Natural and Doubly Natural Dualities

Representable dualities between categories of modules satisfying natural closure properties are investigated and shown to be determined by homological properties shared by various classical and recently investigated types of dualities.     

Elusive Double Perovskite Iodides: Structural,Optical, and Magnetic Properties

Halide double perovskites [A₂M^IM^IIIX₆] are an important class of materials that have garnered substantial interest as non-toxic alternatives to conventional lead iodide perovskites for optoelectronic applications. While numerous studies have examined chloride and bromide double perovskites, reports of iodide double perovskites are rare, and their definitive structural characterization has not been reported. Predictive models have aided us here in the synthesis and characterization of five iodide double perovskites of general formula Cs₂NaLnI₆ (Ln=Ce, Nd, Gd, Tb, Dy). The complete crystal structures, structural phase transitions, optical, photoluminescent, and magnetic properties of these compounds are reported.     

Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment

A pathogenetic feature of Alzhemier disease is the aggregation of monomeric beta-amyloid proteins (Abeta) to form oligomers. Usually these oligomers of long peptides aggregate on time scales of microseconds or longer, making computational studies using atomistic molecular dynamics models prohibitively expensive and making it essential to develop computational models that are cheaper and at the same time faithful to physical features of the process. We benchmark the ability of our implicit solvent model to describe equilibrium and dynamic properties of monomeric Abeta(10-35) using all-atom Langevin dynamics (LD) simulations, since Alphabeta(10-35) is the only fragment whose monomeric properties have been measured. The accuracy of the implicit solvent model is tested by comparing its predictions with experiment and with those from a new explicit water MD simulation, (performed using CHARMM and the TIP3P water model) which is approximately 200 times slower than the implicit water simulations. The dependence on force field is investigated by running multiple trajectories for Alphabeta(10-35) using the CHARMM, OPLS-aal, and GS-AMBER94 force fields, whereas the convergence to equilibrium is tested for each force field by beginning separate trajectories from the native NMR structure, a completely stretched structure, and from unfolded initial structures. The NMR order parameter, S2, is computed for each trajectory and is compared with experimental data to assess the best choice for treating aggregates of Alphabeta. The computed order parameters vary significantly with force field. Explicit and implicit solvent simulations using the CHARMM force fields display excellent agreement with each other and once again support the accuracy of the implicit solvent model. Alphabeta(10-35) exhibits great flexibility, consistent with experiment data for the monomer in solution, while maintaining a general strand-loop-strand motif with a solvent-exposed hydrophobic patch that is believed to be important for aggregation. Finally, equilibration of the peptide structure requires an implicit solvent LD simulation as long as 30 ns.     

Concurrent sensing of benzene and oxygen by a crystalline salt of tris(5,6-dimethyl-1,10-phenanthroline)ruthenium(II)

The complex [Ru(5,6-Me2Phen)3]tfpb2 has been examined as a solid-state benzene and oxygen sensor. The crystalline solid undergoes a reversible vapochromic shift of the emission lambda max to higher energy in the presence of benzene. Additionally, in the presence of oxygen the solid exhibits linear Stern-Volmer quenching behavior. When simultaneously exposed to benzene vapor and oxygen the crystals uptake benzene which inhibits the diffusion of oxygen in the lattice; very little quenching is observed. However, when benzene is removed from the carrier gas, partial loss of benzene occurs and oxygen diffusion is restored resulting in quenching of the emission. The practicality of this crystalline solid as a benzene sensor was investigated by examination of a lower concentration of benzene vapor (0.76%).     

Selective desulfurization of cysteine in the presence of Cys(Acm) in polypeptides obtained by native chemical ligation

Increased versatility for the synthesis of proteins and peptides by native chemical ligation requires the ability to ligate at positions other than Cys. Here, we report that Raney nickel can be used under standard conditions for the selective desulfurization of Cys in the presence of Cys(Acm). This simple and practical tactic enables the more common Xaa-Ala junctions to be used as ligation sites for the chemical synthesis of Cys-containing peptides and proteins. [reaction: see text].     

Secretory phospholipase A2 hydrolysis of phospholipid analogues is dependent on water accessibility to the active site

A new and unnatural type of phospholipids with the head group attached to the 2-position of the glycerol backbone has been synthesized and shown to be a good substrate for secretory phospholipase A2 (sPLA2). To investigate the unexpected sPLA2 activity, we have compared three different phospholipids by using fluorescence techniques and HPLC, namely: (R)-1,2-dipalmitoyl-glycero-3-phosphocholine (hereafter referred to as 1R), (R)-1-O-hexadecyl-2-palmitoyl-glycero-3-phoshocholine (2R), and (S)-1-O-hexadecyl-3-palmitoyl-glycero-2-phosphocholine (3S). Furthermore, to understand the underlying mechanisms for the observed differences, we have performed molecular dynamics simulations to clarify on a structural level the substrate specificity of sPLA2 toward phospholipid analogues with their head groups in the 2-position of the glycerol backbone. We have studied the lipids above 1R, 2R, and 3S as well as their enantiomers 1S, 2S, and 3R. In the simulations of sPLA2-1S and sPLA2-3R, structural distortion in the binding cleft induced by the phospholipids showed that these are not substrates for sPLA2. In the case of the phospholipids 1R, 2R, and 3S, our simulations revealed that the difference observed experimentally in sPLA2 activity might be caused by reduced access of water molecules to the active site. We have monitored the number of water molecules that enter the active site region for the different sPLA2-phospholipid complexes and found that the probability of a water molecule reaching the correct position such that hydrolysis can occur is reduced for the unnatural lipids. The relative water count follows 1R > 2R > 3S. This is in good agreement with experimental data that indicate the same trend for sPLA2 activity: 1R > 2R > 3S.     

Ion trap mass spectrometry on a comet nucleus: the Ptolemy instrument and the Rosetta space mission

In May 2014, the Rosetta spacecraft is scheduled to rendezvous with the comet Churyumov-Gerasimenko ('67P'). One of the instruments on board the 'Lander' which will descend on to the surface of the comet is a miniaturised GC/MS system that incorporates an ion trap mass spectrometer, specially developed for isotope ratio analysis. This article describes the development and optimisation of the ion trap for this unique application, and presents a summary of the range of pre-programmed experiments that will contribute to the characterisation of the solid and volatile cometary materials.     

Tilting objects in abelian categories and quasitilted rings

D. Happel, I. Reiten and S. Smalø initiated an investigation of quasitilted artin -algebras that are the endomorphism rings of tilting objects in hereditary abelian categories whose Hom and Ext groups are all finitely generated over a commutative artinian ring . Here, employing a notion of -objects, tilting objects in arbitrary abelian categories are defined and are shown to yield a version of the classical tilting theorem between the category and the category of modules over their endomorphism rings. This leads to a module theoretic notion of quasitilted rings and their characterization as endomorphism rings of tilting objects in hereditary cocomplete abelian categories.