A novel unexpected luminescent quarternary coordination polymer {Sm3(C8H4O4)4(C12N2H8)2(NO3)}n with three high asymmetrical central Sm fragments by hydrothermal assembly

A novel chain-like luminescent samarium coordination polymer {Sm₃(C₈H₄O₄)₄(C₁₂N₂H₈)₂(NO₃)}_n (C₈H₄O₄ = phthalate, C₁₂N₂H₈ = 1,10-phenanthroline) has been assembled by hydrothermal process. The title complex crystallizes in the monoclinic system, space group P2(1)/c, with lattice parameters a = 22.56(3) Å, b = 11.155(15) Å, c = 20.32(3) Å, β = 96.70(2)°, V = 5078(12) ų, F(000) = 2964, GOF = 0.857, R₁ = 0.0358, wR₂ = 0.0597, Z = 4. Samarium ions exhibit different coordination modes from each other and lead to the unexpected high asymmetrical structure. To our knowledge, it is the first example of lanthanide coordination polymers comprising the three asymmetrical central Sm³⁺ fragments. The photophysical properties have been studied with excitation and emission spectra.     

Modeling of metal interaction geometries for protein-ligand docking

The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements.     

N,O versus O,O coordination in β-imino diketonato complexes: Role of the metal center and of the imino substituent

β-Imino carbonyl enolato metal(II) complexes of general formula [M((RCO)(R′CO)CC(R″)NH)₂] (M = Mn, Fe, Co, Ni, Cu, Zn, Pd, R = R′ = Me, R″ = CCl₃; M = Cu, Pd, R = R′ = Me, R″ = PhCO; R = Me, R′ = Ph, R″ = PhCO; R = R′ = Ph, R″ = PhCO) are easily synthesized by the reaction of metal(II) acetates with the proper β-enaminodiones in 1/2 molar ratio in ethanol at room temperature. In all the cases the trifunctional NOO β-imino carbonyl enolate ligand acts as bidentate to give ML₂ complexes, whose structure depends on the metal center and on the nature of the substituent R″ at the imino carbon. With R″ = CCl₃ an O,O coordination is observed for all the metal centers but one, in fact palladium(II) exhibits an N,O coordination through the imino nitrogen and one keto oxygen. By contrast with R″ = PhCO the ligand is always coordinated through the imino nitrogen and one keto oxygen atom.     

Tuning the formation of copper(I) coordination architectures with quinoxaline-based N,S-donor ligands by varying terminal groups of ligands and reaction temperature

Five new complexes [Cu₂(L¹)I₂]_∞ (1), [Cu(L²)I]₂ (2), {[Cu₂(L²)I₂](CH₃CN)₃}_∞ (3), [Cu₂(L³)I₂]_∞ (4) and {[Cu(L³)I](CH₃CN)}₂ (5) have been obtained by reacting three structurally related ligands, 2,3-bis(n-propylthiomethyl)quinoxaline (L¹), 2,3-bis(tert-butylthiomethyl)quinoxaline (L²) and 2,3-bis[(o-aminophenyl)thiomethyl]quinoxaline (L³) with CuI, respectively, at different temperatures. Single crystal X-ray analyses show that 1, 3, 4 possess 1D chain structures, while 2 and 5 are discrete dinuclear molecules. It is interesting that the reactions of CuI with L¹ at room temperature and 0 °C, respectively, only afforded same structure of 1 (1a and 1b), while using L² (or L³) instead, two different frameworks 2 and 3 (or 4 and 5) have been obtained. The structural changes mainly resulted from the different conformations that L² or L³ adopted at different temperatures. Our research indicates that terminal groups of ligands take an essential role in the framework formation, and the reaction temperature also has important effect on the construction of such Cu(I) coordination architectures. Furthermore, the influence of hydrogen bonds on the conformation of ligands and the supramolecular structures of these complexes have also been explored. The luminescence properties of complexes 1, 2, and 4 have been studied in solid state at room temperature.     

Construction of crystal structures of metal(II)-benzoates (M = Mn, Ni, Co, Cu, Zn, and Cd) and 1,2-bis(4-pyridyl)ethane: Effects of metal coordination modes and their catalytic activities

Five polymeric metal(II)-benzoate complexes of formula [Mn(O₂CPh)₂(CH₃OH)₂(bpa)]_n (1-Mn), [Co(O₂CPh)₂(H₂O)(bpa)_1.5]_n (2-Co), [Ni(O₂CPh)₂(H₂O)(bpa)_1.5]_n (3-Ni), [Cu(O₂CPh)₂(CH₃OH)₂(bpa)]_n (4-Cu), and [Cd(O₂CPh)₂(bpa)_1.5]_n (6-Cd) have been synthesized and characterized (bpa = 1,2-bis(4-pyridyl)ethane). They showed two kinds of structures: parallelogram-like two-dimensional sheets for Co, Ni, and Cd, and one-dimensional chains for Mn, Cu, and Zn. Since similar structures provide similar coordination geometries, the structures depend on the coordination geometries of metal ions. The compounds 1-Mn, 2-Co, 4-Cu, 5-Zn, and 6-Cd have catalyzed efficiently the transesterification of a variety of esters, while 3-Ni has displayed a very slow conversion. The reactivity of catalyst 6-Cd containing Cd ion, well known as an inert metal ion for the ligand substitution, was found to be comparable to that of 5-Zn. The reactivities of the compounds used in this study are in the order of 5-Zn > 6-Cd > 1-Mn > 4-Cu > 2-Co ? 3-Ni, indicating that the non-redox metal-containing compounds (5-Zn and 6-Cd) show better activity than the redox-active metal-containing compounds (1-Mn, 4-Cu, 2-Co, and 3-Ni).     

Oxidovanadium(IV) complexes containing ligands derived from dithiocarbazates - Models for the interaction of VO with thiofunctional ligands

The tetragonal-pyramidal VO²⁺ complexes [VO{(RSC-S)N-NX}₂] (1-6) were synthesised by the reactions of VO(OCHMe₂)₃ with the dithiocarbazate ligands RSC(S)-NH-NX, where X = cyclo-pentyl, cyclo-hexyl or 4-Me₂N-C₆H₄-CH, and R = CH₃ or CH₂C₆H₅. The compounds were characterised by elemental analysis, IR- and mass spectrometries, and in cases of compounds 1, 3, 4 and 5, by X-ray diffraction. The chiral compound 4 (X = cyclo-hexyl, R = CH₂C₆H₅) crystallises in the C configuration. In compound 5, the VO moiety is disordered (83.3:16.7%) with respect to the plane spanned by the four equatorial ligand functions.     

Microwave synthesis, spectroscopy, thermal analysis and crystal structure of an one-dimensional polymeric {[Cu(4,4′-bipy)(H2O)3(SO4)] · 2H2O}n complex

A metal organic-inorganic coordination framework formulated as {[Cu(4,4′-bipy)(H₂O)₃(SO₄)] · 2H₂O}_n (1) (where 4,4′-bipy = 4,4′-bipyridine) has been successfully prepared by microwave synthesis. The title complex has been characterized by single crystal X-ray crystallography, FT-IR spectroscopy and thermal analysis. Complex (1) is an one-dimensional (1D) polymer in which 4,4′-bipy acts as a bridging ligand supporting the formation of infinite [Cu(4,4′-bipy)(H₂O)₃(SO₄)] chains. The packing diagram shows that a 3D network is formed via hydrogen bonds. The infrared spectra and thermographic data are consistent with the chemical formula.     

Towards predicting Ca2+‐binding sites with different coordination numbers in proteins with atomic resolution

Ca²⁺‐binding sites in proteins exhibit a wide range of polygonal geometries that directly relate to an equally‐diverse set of biological functions. Although the highly‐conserved EF‐Hand motif has been studied extensively, non‐EF‐Hand sites exhibit much more structural diversity which has inhibited efforts to determine the precise location of Ca²⁺‐binding sites, especially for sites with few coordinating ligands. Previously, we established an algorithm capable of predicting Ca²⁺‐binding sites using graph theory to identify oxygen clusters comprised of four atoms lying on a sphere of specified radius, the center of which was the predicted calcium position. Here we describe a new algorithm, MUG (MUltiple Geometries), which predicts Ca²⁺‐binding sites in proteins with atomic resolution. After first identifying all the possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca²⁺ position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures. This algorithm, which predicts both Ca²⁺ positions and ligand groups, has been shown to successfully predict over 90% of the documented Ca²⁺‐binding sites in three datasets of highly‐diversified protein structures with 0.22 to 0.49 Å accuracy. All multiple‐binding sites (i.e. sites with a single ligand atom associated with multiple calcium ions) were predicted, as were half of the low‐coordination sites (i.e. sites with less than four protein ligand atoms) and 14/16 cofactor‐coordinating sites. Additionally, this algorithm has the flexibility to incorporate surface water molecules and protein cofactors to further improve the prediction for low‐coordination and cofactor‐coordinating Ca²⁺‐binding sites. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Management on the basis of the best scientific data or integration of ecological research within management? Lessons learned from the Northern spotted owl saga on the connection between research and management in conservation biology

The case of the Northern spotted owl (Strix occidentalis caurina) has now become a classic case study in conservation biology, characterized by a harsh social battle but also by the quantity and quality of the research performed. Based on this example, I study the way the research-management interface was organized. The main lessons I have learned were: 1. laws that involve science in management are crucial but should be more precise; 2. scientific ad-hoc groups are useful reviewers of management plans and interpreters of the best scientific data available, even if more transparent scientific argumentation is needed on some points; 3. in such applied cases, even science that has not been strongly integrated with management can produce results that are useful for management; 4. stronger links between science and management appear necessary, but difficult to implement. This last point makes me wonder whether environmental laws should not more frequently target the incorporation of science into the management process itself rather than “only” basing management on the best scientific data available. On a more ecological level, perhaps the habitat issue has been underrated during the last few years compared to other emerging threats such as the invasion of the spotted owl range by barred owls.     

Nano-channels in the spider fang for the transport of Zn ions to cross-link His-rich proteins pre-deposited in the cuticle matrix

We identify the presence of multiple vascular channels within the spider fang. These channels seem to serve the transport of zinc to the tip of the fang to cross-link the protein matrix by binding to histidine residues. According to amino acid and elemental analysis of fangs extracted shortly after ecdysis, His-rich proteins are deposited before Zn is incorporated into the cuticle. Microscopic and spectroscopic investigations in the electron microscope and synchrotron radiation experiments suggest that Zn ions are transported through these channels in a liable (yet unidentified) form, and then form stable complexes upon His binding. The resulting cross-linking through the Zn–His complexes is conferring hardness to the fang. Our observations of nano-channels serving the Zn-transport within the His-rich protein matrix of the fibre reinforced spider fang may also support recent bio-inspired attempts to design artificial polymeric vascular materials for self-healing and in-situ curing.