jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Grant J. Sherborne | Paul D. Kemmitt | Callum Prentice | Eli Zysman‐Colman | Andrew D. Smith | Charlene Fallan
Source: Angewandte Chemie International Edition (article, 2022-11-07)
Field: Chemistry — Organic Chemistry

Visible Light‐Mediated Cyclisation Reaction for the Synthesis of Highly‐Substituted Tetrahydroquinolines and Quinolines Condensation of 2-vinylanilines and conjugated aldehydes followed by an efficient light-mediated cyclisation selectively yields either substituted tetrahydroquinolines with typically high dr, or in the presence of an iridium photocatalyst the synthesis of quinoline derivatives is demonstrated. These atom economical processes require mild conditions, with the substrate scope demonstrating excellent site selectivity and functional group tolerance, including azaarene-bearing substrates. A thorough experimental mechanistic investigation explores multiple pathways and the key role that imine and iminium intermediates play in the absorption of visible light to generate reactive excited states. The synthetic utility of the reactions is demonstrated on gram scale quantities in both batch and flow, alongside further manipulation of the medicinally relevant products. Iminium ; Chemistry ; Quinoline ; Imine ; Combinatorial chemistry ; Iridium ; Substrate (aquarium) ; Conjugated system ; Photochemistry ; Organic chemistry ; Catalysis Radical Photochemical Reactions ; Catalytic C–H Functionalization Methods ; Sulfur-Based Synthesis Techniques
Authors: Emanuele Falbo | Marco Fusè | Federico Lazzari | Giordano Mancini | Vincenzo Barone
Source: Journal of Chemical Theory and Computation (article, 2022-09-27)
Field: Chemistry — Physical and Theoretical Chemistry

Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV–Vis Spectrum of TEMPO Radical in Different Solvents The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper we report our latest developments with specific reference to unsupervised atomistic simulations employing non periodic boundary conditions (NPBC) followed by clustering of the trajectories employing optimized feature spaces. Next accurate variational computations are performed for a representative point of each cluster, whereas intracluster fluctuations are taken into account by a cheap yet reliable perturbative approach. A number of methodological improvements have been introduced including, e.g., more realistic reaction field effects at the outer boundary of the simulation sphere, automatic definition of the feature space by continuous perception of solute-solvent interactions, full account of polarization and charge transfer in the first solvation shell, and inclusion of vibronic contributions. After its validation, this new approach has been applied to the challenging case of solvatochromic effects on the UV-vis spectra of a prototypical nitroxide radical (TEMPO) in different solvents. The reliability, effectiveness, and robustness of the new platform is demonstrated by the remarkable agreement with experiment of the results obtained through an unsupervised approach characterized by a strongly reduced computational cost as compared to that of conventional quantum mechanics and molecular mechanics models without any accuracy reduction. Computer science ; Statistical physics ; Chemistry ; Dimensionality reduction ; Chromophore ; Cluster analysis ; Robustness (evolution) ; Solvation ; Computational chemistry ; Physics ; Artificial intelligence ; Molecule ; Organic chemistry Photochemistry and Electron Transfer Studies ; Free Radicals and Antioxidants ; Spectroscopy and Quantum Chemical Studies
Authors: Haoyang Wu | Alon Grinberg Dana | Duminda S. Ranasinghe | Frank C. Pickard | Geoffrey P. F. Wood | Todd Zelesky | Gregory W. Sluggett | Jason Mustakis | William H. Green
Source: Molecular Pharmaceutics (article, 2022-04-18)
Field: Chemistry — Analytical Chemistry

Kinetic Modeling of API Oxidation: (2) Imipramine Stress Testing Gauging the chemical stability of active pharmaceutical ingredients (APIs) is critical at various stages of pharmaceutical development to identify potential risks from drug degradation and ensure the quality and safety of the drug product. Stress testing has been the major experimental method to study API stability, but this analytical approach is time-consuming, resource-intensive, and limited by API availability, especially during the early stages of drug development. Novel computational chemistry methods may assist in screening for API chemical stability prior to synthesis and augment contemporary API stress testing studies, with the potential to significantly accelerate drug development and reduce costs. In this work, we leverage quantum chemical calculations and automated reaction mechanism generation to provide new insights into API degradation studies. In the continuation of part one in this series of studies [Grinberg Dana et al., <i>Mol. Pharm.</i> 2021 18 (8), 3037-3049], we have generated the first <i>ab initio</i> predictive chemical kinetic model of free-radical oxidative degradation for API stress testing. We focused on imipramine oxidation in an azobis(isobutyronitrile) (AIBN)/H<sub>2</sub>O/CH<sub>3</sub>OH solution and compared the model's predictions with concurrent experimental observations. We analytically determined iminodibenzyl and desimipramine as imipramine's two major degradation products under industry-standard AIBN stress testing conditions, and our <i>ab initio</i> kinetic model successfully identified both of them in its prediction for the top three degradation products. This work shows the potential and utility of predictive chemical kinetic modeling and quantum chemical computations to elucidate API chemical stability issues. Further, we envision an automated digital workflow that integrates first-principle models with data-driven methods that, when actively and iteratively combined with high-throughput experiments, can substantially accelerate and transform future API chemical stability studies. Chemistry ; Chemical stability ; Computer science ; Computational chemistry ; Biochemical engineering ; Organic chemistry Analytical Methods in Pharmaceuticals ; Cholinesterase and Neurodegenerative Diseases ; Computational Drug Discovery Methods
Authors: Feng Tang | Yanzhou Li | Baoxing Zeng | Guoping Liu | Junwei Zhao | Lijuan Chen
Source: ACS Applied Materials & Interfaces (article, 2022-10-18)
Field: Materials Science — Materials Chemistry

Lamellar Nanocomposite Based on a 1D Crayfish-like Ce<sup>III</sup>-Substituted Phospho(III)tungstate Semiconductor and Polyaniline Used as a High-Performance Humidity Sensing Device In order to meet people's demand for intelligent management of daily life and health, manufacturing and developing humidity monitoring equipment with convenience, high sensitivity, easy miniaturization, and low cost is particularly important in the era of rapid development of artificial intelligence and the Internet of Things. Polyaniline (PANI) is an attractive humidity sensing material due to its designable functional properties. However, PANI modified polyoxometalates (POMs) for humidity sensing are still rare. As a proof of concept, a novel moisture sensing composite material was obtained based on PANI and a novel 1D rare-earth-substituted phospho(III)tungstate [H<sub>2</sub>N(CH<sub>3</sub>)<sub>2</sub>]<sub>9</sub>Na<sub>3</sub>H<sub>6</sub>[Ce<sub>2</sub>(H<sub>2</sub>O)<sub>3</sub>W<sub>5</sub>O<sub>13</sub>(C<sub>2</sub>O<sub>4</sub>)][HP<sup>III</sup>W<sub>9</sub>O<sub>33</sub>]<sub>2</sub>[(HP<sup>III</sup>)<sub>2</sub>W<sub>15</sub>O<sub>54</sub>]·42H<sub>2</sub>O (<b>1</b>). Notably, the anion structure of <b>1</b> contains trivacant Keggin-type [B-α-HP<sup>III</sup>W<sub>9</sub>O<sub>33</sub>]<sup>8-</sup> and Dawson-like [(HP<sup>III</sup>)<sub>2</sub>W<sub>15</sub>O<sub>54</sub>]<sup>10-</sup> subunits linked by a heterometallic [Ce<sub>2</sub>(H<sub>2</sub>O)<sub>3</sub>W<sub>5</sub>O<sub>32</sub>(C<sub>2</sub>O<sub>4</sub>)]<sup>30-</sup> cluster. Furthermore, the <b>1</b>/PANI composite shows a typical semiconductive characteristic with a "band-like" conductive mechanism. The fabricated <b>1</b>/PANI-based humidity sensing device exhibits a broad sensing range (11∼97% relative humidity), fast response/recovery time (3.45 s/3.24 s), good repeatability, and long-term stability (over 3 months). Additionally, the possible sensing mechanism is proposed. This work offers an enormous possibility for the design of high-performance humidity sensing materials through POM material chemistry. Materials science ; Humidity ; Tungstate ; Nanocomposite ; Polyaniline ; Semiconductor ; Composite number ; Nanotechnology ; Relative humidity ; Hygrometer ; Chemical engineering ; Optoelectronics ; Composite material ; Polymer ; Polymerization Polyoxometalates: Synthesis and Applications ; Conducting polymers and applications ; Gas Sensing Nanomaterials and Sensors
Authors: Igor Levchenko | Oleg Baranov | C. ̃Riccardi | H. Eduardo Roman | Uroš Cvelbar | Elena P. Ivanova | Mandhakini Mohandas | Patrik Ščajev | T. Malinauskas | Shuyan Xu | Kateryna Bazaka
Source: Advanced Materials Interfaces (article, 2022-11-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Nanoengineered Carbon‐Based Interfaces for Advanced Energy and Photonics Applications: A Recent Progress and Innovations Abstract As famed quantum physicist W. Pauli once said, “The surface was invented by the devil”. The nonequilibrium state of particles forming the surface, and the presence of dangling bonds transform the surfaces into a 2D reactor with high physical and chemical reactivity. When two such active surfaces are matched, their interface becomes even more reactive, giving rise to novel properties or enhanced performance. For this reason, much effort is applied to design nanoengineered interfacial systems for applications spanning all facets of human life. This review article discusses recent, mostly within two years, progress in the design of complex, sophisticated carbon‐based interfacial material systems for energy and photonics applications, with the aim to emphasize some of the most interesting and important examples of such systems. Differences in the processes that take place on flat and 3D (curved) surfaces are discussed, with the view of guiding the design and construction of complex functional interfaces, focusing on several points that are of particular importance to the ongoing development of advanced interfacial material systems. Nanotechnology ; Materials science ; Photonics ; Interface (matter) ; Surface (topology) ; Carbon fibers ; Engineering physics ; Physics ; Optoelectronics ; Composite material Supercapacitor Materials and Fabrication ; Advancements in Battery Materials ; Advanced battery technologies research
Authors: Rafael G. Araújo | Reyna Berenice González-González | Manuel Martínez-Ruiz | Karina G. Coronado-Apodaca | Humberto Reyes-Pardo | Zoé P. Morreeuw | Mariel Araceli Oyervides-Muñoz | Juan Eduardo Sosa‐Hernández | ‪Damià Barceló | Roberto Parra‐Saldívar | Hafiz M.N. Iqbal
Source: ACS Omega (review, 2022-09-08)
Field: Materials Science — Materials Chemistry

Expanding the Scope of Nanobiocatalysis and Nanosensing: Applications of Nanomaterial Constructs The synergistic interaction between advanced biotechnology and nanotechnology has allowed the development of innovative nanomaterials. Those nanomaterials can conveniently act as supports for enzymes to be employed as nanobiocatalysts and nanosensing constructs. These systems generate a great capacity to improve the biocatalytic potential of enzymes by improving their stability, efficiency, and product yield, as well as facilitating their purification and reuse for various bioprocessing operating cycles. The different specific physicochemical characteristics and the supramolecular nature of the nanocarriers obtained from different economical and abundant sources have allowed the continuous development of functional nanostructures for different industries such as food and agriculture. The remarkable biotechnological potential of nanobiocatalysts and nanosensors has generated applied research and use in different areas such as biofuels, medical diagnosis, medical therapies, environmental bioremediation, and the food industry. The objective of this work is to present the different manufacturing strategies of nanomaterials with various advantages in biocatalysis and nanosensing of various compounds in the industry, providing great benefits to society and the environment. Bioprocess ; Biochemical engineering ; Nanotechnology ; Reuse ; Scope (computer science) ; Nanocarriers ; Applications of nanotechnology ; Risk analysis (engineering) ; Computer science ; Materials science ; Drug delivery ; Engineering ; Business ; Waste management Advanced Nanomaterials in Catalysis ; Carbon and Quantum Dots Applications ; Electrochemical sensors and biosensors
Authors: Rupert L. Mayer | Manuel Matzinger | Anna Schmücker | Karel Stejskal | Gabriela Krššáková | Frédéric Berger | Karl Mechtler
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-09-02)
Field: Chemistry — Spectroscopy

Wide Window Acquisition and AI-based data analysis to reach deep proteome coverage for a wide sample range, including single cell proteomic inputs ABSTRACT A comprehensive proteome map is essential to elucidate molecular pathways and protein functions. Although great improvements in sample preparation, instrumentation and data analysis already yielded impressive results, current studies suffer from a limited proteomic depth and dynamic range therefore lacking low abundant or highly hydrophobic proteins. Here, we combine and benchmark advanced micro pillar array columns (µPAC™) operated at nanoflow with Wide Window Acquisition (WWA) and the AI-based CHIMERYS™ search engine for data analysis to maximize chromatographic separation power, sensitivity and proteome coverage. Our data shows that µPAC™ columns clearly outperform classical packed bed columns boosting peptide IDs by up to 140%. Already at classical narrow isolation widths CHIMERYS™ boosted ID rates by a factor of 2.6 compared to the conventional search engine MS Amanda 2.0. By combining CHIMERYS™ with WWA, even a 4.6-fold increase in ID rates could be achieved. Using our optimized workflow, we were further able to identify more than 10,000 proteins from a single 2 h gradient shotgun analysis. We further investigated the applicability of WWA for single cell inputs and found that the choice of the optimal isolation window width depends on sample input and complexity. Using a short 5.5 cm column and very high flow rates during loading and column equilibration we improved sample throughput to ∼100 samples per day while maintaining high protein ID numbers. We believe that this is especially important for the single cell field where throughput is one of the most limiting factors. Finally, we applied our optimized workflow on immunoprecipitations of Smarca5/SNF2H and found 32 additional interaction partners compared to the original workflow utilizing a packed bed column. These additional interaction partners include previously described interaction partners of Smarca5 like Baz2b as well as undescribed interactors including Arid1a, which is also involved in chromatin remodeling and has been described as key player in neurodevelopmental and malignant disorders. Proteome ; Chromatography ; Chemistry ; Microfluidics ; Benchmark (surveying) ; Computer science ; Sample (material) ; Throughput ; Biological system ; Analytical Chemistry (journal) ; Nanotechnology ; Materials science ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Protein Degradation and Inhibitors ; Monoclonal and Polyclonal Antibodies Research
Authors: Muhammad Naeem | Muhammad Omer Iqbal | Humaira Khan | Muhammad Masood Ahmed | Muhammad Farooq | Muhammad Moeen Aadil | Mohamad Ikhwan Jamaludin | Abu Hazafa | Wan-Chi Tsai
Source: Molecules (review, 2022-05-25)
Field: Chemistry — Organic Chemistry

A Review of Twenty Years of Research on the Regulation of Signaling Pathways by Natural Products in Breast Cancer Breast cancer (BC) is the second leading cause of death among women, and it has become a global health issue due to the increasing number of cases. Different treatment options, including radiotherapy, surgery, chemotherapy and anti-estrogen therapy, aromatase inhibitors, anti-angiogenesis drugs, and anthracyclines, are available for BC treatment. However, due to its high occurrence and disease progression, effective therapeutic options for metastatic BC are still lacking. Considering this scenario, there is an urgent need for an effective therapeutic strategy to meet the current challenges of BC. Natural products have been screened as anticancer agents as they are cost-effective, possess low toxicity and fewer side effects, and are considered alternative therapeutic options for BC therapy. Natural products showed anticancer activities against BC through the inhibition of angiogenesis, cell migrations, proliferations, and tumor growth; cell cycle arrest by inducing apoptosis and cell death, the downstream regulation of signaling pathways (such as Notch, NF-κB, PI3K/Akt/mTOR, MAPK/ERK, and NFAT-MDM2), and the regulation of EMT processes. Natural products also acted synergistically to overcome the drug resistance issue, thus improving their efficacy as an emerging therapeutic option for BC therapy. This review focused on the emerging roles of novel natural products and derived bioactive compounds as therapeutic agents against BC. The present review also discussed the mechanism of action through signaling pathways and the synergistic approach of natural compounds to improve their efficacy. We discussed the recent in vivo and in vitro studies for exploring the overexpression of oncogenes in the case of BC and the current status of newly discovered natural products in clinical investigations. PI3K/AKT/mTOR pathway ; MAPK/ERK pathway ; Protein kinase B ; Medicine ; Breast cancer ; Cancer ; Angiogenesis ; Cancer research ; Aromatase ; Pharmacology ; Signal transduction ; Biology ; Internal medicine Synthesis and biological activity ; Phytochemical compounds biological activities ; Biological Activity of Diterpenoids and Biflavonoids
Authors: Massih Sarif | Olga Jegel | Athanasios Gazanis | Jens Hartmann | Sergi Plana‐Ruiz | Jan Hilgert | Hajo Frerichs | Melanie Viel | Martin Panthöfer | Ute Kolb | Muhammad Nawaz Tahir | Jörg Schemberg | Michael Kappl | Ralf Heermann | Wolfgang Tremel
Source: Scientific Reports (article, 2022-03-10)
Field: Materials Science — Materials Chemistry

High-throughput synthesis of CeO2 nanoparticles for transparent nanocomposites repelling Pseudomonas aeruginosa biofilms Preventing bacteria from adhering to material surfaces is an important technical problem and a major cause of infection. One of nature's defense strategies against bacterial colonization is based on the biohalogenation of signal substances that interfere with bacterial communication. Biohalogenation is catalyzed by haloperoxidases, a class of metal-dependent enzymes whose activity can be mimicked by ceria nanoparticles. Transparent CeO<sub>2</sub>/polycarbonate surfaces that prevent adhesion, proliferation, and spread of Pseudomonas aeruginosa PA14 were manufactured. Large amounts of monodisperse CeO<sub>2</sub> nanoparticles were synthesized in segmented flow using a high-throughput microfluidic benchtop system using water/benzyl alcohol mixtures and oleylamine as capping agent. This reduced the reaction time for nanoceria by more than one order of magnitude compared to conventional batch methods. Ceria nanoparticles prepared by segmented flow showed high catalytic activity in halogenation reactions, which makes them highly efficient functional mimics of haloperoxidase enzymes. Haloperoxidases are used in nature by macroalgae to prevent formation of biofilms via halogenation of signaling compounds that interfere with bacterial cell-cell communication ("quorum sensing"). CeO<sub>2</sub>/polycarbonate nanocomposites were prepared by dip-coating plasma-treated polycarbonate panels in CeO<sub>2</sub> dispersions. These showed a reduction in bacterial biofilm formation of up to 85% using P. aeruginosa PA14 as model organism. Besides biofilm formation, also the production of the virulence factor pyocyanin in is under control of the entire quorum sensing systems P. aeruginosa. CeO<sub>2</sub>/PC showed a decrease of up to 55% in pyocyanin production, whereas no effect on bacterial growth in liquid culture was observed. This indicates that CeO<sub>2</sub> nanoparticles affect quorum sensing and inhibit biofilm formation in a non-biocidal manner. Pyocyanin ; Biofilm ; Quorum sensing ; Pseudomonas aeruginosa ; Nanoparticle ; Chemistry ; Bacterial growth ; Oleylamine ; Bacteria ; Microbiology ; Chemical engineering ; Materials science ; Nanotechnology ; Biology Advanced Nanomaterials in Catalysis ; Bacterial biofilms and quorum sensing ; Nanoparticles: synthesis and applications
Authors: Changyu Shang | Junyu Bu | Cui Song
Source: Materials (review, 2022-08-24)
Field: Materials Science — Materials Chemistry

Preparation, Antimicrobial Properties under Different Light Sources, Mechanisms and Applications of TiO2: A Review Traditional antimicrobial methods, such as antibiotics and disinfectants, may cause adverse effects, such as bacterial resistance and allergic reactions. Photocatalysts based on titanium dioxide (TiO<sub>2</sub>) have shown great potential in the field of antimicrobials because of their high efficiency, lack of pollution, and lack of side effects. This paper focuses on the antimicrobial activity of TiO<sub>2</sub> under different light sources. To improve the photocatalytic efficiency of TiO<sub>2</sub>, we can reduce electron-hole recombination and extend the photocatalytic activity to the visible light region by doping with different ions or compounds and compounding with polymers. We can also improve the surface properties of materials, increase the contact area with microorganisms, and further enhance the resistance to microorganisms. In addition, we also reviewed their main synthesis methods, related mechanisms, and main application fields to provide new ideas for the enhancement of photocatalytic microorganism performance and application popularization in the future. Photocatalysis ; Antimicrobial ; Compounding ; Materials science ; Titanium dioxide ; Nanotechnology ; Doping ; Microorganism ; Biochemical engineering ; Chemistry ; Optoelectronics ; Composite material ; Organic chemistry ; Biology ; Bacteria ; Catalysis Advanced Nanomaterials in Catalysis ; Advanced Photocatalysis Techniques ; TiO2 Photocatalysis and Solar Cells