jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Franco Pellegrini | Ruggero Lot | Yusuf Shaidu | Emine Küçükbenli
Source: The Journal of Chemical Physics (article, 2023-08-28)
Field: Materials Science — Materials Chemistry

PANNA 2.0: Efficient neural network interatomic potentials and new architectures We present the latest release of PANNA 2.0 (Properties from Artificial Neural Network Architectures), a code for the generation of neural network interatomic potentials based on local atomic descriptors and multilayer perceptrons. Built on a new back end, this new release of PANNA features improved tools for customizing and monitoring network training, better graphics processing unit support including a fast descriptor calculator, new plugins for external codes, and a new architecture for the inclusion of long-range electrostatic interactions through a variational charge equilibration scheme. We present an overview of the main features of the new code, and several benchmarks comparing the accuracy of PANNA models to the state of the art, on commonly used benchmarks as well as richer datasets. Computer science ; Artificial neural network ; Plug-in ; Code (set theory) ; Computational science ; Perceptron ; Range (aeronautics) ; Graphics processing unit ; Computer architecture ; Artificial intelligence ; Materials science ; Parallel computing ; Operating system ; Programming language ; Set (abstract data type) Machine Learning in Materials Science ; X-ray Diffraction in Crystallography ; Computational Drug Discovery Methods
Authors: Alisha Kamra | Sourav Das | Preeti Bhatt | Manju Solra | Tanmoy Maity | Subinoy Rana
Source: Chemical Science (article, 2023-01-01)
Field: Materials Science — Biomaterials

A transient vesicular glue for amplification and temporal regulation of biocatalytic reaction networks Regulation of enzyme activity and biocatalytic cascades on compartmentalized cellular components is key to the adaptation of cellular processes such as signal transduction and metabolism in response to varying external conditions. Synthetic molecular glues have enabled enzyme inhibition and regulation of protein-protein interactions. So far, all the molecular glue systems based on covalent interactions operated under steady-state conditions. To emulate dynamic biological processes under dissipative conditions, we introduce herein a transient supramolecular glue with a controllable lifetime. The transient system uses multivalent supramolecular interactions between guanidinium group-bearing surfactants and adenosine triphosphate (ATP), resulting in bilayer vesicle structures. Unlike the conventional chemical agents for dissipative assemblies, ATP here plays the dual role of providing a structural component for the assembly as well as presenting active functional groups to "glue" enzymes on the surface. While gluing of the enzymes on the vesicles achieves augmented catalysis, oscillation of ATP concentration allows temporal control of the catalytic activities similar to the dissipative cellular nanoreactors. We further demonstrate temporal upregulation and control of complex biocatalytic reaction networks on the vesicles. Altogether, the temporal activation of biocatalytic cascades on the dissipative vesicular glue presents an adaptable and dynamic system emulating heterogeneous cellular processes, opening up avenues for effective protocell construction and therapeutic interventions. Nanoreactor ; Chemistry ; Supramolecular chemistry ; Synthetic biology ; Biophysics ; Vesicle ; Protocell ; Dissipative system ; Enzyme ; Nanotechnology ; Membrane ; Biochemistry ; Catalysis ; Materials science ; Computational biology ; Biology ; Molecule Supramolecular Self-Assembly in Materials ; Supramolecular Chemistry and Complexes ; Lipid Membrane Structure and Behavior
Authors: Christian Tüting | Lisa Schmidt | Ioannis Skalidis | Andrea Sinz | Panagiotis L. Kastritis
Source: PROTEOMICS (article, 2023-04-04)
Field: Materials Science — Materials Chemistry

Enabling cryo‐EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures In the cellular context, proteins participate in communities to perform their function. The detection and identification of these communities as well as in-community interactions has long been the subject of investigation, mainly through proteomics analysis with mass spectrometry. With the advent of cryogenic electron microscopy and the "resolution revolution," their visualization has recently been made possible, even in complex, native samples. The advances in both fields have resulted in the generation of large amounts of data, whose analysis requires advanced computation, often employing machine learning approaches to reach the desired outcome. In this work, we first performed a robust proteomics analysis of mass spectrometry (MS) data derived from a yeast native cell extract and used this information to identify protein communities and inter-protein interactions. Cryo-EM analysis of the cell extract provided a reconstruction of a biomolecule at medium resolution (∼8 Å (FSC = 0.143)). Utilizing MS-derived proteomics data and systematic fitting of AlphaFold-predicted atomic models, this density was assigned to the 2.6 MDa complex of yeast fatty acid synthase. Our proposed workflow identifies protein complexes in native cell extracts from Saccharomyces cerevisiae by combining proteomics, cryo-EM, and AI-guided protein structure prediction. Proteomics ; Context (archaeology) ; Computational biology ; Mass spectrometry ; Yeast ; Visualization ; Saccharomyces cerevisiae ; Function (biology) ; Biology ; Computer science ; Chemistry ; Bioinformatics ; Biochemistry ; Artificial intelligence ; Chromatography ; Cell biology ; Gene Enzyme Structure and Function ; Protein Structure and Dynamics ; Advanced Proteomics Techniques and Applications
Authors: Kostas Blekos | Kostas Chairetakis | Iseult Lynch | Effie Marcoulaki
Source: Journal of Cheminformatics (article, 2023-04-12)
Field: Materials Science — Materials Chemistry

Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools Efficient and machine-readable representations are needed to accurately identify, validate and communicate information of chemical structures. Many such representations have been developed (as, for example, the Simplified Molecular-Input Line-Entry System and the IUPAC International Chemical Identifier), each offering advantages specific to various use-cases. Representation of the multi-component structures of nanomaterials (NMs), though, remains out of scope for all the currently available standards, as the nature of NMs sets new challenges on formalizing the encoding of their structure, interactions and environmental parameters. In this work we identify a set of principles that a NM representation should adhere to in order to provide "machine-friendly" encodings of NMs, i.e. encodings that facilitate machine processing and cooperation with nanoinformatics tools. We illustrate our principles by showing how the recently introduced InChI-based NM representation, might be augmented, in principle, to also encode morphology and mixture properties, distributions of properties, and also to capture auxiliary information and allow data reuse. Computer science ; ENCODE ; Representation (politics) ; Reuse ; Identifier ; Scope (computer science) ; Set (abstract data type) ; Component (thermodynamics) ; Chemical nomenclature ; Encoding (memory) ; Theoretical computer science ; Data mining ; Artificial intelligence ; Programming language ; Chemistry Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Scientific Computing and Data Management
Authors: Karolina Zawadzińska | Bartłomiej Gostyński
Source: Scientiae Radices (article, 2023-02-14)
Field: Chemistry — Organic Chemistry

Nitrosubstituted analogs of isoxazolines and isoxazolidines: a surprising estimation of their biological activity via molecular docking. The biological activities in the field of antimicrobial application of trihalomethylated isoxazolines and isoxazolidines were investigated by means of molecular docking. In our work, we compared these two groups of heterocyclic compounds due to their strength of non-covalent binding affinity with several exemplary proteins that are known to partake in various biological processes. The obtained results show that the investigated compounds possess higher binding affinities to selected proteins than many hitherto known and applied compounds. Docking (animal) ; Chemistry ; Binding affinities ; Affinities ; Combinatorial chemistry ; Biological activity ; Antimicrobial ; Covalent bond ; Molecular model ; Stereochemistry ; Computational biology ; Biochemistry ; Computational chemistry ; Organic chemistry ; Biology ; In vitro ; Receptor Synthesis of heterocyclic compounds ; Synthesis and Reactions of Organic Compounds ; Synthesis and Catalytic Reactions
Authors: Mirjana Antonijevic | Christophe Rochais | Patrick Dallemagne
Source: Molecules (review, 2023-01-10)
Field: Chemistry — Organic Chemistry

C3-Symmetric Ligands in Drug Design: When the Target Controls the Aesthetics of the Drug A number of proteins are able to adopt a homotrimeric spatial conformation. Among these structures, this feature appears as crucial for biologic targets, since it facilitates the design of C3-symmetric ligands that are especially suitable for displaying optimized ligand-target interactions and therapeutic benefits. Additionally, DNA as a therapeutic target, even if its conformation into a superhelix does not correspond to a C3-symmetry, can also take advantage of these C3-symmetric ligands for better interactions and therapeutic effects. For the moment, this opportunity appears to be under-exploited, but should become more frequent with the discovery of new homotrimeric targets such as the SARS-CoV2 spike protein. Besides their potential therapeutic interest, the synthetic access to these C3-symmetric ligands often leads to chemical challenges, although drug candidates with an aesthetic structure are generally obtained. Drug ; Aesthetics ; Chemistry ; Computer science ; Medicine ; Philosophy ; Pharmacology Click Chemistry and Applications ; RNA Interference and Gene Delivery ; Photochromic and Fluorescence Chemistry
Authors: Jan P. Unsleber
Source: Journal of Chemical Information and Modeling (article, 2023-05-22)
Field: Materials Science — Materials Chemistry

Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application Autonomously exploring chemical reaction networks with first-principles methods can generate vast data. Especially autonomous explorations without tight constraints risk getting trapped in regions of reaction networks that are not of interest. In many cases, these regions of the networks are only exited once fully searched. Consequently, the required human time for analysis and computer time for data generation can make these investigations unfeasible. Here, we show how simple reaction templates can facilitate the transfer of chemical knowledge from expert input or existing data into new explorations. This process significantly accelerates reaction network explorations and improves cost-effectiveness. We discuss the definition of the reaction templates and their generation based on molecular graphs. The resulting simple filtering mechanism for autonomous reaction network investigations is exemplified with a polymerization reaction. Computer science ; Template ; Simple (philosophy) ; Process (computing) ; Programming language Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Various Chemistry Research Topics
Authors: Reem Mahmoud | F. Gitzhofer | Jasmin Blanchard | Nicolas Abatzoglou
Source: Plasma Chemistry and Plasma Processing (article, 2023-10-25)
Field: Materials Science — Materials Chemistry

In Situ Graphene Synthesis Study in Inductively Coupled Radiofrequency Thermal Plasma Reactor Using Methane Precursor Graphene ; Nucleation ; Methane ; Materials science ; Chemical engineering ; Raman spectroscopy ; Analytical Chemistry (journal) ; Chemistry ; Nanotechnology ; Organic chemistry Graphene research and applications ; Diamond and Carbon-based Materials Research ; Plasma Applications and Diagnostics
Authors: Seyyed Mohammad Mousavifard | Hassan Ghermezcheshme | Alireza Mirzaalipour | Mohsen Mohseni | Gijsbertus de With | Hesam Makki
Source: Materials Horizons (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

PolySMart: a general coarse-grained molecular dynamics polymerization scheme The development of simulation methods to study the structure and dynamics of a macroscopically sized piece of polymer material is important as such methods can elucidate structure-property relationships. Several methods have been reported to construct initial structures for homo- and co-polymers; however, most of them are only useful for short linear polymers since one needs to pack and equilibrate the far-from-equilibrium initial structures, which is a tedious task for long or hyperbranched polymers and unfeasible for polymer networks. In this method article, we present PolySMart, <i>i.e.</i>, an open-source python package, which can effectively produce fully equilibrated homo- and hetero-polymer melts and solutions with no limitation on the polymer topology and size, at a coarse-grained resolution and through a bottom-up approach. This python package is also capable of exploring the polymerization kinetics through its reactive scheme in realistic conditions so that it can model the multiple co-occurring polymerization reactions (with different reaction rates) as well as consecutive polymerizations under stoichiometric and non-stoichiometric conditions. Thus, the equilibrated polymer models are generated through correct polymerization kinetics. A benchmark and verification of the performance of the program for several realistic cases, <i>i.e.</i>, for homo-polymers, co-polymers, and crosslinked networks, is given. We further discuss the capability of the program to contribute to the discovery and design of new polymer materials. Polymerization ; Molecular dynamics ; Dynamics (music) ; Materials science ; Scheme (mathematics) ; Chemistry ; Polymer ; Physics ; Computational chemistry ; Composite material ; Mathematics ; Mathematical analysis Advanced Polymer Synthesis and Characterization ; Polymer Surface Interaction Studies ; Dendrimers and Hyperbranched Polymers
Authors: Mauro E. Silva Júnior | Maíra Oliveira Palm | Diego Alexandre Duarte | Rafael C. Catapan
Source: ACS Omega (article, 2023-02-08)
Field: Materials Science — Materials Chemistry

Catalytic Pt/Al<sub>2</sub>O<sub>3</sub> Monolithic Foam for Ethanol Reforming Fabricated by the Competitive Impregnation Method Here, the synthesis of Pt/Al<sub>2</sub>O<sub>3</sub> catalysts on a monolithic foam employing the competitive impregnation method is presented. NO<sub>3</sub> <sup>-</sup> was used as a competitive adsorbate at different concentrations in order to delay the adsorption of Pt, minimizing the formation of Pt concentration gradients throughout the monolith. The catalysts' characterization includes the BET, H<sub>2</sub>-pulse titration, SEM, XRD and XPS techniques. The catalytic activity evaluation was performed under partial oxidation and autothermal reforming of ethanol in a short contact time reactor. The competitive impregnation method was able to produce better dispersion of the Pt particles through the Al<sub>2</sub>O<sub>3</sub> foams. XPS analysis indicated the catalytic activity of the samples, by the presence of metallic Pt and Pt oxides (PtO and PtO<sub>2</sub>) in the internal regions of the monoliths. Compared to other Pt catalysts reported in the literature, the catalyst produced by the competitive impregnation method was revealed to be selective toward H<sub>2</sub>. Overall, the results showed that the competitive impregnation method employing NO<sub>3</sub> <sup>-</sup> as the co-adsorbate is a promising technique to synthesize well dispersed Pt catalysts over α-Al<sub>2</sub>O<sub>3</sub> foams. Catalysis ; Monolith ; X-ray photoelectron spectroscopy ; Materials science ; Platinum ; Dispersion (optics) ; Chemical engineering ; Adsorption ; Titration ; Metal ; Inorganic chemistry ; Chemistry ; Metallurgy ; Organic chemistry Catalytic Processes in Materials Science ; Catalysis and Hydrodesulfurization Studies ; Electrocatalysts for Energy Conversion
Authors: S. H. Kim | Cigdem Yumusak | CRISTIAN-VLAD IRIMIA | Mateusz Bednorz | Esma Yenel | Mahmut Kuş | Niyazi Serdar Sariçiftçi | Bong Sup Shim | MIHAI IRIMIA
Source: TURKISH JOURNAL OF CHEMISTRY (article, 2023-10-31)
Field: Materials Science — Polymers and Plastics

Amplifying the dielectric constant of shellac by incorporating natural clays for organic field effect transistors (OFETs) We demonstrate in this work the practical use of uniform mixtures of a bioresin shellac and four natural clays, i.e. montmorillonite, sepiolite, halloysite and vermiculate as dielectrics in organic field effect transistors (OFETs). We present a thorough characterization of their processability and film forming characteristic, surface characterization, elaborate dielectric investigation and the fabrication of field effect transistors with two classic organic semiconductors, i.e. pentacene and fullerene C60. We show that low operating voltage of approximately 4 V is possible for all the OFETs using several combinations of clays and shellac. The capacitance measurements show an improvement of the dielectric constant of shellac by a factor of 2, to values in excess of 7 in the uniform mixtures of sepiolite and montmorillonite with this bioresin. Shellac ; Dielectric ; Pentacene ; Chemistry ; Sepiolite ; Field-effect transistor ; Optoelectronics ; Transistor ; Materials science ; Organic chemistry ; Voltage ; Electrical engineering ; Layer (electronics) Conducting polymers and applications ; Analytical Chemistry and Sensors ; Polymer Nanocomposite Synthesis and Irradiation
Authors: Andrey A. Kistanov | S. A. Shcherbinin | Elena A. Korznikova | Oleg V. Prezhdo
Source: The Journal of Physical Chemistry Letters (article, 2023-01-27)
Field: Materials Science — Materials Chemistry

Prediction and Characterization of Two-Dimensional Zn<sub>2</sub>VN<sub>3</sub> A two-dimensional (2D) monolayer of a novel ternary nitride Zn<sub>2</sub>VN<sub>3</sub> is computationally designed, and its dynamical and thermal stability is demonstrated. A synthesis strategy is proposed based on experimental works on production of ternary nitride thin films, calculations of formation and exfoliation energies, and <i>ab initio</i> molecular dynamics simulations. A comprehensive characterization of 2D Zn<sub>2</sub>VN<sub>3</sub>, including investigation of its optoelectronic and mechanical properties, is conducted. It is shown that 2D Zn<sub>2</sub>VN<sub>3</sub> is a semiconductor with an indirect band gap of 2.75 eV and a high work function of 5.27 eV. Its light absorption covers visible and ultraviolet regions. The band gap of 2D Zn<sub>2</sub>VN<sub>3</sub> is found to be well tunable by applied strain. At the same time 2D Zn<sub>2</sub>VN<sub>3</sub> possesses high stability against mechanical loads, point defects, and environmental impacts. Considering the unique properties found for 2D Zn<sub>2</sub>VN<sub>3</sub>, it can be used for application in optoelectronic and straintronic nanodevices. Ternary operation ; Characterization (materials science) ; Materials science ; Monolayer ; Band gap ; Exfoliation joint ; Semiconductor ; Optoelectronics ; Nitride ; Ab initio ; Wide-bandgap semiconductor ; Thermal stability ; Direct and indirect band gaps ; Chemical physics ; Nanotechnology ; Chemical engineering ; Chemistry ; Layer (electronics) ; Computer science MXene and MAX Phase Materials ; 2D Materials and Applications ; Advanced Photocatalysis Techniques
Authors: Michael A. Hough | Filippo Prischi | Jonathan A. R. Worrall
Source: Frontiers in Molecular Biosciences (article, 2023-01-23)
Field: Materials Science — Materials Chemistry

Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches The interaction between macromolecular proteins and small molecule ligands is an essential component of cellular function. Such ligands may include enzyme substrates, molecules involved in cellular signalling or pharmaceutical drugs. Together with biophysical techniques used to assess the thermodynamic and kinetic properties of ligand binding to proteins, methodology to determine high-resolution structures that enable atomic level interactions between protein and ligand(s) to be directly visualised is required. Whilst such structural approaches are well established with high throughput X-ray crystallography routinely used in the pharmaceutical sector, they provide only a static view of the complex. Recent advances in X-ray structural biology methods offer several new possibilities that can examine protein-ligand complexes at ambient temperature rather than under cryogenic conditions, enable transient binding sites and interactions to be characterised using time-resolved approaches and combine spectroscopic measurements from the same crystal that the structures themselves are determined. This Perspective reviews several recent developments in these areas and discusses new possibilities for applications of these advanced methodologies to transform our understanding of protein-ligand interactions. Ligand (biochemistry) ; Macromolecule ; Small molecule ; Structural biology ; Protein crystallization ; Chemistry ; Function (biology) ; Resolution (logic) ; Protein ligand ; Molecule ; Computational biology ; Nanotechnology ; Biophysics ; Materials science ; Computer science ; Biochemistry ; Biology ; Crystallization Enzyme Structure and Function ; Protein Structure and Dynamics ; Metal complexes synthesis and properties
Authors: Taishi Nakanishi | Masahiro Terada
Source: Chemical Science (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Computational molecular refinement to enhance enantioselectivity by reinforcing hydrogen bonding interactions in major reaction pathway Computational analyses have revealed that the distortion of a catalyst and the substrates and their interactions are key to determining the stability of the transition state. Hence, two strategies "distortion strategy" and "interaction strategy" can be proposed for improving enantiomeric excess in enantioselective reactions. The "distortion strategy" is used as a conventional approach that destabilizes the TS (transition state) of the minor pathway. On the other hand, the "interaction strategy" focuses on the stabilization of the TS of the major pathway in which an enhancement of the reaction rate is expected. To realize this strategy, we envisioned the TS stabilization of the major reaction pathway by reinforcing hydrogen bonding and adopted the chiral phosphoric acid-catalysed enantioselective Diels-Alder reaction of 2-vinylquinolines with dienylcarbamates. The intended "interaction strategy" led to remarkable improvements in the enantioselectivity and reaction rate. Phosphoric acid ; Hydrogen bond ; Chemistry ; Catalysis ; Combinatorial chemistry ; Computational chemistry ; Diels–Alder reaction ; Organic chemistry ; Molecule Asymmetric Synthesis and Catalysis ; Molecular spectroscopy and chirality ; Axial and Atropisomeric Chirality Synthesis