ResearchPad - General Chemistry Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Iron-catalyzed urea synthesis: dehydrogenative coupling of methanol and amines]]>

An iron catalyzed method for selective urea synthesis is described. This approach couples methanol and amines to generate diverse organic ureas.

<![CDATA[Quantifying Reversible Surface Binding via Surface-Integrated Fluorescence Correlation Spectroscopy]]>


We present a simple and versatile single-molecule-based method for the accurate determination of binding rates to surfaces or surface bound receptors. To quantify the reversible surface attachment of fluorescently labeled molecules, we have modified previous schemes for fluorescence correlation spectroscopy with total internal reflection illumination (TIR-FCS) and camera-based detection. In contrast to most modern applications of TIR-FCS, we completely disregard spatial information in the lateral direction. Instead, we perform correlation analysis on a spatially integrated signal, effectively converting the illuminated surface area into the measurement volume. In addition to providing a high surface selectivity, our new approach resolves association and dissociation rates in equilibrium over a wide range of time scales. We chose the transient hybridization of fluorescently labeled single-stranded DNA to the complementary handles of surface-immobilized DNA origami structures as a reliable and well-characterized test system. We varied the number of base pairs in the duplex, yielding different binding times in the range of hundreds of milliseconds to tens of seconds, allowing us to quantify the respective surface affinities and binding rates.

<![CDATA[Second-generation CK2α inhibitors targeting the αD pocket]]>

We describe the development of a CAM4712, a novel CK2α inhibitor which does not interact with the ATP binding site and shows improved properties over the first-generation inhibitor CAM4066.

<![CDATA[A catalytic highly enantioselective allene approach to oxazolines]]>

A completely different approach for the asymmetric construction of oxazoline derivatives with an excellent enantioselectivity via the palladium-catalyzed coupling-cyclization of N-(buta-2,3-dienyl)amides with aryl iodides has been reported.

<![CDATA[Photosensitizer synergistic effects: D–A–D structured organic molecule with enhanced fluorescence and singlet oxygen quantum yield for photodynamic therapy]]>

Novel photosensitizers have been developed with high 1O2 quantum yields and strong fluorescence for cancer diagnosis and PDT.

<![CDATA[Discrimination of saturated alkanes and relevant volatile compounds via the utilization of a conceptual fluorescent sensor array based on organoboron-containing polymers]]>

A conceptual sensor array for the efficient discrimination and fast detection of saturated alkanes and commonly found volatile solvents is reported.

<![CDATA[Coupling of sterically demanding peptides by β-thiolactone-mediated native chemical ligation]]>

β-Thiolactones have enabled the sterically demanding peptidyl ligations of Val–Leu, Val–Val and Val–Pro using a one-pot NCL and desulfurization protocol.

<![CDATA[Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with eMolFrag]]>


Constructing high-quality libraries of molecular building blocks is essential for successful fragment-based drug discovery. In this communication, we describe eMolFrag, a new open-source software to decompose organic compounds into nonredundant fragments retaining molecular connectivity information. Given a collection of molecules, eMolFrag generates a set of unique fragments comprising larger moieties, bricks, and smaller linkers connecting bricks. These building blocks can subsequently be used to construct virtual screening libraries for targeted drug discovery. The robustness and computational performance of eMolFrag is assessed against the Directory of Useful Decoys, Enhanced database conducted in serial and parallel modes with up to 16 computing cores. Further, the application of eMolFrag in de novo drug design is illustrated using the adenosine receptor. eMolFrag is implemented in Python, and it is available as stand-alone software and a web server at and

<![CDATA[Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering]]>

Influenza virus infects cells by binding to sialylated glycans on the cell surface. While the chemical structure of these glycans determines hemagglutinin–glycan binding affinity, bimolecular affinities are weak, so binding is avidity-dominated and driven by multivalent interactions. Here, we show that membrane spatial organization can control viral binding. Using single-virus fluorescence microscopy, we demonstrate that the sterol composition of the target membrane enhances viral binding avidity in a dose-dependent manner. Binding shows a cooperative dependence on concentration of receptors for influenza virus, as would be expected for a multivalent interaction. Surprisingly, the ability of sterols to promote viral binding is independent of their ability to support liquid–liquid phase separation in model systems. We develop a molecular explanation for this observation via molecular dynamics simulations, where we find that cholesterol promotes small-scale clusters of glycosphingolipid receptors. We propose a model whereby cholesterol orders the monomeric state of glycosphingolipid receptors, reducing the entropic penalty of receptor association and thus favoring multimeric complexes without phase separation. This model explains how cholesterol and other sterols control the spatial organization of membrane receptors for influenza and increase viral binding avidity. A natural consequence of this finding is that local cholesterol concentration in the plasma membrane of cells may alter the binding avidity of influenza virions. Furthermore, our results demonstrate a form of cholesterol-dependent membrane organization that does not involve lipid rafts, suggesting that cholesterol’s effect on cell membrane heterogeneity is likely the interplay of several different factors.

<![CDATA[Evaluating the Energetic Driving Force for Cocrystal Formation]]>


We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol–1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems—hydrogen-bonded, halogen-bonded, and weakly bound cocrystals—finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition—more densely packed cocrystals with stronger hydrogen bonding tend to be more stable—but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems.

<![CDATA[Strong Magneto-Optical Response of Nonmagnetic Organic Materials Coupled to Plasmonic Nanostructures]]>


Plasmonic nanoparticles (PNPs) can significantly modify the optical properties of nearby organic molecules and thus present an attractive opportunity for sensing applications. However, the utilization of PNPs in conventional absorption, fluorescence, or Raman spectroscopy techniques is often ineffective due to strong absorption background and light scattering, particularly in the case of turbid solutions, cell suspensions, and biological tissues. Here we show that nonmagnetic organic molecules may exhibit magneto-optical response due to binding to a PNP. Specifically, we detect strong magnetic circular dichroism signal from supramolecular J-aggregates, a representative organic dye, upon binding to silver-coated gold nanorods. We explain this effect by strong coupling between the J-aggregate exciton and the nanoparticle plasmon, leading to the formation of a hybrid state in which the exciton effectively acquires magnetic properties from the plasmon. Our findings are fully corroborated by theoretical modeling and constitute a novel magnetic method for chemo- and biosensing, which (upon adequate PNP functionalization) is intrinsically insensitive to the organic background and thus offers a significant advantage over conventional spectroscopy techniques.

<![CDATA[Exposure Assessment of Acetamide in Milk, Beef, and Coffee Using Xanthydrol Derivatization and Gas Chromatography/Mass Spectrometry]]>


Acetamide has been classified as a possible human carcinogen, but uncertainties exist about its levels in foods. This report presents evidence that thermal decomposition of N-acetylated sugars and amino acids in heated gas chromatograph injectors contributes to artifactual acetamide in milk and beef. An alternative gas chromatography/mass spectrometry protocol based on derivatization of acetamide with 9-xanthydrol was optimized and shown to be free of artifactual acetamide formation. The protocol was validated using a surrogate analyte approach based on d3-acetamide and applied to analyze 23 pasteurized whole milk, 44 raw sirloin beef, and raw milk samples from 14 different cows, and yielded levels about 10-fold lower than those obtained by direct injection without derivatization. The xanthydrol derivatization procedure detected acetamide in every food sample tested at 390 ± 60 ppb in milk, 400 ± 80 ppb in beef, and 39 000 ± 9000 ppb in roasted coffee beans.

<![CDATA[Exposure to selected limonene oxidation products: 4-OPA, IPOH, 4-AMCH induces oxidative stress and inflammation in human lung epithelial cell lines]]> <![CDATA[Microsomal Metabolism of Prochiral Polychlorinated Biphenyls Results in the Enantioselective Formation of Chiral Metabolites]]> <![CDATA[Seagrass-Mediated Phosphorus and Iron Solubilization in Tropical Sediments]]>


Tropical seagrasses are nutrient-limited owing to the strong phosphorus fixation capacity of carbonate-rich sediments, yet they form densely vegetated, multispecies meadows in oligotrophic tropical waters. Using a novel combination of high-resolution, two-dimensional chemical imaging of O2, pH, iron, sulfide, calcium, and phosphorus, we found that tropical seagrasses are able to mobilize the essential nutrients iron and phosphorus in their rhizosphere via multiple biogeochemical pathways. We show that tropical seagrasses mobilize phosphorus and iron within their rhizosphere via plant-induced local acidification, leading to dissolution of carbonates and release of phosphate, and via local stimulation of microbial sulfide production, causing reduction of insoluble Fe(III) oxyhydroxides to dissolved Fe(II) with concomitant phosphate release into the rhizosphere porewater. These nutrient mobilization mechanisms have a direct link to seagrass-derived radial O2 loss and secretion of dissolved organic carbon from the below-ground tissue into the rhizosphere. Our demonstration of seagrass-derived rhizospheric phosphorus and iron mobilization explains why seagrasses are widely distributed in oligotrophic tropical waters.

<![CDATA[Experimental and Kinetic Modeling Studies on the Conversion of Sucrose to Levulinic Acid and 5-Hydroxymethylfurfural Using Sulfuric Acid in Water]]>


We here report experimental and kinetic modeling studies on the conversion of sucrose to levulinic acid (LA) and 5-hydroxymethylfurfural (HMF) in water using sulfuric acid as the catalyst. Both compounds are versatile building blocks for the synthesis of various biobased (bulk) chemicals. A total of 24 experiments were performed in a temperature window of 80–180 °C, a sulfuric acid concentration between 0.005 and 0.5 M, and an initial sucrose concentration between 0.05 and 0.5 M. Glucose, fructose, and HMF were detected as the intermediate products. The maximum LA yield was 61 mol %, obtained at 160 °C, an initial sucrose concentration of 0.05 M, and an acid concentration of 0.2 M. The maximum HMF yield (22 mol %) was found for an acid concentration of 0.05 M, an initial sucrose concentration of 0.05 M, and a temperature of 140 °C. The experimental data were modeled using a number of possible reaction networks. The best model was obtained when using a first order approach in substrates (except for the reversion of glucose) and agreement between experiment and model was satisfactorily. The implication of the model regarding batch optimization is also discussed.

<![CDATA[Global Cryptosporidium Loads from Livestock Manure]]>


Understanding the environmental pathways of Cryptosporidium is essential for effective management of human and animal cryptosporidiosis. In this paper we aim to quantify livestock Cryptosporidium spp. loads to land on a global scale using spatially explicit process-based modeling, and to explore the effect of manure storage and treatment on oocyst loads using scenario analysis. Our model GloWPa-Crypto L1 calculates a total global Cryptosporidium spp. load from livestock manure of 3.2 × 1023 oocysts per year. Cattle, especially calves, are the largest contributors, followed by chickens and pigs. Spatial differences are linked to animal spatial distributions. North America, Europe, and Oceania together account for nearly a quarter of the total oocyst load, meaning that the developing world accounts for the largest share. GloWPa-Crypto L1 is most sensitive to oocyst excretion rates, due to large variation reported in literature. We compared the current situation to four alternative management scenarios. We find that although manure storage halves oocyst loads, manure treatment, especially of cattle manure and particularly at elevated temperatures, has a larger load reduction potential than manure storage (up to 4.6 log units). Regions with high reduction potential include India, Bangladesh, western Europe, China, several countries in Africa, and New Zealand.

<![CDATA[Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry]]>


Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.

<![CDATA[Photosensitized Formation of Secondary Organic Aerosols above the Air/Water Interface]]> <![CDATA[pH Responsive and Oxidation Resistant Wet Adhesive based on Reversible Catechol–Boronate Complexation]]>