Forazoline A: Marine‐Derived Polyketide with Antifungal In Vivo Efficacy

Forazoline A, a novel antifungal polyketide with in vivo efficacy against Candida albicans, was discovered using LCMS‐based metabolomics to investigate marine‐invertebrate‐associated bacteria. Forazoline A had a highly unusual and unprecedented skeleton. Acquisition of ¹³C–¹³C gCOSY and ¹³C–¹⁵N HMQC NMR data provided the direct carbon–carbon and carbon–nitrogen connectivity, respectively. This approach represents the first example of determining direct ¹³C–¹⁵N connectivity for a natural product. Using yeast chemical genomics, we propose that forazoline A operated through a new mechanism of action with a phenotypic outcome of disrupting membrane integrity.     

2‐D solitary waves in thermal media with nonsymmetric boundary conditions

Optical solitary waves and their stability in focusing thermal optical media, such as lead glasses, are studied numerically and theoretically in (2 + 1) dimensions. The optical medium is a square cell and mixed boundary conditions of Newton cooling and fixed temperature on different sides of the cell are used. Nonlinear thermal optical media have a refractive index which depends on temperature, so that heating from the optical beam and heat flow across the boundaries can change the refractive index of the medium. Solitary wave solutions are found numerically using the Newton conjugate‐gradient method, while their stability is studied using a linearized stability analysis and also via numerical simulations. It is found that the position of the solitary wave is dependent on the boundary conditions, with the center of the beam moving toward the warmer boundaries, as the parameters are varied. The stability of the solitary waves depends on the symmetry of the boundary conditions and the amplitude of the solitary waves.     

On the SQH Scheme to Solve Nonsmooth PDE Optimal Control Problems

A sequential quadratic Hamiltonian (SQH) scheme for solving different classes of nonsmooth and nonconvex partial differential equation (PDE) optimal control problems is investigated considering seven different benchmark problems with increasing difficulty. These problems include linear and nonlinear PDEs with linear and bilinear control mechanisms, nonconvex, and discontinuous costs of the controls, L¹ tracking terms, and the case of state constraints. The SQH method is based on the characterization of optimality of PDE optimal control problems by the Pontryagin’s maximum principle (PMP). For each problem, a theoretical discussion of the PMP optimality condition is given and results of numerical experiments are presented that demonstrate the large range of applicability of the SQH scheme.     

Oxidation of Sulfides with N‐Bromosuccinimide in the Presence of Hydrated Silica Gel

An efficient and highly selective procedure for oxidation of sulfides to sulfoxides with N‐bromosuccinimide (NBS) in the presence of hydrated silica gel has been developed. Hydrated silica gel supplies the water necessary for decomposition of the intermediate bromosulfonium salt to the product, allowing the reaction to employ a nonaqueous media. Also, this procedure has increased the scope of the reaction by oxidizing a wider variety of sulfides, which was not possible until now.     

PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure

We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force‐fields are available within the framework: PROFASI and OPLS‐AA/L, the latter including the generalized Born surface area solvent model. A flexible command‐line and configuration‐file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net . The software is implemented in C++ and has been tested on Linux and OSX platforms. © 2013 Wiley Periodicals, Inc.     

LC‐MS analysis of estradiol in human serum and endometrial tissue: Comparison of electrospray ionization,atmospheric pressure chemical ionization and atmospheric pressure photoionization

Accurate measurement of estradiol (E2) is important in clinical diagnostics and research. High sensitivity methods are critical for specimens with E2 concentrations at low picomolar levels, such as serum of men, postmenopausal women and children. Achieving the required assay performance with LC–MS is challenging due to the non‐polar structure and low proton affinity of E2. Previous studies suggest that ionization has a major role for the performance of E2 measurement, but comparisons of different ionization techniques for the analysis of clinical samples are not available. In this study, female serum and endometrium tissue samples were used to compare electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) in both polarities. APPI was found to have the most potential for E2 analysis, with a quantification limit of 1 fmol on‐column. APCI and ESI could be employed in negative polarity, although being slightly less sensitive than APPI. In the presence of biological background, ESI was found to be highly susceptible to ion suppression, while APCI and APPI were largely unaffected by the sample matrix. Irrespective of the ionization technique, background interferences were observed when using the multiple reaction monitoring transitions commonly employed for E2 (m/z 271 > 159; m/z 255 > 145). These unidentified interferences were most severe in serum samples, varied in intensity between ionization techniques and required efficient chromatographic separation in order to achieve specificity for E2. Copyright © 2013 John Wiley & Sons, Ltd.     

Protein folding at emulsion oil/water interfaces

It has long been known that proteins change their conformation upon adsorption to emulsion oil/water interfaces. However, it is only recently that details of the specifics of these structural changes have emerged. The development of synchrotron radiation circular dichroism (SRCD), combined with advances in FTIR spectroscopy, has allowed the secondary and tertiary structure of proteins adsorbed at emulsion oil/water interfaces to be studied. SRCD in particular has provided quantitative information and has enabled new insights into the mechanisms and forces driving protein structure re-arrangement to be achieved.The extent of conformational re-arrangement of proteins at emulsion interfaces is influenced by several factors including; the inherit flexibility of the protein, the distribution of hydrophobic/hydrophilic domains within the protein sequence and the hydrophobicity of the oil phase. In general, proteins lose much of their tertiary structure upon adsorption to the oil/water interface and have considerable amounts of non-native secondary structure. Two key conformations have been identified in the structure of proteins at interfaces, intermolecular β-sheet and α-helix. The preferred conformation appears to be the α-helix which is the most compact amphipathic conformation at the oil/water interface. The polarity of the oil phase can have a considerable influence on the degree of protein conformational re-arrangement because it acts as a solvent for hydrophobic amino acids. The new conformation of proteins at interfaces also means that proteins undergo less heat induced re-arrangement at interfaces than in solution. Different conformations of proteins at interfaces impact on emulsification capability, emulsion stability and protein/emulsion digestion. Hence advances in the understanding of protein conformation at interfaces can help to identify suitable proteins and conditions for the preparation of emulsion based food products.     

Universal Algorithm for Simulating and Evaluating Cyclic Voltammetry at Macroporous Electrodes by Considering Random Arrays of Microelectrodes

An algorithm for the simulation and evaluation of cyclic voltammetry (CV) at macroporous electrodes such as felts, foams, and layered structures is presented. By considering 1D, 2D, and 3D arrays of electrode sheets, cylindrical microelectrodes, hollow-cylindrical microelectrodes, and hollow-spherical microelectrodes the internal diffusion domains of the macroporous structures are approximated. A universal algorithm providing the time-dependent surface concentrations of the electrochemically active species, required for simulating cyclic voltammetry responses of the individual planar, cylindrical, and spherical microelectrodes, is presented as well. An essential ingredient of the algorithm, which is based on Laplace integral transformation techniques, is the use of a modified Talbot contour for the inverse Laplace transformation. It is demonstrated that first-order homogeneous chemical kinetics preceding and/or following the electrochemical reaction and electrochemically active species with non-equal diffusion coefficients can be included in all diffusion models as well. The proposed theory is supported by experimental data acquired for a reference reaction, the oxidation of [Fe(CN)₆]⁴⁻ at platinum electrodes as well as for a technically relevant reaction, the oxidation of VO₂⁺ at carbon felt electrodes. Based on our calculation strategy, we provide a powerful open source tool for simulating and evaluating CV data implemented into a Python graphical user interface (GUI).     

Amide Synthesis by Nickel/Photoredox‐Catalyzed Direct Carbamoylation of (Hetero)Aryl Bromides

Herein, we report a one‐electron strategy for catalytic amide synthesis that enables the direct carbamoylation of (hetero)aryl bromides. This radical cross‐coupling approach, which is based on the combination of nickel and photoredox catalysis, proceeds at ambient temperature and uses readily available dihydropyridines as precursors of carbamoyl radicals. The method's mild reaction conditions make it tolerant of sensitive‐functional‐group‐containing substrates and allow the installation of an amide scaffold within biologically relevant heterocycles. In addition, we installed amide functionalities bearing electron‐poor and sterically hindered amine moieties, which would be difficult to prepare with classical dehydrative condensation methods.     

Laser Access to Quercetin Radicals and Their Repair by Co-antioxidants

We have demonstrated the feasibility and ease of producing quercetin radicals by photoionization with a pulsed 355 nm laser. A conversion efficiency into radicals of 0.4 is routinely achieved throughout the pH range investigated (pH 2–9), and the radical generation is completed within a few ns. No precursor other than the parent compound is needed, and the ionization by-products do not interfere with the further fate of the radicals. With this generation method, we have characterized the quercetin radicals and studied the kinetics of their repairs by co-antioxidants such as ascorbate and 4-aminophenol. Bell-shaped pH dependences of the observed rate constants reflect opposite trends in the availability of the reacting protonation forms of radical and co-antioxidant and even at their maxima mask the much higher true rate constants. Kinetic isotope effects identify the repairs as proton-coupled electron transfers. An examination of which co-antioxidants are capable of repairing the quercetin radicals and which are not confines the bond dissociation energies of quercetin and its monoanion experimentally to 75–77 kcal mol⁻¹ and 72–75 kcal mol⁻¹, a much narrower interval in the case of the former than previously estimated by theoretical calculations.