jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Marwa N. El‐Nahass | Tarek A. Fayed | Mohammed M. El‐Gamil | A. S. Fouda
Source: BMC Chemistry (article, 2024-10-05)
Field: Materials Science — Materials Chemistry

Synergistic inhibition effect of diolefinic dye and silver nanoparticles for carbon steel corrosion in hydrochloric acid solution The current work looks at the inhibitory effects of a diolefinic dye, namely 1,4-bis((E)-2-(3-methyl-2,3-dihydrobenzo[d]thiazol-2-yl) vinyl) benzene iodide salt, in relation to CS corrosion mitigation in hydrochloric acid (HCl) environment. This study uses a variety of experimental methodologies, including weight loss (WL) analysis, electrochemical tests, and theoretical considerations. The synergistic effect of diolefinic dye and AgNPs on the corrosion inhibition of CS in 1 M HCl was investigated. The inhibition efficiency (IE) displays a notable enhancement as the concentration of the dye is elevated and as the temperature raises the IE increases. The diolefinic dye exhibited % IE of 83% even at low concentration (1 × 10<sup>-4</sup> M) whereas 90% in the presence of (2.26 × 10<sup>-10</sup>) AgNPs. Tafel graphs demonstrate that the dye follows a mixed type inhibitor. The adsorption of the dye on CS surface follows Langmuir model. Moreover, the influence of temperature and the activation parameters disclose that diolefinic dye is chemisorbed on the CS surface. The synergistic coefficient of the diolefinic dye and AgNPs under various concentration conditions was greater than unity. The surface morphology of CS sheets was confirmed by scanning electron microscopy (SEM) and energy dispersive X-ray analysis (EDX). Density Functional Theory (DFT) calculations provide theoretical support for the inhibitory effects of the examined dye. Notably, there is a high agreement between the findings of practical studies and theoretical expectations. Tafel equation ; Hydrochloric acid ; Corrosion ; Adsorption ; Chemistry ; Nuclear chemistry ; Scanning electron microscope ; Inorganic chemistry ; Langmuir adsorption model ; Salt (chemistry) ; Electrochemistry ; Materials science ; Organic chemistry ; Physical chemistry ; Electrode ; Composite material Corrosion Behavior and Inhibition ; Concrete Corrosion and Durability ; Anodic Oxide Films and Nanostructures
Authors: Mazaya Najmina | Shingo Kobayashi | Rena Shimazui | Haruka Takata | Mayuka Shibata | Kenta Ishibashi | Hiroshi Kamizawa | Akihiro Kishimura | Yoshihito Shiota | Daichi Ida | Taro Shimizu | Tatsuhiro Ishida | Yoshiki Katayama | Masaru Tanaka | Takeshi Mori
Source: Pharmaceutics (article, 2024-09-28)
Field: Materials Science — Materials Chemistry

A Stealthiness Evaluation of Main Chain Carboxybetaine Polymer Modified into Liposome <b>Background:</b> Acrylamide polymers with zwitterionic carboxybetaine (CB) side groups have attracted attention as stealth polymers that do not induce antibodies when conjugated to proteins. However, they induce antibodies when modified onto liposomes. We hypothesized that antibodies are produced against polymer backbones rather than CB side groups. <b>Objectives:</b> In this study, we designed and synthesized a polymer employing CB in its main chain, poly(<i>N</i>-acetic acid-<i>N</i>-methyl-propyleneimine) (PAMPI), and evaluated the blood retention of PAMPI-modified liposomes in mice. <b>Results:</b> The non-fouling nature of PAMPI-modified liposomes estimated from serum protein adsorption was found to be not inferior to PCB- and PEG-modified liposomes. However, to our surprise, the PAMPI-modified liposomes showed an instantaneous clearance less than 1 h post-injection, comparable to the naked liposomes. <b>Conclusions:</b> The extent of the blood retention of polymer-modified liposomes cannot be predicted by their susceptibility to serum protein adsorption and semi-flexible conformation. Liposome ; Chain (unit) ; Polymer ; Polymer science ; Chemistry ; Computer science ; Biochemistry ; Organic chemistry ; Physics Luminescence and Fluorescent Materials ; Supramolecular Self-Assembly in Materials ; Conducting polymers and applications
Authors: Sumaya K. Al-Rawe | Daniil Baranov | Agnieszka K. Bronowska | Céline Cano | Michael A. Carroll | Paul G. Waddell
Source: Crystals (article, 2024-12-12)
Field: Chemistry — Organic Chemistry

Polymorphism in N-(3-Hydroxyphenyl)-3-methoxybenzamide N-(3-hydroxyphenyl)-3-methoxybenzamide was synthesised by amide coupling. After crystallisation, single-crystal X-ray diffraction revealed two distinct polymorphs of the compound: one in the orthorhombic space group Pna21 with one molecule in the asymmetric unit (Z′ = 1) and a second in the triclinic space group P-1 with two molecules in the asymmetric unit (Z′ = 2). A comparison of the structures reveals that the differences between the two can be attributed to conformational variations, disorder, and the dimensionality of the hydrogen bonding networks, with one forming a three-dimensional net and the other forming layers that exhibit approximate p21/b11 layer group symmetry. Molecular dynamics simulations and well-tempered metadynamics-enhanced sampling calculations provide insight into the transition of one polymorph into the other at room temperature. The efficiency of the crystal packing is assessed by a comparison of the densities and melting points of the two structures. Medicine Structural and Chemical Analysis of Organic and Inorganic Compounds ; Synthesis and Reactions of Organic Compounds ; Synthesis and Reactivity of Sulfur-Containing Compounds
Authors: Gökberk Özcelik | David Bienek | Michael Hardt | Dana Glikman | Björn Braunschweig | Andreas Heuer
Source: ChemRxiv (preprint, 2024-04-08)
Field: Chemistry — Organic Chemistry

Photoswitchable arylazopyrazoles surfactants at the water-air interface: a microscopic perspective Surfactants play an important role in modifying the properties of water-air interfaces. However, information on the microscopic behavior of the mechanisms is scarce. Here, we combine information from molecular dynamics simulations, surface tensiometry, and vibrational sum frequency generation spectroscopy to study the behavior of arylazopyrazole (AAP) as a surfactant. This combination of the experimental techniques allows a direct relation between surface tension and surface excess rather than just bulk concentration. Specifically, we compare the case with (O-AAP) and without (H-AAP) the addition of an octyl carbon chain, as well as for two different isomers (E and Z). From the simulations of these four systems, we see that a stronger cluster formation is accompanied by a weaker reduction of the surface tension for intermediate surface excesses. In some cases, even a small but noticeable maximum in the surface tension isotherm is observed. This correlation is expected from the general properties of the Frumkin isotherm. Both the addition of the carbon chain and the consideration of the E isomer compared to the Z isomer increase this effect. Although the experimental data of the surface tension vs. surface excess do not show a maximum, the general features of the surface tension isotherm are consistent between experiment and simulation. Evidence is also provided that it is primarily the interaction of the aromatic benzene rings that determines the strength of the surfactant interactions. Perspective (graphical) ; Interface (matter) ; Air water ; Materials science ; Chemical engineering ; Chemistry ; Pulmonary surfactant ; Nanotechnology ; Computer science ; Physics ; Engineering ; Mechanics ; Artificial intelligence Surfactants and Colloidal Systems ; Photochromic and Fluorescence Chemistry ; Polydiacetylene-based materials and applications
Source: Letters in Applied NanoBioScience (article, 2024-06-30)
Field: Chemistry — Organic Chemistry

In silico Identification of Natural Chromones against SARS-CoV-2 Mpro and Mutated Spike RBDs. Molecular Docking, Dynamics Simulations, and Pharmacokinetic Prediction Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) is the virus behind the deadly disease COVID-19. The present work reports the in-silico analysis of 173 natural chromones against the SARS-CoV-2 Main Protease (Mpro) and spike Receptor Binding Domain (RBD) of the wild type and its variants. The docking studies revealed that chromones have good binding energy against the targets. They were found to be better than the recently reported drug molecules such as Nirmatrelvir, Dipyridamole, and inhibitor N3 (for Mpro) and ceftazidime, kobophenol A (for spike RBDs). Structure-activity relationships emphasized the significance of hydroxyl groups and chromone rings in the ligand system for better binding. Molecular Dynamics (MD) simulations such as Free Energy Landscape, RMSD, RMSF, Rg, and H-bond analysis revealed a positive outcome. MM-PBSA calculations evaluated the binding free energy of the docked complexes and ensured their stability. The stabilizing and destabilizing residues of the proteins were identified through residue-wise decomposition analysis. The pharmacokinetic properties and drug-likeness of the selected chromones were also analyzed. This study emphasizes that the selected chromones could be considered for in-vitro studies to obtain promising leads for drug discovery against SARS-CoV-2. In silico ; Chemistry ; Docking (animal) ; Molecular dynamics ; Stereochemistry ; Drug discovery ; Molecular model ; OPLS ; Protease ; Computational biology ; Combinatorial chemistry ; Pharmacology ; Computational chemistry ; Biochemistry ; Enzyme ; Biology ; Water model ; Medicine Synthesis and biological activity ; Computational Drug Discovery Methods ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Akash Ghosh | Mahesh Bandi | Shankar Ghosh
Source: Physical Review Research (article, 2024-09-06)
Field: Materials Science — Materials Chemistry

Popping: A granular transition In experiments conducted on a weakly confined 2D assembly of deformable cylinders subject ed to rapid in-plane shear loading, we have identified the key obstacle in achieving compaction. This obstacle involves a dynamic transition between mechanical instabilities, progressing from in-plane rearrangement to out-of-plane popping as the density increases. The popping effect reinforces the frictional constraints from the confining wall and restricts particle mobility, impeding the system from attaining greater compaction. We quantify this transition and demonstrate that interparticle friction contributes to smoothing the transition. Published by the American Physical Society 2024 Transition (genetics) ; Chemistry Material Dynamics and Properties ; Music Technology and Sound Studies ; Pickering emulsions and particle stabilization
Authors: J. D. Nam
Source: arXiv (Cornell University) (preprint, 2024-10-02)
Field: Materials Science — Materials Chemistry

Data for: Flow Matching for Accelerated Simulation of Atomic Transport in Materials Atomic transport underpins the performance of materials in technologies such as energy storage and electronics, yet its simulation remains computationally demanding. In particular, modeling ionic diffusion in solid-state electrolytes (SSEs) requires methods that can overcome the scale limitations of traditional ab initio molecular dynamics (AIMD). We introduce LiFlow, a generative framework to accelerate MD simulations for crystalline materials that formulates the task as conditional generation of atomic displacements. The model uses flow matching, with a Propagator submodel to generate atomic displacements and a Corrector to locally correct unphysical geometries, and incorporates an adaptive prior based on the Maxwell-Boltzmann distribution to account for chemical and thermal conditions. We benchmark LiFlow on a dataset comprising 25-ps trajectories of lithium diffusion across 4,186 SSE candidates at four temperatures. The model obtains a consistent Spearman rank correlation of 0.7-0.8 for lithium mean squared displacement (MSD) predictions on unseen compositions. Furthermore, LiFlow generalizes from short training trajectories to larger supercells and longer simulations while maintaining high accuracy. With speed-ups of up to 600,000$\times$ compared to first-principles methods, LiFlow enables scalable simulations at significantly larger length and time scales. Matching (statistics) ; Flow (mathematics) ; Computer science ; Mechanics ; Simulation ; Physics ; Mathematics Nuclear Materials and Properties ; Advanced Materials Characterization Techniques ; Fusion materials and technologies
Authors: André Brasil Vieira Wyzykowski
Source:  (preprint, 2024-02-29)
Field: Chemistry — Spectroscopy

[Poster Board #1935] Advancing efficient molecular structure extraction: A novel computational framework leveraging equivariant Transformers and diffusion models for enhanced drug discovery Drug discovery ; Computer science ; Equivariant map ; Transformer ; Engineering ; Mathematics ; Bioinformatics ; Electrical engineering ; Biology Analytical Chemistry and Chromatography ; Computational Drug Discovery Methods
Authors: Siva Pavan Josyula | M. Brede | Olaf Hesebeck | Katharina Koschek | W. Possart | Andreas Wulf | Bernhard Zimmer | Stefan Diebels
Source: Computational Materials Science (article, 2024-10-19)
Field: Materials Science — Polymers and Plastics

Modelling the influence of moisture on the mechanical behaviour of crosslinked polyurethane adhesives Crosslinked polymers are typically viscoelastic in nature and show non-linear behaviour due to large deformation. The mechanical behaviour of these polymers is influenced by moisture diffusion because of the hygroscopic properties of the material. The crosslinked polymers are formed by the shorter and longer chain length distribution. The shorter chains tend to break/debond from the network with an increase in the deformation thus leading to the softening of the material. In this paper, the crosslinked polymer mechanical behaviour is modelled with a micro-mechanical polymer network model that considers the softening of the elastomer. The network evolution concept used in the micro-mechanical model formulation considers the shorter and longer chain length distribution allowing the softening of material. The moisture diffusion in the material is anomalous behaviour, therefore, the Langmuir-type diffusion model is used to model the moisture diffusion in the crosslinked polymer. The influence of moisture on the mechanical behaviour is modelled by coupling the micro-mechanical network model with the diffusion model. The coupled diffusion and deformation model uses the moisture-dependent mechanical parameter to compute the local parameter for the evaluation of the mechanical behaviour with inhomogeneous moisture distribution. In this paper, crosslinked polyurethane adhesives are used in the numerical investigation of ageing under the influence of moisture with the coupled material model. The experimental investigation for tensile and diffusion behaviours is investigated for different humid conditions at an isothermal condition of 60 ° C . • Micromechanical model is used to study mechanical behaviour of crosslinked polymers. • Micromehcanical model considers the shorter and longer chain length distribution. • Model accounts for softening due to shorter and longer chain distribution. • Langmuir-type diffusion model is used to model the anomalous diffusion behaviour. • Coupled material model to study moisture influence on mechanical behavior. • Moisture-dependent stiffness parameters are used in the coupled material model formulation. Polyurethane ; Adhesive ; Moisture ; Composite material ; Materials science ; Polymer science Polymer composites and self-healing ; Epoxy Resin Curing Processes ; Polymer Nanocomposites and Properties
Authors: Jiangcheng Xu | Wenbo Yu | Yanlin Luo | Tiantao Liu | An Su
Source: Processes (article, 2024-07-22)
Field: Chemistry — Organic Chemistry

Developing Lead Compounds of eEF2K Inhibitors Using Ligand–Receptor Complex Structures The eEF2K, a member of the α-kinase family, plays a crucial role in cellular differentiation and the stability of the nervous system. The development of eEF2K inhibitors has proven to be significantly important in the treatment of diseases such as cancer and Alzheimer’s. With the advancement of big data in pharmaceuticals and the evolution of molecular generation technologies, leveraging artificial intelligence to expedite research on eEF2K inhibitors shows great potential. Based on the recently published structure of eEF2K and known inhibitor molecular structures, a generative model was used to create 1094 candidate inhibitor molecules. Analysis indicates that the model-generated molecules can comprehend the principles of molecular docking. Moreover, some of these molecules can modify the original molecular frameworks. A molecular screening strategy was devised, leading to the identification of five promising eEF2K inhibitor lead compounds. These five compound molecules demonstrated excellent thermodynamic performance when docked with eEF2K, with Vina scores of −12.12, −16.67, −15.07, −15.99, and −10.55 kcal/mol, respectively, showing a 24.27% improvement over known active inhibitor molecules. Additionally, they exhibited favorable drug-likeness. This study used deep generative models to develop eEF2K inhibitors, enabling the treatment of cancer and neurological disorders. Computational biology ; Virtual screening ; Chemistry ; Docking (animal) ; Drug discovery ; Nanotechnology ; Biology ; Biochemistry ; Materials science ; Medicine Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Synthesis and Biological Evaluation
Authors: Fabrizio Mastrolorito | Fulvio Ciriaco | Maria Vittoria Togo | Nicola Gambacorta | Daniela Trisciuzzi | Cosimo Altomare | Nicola Amoroso | Francesca Grisoni | Orazio Nicolotti
Source: ChemRxiv (preprint, 2024-07-23)
Field: Chemistry — Spectroscopy

fragSMILES: a Chemical String Notation for Advanced Fragment and Chirality Representation Generative models have revolutionized de novo drug design, allowing to produce molecules on-demand with desired physicochemical and pharmacological properties. String based molecular representations, such as SMILES (Simplified Molecular Input Line Entry System) strings and SELFIES (Self-Referencing Embedded Strings), have played a pivotal role in the success of generative approaches, thanks to their capacity to encode atom- and bond- information and ease-of-generation. However, such ‘atom-level’ string representations have certain limitations, in terms of capturing information on chirality, and synthetic accessibility of the corresponding designs. In this paper, we present fragSMILES, a novel fragment-based molecular representation in the form of string. fragSMILES encode fragments in a ‘chemically-meaningful’ way via a novel graph-reduction approach, allowing to obtain an efficient, interpretable, and expressive molecular representation, which also avoids fragment redundancy. fragSMILES advances the state-of-the-art of fragment-based representations, by reporting fragments and their ‘breaking’ bonds independently, without fragment redundancy. Moreover, fragSMILES also embeds information of molecular chirality, thereby overcoming known limitations of existing string notations. When compared with SMILES and SELFIES for de novo design, the fragSMILES notation showed its promise in generating molecules with desirable biochemical and scaffolds properties. Notation ; Fragment (logic) ; String (physics) ; Representation (politics) ; Chirality (physics) ; Computer science ; Chemistry ; Physics ; Theoretical physics ; Mathematics ; Programming language ; Arithmetic ; Quantum mechanics ; Political science Molecular spectroscopy and chirality ; Analytical Chemistry and Chromatography ; Mass Spectrometry Techniques and Applications
Authors: Marola W. Issa | Steve V. Barancyk | Reza M. Rock | James F. Gilchrist | Christopher L. Wirth
Source: arXiv (Cornell University) (preprint, 2024-03-28)
Field: Materials Science — General Materials Science

Impact of Resin Molecular Weight on Drying Kinetics and Sag of Coatings The work herein investigates the impact of resin molecular weight and solvent choice on drying kinetics and sag velocity in polymer films. These films, ranging in thickness from ~60 micrometer to ~120 micrometer were formulated with 45% by weight polymer resin in one of two solvent packages with different relative evaporation rates (RER). Gravimetry was initially used to track drying kinetics and a one-dimensional diffusion model was utilized to compute the apparent solvent diffusivity. In addition, the film thickness was tracked with optical profilometry. Results from these measurements showed that for fixed molecular weight the drying kinetics increased by approximately two-fold for the high RER solvent, whereas the apparent diffusivity tended to increase with increasing polymer molecular weight. Films formulated from higher molecular weight resins had greater initial viscosities and thicknesses for identical draw down blade clearance. By extension, the higher apparent diffusivities at greater molecular weights were attributed to effects of prolonged evaporation times for the thicker films. The sag velocity was measured through the thickness of the film for these systems at a 5 degree incline using the Variable Angle Inspection Microscope (VAIM). Measurements showed an increase in sag velocity for thinner and less viscous films, which was somewhat surprising both because a thinner film will experience lower gravitational stress and quicker drying times as compared to a thicker film. From these data we conclude that formulating a coating with higher molecular weight resin, although likely to increase drying time, will tend to deter sag because of the large impact of viscosity on these phenomena. Kinetics ; Chemical engineering ; Chemistry ; Materials science ; Pulp and paper industry ; Polymer chemistry ; Composite material ; Engineering ; Physics Material Properties and Applications ; Epoxy Resin Curing Processes
Authors: Jichao Zhu | Xiaoran Dong | Kunhao Li | Siyu Tian | Yao Kong | Weitong Chen | Shuping Zhou
Source: Ceramics International (article, 2024-12-30)
Field: Materials Science — Materials Chemistry

In vitro controlled release of 5-aminosalicylate from ZnAl-NO3(-CO3) layered double hydroxide drug delivery system Hydroxide ; Drug delivery ; Materials science ; In vitro ; Drug ; Nuclear chemistry ; Chemical engineering ; Controlled release ; Pharmacology ; Nanotechnology ; Chemistry ; Biochemistry ; Medicine ; Engineering Layered Double Hydroxides Synthesis and Applications ; Mesoporous Materials and Catalysis ; Polyoxometalates: Synthesis and Applications