[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)

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.

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

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

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.

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.

Table 1. Selected bond-distances (Å) in 1.

K1–O19	2.885(2)	K1–O23	2.946(2)
K1–O4	2.949(2)	K1–O15 i	2.958(2)
K1–O13 ii	3.025(2)	K1–O11 iii	3.073(2)
K1–N4	3.074(2)	K1–O7 ii	3.201(2)
K1–O12 iii	3.388(3)	K1–O1 ii	3.432(3)
Dy1–O1	2.366(2)	Dy1–O17	2.392(2)
Dy1–O13	2.397(2)	Dy1–O11	2.397(2)
Dy1–O5	2.440(2)	Dy1–N1	2.481(2)
Dy1–O7	2.4838(19)	Dy1–N3	2.500(2)
Dy1–N2	2.523(2)

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

Table 1. Selected bond-distances (Å) in 1.

K1–O19	2.885(2)	K1–O23	2.946(2)
K1–O4	2.949(2)	K1–O15 i	2.958(2)
K1–O13 ii	3.025(2)	K1–O11 iii	3.073(2)
K1–N4	3.074(2)	K1–O7 ii	3.201(2)
K1–O12 iii	3.388(3)	K1–O1 ii	3.432(3)
Dy1–O1	2.366(2)	Dy1–O17	2.392(2)
Dy1–O13	2.397(2)	Dy1–O11	2.397(2)
Dy1–O5	2.440(2)	Dy1–N1	2.481(2)
Dy1–O7	2.4838(19)	Dy1–N3	2.500(2)
Dy1–N2	2.523(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.

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.

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.

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).

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.

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.

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.

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.

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 2. Hydrogen-bond geometries for 1.

O3–H3o…O7 ii	0.81	1.79	2.537(3)	153
O9–H9o…O4w iv	0.92	1.60	2.511(4)	169
O16–H16o…O12 v	0.85	1.63	2.458(3)	163
O19–H19o…O5 iii	0.96	1.57	2.502(3)	162
O21–H21o…O1w vi	0.93	1.65	2.515(3)	152
O23–H23o…O14 ii	0.96	1.57	2.514(3)	168
N5–H5n…O8	0.95	1.96	2.772(3)	142
N7–H7n…O10	0.87	2.23	2.882(3)	132
O1w–H1w…O2 vii	0.92	1.80	2.702(4)	167
O1w–H2w…O18	0.92	1.77	2.672(4)	165
O2w–H3w…O1w	0.92	2.37	3.044(5)	130
O2w–H4w…O17	0.92	2.05	2.865(4)	146
O3w–H5w…O5w	0.92	1.92	2.816(5)	163
O3w–H6w…O22 viii	0.92	1.97	2.878(4)	171
O4w–H7w…O3w	0.92	1.87	2.709(6)	151
O4w–H8w…O2w	0.85	2.06	2.909(6)	180
O5w–H9w…O1	0.92	1.95	2.844(4)	164
O5w–H10w…O15 ix	0.92	2.01	2.891(4)	161

The four columns specify the D–H, H…A and D…A 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.

Table 2. Hydrogen-bond geometries for 1.

O3–H3o…O7 ii	0.81	1.79	2.537(3)	153
O9–H9o…O4w iv	0.92	1.60	2.511(4)	169
O16–H16o…O12 v	0.85	1.63	2.458(3)	163
O19–H19o…O5 iii	0.96	1.57	2.502(3)	162
O21–H21o…O1w vi	0.93	1.65	2.515(3)	152
O23–H23o…O14 ii	0.96	1.57	2.514(3)	168
N5–H5n…O8	0.95	1.96	2.772(3)	142
N7–H7n…O10	0.87	2.23	2.882(3)	132
O1w–H1w…O2 vii	0.92	1.80	2.702(4)	167
O1w–H2w…O18	0.92	1.77	2.672(4)	165
O2w–H3w…O1w	0.92	2.37	3.044(5)	130
O2w–H4w…O17	0.92	2.05	2.865(4)	146
O3w–H5w…O5w	0.92	1.92	2.816(5)	163
O3w–H6w…O22 viii	0.92	1.97	2.878(4)	171
O4w–H7w…O3w	0.92	1.87	2.709(6)	151
O4w–H8w…O2w	0.85	2.06	2.909(6)	180
O5w–H9w…O1	0.92	1.95	2.844(4)	164
O5w–H10w…O15 ix	0.92	2.01	2.891(4)	161

The four columns specify the D–H, H…A and D…A 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 3. Bacteriological data.

Minimum Inhibitory Concenteration (MIC)
M. leuteus	S. aureus	Ent. bac	B. step	E. coli	S.typhi
30 ppm	150 ppm	200 ppm	70 ppm	110 ppm	Nil

Table 3. Bacteriological data.

Minimum Inhibitory Concenteration (MIC)
M. leuteus	S. aureus	Ent. bac	B. step	E. coli	S.typhi
30 ppm	150 ppm	200 ppm	70 ppm	110 ppm	Nil

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[ν_asym(O–C–O)], 1373 [ν(C_ar–C)], 1265 [ν_sym(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 U_iso(H) = 1.2U_eq(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, M_r = 1444.54, triclinic, (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) ų, F(000) = 1454, T = 296(2) K, ρ_calc = 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°), R_Int = 0.025, 13445 merged reflections, 12100 with I > 2σ(I), 825 variable parameters, R(F) = 0.029, wR(F²) = 0.084, w = 1/[σ²(F_o²) + (0.0387P)² + 3.7247P], where P = (F_o² + 2F_c²)/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.