Workshop Nanoscience C: Controlling interactions in complex materials

The second international workshop of the Soochow University—Western University Centre for Synchrotron Radiation Research took place at Soochow University, Suzhou, China, on May 6–8, 2014. The host organizations for this workshop were Soochow University in China and the University of Western Ontario (also known as Western University) in Canada.     

Ion trap collisional activation of disulfide linkage intact and reduced multiply protonated polypeptides.

The presence of disulfide linkages in multiply charged polypeptide ions tends to inhibit the formation of structurally informative product ions under conventional quadrupole ion trap collisional activation conditions. In particular, fragmentation that requires two cleavages (i.e., cleavage of a disulfide linkage and a peptide linkage) is strongly suppressed. Reduction of the disulfide linkage(s) by use of dithiothreitol yields parent ions upon electrospray without this complication. Far richer structural information is revealed by ion trap collisional activation of the disulfide-reduced species than from the native species. These observations are illustrated with doubly protonated native and reduced somatosin, the [M + 5H](5+) ion of native bovine insulin and the [M + 4H](4+) and [M + 3H](3+) ions of the B-chain of bovine insulin produced by reduction of the disulfide linkages in insulin, and the [M + 11H](11+) ion of native chicken lysozyme and the [M + 11H](11+) and [M + 14H](14+) ions of reduced lysozyme. In each case, the product ions produced by ion trap collisional activation were subjected to ion/ion proton transfer reactions to facilitate interpretation of the product ion spectra. These studies clearly suggest that the identification of polypeptides with one or more disulfide linkages via application of ion trap collisional activation to the multiply charged parent ions formed directly by electrospray could be problematic. Means for cleaving the disulfide linkage, such as reduction by dithiothreitol prior to electrospray, are therefore desirable in these cases.     

High-order cycles in the logistic map or centers of cardioids in the mandelbrot set

Asymptotic expressions for the positions of the centres (along the real axis) of high-order cycle cardioids closest to the limit point –2 in the Mandelbrot set are obtained by a combination of numerical and analytical methods.     

Stress Inhomogeneity in Powder Specimens Tested in the Jenike Shear Cell: Myth or Fact?

In the mechanical characterization of powders using the direct shear testers such as the Jenike shear cell, the existence of a uniform or well‐defined stress field in a powder specimen is assumed. This assumption has not been subjected to any serious scrutiny in the literature. In this study, the normal stress variation in a silica powder was locally determined by locating a pressure‐sensitive TekScan pad at the bottom section of a Jenike shear cell. A computer simulation of the consolidation and pre‐shearing stages of the Jenike test procedure was performed using the Discrete Element Method (DEM). The paper presents both experimental and computational evidence for the existence of a complex stress field in the powder specimen, thus clearly invalidating the long‐standing stress homogeneity assumption in the direct shear testing of powders. The implications of the stress inhomogeneity in terms of the accuracy of the material properties extracted from the Jenike test are also presented.     

Simulating Multivariate Extreme Value Distributions of Logistic Type

Methods are given for simulating from symmetric and asymmetric versions of the multivariate logistic distribution, and from other multivariate extreme value distributions based on the well known logistic model. We consider two general approaches. The first approach uses transformations to derive random variables with a joint distribution function from which it is easy to simulate. The second approach derives from a specification of conditionally independent marginal components, conditioning on positive stable random variables. This specification extends to models of nested or hierarchical type and leads to an efficient way of incorporating marginal censoring. The algorithms presented in Sections 2 and 3 are available on request from the author. They are also included in the R (Ihaka and Gentleman, 1996) package evd (Stephenson, 2002), which is available from http://www.maths.lancs.ac.uk/~stephena/.     

A Visible‐Light‐Mediated Radical Smiles Rearrangement and its Application to the Synthesis of a Difluoro‐Substituted Spirocyclic ORL‐1 Antagonist

A visible‐light‐mediated radical Smiles rearrangement has been developed to address the challenging synthesis of the gem‐difluoro group present in an opioid receptor‐like 1 (ORL‐1) antagonist that is currently in development for the treatment of depression and/or obesity. This method enables the direct and efficient introduction of the difluoroethanol motif into a range of aryl and heteroaryl systems, representing a new disconnection for the synthesis of this versatile moiety. When applied to the target compound, the photochemical step could be conducted on 15 g scale using industrially relevant [Ru(bpy)₃Cl₂] catalyst loadings of 0.01 mol %. This transformation is part of an overall five‐step route to the antagonist that compares favorably to the current synthetic sequence and demonstrates, in this specific case, a clear strategic benefit of photocatalysis.     

A Scalable Biomimetic Synthesis of Resveratrol Dimers and Systematic Evaluation of their Antioxidant Activities

An efficient synthetic route to the resveratrol oligomers quadrangularin A and pallidol is reported. It features a scalable biomimetic oxidative dimerization that proceeds in excellent yield and with complete regioselectivity. A systematic evaluation of the natural products and their synthetic precursors as radical‐trapping antioxidants has revealed that, contrary to popular belief, this mode of action is unlikely to account for their observed biological activity.     

Synthesis of β-pyrrolic-modified porphyrins and their incorporation into DNA

A synthetic methodology for the synthesis of various β-pyrrolic-functionalised porphyrins and their covalent attachment to 2'-deoxyuridine and DNA is described. Palladium(0)-catalysed Sonogashira and copper(I)-catalysed Huisgen 1,3-dipolar cycloaddition reactions were used to insert porphyrins into the structure of 2'-deoxyuridine and DNA. Insertion of a porphyrin into the middle of single-stranded CT oligonucleotides possessing a 5'-terminal run of four cytosines was shown to trigger the formation of pH- and temperature-dependent i-motif structures. Porphyrin insertion also led to the aggregation of single-stranded purine-pyrimidine sequences, which could be dissociated by heating at 90 °C for 5 min. Parallel triplexes and anti-parallel duplexes were formed in the presence of the appropriate complementary strand(s). Depending on the modification, porphyrins were placed in the major and minor grooves of duplexes and were used as bulged intercalating insertions in duplexes and triplexes. In general, the thermal stabilisation of parallel triplexes possessing porphyrin-modified triplex-forming oligonucleotide (TFO) strands was observed, whereas anti-parallel duplexes were destabilised. These results are compared and discussed on the basis of the results of molecular modelling calculations.     

Experimental characterization of the weakly anisotropic CN X 2Σ+ + Ne potential from IR-UV double resonance studies of the CN-Ne complex

IR-UV double resonance spectroscopy has been used to characterize hindered internal rotor states (n(K) = 0(0), 1(1), and 1(0)) of the CN-Ne complex in its ground electronic state with various degrees of CN stretch (ν(CN)) excitation. Rotationally resolved infrared overtone spectra of the CN-Ne complex exhibit perturbations arising from Coriolis coupling between the closely spaced hindered rotor states (1(1) and 1(0)) with two quanta of CN stretch (ν(CN) = 2). A deperturbation analysis is used to obtain accurate rotational constants and associated average CN center-of-mass to Ne separation distances as well as the coupling strength. The energetic ordering and spacings of the hindered internal rotor states provide a direct reflection of the weakly anisotropic intermolecular potential between CN X (2)Σ(+) and Ne, with only an 8 cm(-1) barrier to CN internal rotation, from which radially averaged anisotropy parameters (V(10) and V(20)) are extracted that are consistent for ν(CN) = 0-3. Complementary ab initio calculation of the CN X (2)Σ(+) + Ne potential using MRCI+Q extrapolated to the complete one-electron basis set limit is compared with the experimentally derived anisotropy by optimizing the radial potential at each angle. Experiment and theory are in excellent accord, both indicating a bent minimum energy configuration and nearly free rotor behavior. Analogous experimental and theoretical studies of the CN-Ne complex upon electronic excitation to the CN B (2)Σ(+) state indicate a slightly more anisotropic potential with a linear CN-Ne minimum energy configuration. The results from these IR-UV double resonance studies are compared with prior electronic spectroscopy and theoretical studies of the CN-Ne system.     

An octanuclear coordination cage with a 'cuneane' core--a topological isomer of a cubic cage

The octanuclear coordination cage [Ni(8)(L(14Naph))(12)](BF(4))(16) has the core structure of a 'cuneane'--a toplogical isomer of a cube--with a metal ion at each of the eight vertices and bridging ligand spanning each of the twelve edges; this is the only possible 8-vertex polyhedron other than a cube that will form a cage in which each metal is connected to three others.