Pentagonal Bipyramidal Coordination Research Articles

Integrating Polyoxometalate into Dy(III)-based Single-molecule Magnets with Pentagonal Bipyramidal Symmetry.

Polyoxometalates (POMs) with various coordination fashions are versatile ligands for constructing single-ion magnets (SIMs), but enforcing POM-SIMs with a specific geometry remains a synthetic challenge. Herein, we synthesized a POM-cocrystallized DyIII-SIM [Dy(OPPh3)4(H2O)3][PW12O40]·4EtOH (1Dy) and a POM-ligated DyIII-SIM [{Dy(OPPh3)3(H2O)3}{PW12O40}]·Ph3PO·H2O (2Dy) with pentagonal bipyramidal local coordination geometry. Magnetic measurements indicate that 1Dy displays field-induced single-molecule magnet (SMM) behavior and the relaxation is dominated by under-barrier processes. 2Dy exhibits spin-lattice relaxation at a broader temperature region with a reversal barrier over 300 K. Magneto-structural analysis reveals that the enhancement of SMM behavior originated from the equatorial replacement of Ph3PO by POM, which strengthens the axial anisotropy in 2Dy. Luminescent experiments indicate that the characteristic DyIII emissions of 1Dy are covered up by the strong π-π* emission of Ph3PO at low-temperature regions. As for 2Dy, partial DyIII emission persists thanks to the antenna effect between DyIII and POM.

Synthesis, spectral elucidation and DNA binding studies of cadmium(II) carboxylates with nitrogen donor heteroligands

A new series of novel homoleptic and heteroleptic Cd(II) complexes using cyclopropanecarboxylic acid (HL1) and cyclopentanecarboxylic acid (HL2) as main ligands and N-donor species like 2,2′-bipyridine (bpy), 1,10-phenanthroline (phen), and 2,9-dimethyl-1,10-phenanthroline (Me2phen) as co-ligands were prepared and characterized by FT-IR, multinuclear (1H and 13C) NMR, and UV–Visible spectroscopies. Furthermore, the crystal structure of the Cd(II) complex coordinated by cyclopentanecarboxylic acid (HL2) and 1,10-phenanthroline (phen) was explored by single crystal X-ray diffraction (SC-XRD) analysis. The crystal structure was binuclear, in which the coordination geometry around each cadmium center was distorted pentagonal bipyramidal coordination geometry. Various intermolecular interactions were accountable for stabilizing the supramolecular associations, which were seen by Hirshfeld surface analysis in terms of interatomic contacts. The spectroanalytical data of the synthesized complexes confirm the absence of the –OH band in the spectra of complexes as compared to the spectra of the free ligands, which favour the formation of complexes. The nature of complex-DNA interaction and the effect of the coordination of heteroligands on the binding strength of complexes were probed through UV–Visible spectroscopy and cyclic voltammetry. The obtained data confirm that the interaction of DNA with the complexes is dual: intercalation as well as groove binding. The DNA binding constants (Kb) and Gibb’s free energy changes (ΔG) were also determined for these complexes. This study aims to project effective drugs with the least harmful effects that could be useful for mankind against dreadful diseases.

The Chlorido-Bismuth Dication: A Potent Lewis Acid Captured in a Hepta-Coordinate Species with a Stereochemically Active Lone Pair.

The stabilization of simple, highly reactive cationic species in molecular complexes represents an important strategy to isolate and characterize compounds with uncommon or even unprecedented structural motifs and properties. Here we report the synthesis, isolation, and full characterization of chlorido-bismuth dications, stabilized only by monodentate dimethylsulfoxide (dmso) ligands: [BiCl(dmso)6][BF4]2 (1) and [BiCl(μ2-dmso)(dmso)4]2[BF4]4 (2). These compounds show unusual distorted pentagonal bipyramidal coordination geometries along with high Lewis acidities and have been analyzed by multinuclear NMR spectroscopy, elemental analysis, IR spectroscopy, single-crystal X-ray diffraction, and density functional theory calculations. Attempts to generate the bromido- and iodido-analogs gave dmso-stabilized tricationic bismuth species.

Constructing high axiality mononuclear dysprosium molecular magnets via a regulation-of-co-ligands strategy.

Two lanthanide complexes with formulae [DyIII(LN5)(pentafluoro-PhO)3] (1) and [DyIII(LN5)(2,6-difluoro-PhO)2](BPh4) (2) (LN5 = 2,14-dimethyl-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadecal (19),2,13,15,17-pentaene) were structurally and magnetically characterized. DyIII ions lie in the cavity of a five coordinate nitrogen macrocycle, and in combination with the introduction of multi-fluorinated monodentate phenoxyl coligands a high axiality coordination symmetry is built. Using the pentafluorophenol co-ligand, complex 1 with a D2d coordination environment, is obtained and displays moderate single-molecule magnets (SMMs) behavior. When difluorophenol co-ligands were used, a higher local axisymmetric pentagonal bipyramidal coordination geometry was observed in complex 2, which displays apparent slow magnetic relaxation behavior with a hysteresis temperature of up to 5 K. Further magnetic studies of diluted samples combined with ab initio calculations indicate that the high axiality plays a crucial role in suppressing quantum tunneling of magnetization (QTM) and consequently results in good slow magnetic relaxation behavior. Different fluoro-substituted phenoxyl co-ligands have phenoloxy oxygen atoms with different electrostatic potentials as well as a different number of phenoloxy coligands along the magnetic axis, resulting in different ligand field strengths and coordination symmetries.

The Anion Impact on Dimensionality of Cadmium(II) Complexes with Nicotinamide

Three novel cadmium(II) coordination compounds, the dimeric [Cd(CH3COO)2(nia)2]2 (1), the polymeric {[Cd(nia)4](ClO4)2}n (2), and the monomeric [Cd(H2O)3(nia)3](ClO4)2·nia (3), were prepared in the reactions of the nicotinamide (pyridine-3-carboxamide, nia) with the corresponding cadmium(II) salts. All prepared compounds were characterized by elemental analyses, FT-IR spectroscopy, TGA/DTA, and single crystal X-ray analysis. The impact of anions (acetate, perchlorate) and solvent used on the dimensionality of cadmium(II) complexes and the cadmium(II) coordination environment was investigated. The bridging capabilities of acetate ions enabled the formation of dimers in the crystal structure of 1. It was shown that the dimensionality of perchlorate complexes depends on the solvent used. The coordination polymer 2 is isolated from an ethanol solution, while monomeric compound 3 was obtained by using a water/ethanol mixture as a solvent. The pentagonal-bipyramidal coordination of cadmium(II) was found in the presence of chelating and bridging acetate ions in 1. In the presence of non-coordinating perchlorate anions in 2 and 3, the coordination geometry of cadmium(II) is found to be octahedral. The supramolecular amide-amide homosynthon R22(8) was preserved in the hydrogen-bonded frameworks of all three compounds.

Flux Crystal Growth of the Extended Structure Pu(V) Borate Na2(PuO2)(BO3).

As part of our exploration of plutonium-containing materials as potential nuclear waste forms, we report the first extended structure Pu(V) material and the first Pu(V) borate. Crystals of Na2(PuO2)(BO3) were grown out of mixed hydroxide/boric acid flux and found to crystallize in the orthorhombic space group Cmcm with lattice parameters of a = 9.9067(4) Å, b = 6.5909(2) Å, and c = 6.9724(2) Å. Na2(PuO2)(BO3) adopts a layered structure in which layers of PuO2(BO3)2- are separated by sodium cations. Plutonium is found in a pentagonal bipyramidal coordination environment, with axial Pu(V)-O plutonyl bond lengths of 1.876(3) Å and equatorial Pu-O bond lengths ranging from 2.325(5) to 2.467(3) Å. We find that the Pu(V)-O plutonyl bond lengths are approximately 0.1 Å longer than the reported Pu(VI)-O plutonyl bond lengths and shorter by approximately 0.033 Å than the corresponding U(V) uranyl bond lengths. Raman spectroscopy on single crystals was used to determine the PuO2+ plutonyl stretching and the equatorial breathing mode frequencies of the pentagonal bipyramidal coordination environment around plutonium. Density functional theory calculations were used to calculate the Raman spectrum to help identify the Raman bands at 690 and 630 cm-1 as corresponding to the plutonyl(V) ν1 stretch and the equatorial PuO5 breathing mode, respectively. UV-vis measurements on single crystals indicate semiconducting behavior with a band gap of ∼2.60 eV.

Single molecule magnet features in luminescent lanthanide coordination polymers with heptacoordinate Dy/Yb(III) ions as nodes.

Two sets of 1D/2D lanthanide coordination polymers with formulas of Ln(oqa)3·2H2O [Hoqa = 2-(4-oxoquinolin-1(4H)-yl) acetic acid, Ln = Dy (1), Yb (2)] and Ln(oaa)2(HCOO)(H2O) [Hoaa = 2-(9-oxoacridin-10(9H)-yl) acetic acid, Ln = Dy (3), Yb (4)] have been synthesized and their physical properties were investigated. All four complexes are constructed from seven-coordinate lanthanide ions and corresponding organic linkers. The lanthanide ions in 1 and 2 adopt a pentagonal bipyramid coordination geometry, whereas the coordination geometry of lanthanide ions in 3 and 4 can be described as a capped octahedron. Slow magnetic relaxation behaviors were observed in these four products at a zero/non-zero static magnetic field. Complexes 1, 2 and 4 exhibit the characteristic emission of Ln(III) ions, whereas complex 3 shows ligand-based emission. Bright yellow light emission was also observed when a voltage was applied, demonstrating the potential of 1 for application in light-emitting diodes (LEDs). Compounds 3 and 4 are the first examples of lanthanide complexes based on Hoaa ligands.

Molecular Structures of the Pyridine-2-olates PhE(pyO)3 (E = Si, Ge, Sn)—[4+3]-Coordination at Si, Ge vs. Heptacoordination at Sn

The phenyltetrel pyridine-2-olates PhE(pyO)3 (E = Si, Ge, Sn; pyO = pyridine-2-olate) were synthesized from the respective chlorides PhECl3 and 2-hydroxypyridine (2-pyridone) with the aid of a sacrificial base (triethylamine). Their solid-state structures were determined by single-crystal X-ray diffraction. PhSi(pyO)3 exhibits a three-fold capped tetrahedral Si coordination sphere ([4+3]-coordination, Si···N separations ca. 3.0 Å), in accordance with structures of previously reported silicon pyridine-2-olates. PhGe(pyO)3 adopts a related [4+3]-coordination mode, which differs in terms of the tetrahedral faces capped by the pyridine N atoms. Additionally, shorter Ge···N separations (2.8–2.9 Å) indicate a trend toward tetrel hypercoordination. PhSn(pyO)3 features heptacoordinate tin within a pentagonal bipyramidal Sn coordination sphere (Sn···N separations 2.2–2.4 Å). For the Si and Sn compounds, 29Si and 119Sn NMR spectroscopy indicates retention of their tetrel coordination number in chloroform solution.

Synthesis and structures of polynuclear organotin(IV) complexes of a polyaromatic carboxylate ligand and cytotoxic evaluation in tumor cell lines

Three polynuclear organotin(IV) derivatives of composition [n-Bu3Sn(HL)]n1, [Ph3Sn(HL)]n2 and [n-Bu2Sn(HL)2]23 were synthesized by reacting 2-((E)-(4-hydroxy-3-((E)-((4-(methoxycarbonyl)phenyl)imino)methyl)phenyl)diazenyl)benzoic acid (H'HL) with (n-Bu3Sn)2O, Ph3SnOH and n-Bu2SnO, respectively. The structures 1–3 were fully characterized by elemental analysis, IR and NMR (1H, 13C, and 119Sn), 119Sn Mössbauer spectroscopy, and additionally, the molecular and crystal structures of 1–3 and its pro-ligand (H'HL) were established by single-crystal X-ray diffraction analysis. The tributyltin(IV) complex 1 is a one-dimensional coordination polymer, in which the azo ligand bridges adjacent Sn(IV) centres solely via the two carboxylate O-atoms. The hydroxy H atom forms an intramolecular O–H···N hydrogen bond with the imine N-atom, as observed in the crystal structure of H'HL. The triphenyltin(IV) complex 2 is also a one-dimensional coordination polymer, but in this case the azo ligand bridges adjacent Sn(IV) centres via its carboxylate group and the deprotonated phenol O-atom. Unlike in 1, the phenol H-atom has migrated to the imine N-atom, to give a zwitterionic form of the azo ligand. The tin centers in 1 and 2 are pentacoordinated and reveal a distorted trans-R3SnO2 trigonal-bipyramidal environment. The dibutyltin(IV) complex 3 crystallizes as discrete centrosymmetric dinuclear entities where the unique Sn(IV) center is heptacoordinated in a distorted pentagonal bipyramid coordination geometry. In vitro cytotoxicity studies of compound 1 were performed and compared with 2 across a panel of human tumor cell lines and the results were compared with the data of six clinically used anticancer drugs.

Synthesis and Characterization of a Calcium‐Pyrazolonato Complex. Observation of In‐Situ Desolvation During Micro‐Electron Diffraction

AbstractThe synthesis and characterization of a calcium pyrazolonato complex is reported. X‐ray diffraction (XRD) of single crystals revealed an octahedral geometry with two axial solvent ligands. Analysis of the bulk sample by means of microcrystal electron diffraction (micro‐ED) measurement revealed a polymeric pentagonal bipyramidal coordination geometry joined via a central Ca2O2 ring with axial water ligands. During the micro‐ED measurement, loss of water was observed resulting in a secondary structure with a polymeric distorted octahedral coordination geometry joined via a central Ca2O2 ring. These findings demonstrate that XRD and micro‐ED methods can provide complementary data during structural determination, and that even electrophilic metals are susceptible to desolvation under micro‐ED measurements.

Two uranyl-organic frameworks based on pyridine carboxylic acid and their electrochemistry properties study

In this paper, two novel 1D uranyl coordination polymers, [(UO2)(HPDTC)(H2O)]Cl (1) and [(UO2)(DPA)(H2O) (2) based on pyridine acid have been synthesized using hydrothermal method. The structure was obtained with the help of a Single Crystal X-ray diffraction meter and further characterized by IR, UV–vis, TG and others. The compounds show good luminescence properties and the uranium center exhibits the same pentagonal bipyramid coordination geometry among the compounds. Their electrochemical properties have been investigated through Cyclic Voltammetry (CV) and Galvanostatic Charge/Discharge (GCD). It reveals the counterion ions in compound 1 improve the electrical properties as the capacity is 56.94 ​F ​g−1.

Trinuclear cyanido-bridged MII-WV complexes (M = Mn, Co): Crystal structures and magnetic properties

Two new trinuclear heterometallic complexes, [{MnII(L)(CH3OH)}2{WV(CN)8}](NO3)·CH3OH·H2O (2) and [{CoII(L)(CH3OH)}2{WV(CN)8}](NO3)·CH3OH·H2O (3), have been assembled from mononuclear cationic modules, [M(L)(H2O)2]2+, and [W(CN)8]3– as a metalloligand (M = MnII; CoII, L is the pentadentate ligand resulting from the condensation reaction between 2,6-diacetylpyridine and semicarbazide). The crystal structure of the manganese(II) precursor, [MnII(L)(H2O)2](NO3)2·H2O 1, and of the trinuclear compounds 2 and 3 have been solved. Within the three compounds the 3d metal ions show a pentagonal bipyramidal coordination geometry. The magnetic properties of compounds 2 and 3 have been investigated. Compound 2 shows an irregular spin state structure with S = 9/2 arising from MnII-WV antiferromagnetic interactions (J = −8.00 cm−1, H = -2JS1S2). In compound 3, the CoII-WV exchange interaction was found ferromagnetic (J = +12.3 cm−1).

Dihalo bismuth cations: unusual coordination properties and inverse solvent effects in Lewis acidity

Dihalo bismuth cations show an unusual pentagonal bipyramidal coordination geometry with a stereochemically inactive lone pair. Their relevance for the Lewis acidity of BiX3 is discussed.

Magnetic anisotropy of transition metal and lanthanide ions in pentagonal bipyramidal geometry.

The magnetic anisotropy associated with a pentagonal bipyramidal (PBP) coordination sphere is examined on the basis of experimental and theoretical investigations. The origin and the characteristics of this anisotropy are discussed in relation to the electronic configuration of the metal ions. The effects of crystal field, structural distortion, and a second-coordination sphere on the observed anisotropies for transition meal and lanthanide ions are outlined. For the Ln derivatives, we focus on compounds showing SMM-like behavior (i.e. slow relaxation of their magnetization) in order to highlight the essential chemical and structural parameters for achieving strong axial anisotropy. The use of PBP complexes to impart controlled magnetic anisotropy in polynuclear species such as SMMs or SCMs is also addressed. This review of the magnetic anisotropies associated with a pentagonal bipyramidal coordination sphere for transition metal and lanthanide ions is intended to highlight some general trends that can guide chemists towards designing a compound with specific properties.

Deciphering the Role of Anions and Secondary Coordination Sphere in Tuning Anisotropy in Dy(III) Air-Stable D5h SIMs.

Precise control of the crystal field and symmetry around the paramagnetic spin centre has recently facilitated the engineering of high-temperature single-ion magnets (SIMs), the smallest possible units for future spin-based devices. In the present work, we report a series of air-stable seven coordinate Dy(III) SIMs {[L2 Dy(H2 O)5 ][X]3 ⋅L2 ⋅n(H2 O), n = 0, X = Cl (1), n=1, X = Br (2), I (3)} possessing pseudo-D5h symmetry or pentagonal bipyramidal coordination geometry with high anisotropy energy barrier (Ueff ) and blocking temperature (TB ). While the strong axial coordination from the sterically encumbered phosphonamide, t BuPO(NHi Pr)2 (L), increases the overall anisotropy of the system, the presence of high symmetry significantly quenches quantum tunnelling of magnetization, which is the prominent deactivating factor encountered in SIMs. The energy barrier (Ueff ) and the blocking temperature (TB ) decrease in the order 3>2>1 with the change of anions from larger iodide to smaller strongly hydrogen-bonded chloride in the secondary coordination sphere, albeit the local coordination geometry and the symmetry around the Dy(III) display only slight deviations. Ab initio CASSCF/RASSI-SO/SINGLE_ANISO calculations provide deeper insights into the dynamics of magnetic relaxation in addition to the role of the secondary coordination sphere in modulating the anisotropy of the D5h systems, using diverse models. Thus, in addition to the importance of the crystal field and the symmetry to obtain high-temperature SIMs, this study also probes the significance of the secondary coordination sphere that can be tailored to accomplish novel SIMs.

Discrete versus 1D Compounds based on Pentagonal Bipyramid Coordination Geometries: A Matter of Solubility?

AbstractA series of heterometallic compounds based on the association of trans‐dicyanido Cr(III) complex [Cr(L)(CN)2]K ⋅ 2H2O and several divalent [MnII(H2Ln)Cl2] heptacoordinated complexes, where Ln stands for pentadentate ligands featuring a planar N3O2 coordination pocket and various substituents (NH2, cyclohexyl, S,S‐mandelic), is described. A dinuclear compound [Cr(L)(CN)2M(H2L2)] and 1D coordination polymers of general formula [Cr(L)(CN)2M(H2Ln)]X (X=PF6− or [Cr(L)(CN)2]−) were rationally prepared by a simple adjustment of the Cr : M stoichiometry for R=NH2 or tuning the solvent mixtures to promote the crystallization of discrete complexes or chains. The crystal structures, phase purities and magnetic properties of all the compounds are reported.

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin.

Calmodulin (CaM) is a calcium-binding protein that transduces signals to downstream proteins through target binding upon calcium binding in a time-dependent manner. Understanding the target binding process that tunes CaM’s affinity for the calcium ions (Ca2+), or vice versa, may provide insight into how Ca2+-CaM selects its target binding proteins. However, modeling of Ca2+-CaM in molecular simulations is challenging because of the gross structural changes in its central linker regions while the two lobes are relatively rigid due to tight binding of the Ca2+ to the calcium-binding loops where the loop forms a pentagonal bipyramidal coordination geometry with Ca2+. This feature that underlies the reciprocal relation between Ca2+ binding and target binding of CaM, however, has yet to be considered in the structural modeling. Here, we presented a coarse-grained model based on the Associative memory, Water mediated, Structure, and Energy Model (AWSEM) protein force field, to investigate the salient features of CaM. Particularly, we optimized the force field of CaM and that of Ca2+ ions by using its coordination chemistry in the calcium-binding loops to match with experimental observations. We presented a “community model” of CaM that is capable of sampling various conformations of CaM, incorporating various calcium-binding states, and carrying the memory of binding with various targets, which sets the foundation of the reciprocal relation of target binding and Ca2+ binding in future studies.

Rare cis‐Dioxido Uranyl Framework Crystalline Complexes: Synthesis, Structure, Characterization and Properties

AbstractThe trans‐dioxido uranyl frameworks named as [(UO2)(Aip)(DMA)] (1), H[(UO2)(Aib)3] (2) and rare cis‐dioxido [(UO2)Co(Suc)2(H2O)4] (3), and [(UO2)Ni(Suc)2(H2O)4] (4) have been synthesized, which based on 5‐aminoisophthalic acid (H2Aip), 3‐aminobenzoic acid (HAib), and succinic acid (H2Suc) as ligands. They were characterized by Fourier Transform Infrared spectra, UV‐vis absorption spectra, single‐crystal X‐ray diffraction, powder X‐ray diffraction and thermogravimetry analysis. It was found that uranium ion of the complex 1 is in the pentagonal bipyramidal coordination environment, while those of the complexes 2–4 are in the hexagonal bipyramidal coordination environment. Complexes 1, 3, and 4 are 3D network structures, 2 is a discrete structure. In particular, geometry of O=U=O for 1 and 2 are trans, ones for 3 and 4 are cis. The highest removal rate of methylene blue was almost to 96 % by complex 1 as an adsorbent, which illustrates that potential application on dye adsorption.

Magneto-structural studies of a one dimensional Mn(II) coordination polymer derived from a flexible polydentate ligand

The polydentate ligand LHμ contains bipyridine, hydrazone and oxime functionalities and reacts with Mn(CH3COO)2·4H2O to afford an alternating one dimensional chain comprising Mn(II) ions, [{Mn2(LH)(CH3COO)3(CH3OH)2}·CH3OH]n(1). The structure of 1 contains two Mn(II) ions in the asymmetric unit; Mn1 adopts an unusual pentagonal bipyramidal coordination geometry comprising an [N3O4] donor set, while Mn2 adopts a more conventional octahedral geometry coordinated by an [NO5] donor set. The two manganese ions within the dinuclear unit are connected to each either via Ohydrazone and syn-syn Oacetate bridges. These dinuclear units are then linked by anti-anti Oacetate bridges, affording a magnetic 1-D alternating chain topology. Magnetic studies on 1 reveal the presence of weak antiferromagnetic interactions via Ohydrazone and acetate bridges. The magnetism of 1 was modelled using a dimer model [Ĥ = −2JŜ1Ŝ2], with inter-dimer exchange modelled using a mean field term (zJ’) to afford g = 2.046 ± 0.002, J/k = -1.03 ± 0.02 cm−1 and zJ’ = −0.06 ± 0.01 cm−1.

Triple M as Manganese: Medicine, magnetism and macrocycles. Seven-coordinate Mn(II) complexes with pyridine-based macrocyclic ligands

Manganese, or more accurately manganese(II) complexes, are extensively used in various scientific and research fields. In this work, we present the preparation and characterization of three manganese(II) complexes with three structurally-new pyridine-based macrocyclic ligands, which differ from each other by functional group in pendant arms. The ligands’ backbone consists of a parental 17-membered macrocycle (LdiProp) containing pyridine and piperazine rings, which are part of the macrocyclic scaffold. The original aliphatic NH groups in LdiProp were successively substituted with three different pendant arms – benzyl (bn2-LdiProp), 2-pyridylmethyl (py2-LdiProp) and 2-aminoethyl ((NH2et)2-LdiProp). A series of manganese(II) complexes with structural formulas [Mn(bn2-LdiProp)Cl2]·CH3OH (1), [Mn(py2-LdiProp)](ClO4)2·0.5CH3CN·0.35H2O (2) and [Mn((NH2et)2-LdiProp)](ClO4)2 (3) were subsequently prepared. In all cases, the presence of coordination number seven with a close to pentagonal bipyramid geometry was confirmed by X-ray diffraction analysis. The axial positions were occupied by chlorido coligands (1) or nitrogen atoms of the pendant arms (2 and 3). The pentagonal bipyramidal coordination sphere was distorted in case of all complexes 1–3 and axially compressed for 2 and 3. The equatorial Mn–Naliphatic bond distances were significantly lengthened up to 2.61 Å.