jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Aleks Reinhardt | Pin Yu Chew | Bingqing Cheng
Source: The Journal of Chemical Physics (article, 2023-11-14)
Field: Materials Science — Materials Chemistry

A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances. Solubility ; Molecular dynamics ; Crystal (programming language) ; Molecule ; Ionic bonding ; Solvent ; Chemistry ; Thermodynamics ; Chemical physics ; Materials science ; Physical chemistry ; Computational chemistry ; Computer science ; Physics ; Ion ; Organic chemistry Crystallization and Solubility Studies ; Phase Equilibria and Thermodynamics ; Spectroscopy and Quantum Chemical Studies
Authors: Miguel Alberto Flores-Ortiz | Ricardo A. Gutiérrez-Márquez | Rogelio S. Mier-Jiménez | Martha M. Flores‐Leonar | Andrés Aguilar‐Granda
Source: ChemRxiv (preprint, 2023-09-05)
Field: Chemistry — Organic Chemistry

Building C-C bonds using a cheap automated synthesis platform The formation of C-C bonds through automated synthesis platforms seeks to accelerate the preparation of molecules, simplify the operational processes, and reduce the human time required for synthesis. Here, we report C-C bond formation using a low-cost automated synthesis platform that seeks to democratize automated organic synthesis. MIK-I can run reactions widely used in organic chemistry: Claisen-Schmidt condensations, Suzuki-Miyaura coupling, Knoevenagel condensations, and Morita-Baylis-Hillman reactions, showing similar yields obtained manually, which highlights the potential of this platform for the synthesis of building blocks. Knoevenagel condensation ; Organic synthesis ; Computer science ; Chemistry ; Combinatorial chemistry ; Nanotechnology ; Organic chemistry ; Catalysis ; Materials science Advanced Synthetic Organic Chemistry ; Synthetic Organic Chemistry Methods ; Chemical Synthesis and Analysis
Authors: Magenta J. Hensinger | Andreas Eitzinger | Oliver Trapp | Armin R. Ofial
Source: Chemistry - A European Journal (article, 2023-10-18)
Field: Chemistry — Organic Chemistry

Nucleophilicity of 4‐(Alkylthio)‐3‐imidazoline Derived Enamines Imidazolidine-4-thiones (ITOs) are cyclic, secondary amines that were considered as potential prebiotic organocatalysts for light-driven α-alkylations of aldehydes by bromoacetonitrile (BAN). Recent studies showed that the initially supplied ITOs represent the pre-catalyst because they undergo S-alkylation with BAN to give 4-(alkylthio)-3-imidazolines (TIMs). Given that the same reagent mix that undergoes light-driven α-alkylations is also effective in the dark, we synthesized ten ITO- or TIM-derived enamines of aldehydes and characterized their nucleophilic reactivities by kinetic studies in acetonitrile. The experimental second-order rate constants k<sub>2</sub> for reactions of enamines with benzhydrylium ions (reference electrophiles) were evaluated by the Mayr-Patz equation, lg k<sub>2</sub> (20 °C)=s<sub>N</sub> (N+E). The determined nucleophilicities N (and s<sub>N</sub> ) reveal the reactivity profiles of these enamines under prebiotically relevant conditions as well as their potential for use in organocatalytic synthesis. Chemistry ; Nucleophile ; Electrophile ; Alkylation ; Reagent ; Reactivity (psychology) ; Acetonitrile ; Catalysis ; Medicinal chemistry ; Combinatorial chemistry ; Organic chemistry Chemical Reaction Mechanisms ; Sulfur-Based Synthesis Techniques ; Chemical Synthesis and Reactions
Authors: Yésica Vicente-Martínez | María J. Muñoz-Sandoval | Manuel Hernández‐Córdoba | Ignacio López-Garcı́a
Source: Molecules (article, 2023-03-10)
Field: Chemistry — Analytical Chemistry

Using a Simple Magnetic Adsorbent for the Preconcentration and Determination of Ga(III) and In(III) by Electrothermal Atomic Absorption Spectrometry A solid-phase dispersive microextraction procedure has been developed using ferrite (Fe<sub>3</sub>O<sub>4</sub>), an inexpensive magnetic material, as an adsorbent for the separation and subsequent determination of Ga(III) and In(III). The ions were removed from an aqueous solution by adsorption on Fe<sub>3</sub>O<sub>4</sub>, which was next easily collected from the medium by the action of a magnet. The analytes were then desorbed using 50 µL of 2 M NaOH or 50 µL of a 4:1 mixture of 0.1 M EDTA and 2 M HNO<sub>3</sub> for the determination of Ga(III) or In(III), respectively. The level of the elements in the desorption phase was measured by electrothermal atomic absorption spectrometry (ETAAS) by injecting 10 µL of this phase into the atomizer. The enrichment factor was 163, and detection limits of 0.02 and 0.01 µg L<sup>-1</sup> were achieved for Ga(III) and In(III), respectively. The reliability of the procedure has been verified by means of standard reference materials and by means of standard additions. Results are given for waters, soils and samples obtained from various electronic devices. It is of note that the procedure could be the basis for a useful way of recovering these valuable elements from different matrices for reuse. Adsorption ; Atomic absorption spectroscopy ; Analytical Chemistry (journal) ; Desorption ; Chemistry ; Detection limit ; Aqueous solution ; Analyte ; Standard solution ; Standard addition ; Chromatography Analytical chemistry methods development ; Electrochemical Analysis and Applications ; Extraction and Separation Processes
Authors: Hyunsoo Park | Sauradeep Majumdar | Xiaoqi Zhang | Jihan Kim | Berend Smit
Source: ChemRxiv (preprint, 2023-04-24)
Field: Chemistry — Inorganic Chemistry

Inverse design of metal-organic frameworks for direct air capture of CO2 via deep reinforcement learning The combination of several interesting characteristics makes metal-organic frameworks (MOFs) a highly sought-after class of nanomaterials for a broad range of applications like gas storage and separation, catalysis, drug delivery, and so on. However, the ever-expanding and nearly infinite chemical space of MOFs makes it extremely challenging to identify the most optimal materials for a given application. In this work, we present a novel approach using deep reinforcement learning for the inverse design of MOFs, our motivation being designing promising materials for the important environmental application of direct air capture of CO2 (DAC). We demonstrate that the reinforcement learning framework can successfully design MOFs with critical characteristics important for DAC. Our top-performing structures populate two separate subspaces of the MOF chemical space: the subspace with high CO2 heat of adsorption and the subspace with preferential adsorption of CO2 from humid air, with few structures having both characteristics. Our model can thus serve as an essential tool for the rational design and discovery of materials for different target properties and applications. Subspace topology ; Reinforcement learning ; Computer science ; Metal-organic framework ; Linear subspace ; Chemical space ; Inverse ; Spacecraft ; Rational design ; Adsorption ; Nanotechnology ; Artificial intelligence ; Materials science ; Chemistry ; Engineering ; Aerospace engineering ; Mathematics ; Drug discovery Metal-Organic Frameworks: Synthesis and Applications ; Carbon Dioxide Capture Technologies ; Covalent Organic Framework Applications
Authors: Runying Guo | Daorun Hu | Danrui Liu | Qingkun Jiang | Jiaxuan Qiu
Source: Frontiers in Bioengineering and Biotechnology (review, 2023-04-19)
Field: Materials Science — Materials Chemistry

MXene nanomaterials in biomedicine: A bibliometric perspective <b>Purpose:</b> MXene is two-dimensional (2D) nanomaterials that comprise transition metal carbides, nitrides, and carbonitrides. Their unique nanostructure attributes it a special role in medical applications. However, bibliometric studies have not been conducted in this field. Therefore, the aim of the present study was to conduct a bibliometric analysis to evaluate the global scientific output of MXene in biomedical research, explore the current situation of this field in the past years and predicte its research hotpots. <b>Methods:</b> We utilized visual analysis softwares Citespace and Bibliometrix to analyze all relevant documents published in the period of 2011-2022. The bibliometric records were obtained from the Web of Science Core Collection. <b>Results:</b> A total of 1,489 publications were analyzed in this study. We observed that China is the country with the largest number of publications, with Sichuan University being the institution with the highest number of publications in this field. The most publications on MXene medicine research in the past year were found primarily in journals about Chemistry/Materials/Physics. Moreover, ACS Applied Materials and Interfaces was found to be the most productive journal in this field. Co-cited references and keyword cluster analysis revealed that #antibacterial# and #photothermal therapy# are the research focus keyword and burst detection suggested that driven wearable electronics were newly-emergent research hot spots. <b>Conclusion:</b> Our bibliometric analysis indicates that research on MXene medical application remains an active field of study. At present, the research focus is on the application of MXene in the field of antibacterial taking advantage of its photothermal properties. In the future, wearable electronics is the research direction of MXene medical application. Bibliometrics ; Web of science ; Nanotechnology ; Field (mathematics) ; Biomedicine ; Computer science ; Data science ; Materials science ; Library science ; Political science ; MEDLINE ; Mathematics ; Bioinformatics MXene and MAX Phase Materials ; Nanoplatforms for cancer theranostics ; Graphene and Nanomaterials Applications
Authors: Ivan V. Moskalenko | Vladimir V. Shilovskikh | Pavel V. Nesterov | Alexander S. Novikov | Malika Omarova | R. V. Sadovnichii | Vladislav V. Gurzhiy | Nikita Orekhov | Ekaterina V. Skorb
Source: Crystals (article, 2023-08-25)
Field: Chemistry — Physical and Theoretical Chemistry

Supramolecular Assemblies of Melamine-2-Thiobarbiturate and Melamine-Barbiturate-2-Thiobarbiturate: Experimental and Theoretical Studies In this work, we considered the formation of supramolecular assemblies of melamine-thiobarbiturate and melamine-barbiturate-thiobarbiturate. It is known that thiobarbituric acid can form many tautomers, as well as different motifs due to the change of C2=O to C2=S hydrogen bonds. We formed the crystal. The resulting crystals were studied with scanning electron microscopy (SEM), optical fluorescence microscopy, single crystal and powder (PXRD) X-ray diffraction analyses, and solid state nuclear magnetic resonance (ss NMR). These systems were theoretically studied using density functional theory (DFT) and classical molecular dynamics (MD) simulations. Interestingly, just as in the case of melamine barbiturate, during the crystallization process, hydrogen from the C5 moiety of thiobarbituric acid migrates to the melamine molecule. In addition, the resulting melamine thiobarbiturate crystals exhibit fluorescence behavior in the red region (~565–605 nm), while the melamine barbiturate crystals are fluorescent in the green region (512–542 nm). Melamine ; Density functional theory ; Chemistry ; Supramolecular chemistry ; Hydrogen bond ; Powder diffraction ; Photochemistry ; Physical chemistry ; Molecule ; Crystallography ; Organic chemistry ; Computational chemistry Crystallography and molecular interactions ; Molecular Sensors and Ion Detection ; Crystal structures of chemical compounds
Authors: Alisa R. Bogdanova | Dmitry V. Krasnikov | Eldar M. Khabushev | Javier A. Ramirez B. | Yakov Matyushkin | Albert G. Nasibulin
Source: Nanomaterials (article, 2023-04-28)
Field: Materials Science — Materials Chemistry

Role of Hydrogen in Ethylene-Based Synthesis of Single-Walled Carbon Nanotubes We examined the effect of hydrogen on the growth of single-walled carbon nanotubes in the aerosol (a specific case of the floating catalyst) chemical vapor deposition process using ethylene as a carbon source and ferrocene as a precursor for a Fe-based catalyst. With a comprehensive set of physical methods (UV-vis-NIR and Raman spectroscopies, transmission electron microscopy, scanning electron microscopy, differential mobility analysis, and four-probe sheet resistance measurements), we showed hydrogen to inhibit ethylene pyrolysis extending the window of synthesis parameters. Moreover, the detailed study at different temperatures allowed us to distinguish three different regimes for the hydrogen effect: pyrolysis suppression at low concentrations (I) followed by surface cleaning/activation promotion (II), and surface blockage/nanotube etching (III) at the highest concentrations. We believe that such a detailed study will help to reveal the complex role of hydrogen and contribute toward the synthesis of single-walled carbon nanotubes with detailed characteristics. Carbon nanotube ; Materials science ; Hydrogen ; Catalysis ; Chemical engineering ; Ferrocene ; Ethylene ; Raman spectroscopy ; Nanotechnology ; Pyrolysis ; Carbon fibers ; Transmission electron microscopy ; Chemical vapor deposition ; Scanning electron microscope ; Sheet resistance ; Chemistry ; Organic chemistry ; Composite material ; Physical chemistry ; Electrochemistry ; Optics Carbon Nanotubes in Composites ; Graphene research and applications ; Chemical and Physical Properties of Materials
Authors: Samira Chouikh | Sabrina Cheikh | Ali Imessaoudene | Lotfi Mouni | Abdeltif Amrane | A. Benahmed | Noureddine Bettahar
Source: Sustainability (article, 2023-05-12)
Field: Materials Science — Materials Chemistry

Synthesis and Characterization of the Carbonate Hydrotalcites (NiAl-HT, CoAl-HT, and NiCoAl-HT), and Its Application for Removal of the Anionic Azo Dye Titan Yellow from Aqueous Solution This work focuses on studying the removal of Titan Yellow (TY) dye, which is a water pollutant using three matrices of layered double hydroxide (LDHs; M+2Al-HT), with M+2 = Ni, Co, or NiCo were synthesized using the co-precipitation technique in a solution with a constant pH. The X-ray diffraction (XRD) pattern of the formed solids shows that the synthesized phase is the LDH type with the average interlamellar distance (dspacing ≈ 7.595 Å). The Fourier-transform infrared spectroscopy (FT-IR) spectra were compared, before and after adsorption, confirming the displacement of the carbonated interlayers and confirmed the presence of the S=O bond in the dye under study. Thermogravimetric-differential thermal analysis (TG/DTG) shows temperatures of decarbonation of the LDHs. The BET specific surface areas of NiAl-HT, NiCoAl-HT, and CoAl-HT were found equal to 156.819 m2∙g−1, 142.72 m2∙g−1, and 56.98 m2∙g−1, respectively, and the SEM-EDX micrographs results confirmed the creation of the hydrotalcite type material. The UV–visible study of the adsorption of TY is performed by varying different parameters such as pH of the solution, mass, contact time, and temperature. The obtained isotherms from this kinetic study show that the adsorption of TY dye is more efficient in NiAl-HT. It can, therefore, be stated that the adsorption process of TY is endothermic and spontaneous. The results of this study could be extended to other anionic azo dyes having similar chemical structures. Hydrotalcite ; Layered double hydroxides ; Adsorption ; Endothermic process ; Aqueous solution ; BET theory ; Thermogravimetric analysis ; Fourier transform infrared spectroscopy ; Specific surface area ; Materials science ; Nial ; Chemistry ; Nuclear chemistry ; Chemical engineering ; Inorganic chemistry ; Physical chemistry ; Organic chemistry ; Catalysis Layered Double Hydroxides Synthesis and Applications ; Adsorption and biosorption for pollutant removal ; Nanomaterials for catalytic reactions
Authors: M. Shaheer Malik | Hissana Ather | Shaik Mohammad Asif Ansari | Ayesha Siddiqua | Qazi Mohammad Sajid Jamal | Ali Alharbi | Munirah M. Al‐Rooqi | Rabab S. Jassas | Essam M. Hussein | Ziad Moussa | Rami J. Obaid | Saleh A. Ahmed
Source: Pharmaceuticals (article, 2023-02-22)
Field: Chemistry — Organic Chemistry

Novel Indole-Tethered Chromene Derivatives: Synthesis, Cytotoxic Properties, and Key Computational Insights Indole-tethered chromene derivatives were synthesised in a one-pot multicomponent reaction using <i>N</i>-alkyl-1<i>H</i>-indole-3-carbaldehydes, 5,5-dimethylcyclohexane-1,3-dione, and malononitrile, catalysed by DBU at 60-65 °C in a short reaction time. The benefits of the methodology include non-toxicity, an uncomplicated set-up procedure, a faster reaction time, and high yields. Moreover, the anticancer properties of the synthesised compounds were tested against selected cancer cell lines. The derivatives <b>4c</b> and <b>4d</b> displayed very good cytotoxic activity, with IC<sub>50</sub> values ranging from 7.9 to 9.1 µM. Molecular docking revealed the potent derivatives have good binding affinity towards tubulin protein, better than the control, and the molecular dynamic simulations further demonstrated the stability of ligand-receptor interactions. Moreover, the derivatives followed all the drug-likeness filters. Malononitrile ; Indole test ; Chemistry ; Combinatorial chemistry ; Alkyl ; Stereochemistry ; Organic chemistry ; Catalysis Multicomponent Synthesis of Heterocycles ; Synthesis and biological activity ; Bioactive Compounds and Antitumor Agents
Authors: Jackson J. Alcázar | Alessandra C. Misad Saide | Paola R. Campodónico
Source: Journal of Cheminformatics (article, 2023-09-28)
Field: Chemistry — Organic Chemistry

Reliable and accurate prediction of basic pKa values in nitrogen compounds: the pKa shift in supramolecular systems as a case study This article presents a quantitative structure-activity relationship (QSAR) approach for predicting the acid dissociation constant (pK<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi></mml:mi> <mml:mi>a</mml:mi> </mml:msub> </mml:math>) of nitrogenous compounds, including those within supramolecular complexes based on cucurbiturils. The model combines low-cost quantum mechanical calculations with QSAR methodology and linear regressions to achieve accurate predictions for a broad range of nitrogen-containing compounds. The model was developed using a diverse dataset of 130 nitrogenous compounds and exhibits excellent predictive performance, with a high coefficient of determination (R<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mi></mml:mi> <mml:mn>2</mml:mn> </mml:msup> </mml:math>) of 0.9905, low standard error (s) of 0.3066, and high Fisher statistic (<i>F</i>) of 2142. The model outperforms existing methods, such as Chemaxon software and previous studies, in terms of accuracy and its ability to handle heterogeneous datasets. External validation on pharmaceutical ingredients, dyes, and supramolecular complexes based on cucurbiturils confirms the reliability of the model. To enhance usability, a script-like tool has been developed, providing a streamlined process for users to access the model. This study represents a significant advancement in pK<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi></mml:mi> <mml:mi>a</mml:mi> </mml:msub> </mml:math> prediction, offering valuable insights for drug design and supramolecular system optimization. Computer science ; Quantitative structure–activity relationship ; Usability ; Algorithm ; Machine learning ; Artificial intelligence ; Database ; Data mining Free Radicals and Antioxidants ; Crystallography and molecular interactions ; Computational Drug Discovery Methods
Authors: Hugo Cortes-Cano | Lilian I. Olvera | Emilia M. Méndez‐Aguilar | Beatriz Liliana España‐Sánchez | L.G. Arríaga | Goldie Oza | José Herrera-Celis
Source: Biosensors (article, 2023-11-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Surface Functionalization and Escherichia coli Detection Using Surface-Enhanced Raman Spectroscopy Driven by Functional Organic Polymer/Gold Nanofilm-Based Microfluidic Chip In this work, a microfluidic prototype based on polymeric materials was developed to monitor surface processes using surface-enhanced Raman spectroscopy (SERS), keeping the reagents free of environmental contamination. The prototype was fabricated on poly(methyl methacrylic acid) (PMMA). A micrometric membrane of a functional organic polymer (FOP) based on <i>p</i>-terphenyl and bromopyruvic acid monomers was formed on the PMMA surface to promote the formation of metal nanoclusters. Au nanosized film was deposited on the FOP membrane to give rise to the SERS effect. A microchannel was formed on another piece of PMMA using micromachining. A representative 3D model of the prototype layer arrangement was built and simulated in COMSOL Multiphysics<sup>®</sup> to approximate the electric field distribution and calculate the power enhancement factor as the Au film changes over time. The fabrication process was characterized using UV-visible and Raman spectroscopies and XPS. The prototype was tested using a Raman microscope and liquid solutions of cysteamine and <i>Escherichia coli</i> (<i>E. coli</i>). The simulation results demonstrated that the morphological characteristics of the Au layer give rise to the SERS effect, and the power enhancement factor reaches values as high as 8.8 × 10<sup>5</sup> on the FOP surface. The characterization results showed the formation of the FOP and the Au film on PMMA and the surface functionalization with amine groups. The Raman spectra of the prototype showed temporal evolution as different compounds were deposited on the upper wall of the microchannel. Characteristic peaks associated with these compounds were detected with continuous monitoring over time. This prototype offers many benefits for applications like monitoring biological processes. Some advantages include timely surface evaluation while avoiding environmental harm, decreased use of reagents and samples, minimal interference with the process by measuring, and detecting microorganisms in just 1 h, as demonstrated with the <i>E. coli</i> sample. Raman spectroscopy ; Surface modification ; Materials science ; Microchannel ; X-ray photoelectron spectroscopy ; Surface-enhanced Raman spectroscopy ; Polymer ; Chemical engineering ; Analytical Chemistry (journal) ; Microfluidics ; Nanotechnology ; Chemistry ; Organic chemistry ; Raman scattering ; Composite material Gold and Silver Nanoparticles Synthesis and Applications ; Biosensors and Analytical Detection ; Electrochemical Analysis and Applications