jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Hamed Barabadi | Faraz Mojab | Fatemeh Ashouri | Kamyar Jounaki | Reza Jahani | Ali Ramezani
Source: Green Processing and Synthesis (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

<i>Trachyspermum copticum</i> aqueous seed extract-derived silver nanoparticles: Exploration of their structural characterization and comparative antibacterial performance against gram-positive and gram-negative bacteria Abstract In this study, the aqueous seed extract of Trachyspermum copticum was employed to fabricate silver nanoparticles (AgNPs) for their antibacterial performance. The structural characteristics of the phytofabricated AgNPs were investigated using ultraviolet–visible, energy dispersive X-ray, dynamic light scattering, zeta potential, field emission scanning electron microscope, and Fourier transform infrared spectroscopy. Further, the antibacterial effects of AgNPs were evaluated against two standard gram-positive strains of Staphylococcus aureus and Streptococcus pyogenes and two standard gram-negative strains of Escherichia coli and Klebsiella pneumoniae . The findings showed the phytofabrication of spherical-shaped AgNPs with a Z -average diameter of 119.7 nm and the polydispersity index of 0.56. The minimum inhibitory concentration of AgNPs against S. aureus , S. pyogenes , E. coli , and K. pneumoniae strains was 0.25, 1, 0.5, and 0.5 μg·mL −1 , respectively. In addition, the minimum bactericidal concentration of these nanoparticles (NPs) against the mentioned strains was 8, 16, 4, and 4 μg·mL −1 , respectively. Furthermore, the AgNPs enhanced the generation of reactive oxygen species significantly in all studied bacteria compared to the control ( P &lt; 0.05) suggesting an oxidative-associated antibacterial mechanism of AgNPs. Moreover, a dose-dependent cell death was found in all bacterial samples based on flow cytometry analysis. Overall, this study showed a biological approach for the biosynthesis of AgNPs with significant antibacterial effects. Silver nanoparticle ; Antibacterial activity ; Gram-positive bacteria ; Zeta potential ; Chemistry ; Minimum inhibitory concentration ; Nuclear chemistry ; Bacteria ; Dispersity ; Gram-negative bacteria ; Escherichia coli ; Microbiology ; Antimicrobial ; Nanoparticle ; Materials science ; Biology ; Nanotechnology ; Biochemistry ; Organic chemistry Nanoparticles: synthesis and applications ; Essential Oils and Antimicrobial Activity ; Moringa oleifera research and applications
Authors: Yashirdisai Sampasivam | Khalisah Khairina Razman | N. Mazlan | Kamalrul Azlan Azizan | Yogesh K. Ahlawat | Roohaida Othman
Source: Journal of Industrial Microbiology & Biotechnology (article, 2024-12-31)
Field: Chemistry — Organic Chemistry

Towards sustainable agarwood production: integrating microbial interactions, anatomical changes, and metabolite biosynthesis Agarwood is a highly valuable non-timber forest product mainly derived from the Aquilaria genus, widely traded in the perfumery, religious items, and traditional medicine industries. Naturally, agarwood forms within the xylem as part of the tree's defense mechanism against environmental stressors and microbial infection. The escalating demand for agarwood has led to the overexploitation of Aquilaria species, with some now classified as critically endangered. Despite advancements in artificial induction methods for sustainable agarwood supply, the intricate links between physiological and molecular mechanisms governing its formation remain poorly understood. This review addresses these knowledge gaps by examining the interplay between morphological changes in xylem structure during tylose formation and molecular alterations, particularly the biosynthesis of 2-(2-phenylethyl)chromones (PECs), key compounds in agarwood. Additionally, it integrates findings from multi-omics approaches including genomics, transcriptomics, proteomics, and metagenomics to reveal how secondary metabolite biosynthesis, including PECs and terpenes, is regulated across various Aquilaria species, regions, and induction techniques. The role of microbial communities, particularly endophytes such as Fusarium, in regulating agarwood formation is also discussed, emphasizing their involvement in both natural and artificial induction strategies. Furthermore, this review explores the role of reactive oxygen species in mediating morphological and biochemical defense responses, alongside the functions of transcription factors (TFs), protein kinases, and signaling molecules in balancing defense and growth. However, the crosstalk between key genes such as chalcone synthases, MAPK, cytochromes, NADPH oxidases, TFs, and miRNAs require further study to fully understand the complex defense mechanisms in Aquilaria trees. Overall, this review aims to bridge the current knowledge gaps by linking morphological and biochemical changes in agarwood formation, particularly PEC biosynthesis, while proposing metabolite engineering using microbial hosts as a promising tool for sustainable and technology-driven agarwood production. One-Sentence Summary: This review explores the physiological and molecular processes behind agarwood formation in Aquilaria malaccensis, highlighting the roles of tyloses, microbial interactions, secondary metabolite biosynthesis particularly 2-(2-phenylethyl)chromones and the integration of biotechnology for sustainable production and metabolic engineering. Agarwood ; Biology ; Computational biology Wood and Agarwood Research ; Microbial Metabolism and Applications ; Plant Gene Expression Analysis
Authors: Mohana Reddy Mutra | T. L. Chandana | Yun-Jou Wang | Jeh‐Jeng Wang
Source: Chemistry - An Asian Journal (article, 2024-11-29)
Field: Chemistry — Organic Chemistry

Metal Additive–Free Iodine–Promoted Reorganization of Ynamide‐Ynes and Stereoselective 1,2‐Diiodination We report a metal additive-free iodine-promoted one-step structural reorganization of ynamide-ynes and simultaneous stereoselective 1,2-diiodination of the migrated alkyne to form stereospecific tetrasubstituted alkenyl diiodo-tethered indoles (E-isomer). Molecular iodine is cost effective, user friendly, less toxic, commercially available, and easy to handle. The key features of the reaction include metal-and additive-free environment, selectivity, structural reorganization, mild reaction conditions, simple workup, and gram-scale synthesis. This transformation generates multiple bonds [nitrogen (N)-carbon (C)sp2, Csp2-Csp2, 2 Csp2-iodine (I)] via N-Csp bond cleavage in ynamide-ynes. Stereoselectivity ; Chemistry ; Stereospecificity ; Iodine ; Alkyne ; Metal ; Combinatorial chemistry ; Organic chemistry ; Catalysis Catalytic Alkyne Reactions ; Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions
Authors: Aaron Miller | Adam Glos | Zoltán Zimborás
Source: arXiv (Cornell University) (preprint, 2024-03-06)
Field: Materials Science — Materials Chemistry

Treespilation: Architecture- and State-Optimised Fermion-to-Qubit Mappings Quantum computers hold great promise for efficiently simulating Fermionic systems, benefiting fields like quantum chemistry and materials science. To achieve this, algorithms typically begin by choosing a Fermion-to-qubit mapping to encode the Fermioinc problem in the qubits of a quantum computer. In this work, we introduce "treespilation," a technique for efficiently mapping Fermionic systems using a large family of favourable tree-based mappings previously introduced by some of the authors. We use this technique to minimise the number of CNOT gates required to simulate chemical groundstates found numerically using the ADAPT-VQE algorithm. We observe significant reductions, up to $74\%$, in CNOT counts on full connectivity and for limited qubit connectivity-type devices such as IBM Eagle and Google Sycamore, we observe similar reductions in CNOT counts. In many instances, the reductions achieved on these limited connectivity devices even surpass the initial full connectivity CNOT count. Additionally, we find our method improves the CNOT and parameter efficiency of QEB- and qubit-ADAPT-VQE, which are, to our knowledge, the most CNOT-efficient VQE protocols for molecular state preparation. Qubit ; Architecture ; Fermion ; State (computer science) ; Physics ; Theoretical physics ; Computer science ; Quantum mechanics ; Quantum ; Geography ; Algorithm Machine Learning in Materials Science ; Quantum Computing Algorithms and Architecture
Authors: Mounika Sarvepalli | Aditya Velidandi | Arun Kumar | Korrapati Narasimhulu | A Khan | P Singh | A Srivastava | K Acquah | D Beukes | D Warner | P Meyers | S Sunassee | J Neilands | R Bergeron | G Huang | R Smith | N Bharti | J Mcmanis | B Holinsworth | J Martin | M Sandy | A Butler | L Devireddy | D Hart | D Goetz | M Green | B Nagoba | D Vedpathak | C Imada | N Koseki | M Kamata | T Kobayashi | N Hamada-Sato | P Jensen | W Fenical | L Zhang | An Wang | J Sun | N Zhang | S | S Ramesh | N Mathivanan | L Liermann | B Kalinowski | S Brantley | J Ferry | J Francis | J Madinaveitia | H Macturk | G Snow | C Hesseltine | C Pidacks | A Whitehill | N Bohonos | B Hutchings | J Garibaldi | Cccr De Carvalho | Mpc Marques | P Fernandes | E Wilde | E Blagova | T Sanderson | D Raines | R Thomas | B Matzanke | S Anemller | V Schnemann | A Trautwein | K Hantke | J Martinez | J Carter-Franklin | E Mann | M Haygood | T Owen | R Pynn | M Saha | S Sarkar | B Sarkar | B Sharma | S Bhattacharjee | B Dave | K Anshuman | P Hajela | A Nielsen | M Mansson | M Wietz | A Varming | R Phipps | S Prez-Miranda | N Cabirol | R George-Tllez | L Zamudio-Rivera | F Fernndez
Source: NanoWorld Journal (review, 2024-02-12)
Field: Materials Science — Biomaterials

Marine Actinomycetes Siderophores: Types, High Throughput Characterization Techniques, Applications, and Their Association with Nanotechnology: A Comprehensive Review Mounika Sarvepalli, Aditya Velidandi, Arun Kumar Ramachandravarapu and Narasimhulu Korrapati Iron is one of the most essential micronutrients for all the existing life systems. However, at biological pH, iron gets oxidised to insoluble oxyhydroxide polymers. In low iron conditions, microbes secrete specialised molecules called siderophores, which are high affinity and low molecular weight chelating agents that increase the availability of iron for microbial usage. Siderophore ; Nanotechnology ; Characterization (materials science) ; Throughput ; Biology ; Computational biology ; Engineering ; Materials science ; Bacteria ; Genetics ; Telecommunications Diatoms and Algae Research ; Microbial Natural Products and Biosynthesis
Authors: Bapan Saha | Chandrani Pal | Himani Malik | Thiruvancheril G. Gopakumar | Sankar Prasad Rath
Source: Chemistry - A European Journal (article, 2024-09-09)
Field: Materials Science — Materials Chemistry

Conformational Switching of a Nano‐Size Urea‐Bridged Zn(II)Porphyrin Dimer by External Stimuli For the first time, explicit stabilization of all the three conformers, viz. (cis,cis), (cis,trans) and (trans,trans), of a 'nano-sized' highly-flexible urea-bridged Zn(II)porphyrin dimer have been achieved via careful manipulations of external stimuli such as solvent dielectrics, temperature, anionic interactions, axial ligation and surface-induced stabilization. The conformers differ widely in their structures, chemical and photophysical properties and thus have vast potential applicability. X-ray structural characterizations have been reported for the (cis,cis) and (cis,trans)-conformers. While (cis,cis) conformer stabilized exclusively in dichloromethane, more polar solvents resulted in the stabilization of (cis,trans) and (trans,trans)-conformers. Low temperature promotes the stabilization of (cis,trans)-conformer while rise in temperature facilitates flipping to the (cis,cis) one. Significantly, exclusive stabilization of the (trans,trans)-isomer has been illustrated using acetate anion which facilitates H-bonding with the two amide linkages of the urea spacer. Remarkably, HOPG surface facilitates stabilization of the energetically challenging (trans,trans)-conformer via CH⋅⋅⋅π and π⋅⋅⋅π interactions with the solid surface to the porphyrinic cores. DFT calculations demonstrate that the relative stability of the conformers can be modulated upon slight external perturbations as also observed in the experiment. Several factors contributing towards the conformational landscape for the highly flexible urea-bridged porphyrin dimers have been mapped. Porphyrin ; Dimer ; Urea ; Chemistry ; Photochemistry ; Biochemistry ; Organic chemistry Porphyrin and Phthalocyanine Chemistry ; Molecular Sensors and Ion Detection ; Supramolecular Chemistry and Complexes
Authors: Rajendran Muthukumar Sivaraman | Kirubaharan Daphne Jacinth Gracia | Seth Sheeba Thavamani | Thomas Peter Amaladhas | Sandhanasamy Devanesan | Mohamad S. AlSalhi
Source: Green Processing and Synthesis (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Green synthesis of La <sub>2</sub> O <sub>3</sub> –LaPO <sub>4</sub> nanocomposites using <i>Charybdis natator</i> for DNA binding, cytotoxic, catalytic, and luminescence applications Abstract A one-step biosynthetic pathway for the fabrication of La 2 O 3 –LaPO 4 nanocomposites (NCs) was developed, employing Charybdis natator . The structure and phase changes of the NCs were confirmed, and their diverse applications were explored. The peaks at 206, 332, and 442 nm in UV-DRS studies confirmed the formation of La 2 O 3 –LaPO 4 NCs. Fourier transform infrared spectral analysis revealed La–O stretching at 716 cm −1 and the presence of <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msubsup> <m:mrow> <m:mtext>PO</m:mtext> </m:mrow> <m:mrow> <m:mn>4</m:mn> </m:mrow> <m:mrow> <m:mn>3</m:mn> <m:mo>−</m:mo> </m:mrow> </m:msubsup> </m:math> {\text{PO}}_{4}^{3-} bands at 532, 560, 578, and 618 cm −1 . X-ray diffraction patterns showed a hexagonal phase of La 2 O 3 with peaks at 2 θ 11.04 and 28.57 and monoclinic LaPO 4 phases at 2 θ = 18.79 and 41.88. X-ray photoelectron spectroscopy data showed binding energy peaks at 836.04 and 852.77 eV, corresponding to 3d 5/2 and 3d 3/2 of the lanthanum. The average particle size from HR-TEM analysis was 28.95 nm after annealing at 800°C and SAED patterns confirmed their crystalline nature. The high affinity of the NCs towards ctDNA was established by a binding constant value of 2.08 (mg·mL −1 ) −1 . Under UV exposure, 96% degradation efficiency for methyl orange within 120 min at pH 4 was displayed, with a rate constant of 2.72 × 10 −2 min −1 affirming their photocatalytic potential. Their biocompatibility was assessed through MTT assay and luminescence characteristics were evaluated. Luminescence ; Catalysis ; Nanocomposite ; DNA ; Chemistry ; Nanotechnology ; Materials science ; Organic chemistry ; Biochemistry ; Optoelectronics Luminescence Properties of Advanced Materials ; Advanced Nanomaterials in Catalysis ; Nanomaterials for catalytic reactions
Authors: Mingyan Ding | Charles Bell | Michael C. Willis
Source: Angewandte Chemie (article, 2024-06-26)
Field: Chemistry — Organic Chemistry

The Modular Synthesis of Sulfondiimidoyl Fluorides and their Application to Sulfondiimidamide and Sulfondiimine Synthesis Abstract A modular synthesis of sulfondiimidoyl fluorides—the double aza‐analogues of sulfonyl fluorides—allowing variation of the carbon and both nitrogen‐substituents is reported. The chemistry uses readily available organometallic reagents, commercial sulfinylamines, simple electrophiles, and N‐fluorobenzenesulfonimide (NFSI), as the starting materials. The reactions are broad in scope, efficient, and scalable. We show that the sulfondiimidoyl fluoride products can be combined with amines to provide sulfondiimidamides, and with organolithium reagents to provide sulfondiimines, and that reactivity in these transformations can be modulated by variation of the N‐substituents. Modular design ; Chemistry ; Computer science ; Programming language Synthesis and Catalytic Reactions ; Fluorine in Organic Chemistry ; Cyclopropane Reaction Mechanisms
Authors: Md. Nuruzzaman | Zeinab M. Nizam | Jun Ohata
Source: Tetrahedron Chem (article, 2024-08-01)
Field: Chemistry — Organic Chemistry

Fluoroalcohols for chemical modification of biomolecules While their broad utility in various chemistry fields were well recognized for decades, fluoroalcohols have recently emerged as a unique solvent system for bioconjugation development. This review describes examples and roles of fluoroalcohols such as trifluoroethanol (TFE) and hexafluoroisopropanol (HFIP) for chemical modification of biomolecules such as polypeptides, nucleic acids, and saccharides. Many chemical modification processes were facilitated by notable functions of those fluoroalcohols such as a proton shuttle, reversible adduct formation with reactive species, and compatibility with electrochemistry/photochemistry. The usefulness of the fluoroalcohol solvents can be even promoted by its combination with a different solvent system for reaction enhancement and protein stabilization. The collection of the various chemical transformations in this review is an indication of the rapid growth of the solvent-assisted bioconjugation field. Bioconjugation ; Biomolecule ; Combinatorial chemistry ; Nanotechnology ; Chemical modification ; Chemistry ; Chemical biology ; Adduct ; Solvent ; Materials science ; Organic chemistry ; Biochemistry Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Fluorine in Organic Chemistry
Authors: A. N. Koval
Source: Health and Ecology Issues (article, 2024-03-31)
Field: Materials Science — Materials Chemistry

Changes in energy metabolism of rat myocardium during exposure to ionizing radiation Objective. To study the effect of incorporated 137 Cs on the energy metabolism of the myocardium of white rats. Materials and methods. The work was carried out on 8 male white rats divided into 2 experimental groups, which were fed products contaminated with 137 Cs for 7 days. Polarography was used to study the rate of oxygen consumption by myocardial tissue preparations on endogenous substrates, with the addition of exogenous succinic and glutamic acids, and with the addition of an uncoupler of oxidative phosphorylation, 2,4-dinitrophenol.Results. An increase in the rate of respiration on endogenous substrates caused by the uncoupling of oxidative phosphorylation was noted. At the same time, no statistically significant change in the amount of endogenous substrates was found. Conclusion. The revealed violation of energy production in the myocardium of experimental animals is caused by the uncoupling of oxidative phosphorylation, and can be explained by a change in the operation of potassium channels, which can explain the development of cardiovascular pathology under the action of ionizing radiation. Ionizing radiation ; Energy metabolism ; Metabolism ; Radiation ; Nuclear medicine ; Chemistry ; Internal medicine ; Medicine ; Irradiation ; Physics ; Nuclear physics Carbon Nanotubes in Composites ; Radiation Therapy and Dosimetry ; Mitochondrial Function and Pathology
Authors: José C. S. Costa | Ana I.M.C. Lobo Ferreira | Carlos F. R. A. C. Lima | Luı́s M. N. B. F. Santos
Source: The Journal of Physical Chemistry A (article, 2024-05-30)
Field: Chemistry — Organic Chemistry

The Cohesive Interactions in Phenylimidazoles This work presents a comprehensive study exploring the thermodynamics of the solid phase of a series of phenylimidazoles, encompassing experimental measurements of heat capacity, volatility, and thermal behavior. The influence of successive phenyl group insertions on the imidazole ring on thermodynamic properties and supramolecular behavior was thoroughly examined through the evaluation of 2-phenylimidazole (2-PhI), 4-phenylimidazole (4-PhI), 4,5-diphenylimidazole (4,5-DPhI), and 2,4,5-triphenylimidazole (2,4,5-TPhI). Structural correlations between molecular structure and thermodynamic properties were established. Furthermore, the investigation employed UV-vis spectroscopy and quantum chemical calculations. Additive effects arising from the introduction of phenyl groups were found through the analysis of the solid-liquid and solid-gas equilibria, as well as heat capacities. A good correlation emerged between the thermodynamic properties of sublimation and the molar volume of the unit cell, evident across 2-PhI, 4,5-DPhI, and 2,4,5-TPhI. In contrast to its isomer 2-PhI, 4-PhI exhibited greater cohesive energy due to the stronger N-H···N intermolecular interactions, leading to the disruption of coplanar geometry in the 4-PhI molecules. The observed higher entropies of phase transition (fusion and sublimation) are consistent with the higher structural order observed in the crystalline lattice of 4-PhI. Psychology Chemical Thermodynamics and Molecular Structure ; Chemistry and Chemical Engineering ; Thermal and Kinetic Analysis
Authors: Seyedmojtaba Seyedraoufi | Graeme M. Day | Kristian Berland
Source: arXiv (Cornell University) (preprint, 2024-10-27)
Field: Materials Science — Polymers and Plastics

Design of novel organic proton-transfer acid-base (anti-)ferroelectric salts with crystal structure prediction Organic molecular ferroelectrics, including organic proton-transfer ferroelectrics and antiferroelectrics, are potentially attractive in organic electronics and have significant chemical tunability. Among these, acid-base proton transfer (PT) salts stand out due to their low coercive fields and the possibility to tune their properties with different acid-base combinations. Using crystal structure prediction, combining small acid and base organic molecular species, we here predict three novel acid-base PT ferroelectric salts with higher polarization than existing materials. We also report two combinations that form antiferroelectric crystal structures. However, some combinations also result in unfavorable packing or the formation of co-crystal or in one case a divalent salt. The protonation state is found to be highly linked to the crystal structure, with cases where salt crystal structures have the same energetic preferability as co-crystals with a different crystalline packing. Ferroelectricity ; Proton ; Base (topology) ; Crystal structure ; Materials science ; Transfer (computing) ; Crystallography ; Chemistry ; Optoelectronics ; Computer science ; Physics ; Parallel computing Synthesis and properties of polymers ; Solid-state spectroscopy and crystallography ; Nonlinear Optical Materials Research