The Blue Obelisk-interoperability in chemical informatics

The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.     

Doubly Bridged Dinuclear Cadmium(II)azido Schiff Base Complexes: Synthesis, X-Ray Structure and Luminescence Properties of [Cd(L)(N3)]2(Y)2 [L = Schiff Bases, Y = ClO4 −, PF6 −]

Three new Schiff bases, -(bis(pyridin-2-yl)alkylidene)butane-1,4-diamine [(py)(R)C=N-(CH)N=C(R)(py), L: py = pyridine; R = H, -(bis(pyridin-2-yl)formylidene)butane-1,4-diamine (bpfd); R = Me, -(bis(pyridin-2-yl)methylidene)butane-1,4-diamine (bpmd); R = C, -(bis(pyridin-2-yl)bezylidene)butane-1,4-diamine (bpbd)] were prepared and used to synthesize six dinuclear cadmium(II)azido complexes of type [Cd(L)(N)](Y) [L = bpfd, Y = ClO (1a); L = bpfd, Y = PF (1b); L = bpmd, Y = ClO (2a); L = bpmd, Y = PF (2b); L = bpbd, Y = ClO (3a); and L = bpbd, Y = PF (3b)]. Two representative members of the series, 3a and 3b, have been characterized by single crystal X-ray diffraction measurements. Structural study reveals that each cadmium center in both dinuclear compounds is located in a distorted octahedral coordination environment surrounded by six nitrogen atoms—four (N1, N2, N3, N4) from tetradentate ligand, and the fifth and sixth positions occupied by nitrogen atoms (N5, N5^*) of doubly end-on bridging azides. The complexes display intraligand ¹ fluorescence and intraligand ³ phosphorescence in glassy solutions (MeOH at 77 K).     

Dynamics of end-to-end loop formation for an isolated chain in viscoelastic fluid

We theoretically investigate the looping dynamics of a linear chain immersed in a viscoelastic fluid. The dynamics of the chain is governed by a Rouse model with a fractional memory kernel recently proposed by Weber et al. [S.C. Weber, J.A. Theriot, A.J. Spakowitz, Phys. Rev. E 82 (2010) 011913]. Using the Wilemski–Fixman [G. Wilemski, M. Fixman, J. Chem. Phys. 60 (1974) 866] formalism we calculate the looping time for a chain in a viscoelastic fluid where the mean square displacement of the center of mass of the chain scales as t^1/2$t^{1/2}$. We observe that the looping time is faster for the chain in a viscoelastic fluid than for a Rouse chain in a Newtonian fluid up to a chain length and above this chain length the trend is reversed. Also no stable scaling of the looping time with the length of the chain seems to exist for the chain in a viscoelastic fluid.