An in situ electrochemical cell for Q- and W-band EPR spectroscopy

A simple design for an in situ, three-electrode spectroelectrochemical cell is reported that can be used in commercial Q- and W-band (ca. 34 and 94 GHz, respectively) electron paramagnetic resonance (EPR) spectrometers, using standard sample tubing (1.0 and 0.5 mm inner diameter, respectively) and within variable temperature cryostat systems. The use of the cell is demonstrated by the in situ generation of organic free radicals (quinones and diimines) in fluid and frozen media, transition metal ion radical anions, and on the enzyme nitric oxide synthase reductase domain (NOSrd), in which a pair of flavin radicals are generated.     

Assessing and accounting for time heterogeneity in stochastic actor oriented models

This paper explores time heterogeneity in stochastic actor oriented models (SAOM) proposed by Snijders (Sociological Methodology. Blackwell, Boston, pp 361-395, 2001) which are meant to study the evolution of networks. SAOMs model social networks as directed graphs with nodes representing people, organizations, etc., and dichotomous relations representing underlying relationships of friendship, advice, etc. We illustrate several reasons why heterogeneity should be statistically tested and provide a fast, convenient method for assessment and model correction. SAOMs provide a flexible framework for network dynamics which allow a researcher to test selection, influence, behavioral, and structural properties in network data over time. We show how the forward-selecting, score type test proposed by Schweinberger (Chapter 4: Statistical modeling of network panel data: goodness of fit. PhD thesis, University of Groningen 2007) can be employed to quickly assess heterogeneity at almost no additional computational cost. One step estimates are used to assess the magnitude of the heterogeneity. Simulation studies are conducted to support the validity of this approach. The ASSIST dataset (Campbell et al. Lancet 371(9624):1595-1602, 2008) is reanalyzed with the score type test, one step estimators, and a full estimation for illustration. These tools are implemented in the RSiena package, and a brief walkthrough is provided.     

Softness of atherogenic lipoproteins: a comparison of very low density lipoprotein (VLDL) and low density lipoprotein (LDL) using elastic incoherent neutron scattering (EINS)

Apolipoprotein B100 (apoB100)-containing plasma lipoproteins (LDL and VLDL) supply tissues and cells with cholesterol and fat. During lipolytic conversion from VLDL to LDL the size and chemical composition of the particles change, but the apoB100 molecule remains bound to the lipids and regulates the receptor mediated uptake. The molecular physical parameters which control lipoprotein remodeling and enable particle stabilization by apoB100 are largely unknown. Here, we have compared the molecular dynamics and elasticities of VLDL and LDL derived by elastic neutron scattering temperature scans. We have determined thermal motions, dynamical transitions, and molecular fluctuations, which reflect the temperature-dependent motional coupling between lipid and protein. Our results revealed that lipoprotein particles are extremely soft and flexible. We found substantial differences in the molecular resiliences of lipoproteins, especially at higher temperatures. These discrepancies not only can be explained in terms of lipid composition and mobility but also suggest that apoB100 displays different dynamics dependent on the lipoprotein it is bound to. Hence, we suppose that the inherent conformational flexibility of apoB100 permits particle stabilization upon lipid exchange, whereas the dynamic coupling between protein and lipids might be a key determinant for lipoprotein conversion and atherogenicity.     

Genome-based deletion analysis reveals the prenyl xanthone biosynthesis pathway in Aspergillus nidulans

Xanthones are a class of molecules that bind to a number of drug targets and possess a myriad of biological properties. An understanding of xanthone biosynthesis at the genetic level should facilitate engineering of second-generation molecules and increasing production of first-generation compounds. The filamentous fungus Aspergillus nidulans has been found to produce two prenylated xanthones, shamixanthone and emericellin, and we report the discovery of two more, variecoxanthone A and epishamixanthone. Using targeted deletions that we created, we determined that a cluster of 10 genes including a polyketide synthase gene, mdpG, is required for prenyl xanthone biosynthesis. mdpG was shown to be required for the synthesis of the anthraquinone emodin, monodictyphenone, and related compounds, and our data indicate that emodin and monodictyphenone are precursors of prenyl xanthones. Isolation of intermediate compounds from the deletion strains provided valuable clues as to the biosynthetic pathway, but no genes accounting for the prenylations were located within the cluster. To find the genes responsible for prenylation, we identified and deleted seven putative prenyltransferases in the A. nidulans genome. We found that two prenyltransferase genes, distant from the cluster, were necessary for prenyl xanthone synthesis. These genes belong to the fungal indole prenyltransferase family that had previously been shown to be responsible for the prenylation of amino acid derivatives. In addition, another prenyl xanthone biosynthesis gene is proximal to one of the prenyltransferase genes. Our data, in aggregate, allow us to propose a complete biosynthetic pathway for the A. nidulans xanthones.     

Stereodivergent Anion Binding Catalysis with Molecular Motors

A photoresponsive chiral catalyst based on an oligotriazole‐functionalized unidirectional molecular motor has been developed for stereodivergent anion binding catalysis. The motor function controls the helical chirality of supramolecular assemblies with chloride anions, which by means of chirality transfer enables the enantioselective addition of a silyl ketene acetal nucleophile to oxocarbenium cations. Reversal of stereoselectivity (up to 142 % Δee) was achieved through rotation of the motor core induced by photochemical and thermal isomerization steps.     

Gold Nanocage Assemblies for Selective Second Harmonic Generation Imaging of Cancer Cell

Second harmonic generation (SHG) imaging using near infrared laser light is the key to improving penetration depths, leading to biological understanding. Unfortunately, currently SHG imaging techniques have limited capability due to the poor signal‐to‐noise ratio, resulting from the low SHG efficiency of available dyes. Targeted tumor imaging over nontargeted tissues is also a challenge that needs to be overcome. Driven by this need, in this study, the development of two‐photon SHG imaging of live cancer cell lines selectively by enhancement of the nonlinear optical response of gold nanocage assemblies is reported. Experimental results show that two‐photon scattering intensity can be increased by few orders of magnitude by just developing nanoparticle self‐assembly. Theoretical modeling indicates that the field enhancement values for the nanocage assemblies can explain, in part, the enhanced nonlinear optical properties. Our experimental data also show that A9 RNA aptamer conjugated gold nanocage assemblies can be used for targeted SHG imaging of the LNCaP prostate cancer cell line. Experimental results with the HaCaT normal skin cell lines show that bioconjugated nanocage‐based assemblies demonstrate SHG imaging that is highly selective and will be able to distinguish targeted cancer cell lines from other nontargeted cell types. After optimization, this reported SHG imaging assay could have considerable application for biology.     

Multiple approaches for enhancing all-organic electronics photoluminescent sensors: Simultaneous oxygen and pH monitoring

Key issues in using organic light emitting diodes (OLEDs) as excitation sources in structurally integrated photoluminescence (PL)-based sensors are the low forward light outcoupling, the OLEDs’ broad electroluminescence (EL) bands, and the long-lived remnant EL that follows an EL pulse. The outcoupling issue limits the detection sensitivity (S) as only ~20% of the light generated within standard OLEDs can be forward outcoupled and used for sensor probe excitation. The EL broad band interferes with the analyte-sensitive PL, leading to a background that reduces S and dynamic range. In particular, these issues hinder designing compact sensors, potentially miniaturizable, that are devoid of optical filters and couplers. We address these shortcomings by introducing easy-to-employ multiple approaches for outcoupling improvement, PL enhancement, and background EL reduction leading to novel, compact all-organic device architectures demonstrated for simultaneous monitoring of oxygen and pH. The sensor comprises simply-fabricated, directionally-emitting, narrower-band, multicolor microcavity OLED excitation and small molecule- and polymer-based organic photodetectors (OPDs) with a more selective spectral response. Additionally, S and PL intensity for oxygen are enhanced by using polystyrene (PS):polyethylene glycol (PEG) blends as the sensing film matrix. By utilizing higher molecular weight PS, the ratio τ₀/τ₁₀₀ (PL decay time τ at 0% O₂/τ at 100% O₂) that is often used to express S increases ×1.9 to 20.7 relative to the lower molecular weight PS, where this ratio is 11.0. This increase reduces to ×1.7 when the PEG is added (τ₀/τ₁₀₀ = 18.2), but the latter results in an increase ×2.7 in the PL intensity. The sensor's response time is <10 s in all cases. The microporous structure of these blended films, with PEG decorating PS pores, serves a dual purpose. It results in light scattering that reduces the EL that is waveguided in the substrate of the OLEDs and consequently enhances light outcoupling from the OLEDs by ~60%, and it increases the PL directed toward the OPD. The multiple functional structures of multicolor microcavity OLED pixels/microporous scattering films/OPDs enable generation of enhanced individually addressable sensor arrays, devoid of interfering issues, for O₂ and pH as well as for other analytes and biochemical parameters.     

Bidentate substrate binding in Brønsted acid catalysis: structural space,hydrogen bonding and dimerization

BINOL derived chiral phosphoric acids (CPAs) are a prominent class of catalysts in the field of asymmetric organocatalysis, capable of transforming a wide selection of substrates with high stereoselectivities. Exploiting the Brønsted acidic and basic dual functionality of CPAs, substrates with both a hydrogen bond acceptor and donor functionality are frequently used as the resulting bidentate binding via two hydrogen bonds is expected to strongly confine the possible structural space and thus yield high stereoselectivities. Despite the huge success of CPAs and the popularity of a bidentate binding motif, experimental insights into their organization and origin of stereoinduction are scarce. Therefore, in this work the structural space and hydrogen bonding of CPAs and N-(ortho-hydroxyaryl) imines (19 CPA/imine combinations) was elucidated by low temperature NMR studies and corroborated by computations. The postulated bidentate binding of catalyst and substrate by two hydrogen bonds was experimentally validated by detection of trans-hydrogen bond scalar couplings. Counterintuitively, the resulting CPA/imine complexes showed a broad potential structural space and a strong preference towards the formation of [CPA/imine]₂ dimers. Molecular dynamics simulations showed that in these dimers, the imines form each one hydrogen bond to two CPA molecules, effectively bridging them. By finetuning steric repulsion and noncovalent interactions, rigid and well-defined CPA/imine monomers could be obtained. NOESY studies corroborated by theoretical calculations revealed the structure of that complex, in which the imine is located in between the 3,3′-substituents of the catalyst and one site of the substrate is shielded by the catalyst, pinpointing the origin or stereoselectivity for downstream transformations.

Brønsted acid/substrate complexes with bidentate binding motif were studied by NMR and molecular dynamics. A variety of different arrangements was found, including bridged dimers and monomers were characterised in detail.