jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sreelakshmi Mekkattu Tharayil | Mithun C. Mahawaththa | Akiva Feintuch | Ansis Maļeckis | Sven Ullrich | Richard Morewood | Thomas Huber | Christoph Nitsche | Daniella Goldfarb | Gottfried Otting
Source:  (preprint, 2022-06-10)
Field: Materials Science — Materials Chemistry

Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine Abstract. The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag that reacts selectively with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between lanthanoid ion and protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP), (ii) reaction of the cyano groups with α-cysteine, penicillamine or β-cysteine to complete the lanthanide chelating moiety and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb3+ and Tm3+ ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-amino thiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron–electron resonance experiments after titration with Gd3+ ions. Lanthanide ; Chemistry ; Selenocysteine ; Cysteine ; Electron paramagnetic resonance ; Titration ; Crystallography ; Ion ; Stereochemistry ; Inorganic chemistry ; Nuclear magnetic resonance ; Organic chemistry Lanthanide and Transition Metal Complexes ; Electron Spin Resonance Studies ; Hemoglobin structure and function
Authors: Pamela Isabel Japura Huanca | Bianca Araújo Fernandes Veras | Igor de Sousa Oliveira | Sávio Benvindo Ferreira
Source:  (article, 2022-11-14)
Field: Chemistry — Spectroscopy

In Silico Analysis Applied to the Study of Cytotoxicity in Natural Products With the emergence of technological advances, computational analysis in research has become promising by enabling the emergence of scientific production without the need for an experimental laboratory, and it has therefore begun to be used in various sectors, including cytotoxicity. From this perspective, the main objective of this study is to understand the importance of computational analysis for the study of cytotoxicity in natural products in addition to understanding scientific advances on this topic. Thus, this is a narrative-type bibliographic review, carried out between March and September 2022, through the digital databases of Pubmed, SciELO, and the Virtual Health Library with the adoption of the search formula configured with the available descriptors: &ldquo;in silico analysis&rdquo;, &ldquo;cytotoxic&rdquo;, and &ldquo;natural products&rdquo;. This work reaffirmed the importance of computer simulations on cytotoxicity in natural products and provided verification that these types of analyses are a source of knowledge about the structures of natural products, emphasizing the use of in silico analysis of cytotoxic agents, anticancer action, and the treatment of other pathologies. With regard to effectiveness, it is clear that the software reflects results that are similar to studies carried out in vivo. It is noteworthy that the in silico method has an accentuated scientific importance as it allows for a greater adaptability and a lower cost of time and space for research. Thus, such methodology becomes essential in the process of cytotoxicity analysis, obtaining great potential in pharmacological research. In silico ; Cytotoxicity ; Computer science ; Natural (archaeology) ; Computational biology ; Biochemical engineering ; Chemistry ; Engineering ; Biology ; Biochemistry ; In vitro Analytical Chemistry and Chromatography ; Computational Drug Discovery Methods ; Essential Oils and Antimicrobial Activity
Authors: Agustami Sitorus | Ravipat Lapcharoensuk
Source: INMATEH Agricultural Engineering (article, 2022-08-31)
Field: Chemistry — Analytical Chemistry

A COMPREHENSIVE OVERVIEW OF NEAR INFRARED AND INFRARED SPECTROSCOPY FOR DETECTING THE ADULTERATION ON FOOD AND AGRO-PRODUCTS—A CRITICAL ASSESSMENT In the past decade, fast and non-destructive methods based on spectroscopy technology have been studied to detect and discriminate against food adulteration and agro-products. Numerous linear and nonlinear chemometric approaches have been developed for spectroscopy analysis. Recently, various approaches have been developed for spectroscopic calibration modeling to detect and discriminate adulteration food and agro-products. This article discusses the application of spectroscopy technology, including near infrared and infrared, in detecting and discriminating the adulteration of food and agro-products based on recent research and delivered a critical assessment on this topic to serve as lessons from current studies and future outlooks. The current state-of-the-art techniques, including detection and classification of various adulteration in food and agro-products, have been addressed in this paper. Key findings from this study, near infrared and infrared spectroscopy is a non-destructive, rapid, simple-preparation, analytical rapidity, and straightforward method for classification and determination of adulteration in the food and agro-products so it is suitable for large-scale screening and on-site detection. Although there are still some unsatisfactory research results, especially in detecting tiny adductors, these technologies can potentially detect any adulteration in the various food and agro-products at an economically viable level, at least for the initial screening process. In that respect, near infrared and infrared spectroscopy should be expanded to cover all food and agro-products sold in the market. Only then will there be an acceptable deterrent in place to stop adulteration activity in widely consumed food and agro-products ingredients. Food products ; Near-infrared spectroscopy ; Biochemical engineering ; Infrared spectroscopy ; Environmental science ; Computer science ; Process engineering ; Food science ; Chemistry ; Engineering ; Biology Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Identification and Quantification in Food
Authors: Ganyu Chen | Peichen Shi | Longhui Zeng | Liubin Feng | Xiuxiu Wang | Xujing Lin | Yibin Sun | Hongxun Fang | Xiaoyu Cao | Xinchang Wang | Liulin Yang | Zhong‐Qun Tian
Source: Chemical Science (article, 2022-01-01)
Field: Materials Science — Biomaterials

Supramolecular copolymerization through self-correction of non-polymerizable transient intermediates Kinetic control over structures and functions of complex assembly systems has aroused widespread interest. Understanding the complex pathway and transient intermediates is helpful to decipher how multiple components evolve into complex assemblies. However, for supramolecular polymerizations, thorough and quantitative kinetic analysis is often overlooked. Challenges remain in collecting the information of structure and content of transient intermediates <i>in situ</i> with high temporal and spatial resolution. Here, the unsolved evolution mechanism of a classical self-sorting supramolecular copolymerization system was addressed by employing multidimensional NMR techniques coupled with a microfluidic technique. Unexpected complex pathways were revealed and quantitatively analyzed. A counterintuitive pathway involving polymerization through the 'error-correction' of non-polymerizable transient intermediates was identified. Moreover, a 'non-classical' step-growth polymerization process controlled by the self-sorting mechanism was unraveled based on the kinetic study. Realizing the existence of transient intermediates during self-sorting can encourage the exploitation of this strategy to construct kinetic steady state assembly systems. Moreover, the strategy of coupling a microfluidic technique with various characterization techniques can provide a kinetic analysis toolkit for versatile assembly systems. The combined approach of coupling thermodynamic and kinetic analyses is indispensable for understanding the assembly mechanisms, the rules of emergence, and the engineering of complex assembly systems. Copolymer ; Supramolecular chemistry ; Transient (computer programming) ; Polymer chemistry ; Chemistry ; Materials science ; Organic chemistry ; Computer science ; Polymer ; Molecule Supramolecular Self-Assembly in Materials ; Advanced Polymer Synthesis and Characterization ; Supramolecular Chemistry and Complexes
Authors: Muhammad Shafiq Bin Mohd Yusof | Hongwei Song | Tushar Debnath | Bethany Lowe | Minghui Yang | Zhi-Heng Loh
Source: Physical Chemistry Chemical Physics (article, 2022-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

Ultrafast proton transfer of the aqueous phenol radical cation Proton transfer (PT) reactions are fundamental to numerous chemical and biological processes. While sub-picosecond PT involving electronically excited states has been extensively studied, little is known about ultrafast PT triggered by photoionization. Here, we employ femtosecond optical pump-probe spectroscopy and quantum dynamics calculations to investigate the ultrafast proton transfer dynamics of the aqueous phenol radical cation (PhOH˙<sup>+</sup>). Analysis of the vibrational wave packet dynamics reveals unusually short dephasing times of 0.18 ± 0.02 ps and 0.16 ± 0.02 ps for the PhOH˙<sup>+</sup> O-H wag and bend frequencies, respectively, suggestive of ultrafast PT occurring on the ∼0.1 ps timescale. The reduced potential energy surface obtained from <i>ab initio</i> calculations shows that PT is barrierless when it is coupled to the intermolecular hindered translation between PhOH˙<sup>+</sup> and the proton-acceptor water molecule. Quantum dynamics calculations yield a lifetime of 193 fs for PhOH˙<sup>+</sup>, in good agreement with the experimental results and consistent with the PT reaction being mediated by the intermolecular O⋯O stretch. These results suggest that photoionization can be harnessed to produce photoacids that undergo ultrafast PT. In addition, they also show that PT can serve as an ultrafast deactivation channel for limiting the oxidative damage potential of radical cations. Aqueous solution ; Phenol ; Proton ; Chemistry ; Ultrashort pulse ; Photochemistry ; Radical ion ; Organic chemistry ; Ion ; Physics ; Laser Photochemistry and Electron Transfer Studies ; Spectroscopy and Quantum Chemical Studies ; Photoreceptor and optogenetics research
Authors: Xu Yang | Dongli Cao | Haiyu Ji | Yingying Feng | Juan Yu | Anjun Liu
Source: Journal of Food Quality (article, 2022-09-15)
Field: Chemistry — Analytical Chemistry

Optimization of Extraction of Compound Flavonoids from Chinese Herbal Medicines Based on Quantification Theory and Evaluation of Their Antioxidant Activity Plant-derived flavonoids have been attracting increasing research interest because of their multiple health promoting effects, where numerous investigations were carried out on the optimization of extraction and bioactivities. This study aims to optimize the extraction process of compound flavonoids (CFs) from Chinese herbal medicines and detect their antioxidant activity in vitro. CFs were extracted from the raw materials named “medicine food homology,” composed of hawthorn, lotus leaf, tartary buckwheat, cassia seed, Lycium barbarum, and Poria cocos in a mass ratio of 4 : 2 : 2 : 1.5 : 1 : 1. L9 (34) orthogonal design, level effect and engineering average estimation, and quantification theory were utilized to improve the extraction method of CFs, and the predictive model for CFs yield was constructed. The 2,2ʹ-diphenyl-1-picrylhydrazyl (DPPH), 2,2ʹ-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), hydroxyl radical scavenging rate, and reducing power of CFs were measured. The highest CFs yield was obtained under the following extraction condition: liquid-solid ratio of 35 : 1 mL/g, extraction temperature of 75°C, extraction duration of 75 min, and extraction mode enzyme-assisted extraction. The forecasted yield was 37.62%. The result was accurate and the established prediction equation was reliable (R = 0.95). The antioxidant activity of CFs was significantly positively correlated with the concentration from 0.05 to 0.4 mg/mL. The DPPH, ABTS, hydroxyl radical scavenging abilities, and the reducing power of CFs were 81.82 ± 1.75%, 49.35 ± 0.09%, 89.78 ± 0.66%, and 0.232 ± 0.001 at the concentration of 0.4 mg/mL, respectively. CFs could be exploited as natural antioxidants in pharmaceuticals and functional foods. DPPH ; ABTS ; Extraction (chemistry) ; Chemistry ; Antioxidant ; Traditional medicine ; Chromatography ; Yield (engineering) ; Food science ; Organic chemistry ; Medicine ; Materials science Chromatography in Natural Products ; Microbial Metabolism and Applications ; Medicinal Plant Pharmacodynamics Research
Authors: Hongyan Chen | Hongda Yang
Source: Spectroscopy (article, 2022-08-01)
Field: Chemistry — Spectroscopy

Online ATR-FT-IR for Real-Time Monitoring of the Aspirin Esterification Process in an Acid-Mediated Reaction The process of aspirin synthesis was studied using in situ real-time attenuated total reflection Fourier transform infrared spectroscopy (ATR-FT-IR) from salicylic acid and acetic anhydride accompanied by a sulfuric acid catalyst. The data collected from the IR analysis process showed that there were obvious changes in the position, shape, and intensity of the carbonyl characteristic peaks in the three-dimensional (3D) spectra. Principal component analysis (PCA) followed by target transformation of the resulting factors was used to analyze the spectra and the relationship of the absorbance and time trendlines of raw materials and products in the reaction system. This method would be enough to monitor reaction progress and determine the end point without further separation and purification of the reaction mixture. The results demonstrated that the acetylation of salicylic acid catalyzed by sulfuric acid was a complicated process, and the conversion rate was high. The reaction was a rapid reaction mechanism and could be divided into two stages with different reaction rate. The ATR-FT-IR spectroscopy technique can monitor and analyze the changes of raw materials and products with time, which is more reliable to determine fundamental data for process analysis and optimization using real-time monitoring of the reaction process. Attenuated total reflection ; Absorbance ; Sulfuric acid ; Chemistry ; Catalysis ; Infrared spectroscopy ; Acetic anhydride ; Fourier transform infrared spectroscopy ; Reaction rate ; Salicylic acid ; Spectroscopy ; Acetic acid ; Infrared ; Reaction mechanism ; Process optimization ; Analytical Chemistry (journal) ; Inorganic chemistry ; Organic chemistry ; Chromatography ; Chemical engineering ; Optics Analytical Chemistry and Chromatography ; Analytical Methods in Pharmaceuticals ; Spectroscopy and Chemometric Analyses
Authors: Boudraa Saliha | Benabed Fadila | Fofana Issouf | Mokhnache Leila
Source: Diagnostyka (article, 2022-05-12)
Field: Materials Science — Materials Chemistry

FTIR and FDS assessment of mineral oil under low electrical discharge Transformers are crucial elements in the transmission and distribution of electrical energy. The importance of diagnosing these equipments are two-fold: (1) the necessity of service reliability and (2) the likelihood to avoid economic and environmental concerns. Under service conditions, the electrical and thermal stresses or chemical contaminants may degrade the insulation oil inside the transformer and cause incipient failures or reduce its service life. Partial discharges well recognized to be among the most common stresses that can lead to slow but steady degradation of insulating oil in transformers. The present work aims at understanding the influence of low energy electrical discharge on mineral oil based on two spectroscopic methods: FTIR spectroscopy and Frequency Domain Spectroscopy (FDS). An electrical fault has been created by continuous discharge of 10 kV on the surface of various oil samples according to the ASTM D6180. From the FDS results, it was found that the amount of charge carriers and moisture increased with the aging time elapsed that influences the conduction phenomena and in turn, increases the dissipation factor. These results are confirmed by the FTIR results, which show that the intensity of the peak absorbance of the C-H and C-C functional group decreased with aging. The application of these two methods may help monitoring the condition of oil. A combined FTIR and FDS measurements highlighted the correlations between modifications in electrical properties and changes in the chemical structure of the oil under electrical accelerated ageing. Thermal runaway ; Mineral oil ; Dielectric ; Materials science ; Thermal ; Engineering physics ; Petroleum engineering ; Analytical Chemistry (journal) ; Electrical engineering ; Environmental science ; Forensic engineering ; Physics ; Geology ; Engineering ; Optoelectronics ; Chemistry ; Metallurgy ; Thermodynamics ; Environmental chemistry ; Battery (electricity) High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation
Authors: Xiaoliang Ji | Yue Yang
Source: Spectroscopy (article, 2022-08-01)
Field: Chemistry — Physical and Theoretical Chemistry

Density Functional Theory Investigation on the Molecular Structure and Vibrational Spectra of Triclosan Density functional theory (DFT) methods possess a strong ability in the molecular modeling of geometrical and spectroscopic parameters because of their high accuracy and consistency with experimental data. In this study, the performances of different DFT methods to predict the molecular structural and vibrational properties of triclosan were investigated and compared. DFT methods comprised of five commonly used functionals, namely B3LYP, LSDA, PBEPBE, CAM-B3LYP, and M06-2X, were examined. The proper choice of the basis set had a significant influence on the DFT simulation results. Therefore, the effects of different basis sets, including LANL2DZ, SDD, LANL2MB, 6-311G, and 6-311++G(d,p), on the theoretical calculations of triclosan, were also evaluated. Results revealed that the M06-2X/6-311++G(d,p) level of theory was superior to other levels in simulating the structure of triclosan. The LSDA/6-311G level of theory showed the best performance in predicting the vibrational spectra of triclosan. These results can provide a fundamental benchmark for the study of environmental pollution mechanisms and ecological effects of triclosan. Triclosan ; Density functional theory ; Basis set ; Computational chemistry ; Materials science ; Molecule ; Spectral line ; Chemistry ; Physics ; Organic chemistry ; Quantum mechanics Various Chemistry Research Topics ; Photochemistry and Electron Transfer Studies ; Chemistry and Chemical Engineering
Authors: Emily Wu | Sneha Sinha | Chelsea Yang | Miles Zhang | William E. Acree
Source: Liquids (article, 2022-07-05)
Field: Chemistry — Spectroscopy

Abraham Solvation Parameter Model: Calculation of L Solute Descriptors for Large C11 to C42 Methylated Alkanes from Measured Gas–Liquid Chromatographic Retention Data Abraham model L solute descriptors have been determined for 149 additional C11 to C42 monomethylated and polymethylated alkanes based on published Kovat’s retention indices based upon gas–liquid chromatographic measurements. The calculated solute descriptors, in combination with previously published Abraham model correlations, can be used to predict a number of very important chemical and thermodynamic properties including partition coefficients, molar solubility ratios, gas–liquid chromatographic and HPLC retention data, infinite dilution activity coefficients, molar enthalpies of solvation, standard molar vaporization and sublimation at 298 K, vapor pressures, and limiting diffusion coefficients. The predictive computations are illustrated by estimating both the standard molar enthalpies of sublimation and the enthalpies of solvation in benzene for the monomethylated and polymethylated alkanes considered in the current study. Solvation ; Sublimation (psychology) ; Chemistry ; Vaporization ; Thermodynamics ; Partition coefficient ; Kovats retention index ; Chromatography ; Dilution ; Vapor pressure ; Alkane ; Solubility ; Enthalpy of vaporization ; Gas chromatography ; Enthalpy ; Physical chemistry ; Organic chemistry ; Hydrocarbon ; Molecule Analytical Chemistry and Chromatography ; Chemical Thermodynamics and Molecular Structure ; Computational Drug Discovery Methods
Authors: Ondrej Dyck | Feng Bao | Maxim Ziatdinov | Ali Yousefzadi Nobakht | Kody J. H. Law | Artem Maksov | Bobby G. Sumpter | Richard Archibald | Stephen Jesse | Sergei V. Kalinin | David B. Lingerfelt
Source: Carbon Trends (article, 2022-07-03)
Field: Materials Science — Materials Chemistry

Strain-Induced asymmetry and on-site dynamics of silicon defects in graphene In the last decade, the atomically-focused electron beams utilized in scanning transmission electron microscopes (STEMs) have been shown to induce a broad set of local structural transformations in materials, opening pathways for directing material synthesis and modification atom-by-atom. The mechanisms underlying these transformations remain largely unknown, due to the intractability of modeling the myriad of reaction pathways that can be accessed through high-energy electron scattering. The information on materials’ structure and dynamics that can be extracted from STEM images is similarly left underexplored. Here, we report the observation of anomalous on-site dynamics of individual silicon impurity atoms in graphene during STEM imaging. Density functional theory-based structural optimizations of anisotropically-strained molecular nanographenes reveal two distinct (but nearly degenerate) stable structures for four-fold coordinated silicon impurities, where interconversion between the two structures manifests slight changes of the silicon position within the lattice site. Implications for defect-based strain engineering in graphene are discussed. Graphene ; Silicon ; Scanning transmission electron microscopy ; Chemical physics ; Materials science ; Molecular dynamics ; Impurity ; Asymmetry ; Degenerate energy levels ; Atom (system on chip) ; Density functional theory ; Electron ; Crystallographic defect ; Nanotechnology ; Scattering ; Transmission electron microscopy ; Molecular physics ; Crystallography ; Chemistry ; Optoelectronics ; Computational chemistry ; Physics ; Optics Graphene research and applications ; Semiconductor materials and devices ; Electronic and Structural Properties of Oxides