Jumping solitary waves in an autonomous reaction-diffusion system with subcritical wave instability

We describe a new type of solitary waves, which propagate in such a manner that the pulse periodically disappears from its original position and reemerges at a fixed distance. We find such jumping waves as solutions to a reaction-diffusion system with a subcritical short-wavelength instability. We demonstrate closely related solitary wave solutions in the quintic complex Ginzburg-Landau equation. We study the characteristics of and interactions between these solitary waves and the dynamics of related wave trains and standing waves.     

Diffusion on a self-assembled monolayer: molecular modeling of a bound + mobile lubricant

The diffusion of tricresyl phosphate molecules on an octadecyltrichlorosilane self-assembled monolayer (SAM) was characterized using molecular dynamics simulations. The simulations predict that when placed on the top of a close-packed SAM, the molecules remain mobile on the surface with an isotropic diffusion activation energy of approximately 9 kJ/mol. In contrast, an anisotropic barrier that results from chain tilt within the SAM is predicted for diffusion into a defect created by reducing the alkane chain length within a cylinderical region of the surface. Once in the defect, the molecules become trapped by embedding part of the molecule into the side of the SAM.     

Shear band formation and ductility in bulk metallic glass

The variations in the chemical compositions of the metallic glasses reported in the literature, as well as the overall lack of experimental data concerning the inhomogeneous deformation behaviour of metallic glass, make the evaluation of the effects of shear band/fracture behaviour on the mechanical properties of metallic glasses difficult. Isolating the effect of local shear band formation on bulk inhomogeneous flow would appear to be a first step in approaching this problem. The mechanical behaviour of Vitreloy metallic glass at room temperature and at various strain rates in tension and compression was investigated. The formation of multiple shear bands was observed at high strain rates. An increase in strain rate leads to enhanced ductility in tension and compression. Some aspects of the deformation processes in tension and compression are discussed.     

Isomerism due to the rotation of an alkyl side-chain attached to a heterocyclic ring: Crystal and molecular structure of two forms of 6-nitro-2,4-bis(1′,1′,2′-trichloropropyl)-1,3-benzdioxin

Compound I crystallizes in the space groupP2₁/c withZ=4,a=5.889(5),b=30.755(10),c=10.815(3) Å,=92.95(6)°. Compound II crystallizes in the space groupP2₁/n withZ=4,a=10.235(2),b=10.144(1),c=18.346(2) Å,=92.00(1)°. The structures were solved by direct methods and refined by full-matrix least squares, from room-temperature data obtained with an Enraf-Nonius CAD4 diffractometer, to conventionalR factors of 0.041 for I and 0.048 for II.In both isomers the dioxin ring has an approximate envelope conformation with a pseudoequatorial –CC1₂·CHCl·CH₃ group in the 2-position and a pseudoaxial –CCl₂·CHCl·CH₃ group in the 4-position. The molecular structures of I and II differ in that the group at the 2-position is rotated by about 120° in one isomer relative to its position in the other. Both compounds have packing patterns with a wave motif. In II there are interactions of the –NO₂ group with other atoms both between molecules in the same wave and also between molecules in adjacent waves. In I the interactions of the –NO₂ group with other atoms are in the same wave only with adjacent waves being packed together by van der Waals forces alone.     

The N,N-diacetylaminobenzene group in the structure of 6-methyl-8-N,N-diacetylamino-2,4-bis(trichloromethyl)-1,3-benzdioxin

Crystals of 6-methyl-8-N,N-diacetylamino-2,4-bis(trichloromethyl)-1,3-benzdioxin are triclinic, P¯1,Z=2,a=9.586(3),b=9.914(2),c=12.308(5) Å,=67.19(3),=71.95(3), =74.14(2)°. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 difFractometer, and refined by least squares to a finalR value of 0.039 using 3038 reflections. The heterocyclic ring has an envelope conformation. Of thecis-CCl₃ groups one CC1₃ group is pseudoequatorial while the –(C_Ar·C)CCl₃ group is pseudoaxial. (C_Ar)O-C 1.405(4); (C_Ar·O)C-O 1.387(4) Å; C_Ar-C(C_ax)-0 112.3(3); C(C_ax)-O-C(C_eq) 116.1(2)°; (C_Ar)O-C-O-C(C_Ar)58.2(3)°. The configuration of the diacetylamino group (DAA) issyn-anti. The -systems of the DAA and of the aromatic ring are approximately orthogonal, the deviations from orthogonality probably being caused by an intermolecular bifurcated hydrogen bond, each such interaction involving two molecules only, between thesyn O(=C) of the DAA and both hydrogen atoms bonded to the heterocyclic ring in a molecule of the enantiomer. The geometry of the DAA-benzene fragment is compared with those found in the other three published X-ray structures containing this group.     

Crystal and molecular structure of 6-nitro-1,3-benzdioxin: Comparison with the molecular structures of the 2,4-bis(dichloromethyl) and 2,4-bis(trichloromethyl) derivatives

6-Nitro-1,3-benzdioxin is orthorhombic,Pbca,a=7.278(4),b=19.292(3),c=10.978(1) Å,Z=8. The structure was solved by direct methods from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer and refined by least squares to a finalR value of 0.041 using 725 reflections. Some parameters associated with the heterocycle are torsion angle (C_Ar)O-C-O-C(C_Ar) 69.1(4)°; bond lengths C_Ar-O 1.362(3), (C_Ar)O-C 1.434(5), (C_Ar.O)C-O 1.377(5), O-C(C_Ar) 1.431(5), C-C_Ar 1.501(5) Å; bond angles C_Ar-O-C 113.5(3), O-C-O 111.5(3), C-O-C(C_Ar) 110.3(3), O-C-C_Ar 109.9(3)°;H_axH_ax 2.52(5) Å.     

Structure of the α-(allcis) form of 2,4,6-tris(trichloromethyl)-1-oxa-3,5-dithian

The higher-melting (mp 236°C)-isomer of dithioparachloral, i.e.,-2,4,6-tris(trichloromethyl)-1-oxa-3,5-dithian, is orthorhombic,Pnma,a=9.983(2),b=15.318(2),c=10.416(2) Å,V=1592.81 ų,Z=4. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least-squares to a finalR value of 0.040 using 1017 reflections. The molecule is in the chair conformation with all threecis-CCl₃ groups located pseudoequatorially. Endocyclic parameters are: torsion angles (deg) C-O-C-S 75.1(3), O-C-S-C –63.2(3), C-S-C-S 62.4(3); angles (deg) C-O-C 111.9(2), O-C-S 112.6(3), C-S-C 94.8(2), S-C-S 113.2(1); bond lengths (Å) O-C 1.426(5), C-S 1.824(4), S-C 1.818(3) (quoted in cyclic order).     

Structure and conformation of 6,8-dinitro-2,4-bis(trichloromethyl)-1,3-benzdioxin: X-ray crystallographic determination

6,8-dinitro-2,4-bis(trichloromethyl)-1,3-benzdioxin is monoclinic,P2₁/c,Z=4,a=12.348(2),b=11.575(3),c=12.183(4) Å,=107.48(2)°. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least-squares to a finalR value of 0.032 using 2192 reflections. The heterocyclic ring is an envelope structure, the dihedral angle between the plane of the aromatic ring and that containing five of the atoms of the heterocycle being 4.98(6)°. One -CCl₃ group is pseudoequatorial while the (Ar-C)CCl₃ group is pseudoaxial. C-C_eq 1.526(3) Å; C-C_ax 1.537(3) Å; C-C(C_ax)-O 112.4(2)°; C(C_ax)-O-C(C_eq) 115.2(2)°.     

Discontinuously propagating waves in the bathoferroin-catalyzed Belousov-Zhabotinsky reaction incorporated into a microemulsion

Three new types of discontinuously propagating waves are reported in the bathoferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction dispersed in water-in-oil Aerosol OT microemulsion. Jumping waves (JWs) are typically observed at or above room temperature and develop from the familiar trigger waves. Bubble waves (BWs) typically emerge from trigger or JWs at similar temperatures, while rotating waves (RWs) evolve from JW at higher temperatures (>40 degrees C). All these waves propagate discontinuously in a saltatory fashion. Other characteristic features include a discontinuous front for BW consisting of small concentric waves (bubbles) and lateral rotation of annular RWs. All three types of waves, as well as segmented but continuously propagating waves, can coexist. A simple model that is able to describe both jumping and segmented waves is described.     

Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant

Inhibition of Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway, provides a route to blocking cancer-induced changes in cell surface oligosaccharide structures. To probe the substrate requirements of GMII, oligosaccharides were synthesized that contained an alpha(1,3)- or alpha(1,6)-linked 1-thiomannoside. Surprisingly, these oligosaccharides were not observed in X-ray crystal structures of native Drosophila GMII (dGMII). However, a mutant enzyme in which the catalytic nucleophilic aspartate was changed to alanine (D204A) allowed visualization of soaked oligosaccharides and led to the identification of the binding site for the alpha(1,3)-linked mannoside of the natural substrate. These studies also indicate that the conformational change of the bound mannoside to a high-energy B 2,5 conformation is facilitated by steric hindrance from, and the formation of strong hydrogen bonds to, Asp204. The observation that 1-thio-linked mannosides are not well tolerated by the catalytic site of dGMII led to the synthesis of a pentasaccharide containing the alpha(1,6)-linked Man of the natural substrate and the beta(1,2)-linked GlcNAc moiety proposed to be accommodated by the extended binding site of the enzyme. A cocrystal structure of this compound with the D204A enzyme revealed the molecular interactions with the beta(1,2)-linked GlcNAc. The structure is consistent with the approximately 80-fold preference of dGMII for the cleavage of substrates containing a nonreducing beta(1,2)-linked GlcNAc. By contrast, the lysosomal mannosidase lacks an equivalent GlcNAc binding site and kinetic analysis indicates oligomannoside substrates without non-reducing-terminal GlcNAc modifications are preferred, suggesting that selective inhibitors for GMII could exploit the additional binding specificity of the GlcNAc binding site.