jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Jan Blasius | Paul Zaby | Jürgen Dölz | Barbara Kirchner
Source: The Journal of Chemical Physics (article, 2022-06-09)
Field: Chemistry — Organic Chemistry

Uncertainty quantification of phase transition quantities from cluster weighting calculations In this work, we investigate how uncertainties in experimental input data influence the results of quantum cluster equilibrium calculations. In particular, we focus on the calculation of vaporization enthalpies and entropies of seven organic liquids, compare two computational approaches for their calculation, and investigate how these properties are affected by changes in the experimental input data. It is observed that the vaporization enthalpies and entropies show a smooth dependence on changes in the reference density and boiling point. The reference density is found to have only a small influence on the vaporization thermodynamics, whereas the boiling point has a large influence on the vaporization enthalpy but only a small influence on the vaporization entropy. Furthermore, we employed the Gauss--Hermite estimator in order to quantify the uncertainty in thermodynamic functions that stems from inaccuracies in the experimental reference data for the example of the vaporization enthalpy of (R)-butan-2-ol. We quantify the uncertainty as 30.95 · 10<sup>-3</sup> kJ mol<sup>-1</sup>. In addition, we compare the convergence behavior and computational effort of the Gauss-Hermite estimator with the Monte Carlo approach and show the superiority of the former. Using this study, we present how uncertainty quantification can be applied to examples from theoretical chemistry. Vaporization ; Enthalpy of vaporization ; Thermodynamics ; Boiling point ; Estimator ; Weighting ; Enthalpy ; Chemistry ; Statistical physics ; Monte Carlo method ; Mathematics ; Physics ; Statistics Chemical Thermodynamics and Molecular Structure ; Phase Equilibria and Thermodynamics ; Advanced Chemical Physics Studies
Authors: Christos Kannas | Samuel Genheden
Source: ChemRxiv (preprint, 2022-07-15)
Field: Chemistry — Spectroscopy

rxnutils – A Cheminformatics Python Library for Manipulating Chemical Reaction Data We introduce the Python package rxnutils that can be used to manipulate chemical reactions, reaction templates and reaction datasets. The package is built entirely on open-source software such as RDKit and is designed with robustness, extendibility, and reproducibility in mind. Currently, it consists of three sub-packages one for working with chemical entities, one provides pipelining capabilities, and one provides an end-to-end pipeline for preparing the US patent reaction dataset for modelling. In this software research note we discuss the design of the package and provide some code examples. The project is open-source with a Apache 2.0 license and available at GitHub: https://github.com/MolecularAI/rxnutils Python (programming language) ; Computer science ; Cheminformatics ; Open source ; Source code ; Template ; Software ; MIT License ; License ; Software engineering ; Open source software ; Programming language ; Robustness (evolution) ; Database ; Computational science ; Operating system ; Chemistry Analytical Chemistry and Chromatography
Authors: Nishant Singh Jamwal | Amirkianoosh Kiani
Source: Energies (article, 2022-08-18)
Field: Materials Science — Materials Chemistry

Synthesis of 3D Nanonetwork Si Structures via Direct Ultrafast Pulsed Nanostructure Formation Technique Silicon is one of the most used semiconductor materials around the world. This research was conducted on silicon to improve its opto-electrical properties including bandgap and optical conductivity using direct ultrafast pulsed nanostructure formation (DUPNF). The power and frequency of high-intensity picosecond laser pulses were varied, and nanostructures were formed. The optical properties were examined using optical spectroscopy in both VIS and NIR. The structural characteristics were examined using EDX and SEM imaging. It was found that varying the power and frequency of the laser processing caused a change in the bandgap, as well as the structural characteristics of the silicon semiconductor. Increasing the frequency and power showed the formation of nanostructures of silicon and their variation in the properties of the formed nanostructures. The critical breakdown field of the silicon nanostructures was higher than the bulk silicon. Materials science ; Silicon ; Nanostructure ; Semiconductor ; Picosecond ; Optoelectronics ; Band gap ; Ultrashort pulse ; Laser ; Nanotechnology ; Optics Silicon Nanostructures and Photoluminescence ; Nanowire Synthesis and Applications ; Thin-Film Transistor Technologies
Authors: Yujie Liu | Binxiao Li | Baohong Liu | Kun Zhang
Source: Biosensors (review, 2022-12-01)
Field: Materials Science — Materials Chemistry

Single-Particle Optical Imaging for Ultrasensitive Bioanalysis The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial–temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis. Bioanalysis ; Nanotechnology ; Biomolecule ; Characterization (materials science) ; Materials science ; Computer science Quantum Dots Synthesis And Properties ; Photoacoustic and Ultrasonic Imaging ; Biosensors and Analytical Detection
Authors: Natalia Szczepanik | Andrzej Kowalczyk | Zofia Piwowarska | Lucjan Chmielarz
Source: Catalysts (article, 2022-10-27)
Field: Materials Science — Materials Chemistry

MCM-41-Type Mesoporous Silicas Modified with Alumina in the Role of Catalysts for Methanol to Dimethyl Ether Dehydration MCM-41-type mesoporous silicas were modified with alumina by the impregnation, co-condensation, and template ion-exchange (TIE) methods. The obtained materials were characterized with respect to their chemical composition (ICP-OES), textural parameters (low-temperature N2 sorption), structure (XRD), and surface acidity (NH3-TPD) and tested as catalysts of methanol to dimethyl ether (DME) dehydration in a flow microreactor system. The catalytic performance of the studied materials was analyzed with respect to their porous structure, as well as their density and the strength of their acid sites. It was shown that the performance of the studied catalysts depends on the contribution of the surface exposed aluminum species, as well as their aggregation. For the most active catalyst, the study of its catalytic stability under rection conditions was performed. It was shown that the catalyst can be effectively regenerated by the incineration of carbon deposits under air flow at 550 °C for 1 h. Dimethyl ether ; Catalysis ; Mesoporous material ; Methanol ; Dehydration ; Chemical engineering ; Sorption ; Materials science ; Inorganic chemistry ; Chemistry ; Organic chemistry ; Adsorption Catalytic Processes in Materials Science ; Mesoporous Materials and Catalysis ; Zeolite Catalysis and Synthesis
Authors: A. I. Rusanov | Н. В. Чижова | Н. Ж. Мамардашвили
Source: Molecules (article, 2022-12-06)
Field: Materials Science — Materials Chemistry

Synthesis, Structure, and Spectral-Luminescent Properties of Peripherally Fluorinated Mg(II) and Zn(II) Octaphenyltetraazaporphyrins The cyclization of di-(2,6-difluorophenyl)maleindinitrile with magnesium(II) and zinc(II) acetates in boiling ethylene glycol is applied to synthesize Mg(II) and Zn(II) complexes of the octa-(2,6-difluorophenyl)tetraazaporphyrin. The compounds are identified by UV-Vis, <sup>1</sup>H NMR, and mass spectrometry methods. A comparative analysis is performed of the spectral-luminescent properties of magnesium and zinc octaaryltetraazaporphyrinates and their dependence on the number and position of the fluorine atoms in the macrocycle phenyl fragments. The DFT method is used to optimize the geometry of the synthesized complexes. Machine learning methods and QSPR are applied to predict the Soret band wavelength in the UV-V is spectra of the complexes described. Zinc ; Chemistry ; Magnesium ; Luminescence ; Ethylene glycol ; Proton NMR ; Ethylene ; Physical chemistry ; Nuclear chemistry ; Photochemistry ; Organic chemistry ; Materials science Porphyrin and Phthalocyanine Chemistry ; Molecular Sensors and Ion Detection ; Photodynamic Therapy Research Studies
Authors: Catrina E. Wilson | Amanda Gibson | Paul M. Cuillier | Cheng-Han Li | Patrice H. N. Crosby | Edward B. Trigg | Stan Najmr | Christopher B. Murray | Joerg R. Jinschek | Vicky Doan‐Nguyen
Source: Scientific Reports (article, 2022-08-30)
Field: Materials Science — Polymers and Plastics

Local structure elucidation of tungsten-substituted vanadium dioxide (V$$_{1-x}$$W$$_x$$O$$_2$$) Initially, vanadium dioxide seems to be an ideal first-order phase transition case study due to its deceptively simple structure and composition, but upon closer inspection there are nuances to the driving mechanism of the metal-insulator transition (MIT) that are still unexplained. In this study, a local structure analysis across a bulk powder tungsten-substitution series is utilized to tease out the nuances of this first-order phase transition. A comparison of the average structure to the local structure using synchrotron x-ray diffraction and total scattering pair-distribution function methods, respectively, is discussed as well as comparison to bright field transmission electron microscopy imaging through a similar temperature-series as the local structure characterization. Extended x-ray absorption fine structure fitting of thin film data across the substitution-series is also presented and compared to bulk. Machine learning technique, non-negative matrix factorization, is applied to analyze the total scattering data. The bulk MIT is probed through magnetic susceptibility as well as differential scanning calorimetry. The findings indicate the local transition temperature ([Formula: see text]) is less than the average [Formula: see text] supporting the Peierls-Mott MIT mechanism, and demonstrate that in bulk powder and thin-films, increasing tungsten-substitution instigates local V-oxidation through the phase pathway VO[Formula: see text] V[Formula: see text]O[Formula: see text] V[Formula: see text]O[Formula: see text]. Phase transition ; Vanadium ; Crystallography ; Tungsten ; Scattering ; Materials science ; Differential scanning calorimetry ; Local field ; Chemistry ; Condensed matter physics ; Physics ; Thermodynamics ; Optics Transition Metal Oxide Nanomaterials ; Multiferroics and related materials ; Ga2O3 and related materials
Authors: Giada Caniglia | Andrea Teuber | Holger Barth | Boris Mizaikoff | Christine Kranz
Source: Analytical and Bioanalytical Chemistry (article, 2022-11-24)
Field: Materials Science — Surfaces, Coatings and Films

Atomic force and infrared spectroscopic studies on the role of surface charge for the anti-biofouling properties of polydopamine films Antibacterial polymer materials have gained interest due to their capability to inhibit or eradicate biofilms with greater efficiency in comparison with their monomeric counterparts. Among the antimicrobial and anti-biofouling polymers, catecholamine-based polymers - and in particular polydopamine - have been studied due to their favorable adhesion properties, which can be tuned by controlling the pH value. In this study, we used atomic force microscopy (AFM)-based spectroscopy to investigate the relation between the adhesion properties and surface charge density and the pH of electrochemically deposited polydopamine films presenting a dissociation constant of polydopamine of 6.3 ± 0.2 and a point of zero charge of 5.37 ± 0.06. Furthermore, using AFM and attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), the influence of the surface charge density of polydopamine on bacterial adhesion and biofilm formation was investigated. It was shown that the adhesion of Escherichia coli at positively charged polydopamine is three times higher compared to a negatively charged polymer, and that the formation of biofilms is favored at positively charged polymers. Biofouling ; Infrared ; Atomic force microscopy ; Nanotechnology ; Infrared spectroscopy ; Surface charge ; Force spectroscopy ; Charge (physics) ; Analytical Chemistry (journal) ; Chemistry ; Materials science ; Polymer science ; Chemical engineering ; Physical chemistry ; Organic chemistry ; Physics ; Optics ; Engineering Polymer Surface Interaction Studies ; Marine Biology and Environmental Chemistry ; Force Microscopy Techniques and Applications
Authors: Alexey A. Orlov | Savva D. Semenov | Gleb D. Rukhovich | Anastasia Sarycheva | Oxana A. Kovaleva | А. Л. Семенов | Elena D. Ermakova | Е. А. Губарева | Anna E. Bugrova | А. С. Кононихин | Elena I. Fedoros | Е. Н. Николаев | Alexander Zherebker
Source: International Journal of Molecular Sciences (article, 2022-12-16)
Field: Chemistry — Analytical Chemistry

Hepatoprotective Activity of Lignin-Derived Polyphenols Dereplicated Using High-Resolution Mass Spectrometry, In Vivo Experiments, and Deep Learning Chronic liver diseases affect more than 1 billion people worldwide and represent one of the main public health issues. Nonalcoholic fatty liver disease (NAFLD) accounts for the majority of mortal cases, while there is no currently approved therapeutics for its treatment. One of the prospective approaches to NAFLD therapy is to use a mixture of natural compounds. They showed effectiveness in alleviating NAFLD-related conditions including steatosis, fibrosis, etc. However, understanding the mechanism of action of such mixtures is important for their rational application. In this work, we propose a new dereplication workflow for deciphering the mechanism of action of the lignin-derived natural compound mixture. The workflow combines the analysis of molecular components with high-resolution mass spectrometry, selective chemical tagging and deuterium labeling, liver tissue penetration examination, assessment of biological activity in vitro, and computational chemistry tools used to generate putative structural candidates. Molecular docking was used to propose the potential mechanism of action of these structures, which was assessed by a proteomic experiment. Chemistry ; Mass spectrometry ; Computational biology ; Steatosis ; In vivo ; Nonalcoholic fatty liver disease ; Lignin ; Polyphenol ; Biochemistry ; Biochemical engineering ; Bioinformatics ; Fatty liver ; Biology ; Medicine ; Biotechnology ; Chromatography ; Disease ; Pathology ; Antioxidant ; Organic chemistry Chromatography in Natural Products ; Drug-Induced Hepatotoxicity and Protection ; Computational Drug Discovery Methods
Authors: Natashya Evangeline Fiorelia | Anthony Dharma Wibowo | Natanael Leonard Lae | A. Manoharan S.S. Ang | Oki Krisbianto
Source: FoodTech Jurnal Teknologi Pangan (review, 2022-05-25)
Field: Chemistry — Spectroscopy

Types of High-Performance Liquid Chromatography (HPLC) Columns: A Review Some chemical analysts, especially those working in the food sector, often find it difficult to choose the HPLC columns for their research. Every so often they tend to modify their method to fit whatever HPLC column available in their laboratory instead of looking for the column type best suited to their experiments. Other than that, HPLC column types are often very limited discussed in the class. This is particularly disadvantageous for those who have sufficient access to select the HPLC column they need for the best result. The lack of insight into the types of HPLC columns available in the market also influenced their decision to select the right column in their analysis to a large extent. This article briefly reviews the differences between the commonly used Particle-Packed Columns with the newer yet less frequently used Monolithic Columns. The types of HPLC columns based on polarity, molecular size, and the electrical charge will be described further, along with the working principle of the columns in brief and various examples of options available on the market. Lastly, the uses of HPLC columns in the food industries are also described. This review is expected to contribute to the field of chemical analysis, such as food analysis. High-performance liquid chromatography ; Column (typography) ; Chromatography ; Chemistry ; Computer science Analytical Chemistry and Chromatography ; Electrochemical sensors and biosensors ; Advanced Chemical Sensor Technologies
Authors: Tie-qing Zhang | Seunghun Jung | Young‐Bae Kim
Source: Energies (article, 2022-11-29)
Field: Materials Science — Materials Chemistry

Hydrogen Production System through Dimethyl Ether Autothermal Reforming, Based on Model Predictive Control In this study, a thermodynamic analysis of the low temperature autothermal reforming (ATR) of dimethyl ether (DME) for hydrogen production was conducted. The Pd/Zn/γ-Al2O3 catalyst coated on the honeycomb cordierite ceramic was applied to catalyze the reaction, and the optimum activity temperature of this catalyst was demonstrated experimentally and through simulations to be 400 °C. Furthermore, an optimal model predictive control (MPC) strategy was designed to control the hydrogen production rate and the catalyst temperature. Experimental and simulation results indicated that the controller was automated and continuously reliable in the hydrogen production system. By establishing the state-space equations of the autothermal reformer, it can precisely control the feed rates of DME, high-purity air and deionized water. Ultimately, the hydrogen production rate can be precisely controlled when the demand curve changed from 0.09 to 0.23 mol/min, while the catalyst temperature was maintained at 400 °C, with a temporary fluctuation of 4 °C during variations of the hydrogen production rate. Therefore, the tracking performance of the hydrogen production and the anti-disturbance were satisfactory. Hydrogen production ; Catalysis ; Dimethyl ether ; Methane reformer ; Hydrogen ; Model predictive control ; Steam reforming ; Reaction rate ; Materials science ; Chemical engineering ; Chemistry ; Organic chemistry ; Computer science ; Engineering ; Control (management) Catalytic Processes in Materials Science ; Catalysts for Methane Reforming ; Catalysis and Hydrodesulfurization Studies
Authors: Daniel T. Murray | David Shin | Scott Classen | Chris A. Brosey | Greg L. Hura
Source: Methods in enzymology on CD-ROM/Methods in enzymology (article, 2022-11-03)
Field: Materials Science — Materials Chemistry

Visualizing and accessing correlated SAXS data sets with Similarity Maps and Simple Scattering web resources Small-angle X-ray scattering ; Similarity (geometry) ; Scattering ; Set (abstract data type) ; Computer science ; Biological system ; Data set ; Biological data ; Data mining ; Simple (philosophy) ; Bioinformatics ; Artificial intelligence ; Physics ; Biology ; Optics Enzyme Structure and Function ; Protein Structure and Dynamics ; Machine Learning in Materials Science
Authors: Xiaomi Guo | Lincan Fang | Yong Xu | Wenhui Duan | Patrick Rinke | Milica Todorović | Xi Chen
Source: Journal of Chemical Theory and Computation (article, 2022-06-13)
Field: Materials Science — Materials Chemistry

Molecular Conformer Search with Low-Energy Latent Space Identifying low-energy conformers with quantum mechanical accuracy for molecules with many degrees of freedom is challenging. In this work, we use the molecular dihedral angles as features and explore the possibility of performing molecular conformer search in a latent space with a generative model named variational auto-encoder (VAE). We bias the VAE towards low-energy molecular configurations to generate more informative data. In this way, we can effectively build a reliable energy model for the low-energy potential energy surface. After the energy model has been built, we extract local-minimum conformations and refine them with structure optimization. We have tested and benchmarked our low-energy latent-space (LOLS) structure search method on organic molecules with 5-9 searching dimensions. Our results agree with previous studies. Conformational isomerism ; Dihedral angle ; Computer science ; Potential energy surface ; Space (punctuation) ; Energy (signal processing) ; Energy minimization ; Potential energy ; Degrees of freedom (physics and chemistry) ; Molecule ; Biological system ; Physics ; Computational chemistry ; Chemistry ; Quantum mechanics ; Hydrogen bond Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Hassan Nezammahalleh | Faezeh Ghanati | Shima Rezaei | Mohsin Ali Badshah | Joobee Park | Naseem Abbas | Ahsan Ali
Source: Polymers (review, 2022-07-13)
Field: Materials Science — Biomaterials

Biochemical Interactions through Microscopic Techniques: Structural and Molecular Characterization Many researchers and scientists have contributed significantly to provide structural and molecular characterizations of biochemical interactions using microscopic techniques in the recent decade, as these biochemical interactions play a crucial role in the production of diverse biomaterials and the organization of biological systems. The properties, activities, and functionalities of the biomaterials and biological systems need to be identified and modified for different purposes in both the material and life sciences. The present study aimed to review the advantages and disadvantages of three main branches of microscopy techniques (optical microscopy, electron microscopy, and scanning probe microscopy) developed for the characterization of these interactions. First, we explain the basic concepts of microscopy and then the breadth of their applicability to different fields of research. This work could be useful for future research works on biochemical self-assembly, biochemical aggregation and localization, biological functionalities, cell viability, live-cell imaging, material stability, and membrane permeability, among others. This understanding is of high importance in rapid, inexpensive, and accurate analysis of biochemical interactions. Characterization (materials science) ; Nanotechnology ; Microscopy ; Materials science ; Pathology ; Medicine Supramolecular Self-Assembly in Materials ; Lipid Membrane Structure and Behavior ; Polydiacetylene-based materials and applications