jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Kevin A. Webster | Alison I. Bernstein | Brian K. Shoichet | Bradley W. Gray | William C. Wetsel | Martilias S. Farrell | Allison K. Doak | Ramona M. Rodriguiz | Bryan L. Roth | Xi‐Ping Huang | William E. Fantegrossi | Gary W. Miller | Kate White | Philippe Giguère | Joseph H. Porter | Daniel J. Urban | Brenda M. Gannon | Kristen A. Stout | Su Mi Park | John D. McCorvy | Andrew P. Norwood | William S. Hyatt
Source: UNC Libraries (article, 2020-04-21)
Field: Chemistry — Analytical Chemistry

In Vitro and In Vivo Characterization of the Alkaloid Nuciferine RationaleThe sacred lotus (Nelumbo nucifera) contains many phytochemicals and has a history of human use. To determine which compounds may be responsible for reported psychotropic effects, we used in silico predictions of the identified phytochemicals. Nuciferine, an alkaloid component of Nelumbo nucifera and Nymphaea caerulea, had a predicted molecular profile similar to antipsychotic compounds. Our study characterizes nuciferine using in vitro and in vivo pharmacological assays.MethodsNuciferine was first characterized in silico using the similarity ensemble approach, and was followed by further characterization and validation using the Psychoactive Drug Screening Program of the National Institute of Mental Health. Nuciferine was then tested in vivo in the head-twitch response, pre-pulse inhibition, hyperlocomotor activity, and drug discrimination paradigms.ResultsNuciferine shares a receptor profile similar to aripiprazole-like antipsychotic drugs. Nuciferine was an antagonist at 5-HT2A, 5-HT2C, and 5-HT2B, an inverse agonist at 5-HT7, a partial agonist at D2, D5 and 5-HT6, an agonist at 5-HT1A and D4 receptors, and inhibited the dopamine transporter. In rodent models relevant to antipsychotic drug action, nuciferine blocked head-twitch responses and discriminative stimulus effects of a 5-HT2A agonist, substituted for clozapine discriminative stimulus, enhanced amphetamine induced locomotor activity, inhibited phencyclidine (PCP)-induced locomotor activity, and rescued PCP-induced disruption of prepulse inhibition without induction of catalepsy.ConclusionsThe molecular profile of nuciferine was similar but not identical to that shared with several approved antipsychotic drugs suggesting that nuciferine has atypical antipsychotic-like actions. In vitro ; Alkaloid ; In vivo ; Characterization (materials science) ; Chemistry ; Biology ; Stereochemistry ; Biochemistry ; Nanotechnology ; Materials science ; Biotechnology Chromatography in Natural Products
Authors: Aleksandra Balliu | Aaltje Roelofje Femmigje Strijker | Michael Oschmann | Monireh Pourghasemi Lati | Oscar Verho
Source: ChemRxiv (preprint, 2020-03-27)
Field: Chemistry — Organic Chemistry

Stereospecific, Palladium-catalyzed C(sp3)–H Alkenylation and Alkynylation of a Proline Derivative Enabled by 8-Aminoquinoline as a Directing Group &lt;p&gt;In this preprint, we present our initial results concerning a stereospecific Pd-catalyzed protocol for the C3 alkenylation and alkynylation of a proline derivative carrying the well utilized 8‑aminoquinoline directing group. Efficient C–H alkenylation was achieved with a wide range of vinyl iodides bearing different aliphatic, aromatic and heteroaromatic substituents, to furnish the corresponding C3 alkenylated products in good to high yields. In addition, we were able show that this protocol can also be used to install an alkynyl group into the pyrrolidine scaffold, when a TIPS-protected alkynyl bromide was used as the reaction partner. Furthermore, two different methods for the removal of the 8-aminoquinoline auxiliary are reported, which can enable access to both &lt;i&gt;cis&lt;/i&gt;- and &lt;i&gt;trans&lt;/i&gt;-configured carboxylic acid building blocks from the C–H alkenylation products.&lt;/p&gt; Chemistry ; Pyrrolidine ; Stereospecificity ; Alkynylation ; Proline ; Catalysis ; Derivative (finance) ; Palladium ; Bromide ; Medicinal chemistry ; Combinatorial chemistry ; Functional group ; Organic chemistry ; Amino acid ; Biochemistry Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions ; Oxidative Organic Chemistry Reactions
Authors: Joshua Nicks | Stephanie A. Boer | Nicholas G. White | Jonathan A. Foster
Source: ChemRxiv (preprint, 2020-12-03)
Field: Chemistry — Inorganic Chemistry

Monolayer Nanosheets Formed by Liquid Exfoliation of Charge-as-Sisted Hydrogen-Bonded Frameworks Hydrogen-bonded organic frameworks (HOFs) are a diverse and tunable class of materials, but their potential as free-standing two-dimensional nanomaterials has yet to be explored. Here we report the self-assembly of two layered hydrogen-bonded frameworks based on strong, charge-assisted hydrogen-bonding between carboxylate and amidinium groups. Ultrasound-assisted liquid exfoliation of both materials readily produces monolayer hydrogen-bonded organic nanosheets (HONs) with micron-sized lateral dimensions. The HONs show remarkable stability and maintain their extended crystallinity and monolayer structures even after being suspended in water at 80 °C for three days. These systems also exhibit efficient fluorescence quenching of an organic dye in organic solvents, superior to the quenching ability of the bulk frameworks. We anticipate that this approach will provide a route towards a diverse new family of molecular two-dimensional materials with great potential for use in separation, sensing, catalysis, delivery, and electronics materials applications. Monolayer ; Exfoliation joint ; Hydrogen bond ; Materials science ; Quenching (fluorescence) ; Nanotechnology ; Hydrogen ; Nanomaterials ; Chemical engineering ; Catalysis ; Fluorescence ; Chemistry ; Graphene ; Organic chemistry ; Molecule Metal-Organic Frameworks: Synthesis and Applications ; Luminescence and Fluorescent Materials ; Covalent Organic Framework Applications
Authors: Nieves Martínez-Peinado | Núria Cortes-Serra | Laura Torras‐Claveria | María‐Jesús Pinazo | Joaquím Gascón | Jaume Bastida | Julio Alonso-Padilla
Source: Research Square (preprint, 2020-05-16)
Field: Chemistry — Organic Chemistry

Amaryllidaceae alkaloids with anti-Trypanosoma cruzi activity. Trypanosoma cruzi ; Amaryllidaceae ; Amaryllidaceae Alkaloids ; Biology ; Botany ; Computer science ; World Wide Web ; Parasite hosting Chemical synthesis and alkaloids ; Alkaloids: synthesis and pharmacology ; Trypanosoma species research and implications
Authors: Nieves Martínez-Peinado | Núria Cortes-Serra | Laura Torras‐Claveria | María‐Jesús Pinazo | Joaquím Gascón | Jaume Bastida | Julio Alonso-Padilla
Source: Research Square (preprint, 2020-03-24)
Field: Chemistry — Organic Chemistry

Amaryllidaceae alkaloids with anti-Trypanosoma cruzi activity Trypanosoma cruzi ; Amaryllidaceae ; Amaryllidaceae Alkaloids ; Biology ; Virology ; Botany ; Chemistry ; Computer science ; Parasite hosting ; World Wide Web Chemical synthesis and alkaloids ; Trypanosoma species research and implications ; Cyclopropane Reaction Mechanisms
Authors: Đặng Thanh Dũng | Nguyễn Thị Thu Thảo
Source: TẠP CHÍ KHOA HỌC ĐẠI HỌC MỞ THÀNH PHỐ HỒ CHÍ MINH - KỸ THUẬT VÀ CÔNG NGHỆ (article, 2020-08-17)
Field: Chemistry — Organic Chemistry

G-quadruplex: Mục tiêu tiềm năng cho những phân tử nhỏ và protein trong việc tạo thuốc trị ung thư G-quadruplex DNA hay RNA là cấu trúc bậc hai xuất hiện ở những vùng giàu Guanine có cấu trúc 4 sợi được hình thành bởi những G-tetrad xếp chồng lên nhau. Sự hình thành cấu trúc G-quadruplex trong DNA hay RNA đóng vai trò quan trọng trong các quá trình sinh học của tế bào như: sao chép DNA, phiên mã, dịch mã và đặc biệt trong quá trình kéo dài của telomer. Do đó, G-quadruplex được xem là mục tiêu quan trọng cho các quá trình điều hòa và kiểm soát các hoạt động của tế bào có liên quan gen. Hiện nay, hầu hết những hoạt động bất thường của gen đều có ảnh hưởng trực tiếp đến quá trình gây ra bệnh ung thư. Hiểu và kiểm soát được quá trình hình thành G-quadruplex là một trong những hướng để tìm ra cách chữa trị ung thư. Chính vì vậy, việc nghiên cứu, phát triển những phân tử nhỏ hay protein có tương tác trực tiếp với G-quadruplex sẽ đóng vai trò quan trọng trong việc điều chế thuốc chữa các bệnh ung thư và hơn nữa phương pháp điều trị ung thư hướng mục tiêu hiện đang là tâm điểm của nhiều nghiên cứu. Trong bài báo này, chúng tôi tập trung phân tích và thảo luận về sự tương tác giữa các phân tử nhỏ hay protein với&#x0D; G-quadruplex cũng như đánh giá tiềm năng của các ligands trong việc điều trị ung thư. Chemistry ; Stereochemistry ; Medicinal chemistry Synthesis and Characterization of Heterocyclic Compounds ; Structural Behavior of Reinforced Concrete
Authors: Yuta Sato | Takashi Yabuki | Naruhiko Adachi | Toshio Moriya | T. Arakawa | Masato Kawasaki | Chihaya Yamada | Toshiya Senda | Shinya Fushinobu | Takayoshi Wakagi
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-05-04)
Field: Chemistry — Inorganic Chemistry

Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from <i>Sulfurisphaera tokodaii</i> Abstract Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from two Acidianus species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon Sulfurisphaera tokodaii (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5∼13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities and the other two cysteines (Cys101 and Cys104) had a supportive role. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM measurements. Highlights Sulfur oxygenase reductase (SOR) was biochemically and structurally characterized. High resolution structures of SOR were determined by crystallography and cryo-EM. Twenty-four identical subunits of SOR form a hollow sphere. Catalytic components exhibited different features in the crystal and cryo-EM structures. Thermophile ; Disproportionation ; Chemistry ; Crystallography ; Cryo-electron microscopy ; Crystal structure ; Reductase ; Molecular replacement ; Sulfur ; Resolution (logic) ; Enzyme ; Stereochemistry ; Catalysis ; Biochemistry ; Organic chemistry Metal-Catalyzed Oxygenation Mechanisms ; Metalloenzymes and iron-sulfur proteins ; Metal Extraction and Bioleaching
Authors: Terry Kenakin
Source: UNC Libraries (article, 2020-10-31)
Field: Chemistry — Analytical Chemistry

New concepts in pharmacological efficacy at 7TM receptors: IUPHAR Review 2: Developing concepts for drug efficacy The present-day concept of drug efficacy has changed completely from its original description as the property of agonists that causes tissue activation. The ability to visualize the multiple behaviours of seven transmembrane receptors has shown that drugs can have many efficacies and also that the transduction of drug stimulus to various cellular stimulus–response cascades can be biased towards some but not all pathways. This latter effect leads to agonist ‘functional selectivity’, which can be favourable for the improvement of agonist therapeutics. However, in addition, biased agonist potency becomes cell type dependent with the loss of the monotonic behaviour of stimulus–response mechanisms, leading to potential problems in agonist quantification. This has an extremely important effect on the discovery process for new agonists since it now cannot be assumed that a given screening or lead optimization assay will correctly predict therapeutic behaviour. This review discusses these ideas and how new approaches to quantifying agonist effect may be used to circumvent the cell type dependence of agonism. This article, written by a corresponding member of the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR), reviews our current understanding of the interaction of ligands with seven transmembrane receptors. Further information on these pharmacological concepts is being incorporated into the IUPHAR/BPS database http://GuideToPharmacology.org. Pharmacology ; Medicine ; Drug ; Efficacy Analytical Methods in Pharmaceuticals
Authors: Seung‐Je Woo | Jang‐Joo Kim
Source: ChemRxiv (preprint, 2020-12-07)
Field: Chemistry — Physical and Theoretical Chemistry

TD-DFT and Experimental Methods for Unraveling the Energy Distribution of Charge-Transfer Triplet/Singlet States of a TADF Molecule in a Frozen Matrix Reverse intersystem crossing (RISC) rate of a thermally activated delayed fluorescence (TADF) molecule is sensitive to the energy alignment of singlet charge-transfer state (1CT), triplet charge-transfer state (3CT), and locally excited triplet state (3LE). However, the energy distribution of the charge-transfer states originating from the conformational distribution of TADF molecules in a solid matrix inevitably generated during the preparation of a solid sample due to the rotatable donor-acceptor linkage is rarely considered. Moreover, the investigation of the energy distribution of the 3CT state is both theoretically and experimentally difficult due to the triplet instabilities of time-dependent density functional (TD-DFT) calculations and difficulties in phosphorescence measurements, respectively. As a result, the relation between conformational distribution, configurations of excited state transition orbitals, and excited state energies/dynamics have not been clearly explained. In this work, we determined the energy distribution of CT states of the TADF emitter TPSA in frozen toluene at 77 K by the measurement of time-resolved spectra in the full time range (1 ns ~ 30 s) of emission including prompt fluorescence, TADF, 3CT phosphorescence, and 3LE phosphorescence. We obtained the energy band of CT states where 1CT and 3CT states are distributed in the range of 2.85-3.00 eV and 2.64-2.96 eV, respectively. We tested various global hybrid and long-range corrected functionals for the TD-DFT calculation of 3CT energy of TPSA and found that only the M11 functional shows consistent results without triplet instability. We performed TD-DFT with the M11* functional optimized for robust dihedral angle scan of 3CT states without triplet instability and reproduced the energy band structure obtained from the experiment. Through TD-DFT and experimental investigations, it is estimated that the dihedral angle of donor-acceptor (θD-A) and acceptor-linker (θA) of TPSA in frozen toluene lie within the range of 70°≤θD-A≤90° and 0°≤θA≤30° respectively. Our results show that the dihedral angle distribution must be considered for further investigation of the photophysics of TADF molecules and the development of stable and efficient TADF emitters. Intersystem crossing ; Phosphorescence ; Excited state ; Singlet state ; Triplet state ; Atomic physics ; Acceptor ; Molecular physics ; Singlet fission ; Density functional theory ; Chemistry ; Fluorescence ; Materials science ; Physics ; Computational chemistry ; Condensed matter physics ; Optics Photochemistry and Electron Transfer Studies ; Organic Light-Emitting Diodes Research
Authors: Xiaorui Wang | Jiezhong Qiu | Yuquan Li | Guangyong Chen | Huanxiang Liu | Ben Liao | Chang‐Yu Hsieh | Xiaojun Yao
Source: ChemRxiv (preprint, 2020-09-18)
Field: Materials Science — Materials Chemistry

RetroPrime: A Chemistry-Inspired and Transformer-based Method for Retrosynthesis Predictions Retrosynthesis prediction is a crucial task for organic synthesis. In this work, we propose a template-free and Transformer-based method dubbed RetroPrime, integrating chemists’ retrosynthetic strategy of (1) decomposing a molecule into synthons then (2) generating reactants by attaching leaving groups. These two steps are accomplished with versatile Transformer models, respectively. While RetroPrime performs competitively against all state-of-the art models on the standard USPTO-50K dataset, it manifests remarkable generalizability and outperforms the only published result by a non-trivial margin of 4.8% for the Top-1 accuracy on the large-scale USPTO-full dataset. It is known that outputs of Transformer-based retrosynthesis model tend to suffer from insufficient diversity and high invalidity. These problems may limit the potential of Transformer-based methods in real practice, yet no prior works address both issues simultaneously. RetroPrime is designed to tackle these challenges. Finally, we provide convincing results to support the claim that RetromPrime can more effectively generalize across chemical space. Retrosynthetic analysis ; Transformer ; Generalizability theory ; Computer science ; Artificial intelligence ; Machine learning ; Engineering ; Mathematics ; Chemistry ; Voltage ; Electrical engineering Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Asymmetric Hydrogenation and Catalysis
Authors: Philippe Schwaller | Teodoro Laino | Antonio Cardinale | Alessandra Toniato
Source:  (preprint, 2020-10-19)
Field: Materials Science — Materials Chemistry

Chemistry puppeteer: Enhancing the diversity of retrosynthetic predictions One of the main issues of AI-based retrosynthesis planning algorithms is that, usually, the proposed disconnection strategies lack in diversity. When the goal is to find a suitable set of precursors for a given target molecule, the generated precursors typically fall in the same chemical macro class (ex. protection, deprotection or same C-C bond formation with a slightly different Diversity (politics) ; Retrosynthetic analysis ; Chemistry ; Sociology ; Stereochemistry ; Anthropology Machine Learning in Materials Science
Authors: Joshua Lee Padgett | Yusup Geldiyev | Sakshi Gautam | Wen‐Ping Peng | Yehia Mechref | A. Ibrabuimov
Source: arXiv (Cornell University) (preprint, 2020-08-06)
Field: Chemistry — Spectroscopy

Object classification in analytical chemistry via data-driven discovery of partial differential equations Glycans are one of the most widely investigated biomolecules, due to their roles in numerous vital biological processes. This involvement makes it critical to understand their structure-function relationships. Few system-independent, LC-MS/MS (Liquid chromatography tandem mass spectrometry) based studies have been developed with this particular goal, however. When studied, the employed methods generally rely on normalized retention times as well as m/z - mass to charge ratio of an ion values. Due to these limitations, there is need for quantitative characterization methods which can be used independently of m/z values, thus utilizing only normalized retention times. As such, the primary goal of this article is to construct an LC-MS/MS based classification of the permethylated glycans derived from standard glycoproteins and human blood serum, using a Glucose Unit Index (GUI) as the reference frame in the space of compound parameters. For the reference frame we develop a closed-form analytic formula, which is obtained from the Green's function of a relevant convection-diffusion-absorption equation used to model composite material transport. The aforementioned equation is derived from an Einstein-Brownian motion paradigm, which provides a physical interpretation of the time-dependence at the point of observation for molecular transport in the experiment. The necessary coefficients are determined via a data-driven learning procedure. The methodology is presented in an abstract manner which allows for immediate application to related physical and chemical processes. Results employing the proposed classification method are validated via comparison with experimental mass spectrometer data. Chemistry ; Mass spectrometry ; Function (biology) ; Biomolecule ; Analytical Chemistry (journal) ; Chromatography Analytical Chemistry and Chromatography ; Protein Structure and Dynamics ; Mass Spectrometry Techniques and Applications
Authors: Schoukens Dterli
Source: International Journal of Swarm Intelligence and Evolutionary Computation (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Advanced Materials Composition and Nanotechnology by Artificial Intelligence Meetings International is announcing Young Scientist Awards through 13th Smart Materials and Polymer Technology (Smart Materials 2020) which is scheduled at Paris, France during February 19-20 , 2020. This Smart Material conference focuses on “Emerging Progress in smart content applications”. Nanotechnology ; Smart material ; Engineering ; Materials science Machine Learning in Materials Science
Authors: Ayana Ghosh | Shizeng Lin | Jian‐Xin Zhu
Source: Bulletin of the American Physical Society (article, 2020-03-03)
Field: Materials Science — Materials Chemistry

Data-driven study of magnetic interactions of transition-metal based 2D materials Materials science ; Transition metal ; Condensed matter physics ; Nanotechnology ; Chemical physics ; Physics ; Chemistry Machine Learning in Materials Science ; Electron and X-Ray Spectroscopy Techniques ; X-ray Diffraction in Crystallography
Authors: 智広 林 | Tomohiro Hayashi
Source: Institutional Repositories DataBase (IRDB) (article, 2020-12-01)
Field: Materials Science — Surfaces, Coatings and Films

Data-driven prediction of protein adsorption on self-assembled monolayers: toward material screening and design Adsorption ; Protein adsorption ; Analyte ; Protein stability Polymer Surface Interaction Studies ; Adsorption and biosorption for pollutant removal ; Diatoms and Algae Research
Source: Journal of Physics Conference Series (article, 2020-07-01)
Field: Materials Science — Polymers and Plastics

Preface This collection focuses on the most recent scientific and technological advances and innovations in the field of smart photonic and optoelectronic materials and systems for a wide range of applications in communications, computations, energy harvesting, bio-chemical sensing and artificial intelligence. It covers a broad range of subjects from 2D, chalcogenide and group IV materials, to organic and quantum dot nanomaterials, to liquid crystals and fluid nanocomposites. Nanotechnology ; Chalcogenide ; Nanomaterials ; Materials science ; Photonics ; Nanocomposite ; Computer science ; Optoelectronics Conducting polymers and applications
Authors: Crystals Editorial Office
Source: Crystals (article, 2020-07-10)
Field: Materials Science — Materials Chemistry

RETRACTED: Leong et al. Artificial Intelligence Algorithm Enabled Industrial-Scale Graphene Characterization. Crystals 2020, 10, 308 The Crystals Editorial Office has been made aware that the data and results in this published paper [...] Characterization (materials science) ; Graphene ; Scale (ratio) ; Materials science ; Artificial intelligence ; Computer science ; Nanotechnology ; Cartography ; Geography Graphene research and applications ; 2D Materials and Applications ; Graphene and Nanomaterials Applications