Next Article in Journal
Synthesis, Structures and Properties of Molecular Conductors Based on Bis-Fused Donors Composed of (Thio)Pyran-4-ylidene-1,3-dithiole and Tetraselenafulvalene
Previous Article in Journal
Photoinduced Phase Transition in Strongly Electron-Lattice and Electron–Electron Correlated Molecular Crystals

Crystals 2012, 2(3), 1084-1091; doi:10.3390/cryst2031084

Short Note
[KDy(Hptc)3(H3ptc)]n·2n(Hbipy)·5n(H2O), a Layered Coordination Polymer Containing DyO6N3 Tri-Capped Trigonal Prisms (H3ptc = Pyridine 2,4,6-Tricarboxylic Acid, C8H5NO6; Bipy = 2,2'-Bipyridine, C10H8N2)
Shoaib Anwar 1, Irfana Mariam 2, Islam Ullah Khan 1,*, William T. A. Harrison 3,* and Sohail Anwar 1
1
Materials Chemistry Laboratory, Department of Chemistry, Government College University, Lahore-54000, Pakistan; Email: shoaib.anwer731@gmail.com; (Sh.A.); ejaz_lhr_pk@yahoo.com (E.); sohail.anwar21@gmail.com (So.A.)
2
Department of Chemistry, Queen Mary College for Girls, Lahore, Pakistan; Email: majied.irfana@yahoo.com
3
Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK
*
Authors to whom correspondence should be addressed; Email: iuklodhi@yahoo.com (I.U.K.); w.harrison@abdn.ac.uk (W.T.A.H.); Tel.: +92-042-99213338 (I.U.K.); +44-1224-272897 (W.T.A.H.); Fax: +44-1224-272921 (W.T.A.H.).
Received: 10 May 2012; in revised form: 7 June 2012 / Accepted: 25 June 2012 /
Published: 3 August 2012

Abstract

: The synthesis, structure and properties of the bimetallic layered coordination polymer, [KDy(C8H3NO6)3(C8H5NO6)]n·2n(C10H9N2)·5n(H2O) = [KDy(Hptc)3(H3ptc)]n·2n(Hbipy)·5n(H2O), are described. The Dy3+ ion is coordinated by three O,N,O-tridentate doubly-deprotonated pyridine tri-carboxylate (Hptc) ligands to generate a fairly regular DyO6N3 tri-capped trigonal prism, with the N atoms acting as the caps. The potassium ion is coordinated by an O,N,O-tridentate H3ptc molecule as well as monodentate and bidentate Hptc ligands to result in an irregular KNO9 coordination geometry. The ligands bridge the metal-atom nodes into a bimetallic, layered, coordination polymer, which extends as corrugated layers in the (010) plane, with the mono-protonated bipyridine cations and water molecules occupying the inter-layer regions: Unlike related structures, there are no dysprosium–water bonds. Many O–H…O and N–H…O hydrogen bonds consolidate the structure. Characterization and bioactivity data are described. Crystal data: C52H42DyKN8O29, Mr = 1444.54, triclinic, Crystals 02 01084 i001 (No. 2), Z = 2, a = 9.188(2) Å, b = 15.7332(17) Å, c = 19.1664(19) Å, α = 92.797(6)°, β = 92.319(7)°, γ = 91.273(9)°, V = 2764.3(7) Å3, R(F) = 0.029, wR(F2) = 0.084.
Keywords:
coordination polymer; layered supramolecular network; dysprosium

1. Introduction

Coordination polymers, in which bridging ligands connect metal atoms into an extended network [1], have been intensively studied for the past 100 years. This area of chemistry is so vast that a journal solely devoted to reviewing the field—Coordination Chemistry Reviews—publishes some 3000 pages per year.

In this paper we describe the synthesis and structure of the new bimetallic coordination polymer [KDy(C8H3NO6)3(C8H5NO6)]n·2n(C10H9N2)·5n(H2O): (1) Related structures containing Dy3+ ions in combination with pyridine 2,4,6-tricarboxylate (ptc) ligands include α-[Dy(C8H2NO6)(H2O)3]n·nH2O [2], [Dy(C8H2NO6)(H2O)]n·nH2O [3], β-[Dy(C8H2NO6)(H2O)3]n·nH2O [4] and [Dy2(C8H2NO6)2(H2O)5]n·nH2O [5]. In all these compounds, the tri-anionic ptc ligand forms an O,N,O-tridentate link to one metal ion and also bridges to other Dy3+ ions to form a coordination network. One or more water molecules are also directly coordinated to the dysprosium ion.

The crystal structures of [K(VO2)(C8H3NO6)]n·nH2O [6], [KCaEr(C8H2NO6)2(H2O)]n [7] and [KBa(C8H2NO6)(H2O)2]n [7] have been reported but there are no mixed-metal K/Dy/ptc coordination polymers yet known.

2. Results and Discussion

2.1. Crystal Structure of [KDy(C8H3NO6)3(C8H5NO6)]n·2n(C10H9N2)·5n(H2O) (1)

Compound 1 is a bimetallic, layered coordination polymer: The complex asymmetric unit contains one K+ cation, one Dy3+ cation, three doubly-deprotonated (C8H3NO6)2− (Hptc2−) dianions, one neutral C8H5NO6 (H3ptc) molecule, two singly protonated bipyridinium (C10H9N2)+ cations and five water molecules (Figure 1).

The dysprosium ion in 1 is coordinated by the three O,N,O-tridentate C8H3NO6 dianions (in which two carboxylate protons have been lost from the C8H5NO6 neutral molecule) to generate a near-regular tri-capped trigonal prismatic DyO6N3 coordination geometry with the N atoms serving as the caps protruding through the prismatic side-faces (Figure 2). Each ligand forms one Dy–O bond to the “top” triangular face and one to the bottom. The dihedral angle between the O1/O7/O13 and O5/O11/O17 triangular faces is 4.30(4)° and the metal ion is displaced by −1.6580(13) Å from the first triplet of O atoms and by 1.6133(13) Å from the second. The Dy–N bond lengths (Table 1) (mean = 2.501 Å) are longer than all but one of the Dy–O bonds (mean = 2.413 Å). The Dy3+ bond-valence sum (BVS), calculated using the Brown–Altermatt [8] formalism, is 3.18, compared to an expected value of 3.00.

Crystals 02 01084 g001 1024
Figure 1. The asymmetric unit of 1 (50% displacement ellipsoids for the non-hydrogen atoms). The water molecules are omitted for clarity.

Click here to enlarge figure

Figure 1. The asymmetric unit of 1 (50% displacement ellipsoids for the non-hydrogen atoms). The water molecules are omitted for clarity.
Crystals 02 01084 g001 1024
Crystals 02 01084 g002 1024
Figure 2. Detail of the structure of 1 showing the tri-capped trigonal prismatic coordination of the Dy3+ ion (50% displacement ellipsoids, arbitrary spheres for the C atoms). Note the overall, approximate, local C3 symmetry of these atoms.

Click here to enlarge figure

Figure 2. Detail of the structure of 1 showing the tri-capped trigonal prismatic coordination of the Dy3+ ion (50% displacement ellipsoids, arbitrary spheres for the C atoms). Note the overall, approximate, local C3 symmetry of these atoms.
Crystals 02 01084 g002 1024
Table Table 1. Selected bond-distances (Å) in 1.

Click here to display table

Table 1. Selected bond-distances (Å) in 1.
K1–O192.885(2)K1–O232.946(2)
K1–O42.949(2)K1–O15 i2.958(2)
K1–O13 ii3.025(2)K1–O11 iii3.073(2)
K1–N43.074(2)K1–O7 ii3.201(2)
K1–O12 iii3.388(3)K1–O1 ii3.432(3)
Dy1–O12.366(2)Dy1–O172.392(2)
Dy1–O132.397(2)Dy1–O112.397(2)
Dy1–O52.440(2)Dy1–N12.481(2)
Dy1–O72.4838(19)Dy1–N32.500(2)
Dy1–N22.523(2)

Symmetry codes: (i) x, y, z−1; (ii) 1−x, 1−y, 1−z; (iii) −x, 1−y, 1−z.

The geometrical parameters for the three Dy-bonded ligands (containing atoms N1, N2 and N3) are unexceptional, and all the carboxylate groups are close to coplanar with their attached rings. In each case, the protonated (carboxylic acid –CO2H) grouping is the one not bonded to the rare-earth ion at the para position with respect to the pyridine N atom.

The potassium ion in 1 is coordinated by the O,N,O-tridentate C8H5NO6 neutral molecule (containing N4), as well as monodentate and bidentate dianions also bonded to the dysprosium ion to generate a KNO9 coordination polyhedron (mean K–O = 3.095 Å) that can only be described as irregular (Figure 3). It is also decidedly asymmetric with the potassium ion displaced by 0.481 Å from the geometric centroid of its attached atoms. The next-nearest O atom is over 4.0 Å from the K+ ion and the BVS for potassium is 0.87 (expected value = 1.00). The existence of a protonated carboxylic acid forming a coordinate bond to a potassium ion from its OH moiety is uncommon, but some examples such as [K(C5H4N2O4)(C5H3N2O4)]n [9] and [K(C8H8O2S)(C8H7O4S)]n [10] have been structurally characterised previously.

Crystals 02 01084 g003 1024
Figure 3. Detail of 1 (50% displacement ellipsoids, arbitrary spheres for the C atoms) showing the potassium-ion coordination. Symmetry codes as in Table 1.

Click here to enlarge figure

Figure 3. Detail of 1 (50% displacement ellipsoids, arbitrary spheres for the C atoms) showing the potassium-ion coordination. Symmetry codes as in Table 1.
Crystals 02 01084 g003 1024

A notable feature of this phase is the sharing of some of the ligand O atoms (i.e., as μ2 bridges) by the dysprosium and potassium ions: In particular, the three oxygen atoms of the O1/O7/O13 triangular face of the Dy-trigonal prism also bond to the K+ ion. This leads to polymeric chains of alternating DyO6N3 and KNO9 units, which propagate in the [100] direction (Figure 4).

Crystals 02 01084 g004 1024
Figure 4. Fragment of a [100] chain of DyO6N3 and KNO9 polyhedra in 1 (50% displacement ellipsoids). Note how Dy1 and K1 ii are linked via a triangular face but Dy1 and K1 i are linked by a single O atom. Symmetry codes: (i) −x, 1−y, 1−z; (ii) 1−x, 1−y, 1−z.

Click here to enlarge figure

Figure 4. Fragment of a [100] chain of DyO6N3 and KNO9 polyhedra in 1 (50% displacement ellipsoids). Note how Dy1 and K1 ii are linked via a triangular face but Dy1 and K1 i are linked by a single O atom. Symmetry codes: (i) −x, 1−y, 1−z; (ii) 1−x, 1−y, 1−z.
Crystals 02 01084 g004 1024
Crystals 02 01084 g005 1024
Figure 5. The packing for 1 viewed approximately down [100] showing the wavy (010) polymeric sheets with the organic cations and water molecules occupying the inter-sheet regions.

Click here to enlarge figure

Figure 5. The packing for 1 viewed approximately down [100] showing the wavy (010) polymeric sheets with the organic cations and water molecules occupying the inter-sheet regions.
Crystals 02 01084 g005 1024

When ligand bridging via the aromatic rings is also considered, a layered anionic network of stoichiometry [KDy(C8H3NO6)3(C8H5NO6)]2n results, which propagates in the (010) plane (Figure 5). The layer is corrugated and the (C10H9N2)+ bipyridinium cations and water molecules occupy the inter-layer regions. The dihedral angles between the aromatic rings of the bipyridinium cations are 5.23(17)° and 3.39(18)° for the N5- and N7-containing ions, respectively. To complete the structure of 1, numerous O–H…O and N–H…O hydrogen bonds occur (Table 2). The acceptor atoms are either carboxylate O atoms or water O atoms.

Table Table 2. Hydrogen-bond geometries for 1.

Click here to display table

Table 2. Hydrogen-bond geometries for 1.
O3–H3o…O7 ii0.811.792.537(3)153
O9–H9o…O4w iv0.921.602.511(4)169
O16–H16o…O12 v0.851.632.458(3)163
O19–H19o…O5 iii0.961.572.502(3)162
O21–H21o…O1w vi0.931.652.515(3)152
O23–H23o…O14 ii0.961.572.514(3)168
N5–H5n…O80.951.962.772(3)142
N7–H7n…O100.872.232.882(3)132
O1w–H1w…O2 vii0.921.802.702(4)167
O1w–H2w…O180.921.772.672(4)165
O2w–H3w…O1w0.922.373.044(5)130
O2w–H4w…O170.922.052.865(4)146
O3w–H5w…O5w0.921.922.816(5)163
O3w–H6w…O22 viii0.921.972.878(4)171
O4w–H7w…O3w0.921.872.709(6)151
O4w–H8w…O2w0.852.062.909(6)180
O5w–H9w…O10.921.952.844(4)164
O5w–H10w…O15 ix0.922.012.891(4)161

The four columns specify the D–H, H…A and DA separations (Å) and the D–H…A angle (°), respectively. Symmetry codes: (ii) 1−x, 1−y, 1−z; (iii) −x, 1−y, 1−z; (iv) x, y−1, z; (v) −x, 1−y, 2−z; (vi) −x, 2−y, 1−z; (vii) x−1, y, z; (viii) 1−x, 2−y, 1−z; (ix) 1−x, 1−y, 2−z.

2.2. Bacteriological Tests

Seven bacterial strains including two Gram positive Staphylococcus aureus and Micrococcus luteus and five Gram negative, Escherichia coli, Salmonella setubal, Salmonella typhimurium, Enterobacter aerogenes and Bordetella bronchiseptica were used. Roxithromycin (R) and Cefixixme (C) drugs were used as positive controls, which had shown maximum growth inhibition at 1 mg·mL−1 concentrations and DMSO was used as a negative control. Compound 1 shows significant antibacterial activity against all these bacterial strains (Table 3) except Salmonella typhimurium.

Table Table 3. Bacteriological data.

Click here to display table

Table 3. Bacteriological data.
Minimum Inhibitory Concenteration (MIC)
M. leuteusS. aureusEnt. bacB. stepE. coliS.typhi
30 ppm150 ppm200 ppm70 ppm110 ppmNil

3. Experimental Section

The nominal pyridine 2,4,6-tricarboxylic acid (H3ptc) starting material was prepared by oxidizing 2,4,6-trimethyl pyridine with KMnO4 solution, as described by Syper et al. [11]. This evidently generated a potassium salt: A 0.5-mmol solution was prepared by heating 0.11 g of the solid product in 10.0 mL water in a 50-mL round bottom flask. Then, 0.0063 g of 2,2-bipyridine in 5 mL methanol was added, and the mixture was refluxed for 25 min. Then, a 0.125 mmol solution of DyCl3·6H2O was prepared by dissolving 0.040 g of the metal chloride in 10 mL distilled water and this solution was added to the flask. The Dy:H3ptc:bipy molar ratio was 1:4:4. The mixture was refluxed for four hours and transferred to a vial for crystallization. After ten days, pale pinkish needle like crystals of the title compound were obtained. IR (cm−1): 3410 [ν(O–H)], 1631[νasym(O–C–O)], 1373 [ν(Car–C)], 1265 [νsym(O–C–O)], 539 [ν(M–O, M–N)]. TGA showed an initial weight loss of about 5% between 70 °C and 120 °C, presumably attributable to the loss of the water molecules of crystallization (calc. = 6%). From 205 °C to 300 °C (the limit of the experiment), a continuous weight loss of 55% occurred.

The single-crystal data for 1 (pale pink block 0.30 × 0.25 × 0.25 mm) were collected using a Bruker Kappa APEX II CCD diffractometer (graphite monochromated Mo Kα radiation, λ = 0.71073 Å) at room temperature. Data reduction with SAINT then proceeded and the structure was solved by direct methods with SHELXS. The resulting atomic model was developed and refined against |F|2 with SHELXL [12] and the “observed data” threshold for calculating the R(F) residuals was set as I > 2σ(I). The model was analyzed and validated with PLATON [13].

The C-bound H atoms were placed in idealised locations (C–H = 0.96–0.97 Å) and refined as riding atoms. The ligand N-bond and O-bound and water H atoms were located in difference maps and refined as riding atoms in their as-found relative locations. The constraint Uiso(H) = 1.2Ueq(carrier) was applied in all cases. The difference maps in the regions around the water molecules O2w and O4w were not very well defined, and the possibility of disorder of the H atoms attached to these O atoms cannot be ruled out. Full refinement details and software references are given in the deposited cif.

Crystal data for 1: C52H42DyKN8O29, Mr = 1444.54, triclinic, Crystals 02 01084 i001 (No. 2), Z = 2, a = 9.188(2) Å, b = 15.7332(17) Å, c = 19.1664(19) Å, α = 92.797(6)°, β = 92.319(7)°, γ = 91.273(9)°, V = 2764.3(7) Å3, F(000) = 1454, T = 296(2) K, ρcalc = 1.736 g·cm−3, μ = 1.532 mm−1, 37880 reflections measured (−7 ≤ h ≤ 12, −20 ≤ k ≤ 20, −25 ≤ l ≤ 25; 4.88° ≤ 2θ ≤ 56.74°), RInt = 0.025, 13445 merged reflections, 12100 with I > 2σ(I), 825 variable parameters, R(F) = 0.029, wR(F2) = 0.084, w = 1/[σ2(Fo2) + (0.0387P)2 + 3.7247P], where P = (Fo2 + 2Fc2)/3, min./max. Dρ = −0.74, +1.12 e Å−3. Cambridge Structural Database deposition number: CCDC-879106.

4. Conclusions

The synthesis and crystal structure of [KDy(Hptc)3(H3ptc)]n·2n(Hbipy)·5n(H2O) has been described. The coordination of the dysprosium ion by three tridentate Hptc ligands in this compound is distinctly different to those of the compounds noted in the introduction, in which only one ptc ligand bonds in this way, as well as monodentate bridging ligands and water molecules.

References

  1. Batten, S.R.; Champness, N.R.; Chen, X.-M.; Garcia-Martinez, J.; Kitagawa, S.; Öhrström, L.; O’Keeffe, M.; Suh, M.P.; Reedijk, J. Coordination polymers, metal-organic frameworks and the need for terminology guidelines. CrystEngComm 2012, 14, 3001–3004. [Google Scholar] [CrossRef]
  2. Wang, H.-S.; Zhao, B.; Zhai, B.; Shi, W.; Cheng, P.; Liao, D.-Z.; Yan, S.-P. Syntheses, structures and photoluminescence of one-dimensional lanthanide coordination polymers with 2,4,6-pyridine-tricarboxylic acid. Cryst. Growth Des. 2007, 7, 1851–1857. [Google Scholar] [CrossRef]
  3. Li, C.-J.; Peng, M.-X.; Leng, J.-D.; Yang, M.-M.; Lin, J.; Tong, M.-L. Synthesis, structure, photoluminescence and magnetic properties of new 3-D lanthanide-pyridine-2,4,6-tricarboxate framework. CrysEngComm 2008, 10, 1645–1652. [Google Scholar] [CrossRef]
  4. Das, M.C.; Ghosh, S.K.; Sanudo, E.C.; Bharadwaj, P.K. Coordination polymers with pyridine-2,4,6-tricarboxylic acid and alkaline-earth/lanthanide/transition metals: Synthesis and X-ray structures. Dalton Trans. 2009, 1644–1658. [Google Scholar]
  5. Lin, J.-L.; Xu, W.; Zhao, L.; Zheng, Y.-Q. Synthesis, crystal structure and properties of a new lanthanide pyridine-2,4,6-tricarboxylato coordination polymer. Z. Naturforsch.B 2011, 66, 570–576. [Google Scholar] [CrossRef]
  6. Holder, A.A.; VanDerveer, D. Potassium (4-carboxypyridine-2,6-dicarboxylato)-dioxido-vanadate(V) monohydrate. Acta Cryst. 2007, E63, m2051–m2052. [Google Scholar]
  7. Zhang, W.-Z.; Lv, T.-Y.; Wei, D.-Z.; Xu, R.; Xiong, G.; Wang, Y.-Q.; Gao, E.-J.; Sun, Y.-G. Synthesis, crystal structures and luminescence properties of two novel 3D heterometallic coordination polymers. Inorg. Chem. Commun. 2011, 14, 1245–1249. [Google Scholar] [CrossRef]
  8. Brown, I.D.; Altermatt, D. Bond-Valence parameters obtained from a systematic analysis of the Inorganic Crystal Structure Database. Acta Cryst. 1985, B41, 244–247. [Google Scholar]
  9. Nichol, G.S.; Clegg, W. Classical hydrogen bonding and weaker C-H…O interactions in complexes of uracil-5-carboxylic acid with the alkali metals Na-Cs. Polyhedron 2006, 25, 1043–1056. [Google Scholar] [CrossRef]
  10. Mak, T.C.W.; Wai-Hing, Y.; Smith, G.; O’Reilly, E.J.; Kennard, C.H.L. Metal (phenylthio)acetic acid interactions 3. The crystal structures of anhydrous barium (phenylthio)-acetate and the potassium (phenylthio)acetate (phenylthio)acetic acid adduct. Inorg. Chim. Acta 1984, 88, 35–39. [Google Scholar]
  11. Syper, L.; Kloc, K.; Młochowski, K. Synthesis of ubiquinone and menaquinone analogues by oxidative demethylation of alkenylhydroquinine ethers with argentic oxide or ceric ammonium nitrate in the presence of 2,4,6-pyridine tricarboxylic aicd. Tetrahedron 1980, 36, 123–129. [Google Scholar] [CrossRef]
  12. Sheldrick, G.M. A short history of SHELX. Acta Cryst. 2008, A64, 112–122. [Google Scholar]
  13. Spek, A.L. Structure validation in chemical crystallography. Acta Cryst. 2009, D65, 148–155. [Google Scholar]
Crystals EISSN 2073-4352 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert