jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Kenichiro Itami | Maciej Krzeszewski | Hideto Ito
Source:  (preprint, 2021-10-13)
Field: Chemistry — Organic Chemistry

Infinitene: A Helically Twisted Figure-Eight [12]Circulene Topoisomer New forms of molecular nanocarbons particularly looped polyarenes adopting various topologies contribute to the fundamental science and practical applications. Here we report on the synthesis of an infinity-shaped polycyclic aromatic hydrocarbon, infinitene 1 (cyclo[c.c.c.c.c.c.e.e.e.e.e.e]dodecakisbenzene) comprising consecutively fused 12-benzene rings forming an enclosed loop with a strain energy of 60.2 kcal·mol-1. Infinitene 1 represents a topoisomer of still-hypothetical [12]circulene, and its scaffold can be formally visualized as the outcome of the “stitching” of two homochiral [6]helicene subunits by their both ends. The synthetic strategy encompasses transformation of a rationally designed dithiacyclophane to cyclophadiene through the Stevens rearrangement and pyrolysis of the corresponding S,S′-bis(oxide) followed by the UV-light mediated twofold photocyclization. The structure of infinitene 1 is a unique hybrid of helicene and circulene with a molecular formula C48H24, which can be regarded as an isomer for kekulene, [6,6]carbon nanobelt ([6,6]CNB), [12]cyclacene, and tetrabenzo[8]circulene as well. Infinitene 1 is a bench-stable yellow solid with green fluorescence, and soluble to common organic solvents. The figure-eight molecular structure of 1 was unambiguously confirmed by X-ray crystallography. The scaffold of 1, reminiscent of a squeezed spring, stem from its enclosed, fully-fused architecture, is significantly compressed as manifested by a remarkably shortened distance (3.152–3.192 Å) between the centroids of two π-π stacked central benzene rings and the closest C···C distance of 2.920 Å. Combined lamellar and herringbone-like crystal packing suggested three-dimensional electronic inter-actions. Fundamental photophysical properties of infinitene 1 were thoroughly elucidated by means of UV-vis absorption and fluorescence spectroscopic studies as well as density functional theory (DFT) calculations. Its configurational stability enabled separation of the corresponding enantiomers (P,P) and (M,M) by a chiral HPLC. Circular dichroism (CD) and circularly polarized luminescence (CPL) measurements revealed that 1 has moderate |gCD| and |gCPL| values. Helicene ; Chemistry ; Crystallography ; Stereochemistry ; Materials science ; Molecule ; Organic chemistry Synthesis and Properties of Aromatic Compounds ; Fullerene Chemistry and Applications ; Photochromic and Fluorescence Chemistry
Authors: Evelyne Bartholomeeusen | Gert De Cremer | Koen Kennes | Ceri Hammond | Ive Hermans | Jiangbo Lu | D. Schryvers | Pierre A. Jacobs | Maarten B. J. Roeffaers | Johan Hofkens | Bert F. Sels | Eduardo Coutiño‐González
Source: Chemical Communications (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Optical encoding of luminescent carbon nanodots in confined spaces Stable emissive carbon nanodots were generated in zeolite crystals using near infrared photon irradiation gradually converting the occluded organic template, originally used to synthesize the zeolite crystals, into discrete luminescent species consisting of nano-sized carbogenic fluorophores, as ascertained using Raman microscopy, and steady-state and time-resolved spectroscopic techniques. Photoactivation in a confocal laser fluorescence microscope allows 3D resolved writing of luminescent carbon nanodot patterns inside zeolites providing a cost-effective and non-toxic alternative to previously reported metal-based nanoclusters confined in zeolites, and opens up opportunities in bio-labelling and sensing applications. Nanoclusters ; Luminescence ; Nanodot ; Fluorescence ; Materials science ; Carbon fibers ; Nanotechnology ; Raman spectroscopy ; Microscopy ; Microscope ; Photochemistry ; Optoelectronics ; Chemistry ; Optics Carbon and Quantum Dots Applications ; Graphene and Nanomaterials Applications ; Nanocluster Synthesis and Applications
Authors: Prabhleen Kaur | Md. Ehesan Ali
Source: ChemRxiv (preprint, 2021-05-04)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Influence of the Radicaloid Character of Polyaromatic Hydrocarbon Couplers on Magnetic Exchange Interactions Understanding the properties of the coupler influencing spin-spin interactions in organic diradicals are crucial for designing of molecular spintronic systems with long-range effects. In this quest, using density functional theory (DFT) based broken symmetry method, magnetic exchange coupling (2J) between localized radical centers at a given length connected via spacers with different radicaloid character (y) is investigated. The nitroxy radical sites are coupled through prototypical decacene coupler keeping them ~ 27 Å apart. Couplers with different y values, modeled by addition of benzenoid rings in the spin confining region of decacene are used as different spacers between nitroxide diradicals. The strength of magnetic coupling between the localized spin centers is found to be correlated with the radicaloid character of polyaromatic hydrocarbon (PAH) spacers. The stronger exchange interaction is observed for the diradical with higher radicaloid character. It is further observed that the fractional occupied molecular orbitals (MOs) responsible for the open-shell nature of the coupler predominantly constitute the Frontier MOs (FMOs), while in diradicals SOMOs constitute the FMOs. Diradical ; Character (mathematics) ; Atomic orbital ; Chemical physics ; Coupling (piping) ; Spin (aerodynamics) ; Density functional theory ; Molecular orbital ; Combing ; Coupling strength ; Chemistry ; Molecular physics ; Materials science ; Condensed matter physics ; Computational chemistry ; Physics ; Molecule ; Atomic physics ; Electron ; Quantum mechanics ; Singlet state ; Organic chemistry ; Thermodynamics Magnetism in coordination complexes ; Electron Spin Resonance Studies ; Lanthanide and Transition Metal Complexes
Authors: Yongmei Xu | Bin Sun | Xuefei Huang | Gopinath Tirachinapally | Steven B. Dulaney | Zhen Wang | Renpeng Liu | Jian Liu | Bo Yang
Source: UNC Libraries (article, 2021-07-01)
Field: Chemistry — Organic Chemistry

Preactivation-Based, One-Pot Combinatorial Synthesis of Heparin-like Hexasaccharides for the Analysis of Heparin-Protein Interactions Heparin (HP) and heparan sulfate (HS) play important roles in many biological events. Increasing evidence has shown that the biological functions of HP and HS can be critically dependent upon their precise structures, including the position of the iduronic acids and sulfation patterns. However, unraveling the HP code has been extremely challenging due to the enormous structural variations. To overcome this hurdle, we investigated the possibility of assembling a library of HP/HS oligosaccharides using a preactivation-based, one-pot glycosylation method. A major challenge in HP/HS oligosaccharide synthesis is stereoselectivity in the formation of the cis-1,4-linkages between glucosamine and the uronic acid. Through screening, suitable protective groups were identified on the matching glycosyl donor and acceptor, leading to stereospecific formation of both the cis-1,4- and trans-1,4-linkages present in HP. The protective group chemistry designed was also very flexible. From two advanced thioglycosyl disaccharide intermediates, all of the required disaccharide modules for library preparation could be generated in a divergent manner, which greatly simplified building-block preparation. Furthermore, the reactivity-independent nature of the preactivation-based, one-pot approach enabled us to mix the building blocks. This allowed rapid assembly of twelve HP/HS hexasaccharides with systematically varied and precisely controlled backbone structures in a combinatorial fashion. The speed and the high yields achieved in glycoassembly without the need to use a large excess of building blocks highlighted the advantages of our approach, which can be of general use to facilitate the study of HP/HS biology. As a proof of principle, this panel of hexasaccharides was used to probe the effect of backbone sequence on binding with the fibroblast growth factor-2 (FGF-2). A trisaccharide sequence of 2-O-sulfated iduronic acid flanked by N-sulfated glucosamines was identified to be the minimum binding motif and N-sulfation was found to be critical. This provides useful information for further development of more potent compounds towards FGF-2 binding, which can have potential applications in wound healing and anticancer therapy. Heparin ; Chemistry ; Biochemistry Carbohydrate Chemistry and Synthesis ; Proteoglycans and glycosaminoglycans research ; Glycosylation and Glycoproteins Research
Authors: Laurens C. J. M. Peters | Peter C. M. Christianen | Hans Engelkamp | Gerrit C. Groenenboom | J. C. Maan | Erik Kampert | Paul Tinnemans | Alan E. Rowan | U. Zeitler
Source: Physical Review Research (article, 2021-12-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Magnetic anisotropy of individually addressed spin states Controlling magnetic anisotropy is a key requirement for the fundamental understanding of molecular magnetism and is a prerequisite for numerous applications in magnetic storage, spintronics, and all-spin logic devices. In order to address the question of molecular magnetic anisotropy experimentally, we have synthesized single crystals of a molecular spin system containing four antiferromagnetically coupled s = 5/2 manganese(II) ions. Using low-temperature cantilever magnetometry, we demonstrate the selective population of the S = 0, 1, . . . , 10 spin states upon application of magnetic fields up to 33 T and map the magnetic anisotropy of each of these states. We observe a strong dependence of the shape and size of the magnetic anisotropy on the populated spin states, and, in particular, reveal an anisotropy reversal upon going from the lowest to the highest spin state. Condensed matter physics ; Spintronics ; Magnetic anisotropy ; Spin engineering ; Anisotropy ; Spin (aerodynamics) ; Magnetism ; Physics ; Spin states ; Magnetocrystalline anisotropy ; Population ; Chemistry ; Magnetic field ; Spin polarization ; Ferromagnetism ; Quantum mechanics ; Magnetization Magnetism in coordination complexes ; Organic and Molecular Conductors Research ; Physics of Superconductivity and Magnetism
Authors: Xuan‐Hung Pham | Seung Min Park | Bong‐Hyun Jun
Source: International Journal of Molecular Sciences (article, 2021-04-27)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Metal Nano/Microparticles for Bioapplications Nano/micro particles are considered to be the most valuable and important functional materials in the field of materials science and engineering [...]. Nanotechnology ; Nano- ; Materials science ; Metal ; Metallurgy ; Composite material Gold and Silver Nanoparticles Synthesis and Applications ; Nanoparticle-Based Drug Delivery ; Nanoparticles: synthesis and applications
Authors: André Niebur | Tommy Lorenz | Jan‐Ole Joswig | Gotthard Seifert | Sibylle Gemming | Michael Schreiber
Source: physica status solidi (b) (article, 2021-09-19)
Field: Materials Science — Materials Chemistry

Closed‐Loop Defect States in 2D Materials with Honeycomb Lattice Structure: Molybdenum Disulfide Platelets and ribbons of monolayer molybdenum disulfide () exhibit characteristic electronic states along the edges, which tend to decouple from the extended states in the interior of the 2D extended structure. Under sulfur excess specifically triangular platelets are formed, which exhibit 1D extended electronic states with a pronounced catalytic activity along the edges. The present density‐functional‐based investigation shows that very similar electronic states occur also along the edges of holes inside an otherwise perfect, extended monolayer. For triangular defects, the edge states can delocalize around the hole. Density functional molecular dynamics simulations on 150 different nanoscale defect geometries and termination variants prove the high structural stability of hole defects in against further reconstructions and a thermodynamic propensity to participate in sulfur exchange reactions. Monolayer ; Molybdenum disulfide ; Honeycomb ; Density functional theory ; Chemical physics ; Materials science ; Electronic structure ; Sulfur ; Lattice (music) ; Molecular dynamics ; Catalysis ; Molybdenum ; Nanoscopic scale ; Crystallography ; Condensed matter physics ; Chemistry ; Computational chemistry ; Nanotechnology ; Physics ; Composite material 2D Materials and Applications ; Graphene research and applications ; ZnO doping and properties
Authors: P. N. Gajjar | Dhara Raval | Sanjeev K. Gupta | Rajeev Ahuja
Source: Research Square (preprint, 2021-12-03)
Field: Materials Science — Materials Chemistry

Semiconductor Two-Dimensional PdQ2 (Q=S, Se) Monolayer: Strain Modulating Electronic Band Gaps and SQ Efficiencies Abstract We studied the physical, electronic transport and optical properties of a unique pentagonal PdQ 2 (Q= S, Se) monolayers. The dynamic stability of 2D - wrinkle like - PdQ 2 is proven by positive phonon frequencies in the phonon dispersion curve. The optimized structural parameters of wrinkled pentagonal PdQ 2 are in good agreement with the available experimental results. The ultimate tensile strength (UTHS) was calculated and found that, penta-PdS 2 monolayer can withstand up to 16 % (18 % ) strain along x ( y ) direction with 3.44 GPa (3.43 GPa ). While, penta-PdSe 2 monolayer can withstand up to 17 % (19%) strain along x ( y ) dirrection with 3.46 GPa (3.40 GPa). It is found that, the penta-PdQ 2 monolayers has the semiconducting behavior with indirect band gap of 0.94 and 1.26 eV for 2D-PdS 2 and 2D-PdSe 2 , respectively. More interestingly, at room temperacture, the hole mobilty (electron mobility) obtained for 2D-PdS 2 and PdSe 2 are 67.43 (258.06) cm 2 V -1 s -1 and 1518.81 (442.49) cm 2 V -1 s -1 , respectively. In addition, I-V characteristics of PdSe 2 monolayer show strong negative differential conductance (NDC) region near the 3.57 V . The Shockly-Queisser (SQ) effeciency prameters of PdQ 2 monolayers are also explored and the highest SQ efficeinciy obtained for PdS 2 is 33.93 % at -5 % strain and for PdSe 2 is 33.94 % at -2 % strain. The penta-PdQ 2 exhibits high optical absorption intensity in the UV region, up to 4.04 × 10 5 (for PdS 2 ) and 5.28 × 10 5 (for PdSe 2 ), which is suitable for applications in optoelectronic devices. Thus, the ultrathin PdQ 2 monolayers could be potential material for next-generation solar-cell applications and high performance nanodevices. Monolayer ; Semiconductor ; Materials science ; Strain (injury) ; Band gap ; Phonon ; Tensile strain ; Ultimate tensile strength ; Crystallography ; Condensed matter physics ; Chemistry ; Nanotechnology ; Optoelectronics ; Physics ; Composite material 2D Materials and Applications ; MXene and MAX Phase Materials ; Molecular Junctions and Nanostructures
Authors: Praseeda Mol | R.S. Aparna | T. E. Sheeja | K. Deepa
Source: Journal of Plantation Crops (article, 2021-05-26)
Field: Chemistry — Inorganic Chemistry

Novel bHLH and WD40 transcription factors from turmeric (Curcuma longa L.) as putative regulators of curcumin biosynthesis Turmeric, the golden spice belonging to the family Zingiberaceae, is enriched with biologically active curcuminoids composed of curcumin, demethoxycurcumin and bisdemethoxycurcumin. Curcuminoids are phenylpropanoid derivatives, and the biosynthetic pathway is controlled by several transcription factors (TFs). bHLH, WD40 and MYB TFs are the most important TFs regulating phenylpropanoid biosynthesis in plants. Through comparative transcriptome analysis of high and low curcumin germplasm accessions, 20 TFs belonging to the classes bHLH, WD 40, NAC, WRKY and bZIP, which showed differential expression with respect to curcumin, were identified. Among these, two bHLH and one WD40 TFs showed maximum comparative fold change and negative correlation vis-a-vis curcumin content in quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The results of comparative transcriptome and qRT-PCR analyses were in congruence, indicating their putative role as negative regulators. Curcumin ; MYB ; Curcuma ; WRKY protein domain ; Biology ; Transcriptome ; Phenylpropanoid ; Transcription factor ; Zingiberaceae ; Benzylisoquinoline ; Gene ; Biochemistry ; Biosynthesis ; Gene expression ; Botany Coconut Research and Applications ; Curcumin's Biomedical Applications ; Plant Gene Expression Analysis
Authors: Miganoosh Simonian | Mozhan Haji Ghaffari | Ali Salimi | Ebrahim Mirzadegan | Niloufar Sadeghi | Nasim Ebrahimnezhad | Ghazaleh Fazli | Ramina Fatemi | Ali-Ahmad Bayat | Babak Negahdari | Hodjattallah Rabbani
Source: Research Square (preprint, 2021-05-20)
Field: Materials Science — Biomaterials

Monoclonal Antibody Against Sortilin Induces Apoptosis in Human Breast Cancer Cells Abstract Sortilin has an important role to play in various malignances and can be used as a promising target to eradicate cancer cells. The expression of sortilin in 4T1 and MDA-MB231 was evaluated by flow cytometry and immunocytochemistry. Apoptosis test was also performed. Based on cell surface flow cytometry results 2D8-E3 mAb could recognize sortilin molecules in 45.9% and 90.3% of 4T1 and MDA-MB231 cells respectively. The immunocytochemistry staining results verified sortilin surface expression. Apoptosis assay indicated that 2D8-E3 mAb could induce apoptosis in 4T1 and MDA-MB231 cell lines. Our study revealed the important role of surface sortilin in breast carcinoma cell survival and its possible usage as a therapeutic agent in cancer targeted therapies. Monoclonal antibody ; Apoptosis ; Human breast ; Antibody ; Breast cancer ; Cancer research ; Cancer ; Chemistry ; Biology ; Immunology ; Biochemistry ; Genetics Silk-based biomaterials and applications ; Glycosylation and Glycoproteins Research ; Proteoglycans and glycosaminoglycans research
Authors: Pei Liu | Suna Chen | Wenxuan Zhao | Qiutang Wang | Shuqi Wu | Liang Xu | Dan Bai
Source: Frontiers in Chemistry (article, 2021-12-01)
Field: Chemistry — Spectroscopy

Novel Pyrazine-Bridged D-A-D Type Charge Neutral Probe for Membrane Permeable Long-Term Live Cell Imaging A novel donor-acceptor-donor (D-A-D) type compound containing pyrazine as the acceptor and triphenylamine as the donor has been designed and synthesized. The photophysical properties and biocompatibility of this probe, namely (OMeTPA)2-Pyr for live cell imaging were systematically investigated, with observed large Stokes shifts, high photostability, and low cytotoxicity. Furthermore, we demonstrated that (OMeTPA)2-Pyr could permeate live cell membranes for labeling. The proposed mechanism of this probe was the binding and shafting through membrane integral transport proteins by electrostatic and hydrophobic interactions. These salient and novel findings can facilitate the strategic design of new pyrazine-fused charge-neutral molecular platforms as fluorescent probes, for long-term <i>in situ</i> dynamic monitoring in live cells. Pyrazine ; Live cell imaging ; Acceptor ; Membrane ; Chemistry ; Triphenylamine ; Photochemistry ; Fluorescence-lifetime imaging microscopy ; Fluorescence ; Biophysics ; Stereochemistry ; Cell ; Biochemistry Molecular Sensors and Ion Detection ; Luminescence and Fluorescent Materials ; Advanced biosensing and bioanalysis techniques
Authors: Chad Nielsen
Source: Digital Commons - USU (Utah State University) (article, 2021-10-08)
Field: Materials Science — Biomaterials

Investigations of Polyhydroxyalkanoate Secretion and Production Using Sustainable Carbon Sources Polyhydroxyalkanoates (PHAs) are a type of biologically-produced plastic known for their biocompatibility and biodegradability. They have the potential to replace petroleum-based plastics as an environmentally-friendly alternative. This is beneficial because the release of plastics into environments such as the ocean and the buildup of plastics in landfills are major concerns facing society today. Currently, however, PHAs are significantly more expensive than their petroleum-based counterparts. This is largely due to the cost of carbon sources and of extracting the bioplastics from bacteria. The goal of these studies was to examine replacing traditional carbon sources used in PHA production like sugar and oils with sustainable carbon sources and to improve extraction procedures by inducing secretion of PHAs in bacteria. A few sustainable carbon sources were examined for use in PHA production. First, studies focused on the conversion of food waste into PHAs were reviewed. It was shown that utilizing food wastes as carbon sources may be a viable approach to producing PHAs. A second carbon source examined was methanol. A novel isolate of Methylobacterium that demonstrated the ability to produce PHAs from methanol was identified. A system of secreting PHAs that was constructed using synthetic biological engineering approach was introduced to this isolate. This secretion system was not shown to improve extraction of PHAs in Methylobacterium in its current form. Polyhydroxyalkanoates ; Production (economics) ; Carbon fibers ; Natural resource economics ; Business ; Pulp and paper industry ; Environmental science ; Economics ; Computer science ; Engineering ; Bacteria ; Biology ; Microeconomics biodegradable polymer synthesis and properties ; Carbon dioxide utilization in catalysis ; Microplastics and Plastic Pollution
Authors: Daniel Bím | Anastassia N. Alexandrova
Source: ChemRxiv (preprint, 2021-01-21)
Field: Chemistry — Inorganic Chemistry

Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity Heme-iron oxidoreductases operating through the high-valent FeIVO intermediates perform crucial and complicated transformations, such as oxidations of unreactive saturated hydrocarbons. These enzymes share the same Fe coordination, only differing by the axial ligation, e.g., Cys in P450 oxygenases, Tyr in catalases, and His in peroxidases. By examining ~200 heme-iron proteins, we show that the protein hosts exert highly specific intramolecular electric fields on the active sites, and there is a strong correlation between the direction and magnitude of this field and the protein function. In all heme proteins, the field is preferentially aligned with the Fe‒O bond (Fz). The Cys-ligated P450 oxygenases have the highest average Fz of 28.5 MV cm-1, i.e., most enhancing the oxyl-radical character of the oxo group, and consistent with the ability of these proteins to activate strong C‒H bonds. In contrast, in Tyr-ligated proteins, the average Fz is only 3.0 MV cm-1, apparently suppressing single-electron off-pathway oxidations, and in His-ligated proteins, Fz is –8.7 MV cm-1. The operational field range is given by the trade-off between the low reactivity of the FeIVO Compound I at the more negative Fz, and the low selectivity at the more positive Fz. Consequently, a heme-iron site placed in the field characteristic of another heme-iron protein class loses its canonical function, and gains an adverse one. Thus, electric fields produced by the protein scaffolds, together with the nature of the axial ligand, control all heme-iron chemistry. Heme ; Chemistry ; Reactivity (psychology) ; Intramolecular force ; Hemeprotein ; Heme oxygenase ; Peroxidase ; Microsome ; Active site ; Stereochemistry ; Enzyme ; Biochemistry Metal-Catalyzed Oxygenation Mechanisms ; Hemoglobin structure and function ; CO2 Reduction Techniques and Catalysts