Reference frames in harmonic coordinates: geometric and physical aspects

This work is focused on the geometrical and physical characteristics of the class of reference frames associated to harmonic coordinates. Precisely, we express in relative form the harmonicity conditions and consider the so called ??spatially harmonicity?? of a reference frame in spherical symmetry. The initial data problem is then analyzed in polar coordinates and the obtained results are applied to special cases of exact solutions.     

Dibenzo[b,f]oxepin‐10(11H)‐one and dibenzo[b,f]thiepin‐10(11H)‐one as useful synthons in the synthesis of various dibenzo[e,h]azulenes

The present review focuses on dibenzo[b,f]oxepin‐10(11H)‐one ( I , X = O) and dibenzo[b,f]thiepin‐10(11H)‐one ( I , X = S) as common synthons in the efficient synthesis of various dibenzoxepino[4,5‐ and dibenzothiepino[4,5]‐fused five‐membered heterocycles: [2,3] fused thiophene ( II ), [3,4] fused thiophene ( III ), furan ( IV ), pyrrole ( V ), imidazole ( VI ), pyrazole ( VII ), oxazole ( VIII ), and thiazole ( IX ). The potential of I to be converted into reactive intermediates that readily undergo heteroaromatic annulation reactions by cyclocondensation with proper binucleophiles allows formation of a range of enumerated functionalized dibenzo[e,h]azulene [4] structures ( II , III , IV , V , VI , VII , VIII , IX ). Dibenzo[e,h]azulenes as heterotetracyclic scaffold can be exploited in further modifications to obtain compounds with altered physicochemical and biological profile. J. Heterocyclic Chem., (2012).     

Synthesis of hexadehydrotribenzo[a,e,i][12]annulenes by acetylene insertion into an open-chain precursor

A simple synthesis of a hexadehydrotribenzo[a,e,i][12]annulene by insertion of acetylene into an open-chain diiodo precursor under Sonogashira coupling conditions has been developed and used to prepare a rigid three-armed star connector for testing as a building block for a two-dimensional hexagonal hydrogen-bonding array.     

A ferrocenyl‐substituted pseudo­titanocene complex

The title compound, (η⁵‐cyclo­penta­dienyl)[(1,2,3,4,5‐η)‐4‐ferro­cenyl‐1,2,5,6‐tetrakis­(tri­methyl­silyl)­cyclo­hexa‐2,4‐dien‐1‐yl]­titanium(II), [TiFe(C₅H₅)₂(C₂₃H₄₂Si₄)] or [Ti{η⁵‐C₆H₂{Fe­(η⁵‐C₅H₄)(η⁵‐C₅H₅)}{Si(CH₃)₃}₄}(η⁵‐C₅H₅)], possesses two directly linked metallocene units that subtend an angle of 52.9 (1)° (defined by the least‐squares planes of the directly connected π‐ligands) associated with the steric requirements of the bulky tri­methyl­silyl substituents. The cyclo­hexa­dienyl ligand adopts an envelope conformation; the perpendicular distance of its η⁵‐plane to the Ti atom is 1.512 (1) Å.     

Phase transitions in n-alkyl­ammonium di­hydrogenphosphates and -arsenates and ferroelastic n-hexyl- and n-octyl­ammonium di­hydrogen­arsenate

-Hexyl­ammonium di­hydrogenarsenate, (C₆­H₁₆N)[AsO₂(OH)₂], and -octyl­ammonium di­hydrogenarsenate, (C₈H₂₀N)[AsO₂(OH)₂], are both ferroelastic at room temperature. The samples used in this study were not subjected to a phase transition after they had been crystallized. The structures are monoclinic (P2₁/n) and isostructural with the corresponding di­hydrogenphosphates. Each sample contained two domains and each structure was refined as a twin. There are strong hydrogen bonds between di­hydrogenarsenates and moderate hydrogen bonds between di­hydrogenarsenates and -alkyl­ammonium groups. The hydrogen-bond distances correspond well to those observed in the di­hydrogenphosphates. All the atoms except two H atoms exist in pairs linked by the lost symmetry operations derived from the prototypic space group P2/b2₁/n2₁/a. Each of these two different H atoms is involved in an asymmetric hydrogen bond between an oxy­gen pair. These oxy­gens are supposed to change their roles as hydrogen-bond donors and acceptors during the ferroelastic switching. The phase-transition sequences are affected by interactions between the neighbouring organic chains in the structure.     

Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori

Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, respectively. Within the conserved amino acid motif, HpCrdA contains two additional methionines and two glutamic acid residues (MMXEMPGMXXMXEM) in comparison to CopC and PcoC but lacks the canonical Cu(II) binding site (two His) since the sequence has no His residues. The methionine-rich site is in a flexible loop and can adopt different geometries for the two copper oxidation states. It could bind copper in both oxidation states (I and II), but with different binding affinities, micromolar was found for Cu(II), and less than nanomolar is proposed for Cu(I). Considering that CrdA is a periplasmic protein involved in chaperoning copper export and delivery in the H. pylori cell and that the affinity of the interaction corresponds to a middle or strong metal–protein interaction depending on the copper oxidation state, we conclude that the interaction also occurs in vivo and is physiologically relevant for H. pylori.     

Field Effect and Local Gating in Nitrogen-Terminated Nanopores (NtNP) and Nanogaps (NtNG) in Graphene

Functionalization of electrodes is a wide-used strategy in various applications ranging from single-molecule sensing and protein sequencing, to ion trapping, to desalination. We demonstrate, employing non-equilibrium Green′s function formalism combined with density functional theory, that single-species (N, H, S, Cl, F) termination of graphene nanogap electrodes results in a strong in-gap electrostatic field, induced by species-dependent dipoles formed at the electrode ends. Consequently, the field increases or decreases electronic transport through a molecule (benzene) placed in the nanogap by shifting molecular levels by almost 2 eV in respect to the electrode Fermi level via a field effect akin to the one used for field-effect transistors. We also observed the local gating in graphene nanopores terminated with different single-species atoms. Nitrogen-terminated nanogaps (NtNGs) and nanopores (NtNPs) show the strongest effect. The in-gap potential can be transformed from a plateau-like to a saddle-like shape by tailoring NtNG and NtNP size and termination type. In particular, the saddle-like potential is applicable in single-ion trapping and desalination devices.     

A Memetic Algorithm for Minimum-Cost Vertex-Biconnectivity Augmentation of Graphs

This paper considers the problem of augmenting a given graph by a cheapest possible set of additional edges in order to make the graph vertex-biconnected. A real-world instance of this problem is the enhancement of an already established computer network to become robust against single node failures. The presented memetic algorithm includes effective preprocessing of problem data and a fast local improvement strategy which is applied before a solution is included into the population. In this way, the memetic algorithm's population consists always of only feasible, locally optimal solution candidates. Empirical results on two sets of test instances indicate the superiority of the new approach over two previous heuristics and an earlier genetic algorithm.