Coordination Of Metal Cations Research Articles

Exploring the capabilities of X-ray absorption spectroscopy for determining the structure of electrolyte solutions: computed spectra for Cr(3+) or Rh(3+) in water based on molecular dynamics.

Extended X-ray absorption fine structure (EXAFS) spectra of Cr(3+) and Rh(3+) in aqueous solution are analyzed and compared with computed spectra derived from structural results obtained by molecular dynamics (MD) simulation. This procedure quantifies the reliability of the EXAFS structural determination when applied to ions in solution. It provides guidelines for interpreting experimental spectra of octahedrally coordinated metal cations in aqueous solution. A set of relationships among Debye-Waller factors is proposed on the basis of MD results to reduce the number of independent fit parameters. The determination of the second hydration shell is examined. Calculated XANES spectra compare well with experimental ones. Indeed, the splitting observed on the main peak of the Rh K-edge was anticipated by the calculations. Simulated spectra from MD structures of increasing cluster size show a relationship between the second hydration shell and features of the XANES region at energies just above the edge. The combination of quantum and statistical calculations with the XANES spectrum is found to be very fruitful to get insight into the quantitative estimation of structural properties of electrolyte solutions.

Design, synthesis and solid state structural characterisation of a metallacyclophane formed by a diazadioxamacrocycle bearing two pyridines and silver(I) cation

Upon functionalisation of 1,7-diaza-4,10-dioxacyclododecane 2 on both nitrogen atoms by two pyridine units using the para-position with respect to the nitrogen of the pyridine, the bismonodentate ligand 1 was obtained and structurally characterised in the solid state by X-ray diffraction on single-crystal. Under self-assembly condition, in the presence of AgPF 6, the above mentioned ligand 1 forms the macrotricyclic metallamacrocycle 4 composed of two ligands and two silver cations with linear coordination of both metal cations. The barrel type structure thus obtained was also characterised in the solid state by X-ray diffraction methods.

Crown-containing spironaphthoxazines and spiropyrans. 3. Synthesis and investigation of the merocyanine form of crown-containing spirobenzothiazolinonaphthoxazine

A method for the synthesis of the spirobenzothiazolinonaphthoxazine, stable in the merocyanine form and containing a crown-ether fragment was developed. The complexing properties of the prepared merocyanine compound and the spectroscopic and photochromic characteristics of its complexes with alkaline earth metal cations were studied by NMR and UV spectroscopy. The results were analyzed using quantum-chemical calculations. The addition of alkaline earth metal perchlorates to a solution of a crown ether-containing merocyanine dye in MeCN results in the coordination of metal cations to two binding centers, namely, the crown-ether fragment and the merocyanine oxygen atom. This gives rise to two types of complexes, which differ substantially in their structurally. The complexation induces changes in the UV spectra and influences on the photochromic behavior of the prepared compound.

MALDI-TOF-MS of Saturated Polyolefins by Coordination of Metal Cations: A Theoretical Study

Density functional calculations were applied to obtain binding energies for metal cation-oligomer complexes of n-alkanes and poly(ethylene glycol)s (PEG). The B3LYP/6-31G* energies for complexing metal cations (Na+, Li+, Co+, Cu+, Zn+, and Zn2+) with straight chain aliphatics (CnH2n+2, n = 1−12) are in excellent agreement with the limited available experimental and theoretical data. The strength of the complexes increases with an increasing degree of polymerization and with a decreasing size of the metal ion. The weakest calculated complex is Na+−CH4 (7.8 kcal/mol) and the strongest is Co+−dodecane (52.0 kcal/mol). Smaller sized cations, such as Li+, induce more polarized hydrocarbons. Transition metals give stronger complexes than the main group metals because their d-electrons shield the nuclear charge less effectively. M+−methane binding energies, ranging from 12.6 to 23.1 kcal/mol, are also reported for Sc+, Y+, La+, Cu+, Ag+, and Au+. Doubly charged metal ions give much stronger complexes, that is, 67.1 kcal/mol for Zn2+−CH4. Methane binding energies of ca. 20 kcal/mol are obtained when the Be2+, Mg2+, Fe2+, and Zn2+ dications are ligated with a cyclopentadienyl anion. The poly(ethylene glycol)s (HO−[C2H4O]n−H, n = 1−5) bind significantly stronger to the metal cations (Na+ and Cu+) than the aliphatics. The Na+−monomer (C2H6O2) already has a complex strength of 48.5 kcal/mol, while that of the pentamer (C10H22O6), which is the smallest observable Na+−complex by MALDI-TOF-MS, amounts to 88 kcal/mol. The corresponding Cu+ complexes are even stronger with a value of 79.6 kcal/mol for Cu+−C2H6O2. Binding energies of 53.3 and 64.1 kcal/mol are calculated for the respective K+−tetramer and K+−pentamer of which the pentamer is also observed spectroscopically.

Effect of Metal Coordination on the Charge Distribution over the Cation Binding Sites of Zeolites. A Combined Experimental and Theoretical Study

Simplified cluster models representing cation binding sites in a zeolite of ferrierite structure have been optimized with a series of divalent (MgII, MnII, CoII, NiII) and monovalent (NaI, CuI, AgI) metal cations. It has been found that the coordination of metal cations significantly perturbs the charge distribution over the cation binding sites. The perturbation is of electronic origin and arises from the strong electric field concentrated on the metal cation and from framework to metal charge-transfer effects. Its extent is specific to the type of cation and can be expressed with an empirical formula, which contains the formal charge of the cation and bond distance parameters. A sound correlation has been found between the extent of perturbation and the measured infrared vibrational wavenumbers of the shifted T−O−T antisymmetric skeletal vibrations, appearing in the 1020−780 cm-1 region of the FTIR spectra of ferrierite exchanged with metal cations.

Tris(2-succinimidoethyl)amine hydrate (1/0.075)

The title compound, C18H24N4O6·0.075H2O, (I), was prepared as part of a research programme to prepare and identify new tripodal ligands which exhibit instability at low pH, thereby releasing coordinated metal cations under such conditions. Each mol­ecule lies on a crystallographic threefold axis with the three arms arranged in the form of a claw. Angles within the five-membered succin­imide ring, where the r.m.s. deviation of the five atoms from the least-squares ring plane is only 0.004 A, vary from 104.8 (3)° at a methyl­ene C atom to 112.7 (3)° at the formally sp2 N atom. The structure contains a partially occupied disordered water mol­ecule, the source of which is presumably the water produced as a by-product of the synthetic reaction.

Calixphyrins. Hybrid macrocycles at the structural crossroads between porphyrins and calixpyrroles

Calixphyrins are a class of hybrid molecules that lie at the structural crossroads between porphyrins and calixpyrroles. Porphyrins, long known for their versatile metal cation coordination chemistry, are macrocycles that contain only sp2-hybridized bridging meso carbon atoms within their framework. Calix[n]pyrroles, on the other hand, are porphyrin analogs that contain pyrroles bridged exclusively by sp3 meso carbon centers, and in recent years have been shown to display remarkable anion-binding properties. Calix[n]phyrins bear analogy to both the porphyrins and calixpyrroles and are macrocyclic analogs that contain a mixture of sp2- and sp3-hybridized meso carbon bridges. This leads to partial interruptions in the conjugation pathway of the molecule, introduces novel structural features, and leads to interesting anion and cation recognition properties. It also allows for modular syntheses. In the present paper, the chemistry of calix[n]phyrins, still at an early stage of exploration, is reviewed.

METAL COMPLEXES OF NOVEL SYMMETRICAL SCHIFF BASE LIGANDS

Two novel symmetrical Schiff base ligands, H2L1 and H2L2, with tetradentate N2O2 and pentadentate N3O2 coordinating sites were prepared by the reaction of the aldehyde 2-methyl-7-formyl-8-hydroxy-quinoline with 1,3-diaminopropane or diethylenetriamine, respectively, in the molar ratio 2:1. Cu(II), Ni(II), Co(II), Mn(II), Fe(III) and VO(IV) complexes of both ligands were synthesized. The ligands and their metal complexes were characterized by elemental analyses, IR, UV-Vis, ESR, NMR and mass spectra and also by magnetic moment measurements. Both ligands behave as tetradentate ones when coordinating metal cations. The ligand H2L1 has a smaller cavity than the ligand H2L2, thus the former ligand yielded mononuclear products, through chelation of one ligand molecule to a metal cation, while the latter ligand yielded binuclear products, through the coordination of two metal cations to two ligand molecules. Each of the Fe(III) cations was coordinated to three halves of both ligand molecules yielding also a mononuclear product with ligand H2L1 and a binuclear product with ligand H2L2. Either mononuclear or binuclear complex molecules link together forming polymeric chains. The mononuclear and binuclear complex forms were well manifested in the ESR spectra of the vanadyl complexes. The polymeric structures of the metal complexes led to an enhanced decrease of their magnetic moments through antiferromagnetic exchange between neighbouring metal cations.

Wechselwirkungen in Molekülkristallen, 160 [1,2]. Kristallzüchtung und Strukturbestimmung der verschiedenartigen Polyphenyl-Kontaktionenmultipel [p-Quaterphenylee⊖⊖][Na⊕(DME)3]2, [p-Quaterphenyl⊖⊖(Na⊕(THF)3)2] und [p-Terphenyl⊖⊖Na⊕(DME)2Na⊕(DME)]2 / Interaction in Molecular Crystals, 160 [1, 2]. Crystallization and Structure Determination of the Different Polyphenyl Contact Ion Multiples [p-Quaterphenylee⊖⊖][Na⊕(DME)3]2, [p-Quaterphenyl⊖⊖(Na⊕(THF)3)2] und [p-Terphenyl⊖⊖Na⊕(DME)2Na⊕(DME)]2

The π-hydrocarbons p-terphenyl and p-quaterphenyl are reduced to their dianions in aprotic solutions of different ethers at sodium metal mirrors. Single crystal structure determinations of the solvent-separated or solvens-shared contact ion multiples, [p-terphenyl⊖⊖ Na⊕(DME)2Na⊕DME]2, p-quaterphenyl⊖⊖ ][Na⊕(DME)3]2 and [p-quaterpheny⊖⊖( Na⊕(THF)3)2], prove the essential cation solvation by the chelating dimethoxyethane (DME) versus the bulky tetrahydrofuran (THF) ligands: The solution network of equilibria between solvent separated and solvent shared ion aggregates can be considerably and transparently modified by the ether solvent selected. In addition, the structures of the monomeric sodium salts reveal partly novel details of metal cation coordination by contacts Na⊕ ··· O as well as Na⊕ ··· Cπ such as in the dimeric sodium salt of p-terphenyl dianion, [(DME)2Na⊕ (terphenyl⊖⊖)(Na⊕ DME)(terphenyl⊖⊖)Na⊕ (DME)2].

Gas phase intramolecular proton transfer in cationized glycine and chlorine substituted derivatives (M-Gly, M = Na+, Mg2+, Cu+, Ni+, and Cu2+): existence of Zwitterionic structures?

The intramolecular proton transfer in cationized glycine and chlorine substituted derivatives with M = Na+, Mg2+, Ni+, Cu+, and Cu2+ has been studied with the three parameter B3LYP density functional method. The coordination of metal cations to the oxygens of the carboxylic group of glycine stabilizes the zwitterionic structure. For all monocations the intramolecular proton transfer occurs readily with small energy barriers (1-2 kcalmol(-1)). For the dication Mg2+ and Cu2+ systems, the zwitterionic structure becomes very stable. However, whereas for Mg2+, the proton transfer process takes place spontaneously, for Cu2+ the reaction occurs with an important energy barrier. The substitution of the hydrogens of the amino group by chlorine atoms decreases the basicity of nitrogen, which destabilizes the zwitterionic structure. For monosubstituted glycine complexed with Na+, the zwitterionic structure still exists as a minimum, but for disubstituted glycine no minimum appears for this structure. In contrast, for Mg2+ complexed to mono- and disubstituted glycine, the zwitterionic structure remains the only minimum, since the enhanced electrostatic interaction with the dication overcomes the destabilizing effect of the chlorine atoms.

Theoretical Studies of the Coordination and Stability of Divalent Cations in ZSM-5

The coordination of divalent metal cations to ZSM-5 has been investigated using gradient-corrected density functional theory (DFT). Coordination at both isolated charge-exchange sites and pairs of charge-exchange sites was considered for Co2+, Cu2+, Fe2+, Ni2+, Pd2+, Pt2+, Ru2+, Rh2+, and Zn2+. Thermodynamic calculations of the stability of M2+ to reduction to M0 and demetalation to form MOx particles were also carried out. The results indicate that Cu2+, Co2+, Fe2+, and Ni2+ are coordinated preferentially to five-membered rings containing two Al atoms, which are located on the walls of the sinusoidal channels, whereas Pd2+, Pt2+, Ru2+, Rh2+, and Zn2+ are coordinated preferentially to six-membered rings located on the walls of the sinusoidal channels. Examination of the stability of dimer cations of the form [M−O−M]2+ shows that such structures are not generally stable to hydrolysis, with the possible exception of [Cu−O−Cu]2+. The findings of these calculations are in good general agreement with experimental results.

Structure and function of the hairpin ribozyme

The hairpin ribozyme belongs to the family of small catalytic RNAs that cleave RNA substrates in a reversible reaction that generates 2′,3′-cyclic phosphate and 5′-hydroxyl termini. The hairpin catalytic motif was discovered in the negative strand of the tobacco ringspot virus satellite RNA, where hairpin ribozyme-mediated self-cleavage and ligation reactions participate in processing RNA replication intermediates. The self-cleaving hairpin, hammerhead, hepatitis delta and Neurospora VS RNAs each adopt unique structures and exploit distinct kinetic and catalytic mechanisms despite catalyzing the same chemical reactions. Mechanistic studies of hairpin ribozyme reactions provided early evidence that, like protein enzymes, RNA enzymes are able to exploit a variety of catalytic strategies. In contrast to the hammerhead and Tetrahymena ribozyme reactions, hairpin-mediated cleavage and ligation proceed through a catalytic mechanism that does not require direct coordination of metal cations to phosphate or water oxygens. The hairpin ribozyme is a better ligase than it is a nuclease while the hammerhead reaction favors cleavage over ligation of bound products by nearly 200-fold. Recent structure-function studies have begun to yield insights into the molecular bases of these unique features of the hairpin ribozyme.

Structural analysis and magnetic properties of the 2-D compounds [M(N3)2(bpa)]n (M = Mn, Co or Ni; bpa = 1,2-bis(4-pyridyl)ethane) †

Isomorphous compounds exhibiting the general formula [M(N3)2(bpa)]n (M = MnII1, CoII2 or NiII3; bpa = 1,2-bis(4-pyridyl)ethane) have been prepared and magnetostructurally characterised. X-Ray diffraction analysis revealed a 2-D arrangement of octahedrally co-ordinated metal cations where di-μ-(1,3)-N3-bridged metallic chains are connected through bpa ligands. IR and UV-VIS spectra were consistent with this structural characterisation. Magnetic analysis carried out by means of ESR spectroscopy and susceptibility measurements indicated that the three compounds are antiferromagnetic, J values being −5.7, −14.0 and −80 cm−1 for 1, 2 and 3, respectively.

1,1′-substituted pyridinothiaferrocene derivatives

The syntheses and characterisation of three new ferrocene ligands containing N and S as heteroatoms are described. In addition, the coordination of guest metal cations into each host binding site has been studied by spectroscopic and electrochemical methods and the results for zinc complexation are presented.

Hydrogen-bonded Trimers of DNA Bases and their Interaction with Metal Cations: Ab initio Quantum-chemical and Empirical Potential Study

Neutral (G.GC, A. AT, G.AT, T. AT, and C (imino).GC) and protonated (CH+.GC and AH+.GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion—;molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to metal cation coordination to the N7/06 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly nonadditive; the three-body term is above -10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.

Self-Assembled Ionophores. An Isoguanosine-K+ Octamer

The mononucleoside, 5‘-(tert-butyldimethylsilyl)-2‘,3‘-O-isopropylidene isoguanosine (isoG) 2, has a strong affinity for alkali metal cations. Previously, it was shown that isoG 2 self-assembles via hydrogen bonds to give a stable tetramer, (isoG)4 4, in organic solvents (Davis et al. J. Org. Chem. 1995, 60, 4167−4176). The isoG tetramer 4 can then coordinate metal cations. In this present study, vapor phase osmometry and further 1H NMR experiments confirmed that isoG 2 self-assembles via complementary hydrogen bonds to form tetramer 4. Molecular models obtained from molecular dynamics and MM2 energy minimization indicate that the isoG tetramer 4 is bowl-shaped, with four C2 oxygens located on the tetramer's convex surface. It is likely that these four oxygens on the tetramer's convex face coordinate cations. Potassium picrate was used to determine the stoichiometry of the isoG-K+ complex and its K+ binding affinity. Both 1H NMR and UV−vis spectroscopic analysis demonstrated that isoG 2 forms an octamer, ...

A detailed 1H and 13C NMR study of a repeating disaccharide of hyaluronan: the effect of sodium and calcium ions

Hyaluronan (HA), a polyanionic polysaccharide consisting of repeating glucuronate and N-acetylglucosamine residues, exists surrounded by ions in its physiological milieu. For example, the average concentration of sodium is 300 mM in bovine hyaline cartilage, or roughly twice that of typical extracellular fluid [1]. It has been shown that salts can modify strongly the properties of HA [2,3] and its constituent monomers [4,5]. For example, Van Damme et al. [2] reported that binding of HA to lysozyme is most efficient at pH 7.5 and 10-15 mM NaCI. Self-association of hyaluronate segments in aqueous solution requires a sodium concentration of 150 mM [3]. Several physical techniques (NMR [6-13], X-ray [14-17], CD [8,18], and IR [9,14]) have been employed to determine if salts interact with uronate residues non-specifically (via electrostatic interaction) [7] or through chelation by several ligands acting in concert. Most authors have postulated the existence of chelation sites. A review of studies conducted on HA in the solid and liquid states leads to the conclusion that the oxygens of the carboxyl groups on HA and of water molecules always take part in coordination of metal cations, while other oxygens around the sugar ring are sometimes involved as well. The type of

First sphere coordination of divalent metal cations by cyclodextrin: structure of the β-cyclodextrin–calcium chloride–water (1/2/11.25) compound

The structure of the title compound provides the first illustration of direct coordination of a polyvalent cation, as well as an inorganic anion, by β-cyclodextrin (β-CD). Crystal data: P212121, Z = 4, a = 15.875 (1), b = 17.583 (1), c = 24.270 (2) Å, V = 6775 (1) Å3, R = 0.059 for 4744 unique observed reflections with I > 3σ(I). There are two CaCl2 per β-CD, with no direct contacts between the ions. None of the ions are included within the cyclodextrin cavity. The cations are in direct interaction simultaneously with two or three β-CD molecules and an eightfold coordination occurs for both. No disorder was found except for the two water molecules situated inside the cavity. The crystalline form is a novel monomer-type structure. The β-CD molecules are stacked as monomer entities inclined at ~50° along a twofold screw axis, such that they are arranged in a new herringbone-like scheme. The overall packing is stabilized by intermolecular interactions between cyclodextrin monomers and by direct coordination to the ions. Moreover, the cohesion is reinforced by hydrogen bonds involving water molecules arranged in infinite chain motifs traversing the whole structure.

Ferromagnetic coupling by diamagnetic metal cation coordination: magnetism and structure of the alkali-metal salts of nitroxide carboxylates

Sodium and potassium salts of the free radical 4-carboxy-TEMPO (1-H) form extended one-dimensional ferromagnetically coupled systems: the salt (1-Na) is structurally characterized.

Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from Escherichia coli

Crystal structures of unligated adenylosuccinate synthetase from Escherichia coliin space groups P2 1and P2 12 12 1have been refined to R-factors of 0.199 and 0.206 against data to 2.0 and 2.5 Å, respectively. Bond lengths and angles deviate from expected values by 0.011 Å and 1.7° for the P2 1crystal form and by 0.015 Å and 1.7° for the P2 12 12 1crystal form. The fold of the polypeptide chain is dominated by a central β-sheet, which is composed of nine parallel strands and a tenth antiparallel strand. Extending off from this central β-sheet are four subdomains. The four subdomains contribute loops of residues that are disordered or have high thermal parameters. At least three of these loops (residues 42 to 52, 120 to 131 and 298 to 304) contribute essential residues to the putative active site of the synthetase. In the absence of ligands, much of the active site of the synthetase exists in an ill-defined conformational state. Two, nearly independent regions contribute residues to the interface between polypeptide chains of the synthetase dimer. A pair of helices (H4 and H5) interact with their symmetry-equivalent mates by way of residues that are not conserved amongst the known sequences of the synthetase. The second interface region involves conserved residues belonging to structural elements that connect strands of the central β-sheet. Residues putatively involved in the binding of IMP lie at or near the interface between polypeptide chains of the dimer. Of the four sequence elements putatively common to all GTP hydrolases, the synthetase has only the guanine recognition element and a glycine-rich loop (P-loop). Although the base recognition element is essentially identical with those of the p21 rasand G αproteins, the P-loop of the synthetase is extended in size relative to the P-loops of other GTP hydrolases. The P-loop has two acid residues (Asp13 and Glu14), which are found in the P-loops of only the synthetase family. Glu14 may be involved in the stabilization of the enlarged P-loop of the synthetase, whereas Asp13 may play a role in catalysis and in the coordination of Mg 2+. The structural elements of the p21 rasand G αproteins responsible for binding Mg 2+are either absent from the synthetase or unavailable for the coordination of metal cations.