jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Alisha Kamra | Sourav Das | Preeti Bhatt | Manju Solra | Tanmoy Maity | Subinoy Rana
Source: ChemRxiv (preprint, 2022-11-14)
Field: Chemistry — Organic Chemistry

A Dissipative Supramolecular Glue for Temporal Control of Amplified Enzyme Activity and Biocatalytic Cascades Regulation of enzyme activity is key to the adaptation of cellular processes such as signal transduction and metabolism in response to varying external conditions. Synthetic molecular glues have provided effective systems for enzyme inhibition and regulation of protein-protein interactions. So far, all the molecular glue systems based on covalent interactions operated in equilibrium conditions. To emulate dynamic far-from-equilibrium biological processes, we introduce herein a transient supramolecular glue with controllable lifetime. The transient system uses multivalent supramolecular interactions between guanidium group-bearing surfactants and adenosine triphosphates (ATP), resulting in bilayer vesicle structures. Unlike the conventional fuels for non-equilibrium 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. We further demonstrate temporal activation and control of biocatalytic cascade networks on the vesicles, which represents an essential cellular component. 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. Supramolecular chemistry ; Vesicle ; Chemistry ; Synthetic biology ; Dissipative system ; Biophysics ; Enzyme ; Protocell ; Transduction (biophysics) ; Nanotechnology ; Membrane ; Biochemistry ; Materials science ; Computational biology ; Biology ; Molecule Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials ; Porphyrin and Phthalocyanine Chemistry
Authors: Amir Jahangiri | Han Xiao | Dmitry Lesovoy | Tatiana Agback | Peter Agback | Adnane Achour | Vladislav Orekhov
Source: arXiv (Cornell University) (preprint, 2022-08-04)
Field: Chemistry — Analytical Chemistry

NMR spectrum reconstruction as a pattern recognition problem A new deep neural network based on the WaveNet architecture (WNN) is presented, which is designed to grasp specific patterns in the NMR spectra. When trained at a fixed non-uniform sampling (NUS) schedule, the WNN benefits from pattern recognition of the corresponding point spread function (PSF) pattern produced by each spectral peak resulting in the highest quality and robust reconstruction of the NUS spectra as demonstrated in simulations and exemplified in this work on 2D 1H-15N correlation spectra of three representative globular proteins with different sizes: Ubiquitin (8.6 kDa), Azurin (14 kDa), and Malt1 (44 kDa). The pattern recognition by WNN is also demonstrated for successful virtual homo-decoupling in a 2D methyl 1H-13 HMQC spectrum of MALT1. We demonstrate using WNN that prior knowledge about the NUS schedule, which so far was not fully exploited, can be used for designing new powerful NMR processing techniques that surpass the existing algorithmic methods. Pattern recognition (psychology) ; Computer science ; Artificial intelligence ; Decoupling (probability) ; Schedule ; Engineering Spectroscopy and Chemometric Analyses ; Molecular spectroscopy and chirality ; NMR spectroscopy and applications
Authors: Susi Lehtola | Antti J. Karttunen
Source: ChemRxiv (preprint, 2022-02-03)
Field: Chemistry — Physical and Theoretical Chemistry

Free and Open Source Software for Computational Chemistry Education Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. Our brief review on free and open source software (FOSS) packages points out the existence of software offering a wide range of functionality, all the way from approximate semiempirical calculations with tight-binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, covering both molecular and solid-state systems. Combined with the remarkable increase in the computing power of personal devices, which now rivals that of the fastest supercomputers in the world in the 1990s, we demonstrate that a decentralized model for teaching computational chemistry is now possible thanks to FOSS packages, enabling students to perform reasonable modeling on their own computing devices in the bring your own device (BYOD) scheme. FOSS software can be made trivially simple to install and keep up to date, eliminating the need for departmental support, and also enables comprehensive teaching strategies, as various algorithms' actual implementations can be used in teaching. We exemplify what kinds of calculations are feasible with four FOSS electronic structure programs, assuming only extremely modest computational resources, to illustrate how FOSS packages enable decentralized approaches to computational chemistry education within the BYOD scheme. FOSS also has further benefits driving its adoption: the open access to the source code of FOSS packages democratizes the science of computational chemistry, and FOSS packages can be used without limitation also beyond education, in academic and industrial applications, for example. Computer science ; Software ; Computational science ; Implementation ; Function (biology) ; Theoretical computer science ; Software engineering ; Operating system Various Chemistry Research Topics ; Scientific Computing and Data Management ; Distributed and Parallel Computing Systems
Authors: Pelin Koparır | Rebaz Anwar Omar | S Scholz | J Kidd | L Capaldo | N Flikweert | R Littlefield | T Yoon | M Horst | J Yang | J Meisner | T Kouznetsova | T Martnez | S Craig | Y Xia | Yilmaz | A ukurovali | B Sepehri | R Ghavami | S Farahbakhsh | R Ahmadi | Y Huang | T Cohen | B Sperry | H Larson | H Nguyen | M Homer | F Dou | L Jacoby | B Cossairt | D Gamelin | R Omar | P Koparir | M Koparir | T Rosen | M Akhmedov | I Sardarov | I Akhmedov | R Kostikov | A Kisin | N Babaev | M Koca | C Kirilmi | C Arici | A ukuroval | N zdemir | I Ylmaz | M Diner | Ylmaz | O Bykgngr | L Ahmed | O Rebaz | R Anwar | I Qader | R Omer | D Lee | N Galant | H Wang | Z Mucsi | D Setiadi | B Viskolcz | I Csizmadia | R Sure | S Grimme | L Omer | R Anwer | H Oelichmann | D Bougeard | B Schrader | A Jayaprakash | V Arjunan | S Jose | S Mohan | L Gundelach | T Fox | C Tautermann | C.-K Skylaris | R Sarkar
Source: Letters in Applied NanoBioScience (article, 2022-09-18)
Field: Chemistry — Organic Chemistry

DFT Calculation for Newly Synthesized 2-Chloro-1-(3-methyl-3-mesityl-cyclobutyl)– ethanone The synthesis of cyclobutane rings, particularly stereospecifically, poses significant challenges in synthetic chemistry due to the highly strained ring topologies. The cyclobutane-containing natural products are appealing targets for total synthesis due to their new chemical structures and exceptional biological activity. In this study, we have presented the synthesis and structure analysis of 2-chloro-1-(3-methyl-3-mesityl-cyclobutyl)–ethanone. The molecular elucidation was conducted by Fourier transform infrared (IR) and Nuclear magnetic spectroscopy (NMR). The I recording in 4000-500cm-1 was done in the potassium bromide solid phase, while the NMR for both Hydrogen and Carbon was done in the Dimethyl sulfoxide-6. Density functional theory (DFT) was used to stimulate and confirm the structure and molecular characterization. Using DFT/cc-pVDZ method to study various conformers of the compound and their minimum energies by the scanning potential energy surface. In addition, the molecular electrostatic potential map (MEP) and charge spreading have been plotted for the molecule to account for the chemical reactivity and site selectivity. Furthermore, the thermodynamic properties of the molecule have been studied. A good correlation was found between experimental and stimulation studies for Fourier transform infrared and Nuclear magnetic spectroscopy results. In the stimulation data, the conformer's energy differences were very small. Chemistry ; Cyclobutane ; Conformational isomerism ; Molecule ; Density functional theory ; Potassium bromide ; Chemical shift ; Reactivity (psychology) ; Fourier transform infrared spectroscopy ; Infrared spectroscopy ; Computational chemistry ; Potential energy surface ; Proton NMR ; Bromide ; Ring (chemistry) ; Physical chemistry ; Stereochemistry ; Organic chemistry ; Chemical engineering Inorganic and Organometallic Chemistry ; Molecular spectroscopy and chirality ; Organic Chemistry Cycloaddition Reactions
Authors: Max C. Lemme | Deji Akinwande | Cedric Huyghebaert | Christoph Stampfer
Source: RePEc: Research Papers in Economics (article, 2022-03-16)
Field: Materials Science — Materials Chemistry

2D materials for future heterogeneous electronics Graphene and two-dimensional materials (2DM) remain an active field of research in science and engineering over 15 years after the first reports of 2DM. The vast amount of available data and the high performance of device demonstrators leave little doubt about the potential of 2DM for applications in electronics, photonics and sensing. So where are the integrated chips and enabled products? We try to answer this by summarizing the main challenges and opportunities that have thus far prevented 2DM applications. Electronics ; Nanotechnology ; Materials science ; Engineering physics ; Engineering ; Electrical engineering 2D Materials and Applications ; Graphene research and applications ; MXene and MAX Phase Materials
Authors: Wai-Yan Ryana Fok | Martin Grashei | Jason G. Skinner | Bjoern Menze | Franz Schilling
Source: EJNMMI Research (article, 2022-04-23)
Field: Chemistry — Spectroscopy

Prediction of multiple pH compartments by deep learning in magnetic resonance spectroscopy with hyperpolarized 13C-labelled zymonic acid The results of this study indicate that CNNs offer a reliable, accurate, fast and non-interactive method for analysis of hyperpolarized <sup>13</sup>C MRS and MRSI data, where low amounts of acquired data can be complemented to achieve suitable network training. Medicine ; Nuclear magnetic resonance ; Magnetic resonance imaging ; Nuclear magnetic resonance spectroscopy ; Cardiac imaging ; Spectroscopy ; Nuclear medicine ; Radiology Advanced NMR Techniques and Applications ; Molecular spectroscopy and chirality ; Protein Structure and Dynamics
Authors: Benjamin T. Boyle | Jeffrey N. Levy | Louis de Lescure | Robert S. Paton | Andrew McNally
Source: ChemRxiv (preprint, 2022-07-06)
Field: Chemistry — Organic Chemistry

3-Selective Halogenation of Pyridines via Zincke Imine Intermediates Pyridine halogenation reactions are crucial for obtaining the vast array of derivatives required for drug and agrochemical development. Yet, despite more than a century of synthetic endeavors, there are no broadly applicable 3-selective halogenation processes that function directly from pyridine C–H precursors. We have developed a ring-opening, halogenation, ring-closing sequence that temporarily transforms pyridines into a reactive series of alkenes. These Zincke imine intermediates undergo highly regioselective halogenation reactions under mild conditions. Experimental and computational mechanistic studies indicate that the selectivity-determining step changes based on the halogen electrophile. Using this method, we formed a diverse set of 3-halopyridines and demonstrated late-stage halogenation of complex pharmaceuticals and agrochemicals. Halogenation ; Chemistry ; Regioselectivity ; Imine ; Electrophile ; Pyridine ; Ring (chemistry) ; Selectivity ; Halogen ; Combinatorial chemistry ; Organic chemistry ; Catalysis Catalytic C–H Functionalization Methods ; Advanced Synthetic Organic Chemistry ; Synthesis and Catalytic Reactions
Authors: Charles Buchanan | Gogulan Karunanithy | Olga Tkachenko | M. Barber | Michael T. Marty | Andrew J. Baldwin
Source: Research Square (preprint, 2022-11-23)
Field: Chemistry — Analytical Chemistry

UnidecNMR: Automatic peak detection for NMR spectra in 1-4 dimensions Deconvolution ; Pipeline (software) ; Spectral line ; NMR spectra database ; Computer science ; Heteronuclear single quantum coherence spectroscopy ; Software ; Function (biology) ; Two-dimensional nuclear magnetic resonance spectroscopy ; Quality (philosophy) ; Range (aeronautics) ; Biological system ; Algorithm ; Nuclear magnetic resonance ; Physics ; Materials science Spectroscopy and Chemometric Analyses ; Gene expression and cancer classification ; Metabolomics and Mass Spectrometry Studies
Authors: Davide Romani | María B. Márquez | Silvia Antonia Brandán | S Grant | H Langtry | R Brogden | Ranitidine | K Bardhan | G Bianchi Porro | K Bose | M Daly | R Hinchliffe | E Jonsson | M Lazzaroni | J Naesdal | L Rikner | A Walan | P Bauerfeind | T Cilluffo | C Emde | C Fimmel | W Kohler | T Gasser | A Blum | A Oliva | S Partemi | V Arena | F De Giorgio | C Colecchi | N Fucci | V Pascali | S Jain | M Srinath | C Narendra | S Reddy | A Sindhu | R Pahwa | S Sharma | V Kumar | K Kohli | P Stephens | A Huq | T Ishida | Y In | M Inoue | A Hempel | N Camerman | D Mastropaolo | A Camerman | S Mondal | K Aikat | G Halder | F Lanza | F Chan | E Quigley | R Crowther | R Bellanger | K Szauter | K Demirkan | B Bozkurt | G Karakaya | A Kalyoncu | E Stepanova | A Arzamastsev | A Titova | M Jamrgiewicz | J ukasiak | P Ramesh | S Gunasekaran | G Ramkumar | S Brandn | T Cholerton | J Hunt | G Klinkert | M Martin-Smith | G Rauhut | P Pulay | T Sundius | J Ruiz Hidalgo | R Rudyk | M Checa | C Cataln | Structural | M Mrquez | K Guzzetti | M Iramain | M Manzur | F Biegler-Kning | J Schnbohm | D Bayles | Aim | D Romani | O Noureddine | N Issaoui
Source: Biointerface Research in Applied Chemistry (article, 2022-06-07)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Vibrational Study of Mono and Diprotonated Species of Potent Anti-acid Ranitidine Hydrochloride Combining DFT with SQMFF Calculations Structural and vibrational studies of mono (M) and diprotonated (D) species of ranitidine hydrochloride (RH) have been performed by combining B3LYP/6-31G* calculations with the scaled quantum mechanical force field (SQMFF) methodology. Four M structures in the gas phase and aqueous solution and two D E/Z and Z/E isomers in solution were considered. The M and D free base, cationic, and hydrochloride species show higher dipole moment values and expansion of volumes in solution, while higher solvation energies are predicted for both D (E/Z) and (Z/E) species. NBO and AIM studies suggest high stabilities of D (Z/E) cationic and hydrochloride species in solution. Gap values show that the M and D species are the most reactive in both media. M and two D forms were completely assigned, and their force constants were reported. The D hydrochloride (E/Z) form shows two IR bands at 2718 and 2625 cm-1 assigned to νN6-H34 and νN5-H44 stretching modes where the formation of O3-H34···N6 bond justifies the strong shifting of N6-H34 stretching mode towards lower wavenumbers. The IR bands at 2563, 2515, and 2475 cm-1 assigned to the two D species, together with the absence of an intense band at 1764 cm-1, show clearly that M species is not present in the solid phase, but the two D hydrochloride (E/Z) and (Z/E) species. Cationic polymerization ; Chemistry ; Solvation ; Natural bond orbital ; Hydrochloride ; Dipole ; Physical chemistry ; Density functional theory ; Computational chemistry ; Organic chemistry ; Molecule Nonlinear Optical Materials Research ; Synthesis and Characterization of Heterocyclic Compounds ; Structural and Chemical Analysis of Organic and Inorganic Compounds
Authors: David G. Madden | Daniel O’Nolan | Nakul Rampal | Robin Babu | Ceren Çamur | Ali Al Shakhs | Shi‐Yuan Zhang | Graham A. Rance | Javier Pérez | Nicola Casati | Carlos Cuadrado‐Collados | D. O’Sullivan | Nicholas Rice | Thomas Gennett | Philip A. Parilla | Sarah Shulda | Katherine E. Hurst | Vitalie Stavila | Mark D. Allendorf | Joaquín Silvestre‐Albero | Alexander C. Forse | Neil R. Champness | Karena W. Chapman | David Fairen‐Jiménez
Source: ChemRxiv (preprint, 2022-02-23)
Field: Chemistry — Inorganic Chemistry

Densified HKUST-1 Monoliths as a Route to High Volumetric and Gravimetric Hydrogen Storage Capacity We are currently witnessing the dawn of the hydrogen (H2) economy, where H2 will become a primary fuel for heating, transportation, and long-distance and long-term energy storage. Among the diverse possibilities, H2 can be stored as a pressurized gas, cryogenic liquid, or solid fuel via adsorption onto porous materials. Metal-organic frameworks (MOFs) have emerged as the adsorbent materials with the theoretical highest H2 storage densities on both a volumetric and gravimetric basis. However, a critical bottleneck for the use of H2 as a transportation fuel has been the lack of densification methods capable of shaping MOFs into practical formulations whilst maintaining their adsorptive performance. Here, we report a high-throughput screening and deep analysis of a database of MOFs to find optimal materials, followed by the synthesis, characterisation, and performance evaluation of an optimal monolithic MOF (monoMOF) for H2 storage. After densification, this monoMOF stores 46 g L-1 H2 at 50 bar, 77 K, and delivers 41 and 42 g L-1 H2 at operating pressures of 25 and 50 bar, respectively, when deployed in a combined temperature–pressure (25-50 bar/77 K → 5 bar/160 K) swing gas delivery system. This performance represents up to an 80% reduction in the operating pressure requirements for delivering H2 gas when compared with benchmark materials, and an 83% reduction compared to compressed H2 gas. Our findings represent a substantial step forward in the application of high-density materials for volumetric H2 storage applications. Gravimetric analysis ; Hydrogen storage ; Materials science ; Pressure swing adsorption ; Bar (unit) ; Process engineering ; Metal-organic framework ; Adsorption ; Bottleneck ; Porosity ; Chemical engineering ; Energy storage ; Fuel gas ; Hydrogen ; Computer science ; Composite material ; Chemistry ; Thermodynamics ; Organic chemistry ; Engineering Metal-Organic Frameworks: Synthesis and Applications ; Boron and Carbon Nanomaterials Research ; Carbon dioxide utilization in catalysis
Authors: Tie-qing Zhang | Seunghun Jung | Young‐Bae Kim
Source: Preprints.org (preprint, 2022-11-24)
Field: Materials Science — Materials Chemistry

Hydrogen Production System through Dimethyl Ether Autothermal Reforming based on Model Predictive Control The objective of this study is to design an optimal model predictive control (MPC) strategy using manipulated variables to control the production of a sufficient amount of hydrogen through low temperature autothermal reforming of dimethyl ether (DME), a reforming reaction performed using PdO/ZnO/&amp;gamma;-Al2O3 catalysts coated on honeycomb cordierite ceramics. Experiments and simulation have verified that the optimal activity temperature of the catalyst is 400 &amp;deg;C, and the hydrogen volume fraction in syngas is over 43%. In the implementation of the hydrogen production system, the MPC controller can precisely determine the feed rates of DME, high-purity air, and water based on the space state equation of the reformer, to achieve the anti-disturbance of the reformer temperature. Thus, the reduction of hydrogen yield and sintering of the catalyst as a result of overheating are prevented. As the static and dynamic performance of hydrogen production exhibits excellent tracking of the setpoints, an autonomous, automated, and reliable continuous system was designed to meet the desired hydrogen demand situation. This study shows that an autonomous, automated, and reliable continuous hydrogen production reforming system can be designed to actively respond to the on-board hydrogen usage situation. Hydrogen production ; Steam reforming ; Methane reformer ; Model predictive control ; Hydrogen ; Dimethyl ether ; Process engineering ; Materials science ; Catalysis ; Chemical engineering ; Computer science ; Chemistry ; Engineering ; Organic chemistry Catalytic Processes in Materials Science ; Catalysts for Methane Reforming ; Catalysis and Hydrodesulfurization Studies
Authors: Martin Morgeneyer | H. J. Feise | Jerry Y. Y. Heng | Martin Lehmann | Daniele Marchisio | Maria G. Rasteiro | Steve Ward-Smith
Source: Process Safety and Environmental Protection (article, 2022-09-16)
Field: Materials Science — Materials Chemistry

Particle technology’s contributions to the major challenges of the 21st century A predictive retrospective as a particular birthday present of IChemE Vision ; Field (mathematics) ; Engineering ethics ; Political science ; Engineering ; Data science ; Environmental ethics ; Computer science ; Sociology Graphite, nuclear technology, radiation studies
Authors: Matthias T. Agne | Shashwat Anand | G. Jeffrey Snyder
Source: Research Square (preprint, 2022-01-10)
Field: Materials Science — Materials Chemistry

Inherent anharmonicity of harmonic solids Abstract Atomic vibrations, in the form of phonons, are foundational in describing the thermal behavior of materials. The possible frequencies of phonons in materials are governed by the complex bonding between atoms, which is physically represented by a spring-mass model that can account for interactions (spring forces) between the atoms (masses). The lowest order, harmonic, approximation only considers linear forces between atoms and is thought incapable of explaining phenomena like thermal expansion and thermal conductivity, which are attributed to non-linear, anharmonic, interactions. Here we show that the kinetic energy of atoms in a solid produces a pressure much like the kinetic energy of atoms in a gas does. This vibrational or phonon pressure naturally increases with temperature, as it does in a gas, and therefore results in a thermal expansion. Because thermal expansion thermodynamically defines a Grüneisen parameter, which is a typical metric of anharmonicity, we show that even a harmonic solid will necessarily have some anharmonicity. A consequence of this phonon pressure model is a harmonic estimation of the Grüneisen parameter from the ratio of the transverse and longitudinal speeds of sound. We demonstrate the immediate utility of this model by developing a high-throughput harmonic estimate of lattice thermal conductivity that is comparable to other state-of-the-art estimations. By linking harmonic and anharmonic properties explicitly, this study provokes new ideas about the fundamental nature of anharmonicity, while also providing a basis for new materials engineering design metrics. Anharmonicity ; Harmonic ; Materials science ; Physics ; Acoustics ; Condensed matter physics Thermal and Kinetic Analysis ; Thermodynamic and Structural Properties of Metals and Alloys ; Material Science and Thermodynamics