jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yongbin Kuang | Weiwei Ni | Liu Han | Jinsong Han
Source: ChemMedChem (review, 2024-11-24)
Field: Materials Science — Materials Chemistry

Poly(<i>p</i>‐Phenyleneethynylene)s‐Based Sensor Array for Diagnosis of Clinical Diseases Inspired by the mammalian taste and olfactory systems, array-based pattern recognition technology has demonstrated significant potential in discerning subtle differences between highly similar compounds and complex mixtures, owing to their unique parallel detection mechanism based on cross-reactive signals. While optical sensor array has been extensively employed in the field of chemical sensing, they encounter significant challenges in non-specific recognition of multiple analytes at low concentrations, particularly in rife environments with complex interferences. Poly(p-phenylene ethynylene)s (PPEs) offer substantial advantages in detecting multi-analytes at low concentrations, owing to its distinctive optical properties, including the "molecular wire" effect, fluorescence super-amplification and super-quenching. This is particularly promising for the parallel detection of ultra-low concentration multi-biomarkers in clinical diseases. As the continuous development of PPEs sensor array, more sensitive methods for rapid detection of clinical disease will be further developed. It will promote the further development of the field of early diagnosis of clinical diseases. Medicine ; Materials science Luminescence and Fluorescent Materials ; Advanced biosensing and bioanalysis techniques ; Polydiacetylene-based materials and applications
Authors: Junhui Peng | Evgenii Tikhonov
Source: physica status solidi (b) (article, 2024-12-18)
Field: Materials Science — Ceramics and Composites

Computational Search for Compounds with the Highest Melting Temperature in the Ternary HfC‐Based Ceramics The melting temperature ( T m ) determines the service temperature of ultrahigh‐temperature ceramics (UHTCs), so it is of great significance to search for compound with the highest T m in UHTCs. In present work, the formula to calculate the T m of UHTCs with the rock salt structure is modified first: T m = f ( c ) EV m /(100 k B ), f ( c ) = 0.6412* c + 0.9947, which considers the influence of vacancy concentration ( c ) on the T m . The calculated T ms are in good agreement with the experimental values of UHTCs, and the calculation accuracy exceeds 91%. The T m could be obtained by only calculating the elastic modulus and volume per atom. Using this formula, the T ms of ternary HfC‐based UHTCs with the rock salt structure are predicted, and a new compound with the highest melting temperature, HfTa 2 C 3 , is found. Finally, the empirical relationship between the T m and shear modulus or Vickers hardness of UHTCs with the rock salt structure is also investigated. Ternary operation ; Ceramic ; Melting temperature ; Materials science ; Thermodynamics ; Metallurgy ; Computer science ; Composite material ; Physics Advanced ceramic materials synthesis ; Intermetallics and Advanced Alloy Properties ; Inorganic Chemistry and Materials
Authors: Faranak Karamifard | Mahta Mazaheri | Ali Dadbinpour
Source: In Silico Pharmacology (article, 2024-04-11)
Field: Materials Science — Materials Chemistry

Abatement of the binding of human hexokinase II enzyme monomers by in-silico method with the design of inhibitory peptides In silico ; Hexokinase ; Enzyme ; Inhibitory postsynaptic potential ; Chemistry ; Biochemistry ; Computational biology ; Biology ; Glycolysis ; Neuroscience ; Gene Enzyme Structure and Function ; Biochemical and Molecular Research ; Cancer, Hypoxia, and Metabolism
Authors: Arshi Abbas | Syed Salman Shafqat | Muhammad Faizan Nazar | Hafeez Ullah Khan | Asma Mukhtar | Muhammad Tayyab | Asad Syed | Muhammad Nadeem Zafar | Syeda Amna Masood | Kashif Kamran
Source: International Journal of Chemical Kinetics (article, 2024-03-15)
Field: Chemistry — Organic Chemistry

Molecular interaction of nonsteroidal anti‐inflammatory prodrug nepafenac with ionic surfactants Abstract Drug‐surfactant interaction increases the solubility of poorly water‐soluble drugs and design better pharmaceutical formulations. The degree of interaction of nepafenac (NP), a nonsteroidal anti‐inflammatory prodrug was studied with ionic surfactant molecules such as cationic surfactant cetrytrimethyl ammonium bromide (CTAB) and anionic surfactant sodium dodecyl sulphate (SDS) in an aqueous medium at room temperature. NP made mixed micelles with CTAB and SDS. To investigate the influence of interactions, conductivity measurements, UV–visible spectroscopy, and fluorescence measurements were recorded. The quantification of NP–surfactant interactions was investigated using various mathematical models. The CMC values determined from conductivity measurements of pure surfactants were 0.96 mM for CTAB and 8.14 mM for SDS near to their literature values. At different mole fractions of NP in UV measurements, binding constants from lnKb were found 0.025 and 0.123 and number of NP molecules per micelles ( n ) 67, 46 for CTAB and SDS, respectively. The mixed micelles of NP–CTAB and NP–SDS revealed that CTAB has a strong interaction with NP than SDS. The Benesi–Hildebrand relationship, Stern–Volmer and Kawamura replica for the partition coefficient were used to confirm the findings. We are confident that the host–guest interaction mechanism can contribute to a better understanding of molecular recognition in the phospholipid membrane model. Chemistry ; Nonsteroidal ; Prodrug ; Ionic bonding ; Anti-inflammatory ; Pharmacology ; Combinatorial chemistry ; Organic chemistry ; Biochemistry ; Ion Surfactants and Colloidal Systems ; Analytical Chemistry and Chromatography ; Protein Interaction Studies and Fluorescence Analysis
Authors: Xiaohong Ji | Zhen Wang | Zhifeng Gao | Hang Zheng | Linfeng Zhang | Guolin Ke | E Weinan
Source: arXiv (Cornell University) (preprint, 2024-06-21)
Field: Chemistry — Physical and Theoretical Chemistry

Uni-Mol2: Exploring Molecular Pretraining Model at Scale In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining models remains unexplored. In this work, we present Uni-Mol2 , an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, characterizing the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale Uni-Mol2 to 1.1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show consistent improvement in the downstream tasks as the model size grows. The Uni-Mol2 with 1.1B parameters also outperforms existing methods, achieving an average 27% improvement on the QM9 and 14% on COMPAS-1D dataset. Scale (ratio) ; Scale model ; Psychology ; Computer science ; Geography ; Engineering ; Cartography ; Aerospace engineering Various Chemistry Research Topics
Authors: Ismet Can Sahin | Can Eyüpoğlu
Source: İstanbul Ticaret Üniversitesi Teknoloji ve Uygulamalı Bilimler Dergisi (article, 2024-01-29)
Field: Chemistry — Analytical Chemistry

TEXTILE DYEING PROCESS AND DYEING RECIPE PREDICTION USING ARTIFICAL INTELLIGENCE In this study, a comprehensive analysis is presented on the determination and estimation of the sample color or target color taken from the customer in the laboratory department of textile dyeing companies. The importance of the textile industry in the world and Turkey is also mentioned. In the report published by Statista, it is seen that the textile industry has a share of 3.3% in Turkey and the world. In this work, a sample study was conducted in a textile finishing company and the processes were shared. First, the classical processes used to determine the target color are explained in detail. Then, it was mentioned how the data obtained with the spectrophotometer device is used in color estimation using machine learning methods and artificial neural networks According to the results of the examination, it is seen that the data obtained with the hyperspectral camera device is estimated by the long short-term memory (LSTM) model, since the spectrophotometer device is expensive and does not give accurate results recently. In addition, it has been observed that this model gives better results than the same model created from the data obtained with the spectrophotometer device Dyeing ; Textile ; Sample (material) ; Artificial intelligence ; Recipe ; Process (computing) ; Computer science ; Textile industry ; Artificial neural network ; Hyperspectral imaging ; Process engineering ; Pulp and paper industry ; Engineering ; Materials science ; Geography ; Chromatography ; Chemistry ; Composite material Spectroscopy and Chemometric Analyses ; Color Science and Applications ; Dyeing and Modifying Textile Fibers
Authors: Roberta Puglisi | Alessia Cavallaro | Andrea Pappalardo | Manuel Petroselli | Rossella Santonocito | Giuseppe Trusso Sfrazzetto
Source: Molecules (article, 2024-08-05)
Field: Materials Science — Materials Chemistry

A New BODIPY-Based Receptor for the Fluorescent Sensing of Catecholamines The human body synthesizes catecholamine neurotransmitters, such as dopamine and noradrenaline. Monitoring the levels of these molecules is crucial for the prevention of important diseases, such as Alzheimer's, schizophrenia, Parkinson's, Huntington's, attention-deficit hyperactivity disorder, and paragangliomas. Here, we have synthesized, characterized, and functionalized the BODIPY core with picolylamine (BDPy-pico) in order to create a sensor capable of detecting these biomarkers. The sensing properties of the BDPy-pico probe in solution were studied using fluorescence titrations and supported by DFT studies. Catecholamine sensing was also performed in the solid state by a simple strip test, using an optical fiber as the detector of emissions. In addition, the selectivity and recovery of the sensor were assessed, suggesting the possibility of using this receptor to detect dopamine and norepinephrine in human saliva. BODIPY ; Catecholamine ; Fluorescence ; Dopamine ; Chemistry ; Receptor ; Norepinephrine ; Biophysics ; Biochemistry ; Neuroscience ; Biology ; Physics Luminescence and Fluorescent Materials ; Electrochemical sensors and biosensors ; Carbon and Quantum Dots Applications
Authors: Nathalie Proos Vedin | Sílvia Escayola | Slavko Radenković | Miquel Solà | Henrik Ottosson
Source: ChemRxiv (preprint, 2024-02-01)
Field: Chemistry — Organic Chemistry

The n,π* States of Heteroaromatics: When are They the Lowest Excited States and in What Way Can They Be Aromatic or Antiaromatic? Heteroaromatic molecules are found in areas ranging from biochemistry to photovoltaics. We analyze the n,π* excited states of 6π-electron heteroaromatics with in-plane lone-pairs (n(sigma), herein n), and use qualitative theory and quantum chemical computations, starting at Mandado’s 2n+1 rule for aromaticity of separate spins. After excitation of an electron from n to π*, a (4n+2)π-electron species has 2n+2 π(alpha)-electrons and 2n+1 π(beta)-electrons (or vice versa), and becomes π(alpha)-antiaromatic and π(beta)-aromatic. Yet, the antiaromatic π(alpha)- and aromatic π(beta)-components seldom cancel, leading to residuals with aromatic or antiaromatic character. We explore vertically excited triplet n,π* states (3n,π*), which are most readily analyzed, but also singlet n,π* states (1n,π*), and explain which compounds have n,π* states with aromatic residuals as their lowest excited states (e.g., pyrazine and the phenyl anion). If the π-electron population becomes more (less) uniformly distributed upon excitation, the system will have an (anti-)aromatic residual. Among isomers, the one which has the most aromatic residual in 3n,π* is often of lowest energy in this state. Five-membered ring heteroaromatics with one or two N, O and/or S atoms never have n,π* states as their first excited states (T1 and S1), while this is nearly always the case for six-membered ring heteroaromatics with electropositive heteroatoms and/or highly symmetric (D2h) diheteroaromatics. For the complete compound set, there is a modest correlation between the (anti)aromatic character of the n,pi* state and the energy gap between the lowest n,π* and π,π* states (R2 = 0.42), while it is stronger for monosubstituted pyrazines (R2 = 0.84). Antiaromaticity ; Excited state ; Aromaticity ; Chemistry ; Ring (chemistry) ; Heteroatom ; Singlet state ; Population ; Pi interaction ; Electron ; Computational chemistry ; Crystallography ; Molecule ; Atomic physics ; Physics ; Quantum mechanics ; Organic chemistry Synthesis and Properties of Aromatic Compounds ; Molecular Junctions and Nanostructures ; Fullerene Chemistry and Applications
Authors: Vipin Kumar | Pushpendra Kumar | Akash Akash | Ajay Saini | Jin Seog Gwag
Source: ChemistrySelect (article, 2024-09-30)
Field: Materials Science — Materials Chemistry

Tunable Electronic, Optoelectronic, and Photocatalytic Properties of MoS <sub>2</sub> and GaS Monolayers in the MoS <sub>2</sub> /GaS Heterostructure Abstract The electronic structure calculations show that the GaS and MoS 2 monolayer and MoS 2 /GaS hetero‐bilayer systems are semiconducting materials. It is also justified by the density of states. In the hetero‐bilayer system, the band gap is reduced. It causes an increase in the absorption, compared to their monolayers, of incident light in the visible region. This may be because of the charge transfer and the interlayer interaction between these monolayers in the heterostructure form. The calculated higher extinction coefficient causes the fast absorption of light, hence, the increased absorption coefficient. The heterostructure system makes the refractive index and reflection coefficient of GaS and MoS 2 monolayers tuneable. The static reflection coefficient is in the following order GaS &lt; MoS 2 /GaS &lt; MoS 2 . It means that the MoS 2 /GaS heterostructure system can increase the static refractive index of GaS and decrease that of MoS 2 monolayers simultaneously. The calculated band edge positions show that the MoS 2 and GaS monolayers have excellent water oxidation and reduction capability, respectively. These predictions show that the proposed heterostructure may be a potential candidate for nanoelectronics and optoelectronics. Heterojunction ; Monolayer ; Optoelectronics ; Materials science ; Photocatalysis ; Nanotechnology ; Chemistry ; Catalysis 2D Materials and Applications ; Chalcogenide Semiconductor Thin Films ; MXene and MAX Phase Materials
Authors: P. M. Rafailov | Dimitre Dimitrov | Daniela Kovacheva | Vera Marinova
Source: Nanomaterials (article, 2024-07-27)
Field: Materials Science — Materials Chemistry

Polarized Raman Study of First-Order Phonons in Self-Flux Grown Single-Crystalline WTe2 Bulk single crystals of WTe<sub>2</sub> were grown by the self-flux method and characterized by X-ray diffraction, polarized micro-Raman spectroscopy, and optical microscopy. All methods revealed a high crystalline quality, thus demonstrating the advantages of the growth method used as a starting base for the synthesis of high-quality 2D materials. In each main scattering configuration, we recorded a series of Raman spectra in different sample orientations achieved by rotating the sample around the incident laser beam. In addition to the well-established case of excitation along the c crystal axis, we also applied laser excitation along the a and b axes. Thus, scattering configurations were also realized in the XZ and YZ polarization planes, for which no comparative literature data have yet been established. In these experiments, two new Raman-active phonons with B<sub>2</sub> symmetry and frequencies of 89 cm<sup>-1</sup> and 122 cm<sup>-1</sup> were identified. The obtained experimental data enabled us to derive the magnitude ratios of all three tensor elements of the A<sub>1</sub> modes and to find their phase differences. Raman spectroscopy ; Phonon ; Raman scattering ; Excitation ; Materials science ; Diffraction ; Laser ; Optics ; Polarization (electrochemistry) ; Coherent anti-Stokes Raman spectroscopy ; Single crystal ; Scattering ; X-ray Raman scattering ; Molecular physics ; Crystal (programming language) ; Analytical Chemistry (journal) ; Crystallography ; Condensed matter physics ; Chemistry ; Physics 2D Materials and Applications ; Topological Materials and Phenomena ; Advanced Thermoelectric Materials and Devices
Authors: Jiayun Pang | Ivan Vulić
Source: Faraday Discussions (article, 2024-08-19)
Field: Materials Science — Materials Chemistry

Specialising and analysing instruction-tuned and byte-level language models for organic reaction prediction Transformer-based encoder-decoder models have demonstrated impressive results in chemical reaction prediction tasks. However, these models typically rely on pretraining using tens of millions of unlabelled molecules, which can be time-consuming and GPU-intensive. One of the central questions we aim to answer in this work is: can FlanT5 and ByT5, the encoder-decoder models pretrained solely on language data, be effectively specialised for organic reaction prediction through task-specific fine-tuning? We conduct a systematic empirical study on several key issues of the process, including tokenisation, the impact of (SMILES-oriented) pretraining, fine-tuning sample efficiency, and decoding algorithms at inference. Our key findings indicate that although being pretrained only on language tasks, FlanT5 and ByT5 provide a solid foundation to fine-tune for reaction prediction, and thus become 'chemistry domain compatible' in the process. This suggests that GPU-intensive and expensive pretraining on a large dataset of unlabelled molecules may be useful yet not essential, to leverage the power of language models for chemistry. All our models achieve comparable Top-1 and Top-5 accuracy although some variation across different models does exist. Notably, tokenisation and vocabulary trimming slightly affect final performance but can speed up training and inference; the most efficient greedy decoding strategy is very competitive while only marginal gains can be achieved from more sophisticated decoding algorithms. In summary, we evaluate FlanT5 and ByT5 across several dimensions and benchmark their impact on organic reaction prediction, which may guide more effective use of these state-of-the-art language models for chemistry-related tasks in the future. Byte ; Computer science ; Programming language Machine Learning in Materials Science ; Topic Modeling
Authors: B. Srinivas | Deepak B. Huple | Andrei G. Kutateladze
Source: Angewandte Chemie International Edition (article, 2024-09-12)
Field: Chemistry — Organic Chemistry

Complexity‐Building Exhaustive Dearomatization of Benzenoid Aromatics within an ESIPT‐Initiated Three‐Step Photochemical Cascade. Dearomative cycloadditions offer rapid access to complex 3D molecular architectures, commonly via a sp<sup>2</sup>-to-sp<sup>3</sup> rehybridization of two atoms of an aromatic ring. Here we report that the 6e π-system of a benzenoid aromatic pendant could be exhaustively depleted within a single photochemical cascade. An implementation of this approach involves the initial dearomative [4+2] cycloaddition of the Excited State Intramolecular Proton Transfer (ESIPT)-generated azaxylylene, followed by two consecutive [2+2] cycloadditions of auxiliary π moieties strategically positioned in the photoprecursor. Such photochemical cascade fully dearomatizes the benzenoid aromatic ring, saturating all six sp<sup>2</sup> atoms to yield a complex sp<sup>3</sup>-rich scaffold with high control of its 3D molecular shape, rendering it a robust platform for rapid systematic mapping of underexplored chemical space. Significant growth of molecular complexity-starting with a modular synthesis of photoprecursors from readily available building blocks-is quantified by Böttcher score calculations. Intramolecular force ; Cascade ; Cycloaddition ; Chemistry ; Ring (chemistry) ; Modular design ; Aromaticity ; Computational chemistry ; Combinatorial chemistry ; Photochemistry ; Molecule ; Stereochemistry ; Computer science ; Organic chemistry Radical Photochemical Reactions ; Photochromic and Fluorescence Chemistry ; Synthesis and Properties of Aromatic Compounds
Authors: Vladimir A. Pomogaev | E. N. Bocharnikova | O. N. Tchaikovskaya | Павел В. Аврамов
Source: International Journal of Quantum Chemistry (article, 2024-10-22)
Field: Chemistry — Physical and Theoretical Chemistry

Phenol Photostatic Spectra and Quantum‐Classical Photodynamic Deprotonation ABSTRACT The spectral‐luminescence properties and photochemical conversions of phenol were analyzed for an isolated molecule as well as in water solvents in a continuum implicit model and explicit atomistic surroundings. This involved employing cut‐edge hybrid quantum‐classical methodologies to generate static optical spectra and the excited dissipative crossing potential energy curves. A combination of electronic excitations, gradient calculations, and embedding electrostatic potential fitting charges on quantum‐classical molecular dynamic propagation trajectories provided statistically averaged absorption spectra. The mixed‐reference spin‐flip multiconfigurational linear response method based on reference triplet preprocessed in the time‐dependent density‐functional theory was utilized to determine conical intersections between the lowest excited and ground states, as well as two‐stage transitions from the second excitation to the ground state. Non‐adiabatic quantum‐classical molecular dynamics defined photodissipative trajectories of excited states, their lifetimes, and crossing points through trajectory surface hopping together with the mixed‐reference spin‐flip and embedding electrostatic potential fitting approaches. Dyson orbitals of the extended Koopmans' theorem were applied to reveal the nature of molecular states at conical intersections and key points on photodynamic trajectories. Potential hydroxyl group cleavage predicted with conical intersections searching turns to “swift” OH deprotonation through |π→⟩ transition along photodynamic propagations in contrast with “long” processes leading to benzene ring deformation with stable OH bond. Deprotonation ; Phenol ; Quantum ; Spectral line ; Chemistry ; Computational chemistry ; Photochemistry ; Physics ; Quantum mechanics ; Organic chemistry Photochemistry and Electron Transfer Studies ; Various Chemistry Research Topics ; Spectroscopy and Quantum Chemical Studies