jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Daniel J. Fowler
Source: Scholarworks (University of Massachusetts Amherst) (article, 2022-11-30)
Field: Chemistry — Spectroscopy

Quaternary Structure of Chemoreceptors in Active Signaling Complexes Differs From Crystal Structure of Isolated Fragments: Evidence From Solid-State NMR The receptor dimers that mediate bacterial chemotaxis form high-order signaling complexes with CheW and the kinase CheA. From the packing arrangement in two crystal structures of different receptor cytoplasmic fragments, two different models have been proposed for receptor signaling arrays: the trimers-of-dimers and hedgerow models. We identified an interdimer distance that differs substantially in the two models, labeled the atoms defining this distance through isotopic enrichment, and measured it with 13C-19F REDOR. This was done in two types of receptor samples: first, isolated bacterial membranes containing overexpressed, intact receptor, and second, soluble receptor fragments reconstituted into kinase-active signaling complexes. In both cases, the distance found was not compatible with the receptor dimer−dimer contacts observed in the trimers-of-dimers or in the hedgerow models. Comparisons of simulated and observed REDOR dephasing were used to deduce a closest-approach distance at this interface, which provides a constraint for the possible arrangements of kinase-competent receptor assemblies. An alternate model of receptor signaling is proposed, which reconciles this result with existing structural and biochemical data. Additionally, two advances to solid-state NMR methodology are described. The first is a set of strategies to protect protein samples against degradation by solid-state NMR analysis. Biochemical and spectroscopic techniques are prescribed to identify and isolate specific challenges to protein stability, allowing them to be addressed individually. For this purpose a new pulse sequence (Thermal Calibration Under Pulseload, or TCUP) is employed, which allows sample temperature to be measured with exceptional time resolution. The second NMR advance describes the creation and characterization of a 13C-19F REDOR distance-calibration standard. The inclusion compound of 4-fluorotoluene and tert-butylcalix[4]arene was used for this purpose. The compound is easily synthesized from commercially available materials, and provides a long, isolated 13C-19F distance of 4.1 Å. Dynamics within the compound allow direct observation of 19F resonances without 1H-decoupling, and provide exceptionally sharp 13C resonances; these characteristics speed the routine setup of REDOR experiments. Both methodological developments were important to performing accurate distance measurements on functionally relevant chemotaxis signaling complexes; they also pave the way for making similar measurements in other proteins of interest. Quaternary ; Crystallography ; Chemoreceptor ; Crystal structure ; Chemistry ; Stereochemistry ; Biophysics ; Biology ; Paleontology ; Biochemistry ; Receptor Advanced NMR Techniques and Applications ; Molecular Sensors and Ion Detection ; Chemical Synthesis and Analysis
Authors: 美歌 石垣 | Atsushi Ito | Risa Hara | Shun-ichi Miyazaki | Kodai Murayama | Sana Tusji | Miho Inomata | 恵介 吉清 | 達之 山本 | Yukihiro Ozaki
Source: Institutional Repositories DataBase (IRDB) (article, 2022-06-15)
Field: Chemistry — Physical and Theoretical Chemistry

Development of an amino acid sequence-dependent analytical method for peptides using near-infrared spectroscopy Amino acid ; Spectroscopy ; Peptide sequence ; Peptide ; Amino acid analysis thermodynamics and calorimetric analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Spectroscopy and Chemometric Analyses
Authors: Ueon Sang Shin | Ji-Hye Kang | Ji‐Young Hwang | Young‐Jae Cho | Sang-Yu Park | Jung‐Joo Choi | E Sun Paik | Jeong‐Won Lee
Source: Research Square (preprint, 2022-09-07)
Field: Materials Science — Biomaterials

Advanced Drug Delivery of Paclitaxel with Thermoresponsive Water-soluble Micelles for Ovarian Cancer Abstract As an anti-cancer drug, paclitaxel (PTX) is known to be effective for treating patients with ovarian cancer. Not only do dose density and side effects of PTX represent a certain difficulty in chemotherapy, but also cause problems related to its poor water solubility during the administration. From the dose-density concept, we hypothesized that continuous release of PTX could increase the duration of exposure to tumor cells and may be an effective ovarian cancer treatment for patients. Herein, we developed highly water-soluble and multi-temperature-responsive PTX delivery systems to treat ovarian cancer. This was accomplished by entrapping the hydrophobic PTX in poly(NIPAAm-co-BVIm) micelles engineered to deliver drugs (pNIB/PTX). Specifically, the pNIB/PTX-3 complex containing 74 μg PTX loaded at 25 °C showed a rapid release of PTX initially (5.9 %/day) during the first five days at 37 °C. The release rates decreased (1.1 %/day) over the following month, indicating a multi-step release. In orthotopic ovarian cancer mouse models, the pNIB/PTX complex resulted in a six-fold greater therapeutic effect with a single intraperitoneal injection than weekly PTX treatment alone in vitro using two human ovarian cancer cell lines, HeyA8 and SKOV3ip. Moreover, the tumor weights in HeyA8 and SKOV3ip1 models were remarkably decreased with the pNIB/PTX complex compared to the controls. The good water solubility and temperature-dependent release of PTX carriers are highly effective for short-term and long-term delivery. This multi-step drug delivery may be used as a potential candidate for the treatment of patients with ovarian cancer. Paclitaxel ; Ovarian cancer ; Drug delivery ; Pharmacology ; Drug ; Chemotherapy ; Cancer ; Micelle ; Medicine ; In vivo ; Cancer cell ; Chemistry ; Internal medicine ; Biology ; Aqueous solution Nanoparticle-Based Drug Delivery ; Ovarian cancer diagnosis and treatment ; MicroRNA in disease regulation
Authors: Yingfan Liu | Zhiqiang Zhao
Source: Zeitschrift für Kristallographie - New Crystal Structures (article, 2022-08-15)
Field: Chemistry — Organic Chemistry

Crystal structure of (<i>Z</i>)-2-(<i>tert</i>-butyl)-5-((5-(<i>tert</i>- butyl)-2<i>H</i>-pyrrol-2-ylidene)(mesityl)methyl)-1<i>H</i>-pyrrole, C<sub>26</sub>H<sub>34</sub>N<sub>2</sub> Abstract C 26 H 34 N 2 , orthorhombic, Pbca (no. 61), a = 14.8062(2) Å, b = 15.8918(2) Å, c = 20.0121(3) Å, V = 4708.79(11) Å 3 , Z = 8, R gt ( F ) = 0.0548, wR ref ( F 2 ) = 0.1701, T = 296.2 K. Orthorhombic crystal system ; Chemistry ; Pyrrole ; Crystal structure ; Crystal (programming language) ; Medicinal chemistry ; Stereochemistry ; Crystallography ; Organic chemistry Synthesis and Reactivity of Heterocycles ; Synthesis and Characterization of Pyrroles ; Porphyrin and Phthalocyanine Chemistry
Authors: Valentin Théry | Florian Molton | Selim Sirach | Neven Tillet | Jacques Pécaut | Eder Tomas-Mendivil | David Martín
Source: ChemRxiv (preprint, 2022-04-05)
Field: Chemistry — Organic Chemistry

The curious case of a sterically crowded Stenhouse salt We report a peculiar Stenhouse salt. It does not evolve into cyclopentenones upon basification, due to the steric hindrance of its bulky stable carbene patterns. This allowed for the observation and characterization of the transient open-chain neutral derivative, which was isolated as its cyclized form. The latter features an unusually long reactive C–O bond (150 pm) and a rich electrochemistry, including oxidation into an air-persistent radical cation. Steric effects ; Salt (chemistry) ; Carbene ; Chemistry ; Derivative (finance) ; Polymer chemistry ; Photochemistry ; Organic chemistry ; Catalysis ; Business Radical Photochemical Reactions ; Synthetic Organic Chemistry Methods ; Oxidative Organic Chemistry Reactions
Authors: Sunil Varughese | Krzysztof Woźniak | Indira S. Divya | Saravanan Kandasamy
Source: ChemRxiv (preprint, 2022-02-14)
Field: Chemistry — Physical and Theoretical Chemistry

Flexible organic crystals. Understanding the tractable co-existence of elastic and plastic bending As an emerging class of ﬂexible materials, mechanically bendable molecular crystals are broadly classified as either elastic or plastic. Nevertheless, flexible organic crystals having elasticity and plasticity coexisting under different stress settings are exceptional; hence, it is imperative to establish the concurring factors that beget this rare occurrence. We report a series of halogen-substituted benzil crystals showing elastic bending (within ~ 2.45% strain), followed by elastoplastic deformation at ambient conditions. At higher stress settings, they display exceptional plastic flexibility that one could bend, twist, or even coil them around a capillary tube. Structural, computational, and microscopy studies reveal the microscopic and macroscopic basis for the exciting coexistence of elastic, elastoplastic, and plastic properties in the crystals. The isotropic distribution of weak interactions and the dispersive interactions that stitch the interlayer region enables the system to adopt partial molecular movements, restoring the original state within the elastic strain. The novel polymorph of F-derivative (BZF) shows exceptional mechanical deformation characteristics vis-à-vis the brittle nature of the known form (BZF_O). Comparative studies with oxalate compounds, wherein the twisted diketo moiety in benzil replaced with a rigid and coplanar central oxalate moiety, enabled us to understand the effect of the anisotropic factor in the crystal packing induced by the C=O···C tetral interactions. The enhanced anisotropy reduced the elastic regime, making the oxalate crystals more prone to plastic deformation. The work highlights the possible coexistence of orthogonal mechanical characteristics in molecular crystals and further construed the concurrent effect of the microscopic and macroscopic elements in attaining this exceptional mechanical trait. Materials science ; Composite material ; Isotropy ; Benzil ; Crystallography ; Anisotropy ; Bending ; Condensed matter physics ; Chemical physics ; Chemistry ; Optics ; Physics Crystallography and molecular interactions ; Luminescence and Fluorescent Materials ; Supramolecular Chemistry and Complexes
Authors: Ke Luan | Lu Wang | Fang‐Fang Xie | Bin‐Wen Chen | Zuo‐Chang Chen | Lin‐Long Deng | Su‐Yuan Xie | Lan‐Sun Zheng
Source: Nanomaterials (article, 2022-04-22)
Field: Chemistry — Organic Chemistry

Synthesis and Fluorescent Properties of Multi-Functionalized C70 Derivatives of C70(OCH3)10[C(COOEt)2] and C70(OCH3)10[C(COOEt)2]2 Due to the partially reduced π-conjugation of the fullerene cage, multi-functionalized fullerene derivatives exhibit remarkable fluorescent properties compared to pristine fullerenes, which have high potential for application in organic light-emitting diodes (OLEDs). In this study two multi-functionalized C<sub>70</sub> derivatives, C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub>[C(COOEt)<sub>2</sub>] and C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub>[C(COOEt)<sub>2</sub>]<sub>2</sub>, with excellent fluorescence properties, were designed and synthesized. Compared with C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub> containing a single kind of functional group, both the C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub>[C(COOEt)<sub>2</sub>] and C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub>[C(COOEt)<sub>2</sub>]<sub>2</sub> exhibited enhanced fluorescence properties with blue fluorescence emission. The fluorescence quantum yields of the C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub>[C(COOEt)<sub>2</sub>] and C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub>[C(COOEt)<sub>2</sub>]<sub>2</sub> were 1.94% and 2.30%, respectively, which were about ten times higher than that of C<sub>70</sub>(OCH<sub>3</sub>)<sub>10</sub>. The theoretical calculations revealed that the multi-functionalization of the C<sub>70</sub> increased the S<sub>1</sub>-T<sub>1</sub> energy gap, reducing the intersystem crossing efficiency, resulting in the higher fluorescence quantum yield of the C<sub>70</sub> derivatives. The results indicate that multi-functionalization is a viable strategy to improve the fluorescence of fullerene derivatives. Fluorescence ; Materials science ; Chemistry ; Physics ; Optics Fullerene Chemistry and Applications ; Graphene research and applications ; Synthesis and Properties of Aromatic Compounds
Authors: Sunil Varughese | Krzysztof Woźniak | Indira S. Divya | Saravanan Kandasamy | Toshiyuki Sasaki | Hideko Koshima | Shodai Hasebe
Source: ChemRxiv (preprint, 2022-07-04)
Field: Chemistry — Physical and Theoretical Chemistry

Flexible organic crystals. Understanding the tractable co-existence of elastic and plastic bending As an emerging class of ﬂexible materials, mechanically bendable molecular crystals are broadly classified as elastic or plastic. Nevertheless, flexible organic crystals with mutually exclusive elastic and plastic traits, with contrasting structural requirements, co-existing under different stress settings are exceptional; hence, it is imperative to establish the concurring factors that beget this rare occurrence. We report a series of halogen-substituted benzil crystals showing elastic bending (within ~ 2.45% strain), followed by elastoplastic deformation at ambient conditions. At higher stress settings, they display exceptional plastic flexibility that one could bend, twist, or even coil around a capillary tube. X-ray diffraction, microscopy, and computational data reveal the microscopic and macroscopic basis for the exciting co-existence of elastic, elastoplastic, and plastic properties in the crystals. The layered molecular arrangement and the weak dispersive interactions sustaining the interlayer region provide considerable tolerance towards the breaking and making upon engaging or releasing the external stress; it enables restoring the original state within the elastic strain. Comparative studies with oxalate compounds, wherein the twisted diketo moiety in benzil was replaced with a rigid and coplanar central oxalate moiety, enabled us to understand the effect of the anisotropy factor in the crystal packing induced by the C=O···C tetral interactions. The enhanced anisotropy depreciated the elastic domain, making the oxalate crystals more prone to plastic deformation. Three-point bending experiments and the determined Young's moduli further corroborate the co-existence of the elastic and plastic realm and highlights the critical role of the underlying structural elements that determine the elastic to plastic transformation. The work highlights the possible co-existence of orthogonal mechanical characteristics in molecular crystals and further construed the concurrent effect of the microscopic and macroscopic elements in attaining this exceptional mechanical trait. Materials science ; Benzil ; Composite material ; Bending ; Crystallography ; Plastic bending ; Elastic modulus ; Anisotropy ; Deformation (meteorology) ; Bending stiffness ; Chemistry ; Optics ; Physics Crystallography and molecular interactions ; Luminescence and Fluorescent Materials ; Corrosion Behavior and Inhibition
Authors: Caroline R. Carneiro | Isabela B. Serwy | Carolina S. Silva | Ingrid T. Weber
Source: Journal of the Brazilian Chemical Society (article, 2022-01-01)
Field: Chemistry — Analytical Chemistry

Encoding of Luminescent Ink Markers Using Low-Level Data Fusion and Chemometrics The identification and analysis of documentary fraud is always a challenge for forensic science. Document analysis has proven to be an important branch of forensics in elucidating the authenticity of documents. The development and incorporation of luminescent inks in authentic documents have proved to be an excellent security feature. This paper purposes the use of a possible luminescent ink marker for anti-counterfeiting applications, aiming to create a document encoding process that is simple, robust, sensitive, and non-destructive. Since luminescent inks markers provide a visual, chemical, and spectral signature, and can be easily detected by using a UV lamp, the aid of unsupervised chemometric tools makes it possible to differentiate the luminescent markers inserted in the ink. Unsupervised models of principal component analysis (PCA) and K-mean were successful in correctly associating marked inks with their respective pure markers, while a supervised classification model based on partial least squares discriminant analysis (PLS-DA) correctly classified all samples from the prediction set and the blind test samples. For comparison, a soft independent modeling of class analogy (SIMCA) model was also built, which despite showing a misclassified sample it is also a strong candidate for future applications. Chemometrics ; Computer science ; Principal component analysis ; Pattern recognition (psychology) ; Artificial intelligence ; Sample (material) ; Luminescence ; Partial least squares regression ; Linear discriminant analysis ; Data mining ; Machine learning ; Materials science ; Chemistry ; Chromatography Spectroscopy and Chemometric Analyses ; Cultural Heritage Materials Analysis ; Currency Recognition and Detection
Authors: Nicholas J. East | Ben E. Clifton | Colin J. Jackson | Joe A. Kaczmarski
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-09-13)
Field: Materials Science — Materials Chemistry

The role of evolutionarily metastable oligomeric states in the optimization of catalytic activity Abstract The emergence of oligomers is common during the evolution and diversification of protein families, yet the selective advantage of oligomerization is often cryptic or unclear. Oligomerization can involve the formation of isologous head-to-head interfaces (e.g., in symmetrical dimers) or heterologous head-to-tail interfaces (e.g., in cyclic complexes), the latter of which is less well studied and understood. In this work, we retrace the emergence of the trimeric form of cyclohexadienyl dehydratase from Pseudomonas aeruginosa (PaCDT) by introducing residues that form the PaCDT trimer-interface into AncCDT-5 (a monomeric reconstructed ancestor of PaCDT). We find that single interface mutations can switch the oligomeric state of the variants (implying evolutionarily metastable oligomeric states) and that trimerization corresponds with a reduction in the K M value of the enzyme from a promiscuous level to the physiologically relevant range. We show that this can be rationalized at the structural and dynamic level by reduced sampling of a non-catalytic conformational substate, and that trimerization was likely followed by a C-terminal extension that further refined the conformational sampling and kinetic properties of the enzyme. This work provides insight into how neutral sampling of metastable oligomeric states along an evolutionary trajectory can facilitate the evolution and optimization of enzyme function. Importance &amp; Impact Statement Understanding how and why structural complexity (including homo-oligomerization and sequence insertions) emerges during the evolution and diversification of natural enzymes is a key goal in the study and design of protein function. We show that cyclic homo-oligomeric states can emerge via a small number of substitutions, and that trimerization and a C-terminal extension contributed to the tuning of catalytic properties during the evolution of cyclohexadienyl dehydratase from Pseudomonas aeruginosa . Trimer ; Chemistry ; Stereochemistry ; Dimer Enzyme Structure and Function ; Protein Structure and Dynamics ; Microbial Metabolic Engineering and Bioproduction
Authors: Peter Kiplangʼat Koech | Gergely Jócsák | Imre Boldizsár | Kinga Moldován | Sándor Borbély | Ildikó Világi | Árpád Dobolyi | Petra Varró
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-10-18)
Field: Chemistry — Organic Chemistry

Anti-glutamatergic effects of three lignan compounds: arctigenin, matairesinol and trachelogenin - An ex vivo study on rat brain slices Abstract Arctigenin is a bioactive dibenzylbutyrolactone-type lignan exhibiting various pharmacological activities. The neuroprotective effects of arctigenin were demonstrated to be mediated via inhibition of AMPA/KA type glutamate receptors in the somatosensory cortex of the rat brain. The aim of this study was to compare the effects of arctigenin with matairesinol and trachelogenin on synaptic activity in ex vivo rat brain slices. Arctigenin, matairesinol and trachelogenin were isolated from Arctium lappa, Centaurea scabiosa and Cirsium arvense , respectively, and applied on brain slices via perfusion medium at the concentration range of 0.5-40 μM. The effects of the lignans were examined in the CA1 hippocampus and the somatosensory cortex by recording electrically evoked field potentials. Arctigenin and trachelogenin caused a significant dose-dependent decrease in the amplitude of hippocampal population spikes (POPS) and the slope of excitatory postsynaptic potentials (EPSPs), whereas matairesinol (1 μM and 10 μM) decreased EPSP slope but had no effect on POPS amplitude. Trachelogenin effect (0.5 μM, 10 μM, 20 μM) was comparable to arctigenin (1 μM, 20 μM, 40 μM) (p &gt; 0.05). In the neocortex, arctigenin (10 μM, 20 μM) and trachelogenin (10 μM) significantly decreased the amplitude of evoked potential early component, while matairesinol (1 μM and 10 μM) had no significant effect (p&gt;0.05). The results suggest that trachelogenin and arctigenin act via inhibition of AMPA/KA receptors in the brain and trachelogenin has a higher potency than arctigenin. Thus, trachelogenin and arctigenin could serve as lead compounds in the development of alternative neuroprotective drugs. AMPA receptor ; Lignan ; Chemistry ; Population ; Excitatory postsynaptic potential ; Pharmacology ; Biology ; NMDA receptor ; Stereochemistry ; Biochemistry ; Receptor ; Medicine Coordination Chemistry and Organometallics ; Axial and Atropisomeric Chirality Synthesis ; Plant-derived Lignans Synthesis and Bioactivity
Authors: Abraham K. Aworinde | Titus O. Ajewole | Olakunle Olukayode | Joseph O. Dirisu
Source: Pertanika journal of science & technology (article, 2022-04-20)
Field: Materials Science — Biomaterials

Mathematical Models for Predicting the Mechanical Properties of Poly(Lactic Acid) for Load-Bearing Applications In order to widen the areas of application of poly (lactic acid) (PLA), there has been a multiplicity of experiments. This study attempts to develop mathematical models for predicting the mechanical properties of PLA to reduce the number of experimental runs and material wastage. The melt-cast method produced unreinforced PLA samples with different slenderness ratios (λ) in triplicate using. The samples were subjected to a compression test to obtain the mechanical properties captured at three main points on the stress-strain curve: yield, ultimate stress, and fracture. Regression models were developed from the data obtained at the three points, and their validity was examined by testing them against the previous relevant experimental studies from various authors. The coefficient of determination (R2) and coefficient of correlation (ρ) was also examined for each model to establish their degree of correctness further. Analyses show that the developed models give reasonable approximations of some of the properties examined. The mass (M) and the modulus of elasticity (E) were the most accurately predictable properties with [R2, ρ] of [99.97%, 0.9998] and [91.55%, 0.9568], respectively. Results also show that apart from the melt-cast method, the compressive modulus of PLA (both circular and rectangular cross-sections test samples) produced via injection molding and fused filament fabrication can be predicted with near accuracy using the model developed in this study. This study gives researchers the tools needed to avoid material wastage by having close-to-real values of the mechanical properties of PLA through prediction before carrying out any experiment. Materials science ; Young's modulus ; Molding (decorative) ; Composite material ; Modulus ; Compressive strength ; Elastic modulus ; Elasticity (physics) ; Structural engineering ; Engineering biodegradable polymer synthesis and properties ; Additive Manufacturing and 3D Printing Technologies ; Bone Tissue Engineering Materials