Ligands In Coordination Sphere Research Articles

BioMe: biologically relevant metals

In this article, we introduce BioMe (biologically relevant metals), a web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal coordination sphere, distribution of coordination numbers, percentage of metal ions coordinated by the combination of selected ligands, distribution of monodentate and bidentate metal-carboxyl, bindings for ASP and GLU, percentage of particular binuclear metal centers, distribution of coordination geometry, descriptive statistics for a metal ion–donor distance and percentage of the selected metal ions coordinated by each of the selected ligands. Statistics is presented in numerical and graphical forms. The underlying database contains information about all contacts within the range of 3 Å from a metal ion found in the asymmetric crystal unit. The stored information for each metal ion includes Protein Data Bank code, structure determination method, types of metal-binding chains [protein, ribonucleic acid (RNA), deoxyribonucleic acid (DNA), water and other] and names of the bounded ligands (amino acid residue, RNA nucleotide, DNA nucleotide, water and other) and the coordination number, the coordination geometry and, if applicable, another metal(s). BioMe is on a regular weekly update schedule. It is accessible at http://metals.zesoi.fer.hr.

ChemInform Abstract: Functionalized Cyclodextrins as First and Second Coordination Sphere Ligands for Aqueous Organometallic Catalysis

AbstractReview: 46 refs.

Functionalized Cyclodextrins as First and Second Coordination Sphere Ligands for Aqueous Organometallic Catalysis

AbstractSupramolecular catalysis now forms a viable and challenging interdisciplinary topic that drives chemists to design new ligands and their metal complexes. Functionalized cyclodextrins (CDs) have attracted particular attention in this respect because of their molecular recognition and metal coordination ability. They can act both as first‐coordination‐sphere ligands through coordination of a phosphanyl or amino group onto the metal and as second‐coordination‐sphere ligands because of the inclusion of a guest molecule (substrate or ligand) inside their cavity. These combined features make functionalized CDs very special objects. The present review seeks to address the scope of these supramolecular entities as ligands for the elaboration of novel organometallic complexes for aqueous catalysis.

Dinitrogen Complexes of Sulfur-Ligated Iron

We report a unique class of dinitrogen complexes of iron featuring sulfur donors in the ancillary ligand. The ligands utilized are related to the recently studied tris(phosphino)silyl ligands (2-R(2)PC(6)H(4))(3)Si (R = Ph, iPr) but have one or two phosphine arms replaced with thioether donors. Depending on the number of phosphine arms replaced, both mononuclear and dinuclear iron complexes with dinitrogen are accessible. These complexes contribute to a desirable class of model complexes that possess both dinitrogen and sulfur ligands in the immediate iron coordination sphere.

ChemInform Abstract: Crystal Engineering of Hybrid Inorganic—Organic Systems Based Upon Complexes with Dissymmetric Compartmental Ligands

AbstractReview: 74 refs.

Porphyrin Framework Solids. Hybrid Supramolecular Assembly Modes of Tetrapyridylporphyrin and Aqua Nitrates of Lanthanoid Ions

New types of porphyrin-based framework solids were constructed by reacting meso-tetra(4-pyridyl)porphyrin (TPyP) with various aqua nitrate salts of lanthanoid metal ions [Ln(NO3)3(H2O)x]. They represent hybrid organic−inorganic crystalline compounds in which the tetradentate porphyrin units, having both coordination as well as hydrogen bonding functionalities, are interlinked through the inorganic connectors into self-assembled three-dimensional architectures. The lanthanoid complexes bear, in addition to the coordination capacity of the metal ions, multiple molecular recognition sites on their nitrate and water ligands, serving as effective linkers of the supramolecular arrays that form. Several different modes of the intermolecular association were revealed by single-crystal X-ray diffraction. They differ by the nature of the interaction synthons between the component species, the degree of protonation of the porphyrin entities in the given experimental conditions, and the topology of the resulting assemblies. An exceptional structure, in which a doubly protonated porphyrin unit and the lanthanoid species formed separate hydrogen bonded arrays (where one-dimensional chains of the latter are enclathrated within two-dimensional layers of the former) by reacting the meso-tetra(3-pyridyl)porphyrin (TPy(3)P) with a dehydrated La-salt, is described as well. All the compounds are characterized by open architectures, giving rise to lattice-inclusion of solvent species. This study demonstrates that the TPyP building block may effectively engage in supramolecular constructs with the lanthanoid metal ions, either through direct coordination to the metal center and/or by hydrogen bonding to its coordination sphere ligands.

Synthesis and characterization of iron(II) quinaldate complexes.

Treatment of iron(II) chloride or iron(II) bromide with 2 equiv of sodium quinaldate (qn = quinaldate or C(10)H(6)NO(2)(-)) yields the coordinatively unsaturated mononuclear iron(II) quinaldate complexes Na[Fe(II)(qn)(2)Cl].DMF and Na[Fe(II)(qn)(2)Br].DMF (DMF = N,N-dimethylformamide), respectively. When a similar synthesis is carried out using iron(II) triflate, a solvent-derived linear triiron(II) complex, [Fe(II)(3)(qn)(6)(DMF)(2)], with two five-coordinate iron(II) centers and a single six-coordinate iron(II) center is obtained. Each of these species has been characterized using X-ray diffraction. The vibrational features of these complexes are consistent with the observed solid-state structures. Each of these compounds exhibits an iron(II)-to-quinaldate (pi*) charge-transfer band between 520 and 550 nm. These metal-to-ligand charge-transfer bands are sensitive to substitution of the quinaldates as well as alteration of the first coordination sphere ligands. However, the (1)H NMR spectra of these paramagnetic high-spin iron(II) complexes are not consistent with retention of the solid-state structures in a DMF solution. The chemical shifts, longitudinal relaxation times (T(1)), relative integrations, and substitution of the quinaldate ligands provide a means to fully assign the (1)H NMR spectra of the paramagnetic materials. These spectra are consistent with coordination equilibria between five- and six-coordinate species in a DMF solution. Electrochemical studies are reported to place these oxygen-sensitive compounds in a broader context with other iron(II) compounds. Iron complexes of bidentate quinoline-2-carboxylate-derived ligands are germane to metabolic pathways, environmental remediation, and catalytic applications.

Modulation of the heme electronic structure and cystathionine β-synthase activity by second coordination sphere ligands: The role of heme ligand switching in redox regulation

In humans, cystathionine beta-synthase (CBS) is a hemeprotein, which catalyzes a pyridoxal phosphate (PLP)-dependent condensation reaction. Changes in the heme environment are communicated to the active site, which is approximately 20A away. In this study, we have examined the role of H67 and R266, which are in the second coordination sphere of the heme ligands, H65 and C52, respectively, in modulating the heme's electronic properties and in transmitting information between the heme and active sites. While the H67A mutation is comparable to wild-type CBS, interesting differences are revealed by mutations at the R266 site. The pathogenic mutant, R266K, is moderately PLP-responsive while the R266M mutation shows dramatic differences in the ferrous state. The electrostatic interaction between C52 and R266 is critical for stabilizing the ferrous heme and its disruption leads to the facile formation of a 424nm (C-424) absorbing ferrous species, which is inactive, compared to the active 449nm ferrous species for wild-type CBS. Resonance Raman studies on the R266M mutant reveal that the kinetics of C52 rebinding after Fe-CO photolysis are comparable to that of wild-type CBS. EXAFS studies on C-424 CBS are consistent with the presence of two axial N/O low Z scatters with only one being a rigid unit of a histidine residue while the other could be a solvent molecule, an oxygen atom from the peptide backbone or a side chain nitrogen. The redox potential for the heme in full-length CBS is -350+/-4mV and is substantially lower than the value of -287+/-2mV determined for truncated CBS. A redox-regulated ligand change has the potential to serve as an allosteric on/off switch in human CBS and the second sphere ligand, R266, plays an important role in this transition.

Crystal engineering of hybrid inorganic–organic systems based upon complexes with dissymmetric compartmental ligands

This paper illustrates the versatility of mono- and heterobinuclear complexes with dissymmetric compartmental ligands in designing molecular and supramolecular heterometallic systems. Mononuclear complexes with side-off bicompartmental ligands derived from o-vanillin act efficiently, through their empty compartment, as hydrogen-bond receptors and as second coordination sphere ligands. These Schiff- bases are also suitable for synthesizing 3d-3d′ and 3d-4f heterobinuclear complexes. Both 3d-3d′ and 3d-4f complexes can be employed as nodes in obtaining coordination polymers with various dimensionalities and network topologies, as well as interesting magnetic and optical properties.

Modeling the Resting State of Oxalate Oxidase and Oxalate Decarboxylase Enzymes

In view of the biological and commercial interest in models for Oxalate Decarboxylases (OxDC) and Oxalate Oxidases (OxOx), we have synthesized and characterized three new Mn (II) complexes ( 1- 3) employing N3O-donor amino-carboxylate ligands (TCMA, 1,4,7-triazacyclononane- N-acetic acid; K (i) Pr 2TCMA, potassium 1,4-diisopropyl-1,4,7-triazacyclononane- N-acetate; and KBPZG, potassium N,N-bis(3,5-dimethylpyrazolyl methyl)glycinate). These complexes were characterized by several techniques including X-ray crystallographic analysis, X-band electron paramagnetic resonance (EPR), electrospray ionization mass spectrometry (ESI-MS), and cyclic voltammetry. The crystal structures of 1 and 3 revealed that both form infinite polymeric chains of Mn (II) complexes linked by the pendant carboxylate arms of the TCMA (-) and the BPZG (-) ligands in a syn-antipattern. Complex 2 crystallizes as a mononuclear Mn (II) cation, six-coordinate in a distorted octahedral geometry. Although complexes 1 and 3 crystallize as polymeric chains, all compounds present the same N3O-donor set atoms around the metal center as observed in the crystallographically characterized OxDC and OxOx. Moreover, complex 2 also contains two water molecules coordinated to the Mn center as observed in the active site of OxDC and OxOx. ESI-MS spectrometry, combined with EPR, were useful techniques to establish that complexes 1- 3 are present as mononuclear Mn (II) species in solution. Finally, complexes 1- 3 are able to model the resting state active sites, with special attention focused on complex 2 which provides the first exact first coordination sphere ligand structural model for the resting states of both OxDC and OxOx.

Metal Ion Activation of S-Adenosylmethionine Decarboxylase Reflects Cation Charge Density

S-Adenosylmethionine decarboxylase from Escherichia coli is a pyruvoyl cofactor-containing enzyme that requires a metal cation for activity. We have found that the enzyme is activated by cations of varying charge and ionic radius, such as Li+, A13+, Tb3+, and Eu3+, as well as the divalent cations Mg2+, Mn2+, and Ca2+. All of the activating cations provide kcat values within 30-fold of one another, showing that the charge of the cation does not greatly influence the rate-limiting step for decarboxylase turnover. Cation concentrations for half-maximal activation decrease by >100-fold with each increment of increase in the cation charge, ranging from approximately 300 mM with Li+ to approximately 2 microM with trivalent lanthanide ions. The cation affinity is related to the charge/radius ratio of the ion for those ions with exchangeable first coordination sphere ligands. The exchange-inert cation Co(NH3)63+ activates in the presence of excess EDTA (and NH4+ does not activate), indicating that direct metal coordination to the protein or substrate is not required for activation. The binding of metal ions (monitored by changes in the protein tryptophan fluorescence) and enzyme activation are both cooperative with Hill coefficients as large as 4, the active site stoichiometry of this (alphabeta)4 enzyme. The Hill coefficients for Mg2+ binding and activation increase from 1 to approximately 4 as the KCl concentration increases, which is also observed with NaCl or KNO3; neither Na+ nor K+ activates the enzyme. The single tryptophan in the protein is located 16 residues from the carboxyl terminus of the pyruvoyl-containing alpha chain, in a 70-residue segment that is not present in metal ion independent AdoMet decarboxylases from other organisms. The results are consistent with allosteric metal ion activation of the enzyme, congruent with the role of the putrescine activator of the mammalian AdoMet decarboxylase.

A Reaction of 3,6‐Di(tert‐butyl)‐4‐chloro‐1,2‐benzoquinone with Potassium Ethyl Xanthate. New Sulfur‐Containing o‐Quinones.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

A reaction of 3,6-di(tert-butyl)-4-chloro-1,2-benzoquinone with potassium ethyl xanthate. New sulfur-containing o-quinones

In a reaction of 3,6-di(tert-butyl)-4-chloro-1,2-benzoquinone with potassium ethyl xanthate, the halogen atom was replaced by the ethyl xanthate group. Acid hydrolysis of the product gave 4,7-di(tert-butyl)-5,6-dihydroxy-1,3-benzodithiol-2-one containing a pyrocatechol fragment, which was oxidized into the corresponding quinone. When irradiated in solution with visible light, this quinone quantitatively eliminated a CO molecule with contraction of the ring to a five-membered one. The quinones obtained were studied as ligands in coordination spheres of metals by ESR spectroscopy.

The structure of O-phospho-DL-threonine in potassium, sodium and ammonium environments

Summary Interactions of O-phospho-DL-threonine (DL-PThr) in the different ionization states with potassium, sodium and ammonium cations have been studied on five crystals (denoted as I-V). In semipotassium salt of DL-PThr (I), the phosphate group adopts the nearly trans conformation, whereas in mono- and disodium salts (II and III) and in mono- and diammonium salts of DL-PThr (IV and V) the phosphate group is situated anticlinal to the rest of the molecule, showing its conformational flexibility depending on the crystal environment, where significant differences are observed in interactions of K+, Na+ and NH4 + cations with PThr. The crystal packing in each of I-V is dominated by interactions between PThr moieties and the cations and hydrogen bond networks involving the phosphate, carboxyl, and amino groups of PThr moieties and water molecules. In crystal I, water molecules are not involved in potassium cation complexation. In crystals II and III, sodium cations show a preference for water molecules over PThr anions as ligands in coordination spheres. Especially in crystals I-III, water molecules are involved in very extensive networks of hydrogen-bond interactions.

Transformation of copper(I) thiophosphite complexes into copper(I) clusters bridged by diisopropyldisulfides and diethyldisulfides

AbstractThe cleavage of coordination bonds in copper(I) halide thiophosphite complexes with the following transformation of the PS containing ligands in metal coordination sphere results in new cluster compounds bridged by disulfides. Thus, polymeric and tetrameric complexes of Cu(I) halides with thiophosphite ligands (triethyltrithiophosphites and triisopropyltrithiophosphites) were found to be transformed at the storage or upon recrystallization in polar solvents (CHCl3, CH3CN) into polymeric copper(I) clusters with Cu···Cu short contacts: [Cu2X2·L]n (where L = (EtS)2, (i‐PrS)2; X = Cl, Br). A completely different new polymeric complex was obtained by direct interaction of copper bromide with diethyl disulfide. © 2006 Wiley Periodicals, Inc. Heteroatom Chem 17:542–546, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20274

Nickel(II) bis(diphenylphosphino)amide: Redox-coupling of dppa ligands in coordination sphere of Ni 2+ and some other properties

The reactions of Ni II[(PPh 2) 2N] 2 ( 2) with various reagents are described. Addition of two moles of carbon monoxide to 2, at 20 °C and atmospheric pressure leads to the redox coupling of dppa ligands and formation of zero-valent nickel complex (CO) 2Ni(Ph 2P N PPh 2 PPh 2 NPPh 2) ( 4). The nickel atom in 4 has a tetrahedral coordination and is incorporated into the NiP 4N 2 ring adopting a distorted chair conformation with phosphorus–phosphorus bond length 2.2777(5) Å. Contrary to CO, sulphur dioxide reacts with 2 to form simple adduct (SO 2)Ni II[(PPh 2) 2N] 2. The reaction of 2 with allyl bromide runs as alkylation of dppa ligand to form All-N(PPh 2) 2NiBr 2. The reduction of 2 with metallic sodium in THF gives Ni(0) complex, HN(PPh 2) 2Ni(Ph 3P) 2 ( 7). The electrochemical reduction of 2 in CH 2Cl 2 takes place in two steps: reversible one-electron and quasi-reversible three-electron step.

Preparation and X-ray Structures of Metal-Free, Dicobalt and Dimanganese Forms of Soluble Methane Monooxygenase Hydroxylase fromMethylococcus capsulatus(Bath)

A three-component soluble methane monooxygenase (sMMO) enzyme system catalyzes the hydroxylation of methane to methanol at a carboxylate-bridged diiron center housed in the alpha-subunit of the hydroxylase (MMOH). Catalysis is facilitated by the presence of a regulatory protein (MMOB) and inhibited by MMOD, a protein of unknown function encoded in the sMMO operon. Both MMOB and MMOD are presumed to bind to the same region of the MMOH alpha-subunit. A colorimetric method for monitoring removal of Fe(II) from MMOH was developed using 1,10-phenanthroline and yields apo MMOH with <0.1 Fe/homodimer. With the use of this method, it was possible to investigate the X-ray structure of the apoenzyme and to perform metal reconstitution studies. Using MMOH from Methylococccus capsulatus (Bath), the effects of MMOB and MMOD on metal binding were studied and structural perturbations relevant to the function of this enzyme were identified. X-ray crystal structures of the apo, Mn(II)-soaked, and Co(II)-grown MMOH, determined to 2.3 A or greater resolution, reveal that the presence of metal ions is essential for the proper folding of helices E, F, and H of the alpha-subunit. The active sites of Mn(II)-soaked and Co(II)-grown MMOH are similar to that of reduced, native MMOH with notable differences in the metal-metal distances and ligand coordination sphere that may reflect how this dinuclear metal center might change in the presence of MMOB. MMOB and MMOD decrease the rate of removal of Fe(II) from the enzyme by 22- and 16-fold, respectively. On the basis of previous studies, it is hypothesized that MMOB, and perhaps MMOD, function to block solvent access to the MMOH active site. Finally, ITC studies and the observed disorder in helices E, F, and H in the apo and Mn(II)-soaked structures suggest that these regions of MMOH are critical for MMOB and MMOD binding.

Conical cavitands as second coordination spheres and protecting environments. Towards metal-centred, intra-cavity reactions

Metallocavitands are coordination compounds based on rigidified molecular cavities which possess at least one entry. Those in which the metal centre is rigidly held above the entrance are particularly promising for the study of host-guest interactions between metal-bonded substrates and the internal part of a cavity. Such systems also open the way to highly selective intra-cavity reactions. The present review focusses on conical cavities derived from calixarenes and cyclodextrins and examines their possible use as second coordination sphere ligands.

Ligand exchange chiral separations by cyclodextrin derivatives in capillary electrophoresis.

A beta-cyclodextrin substituted by an imidazole-bound histamine (CDmh) was successfully used to separate underivatised tryptophan racemate in capillary electrophoresis in the presence of copper(II) ion by the ligand exchange mechanism. To the best of our knowledge, this is the first example of a cyclodextrin derivative behaving as the first coordination sphere ligand in the complex added to the background electrolyte (BGE).

Observation of ligand effects during alkene hydrogenation catalysed by supported metal clusters.

Homogeneous organometallic catalysts and many enzymes activate reactants through coordination to metal atoms; that is, the reactants are turned into ligands and their reactivity controlled through other ligands in the metal's coordination sphere. In the case of supported metal clusters, catalytic performance is influenced by the support and by adsorbed reactants, intermediates or products. The adsorbates are usually treated as ligands, whereas the influence of the supports is usually ascribed to electronic interactions, even though metal clusters supported on oxides and zeolites form chemical bonds to support oxygen atoms. Here we report direct observations of the structure of supported metal clusters consisting of four iridium atoms, and the identification of hydrocarbon ligands bound to them during propene hydrogenation. We find that propene and molecular hydrogen form propylidyne and hydride ligands, respectively, whereas simultaneous exposure of the reactants to the supported iridium cluster yields ligands that are reactive intermediates during the catalytic propane-formation reaction. These intermediates weaken the bonding within the tetrahedral iridium cluster and the interactions between the cluster and the support, while replacement of the MgO support with gamma-Al2O3 boosts the catalytic activity tenfold, by affecting the bonding between the reactant-derived ligands and the cluster and therefore also the abundance of individual ligands. This interplay between the support and the reactant-derived ligands, whereby each influences the interaction of the metal cluster with the other, shows that the catalytic properties of supported metal catalysts can be tuned by careful choice of their supports.