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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2017 Nov 17;73(Pt 12):1875–1877. doi: 10.1107/S2056989017016231

Crystal structure of aqua­(1H-pyrazole-κN 2)(pyridine-2,6-di­carboxyl­ato-κ3 O 2,N,O 6)copper(II) dihydrate

Daeyoung Kim a, Sung Kwon Kang a,*
PMCID: PMC5730243  PMID: 29250406

The synthesis and crystal structure of tridentate pyridine-2,6-di­carboxyl­ate CuII complex with a heterocyclic pyrazole ligand, a potential candidate for metal catalysts, are reported. The CuII atom is coordinated by three O atoms and two N atoms, provided by a tridentate pyridine-2,6-di­carboxyl­ate, one pyrazole and one water ligand, forming a slightly distorted square-pyramidal geometry.

Keywords: crystal structure; pyridine-2,6-di­carboxyl­ate; pyrazole; square-pyramidal CuII complex

Abstract

In the title compound, [Cu(C7H3NO4)(C3H4N2)(H2O)]·2H2O, the CuII atom is coordinated by three O atoms and two N atoms, provided by a tridentate pyridine-2,6-di­carboxyl­ate (pdc), one pyrazole and one water ligand, forming a slightly distorted square-pyramidal geometry [range of O—Cu—O and O—Cu—N bond angles = 79.55 (8)–166.22 (10)°]. The water mol­ecule is positioned at the apical position. In the crystal, the complex mol­ecule and the two crystallographically independent non-coordinating water mol­ecules are linked into a supra­molecular layer structure parallel to the ab plane via O—H⋯O and N—H⋯O hydrogen bonds.

Chemical context  

Metal complexes with the tridentate ligand 2,6-bis­[(1H-pyrazol-1-yl)meth­yl]pyridine are known to be catalysts of polyethyl­ene polymerization (Singh et al., 2003 ▸; Watson et al., 1987 ▸; Son et al., 2014 ▸; Kim & Kang, 2015 ▸). 2,6-Bis[(1H-pyrazol-1-yl)meth­yl]pyridine was oxidized to pyridine-2,6-di­carboxyl­ate (pdc) by metal nitrate (Unuigboje & Anyile, 2007 ▸). The pdc mol­ecule has been recognized as a component of bacterial spores, and is also useful in a variety of processes as an enzyme inhibitor, plant preservative and food sanitizer (Cui et al., 2011 ▸). The pdc mol­ecule has been selected as a primary dibasic tridentate ligand and a metal complex with pdc was reported to be a new chemical sensor (Mistri et al., 2013 ▸). Attention has been paid to the design of various N-donor ligands with special structural properties in order to investigate the specific stereochemical requirements of a particular metal-binding site (Mukherjee, 2000 ▸). Various substituted N-donor heterocyclic ligands such as imidazole and pyrazole have been selected as a second ligand, so that the structural and electronic effects on the biologically important Cu—N bond could be probed (Ang et al., 1991 ▸; Chen et al., 2011 ▸; Lin et al., 2009 ▸; Liu et al., 2005 ▸). As part of these continuing studies, the title complex has been synthesized and characterized by single crystal X-ray diffraction.

Structural commentary  

The mol­ecular structure of the title compound is shown in Fig. 1 ▸. The CuII atom is coordinated by three O atoms and two N atoms from tridentate pyridine-2,6-di­carboxyl­ate (pdc), pyrazole and water ligands. The coordination geometry around the CuII atom is a distorted square pyramid as indicated by the τ value of 0.113 (Addison et al., 1984 ▸). The CuII atom lies in the center of the basal plane defined by two nitro­gen atoms (N2 from pdc and N14 from pyrazole) and two oxygen atoms (O9 and O12 from pdc). The plane including the CuII atom is almost planar, with an r.m.s. deviation of 0.0847 Å from the corresponding least-squares plane defined by the five constituent atoms. The pyrazole ring is twisted by 66.61 (10)° from the basal plane. The apical Cu1—O19 bond length of 2.217 (2) Å is much longer than those of the basal Cu—O lengths [Cu1—O9 = 2.026 (2) Å and Cu1—O12 = 2.058 (2) Å].graphic file with name e-73-01875-scheme1.jpg

Figure 1.

Figure 1

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The mol­ecular structure of the title compound, showing the atom-numbering scheme and 30% probability ellipsoids for non-H atoms. H atoms are drawn as small spheres of arbitrary radii. The O—H⋯O hydrogen bonds are indicated by dashed lines.

Supra­molecular features  

In the crystal, O—H⋯O hydrogen bonds (O19—H19B⋯O21, O20—H20B⋯O13 and O20—H20A⋯O10iii; symmetry code as in Table 1 ▸) link the complex mol­ecule to the non-coordinating water mol­ecules (Fig. 1 ▸). Two crystallographically independent non-coordinating water mol­ecules are also linked to each other by O—H⋯O hydrogen bonds (O21—H21A⋯O20iv and O21—H21B⋯O20v; Table 1 ▸). Adjacent complex mol­ecules are connected by other O—H⋯O and N—H⋯O hydrogen bonds (N15—H15⋯O12i and O19—H19A⋯O9ii; Table 1 ▸). The above-mentioned inter­molecular inter­actions stabilize and link the components into a two-dimensional network parallel to the ab plane (Fig. 2 ▸).

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O19—H19B⋯O21 0.75 (4) 2.09 (5) 2.831 (5) 169 (4)
O20—H20B⋯O13 0.70 (5) 2.12 (5) 2.807 (4) 172 (6)
N15—H15⋯O12i 0.93 (4) 1.93 (4) 2.832 (3) 164 (4)
O19—H19A⋯O9ii 0.70 (5) 2.12 (5) 2.805 (3) 165 (5)
O20—H20A⋯O10iii 0.78 (5) 2.01 (5) 2.784 (4) 171 (5)
O21—H21A⋯O20iv 0.91 (6) 2.05 (6) 2.933 (5) 163 (5)
O21—H21B⋯O20v 0.81 (6) 2.17 (6) 2.938 (5) 161 (6)
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Symmetry codes: (i) Inline graphic; (ii) Inline graphic; (iii) Inline graphic; (iv) Inline graphic; (v) Inline graphic.

Figure 2.

Figure 2

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Part of the packing diagram of the title compound, showing mol­ecules linked by inter­molecular O—H⋯O and N—H⋯O hydrogen bonds (dashed lines).

Database survey  

A search of the Cambridge Structural Database (Version 5.37 with two updates, Groom et al., 2016 ▸) returned 1448 entries for crystal structures related to the name pyridine-2,6-di­carboxyl­ato. Most of them are crystal structures of metal complexes. However, there are only four entries with a secondary ligand of a pyrazolyl derivative bonded to a transition metal, viz. a Cu complex (Lin et al., 2009 ▸; Wang et al., 2014 ▸) and Zn and Co complexes (Zhang et al., 2011 ▸).

Synthesis and crystallization  

A solution of copper nitrate trihydrate (0.072 g, 0.3 mmol) in aceto­nitrile (5 ml) was added to a solution of 2,6-bis­[(1H-pyra­zol-1-yl)meth­yl]pyridine (0.072 g, 0.3 mmol) in aceto­nitrile (5 ml) in a high-pressure vessel. After sealing the high-pressure vessel, the resulting solution was stirred for three days at 403 K. The precipitate formed was removed by filtration, and the filtrate was washed with aceto­nitrile and di­chloro­methane to get a dark-green powder. Single crystals of the title compound were obtained from its aqueous solution by slow evaporation of the solvent at 333 K within five days.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. H atoms of the water mol­ecules and the NH group were located in a difference-Fourier map and refined freely [refined distances; O—H = 0.70 (5)–0.91 (6) Å and N—H = 0.93 (4) Å]. Other H atoms were positioned geometrically and refined using a riding model, with C—H = 0.93 Å, and with U iso(H) = 1.2U eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula [Cu(C7H3NO4)(C3H4N2)(H2O)]·2H2O
M r 350.77
Crystal system, space group Triclinic, P Inline graphic
Temperature (K) 296
a, b, c (Å) 5.2171 (9), 8.9249 (16), 15.309 (3)
α, β, γ (°) 105.289 (8), 94.523 (8), 93.295 (9)
V (Å3) 683.2 (2)
Z 2
Radiation type Mo Kα
μ (mm−1) 1.64
Crystal size (mm) 0.25 × 0.23 × 0.12
 
Data collection
Diffractometer Bruker SMART CCD area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2012 ▸)
T min, T max 0.546, 0.726
No. of measured, independent and observed [I > 2σ(I)] reflections 15587, 3312, 3110
R int 0.024
(sin θ/λ)max (Å−1) 0.667
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.035, 0.088, 1.15
No. of reflections 3312
No. of parameters 214
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.68, −0.53
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Computer programs: SMART and SAINT (Bruker, 2012 ▸), SHELXS2013 (Sheldrick, 2008 ▸), SHELXL2013 (Sheldrick, 2015 ▸) and ORTEP-3 for Windows and WinGX (Farrugia, 2012 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989017016231/is5480sup1.cif

e-73-01875-sup1.cif (464.2KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017016231/is5480Isup2.hkl

e-73-01875-Isup2.hkl (264.4KB, hkl)

CCDC reference: 1584872

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

[Cu(C7H3NO4)(C3H4N2)(H2O)]·2H2O Z = 2
Mr = 350.77 F(000) = 358
Triclinic, P1 Dx = 1.705 Mg m−3
a = 5.2171 (9) Å Mo Kα radiation, λ = 0.71073 Å
b = 8.9249 (16) Å Cell parameters from 9694 reflections
c = 15.309 (3) Å θ = 2.4–28.2°
α = 105.289 (8)° µ = 1.64 mm−1
β = 94.523 (8)° T = 296 K
γ = 93.295 (9)° Block, green
V = 683.2 (2) Å3 0.25 × 0.23 × 0.12 mm
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Data collection

Bruker SMART CCD area-detector diffractometer 3110 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube Rint = 0.024
φ and ω scans θmax = 28.3°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2012) h = −6→6
Tmin = 0.546, Tmax = 0.726 k = −11→11
15587 measured reflections l = −20→20
3312 independent reflections
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Refinement

Refinement on F2 0 restraints
Least-squares matrix: full Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.035 H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.088 w = 1/[σ2(Fo2) + (0.0181P)2 + 1.271P] where P = (Fo2 + 2Fc2)/3
S = 1.15 (Δ/σ)max < 0.001
3312 reflections Δρmax = 0.68 e Å−3
214 parameters Δρmin = −0.52 e Å−3
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Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
Cu1 0.72303 (6) 0.46457 (4) 0.26827 (2) 0.02692 (10)
N2 0.6036 (4) 0.3633 (2) 0.14415 (14) 0.0245 (4)
C3 0.7285 (5) 0.2455 (3) 0.09966 (17) 0.0262 (5)
C4 0.6564 (6) 0.1715 (3) 0.00900 (19) 0.0332 (6)
H4 0.7444 0.0895 −0.0224 0.040*
C5 0.4473 (6) 0.2238 (3) −0.03373 (19) 0.0363 (6)
H5 0.3942 0.1762 −0.0947 0.044*
C6 0.3182 (6) 0.3459 (3) 0.01379 (19) 0.0328 (6)
H6 0.1778 0.3807 −0.0143 0.039*
C7 0.4036 (5) 0.4151 (3) 0.10435 (17) 0.0253 (5)
C8 0.9466 (5) 0.2086 (3) 0.16040 (18) 0.0288 (5)
O9 0.9876 (4) 0.3056 (2) 0.23975 (13) 0.0327 (4)
O10 1.0648 (5) 0.0935 (3) 0.13212 (15) 0.0443 (5)
C11 0.2971 (5) 0.5503 (3) 0.16952 (18) 0.0282 (5)
O12 0.4307 (4) 0.6002 (2) 0.24738 (13) 0.0319 (4)
O13 0.0961 (4) 0.6013 (3) 0.14620 (15) 0.0417 (5)
N14 0.8880 (4) 0.6023 (3) 0.38160 (16) 0.0330 (5)
N15 1.1120 (5) 0.6903 (3) 0.39067 (18) 0.0409 (6)
H15 1.218 (8) 0.680 (5) 0.344 (3) 0.066 (12)*
C16 1.1553 (7) 0.7888 (4) 0.4734 (2) 0.0530 (9)
H16 1.2963 0.8616 0.4944 0.064*
C17 0.9590 (8) 0.7642 (5) 0.5214 (2) 0.0583 (10)
H17 0.9378 0.8150 0.5814 0.070*
C18 0.7951 (7) 0.6469 (4) 0.4620 (2) 0.0492 (8)
H18 0.6417 0.6053 0.4765 0.059*
O19 0.4765 (5) 0.3250 (3) 0.33442 (17) 0.0397 (5)
H19A 0.356 (9) 0.304 (5) 0.309 (3) 0.061 (15)*
H19B 0.521 (8) 0.246 (5) 0.333 (3) 0.057 (14)*
O20 0.0431 (7) 0.9056 (3) 0.2509 (2) 0.0657 (8)
H20A 0.061 (10) 0.952 (6) 0.215 (4) 0.079*
H20B 0.042 (10) 0.828 (6) 0.226 (4) 0.079*
O21 0.5720 (7) 0.0147 (4) 0.3314 (3) 0.0839 (11)
H21A 0.420 (11) −0.039 (7) 0.303 (4) 0.101*
H21B 0.676 (12) −0.028 (7) 0.299 (4) 0.101*
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Cu1 0.02439 (16) 0.03062 (17) 0.02206 (16) 0.00556 (12) −0.00065 (11) 0.00077 (12)
N2 0.0246 (10) 0.0259 (10) 0.0219 (10) 0.0018 (8) 0.0023 (8) 0.0047 (8)
C3 0.0272 (12) 0.0239 (11) 0.0268 (12) 0.0010 (9) 0.0047 (10) 0.0053 (9)
C4 0.0398 (15) 0.0276 (13) 0.0290 (13) 0.0014 (11) 0.0078 (11) 0.0011 (10)
C5 0.0445 (16) 0.0381 (15) 0.0217 (12) −0.0033 (12) −0.0001 (11) 0.0023 (11)
C6 0.0340 (14) 0.0364 (14) 0.0279 (13) −0.0002 (11) −0.0028 (11) 0.0107 (11)
C7 0.0239 (12) 0.0269 (12) 0.0253 (12) 0.0010 (9) 0.0025 (9) 0.0075 (9)
C8 0.0277 (13) 0.0292 (13) 0.0306 (13) 0.0043 (10) 0.0054 (10) 0.0089 (10)
O9 0.0276 (9) 0.0372 (10) 0.0306 (10) 0.0083 (8) −0.0014 (7) 0.0042 (8)
O10 0.0511 (13) 0.0405 (12) 0.0425 (12) 0.0220 (10) 0.0085 (10) 0.0083 (9)
C11 0.0279 (13) 0.0290 (12) 0.0294 (13) 0.0057 (10) 0.0036 (10) 0.0097 (10)
O12 0.0311 (10) 0.0336 (10) 0.0277 (9) 0.0107 (8) 0.0012 (7) 0.0012 (8)
O13 0.0366 (11) 0.0424 (12) 0.0448 (12) 0.0166 (9) −0.0044 (9) 0.0089 (9)
N14 0.0282 (11) 0.0387 (13) 0.0280 (11) −0.0003 (9) 0.0003 (9) 0.0029 (10)
N15 0.0372 (14) 0.0487 (15) 0.0299 (13) −0.0047 (11) 0.0072 (10) −0.0011 (11)
C16 0.053 (2) 0.054 (2) 0.0371 (17) −0.0137 (16) 0.0027 (15) −0.0095 (15)
C17 0.059 (2) 0.072 (2) 0.0294 (16) −0.0077 (19) 0.0098 (15) −0.0112 (16)
C18 0.0427 (18) 0.068 (2) 0.0308 (15) −0.0053 (16) 0.0080 (13) 0.0026 (15)
O19 0.0297 (12) 0.0496 (14) 0.0428 (13) 0.0017 (10) 0.0000 (10) 0.0188 (11)
O20 0.096 (2) 0.0400 (14) 0.0618 (19) 0.0135 (16) 0.0016 (16) 0.0158 (13)
O21 0.070 (2) 0.0589 (19) 0.106 (3) 0.0035 (16) −0.021 (2) 0.0010 (18)
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Geometric parameters (Å, º)

Cu1—N2 1.913 (2) C11—O13 1.231 (3)
Cu1—N14 1.944 (2) C11—O12 1.288 (3)
Cu1—O9 2.0255 (19) N14—C18 1.329 (4)
Cu1—O12 2.0577 (19) N14—N15 1.347 (3)
Cu1—O19 2.217 (2) N15—C16 1.331 (4)
N2—C3 1.328 (3) N15—H15 0.93 (4)
N2—C7 1.333 (3) C16—C17 1.346 (5)
C3—C4 1.382 (4) C16—H16 0.9300
C3—C8 1.519 (4) C17—C18 1.388 (5)
C4—C5 1.394 (4) C17—H17 0.9300
C4—H4 0.9300 C18—H18 0.9300
C5—C6 1.384 (4) O19—H19A 0.70 (5)
C5—H5 0.9300 O19—H19B 0.75 (4)
C6—C7 1.386 (4) O20—H20A 0.78 (5)
C6—H6 0.9300 O20—H20B 0.70 (5)
C7—C11 1.513 (4) O21—H21A 0.91 (6)
C8—O10 1.226 (3) O21—H21B 0.81 (6)
C8—O9 1.286 (3)
N2—Cu1—N14 166.22 (10) O10—C8—O9 125.9 (3)
N2—Cu1—O9 80.44 (8) O10—C8—C3 119.8 (2)
N14—Cu1—O9 100.39 (9) O9—C8—C3 114.3 (2)
N2—Cu1—O12 79.55 (8) C8—O9—Cu1 114.62 (16)
N14—Cu1—O12 97.91 (9) O13—C11—O12 125.8 (2)
O9—Cu1—O12 159.43 (8) O13—C11—C7 119.7 (2)
N2—Cu1—O19 98.60 (9) O12—C11—C7 114.5 (2)
N14—Cu1—O19 95.05 (10) C11—O12—Cu1 114.43 (16)
O9—Cu1—O19 94.79 (9) C18—N14—N15 105.1 (2)
O12—Cu1—O19 92.87 (9) C18—N14—Cu1 129.0 (2)
C3—N2—C7 122.1 (2) N15—N14—Cu1 125.41 (19)
C3—N2—Cu1 118.43 (17) C16—N15—N14 111.1 (3)
C7—N2—Cu1 119.42 (17) C16—N15—H15 126 (3)
N2—C3—C4 121.0 (2) N14—N15—H15 122 (3)
N2—C3—C8 111.8 (2) N15—C16—C17 108.0 (3)
C4—C3—C8 127.3 (2) N15—C16—H16 126.0
C3—C4—C5 117.7 (3) C17—C16—H16 126.0
C3—C4—H4 121.1 C16—C17—C18 105.3 (3)
C5—C4—H4 121.1 C16—C17—H17 127.4
C6—C5—C4 120.6 (3) C18—C17—H17 127.4
C6—C5—H5 119.7 N14—C18—C17 110.5 (3)
C4—C5—H5 119.7 N14—C18—H18 124.7
C5—C6—C7 118.3 (3) C17—C18—H18 124.7
C5—C6—H6 120.9 Cu1—O19—H19A 110 (4)
C7—C6—H6 120.9 Cu1—O19—H19B 115 (3)
N2—C7—C6 120.3 (2) H19A—O19—H19B 101 (5)
N2—C7—C11 111.7 (2) H20A—O20—H20B 103 (6)
C6—C7—C11 128.0 (2) H21A—O21—H21B 102 (5)
C7—N2—C3—C4 0.4 (4) C4—C3—C8—O9 173.6 (3)
Cu1—N2—C3—C4 −177.8 (2) O10—C8—O9—Cu1 −172.0 (2)
C7—N2—C3—C8 −179.6 (2) C3—C8—O9—Cu1 7.5 (3)
Cu1—N2—C3—C8 2.3 (3) N2—C7—C11—O13 −172.6 (2)
N2—C3—C4—C5 −0.5 (4) C6—C7—C11—O13 7.5 (4)
C8—C3—C4—C5 179.4 (3) N2—C7—C11—O12 6.4 (3)
C3—C4—C5—C6 0.1 (4) C6—C7—C11—O12 −173.5 (3)
C4—C5—C6—C7 0.5 (4) O13—C11—O12—Cu1 171.0 (2)
C3—N2—C7—C6 0.2 (4) C7—C11—O12—Cu1 −7.9 (3)
Cu1—N2—C7—C6 178.3 (2) C18—N14—N15—C16 −1.2 (4)
C3—N2—C7—C11 −179.7 (2) Cu1—N14—N15—C16 170.8 (3)
Cu1—N2—C7—C11 −1.6 (3) N14—N15—C16—C17 1.2 (5)
C5—C6—C7—N2 −0.6 (4) N15—C16—C17—C18 −0.7 (5)
C5—C6—C7—C11 179.2 (3) N15—N14—C18—C17 0.7 (4)
N2—C3—C8—O10 173.0 (3) Cu1—N14—C18—C17 −170.9 (3)
C4—C3—C8—O10 −6.9 (4) C16—C17—C18—N14 0.0 (5)
N2—C3—C8—O9 −6.5 (3)
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Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
O19—H19B···O21 0.75 (4) 2.09 (5) 2.831 (5) 169 (4)
O20—H20B···O13 0.70 (5) 2.12 (5) 2.807 (4) 172 (6)
N15—H15···O12i 0.93 (4) 1.93 (4) 2.832 (3) 164 (4)
O19—H19A···O9ii 0.70 (5) 2.12 (5) 2.805 (3) 165 (5)
O20—H20A···O10iii 0.78 (5) 2.01 (5) 2.784 (4) 171 (5)
O21—H21A···O20iv 0.91 (6) 2.05 (6) 2.933 (5) 163 (5)
O21—H21B···O20v 0.81 (6) 2.17 (6) 2.938 (5) 161 (6)
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Symmetry codes: (i) x+1, y, z; (ii) x−1, y, z; (iii) x−1, y+1, z; (iv) x, y−1, z; (v) x+1, y−1, z.

Funding Statement

This work was funded by Chungnam National University grant .

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989017016231/is5480sup1.cif

e-73-01875-sup1.cif (464.2KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017016231/is5480Isup2.hkl

e-73-01875-Isup2.hkl (264.4KB, hkl)

CCDC reference: 1584872

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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