Radical Formation in the Gas‐Phase Ozonolysis of Deprotonated Cysteine

Although the deleterious effects of ozone on the human respiratory system are well‐known, many of the precise chemical mechanisms that both cause damage and afford protection in the pulmonary epithelial lining fluid are poorly understood. As a key first step to elucidating the intrinsic reactivity of ozone with proteins, its reactions with deprotonated cysteine [Cys?H]^? are examined in the gas phase. Reaction proceeds at near the collision limit to give a rich set of products including 1) sequential oxygen atom abstraction reactions to yield cysteine sulfenate, sulfinate and sulfonate anions, and significantly 2) sulfenate radical anions formed by ejection of a hydroperoxy radical. The free‐radical pathway occurs only when both thiol and carboxylate moieties are available, implicating electron‐transfer as a key step in this reaction. This novel and facile reaction is also observed in small cys‐containing peptides indicating a possible role for this chemistry in protein ozonolysis.     

Synthesis,Structure, and Properties of SrC(NH)3, a Nitrogen‐Based Carbonate Analogue with the Trinacria Motif

Strontium guanidinate, SrC(NH)₃, the first compound with a doubly deprotonated guanidine unit, was synthesized from strontium and guanidine in liquid ammonia and characterized by X‐ray and neutron diffraction, IR spectroscopy, and density‐functional theory including harmonic phonon calculations. The compound crystallizes in the hexagonal space group P6₃/m, constitutes the nitrogen analogue of strontium carbonate, SrCO₃, and its structure follows a layered motif between Sr²⁺ ions and complex anions of the type C(NH)₃^2?; the anions adopt the peculiar trinacria shape. A comparison of theoretical phonons with experimental IR bands as well as quantum‐chemical bonding analyses yield a first insight into bonding and packing of the formerly unknown anion in the crystal.     

On the DFT Ground State of Crystalline Bromine and Iodine

We report on an erroneous ground state within common density functional theory (DFT) methods for the solid elements bromine and iodine. Phonon computations at the GGA level for both molecular crystals yield imaginary vibrational modes, erroneously indicating dynamic instability—that fact alone could easily pass as a computational artefact, but these imaginary modes lead to energetically more favorable and dynamically stable structures, made up of infinite monoatomic chains. In contrast, meta‐GGA and hybrid functionals yield the correct energetic order for bromine, while for iodine, most global hybrids do not improve the GGA result significantly. The qualitatively correct answer, in both cases, is given by the long‐range corrected hybrid LC‐ωPBE, the Minnesota functionals M06L and M06, and by periodic Hartree–Fock and MP2 theory. This poor performance of economic DFT functionals should be kept in mind, for example, during global structure optimizations of systems with significant contributions from halogen bonds.     

Laser Machined Plastic Laminates: Towards Portable Diagnostic Devices for Use in Low Resource Environments

Despite significant progress in development of bioanalytical devices cost, complexity, access to reagents and lack of infrastructure have prevented use of these technologies in resource‐limited regions. To provide a sustainable tool in the global effort to combat infectious diseases the diagnostic device must be low cost, simple to operate and read, robust, and have sensitivity and specificity comparable to laboratory analysis. In this mini‐review we describe recent work using laser machined plastic laminates to produce diagnostic devices that are capable of a wide variety of bioanalytical measurements and show great promise towards future use in low‐resource environments.     

A surface wipe sampling and LC–MS/MS method for the simultaneous detection of six antineoplastic drugs commonly handled by healthcare workers

An effective wipe sampling and LC–MS/MS method was developed to simultaneously analyze six commonly administered antineoplastic drugs in stainless steel surface. The analyzed drugs were methotrexate, paclitaxel, cyclophosphamide, 5-fluorouracil, vincristine, and oxaliplatin, a frequently prepared antineoplastic drug that has not been included among any of the published simultaneous detection methods. The established method was used to evaluate the recoveries of antineoplastic drugs on brand new and worn stainless steel surfaces by wiping the plates with a Whatman filter paper wetted with 0.5 mL of water/methanol (20:80) with 0.1 % formic acid followed by LC–MS/MS before desorbing the filter with a water/methanol (50:50) solution. A significant decrease in the recovery of all evaluated drugs was found when worn plates were used. Additionally, the inter-personnel variability on drug recoveries during wiping procedures was evaluated. Significantly higher recoveries were achieved by the personnel with more training and experience versus personnel without prior experience. Finally, a laboratory stability test was developed to assess the degradation of the antineoplastic drugs during replicated shipping conditions. With the exception of vincristine sulfate which exhibited a significant (p?<?0.05) degradation after 48 h, all evaluated drugs were stable during the first 24–48 h. However, after 144 h, an increase in the degradation of all evaluated drugs was observed, with oxaliplatin and 5-fluorouracil exhibiting the most degradation.     

Efficient chemoenzymatic synthesis of an N-glycan isomer library

Quantification, characterization and biofunctional studies of N-glycans on proteins remain challenging tasks due to the complexity, diversity and low abundance of these glycans. The availability of structurally defined N-glycan (especially isomer) libraries is essential to help solve these tasks. We report herein an efficient chemoenzymatic strategy, namely Core Synthesis/Enzymatic Extension (CSEE), for rapid production of diverse N-glycans. Starting with 5 chemically prepared building blocks, 8 N-glycan core structures containing one or two terminal N-acetyl-d-glucosamine (GlcNAc) residue(s) were chemically synthesized via consistent use of oligosaccharyl thioethers as glycosylation donors in a convergent fragment coupling strategy. Each of these core structures was then extended to 5 to 15 N-glycan sequences by enzymatic reactions catalyzed by 4 robust glycosyltransferases. Success in synthesizing N-glycans with Neu5Gc and core-fucosylation further expanded the ability of the enzymatic extension. Meanwhile, high performance liquid chromatography with an amide column enabled rapid and efficient purification (>98% purity) of N-glycans in milligram scales. A total of 73 N-glycans (63 isomers) were successfully prepared and characterized by MS² and NMR. In summary, the CSEE strategy provides a practical approach for “mass production” of structurally defined N-glycans, which are important standards and probes for glycoscience.     

Origins of the Intermediate Spectral Form in M100 Mutants of Photoactive Yellow Protein

Numerous single‐site mutants of photoactive yellow protein (PYP) from Halorhodospira halophila and as well as PYP homologs from other species exhibit a shoulder on the short wavelength side of the absorbance maximum in their dark‐adapted states. The structural basis for the occurrence of this shoulder, called the “intermediate spectral form,” has only been investigated in detail for the Y42F mutation. Here we explore the structural basis for occurrence of the intermediate spectral form in a M121E derivative of a circularly permuted H. halophila PYP (M121E‐cPYP). The M121 site in M121E‐cPYP corresponds to the M100 site in wild‐type H. halophila PYP. High‐resolution NMR measurements with a salt‐tolerant cryoprobe enabled identification of those residues directly affected by increasing concentrations of ammonium chloride, a salt that greatly enhances the fraction of the intermediate spectra form. Residues in the surface loop containing the M121E (M100E) mutation were found to be affected by ammonium chloride as well as a discrete set of residues that link this surface loop to the buried hydroxyl group of the chromophore via a hydrogen bond network. Localized changes in the conformational dynamics of a surface loop can thereby produce structural rearrangements near the buried hydroxyl group chromophore while leaving the large majority of residues in the protein unaffected.     

Comparison of structural,thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

The prevalence of Mg²⁺ ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg²⁺ ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion‐centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg²⁺ model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion–water and ion–solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single‐site Mg²⁺ ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12‐6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12‐6‐4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg²⁺ ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next‐generation models that target specific binding sites in biomolecules. © 2015 Wiley Periodicals, Inc.