A supramolecular copper(II) compound with double bridging water ligands: synthesis, crystal structure, spectroscopy, thermal analysis, and magnetism

A complex of composition {[{Cu(NDC)(OH₂)(tn)(μ-OH₂)}₂]·2H₂O}_∞ (1) and a mononuclear complex salt [Cu(OH₂)₂(tn)₂](NDC)·3H₂O (2), where NDC = 2,6-naphthalenedicarboxylate dianion and tn = 1,3-diaminopropane, were simultaneously crystallized from an aqueous solution of the copper(II) naphthalenedicarboxylate—1,3-diaminopropane—methanol system. The crystal and molecular structures of both complexes were determined by single-crystal X-ray diffraction. Compound (1) consists of a supramolecular coordination complex in which the monomeric unit is assembled from a homodinuclear Cu(II) bridged by two water ligands. The Cu(II) centers exhibit distorted octahedral coordination; the equatorial plane is provided by one chelating tn ligand, one NDC^2? ligand, one μ-H₂O while the axial positions are occupied by H₂O and μ-H₂O. Strong intra- and/or intermolecular hydrogen bonds, also involving the crystallization water molecules, together with π–π stacking interactions, are involved in building up the supramolecule. The solid structure of compound (2) includes three water molecules of crystallization, the counter ion NDC^2?, and a Cu(II) cationic complex in which the metal is six-coordinated in an axially elongated octahedron defined by two chelating tn ligands in the equatorial plane and two water ligands in the axial positions. Thermal analyses of (1) show two significant weight losses corresponding to water molecules (lattice and coordinated), followed by the decomposition of the network.     

Varieties in structures of Co(II), Ni(II) and Cu(II) coordination compounds based on dimethyl pyridin-2-ylcarbamoylphosphoramidate

A series of new 3d metal complexes based on dimethyl pyridin-2-ylcarbamoylphosphoramidate (HL) was synthesized. The compounds with general formula M(HL)₂Cl₂·nH₂O and M(L)₂·nH₂O (M=Co²⁺, Cu²⁺, Ni²⁺) were characterized by means of single-crystal X-ray analysis and IR spectroscopy. The organic ligands in all complexes are coordinated via oxygen atom of the carbonyl group and nitrogen atom of the heterocycle. The coordination environment of the central atoms is a distorted octahedron. The axial positions in the Co(II) and Ni(II) complexes with deprotonated ligands are occupied by water molecules. The Co(II) and Cu(II) complexes with phosphoryl ligands in a neutral form have different ligands in the axial positions: in the Co(II) complex, the positions are occupied by two water molecules, whereas in the Cu(II) complex, the positions are occupied by two chlorine anions. The structure of HL was experimentally and theoretically obtained by utilizing single-crystal X-ray analysis and DFT calculations. The computationally optimized geometric parameters for HL show a good agreement with the experimental results.     

Derivation of structural models for two intercalated compounds of α-zirconium phosphate

Reasonable structural models are proposed for two intercalated compounds of-Zr(HPO₄)₂·H₂O (-ZrP), one with 2,2-bipyridyl (A) and another one with 1,10-phenanthroline (B). The models are derived by considerations of the unit-cell geometry changes undergone by-ZrP upon insertion of the organic molecules and on a set of general criteria of structural analysis, already developed by us and called the comparison method. If it is assumed that the water molecules in A and B keep the positions they have in-ZrP, as fixed by their links to the phosphate-OH groups, the inserted molecules, while obeying the general conditions of optimum packing, establish interactions of the hydrogen-bonding type with the water molecules. This modeling gives for A and B a possible structural explanation to the maximum number of inserted molecules of the two species, as fixed by their stoichiometry.     

A single amino acid determines preference between phospholipids and reveals length restriction for activation ofthe S1P<Subscript>4</Subscript> receptor

Background

Sphingosine-1-phosphate and lysophosphatidic acid (LPA) are ligands for two related families of G protein-coupled receptors, the S1P and LPA receptors, respectively. The lysophospholipid ligands of these receptors are structurally similar, however recognition of these lipids by these receptors is highly selective. A single residue present within the third transmembrane domain (TM) of S1P receptors is thought to determine ligand selectivity; replacement of the naturally occurring glutamic acid with glutamine (present at this position in the LPA receptors) has previously been shown to be sufficient to change the specificity of S1P₁ from S1P to 18:1 LPA.

Results

We tested whether mutation of this "ligand selectivity" residue to glutamine could confer LPA-responsiveness to the related S1P receptor, S1P₄. This mutation severely affected the response of S1P₄ to S1P in a [³⁵S]GTPγS binding assay, and imparted sensitivity to LPA species in the order 14:0 LPA > 16:0 LPA > 18:1 LPA. These results indicate a length restriction for activation of this receptor and demonstrate the utility of using LPA-responsive S1P receptor mutants to probe binding pocket length using readily available LPA species. Computational modelling of the interactions between these ligands and both wild type and mutant S1P₄ receptors showed excellent agreement with experimental data, therefore confirming the fundamental role of this residue in ligand recognition by S1P receptors.

Conclusions

Glutamic acid in the third transmembrane domain of the S1P receptors is a general selectivity switch regulating response to S1P over the closely related phospholipids, LPA. Mutation of this residue to glutamine confers LPA responsiveness with preference for short-chain species. The preference for short-chain LPA species indicates a length restriction different from the closely related S1P₁ receptor.

     

(18-Crown-6)(hydrogennitrato)potassium: Synthesis and crystal structure

A new complex, [K(18-crown-6)(NO₃)(HNO₃)] (I), is synthesized, and its crystal structure is studied using X-ray diffraction analysis: space group P \(\bar 1\), a = 8.253 Å, b = 9.277 Å, c = 13.903 Å, α = 95.89°, β = 104.30°, γ = 91.89°, Z = 2. The triclinic structure of compound I was solved by a direct method and refined by the full-matrix least-squares method in the anisotropic approximation to R = 0.059 for all 3573 independent reflections (CAD4 automated diffractometer, γMoK _α radiation). The structure of compound I contains two independent halves of two centrosymmetric complex molecules with different coordination modes of the K⁺ cations. Two NO ₃ ^? and HNO₃ ligands are randomly disordered relative to the symmetry center and are presented by two average independent H_0.5N ₃ ^1/2? , ligands, which are also orientationally disordered.     

Bis(Saccharinato)Nickel(II) Complexes with 2-Aminomethyl and -Ethylpyridines. Syntheses,Crystal Structures,Spectral and Thermal Analyses of trans-[Ni(sac-N)2(ampy-N,N′)2] and trans-[Ni(sac-O)2(aepy-N,N′)2]

The trans-bis(saccharinato)nickel(II) complexes with 2-aminomethylpyridine (ampy) and 2-aminoethylpyridine (aepy) have been prepared and characterized by elemental analyses, i.r., u.v.–vis., magnetic measurements and single crystal X-ray diffraction. Both structures consist of discrete molecules of the title complexes, in which the nickel(II) ion lies on an inversion centre and is octahedrally coordinated by two bidentate (N,N) ampy or aepy ligands and two anionic sac ligands, occupying trans positions. The most interesting feature of the complexes is the coordination of sac. In [Ni(sac)₂(ampy)₂], sac is N-bonded, whereas it is O-coordinated in [Ni(sac)₂(aepy)₂]. The i.r. spectra and thermal behaviour of both complexes are discussed in detail.     

New crystal structures of β-[Ni(NCS)2(4-methylpyridine)4] clathrates with furan,tetrahydrofuran, methylene chloride,benzene + ethanol and methylcellosolve as guest molecules

Single crystal X-ray structures of clathrates of -[Ni(NCS)₂(4-methylpyridine)₄] with furan, tetrahydrofuran, benzene + ethanol, methylene chloride, and methylcellosolve as guests molecules are reported. The location of the guest molecule in the partially decomposed clathrate with methylene chloride was defined by X-ray diffraction and compared with the fully occupied one. The host lattices of all clathrates studied are tetragonal (I4₁/a) and do not differ significantly from typical -phase clathrates of [M(NCS)₂(4-methylpyridine)₄] (M = divalent metal cation). Arrangements of guest molecules represent different types of packing: one type of guest molecule occupies both possible types of positions, two different guest molecules occupy different positions, with only one type of positions occupied by one type of guest molecule. Possible stoichiometries of clathrates with -type lattices are discussed.Presented at the Sixth International Seminar on Inclusion Compounds, Istanbul, Turkey, 27–31 August 1995.     

Molecular structure and pseudopolymorphism of squamtin A from Annona squamosa

The cyclopeptide, squamtin A (1, formula: C₃₉H₆₀O₁₁N₈S), was found to crystallized in two pseudopolymorphisms, i.e. 1·(H₂O)_3.5 and 1·(H₂O)_3.9. The composition of the amino acids and their linkage sequences are the same. The main differences between the two kinds of crystals lie in the positions and occupancies of the water molecules, the positions of the sulfur atoms and the conformation of the side chains. The absolute configuration of 1 is established by X-ray analysis in combination with the Marfey's analysis of its hydrolysates.     

Structure of Organic Crystals with Molecules Lying on Twofold Crystallographic Axes. Structural Class P21212, Z = 2(2)

Molecular arrangement in crystals of a rare structural class P2₁2₁2, Z = 2(2), with molecules occupying a system of special positions on 2 axes is considered. The Cambridge Structural Database (CSD) contains 58 organic crystal substances belonging to this class; 54 of these have clear-cut chains P_c2, Z = 1(2) (shashlyks) and form two subclasses. In crystals of the first subclass (23 representatives), there are layers possessing one of two remarkable features: molecules in a layer have an extraordinarily high molecular coordination number (m.c.n. is 8 in a layer), or molecules in a layer are linked by halogen...halogen specific short contacts (m.c.n. in a layer equals 4). In crystals of the second subclass (31 representative), layers are absent, and the structure is formed directly from chains.     

New anionic and dianionic polydentate systems featuring ancillary phosphinosulfides as ligands in coordination chemistry and catalysis

This article provides an overview of the chemistry of monoanionic S–P–S and dianionic S–C–S ligands featuring two phosphinosulfide ligands as pendant groups. These new pincer-type structures are easily assembled from phosphinines and the bis-sulfide derivative of the bis(diphenylphosphino)methane, respectively. Monoanionic S–P–S pincer ligands easily coordinate group 10 and group 9 metal fragments through displacement reactions. Palladium(II) complexes of S–P–S ligands efficiently catalyze cross-coupling processes, allowing the formation of boronic esters and biphenyl derivatives. Rh(I) complexes of S–P–S ligands react in a regioselective way with small molecules (O₂, SO₂, CS₂, MeI) to afford the corresponding Rh(I) or Rh(III) derivatives. S–C–S dianonic ligands, which are readily obtained through a bis-metallation at the central carbon atom of Ph₂P(S)CH₂P(S)Ph₂, react with Pd(II) and Ru(II) precursors to afford new carbene complexes. Samarium and thulium alkylidene complexes of these S–C–S dianionic ligands were synthesized in a similar way. Reaction of the lanthanide derivatives with ketones or aldehydes yields olefinic derivatives through a ‘Wittig-like’ process.     

Solvent effect on intensities off-ftransitions in lanthanide(III) complexes

A general theory of the solvent effect on the intensities of f-f; transitions of lanthanide complexes based on static and dynamic coupling between metal ion and ligands and solvent molecules is presented. New expressions are found correlating the intensity parameters with physical characteristics of the solvent. It is shown that the solvent effect influences only in the parameter ₂.     

Crystal structure and electronic properties of bis(mepirizole) copper(II) perchlorate. Correlation between the electronic spectrum and CuN4 chromophore distortion from tetrahedral symmetry

Summary The crystal structure of the title compound has been determined from single-crystal x-ray diffraction data. The crystals are tetragonal, space group P4₂2₁2, withz=2 in a unit cell of dimensionsa=b=9.575(2),c=16.135(5) Å. The structure was solved by the usual Patterson and Fourier techniques, and was refined by least-squares analysis to an R value of 0.057 for 545 observed reflexions. Two mepirizole molecules are arranged in a flattened tetrahedral manner (average Cu-N, 1.974 Å) around Cu, and coordinated through N atoms. The dihedral angle between N-Cu-N planes of the two ligands is 53.6+°. This geometry seems to result from steric interaction between the ligands.The e.s.r. spectrum is axial (g g > 2.0). A study of the maximum d-d transition as a function of CuN₄ chromophore distortion from T_d symmetry is reported.4-Methoxy-2-(5-methoxy-3-methyl-pyrazol-1-yl) -6-methylpyrimidine.     

Exploring the Reactivity of Rh<Subscript>2</Subscript> (OAc)<Subscript>4</Subscript> with 2, 2′ -Dipyridylamine

A series of three new compounds obtained from the reaction of Rh₂(OAc)₄ and 2, 2 -dipyridylamine (Hdpa) under various conditions have been characterized. All are diamagnetic and have a Rh–Rh single bond. In Rh₂(dpa)₄, 1, there are four bridging dpa anions which bind the two Rh atoms through one pyridyl N atom and one amido N atom though two of these ligands interact further with a rhodium atom through the third N atom. In the other two compounds the Hdpa ligand is neutral. Thus Rh₂(OAc)₄(Hdpa)₂, 2, is an adduct of the well known complex dirhodium tetraacetate in which the two Hdpa ligands occupy axial positions. In the third compound, Rh₂(Hdpa)₂(OAc)₂Cl₂, 3, only two acetate bridges are present. One Hdpa molecule chelates equatorially each rhodium atom and the chloride ions are axially coordinated. The Rh–Rh distances are 2. 4005(6) and 2. 4042(8) Å for 1 and 2, respectively. For 3, the Rh–Rh distance of 2. 593(1) Å is significantly longer than those in 1 and 2 because of the presence of fewer bridging ligands.     

Protein–small molecule docking with receptor flexibility in iMOLSDOCK

We have earlier reported the iMOLSDOCK technique to perform ‘induced-fit’ peptide–protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein–ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/.     

Synthesis and crystal structure of a 1 : 2 adduct of aquatrifluoroboron and triphenylphosphine oxide

A crystalline 1 : 2 adduct of aquatrifluoroboron and triphenylphosphine oxide 1/2[BF₃(H₂O)] · Ph₃PO(I) is synthesized and studied by X-ray diffraction analysis. The crystals are orthorhombic, space group Fdd2, a = 32.283 Å, b = 20.162 Å, c = 10.191 Å, Z = 16. The structure is solved by the direct method and refined by a full-matrix least-squares method in the anisotropic approximation to R = 0.054 against 2528 independent reflections (CAD4 automated diffractometer, MoK). A Ph₃PO molecule has a normal structure. A [BF₃(H₂O)] molecule is randomly disordered relative to axis 2; populations of positions of all its atoms are 0.5. The boron atom has a distorted tetrahedral coordination with a donor-acceptor B-O(w) bond. In crystal, strong hydrogen bonds of the P=OH-O-HO=P type are formed between the H₂O molecule and two Ph₃PO molecules.Translated from Koordinatsionnaya Khimiya, Vol. 31, No. 1, 2005, pp. 12–16.Original Russian Text Copyright © 2005 by Chekhlov.     

Reactions of titanocene dihalides with N,N′,N″-chelates: Preparation,X-ray structure and characterization of bis(chloro){2,6-bis[(3,5-dimethyl)pyrazol-1-yl]pyridine}(η-peroxo)titanium(IV)

The reaction of [Ti^IV(Cp)₂Cl₂] (Cp⁻ = η⁵-C₅H₅⁻) and 2,6-bis(3,5-dimethylpyrazolyl-1-yl)pyridine (bdmpp) in Me₂CO has afforded complex [Ti^IVCl₂(O₂)(bdmpp)] (1). The complex can also be prepared from the 1:1:1 [Ti(Cp)₂Cl₂]/bdmpp/H₂O₂ reaction mixture in various solvents. Single-crystal, X-ray crystallography has revealed that the Ti^IV center is in a distorted pentagonal bipyramidal environment in both of the two, crystallographically independent molecules that are present in the asymmetric unit; the equatorial positions are occupied by the two O atoms of the side-on (η²) O₂²⁻ group and the three N-atoms of the tridentate chelate, while the two chloro ligands are on the axial positions. IR, Raman, electronic and ¹H NMR data are discussed in terms of the known structure and the coordination modes of the peroxo and bdmpp ligands.     

Synthesis,characterization, crystal structure,and electrochemical property of copper(II) complexes with Schiff bases derived from 5-halogenated salicylaldehyde and amantadine

A mixture of copper(II) chloride dihydrate and ligands derived from amantadine and 5-halogenated salicylaldehyde in anhydrous methanol generated two novel complexes C₃₄H₃₈Cl₂CuN₂O₂ (I) and C₃₄H₃₈Br₂CuN₂O₂ (II), respectively. The complexes were characterized by melting point, elemental analysis, molar conductance, IR, UV-Vis, and single-crystal X-ray diffraction (CIF files nos. 1435429 (I), 1435430 (II)). Single-crystal X-ray diffraction analysis reveals that both complexes crystallize in monoclinic system, P2₁/c space group. Each asymmetric unit consists of two mononuclear copper(II) complex molecules and each complex molecule includes one copper(II) atom two corresponding deprotonated ligands. The central copper(II) atom is four-coordinated via two nitrogen atoms and two oxygen atoms from the corresponding Schiff base ligands, forming a distorted tetrahedral geometry. Electrochemical properties of the complexes were studied by cyclic voltammetry.     

Synthesis and crystal structure of diaqua(trinitrato)iron(III) 18-crown-6

A novel complex adduct, diaqua(trinitrato)iron(III) 18-crown-6, [Fe(NO₃)₃(H₂O)₂] · 18-crown-6, was synthesized and its crystal structure was studied by X-ray diffraction: space group C2/c, a = 10.073, b = 18.069, c = 25.326 Å, β = 91.51°, Z = 8. The structure was solved by the direct method and refined by the full-matrix least-squares method in the anisotropic approximation to R = 0.076 for 4090 independent reflections (CAD-4 automated diffractometer, λMoK_α). The structure contains isolated complex molecule [Fe(NO₃)₃(H₂O)₂] and two halves of independent molecules 18-crown-6, one of which is statistically disordered about axis 2, while another one is located around the inversion center and is somewhat disordered with respect to the latter. In the complex molecule, the coordination polyhedron of the Fe³⁺ cation is a distorted pentagonal bipyramid with five O atoms of three NO ₃ ^? ligands in a base and two O atoms of two water molecules in the axial vertices. The alternating complex molecules and the disordered 18-crown-6 molecules are joined by hydrogen bonds into “thick” infinite chains along the z axis.