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“Fluxomics” refers to the systematic analysis of metabolic fluxes in a biological system and may uncover novel dynamic properties of metabolism that remain undetected in conventional metabolomic approaches. In labeling experiments, tracer molecules are used to track changes in the isotopologue distribution of metabolites, which allows one to estimate fluxes in the metabolic network. Because unidentified compounds cannot be mapped on pathways, they are often neglected in labeling experiments. However, using recent developments in de novo annotation may allow to harvest the information present in these compounds if they can be identified. Here, we present a novel tool (HiResTEC) to detect tracer incorporation in high-resolution mass spectrometry data sets. The software automatically extracts a comprehensive, nonredundant list of all compounds showing more than 1% tracer incorporation in a nontargeted fashion. We explain and show in an example data set how mass precision and other filter heuristics, calculated on the raw data, can efficiently be used to reduce redundancy and noninformative signals by 95%. Ultimately, this allows to quickly investigate any labeling experiment for a complete set of labeled compounds (here 149) with acceptable false positive rates. We further re-evaluate a published data set from liquid chromatography-electrospray ionization (LC-ESI) to demonstrate broad applicability of our tool and emphasize importance of quality control (QC) tests. HiResTEC is provided as a package in the open source software framework R and is freely available on CRAN.
Ligand based modification has been performed to synthesize a pair of
mixed ligands d10 MOF based materials related to a previously published compound as a base material. The previous compound was a Zn(II)-MOF, {[Zn(4-bpdh)(H2dht)](MeOH)(H2O)}n (1) [N,N′-bis(1-pyridin-4-yl-ethylidene)hydrazine = 4-bpdh and 2,5-dihydroxyterephthalic acid = H4dht], which is a five-fold interpenetrated framework and highly dynamic in nature. In the first synthetic modification, the central metal is replaced by Cd(II), which has the same framework formula as the base material, but this is a rigid compound and also there is no interpenetration in the framework. In the second modification, along with the metal center, the 4,4′- coordinating N,N′-donor ligand is replaced by an isomeric 3,3′-coordinating N,N′- donor linker. In this compound, the dynamism is regenerated. The dynamic nature can be realized by the extensive PXRD studies and characteristic “step-shaped” gas/solvent adsorption behavior for CO2, water, and ethanol. Furthermore, all these 3D MOFs show excited-state intramolecular proton transfer phenomena and water sensing properties in different organic solvents. Here excitingly, the ease of water sensing property is directly related to the dynamic behavior of the framework which has been studied thoroughly in terms of structural correlation.
A cobalt(III) complex, [Co(L)3](DMF) (1) of Schiff base ligand HL, 2-((E)-(benzylimino)methyl)-4-bromophenol is prepared and single crystal X-ray structural analysis have also been performed. The structures of complex 1 showed hexa-coordinated mononuclear systems that adopt octahedral geometry. The complex has also exhibited the supramolecular networks through non-covalent interactions like H-bonding, C–Hπ stacking. Moreover, the complex 1 is very effective in the catalytic fixation of carbon dioxide in propergyl alcohols to produce α-alkylidene cyclic carbonates. The catalytic production of α-alkylidene cyclic carbonates have been carried out through carboxylative cyclization of propargyl alcohols using CO2 balloon of 1 atm pressure at 80 ◦C. Solvent free condition (green synthesis) made this catalytic protocol eco-friendly towards the environment. Utilizing various substrates of propargyl alcohols moderate to high percentage yield (62–95%) of respective α-alkylidene cyclic carbonates product have been isolated over this catalytic reaction. Besides, the theoretical calculations (DFT) was performed for the prediction of probable mechanism of the catalytic reaction
Mechanically flexible single crystals of molecular materials offer potential for a multitude of new directions in advanced materials design. Before the full potential of such materials can be exploited, insight into their mechanisms of action must be better understood. Such insight can be only obtained through synergistic use of advanced experimentation and simulation. We herein report the first detailed mechanistic study of elasto-plastic flexibility in a molecular solid. An atomistic origin for this mechanical behaviour is proposed through a combination of atomic force microscopy, μ-focus synchrotron X-ray diffraction, Raman spectroscopy, ab initio simulation, and computed elastic tensors. Our findings suggest that elastic and plastic bending are intimately linked and result from extensions of the same molecular deformations. The proposed mechanism bridges the gap between contested mechanisms, suggesting its applicability as a general mechanism for elastic and plastic bending in organic molecular crystals.
Clerodin was isolated from the medicinal plant Clerodendrum infortunatum, and CSD search showed the first crystal structure of clerodin by a single-crystal X-ray diffraction study. We checked its binding potential with target proteins by docking and conducted network pharmacology analysis, ADMET analysis, in silico pathway analysis, normal mode analysis (NMA), and cytotoxic activity studies to evaluate clerodin as a potential anticancer agent. The cell viability studies of clerodin on the human breast carcinoma cell line (MCF-7) showed toxicity on MCF-7 cells but no toxicity toward normal human lymphocyte cells (HLCs). The anticancer mechanism of clerodin was validated by its enhanced capacity to produce intracellular reactive oxygen species (ROS) and to lower the reduced glutathione content in MCF-7 cells.
Mechanical flexibility in single crystals of covalently bound materials is a fascinating and poorly understood phenomenon. We present here the first example of a plastically flexible one-dimensional (1D) coordination polymer. The compound [Zn(m-Cl)2(3,5-dichloropyridine)2]n is flexible over two crystallographic faces. Remarkably, the single crystal remains intact when bent to 1808. A combination of microscopy, diffraction, and spectroscopic studies have been used to probe the structural response of the crystal lattice to mechanical bending. Deformation of the covalent polymer chains does not appear to be responsible for the observed macroscopic bending. Instead, our results suggest that mechanical bending occurs by displacement of the coordination polymer chains. Based on experimental and theoretical evidence, we propose a new model for mechanical flexibility in 1D coordination polymers. Moreover, our calculations propose a cause of the different mechanical properties of this compound and a structurally similar elastic material
Multidrug solids have a potential use to efficiently treat and control a superfluity of medical conditions.
To address the current drawbacks of drug development in R&D, it was targeted to achieve new pharmaceutical solid forms of fenamic acids having improved solubility and thermal stability. Subsequently, five new multicomponent solids consisting of three salt hydrates of trimethoprim (TMP) with mefenamic acid (TMP-MFA-H2O), tolfenamic acid (TMP-TFA-H2O) and flufenamic acid (TMP-FFA-H2O), and two cocrystals of sulfamethazine (SFZ) with flufenamic acid (SFZ-FFA) and niflumic acid (SFZ-NFA) were prepared by liquid assisted grinding. Looking at the structures of active pharmaceutical ingredient (API) molecules, it was quite expected that a wide range of supramolecular synthons would lead to cocrystallization.
New forms were characterized thoroughly by various solid-state techniques, including single crystal X-ray diffraction (SCXRD), which provided details of hydrogen bonding, molecular packing and interactions between drug and coformer. Kinetic solubility at pH 7.4 buffer study has been carried out and a comparison is made with respect to the parent drugs. A significant enhancement of NSAIDs solubility was observed in all salt hydrate systems of TMP. Thus with increasing physicochemical properties such as improved solubility further leads to the enhancement of bioavailability, which has implications to overcoming the formulation related problems of active pharmaceutical ingredients (APIs).
Fluorescent plastically bendable crystals are a promising alternative to silicon-based materials for fabricating photonic integrated circuits, owing to their optical attributes and mechanical compliance. Mechanically bendable plastic organic crystals are rare. Their formation requires anisotropic intermolecular interactions and slip planes in the crystal lattice. This work presents three fluorescent plastically bendable crystalline materials namely, 2-((E)-(6-methylpyridin-2-ylimino)methyl)-4-chlorophenol (SB1), 2-((E)-(6-methylpyridin-2-ylimino)methyl)-4-bromophenol (SB2), and 2-((E)-(6-Bromopyridin-2-ylimino)methyl)-4-bromophenol (SB3) molecules. The crystal plasticity in response to mechanical stress facilitates the fabrication of various monolithic and hybrid (with a tip-to-tip coupling) photonic circuits using mechanical micromanipulation with an atomic force microscope cantilever tip. These plastically bendable crystals act as active (self-guiding of fluorescence) and passive waveguides both in straight and extremely bent (U-, J-, and O-shaped) geometries. These microcircuits use active and passive waveguiding principles and reabsorbance and energy-transfer mechanisms for their operation, allowing input-selective and direction-specific signal transduction.
Pirfenidone is an important drug molecule used in the treatment of idiopathic lung fibrosis. Although approved by the USFDA in 2014, pirfenidone’s aqueous solubility is too high and must be mitigated by additives. In this work, the cocrystallization of pirfenidone is explored as an alternative approach to reducing its solubility. Herein, an anhydrous form of pirfenidone is reported, alongside its first two reported cocrystals. The new crystalline solids are thoroughly characterized by single crystal X-ray diffraction (SCXRD), powder X-ray diffraction analysis (PXRD), Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA).
Equilibrium solubility and intrinsic dissolution rates (IDR) are studied for the cocrystals and compared to that of the parent drug. Both cocrystal forms exhibit drastically lower aqueous solubility (by up to 90%) and dissolution rates, rationalized based on both lattice energy calculations and consideration of intermolecular interactions in the solid state. Furthermore, we compare the physicochemical properties of solution-based material with that of material produced mechanochemically. Importantly, no differences are observed between the two production methods. This work demonstrates the strength of crystal Engineering strategies to beneficially modify important pharmaceutical properties and highlights the potential of mechanochemistry to facilitate this in an environmentally benign way.