated data evaluation strategy based on proteomics and metabolomics to four silica NMs and one titanium dioxide-based NM. For in vitro investigations, alveolar epithelial cells and alveolar macrophages were treated with different doses of NMs, and the results were compared to effects on rat lungs after short-term inhalations and instillations at varying doses with and without a recovery period. Results Since the production of reactive oxygen species (ROS) is described to be a critical biological effect of NMs, and enrichment analyses confirmed oxidative stress as a significant effect upon NM treatment in vitro in the present study, we focused on different levels of oxidative stress. Thus, we found opposite changes for proteins and metabolites that are related to the production of reduced glutathione in alveolar epithelial cells and alveolar macrophages, illustrating that NMs MoAs depend on the used model system. Interestingly, in vivo , pathways related to inflammation were affected to a greater extent than oxidative stress responses. Hence, the assignment of the observed effects to the levels of oxidative stress was different in vitro and in vivo as well. However, the overall classification of “active” and “passive” NMs was consistent in vitro and in vivo . Conclusions The consistent classification indicates both tested cell lines to be suitable for NM toxicity assessment even though the induced levels of oxidative stress strongly depend on the used model systems. Thus, the here presented results highlight that model systems need to be carefully revised to decipher the extent to which they can replace in vivo testing. In vivo ; Oxidative stress ; In vitro ; Glutathione ; Oxidative phosphorylation ; Reactive oxygen species ; Chemistry ; Cell biology ; In vitro toxicology ; Biology ; Biochemistry ; Biotechnology ; Enzyme Nanoparticles: synthesis and applications ; Air Quality and Health Impacts ; Heavy Metal Exposure and Toxicity
Authors: Nieves Martínez-Peinado | Núria Cortes-Serra | Laura Torras‐Claveria | María‐Jesús Pinazo | Joaquím Gascón | Jaume Bastida | Julio Alonso-Padilla
Source: Research Square (preprint, 2020-04-07)
Field: Chemistry — Organic Chemistry

Amaryllidaceae alkaloids with anti-Trypanosoma cruzi activity Amaryllidaceae ; Trypanosoma cruzi ; Amaryllidaceae Alkaloids ; Biology ; Virology ; Botany ; Parasite hosting ; Computer science ; World Wide Web Chemical synthesis and alkaloids ; Trypanosoma species research and implications ; Cyclopropane Reaction Mechanisms
Authors: Jinlong He
Source: Digital Commons - USU (Utah State University) (article, 2020-12-18)
Field: Materials Science — Polymers and Plastics

Molecular Mechanisms and Design of Hydrogen-Bonded Materials for Thermal Applications Heat transfer at the nanoscale plays an important role in determining the reliability and performance of many innovative advanced materials technologies such as nanoelectronics, semiconductor, biomedical devices, polymers, and composites. Extensive efforts have been made to design materials with extraordinary thermal properties. However, fundamental understanding of heat transfer in many of these materials is still not lacking, because the thermal transport processes are governed by several factors including molecular morphology and chemical bonding. Among these factors, the atomic bonding between two dissimilar materials or within single materials is of particular interest due to its ubiquity and importance in physical processes. This work will focus on the demonstration and fundamental understanding of nanoscale thermal transport enhanced by incorporating hydrogen bonds in materials design. Molecular dynamics is performed for studying heat transfer processes in two typical hydrogen-bonded materials: (1) protein secondary structures, and (2) electrode/electrolyte composites in lithium ion batteries. Theoretical calculation and analysis show that heat transfer can be tuned in a wide range by modifying the hydrogen bonds. Results will not only provide new physical insights, but will also guide the rational design of materials for desired thermal properties towards many applications. Thermal ; Materials science ; Physics ; Thermodynamics Synthesis and properties of polymers
Authors: Sapna Pandey | Ekta Dhamija | Sanjay Kumar | Pragya D. Yadav | T. Narender | Arnava Dasgupta | Ravishankar Ramachandran | Kishore K. Srivastava
Source:  (preprint, 2020-11-09)
Field: Chemistry — Organic Chemistry

Identification of active molecules against Mycobacterial Shikimate Kinase from Chemical library and their affinity with different domains Tuberculosis (TB), regardless of being the oldest disease is still a menace that humans have not been able to control. With the advancement in the drug discovery programme, target-based drug discovery appears to be one of the promising techniques for the development of future therapeutics. It involves identifying an essential gene involved in the pathogenesis of the disease and then targeting the protein against a defined chemical library. Shikimate kinase is one such validated target in mycobacterium. It is vital for the growth of bacteria and is absent in mammals, making it an ideal drug target. Here 6427 compounds were screened through structure based virtual screening where compound S-014-1049 was found active against H37Rv and proven non-cytotoxic in in vitro studies. It specifically binds to the core domain of MTSK. Drug discovery ; Mycobacterium tuberculosis ; Shikimate pathway ; Computational biology ; Drug ; Virtual screening ; Biology ; Tuberculosis ; Chemical library ; Drug development ; Kinase ; Small molecule ; Identification (biology) ; Gene ; Chemistry ; Biochemistry ; Pharmacology ; Medicine ; Biosynthesis Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds ; Quinazolinone synthesis and applications