jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yi Yu | Karl Börjesson
Source: arXiv (Cornell University) (preprint, 2022-05-16)
Field: Materials Science — Materials Chemistry

Chemical transformer compression for accelerating both training and inference of molecular modeling Transformer models have been developed in molecular science with excellent performance in applications including quantitative structure-activity relationship (QSAR) and virtual screening (VS). Compared with other types of models, however, they are large, which results in a high hardware requirement to abridge time for both training and inference processes. In this work, cross-layer parameter sharing (CLPS), and knowledge distillation (KD) are used to reduce the sizes of transformers in molecular science. Both methods not only have competitive QSAR predictive performance as compared to the original BERT model, but also are more parameter efficient. Furthermore, by integrating CLPS and KD into a two-state chemical network, we introduce a new deep lite chemical transformer model, DeLiCaTe. DeLiCaTe captures general-domains as well as task-specific knowledge, which lead to a 4x faster rate of both training and inference due to a 10- and 3-times reduction of the number of parameters and layers, respectively. Meanwhile, it achieves comparable performance in QSAR and VS modeling. Moreover, we anticipate that the model compression strategy provides a pathway to the creation of effective generative transformer models for organic drug and material design. Transformer ; Inference ; Computer science ; Quantitative structure–activity relationship ; Machine learning ; Training set ; Artificial intelligence ; Voltage ; Engineering Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Yehor S. Malets
Source: ChemRxiv (preprint, 2022-05-17)
Field: Chemistry — Physical and Theoretical Chemistry

Object approach to the organic molecule representation Object way of thinking about structure of organic molecule (functional groups, cycles) is common for professional synthetic chemists. In contrast, atom-level graph-based approaches mostly used for computing. Space, memory consumption and quantity of CPU/GPU cycles could be significantly reduced using next-level object abstractions which lead to another way of linear molecule recording. Perspectives of this concept are discussed. Object (grammar) ; Computer science ; Representation (politics) ; Graph ; Contrast (vision) ; Theoretical computer science ; Atom (system on chip) ; Organic molecules ; Molecule ; Space (punctuation) ; Artificial intelligence ; Chemistry ; Parallel computing ; Organic chemistry Various Chemistry Research Topics ; Computational Drug Discovery Methods ; Molecular spectroscopy and chirality
Authors: Christoph Selg | Anna Hartmann | I Amaechi | A Youssef | A Drfler | Y Gonzlez | R Katoch | A Ruediger | G Lei | Yu | M Scharnhlz | P Coburger | L Gravogl | D Klose | J Gamboa-Carballo | D Horvth | A Vgner | D Szikra | G Trencsnyi | N Demitri | N Guidolin | A Maiocchi | S Ghiani | F Travagin | G Giovenzana | Z Baranyai | G.-Q Jin | D.-E Sun | X Xia | Z.-F Jiang | B Cheng | Y Ning | F Wang | Y Zhao | X Chen | J.-L Zhang | W Zhang | L Yang | X Yan | W Tian | Z Liu | Z Lin | Z Deng | X Qu | S.-C Wang | Q.-S Zhang | Z Wang | L Zheng | X.-D Zhang | Y.-N Fan | P.-Y Fu | X.-H Xiong | M Pan* E ; | M Vzquez-Nakagawa | L Rodrguez-Prez | N Martn | * Herranz | D Jang | J.-M Heo | F Jannah | M Khazi | Y Son | J Noh | H An | S Park | D Yoon | N Kadamannil | R Jelinek | * J.-M Kim | D Obi | N Frey | D Dickie | C Webster | * Gilliard | Satyam Saurabh | M Mandar | Sujit Shirolkar | Ghosh | Dienes With | Prochiral Silanes | L Wang | W Lu | J Zhang | Q Chong | * Meng | R Sharma | T Rajanbabu | B Raya | S Jing | V Balasanthiran
Source: Angewandte Chemie International Edition (article, 2022-10-18)
Field: Chemistry — Organic Chemistry

Graphical Abstract: Angew. Chem. Int. Ed. 43/2022 is reported by Oleg V. Larionov and co-workers in their Research Article (e202210525), as illustrated in the cover picture.The reaction is enabled by radicalophilic reactivity of the sulfinyl sulfones shown in the top left that is distinct from the known dissociation and nucleophilic substitution pathways.Given the importance of carboxylic acids and sulfoxides for medicinal chemistry, agroscience, and organic synthesis, decarboxylative sulfination addresses the unmet need for a direct interconversion between the two functional groups and provides access to new sulfoxide chemical space. BioanalyticsDual-modal NIRF-SIMS imaging achieved by using clickable lanthanide molecular probes is reported by Yao Zhao, Xing Chen, Jun-Long Zhang et al. in their Research Article (e202208707). Microporous MaterialsZhangjing Zhang and co-workers report in their Communication (e202207579) an ultramicroporous hydrogen-bonded organic framework with a suitable pore environment and electrostatic potential distribution fitting well to C 2 H 2 . INT ; Chemistry ; Computer science ; Materials science ; Programming language Click Chemistry and Applications ; Fluorine in Organic Chemistry ; Cyclopropane Reaction Mechanisms
Authors: M. Antonia Martín
Source: Advances in Analytic Science (article, 2022-04-09)
Field: Chemistry — Organic Chemistry

Natural and synthetic cavitands: Challenges in chemistry and pharmaceutical technology &lt;span&gt;Supramolecular chemistry involves non-covalent interactions and specific molecular recognition of molecules/analytes by host molecules or supramolecules. These events are present in synthesis, catalysis, chiral separations, design of sensors, cell signaling processes and drug transport by carriers. The typical behavior of supramolecules is derived from their ability to build well-structured self-assembled and self-organized entities. Cavitands are a particular group of supramolecules possessing a cavity capable to include a variety of compounds thanks to host-guest non-covalent interactions developed among cavitands and analytes. Some typical cavitands are crown ethers, calixarenes, cucurbiturils, porphyrins and cyclodextrins. The two latter families are natural product cavitands that are generally considered models for molecular recognition of cations and organic and inorganic guest molecules, being attractive host molecules from the sustainability point of view. The natural cyclodextrins (α, β and γ-cd) are obtained with reasonable cost by enzymatic treatment of starch under adequate temperature conditions. They are profusely used in pharmaceutical, food and cosmetic industries due to their very low toxicity and side effects. This review is focused on the relevance andapplications of cyclodextrins in pharmaceuticaltechnology for their ability to increase solubility and stabilize drug molecules, thereby enhancing their bioavailability. The association of cyclodextrins with diverse nanostructured materials, i.e., carbon nanotubes, magnetic nanoparticles, silica and molecularly imprinted polymers, allows to synergize the properties of cyclodextrins and these nanostructured materials to reach highly specific molecular recognition of analytes. The exploitation of these benefits for analytical sample pre-treatment and chiral chromatographic separations are described. The use of cyclodextrins as mobile phases additives in hplc provides interesting results for green and sustainable chromatographic separations. Polymers incorporating cyclodextrins show exceptional adsorption properties for retaining toxic compounds and persistent organic pollutants from soils and water samples, allowing satisfactory recoveries of these environmental samples according to the stockholm convection principles.&lt;/span&gt; Chemistry ; Cucurbituril ; Calixarene ; Supramolecular chemistry ; Combinatorial chemistry ; Molecule ; Host–guest chemistry ; Molecular recognition ; Nanotechnology ; Organic chemistry ; Materials science Inorganic and Organometallic Chemistry
Authors: Safaa Ibrahim Mohammed | Thaer Abed Hallow | Dawood H. Mohammed
Source: International Journal of Health Sciences (article, 2022-08-23)
Field: Chemistry — Physical and Theoretical Chemistry

Improvement of octane number of Gasoline by using rubber waste In this study, the octane number of gasoline was improved by using isobutanol isobutanol prepared in the treatment of tire inner rubber with kerosene at different temperatures and in different quantities, and then treated with concentrated capranic acid and water. Then, the formed alcohol and water are separated from the acid kerosene using fractional distillation, where the water and alcohol are separated, leaving the acid and kerosene, and then the distilled liquid (isertoy mixture) is heated on a column containing sodium tetramer. And mixed by 1, 1.5, 3, and 5% with gasoline, where the octane number was raised. Cassiochromatographic octane number assays were performed. Gasoline ; Kerosene ; Isobutanol ; Octane ; Distilled water ; Distillation ; Chemistry ; Octane rating ; Chromatography ; Natural rubber ; Alcohol ; Organic chemistry Various Chemistry Research Topics
Authors: Athraa Al | Muthana S. Mashkour | Muthana Saleh Mashkour | M Li | W Xu | Y Su | S Grg | S Bonam | M Sekar | G Guntuku | S Nerella | A Pawar | Km | S Challa | I Shogar | U Marx | T Akabane | T Andersson | E Baker | M Beilmann | S Beken | D Freedman | J Song | P Sun | Ji Li | J | J Rose | J Davis | Shaw Tronieri | J Wadden | T Berkowitz | R Chao | A Pearl | R Alamuddin | N | J Hawley | P Sassone-Corsi | J Zierath | E Fottrell | N Ahmed | J Morrison | A Kuddus | S Shaha | C King | X Gao | Y Wen | D Qu | L An | S Luan | W Jiang | S Meena | J Blankenburg | K Maciol | C Hahn | H Frey | N Hussein | R Maeah | Z Sharba | B Aasoon | G Sulaiman | A Taha | G Bayarsaikhan | A Avan | S eki | R ; Apak | Swati Sadhana Rajput ; Mansi Sathe | Patel | A Amal | Bajrai | Essam Ezzeldin | A Khalid | Mohammad Al-Rashood | Muzaffar Raish | Iqbal | T | S | Al-Ghabsha | M | Al-Abachi
Source: Journal of Pharmaceutical Negative Results (article, 2022-01-01)
Field: Chemistry — Analytical Chemistry

Spectrophotometric Determination Of Anti-Obesity Drug (Lorcaserin) By Azo Coupling Reaction With Brady’s Reagent The dedication of lorcaserin in its pure form and pharmaceutical preparations, with a simple, exact, precision, accurate and managed spectrophotometric technique is studied. The azo coupling reaction of dinitrophenylhydrazine (2,4DNPH) reagent oxidized by potassium iodate with lorcaserin in alkaline medium. The optimum conditions for the formation of the azo coupling dye were studied from the impact of the reagent's extent and the volume of concentrated H2SO4, concentration and volume of oxidizing agent KIO3, volume of NaOH, the quick response of time and the temperature effect. This method obeys Beer's law with concentrations ranging from (25-500) g. mL -1 at max wavelength 590 nm. The Calculated values from the current study were LOD = 0.523 g. mL -1 , LOQ = 1.743 g. mL -1 , linearity coefficient = 0.9990, sandals sensitivity =0. 294g.cm - and stabilization constant is 5. 110 8 .The proposed method has been successfully applied for the dedication of lorcaserin in its pharmaceutical preparations. Reagent ; Chemistry ; Drug ; Chromatography ; Pharmacology ; Medicine ; Organic chemistry Analytical Methods in Pharmaceuticals
Authors: Ranjith P. Karuvalam | Angel Ignatious | C. Yohannan Panicker | B. Sureshkumar | Stevan Armaković | Sanja J. Armaković | Christian Van Alsenoy | P.L. Anto
Source: ChemRxiv (preprint, 2022-02-17)
Field: Chemistry — Organic Chemistry

Spectroscopic characterization, docking studies and reactive properties by DFT calculations of halogen substituted 6-Chloro-N-(3-iodo-4-methylphenyl)-pyrazine-2-carboxamide with MD simulations. The spectral characterization of 6-Chloro-N-(3-iodo-4-methylphenyl)-pyrazine-2-carboxamide (CIMPPC) was executed by FT-IR and FT-Raman spectroscopic methods and density functional theory (DFT) computations have been carried using B3LYP/gen method. On the basis of potential energy distribution (PED) the vibrational assignments of the wavenumbers were proposed. NBO analysis was performed to study donor acceptor interactions. Halogen substitution results in increase in the µ (chemical potential) value in comparison with the parent molecule, which is a minimum. Halogen substitution also results a decrease in electrophilicity index. Fundamental reactive properties of the title molecule is investigated by MEP analysis. Visualization of ALIE and Fukui functions evaluated the most probable sites for electrophilic attacks. Exposure of the title compound towards autoxidation and hydrolysis is evaluated using BDE and RDF. The compatible nature of the compound is investigated through the Hildebrand solubility parameter. CIMPPC exhibit inhibitory activity against the anti-inflammatory receptor transient receptor potential cation channel. Natural bond orbital ; Chemistry ; Computational chemistry ; Pyrazine ; Density functional theory ; Molecule ; Electrophilic substitution ; Halogen ; Carboxamide ; Stereochemistry ; Organic chemistry Synthesis and biological activity ; Nonlinear Optical Materials Research ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Mosaad S. Mohamed | Samir M. Awad | Neama Abdallah Abd El-tawab | Naglaa Ahmed
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2022-07-30)
Field: Chemistry — Organic Chemistry

An overview on synthesis and biological activity of pyrimidines Pyrimidines represent an important class of heterocycles containing two nitrogen atoms at position 1 and 3 of the six membered ring show wide range of biological activities. Numerous methods for the synthesis of pyrimidine and their diverse reactions offer enormous scope in the field of medicinal chemistry. Pyrimidine possesses wide spectrum of biological activities including antitubercular, antibacterial, antifungal, antiviral, anti-inflammatory, antimalarial, anticancer, and anti-HIV activity. The present review attempts to give brief information about the synthesis and various biological activities of pyrimidines and their derivatives. Computational biology ; Chemistry ; Biology Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Xing Shi | Zhihui Wu | Tianyun Jin | Cili Wang | Pinglin Li
Source: Research Square (preprint, 2022-04-18)
Field: Chemistry — Organic Chemistry

Structural investigation of aaptourinamine by a time-saving module-assembly based calculation Abstract Unambiguously confirming natural products with high C/H ratio or proton-deficient and multi heteroatoms is challenging. A time-saving module-assembly calculation method named ‘Dooerafa’ including of constructing the meta-structures by a grafting method based on the crucial and the limited two dimensional nuclear magnetic resonance (2D NMR) correlations, ‘ring-contraction strategy’ based on mechanic force field and quantum chemical theory, and self-assemble calculations in Python programing for shaping up the structural candidates along with DFT-GIAO calculation was studied. And this method, verified by a known alkaloid spiroreticulatine with structure determined by X-ray diffraction, was performed for the structural elucidation of aaptourinamine which was isolated from marine sponge Aaptos suberitoides , showing us a brand new scaffold of imidazo[4,5,1-ij]pyrrolo[3,2-f]quinolin-7(8H)-one which has a biosynthetically relationship with the bioactive and structurally unique aaptamine alkaloid. Heteroatom ; Python (programming language) ; Chemistry ; Structural motif ; Stereochemistry ; Ring (chemistry) ; Computational chemistry ; Computer science ; Organic chemistry Synthesis and Reactivity of Heterocycles ; Synthesis and Characterization of Pyrroles ; Chemical synthesis and alkaloids
Authors: Miguel Reina | Eduardo Gabriel Guzmán‐López | Annia Galano
Source:  (preprint, 2022-07-01)
Field: Chemistry — Organic Chemistry

Computational Design of Rasagiline Derivatives: Searching for Enhanced Antioxidant Capability A set of new rasagiline derivatives is presented. They were designed to be antioxidant compounds with the potential to be used for treating neurodegenerative disorders. They are expected to be multifunctional molecules that can help reduce oxidative stress, which is thought to contribute to neurodegenerative disorders. The CADMA-Chem computational protocol was used to produce rasagiline derivatives and to evaluate their likeliness as oral drugs and antioxidants. Three of them were identified as the most promising ones. They are proposed to be better free radical scavengers than rasagiline. In addition, they are expected to keep the parent’s molecule neuroprotective capability. Hopefully, the results presented here would promote further experimental and theoretical investigations on these compounds. Rasagiline ; Neuroprotection ; Antioxidant ; Oxidative stress ; Combinatorial chemistry ; Chemistry ; Pharmacology ; Computer science ; Nanotechnology ; Parkinson's disease ; Materials science ; Organic chemistry ; Biochemistry ; Medicine Free Radicals and Antioxidants ; Synthesis and biological activity ; Computational Drug Discovery Methods
Authors: Colin P. Pilkington | Claudia Contini | Joseph D. Barritt | Paul A Simpson | John M. Seddon | Yuval Elani
Source: ChemRxiv (preprint, 2022-09-26)
Field: Materials Science — Materials Chemistry

A microfluidic platform for the controlled synthesis of higher-order liquid crystalline nanoparticles Soft-matter nanoparticles are of great interest in biotechnology, particularly for fields such as therapeutic delivery and in vivo imaging. Underpinning this is their biocompatibility, potential for selective targeting, attractive pharmacokinetic properties, and amenability to downstream functionalisation. Morphological diversity inherent to soft-matter particles can give rise to enhanced functionality. However, this diversity remains underexplored, and only the simplest of particle architectures (spherical lipid vesicles and lipid/polymer nanoparticles (LNPs)) have been exploited at a clinical level. This is largely due to limitations associated with existing particle synthesis methods that rely on poorly controlled bulk mixing conditions and high-energy input. To address this, we have designed a scalable microfluidic hydrodynamic focusing (MHF) technology for the controllable, rapid, and continuous production of lyotropic liquid crystalline (LLC) nanoparticles (both cubosomes and hexosomes); colloidal dispersions of higher-order lipid assemblies with intricate internal structures of 3-D and 2-D symmetry. These particles have been proposed as the next generation of soft-matter nano-carriers, with unique fusogenic and physical properties. Using our platform, we produce stable nanoparticles with varied architectural features. Crucially, our microfluidic method gives unprecedented control over LLC size, a feature we go on to exploit in fusogenic studies with model cell membranes, in which a dependency on particle diameter is evident. We believe our platform has the potential to serve as a tool for future studies around non-lamellar soft nanoparticles, and anticipate it to allow for the rapid prototyping of LLC particles of diverse functionality, paving the way toward their eventual uptake at an industrial level. Nanotechnology ; Microfluidics ; Nanoparticle ; Soft matter ; Materials science ; Particle (ecology) ; Drug delivery ; Dissipative particle dynamics ; Vesicle ; Membrane ; Polymer ; Chemistry ; Colloid ; Engineering ; Chemical engineering Pickering emulsions and particle stabilization ; Surfactants and Colloidal Systems ; Lipid Membrane Structure and Behavior
Authors: Amarachi G Kalu Chekwube A Ezegbe
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2022-03-04)
Field: Chemistry — Organic Chemistry

POLYMERIC MICROPARTICLES FORMULATION OF INSULIN FOR ORAL DRUG DELIVERY <strong><em>Aim</em></strong><em>: To investigate the use of polymers with mucoadhesive properties. <strong>Method</strong>: Microparticles were formed using double emulsion technique (w/o/w) with the insulin loaded at the core of the particles. Gelatin, Polyethylene glycol 4000 (PEG-4000), Eudragit<sup>®</sup> S 100, snail mucin and sodium alginate polymers were combined at different ratios and investigated. The subsequent batches, W (Gelatin-PEG 4000), were characterized for particle size, morphology and polydispersity index (PDI). The stability of the formulations were evaluated using pH and Differential Scanning Calorimeter (DSC). In vitro drug release profile and in vivo study using diabetic rat model were carried out on the formulations. <strong>Results</strong>: The batches in W, had rough spherical shapes except for batch Z3 which was rod-like and smooth. Particle size ranged from 12.24 µm ± 0.1 to 23.57 µm ± 2.3 (batch W). PDI of the optimized batches were W2 (0.884 ± 0.11), W3 (0.431 ± 0.30), W5 (0.407 ± 0.64). The pH of the formulations showed an increase from 6.4 to 6.6 (at 24 h) to 7.4 – 7.8 (after one month) on storage for batches W, indicating a secondary microbial degradation. The encapsulation efficiency across all batches were greater than 76.4 %, and the loading capacities were between 2.48 to 5.24 %. The DSC thermogram showed that when compared with a commercial sample of insulin, that the sub-batches of batch W showed greater stability than the reference sample. <strong>Conclusion</strong>: Polymers of mucoadhesive properties can be used to formulate insulin for oral drug delivery, and they also have potential control release ability. </em> <em> <strong>Keywords:</strong> Diabetes mellitus, Insulin, Microparticles, Polymers. </em> Insulin delivery ; Drug delivery ; Drug ; Insulin ; Medicine ; Pharmacology ; Diabetes mellitus ; Internal medicine ; Materials science ; Nanotechnology ; Endocrinology ; Type 1 diabetes Chemical Synthesis and Reactions ; Polymer Synthesis and Characterization
Authors: MAGNUS ONYEMAECHI OGBU | M. B. Fugu | A. M. Fulata | C. V. Nnam-Obi | D. E. Ndukwu
Source: Asian Journal of Applied Chemistry Research (article, 2022-04-14)
Field: Chemistry — Organic Chemistry

Isolation and Characterisation of Haemanthamine Alkaloid from Daffolis Extract using NMR and Mass Spectroscopic Techniques The recent surge in drug resistance and failure is belief to be a factor in the trend for the isolation of natural products from plants and other sources. This is largely due to the efficacy and safety of their components. Haemanthamine is an alkaloid of Amaryllidaceae family, the compound was reported to have lots of medicinal effects against microbes and some forms of cancers with significantly low or no side effects. The plant Daffodil is one of the commonest reservour of this alkaloid and used traditionally in the treatment of urinary disease, headache, fever, swelling growth, joint ailments, skin diseases, bruises, sprains, respiratory problems, gastrointestinal disorders among others. These medicinal potential of the plant stimulated our interest to isolate and characterized the Haemanthamine alkaloids from the plant using NMR and Mass Spectroscopic Techniques. The results obtained are in good agreement with the previously reported literatures which indicate that Haemanthamine was successfully isolated. Alkaloid ; Isolation (microbiology) ; Traditional medicine ; Medicine ; Chemistry ; Biology ; Stereochemistry ; Microbiology Chemical synthesis and alkaloids