jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Daniela Dascălu | Diana Larisa Roman | Mǎdǎlina Filip | Alecu Ciorsac | Vasile Ostafe | Adriana Isvoran
Source: ADMET & DMPK (article, 2020-06-28)
Field: Materials Science — Biomaterials

Solubility and ADMET profiles of short oligomers of lactic acid Polylactic acid (PLA) is a polymer with an increased potential to be used in different medical applications, including tissue engineering and drug-carries. The use of PLA in medical applications implies the evaluation of the human organism's response to the polymer inserting and to its degradation products. Consequently, within this study, we have investigated the solubility and ADMET profiles of the short oligomers (having the molecular weight lower than 3000 Da) resulting in degradation products of PLA. There is a linear decrease of the molar solubility of investigated oligomers with molecular weight. The results that are obtained also reveal that short oligomers of PLA have promising pharmacological profiles and limited toxicological effects on humans. These oligomers are predicted as potential inhibitors of the organic anion transporting peptides OATP1B1 and OATP1B3, they present minor probability to affect the androgen and glucocorticoid receptors, have a weak potential of hepatotoxicity, and may produce eye injuries. These outcomes may be used to guide or to supplement in vitro and/or in vivo toxicity tests such as to enhance the biodegradation properties of the biopolymer. Solubility ; Polylactic acid ; Chemistry ; Biodegradation ; Biopolymer ; Polymer ; Lactic acid ; In vivo ; Degradation (telecommunications) ; In vitro ; Organic chemistry ; Biochemistry ; Bacteria ; Biology biodegradable polymer synthesis and properties ; Inflammatory mediators and NSAID effects ; Biopolymer Synthesis and Applications
Authors: Yuehua Chen | Yuzhu Wang | Yonggang Yang | Yuhuan Li | Yafu Wang | Ge Wang | Tony D. James | Xiaopeng Xuan | Hua Zhang | Yufang Liu
Source: Chemical Science (article, 2020-01-01)
Field: Chemistry — Spectroscopy

A molecular-logic gate for COX-2 and NAT based on conformational and structural changes: visualizing the progression of liver disease Lighting up the relevant lesion boundaries during operations is vital for guiding the effective resection of hepatopathic tissue. We envisioned that molecular-logic gates, which are known for their excellent digital correlation between input and output signals, could be used to facilitate differential visualization of lesion boundaries. Herein, a series of flexible molecules, naphthalene imide-indole derivatives (<b>IAN</b>) were prepared and evaluated as molecular-logic gates. The input and output signals of the <b>IAN</b> derivatives were successfully used to highlight different hepatopathic regions in order to facilitate boundary differentiation. The <b>IAN</b> derivatives produce different signals due to collaborative changes in the conformation and structure. The hepatopathy-related enzymes (COX-2 and NAT) were used to induce conformational and structural changes in <b>IAN</b> derivatives. Based on these enzyme induced synergistic effects, <b>IAN</b> can sensitively emit different coloured signals such as green, cyan and blue (output signals) as a function of the different input signals, <i>i.e.</i> the different activity of COX-2 and NAT in solution and living cells. Significantly, the <b>IAN</b> derivatives were successfully used to distinguish the boundaries of hepatopathic lesions in tissues after spraying with <b>IAN</b> derivatives (mild cirrhosis, severe cirrhosis, in addition to early and late hepatocellular carcinoma) under a hand held lamp at 365 nm by naked eye. Nat ; Disease ; Resection ; Lesion ; Computer science ; Computational biology ; Medicine ; Chemistry ; Philosophy ; Biology ; Pathology ; Surgery ; Computer network Molecular Sensors and Ion Detection ; Pharmacological Receptor Mechanisms and Effects ; Computational Drug Discovery Methods
Authors: Jingjing Zhang | Quan Chen | Robert J. Mayer | Jin‐Dong Yang | Armin R. Ofial | Jin‐Pei Cheng | Herbert Mayr
Source: Angewandte Chemie International Edition (article, 2020-04-07)
Field: Chemistry — Organic Chemistry

Predicting Absolute Rate Constants for Huisgen Reactions of Unsaturated Iminium Ions with Diazoalkanes The kinetics and stereochemistry of the reactions of iminium ions derived from cinnamaldehydes and MacMillan's imidazolidinones with diphenyldiazomethane and aryldiazomethanes were investigated experimentally and with DFT calculations. The reactions of diphenyldiazomethane with iminium ions derived from MacMillan's second-generation catalysts gave 3-aryl-2,2-diphenylcyclopropanecarbaldehydes with yields >90 % and enantiomeric ratios of ≥90:10. Predominantly 2:1 products were obtained from the corresponding reactions with monoaryldiazomethanes. The measured rate constants are in good agreement with the rate constants derived from the one-center nucleophilicity parameters N and s<sub>N</sub> of diazomethanes and the one-center electrophilicity parameters E of iminium ions as well as with quantum chemically calculated activation energies. Iminium ; Chemistry ; Electrophile ; Nucleophile ; Reaction rate constant ; Ion ; Thermochemistry ; Enantiomer ; Computational chemistry ; Catalysis ; Kinetics ; Physical chemistry ; Organic chemistry ; Physics Cyclopropane Reaction Mechanisms ; Oxidative Organic Chemistry Reactions ; Asymmetric Synthesis and Catalysis
Authors: Musen Zhou | Jianzhong Wu
Source: The Journal of Chemical Physics (article, 2020-08-17)
Field: Chemistry — Inorganic Chemistry

A GPU implementation of classical density functional theory for rapid prediction of gas adsorption in nanoporous materials Nanoporous materials are promising as the next generation of absorbents for gas storage and separation with ultrahigh capacity and selectivity. The recent advent of data-driven approaches in materials modeling provides alternative routes to tailor nanoporous materials for customized applications. Typically, a data-driven model requires a large amount of training data that cannot be generated solely by experimental methods or molecular simulations. In this work, we propose an efficient implementation of classical density functional theory with a graphic processing unit (GPU) for the fast yet accurate prediction of gas adsorption isotherms in nanoporous materials. In comparison to serial computing with the central processing unit, the massively parallelized GPU implementation reduces the computational cost by more than two orders of magnitude. The proposed algorithm renders new opportunities not only for the efficient screening of a large materials database for gas adsorption but it may also serve as an important stepping stone toward the inverse design of nanoporous materials tailored to desired applications. Nanoporous ; Massively parallel ; Computer science ; Adsorption ; Graphics processing unit ; Density functional theory ; General-purpose computing on graphics processing units ; Inverse ; Computational science ; Nanotechnology ; Materials science ; Parallel computing ; Graphics ; Chemistry ; Computer graphics (images) ; Computational chemistry ; Mathematics Metal-Organic Frameworks: Synthesis and Applications ; Zeolite Catalysis and Synthesis ; Machine Learning in Materials Science
Authors: Eric B. Isaacs | Grace M. Lu | Christopher Wolverton
Source: The Journal of Physical Chemistry Letters (article, 2020-06-23)
Field: Materials Science — Materials Chemistry

Inverse Design of Ultralow Lattice Thermal Conductivity Materials via Materials Database Screening of Lone Pair Cation Coordination Environment The presence of lone pair (LP) electrons is strongly associated with the disruption of lattice heat transport, which is a critical component of strategies to achieve efficient thermoelectric energy conversion. By exploiting an empirical relationship between lattice thermal conductivity, κ<sub>L</sub>, and the bond angles of pnictogen group LP cation coordination environments, we develop an inverse design strategy based on a materials database screening to identify chalcogenide materials with ultralow κ<sub>L</sub> for thermoelectrics. Screening the ∼635 000 real and hypothetical inorganic crystals of the Open Quantum Materials Database based on the constituent elements, nominal electron counting, LP cation coordination environment, and synthesizability, we identify 189 compounds expected to exhibit ultralow κ<sub>L</sub>. As a validation, we explicitly compute the lattice dynamical properties of two of the compounds (Cu<sub>2</sub>AgBiPbS<sub>4</sub> and MnTl<sub>2</sub>As<sub>2</sub>S<sub>5</sub>) using first-principles calculations and successfully find both achieve ultralow κ<sub>L</sub> values at room temperature of ∼0.3-0.4 W/(m·K) corresponding to the amorphous limit. Our data-driven approach provides promising candidates for thermoelectric materials and opens new avenues for the design of phononic properties of materials. Lone pair ; Thermal conductivity ; Lattice (music) ; Inverse ; Materials science ; Database ; Computer science ; Chemistry ; Physics ; Composite material ; Organic chemistry ; Mathematics ; Molecule ; Geometry Advanced Thermoelectric Materials and Devices ; Machine Learning in Materials Science ; Thermal properties of materials
Authors: Robert Dobosz | J. Mućko | Ryszard Gawinecki
Source: Energies (article, 2020-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

Using Chou’s 5-Step Rule to Evaluate the Stability of Tautomers: Susceptibility of 2-[(Phenylimino)-methyl]-cyclohexane-1,3-diones to Tautomerization Based on the Calculated Gibbs Free Energies Gibbs free energies, based on DFT (Density Functional Theory) calculations, prove that enaminone (2-(anilinemethylidene)cyclohexane-1,3-dione) and ketamine (2-[(phenylimino)-methyl]cyclohexane-1,3-dione) are the most and least stable tautomeric forms of the studied systems, respectively. 1H and 13C NMR spectra prove that 2-(anilinemethylidene)cyclohexane-1,3-diones are the only tautomeric species present in dimethylsulfoxide solution (a very weak signal can be seen only for the p-methoxy derivatives). The zwitterionic character of these enaminones is strengthened by naphthoannulation and by the insertion of the electron-withdrawing substituent into the benzene ring (the latter weakens the intramolecular hydrogen bond in the compound). Substituent and naphtoannulation have no effect on the stability of the studied tautomers. Slight twisting of the benzene ring, with respect to the CArNC plane (seen in the crystalline state), was proven to also take place in vacuum and in solution. Tautomer ; Chemistry ; Cyclohexane ; Substituent ; Intramolecular force ; Benzene ; Ring (chemistry) ; Gibbs free energy ; Density functional theory ; Hydrogen bond ; Computational chemistry ; Crystallography ; Medicinal chemistry ; Stereochemistry ; Molecule ; Organic chemistry ; Thermodynamics ; Physics Crystallography and molecular interactions ; Organic Chemistry Cycloaddition Reactions ; Computational Drug Discovery Methods
Authors: Matthew L. Evans | Andrew J. Morris
Source: The Journal of Open Source Software (article, 2020-10-27)
Field: Materials Science — Materials Chemistry

matador: a Python library for analysing, curating and performing high-throughput density-functional theory calculations Evans et al., (2020). matador: a Python library for analysing, curating and performing high-throughput density-functional theory calculations. Journal of Open Source Software, 5(54), 2563, https://doi.org/10.21105/joss.02563 Python (programming language) ; Computer science ; Software ; Density functional theory ; Throughput ; Programming language ; Operating system ; Physics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Huayu Jiang | Yumo Wang | Chaofei Nie | Feng Yan | Xin Ouyang | Jing Gong
Source: Applied Sciences (article, 2020-12-31)
Field: Chemistry — Analytical Chemistry

Oil Sludge Deposition in Storage Tanks: A Case Study for Russian Crude Oil in Mo-he Station The oil tank can form a considerable amount of sludge deposition after continuous accumulation, which cause a seriously negative impact on both the storage capacity and the safe operation of the oil tank. Therefore, it is important to anticipate the rate of sludge deposition in advance so that proper measures can be planned to remove this heavy layer on the bottom. This paper proposes a method using a relatively simple formula for predicting the sludge deposits. The sedimentation mechanism of wax and asphaltene is introduced and summarized from both the micro and macro aspects, the factors causing the interaction between particles and the influence on coalescence were analyzed. We applied our prediction methods to calculate the sludge deposition of four oil tanks in Mo-he Station and compared our results with the data measured by experiments. The results show that our method had a good general accuracy to experimental data and can be used directly for on-site engineers to anticipate real sludge height before measuring the oil level inside the tank. Deposition (geology) ; Coalescence (physics) ; Environmental science ; Asphaltene ; Oil storage ; Sedimentation ; Storage tank ; Oil sludge ; Petroleum engineering ; Waste management ; Crude oil ; Environmental engineering ; Engineering ; Geology ; Sediment ; Chemical engineering Petroleum Processing and Analysis ; Hydrocarbon exploration and reservoir analysis ; Enhanced Oil Recovery Techniques
Authors: В. Г. Кривовичев | Sergey V. Krivovichev | M. V. Charykova
Source: Minerals (article, 2020-07-12)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Tellurium Minerals: Structural and Chemical Diversity and Complexity The chemical diversity and complexity of tellurium minerals were analyzed using the concept of mineral systems and Shannon informational entropy. The study employed data for 176 Te mineral species known today. Tellurium minerals belong to six mineral systems in the range of one-to-six species-defining elements. For 176 tellurium minerals, only 36 chemical elements act as essential species-defining constituents. The numbers of minerals of main elements are calculated as follows (the number of mineral species is given in parentheses): O (89), H (48), Cu (48), Pb (43), Bi (31), S (29), Ag (20), Fe (20), Pd (16), Cl (13), and Zn (11). In accordance with their chemistry, all Te minerals are classified into five types of mineral systems: tellurium, oxides, tellurides and intermetalides, tellurites, and tellurates. A statistical analysis showed positive relationships between the chemical, structural, and crystallochemical complexities and the number of essential species-defining elements in a mineral. A positive statistically significant relationship between chemical and structural complexities was established. It is shown that oxygen-free and oxygen-bearing Te minerals differ sharply from each other in terms of chemical and structural complexity, with the first group of minerals being simpler than the second group. The oxygen-free Te minerals (tellurium, tellurides, and intermetallides) are formed under reducing conditions with the participation of hydrothermal solutions. The most structurally complex oxygen-bearing Te minerals originate either from chemical weathering and the oxidation of ore deposits or from volcanic exhalations (Nabokoite). Tellurium ; Mineral ; Chemistry ; Weathering ; Mineralogy ; Inorganic chemistry ; Geology ; Geochemistry ; Organic chemistry Crystal Structures and Properties ; Chemical Thermodynamics and Molecular Structure ; Solid-state spectroscopy and crystallography
Authors: Liam Yourston | Alexey V. Krasnoslobodtsev
Source: Molecules (article, 2020-07-02)
Field: Materials Science — Materials Chemistry

Micro RNA Sensing with Green Emitting Silver Nanoclusters Micro RNA (miR) are regulatory non-coding RNA molecules, which contain a small number of nucleotides ~18-28 nt. There are many various miR sequences found in plants and animals that perform important functions in developmental, metabolic, and disease processes. miRs can bind to complementary sequences within mRNA molecules thus silencing mRNA. Other functions include cardiovascular and neural development, stem cell differentiation, apoptosis, and tumors. In tumors, some miRs can function as oncogenes, others as tumor suppressors. Levels of certain miR molecules reflect cellular events, both normal and pathological. Therefore, miR molecules can be used as biomarkers for disease diagnosis and prognosis. One of these promising molecules is miR-21, which can serve as a biomarker with high potential for early diagnosis of various types of cancer. Here, we present a novel design of miR detection and demonstrate its efficacy on miR-21. The design employs emissive properties of DNA-silver nanoclusters (DNA/AgNC). The detection probe is designed as a hairpin DNA structure with one side of the stem complimentary to miR molecule. The binding of target miR-21 opens the hairpin structure, dramatically modulating emissive properties of AgNC hosted by the C<sub>12</sub> loop of the hairpin. "Red" fluorescence of the DNA/AgNC probe is diminished in the presence of the target miR. At the same time, "green" fluorescence is activated and its intensity increases several-fold. The increase in intensity of "green" fluorescence is strong enough to detect the presence of miR-21. The intensity change follows the concentration dependence of the target miR present in a sample, which provides the basis of developing a new, simple probe for miR detection. The detection strategy is specific, as demonstrated using the response of the DNA/AgNC probe towards the scrambled miR-21 sequence and miR-25 molecule. Additionally, the design reported here is very sensitive with an estimated detection limit at ~1 picomole of miR-21. microRNA ; DNA ; RNA ; Nanoclusters ; Small hairpin RNA ; Gene silencing ; Fluorescence ; DNA microarray ; Chemistry ; Biophysics ; Cell biology ; Biology ; DNA damage ; Molecule ; Computational biology ; Molecular biology ; Nanotechnology ; Gene expression ; Materials science ; Gene ; Biochemistry ; Physics Nanocluster Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Advanced Nanomaterials in Catalysis
Authors: Massimiliano Chiappini | Alessandro Patti | Marjolein Dijkstra
Source: Physical review. E (article, 2020-10-12)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Helicoidal dynamics of biaxial curved rods in twist-bend nematic phases unveiled by unsupervised machine learning techniques Uniaxial rods in a nematic phase diffuse preferentially in the direction parallel to the nematic director n[over ̂]. The nematic director field n[over ̂](r) of a chiral twist-bend nematic (N_{TB}) phase of achiral banana-shaped particles, recently discovered experimentally, displays a heliconical twist of given handedness and periodicity. Using simulations, we investigate the long-time macroscopic diffusion in N_{TB} phases, and find that the predilection of curved rods to diffuse in the direction of the twisting n[over ̂](r) yields a fascinating chiral dynamics along helices, even though achiral curved rods display Brownian motion with a nontrivial rototranslational coupling. We devise a machine learning protocol to characterize the helicoidal particle trajectories, finding that their pitch and radius are determined by the pitch and conical angle of the N_{TB} phase thereby connecting its structural and dynamical properties. Twist ; Rod ; Liquid crystal ; Condensed matter physics ; Dynamics (music) ; Materials science ; Classical mechanics ; Optics ; Physics ; Geometry ; Mathematics ; Acoustics Liquid Crystal Research Advancements ; Advanced Materials and Mechanics ; Electrowetting and Microfluidic Technologies
Authors: Pavel Korotaev | Alexander V. Shapeev
Source: Physical review. B./Physical review. B (article, 2020-11-19)
Field: Materials Science — Materials Chemistry

Lattice dynamics of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>Yb</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:msub><mml:mi>Co</mml:mi><mml:mn>4</mml:mn></mml:msub><mml:msub><mml:mi>Sb</mml:mi><mml:mn>12</mml:mn></mml:msub></mml:mrow></mml:math> skutterudite by machine-learning interatomic potentials: Effect of filler concentration and disorder Lattice dynamics determines a number of important properties of solids. While computational methods with predictive power have been developed in this area, the task is still difficult for the complex compounds. We present a method for automatic on-the-fly generation of multicomponent interatomic potentials. The method is based on active learning, which ensures effective extrapolation to new atomic environments. The accuracy is then demonstrated on the example of the Yb-filled skutterudite compound ${\mathrm{Yb}}_{x}{\mathrm{Co}}_{4}{\mathrm{Sb}}_{12}$, which is a family of the promising thermoelectric materials. Atomic displacements, vibrational spectrum, and lattice thermal conductivity were obtained and the effect of the Yb filling and ordering was studied as 700 K. The potential allowed us to reproduce fine features of the vibrational spectrum, as well as the reduction of the lattice thermal conductivity with filling. We found only a small effect of the disorder on the vibrational spectrum and the thermal conductivity. Extrapolation ; Skutterudite ; Thermal conductivity ; Lattice (music) ; Interatomic potential ; Physics ; Materials science ; Thermodynamics ; Thermoelectric materials ; Molecular dynamics ; Quantum mechanics ; Mathematical analysis ; Mathematics Advanced Thermoelectric Materials and Devices ; Machine Learning in Materials Science ; Rare-earth and actinide compounds
Authors: Franck Camerel | Marc Fourmigué
Source: European Journal of Inorganic Chemistry (article, 2020-01-02)
Field: Materials Science — Materials Chemistry

(Photo)Thermal Stimulation of Functional Dithiolene Complexes in Soft Matter Square‐planar bis(dithiolene) complexes are characterized with a planar delocalized structure and a strong and tunable near infrared (NIR) absorption; they are highly stable under laser irradiation, and their conversion efficiency (light to heat) reaches up to 40–50 %. Their involvement in soft matter, namely liquid crystals, gels, and nanoparticles, opens many possibilities to control the actual state of a material, particularly under light irradiation. Thus, liquid crystalline phases can easily be modified, (i) with temperature to modulate the extended magnetic interactions of paramagnetic complexes, or (ii) under laser irradiation to unravel these remarkable photothermal properties, toward the development of light‐responsive materials. Dithiolene complexes can be also functionalized to produce very effective gelation agents, while the photothermal effect can be used to destabilize at will their supramolecular organization. Besides photothermal therapy, new therapeutic agents were also developed for photo‐controlled drug delivery and bioimaging, combining chemotherapy and phototherapy. Hydrophobic complexes were accordingly designed for their encapsulation in block copolymer nanoparticles for photothermal therapy and photo‐controlled drug delivery under laser irradiation. This class of complexes can be also used as exogenous contrast agents for photoacoustic bioimaging. Photothermal therapy ; Chemistry ; Photothermal effect ; Irradiation ; Nanoparticle ; Drug delivery ; Copolymer ; Delocalized electron ; Azobenzene ; Laser ; Nanotechnology ; Photochemistry ; Polymer ; Materials science ; Organic chemistry ; Optics Luminescence and Fluorescent Materials ; Perovskite Materials and Applications ; Nanoplatforms for cancer theranostics