Coordination diversity in palladium(II)-picolinamide ligand complexes: structural and quantum chemical studies

The separation of different metal ions can be successfully accomplished by using picolinamide-based ligands. We herein report the first X-ray structure of picolinamide-based ligands of the type C₅H₄NCONR₂ (where R=ⁱC₃H₇ (L1) and ⁱC₄H₉ (L2)) and C₅H₄NCONHR (R=^tC₄H₉ (L3)) with palladium(II) ion. We have synthesized and characterized the structures of two palladium complexes, [PdCl₂(L1)₂] (1) and [PdCl₂L3] (3). In 1, ligand L1 forms a 2?:?1 complex with palladium(II) chloride, whereas in 3, the ligand L3 forms a 1?:?1 complex. Further, in 1, the ligand L1 acts as a monodentate ligand and is bound only through pyridyl-N atom, whereas in 3, the ligand L3 acts as a bidentate chelating ligand and is bound through both the pyridyl-N and amido-O atoms to the Pd(II) center. Electronic structure calculations are carried out to understand the experimental coordination diversity in the Pd complexes. Our calculations clearly suggest that a combination of steric hindrance of the ligand and the electronic effect of metal ions may modulate the coordination preferences.     

Coordination studies of a new unsymmetrical kappa4-PNN'N"-tetradentate ligand: stepwise formation and structural characterization

The two-step synthesis of a new unsymmetrical ligand 2-[Ph2PC6H4C(H)=N]C6H4[N(H)COCH2N(H)CO2Bz], 2.HH, via acid-catalyzed Schiff base condensation of 2-(H2N)C6H4[N(H)COCH2N(H)CO2Bz], 1, with 2-Ph2PC6H4(CHO) in refluxing EtOH is reported. The multidentate ligand 2.HH, isolated in ca. 60% yield, exhibits an array of ligation modes, as exemplified by coordination studies with NiII, PdII, PtII, and AuI mononuclear metal precursors. Hence, reaction of 2.HH with AuCl(tht) (1:1 molar ratio, tht = tetrahydrothiophene) affords AuCl(2.HH), 3, in which the ligand behaves as a classic, neutral two-electron phosphorus donor. In contrast, reaction with MCl2(cod) (M = Pt, Pd; cod = cycloocta-1,5-diene) affords the corresponding dichloro complexes MCl2(2.HH) (4a M = Pt; 4b M = Pd) in which kappa2-P/N-chelation through both P and imino N-donor atoms is observed. Likewise, treatment of Pd(CH3)Cl(cod) with 2.HH gave Pd(CH3)Cl(2.HH), 4c, in which the imino nitrogen is trans to the methyl ligand. Cycloocta-1,5-diene elimination from, and single methyl protonation of, Pt(CH3)2(cod) with 1 equiv of 2.HH in toluene at ambient temperature affords the neutral complex Pt(CH3)(2.H-), 5a, in which 2.H- functions effectively in a kappa3-PNN' coordination mode. The dichloro compounds 4a or 4b undergo smooth N(H) deprotonation with tBuOK to give 6a\6a' and 6b\6b' in which 22- acts as a dianionic kappa4-PNN'N' ' ligand. The corresponding square-planar, diamagnetic, nickel(II) complex 6c\6c' was prepared in excellent yield from NiCl2.6H2O, 2.HH, and tBuOK. Variable-temperature NMR experiments confirm 6a\6a' and 6b\6b' exist, in solution, as a pair of conformational (anti and syn) isomers due to restricted rotation about the N-CO2Bz group. This feature is also borne out by single-crystal X-ray studies of anti-6a.CHCl3, syn-6a'.H2O, anti-6b.CHCl3, and anti-6c.CH2Cl2. To the best of our knowledge, we believe these constitute the first examples of crystallographically characterized conformers of a tetradentate ligand incorporating a P-donor center. All new compounds reported have been fully characterized by a combination of spectroscopic (NMR, FT-IR, ES-MS) and analytical methods. Furthermore, single-crystal X-ray studies have also been undertaken on compounds 2.HH, 3, 4a, and 5a.Et2O.     

Coordination of a triazine ligand with CuII and AgI investigated by spectral,structural, theoretical and docking studies

Two complexes of 5‐phenyl‐3‐(pyridin‐2‐yl)‐1,2,4‐triazine (PPTA), namely (ethanol‐κO)bis(nitrato‐κO)[5‐phenyl‐3‐(pyridin‐2‐yl‐κN)‐1,2,4‐triazine‐κN²]copper(II), [Cu(NO₃)₂(C₁₄H₁₀N₄)(C₂H₆O)] or [Cu(NO₃)₂(PPTA)(EtOH)] ( 1 ), and bis[μ‐5‐phenyl‐3‐(pyridin‐2‐yl)‐1,2,4‐triazine]‐κ³N¹:N²,N³;κ³N²,N³:N¹‐bis[(nitrato‐κO)silver(I)], [Ag₂(NO₃)₂(C₁₄H₁₀N₄)₂] or [Ag₂(NO₃)₂(μ‐PPTA)₂] ( 2 ), were prepared and characterized by elemental analysis, FT–IR spectroscopy and single‐crystal X‐ray diffraction. The X‐ray structure analysis of 1 revealed a copper complex with square‐pyramdial geometry containing two O‐donor nitrate ligands along with an N,N′‐donor PPTA ligand and one O‐donor ethanol ligand. In the binuclear structure of 2 , formed by the bridging of two PPTA ligands, each Ag atom has an AgN₃O environment and square‐planar geometry. In addition to the four dative interactions, each Ag atom interacts with two O atoms of two nitrate ligands on adjacent complexes to complete a pseudo‐octahedral geometry. Density functional theory (DFT) calculations revealed that the geometry around the Cu and Ag atoms in 1 ^opt and 2 ^opt (opt is optimized) for an isolated molecule is the same as the experimental results. In 1 , O—H…O hydrogen bonds form R₁²(4) motifs. In the crystal network of the complexes, in addition to the hydrogen bonds, there are π–π stacking interactions between the aromatic rings (phenyl, pyridine and triazine) of the ligands on adjacent complexes. The ability of the ligand and complexes 1 and 2 to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B‐DNA) was investigated by docking studies. The results show that the studied compounds can interact with proteins better than doxorubicin (except for TrxR and Top II).     

Coordination studies of Al-EDTA in aqueous solution

The degree of aluminum toxicity is based on its complexation with organic ligands. One of these complexes is AlEDTA- (Al = aluminum, EDTA = ethylenediaminetetraacetate), the structure of which in aqueous solution has been debated on the basis of X-ray absorption and NMR measurements with different interpretations proposing different coordination. In addition, there is a lack of consensus regarding the relationship of crystalline AlEDTA- and its geometry in solution. This debate must be resolved, not merely for scientific interest, but because the use of an incorrect coordination might lead to the wrong interpretation of bioactivity and kinetics data. In this work, we predict the coordination of Al in aqueous AlEDTA- by employing ab initio calculations and Car-Parrinello molecular dynamics simulations. Our results indicate that AlEDTA- favors Al in octahedral coordination in aqueous solution. Furthermore, the predicted crystalline and solution-phase structures of AlEDTA- are similar and agree well with recent X-ray measurements, supporting the strong chelating nature of this metal-organic complex in aqueous solution.     

Coordination and structural properties of encumbering 6-mesityl-2-picolinate complexes

In an effort to enforce a sterically hindered environment in transition-metal and main-group 2-picolinate complexes, the synthesis of the encumbering derivative 6-mesityl-2-picolinate ((Mes)pic) is presented. The coordination and structural properties of (Mes)pic are demonstrated with a range of transition-metal and main-group fragments. The 6-position mesityl group of (Mes)pic is shown to alter both the primary and secondary coordination spheres of metal centers relative to the ubiquitous and unencumbered parent 2-picolinate anion.     

Synthetic and structural studies of cobalt-pivalate complexes

The synthesis and characterisation of a range of cobalt pivalate cage complexes are reported. The cages include: a dinuclear Co(II) complex; an oxo-centred Co(III) triangle; tetranuclear Co(II) heterocubanes and butterflies; tetranuclear heterovalent cobalt butterflies and hexanuclear edge-sharing bitetrahedra; heterovalent penta-, hexa- and hepta-nuclear cages based on [M(4)O(4)] heterocubane cores; and a tetradecanuclear cage based on heterocubanes sharing edges and vertices. Spectroscopic studies suggest that some of these cores are retained in solution, but that only in the Co(III) triangle is the structure including ligands retained. A scheme is proposed to account for the many structures observed, which may be applicable to other polymetallic cage complexes.     

Synthesis and structural studies of mixed-ligand complexes

Seven mixed-ligand complexes of cobalt(II), nickel(II) and copper(II) containing benzoylacetone andL-proline (HL¹), 2-pyrrolidone-5-carboxylic acid (HL²) orL-thioproline (HL³) were prepared and characterized by means of elemental analysis, IR, electronic spectra, magnetic moment measurements and molar conductance. Both HL¹ and HL² coordinate with these metal ions in a neutral zwitterionic form (-NH₂-CH-COO^–), whereas HL³ coordinates as a monobasic chelating agent (O/N). The continuous thermochromism of the nickel(II) complex of HL¹ (2) was attributed to a geometry change; it was investigated by DTA, TG, electronic spectra and X-ray powder diffraction techniques.     

Bioactivities and structural studies of withanolides fromWithania somnifera

Four bioactive withanolides withalactone (1), withaoxylactone (2), quresimine-A (4-hydroxy, 3-methoxy-5, 6-epoxy-(22R)-witha-24-enolide) (3) and quresindne-B (4, 27 dihydroxy-3-methoxy-5, 6-epoxy-(22R)-witha-24-enolide (4) have been isolated from the herbs of Withania somnifera, Dunal (Solanaceae). The elucidation of their structures is based on extensive spectroscopic studies, such as¹H-NMR, COSY-45°, HMBC, HMQC HOHAHA, E.I., FAB (+ ve), and HR MS, etc.Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1200–1213, September, 1995.     

Synthesis and structural studies of hydrophilic mesocyclic trithioethers

The functionalized mesocyclic trithioethers, 1,4,7-trithiacyclodecane-9,9-dimethanol (10S3-diMeOH), 9 -methyl-1, 4, 7 - trithiacyclodecane - 9 -carboxylic acid (Me-10S3-acid), 1,4,7-trithiacycloundecane-9,10-diol (dihydroxy-11S3), 1,5,9-trithiacyclododecane-3,3-dimethanol (12S3-diMeOH), 3-methyl-1,5,9-trithiacyclododecane-3-carboxylic acid (Me-12S3-acid), and 1 , 5 , 9 - trit hiacyclo tride cane -11 , 12 - diol ( dihydroxy - 13S3), have been synthesized using the cesium dithiolate technique. The single-crystal X-ray structure has been determined for 3-methyl-1,5,9-trithiacyclododecane-3-carboxylic acid. The compound crystallizes in the monoclinic space group P2₁/n, with a = 9.513(2) Å, b = 5.706(1) Å, c = 25.70(1) Å, β = 96.50(1)°, Z = 4, and R = 0.075. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:123–128, 1998     

Coordination of di- and triimine ligands at ruthenium(II) and ruthenium(III) centers: structural,electrochemical and radical scavenging studies

Herein, we explore the coordination of di- and triimine chelators at ruthenium(II) and ruthenium(III) centers. The reactions of 2,6-bis-((4-tetrahydropyranimino)methyl)pyridine (thppy), N¹,N²-bis((3-chromone)methylene)benzene-1,2-diamine (chb), and tris-((1H-pyrrol-2-ylmethylene)ethane)amine (H₃pym) with trans-[Ru^IICl₂(PPh₃)₃] afforded the diamagnetic ruthenium(II) complex cis-[RuCl₂(thppy)(PPh₃)] (1) and the paramagnetic complexes [mer-Ru₂(μ-chb)Cl₆(PPh₃)₂] (2), and [Ru(pym)] (3), respectively. The complexes were characterized by IR, NMR, and UV–vis spectroscopy and molar conductivity measurements. The structures were confirmed by single crystal X-ray diffraction studies. The redox properties of the metal complexes were probed via cyclic- and squarewave voltammetry. Finally, the radical scavenging capabilities of the metal complexes towards the NO and 2,2-di(4-tert-octylphenyl)-1-picrylhydrazyl (DPPH) radicals were investigated     

Synthesis and structural studies of some copper-benzoate complexes

The reaction of CuCl₂·2H₂O with 3,5-diisopropylpyrazole (Pz^iPr2H) in the presence of sodium parafluorobenzoate (Na-p-FBz) resulted in the formation of an oxo-chloro-bridged tetranuclear complex [Cu₄(Pz^iPr2H)₄(μ-O)(μ-Cl)₆] 1, whereas the reaction of Cu(NO₃)₂·3H₂O with Pz^iPr2H in the presence of different benzoates gave [Cu(Pz^iPr2H)₂(μ-OCH₃)]₂(NO₃)₂ 2, [Cu(Pz^iPr2H)₃(NO₃)(p-ClBz)]·CH₃CN 3, [Cu(p-CH₃Bz)₂(Pz^iPr2H)]₂·2CH₃CN 4, [Cu(p-OCH₃Bz)₂(CH₃CN)]₂·4CH₃CN 5 and [Cu(p-CNBz)(CH₃CN)]₂ 6. Single-crystal X-ray diffraction studies confirmed these formulations. DNA binding studies for these complexes were performed by means of UV-visible absorption titration and viscosity measurements. Gel electrophoresis studies showed that hydroxyl radicals are involved in DNA cleavage in the presence of the complexes.     

Some structural and thermodynamic studies of clathrate hydrates

X-ray and neutron diffraction studies show argon and krypton to preferentially form clathrate hydrates of structure II, rather than structure I as previously assumed; methane and hydrogen sulphide do form structure I. Re-examination of solid-solution thermodynamic theory shows that structure II is basically the more stable; structure I is generally formed only when the guest molecule is in the size range that favours occupancy of the 14-hedral over the 12-hedral cages. For molecules too large to enter the 12-hedra the relative stability of structure II is greatest at 0°C, in agreement with the observed sequence of change of stability of cyclopropane hydrate: I to II at –16° and II to I at 1.5°. Carbon dioxide hydrate is observed to decompose on prolonged standing at 105K in accord with the low-temperature instability predicted by Miller.     

Polyisoprenoid alcohols--recent results of structural studies

Polyisoprenoid alcohols (polyprenols and dolichols) are linear polymers of from several up to more than 100 isoprene units identified in almost all living organisms. Studies of their chemical structures have resulted in the discovery of new variants such as the recently described alloprenols with reversed configuration of the double bond in the alpha-isoprene unit. In parallel, structural elucidation of metabolically labeled plant dolichols has indicated that both the mevalonate and methylerythritol phosphate pathways are involved in the biosynthesis of dolichols in roots, leading to the construction of a spatial model of their biosynthesis. According to this model, in root cells, synthesis of the dolichol molecule is initiated in the plastids, and the resulting intermediates, oligoprenyl diphosphates, are exported to the cytoplasm and are elongated up to the desired chain length. The metabolic consequences of this putative model are discussed in the context of the enzymatic machinery involved.     

Synthetic and structural studies on C-ethynyl- and C-bromo-carboranes

A high-yield preparation of the C-monoethynyl para-carborane, 1-Me(3)SiC[triple bond]C-1,12-C2B10H11, from C-monocopper para-carborane and 1-bromo-2-(trimethylsilyl)ethyne, BrC[triple bond]CSiMe(3) is reported. The low-yield preparation of 1,12-(Me3SiC[triple bond]C)2-1,12-C2B10H10 from the C,C'-dicopper para-carborane derivative with 1-bromo-2-(trimethylsilyl)ethyne, BrC[triple bond]CSiMe3, has been re-investigated and other products were identified including the C-monoethynyl-carborane 1-Me3SiC[triple bond]C-1,12-C2B10H11 and two-cage assemblies generated from cage-cage couplings. The contrast in the yields of the monoethynyl and diethynyl products is due to the highly unfavourable coupling process between 1-RC[triple bond]C-12-Cu-1,12-C2B10H10 and the bromoalkyne. The ethynyl group at the cage carbon C(1) strongly influences the chemical reactivity of the cage carbon at C(12)-the first example of the "antipodal effect" affecting the syntheses of para-carborane derivatives. New two-step preparations of 1-ethynyl- and 1,12-bis(ethynyl)-para-carboranes have been developed using a more readily prepared bromoethyne, 1-bromo-3-methyl-1-butyn-3-ol, BrC[triple bond]CCMe2OH. The molecular structures of the two C-monoethynyl-carboranes, 1-RC[triple bond]C-1,12-C2B10H11 (R = H and Me3Si), were experimentally determined using gas-phase electron diffraction (GED). For R = H (R(G) = 0.053) a model with C(5v) symmetry refined to give a C[triple bond]C bond distance of 1.233(5) A. For R = Me3Si (R(G) = 0.048) a model with C(s) symmetry refined to give a C[triple bond]C bond distance of 1.227(5) A. Molecular structures of 1,12-Br2-1,12-C2B10H10, 1-HC[triple bond]C-12-Br-1,12-C2B10H10 and 1,12-(Me(3)SiC[triple bond]C)2-1,12-C2B10H10 were determined by X-ray crystallography. Substituents at the cage carbon atoms on the C2B10 cage skeleton in 1-X-12-Y-1,12-C2B10H10 derivatives invariably lengthen the cage C-B bonds. However, the subtle substituent effects on the tropical B-B bond lengths in these compounds are more complex. The molecular structures of the ethynyl-ortho-carborane, 1-HC[triple bond]C-1,2-C2B10H11 and the ethene, trans-Me3SiBrC=CSiMe3Br are also reported.     

Thermal and structural studies of nanocrystallization of oxyfluoride glasses

The influence of fluorine content on the structure and crystallization of oxyfluoride glasses from the Na₂O–Al₂O₃–SiO₂–LaF₃ system was studied by DTA/DSC, XRD, FTIR and SEM methods. It has been found that the increase in the fluorine content in the structure of oxyfluoride glasses causes the increase of the flexibility of their structure, which inhibits the process of crystallization of the silicate- aluminium matrix. Simultaneously the ability of the glass for LaF₃ crystallization, which shows a multistage character, is increasing. Analysis of the local atomic interactions in the structure of glasses has been used to explain the course of the crystallization.     

Coordination of Ce(III) and Nd(III) with pentaethylene glycol in the presence of picrate anion: Spectroscopic and X-ray structural studies

¹H NMR evidence for direct coordination between the Ln(III) ion and the oxygen atoms of the pentaethylene glycol (EO5) ligand and the picrate anion (Pic) in [Ln(Pic)₂(EO5)][Pic] {Ln = Ce and Nd} complexes are confirmed by single X-ray diffraction. No dissociation of Ln–O bonds in dimethyl sulfoxide-d solution was observed in NMR studies conducted at different temperatures ranging 25–100 °C. The Ln(III) ion was chelated to nine oxygen atoms from the EO5 ligand in a hexadentate manner and the two Pic anions in each bidentate and monodentate modes. Both compounds are isostructural and crystallized in monoclinic with space group P2₁/c. Coordination environment around the Ce1 and Nd1 atoms can be described as tricapped trigonal prismatic and monocapped square antiprismatic geometries, respectively. The crystal packing of the complexes have stabilized by one dimensional (1D) chains along the [0 0 1] direction to form intermolecular O–HO and C–HO hydrogen bonding. The molar conductance of the complexes in DMSO solution indicated that both compounds are ionic. The complexes had a good thermal stability. Under the UV-excitation, these complexes exhibited the red-shift emission.     

Spectroscopic investigations and structural confirmation studies on thiourea

The Fourier transform infrared and Raman spectra of thiourea have been studied in the region 4000–400 and 4000–10 cm^?1, respectively. A complete vibrational analysis on the molecular structure of thiourea has been made on the basis of C_2υ point group symmetry. The validity of the vibrational assignments on the structure of thiourea is supported by evaluating the molecular constants and the potential energy distribution.     

Synthesis and structural studies of lanthanide substituted bismuth-titanium pyrochlores

The identity of the pyrochlore phase seen during the synthesis of ferroelectric Bi_4−xLn_xTi₃O₁₂ Aurivillius oxides is shown to be Bi_2/3Ln_4/3Ti₂O₇. This pyrochlore is only stable for Ln³⁺=Sm³⁺ or smaller. For larger lanthanides the layered Aurivillius oxide is favoured. The presence of six-fold disorder, associated with the Bi 6s² lone pair electrons, is believed to stabilise the unexpected stoichiometry of this oxide. Precise structures, obtained by Rietveld refinement from synchrotron X-ray diffraction data, of three examples Ln³⁺=Eu, Ho and Yb are presented.     

Dynamic and structural NMR studies of cavitand-based coordination cages

The interionic structure, kinetic stability, and degree of anion encapsulation of coordination cages 1 were studied by PGSE, NOE, and EXSY NMR techniques. The rate constants for the formation/dissociation processes at 296 K were obtained independently via (1)H-NOESY and (19)F-NOESY experiments giving, respectively, k(obs) = 0.30 +/- 0.04 s(-1) in CDCl(3) and k(obs) = 5.2 +/- 0.8 s(-1) in CD(3)NO(2)/CDC(13) (7.1) mixture with the proton probe, and k(obs) = 0.33 +/- 0.06 s(-1) in CDCl(3) and k(obs) = 5.0 +/- 0.8 s(-1) in CD(3)NO(2)/CDC(13) (7/1 mixture) with the (19)F probe. PGSE experiments showed that in CDCl(3) not only the encapsuled anion but also the external anions translate with the same rate as the cage. (19)F,(1)H-HOESY experiments indicated that an average of five external triflate anions are located in the equatorial sites close to the palladium moieties, while two of them approach the polar pockets formed by the alkyl chains. In a CD(3)NO(2)/CDCl(3) (7/1) mixture only one or two anions are in close proximity with the cage, while the others are solvated. In all the considered solvents (benzene, chloroform, methylene chloride, and nitromethane) the inclusion of a single unsolvated triflate anion in the cage is quantitative. (19)F,(1)H-HOESY experiments indicated that the charged guest head points toward one metal center. Therefore, while the ionic aggregation level and kinetic stability of coordination cages 1 are solvent dependent, anion encapsulation is not.