jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Atta Muhammad | Carlos Sáenz Ezquerro | Rajat Srivastava | Pietro Asinari | Manuel Laspalas | A. Chiminelli | Matteo Fasano
Source: Nanomaterials (article, 2023-06-28)
Field: Materials Science — Materials Chemistry

Atomistic to Mesoscopic Modelling of Thermophysical Properties of Graphene-Reinforced Epoxy Nanocomposites This research addresses the need for a multiscale model for the determination of the thermophysical properties of nanofiller-enhanced thermoset polymer composites. Specifically, we analyzed the thermophysical properties of an epoxy resin containing bisphenol-A diglyceryl ether (DGEBA) as an epoxy monomer and dicyandiamide (DICY) and diethylene triamine (DETA) as cross-linking agents. The cross-linking process occurs at the atomistic scale through the formation of bonds among the reactive particles within the epoxy and hardener molecules. To derive the interatomic coarse-grained potential for the mesoscopic model and match the density of the material studied through atomic simulations, we employed the iterative Boltzmann inversion method. The newly developed coarse-grained molecular dynamics model effectively reproduces various thermophysical properties of the DGEBA-DICY-DETA resin system. Furthermore, we simulated nanocomposites made of the considered epoxy additivated with graphene nanofillers at the mesoscopic level and verified them against continuum approaches. Our results demonstrate that a moderate amount of nanofillers (up to 2 wt.%) increases the elastic modulus and thermal conductivity of the epoxy resin while decreasing the Poisson's ratio. For the first time, we present a coarse-grained model of DGEBA-DICY-DETA/graphene materials, which can facilitate the design and development of composites with tunable thermophysical properties for a potentially wide range of applications, e.g., automotive, aerospace, biomedical, or energy ones. Epoxy ; Materials science ; Mesoscopic physics ; Graphene ; Thermosetting polymer ; Composite material ; Nanocomposite ; Diglycidyl ether ; Thermal conductivity ; Molecular dynamics ; Bisphenol A ; Nanotechnology ; Computational chemistry ; Chemistry Thermal properties of materials ; Carbon Nanotubes in Composites ; Polymer Nanocomposites and Properties
Authors: Caihua Liu | Yachao Tian | Zihan Ma | Linyi Zhou
Source: Foods (article, 2023-06-14)
Field: Materials Science — Materials Chemistry

Pickering Emulsion Stabilized by β-Cyclodextrin and Cinnamaldehyde/β-Cyclodextrin Composite A Pickering emulsion was prepared using β-cyclodextrin (β-CD) and a cinnamaldehyde (CA)/β-CD composite as emulsifiers and corn oil, camellia oil, lard oil, and fish oil as oil phases. It was confirmed that Pickering emulsions prepared with β-CD and CA/β-CD had good storage stability. The rheological experiments showed that all emulsions had G' values higher than G″, thus confirming their gel properties. The results of temperature scanning rheology experiments revealed that the Pickering emulsion prepared with β-CD and CA/β-CD composites had high stability, in the range of 20-65 °C. The chewing properties of Pickering emulsions prepared by β-CD and corn oil, camellia oil, lard, and herring oil were 8.02 ± 0.24 N, 7.94 ± 0.16 N, 36.41 ± 1.25 N, and 5.17 ± 0.13 N, respectively. The chewing properties of Pickering emulsions made with the CA/β-CD composite and corn oil, camellia oil, lard, and herring oil were 2.51 ± 0.05 N, 2.56 ± 0.05 N, 22.67 ± 1.70 N, 3.83 ± 0.29 N, respectively. The texture properties confirmed that the CA/β-CD-composite-stabilized-emulsion had superior palatability. After 28 days at 50 °C, malondialdehyde (MDA) was detected in the emulsion. Compared with the β-CD and CA + β-CD emulsion, the CA/β-CD composite emulsion had the lowest content of MDA (182.23 ± 8.93 nmol/kg). The in vitro digestion results showed that the free fatty acid (FFA) release rates of the CA/β-CD composite emulsion (87.49 ± 3.40%) were higher than those of the β-CD emulsion (74.32 ± 2.11%). This strategy provides ideas for expanding the application range of emulsifier particles and developing food-grade Pickering emulsions with antioxidant capacity. Cyclodextrin ; Cinnamaldehyde ; Emulsion ; Composite number ; Pickering emulsion ; Chemistry ; Chemical engineering ; Materials science ; Organic chemistry ; Composite material ; Engineering ; Catalysis Pickering emulsions and particle stabilization ; Proteins in Food Systems ; Polysaccharides Composition and Applications
Authors: Simone Ciarella | Massimiliano Chiappini | Emanuele Boattini | Marjolein Dijkstra | Liesbeth M. C. Janssen
Source: Machine Learning Science and Technology (article, 2023-03-27)
Field: Materials Science — Materials Chemistry

Dynamics of supercooled liquids from static averaged quantities using machine learning Abstract We introduce a machine-learning approach to predict the complex non-Markovian dynamics of supercooled liquids from static averaged quantities. Compared to techniques based on particle propensity, our method is built upon a theoretical framework that uses as input and output system-averaged quantities, thus being easier to apply in an experimental context where particle resolved information is not available. In this work, we train a deep neural network to predict the self intermediate scattering function of binary mixtures using their static structure factor as input. While its performance is excellent for the temperature range of the training data, the model also retains some transferability in making decent predictions at temperatures lower than the ones it was trained for, or when we use it for similar systems. We also develop an evolutionary strategy that is able to construct a realistic memory function underlying the observed non-Markovian dynamics. This method lets us conclude that the memory function of supercooled liquids can be effectively parameterized as the sum of two stretched exponentials, which physically corresponds to two dominant relaxation modes. Supercooling ; Parameterized complexity ; Relaxation (psychology) ; Computer science ; Statistical physics ; Context (archaeology) ; Artificial neural network ; Function (biology) ; Exponential function ; Binary number ; Range (aeronautics) ; Algorithm ; Artificial intelligence ; Mathematics ; Physics ; Thermodynamics ; Materials science ; Mathematical analysis Material Dynamics and Properties ; Theoretical and Computational Physics ; Phase Equilibria and Thermodynamics
Authors: Caleb J. Setzler | Caleb A. Arrington | David J. Lewis | Jeffrey T. Petty
Source: The Journal of Physical Chemistry B (article, 2023-12-06)
Field: Materials Science — Materials Chemistry

Breaching the Fortress: Photochemistry of DNA-Caged Ag<sub>10</sub><sup>6+</sup> [Image: see text] A DNA strand can encapsulate a silver molecule to create a nanoscale, aqueous stable chromophore. A protected cluster that strongly fluoresces can also be weakly photolabile, and we describe the laser-driven photochemistry of the green fluorophore C(4)AC(4)TC(3)GT(4)/Ag(10)(6+). The embedded cluster is selectively photoexcited at 490 nm and then bleached, and we describe how the efficiency, products, and route of this photochemical reaction are controlled by the DNA cage. With irradiation at 496.5 nm, the cluster absorption progressively drops to give a photodestruction quantum yield of 1.5 (±0.2) × 10(–4), ∼10(3)× less efficient than fluorescence. A new λ(abs) = 335 nm chromophore develops because the precursor with 4 Ag(0) is converted into a group of clusters with 2 Ag(0) – Ag(6)(4+), Ag(7)(5+), Ag(8)(6+), and Ag(9)(7+). The 4–7 Ag(+) in this series are chemically distinct from the 2 Ag(0) because they are selectively etched by iodide. This halide precipitates silver to favor only the smallest Ag(6)(4+) cluster, but the larger clusters re-develop when the precipitated Ag(+) ions are replenished. DNA-bound Ag(10)(6+) decomposes because it is electronically excited and then reacts with oxygen. This two-step process may be state-specific because O(2) quenches the red luminescence from Ag(10)(6+). However, the rate constant of 2.3 (±0.2) × 10(6) M(–1) s(–1) is relatively small, which suggests that the surrounding DNA matrix hinders O(2) diffusion. On the basis of analogous photoproducts with methylene blue, we propose that a reactive oxygen species is produced and then oxidizes Ag(10)(6+) to leave behind a loose Ag(+)-DNA skeleton. These findings underscore the ability of DNA scaffolds to not only tune the spectra but also guide the reactions of their molecular silver adducts. Chromophore ; Photochemistry ; Chemistry ; Fluorophore ; Quantum yield ; Fluorescence ; Aqueous solution ; Luminescence ; Excited state ; Singlet oxygen ; Cluster (spacecraft) ; Absorption (acoustics) ; Oxygen ; Materials science ; Physical chemistry ; Organic chemistry Nanocluster Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Ryou Kubota | Itaru Hamachi
Source: Advanced Science (article, 2023-11-28)
Field: Materials Science — Biomaterials

Cell‐Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non‐/Out‐of‐Equilibrium Dynamic Systems Living cells are complex, nonequilibrium supramolecular systems capable of independently and/or cooperatively integrating multiple bio-supramolecules to execute intricate physiological functions that cannot be accomplished by individual biomolecules. These biological design strategies offer valuable insights for the development of synthetic supramolecular systems with spatially controlled hierarchical structures, which, importantly, exhibit cell-like responses and functions. The next grand challenge in supramolecular chemistry is to control the organization of multiple types of supramolecules in a single system, thus integrating the functions of these supramolecules in an orthogonal and/or cooperative manner. In this perspective, the recent progress in constructing multicomponent supramolecular soft materials through the hybridization of supramolecules, such as self-assembled nanofibers/gels and coacervates, with other functional molecules, including polymer gels and enzymes is highlighted. Moreover, results show that these materials exhibit bioinspired responses to stimuli, such as bidirectional rheological responses of supramolecular double-network hydrogels, temporal stimulus pattern-dependent responses of synthetic coacervates, and 3D hydrogel patterning in response to reaction-diffusion processes are presented. Autonomous active soft materials with cell-like responses and spatially controlled structures hold promise for diverse applications, including soft robotics with directional motion, point-of-care disease diagnosis, and tissue regeneration. Supramolecular chemistry ; Nanotechnology ; Self-healing hydrogels ; Biomolecule ; Synthetic biology ; Supramolecular polymers ; Soft materials ; Materials science ; Soft robotics ; Nanofiber ; Computer science ; Chemistry ; Molecule ; Bioinformatics ; Artificial intelligence ; Biology Supramolecular Self-Assembly in Materials ; Supramolecular Chemistry and Complexes ; Hydrogels: synthesis, properties, applications
Authors: Shalini Mathpal | Tushar Joshi | Priyanka Sharma | Priyanka Maiti | Mahesha Nand | Veena Pande | Subhash Chandra
Source: 3 Biotech (article, 2023-12-19)
Field: Chemistry — Organic Chemistry

In silico screening of chalcone derivatives as promising EGFR-TK inhibitors for the clinical treatment of cancer Lipinski's rule of five ; Erlotinib ; Virtual screening ; Chalcone ; EGFR inhibitors ; Epidermal growth factor receptor ; Wnt signaling pathway ; Docking (animal) ; In silico ; Chemistry ; Computational biology ; Chemical space ; Biochemistry ; Cancer research ; Drug discovery ; Biology ; Stereochemistry ; Signal transduction ; Receptor ; Medicine Synthesis and biological activity ; HER2/EGFR in Cancer Research ; Quinazolinone synthesis and applications
Authors: Galen T. Craven | Renai Chen | M. Cooper | Christopher Matthews | Jason Rizk | Walter Malone | Landon Johnson | Tammie Gibson | David A. Andersson
Source: Computational Materials Science (article, 2023-09-04)
Field: Materials Science — Materials Chemistry

Data-driven methods for diffusivity prediction in nuclear fuels Nuclear fuel ; Nuclear engineering ; Thermal diffusivity ; Materials science ; Diffusion ; Uranium ; Creep ; Structural material ; Environmental science ; Thermodynamics ; Composite material ; Engineering ; Physics ; Metallurgy Nuclear Materials and Properties ; Nuclear reactor physics and engineering ; Machine Learning in Materials Science
Authors: Blake Armstrong | Alessandro Silvestri | Raffaella Demichelis | Paolo Raiteri | Julian D. Gale
Source: Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences (article, 2023-05-21)
Field: Materials Science — Biomaterials

Solubility-consistent force field simulations for aqueous metal carbonate systems using graphical processing units Crystallization of alkaline earth metal carbonates from water is important for biomineralization and environmental geochemistry. Here, large-scale computer simulations are a useful approach to complement experimental studies by providing atomistic insights and even by quantitatively determining the thermodynamics of individual steps. However, this is dependent on the existence of force field models that are sufficiently accurate while being computationally efficient enough to sample complex systems. Here, we introduce a revised force field for aqueous alkaline earth metal carbonates that reproduces both the solubilities of the crystalline anhydrous minerals, as well as the hydration free energies of the ions. The model is also designed to run efficiently on graphical processing units thereby reducing the cost of such simulations. The performance of the revised force field is compared against previous results for important properties relevant to crystallization, including ion-pairing and mineral-water interfacial structure and dynamics. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'. Anhydrous ; Crystallization ; Aqueous solution ; Force field (fiction) ; Solubility ; Carbonate ; Field (mathematics) ; Biomineralization ; Alkaline earth metal ; Metal ; Materials science ; Computer science ; Chemistry ; Chemical physics ; Thermodynamics ; Chemical engineering ; Physics ; Physical chemistry ; Metallurgy ; Organic chemistry Calcium Carbonate Crystallization and Inhibition ; Spectroscopy and Quantum Chemical Studies ; Crystallization and Solubility Studies
Authors: Samantha N. Muellers | Karen N. Allen | Adrian Whitty
Source: Proceedings of the National Academy of Sciences (article, 2023-12-01)
Field: Materials Science — Materials Chemistry

MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal stability based on comparison of the amino acid sequences of homologous proteins derived from bacteria that grow at different temperatures. A key feature of the method is that it compares the sequences based not simply on the amino acid identity, but rather on the structural and physicochemical properties of the side chain. The method accurately identified stabilizing substitutions in three well-studied systems and was validated prospectively by experimentally testing predicted stabilizing substitutions in a polyamine oxidase. In each case, the method outperformed the widely used bioinformatic consensus approach. The method can also provide insight into fundamental aspects of protein structure, for example, by identifying how many sequence positions in a given protein are relevant to temperature adaptation. Protein superfamily ; Computational biology ; Amino acid ; Stability (learning theory) ; Computer science ; Protein stability ; Identification (biology) ; Peptide sequence ; Protein engineering ; Thermostability ; Protein design ; Artificial intelligence ; Biological system ; Protein structure ; Machine learning ; Biochemistry ; Chemistry ; Biology ; Gene ; Enzyme Enzyme Structure and Function ; Microbial Metabolic Engineering and Bioproduction ; Genomics and Phylogenetic Studies
Authors: Andreas Will | Denys Oliinyk | Christian Bleiholder | Florian Meier
Source: Analytical and Bioanalytical Chemistry (article, 2023-09-27)
Field: Chemistry — Spectroscopy

Peptide collision cross sections of 22 post-translational modifications Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis. Ion-mobility spectrometry ; Chemistry ; Peptide ; Ion ; Mass spectrometry ; Analytical Chemistry (journal) ; Proteome ; Bottom-up proteomics ; Collision-induced dissociation ; Chemical physics ; Chromatography ; Atomic physics ; Protein mass spectrometry ; Tandem mass spectrometry ; Biochemistry ; Physics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Raashiq Ishraaq | Tanmay Sarkar Akash | Arka Bera | Siddhartha Das
Source: The Journal of Physical Chemistry B (article, 2023-12-26)
Field: Materials Science — Surfaces, Coatings and Films

Hydrophilic and Apolar Hydration in Densely Grafted Cationic Brushes and Counterions with Large Mobilities We employ an all-atom molecular dynamics (MD) simulation framework to unravel water microstructure and ion properties for cationic [poly(2-(methacryloyloxy)ethyl) trimethylammonium chloride] (PMETAC) brushes with chloride ions as counterions. First, we identify locally separate water domains (or first hydration shells) each around {N(CH<sub>3</sub>)<sub>3</sub>}<sup>+</sup> and the C═O functional groups of the PMETAC chain and one around the Cl<sup>-</sup> ion. These first hydration shells around the respective moieties overlap, and the extent of the overlap depends on the nature of the species triggering it. Second, despite the overlap, the water molecules in these domains demonstrate disparate properties dictated by the properties of the atoms and groups around which they are located. For example, the presence of the methyl groups makes the {N(CH<sub>3</sub>)<sub>3</sub>}<sup>+</sup> group trigger apolar hydration as evidenced by the corresponding orientation of the dipole of the water molecules around the {N(CH<sub>3</sub>)<sub>3</sub>}<sup>+</sup> moiety. These water molecules around the {N(CH<sub>3</sub>)<sub>3</sub>}<sup>+</sup> group also have enhanced tetrahedrality compared to the water molecules constituting the hydration layer around the C═O group and the Cl<sup>-</sup> counterion. Our simulations also identify that there is an intervening water layer between the Cl<sup>-</sup> ion and {N(CH<sub>3</sub>)<sub>3</sub>}<sup>+</sup> group: this layer prevents the Cl<sup>-</sup> ion from coming very close to the {N(CH<sub>3</sub>)<sub>3</sub>}<sup>+</sup> group. As a consequence, there is a significantly large mobility of the Cl<sup>-</sup> ions inside the PMETAC brush layer. Furthermore, the C═O group of the polyelectrolyte (PE) chain, due to the partial negative charge on the oxygen atom and the specific structure of the PMETAC brush system, demonstrates strongly hydrophilic behavior and enforces a specific dipole response of water molecules analogous to that experienced by water around anionic species of high charge density. In summary, our findings confirm that PMETAC brushes undergo hydrophilic hydration at one site and apolar hydration at another site and ensure large mobility of the supported Cl<sup>-</sup> counterions. Counterion ; Chemistry ; Cationic polymerization ; Molecule ; Chloride ; Ion ; Moiety ; Crystallography ; Molecular dynamics ; Polymer chemistry ; Computational chemistry ; Stereochemistry ; Organic chemistry Polymer Surface Interaction Studies ; Surfactants and Colloidal Systems ; Electrostatics and Colloid Interactions
Authors: Syeda Abida Ejaz | Aftab Farid | Seema Zargar | Pervaiz Ali Channar | Mubashir Aziz | Tanveer A. Wani | Hafiz Muhammad Attaullah | Rabail Ujhan | Arfa Tehzeeb | Aamer Saeed | Hafiz Saqib Ali | Mauricio F. Erben
Source: BMC Chemistry (article, 2023-08-14)
Field: Chemistry — Organic Chemistry

Computational and theoretical chemistry of newly synthesized and characterized 2,2’-(5,5’-(1,4-phenylene)bis(1H-tetrazole-5,1-diyl))bis-N-acetamides Energetic heterocycles, including pyridines, triazoles, and tetrazoles, exhibit greater density, heats of formation, and oxygen balance compared to their carbocyclic counterparts, making them a promising approach for synthesizing novel bis-tetrazole acetamides. Synthesized compounds A-F, some of which feature a chlorine atom attached to the phenyl ring, serve as valuable synthons for aryl coupling reactions. Analysis via <sup>1</sup>H-NMR and <sup>13</sup>C-NMR spectroscopy, as well as density functional considerations through B3LYP functional correlation with 6-311 + + G(d) and 6-31G(d) basis set, revealed the observed LUMO/HOMO energies and charge transfer within the molecule. Additionally, the dipole moment, chemical hardness, softness, ionization potential, local reactivity potential via Fukui indices and thermodynamic properties (entropy, enthalpy, and Gibbs free energy) of the molecule were calculated through density functional theory studies. In addition, Molecular Docking studies were conducted to investigate the anti-cancer potential of synthesized heterocyclic compounds against caspase 3, NF-KAPPA-B and P53 protein. Molecular docking analysis demonstrated a potent interaction between 2,2'-(5,5'-(1,4-phenylene)bis(1H-tetrazole-5,1-diyl))bis-N-(2,4-dinitrophenyl) acetamides (6d) and TP53 and NF-KAPPA-B with binding energies of - 11.8 kJ/mol and - 10.9 kJ/mol for TP53 and NF-KAPPA-B, respectively. Similarly, 2,2'-(5,5'-(1,4-phenylene)bis(1H-tetrazole-5,1-diyl))bis-N-(2-chlorophenyl) acetamides (6f) exhibited a strong interaction with caspase-3 with binding energy of -10.0 kJ/mol, indicating their potential as therapeutic agents against these proteins. Furthermore, the findings of current study was further strengthen by 100 ns molecular dynamics (MD) simulations. Finally, theoretical studies of oxygen balance and nitrogen percentage suggest that these molecules can be utilized as energetic materials. Tetrazole ; Phenylene ; Chemistry ; Combinatorial chemistry ; Organic chemistry ; Polymer Synthesis of Tetrazole Derivatives ; Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity