Aqua­(oxydiacetato-κ³O,O′,O′′)(pyridine-2-carboxamide-κ²N¹,O)copper(II)

The title compound, [Cu(C₄H₆O₅)(C₆H₂N₂O)(H₂O)], has a six-coordinate Cu^II atom in a Jahn–Teller-distorted octa­hedral environment, coordinated by a tridentate oxydiacetate dianion, a bidentate pyridine-2-carboxamide ligand and a water mol­ecule. The oxydiacetate chelates the Cu^II atom in a facial configuration.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.022
• wR factor = 0.062
• Data-to-parameter ratio = 13.6

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT232_ALERT_2_C Hirshfeld Test Diff (M-X)  Cu1    -   O4      ..       5.84 su
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C8

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

The present work is a continuation of earlier studies of the preparation, and structure of copper(II) complexes with pyridine-2-carboxamide (C₆H₆N₂O, pca) and dicarboxylic acids (Sieroń, 2004; 2007).

The structure of the title compound, (I), is shown in Fig. 1. The Cu^II atom shows a typical Jahn-Teller distorted octahedral environment. In the basal plane Cu is bound to O and N atoms of pca [1.979 (1) and 2.013 (1) Å for Cu1–O1 and Cu1–N1, respectively], to two terminal carboxylate O atoms from the oda ligand [1.944 (1) and 1.958 (1) Å for Cu1–O2 and Cu1–O5, respectively]. The apical positions are occupied by the central O atom of oda [Cu1–O4 = 2.413 (1) Å] and by the water ligand [Cu1–O7 = 2.306 (2) Å]. The octahedral (4 + 2) coordination is distinctly deformed, with the O4–Cu1–O7 angle between the axial bonds measuring to 159.59 (6)°.

The tridentate oda dianion chelates to the Cu^II atom in a facial coordination mode via O2, O4 and O5. The Cu1/O2/C7/C8/O4 ring is essentially planar with only atom C7 being displaced by 0.076 (3) Å out of the mean plane of the other atoms. The Cu1/O4/C9/C10/O5 ring is twisted about the Cu—O4 bond, with the puckering defined by Q(2) = 0.3236 (12) Å and ϕ(2)= 190.0 (3) ° (Cremer & Pople, 1975) and the pseudorotation parameters P = 348.9 (3) and τ(M) = 26.1 (1) ° (Rao et al., 1981).

The individual carboxylate ions are differently involved in the intermolecular hydrogen-bond system. In the C7/O2/O3 group, only O2 is engaged in hydrogen bonding (as an unsymmetrical bifurcated acceptor). The C10/O5/O6 group forms intermolecular hydrogen bonds in which both O5 and O6 (bifurcatedly) are engaged. This causes distinctly different delocalization of π-bonds in both carboxylic groups. The bonds C7—O2 [1.288 (2) Å] and C7—O3 [1.223 (2) Å] are differentiated, while C10—O5 [1.262 (2) Å] and C10—O6 [1.246 (2) Å] are very similar.

Neighbouring Cu^II complex molecules are also linked through π···π stacking interactions, with distances between ring centroids C_g···C_g(2 - x, 1 - y, 1 - z) of 3.7350 (9) Å.

Related literature

For related structures, see: Sieroń (2004, 2007). For related literature, see: Cremer & Pople (1975); Rao et al. (1981); Watanabe et al. (1973).

S2. Experimental

A mixture of 2-pyridinecarbonitrile (2 mmol) and copper(II) oxydiacetate (2 mmol) in water (60 ml) was heated to boiling. When the solution became dark blue, indicating the copper-assisted hydrolysis of 2-pyridinecarbonitrile to pyridine-2-carboxamide (Watanabe et al., 1973), it was filtered and allowed to cool to room temperature. After a few days, blue crystals of the title compound were obtained.

S3. Refinement

The amine and water H atoms were located in a difference Fourier synthesis and their positions and isotropic displacement parameters were refined freely. The remaining H atoms were positioned with idealized geometry, with C–H = 0.93 or 0.97 Å, and refined with fixed isotropic displacement parameters using a riding model, with U_iso(H) = 1.2U_eq(C).

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXTL (Sheldrick, 2003); molecular graphics: SHELXTL and Mercury (Macrae et al., 2006); software used to prepare material for publication: PLATON (Spek, 2003).

Figures

Fig. 1. The structure of (I), showing 30% probability displacement ellipsoids and the atom-numbering scheme.

Aqua(oxydiacetato-κ³O,O',O'')(pyridine-2-carboxamide- κ²N¹,O)copper(II)

Crystal data

[Cu(C4H6O5)(C6H2N2O)(H2O)]	F(000) = 684
Mr = 335.77	Dx = 1.805 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 7383 reflections
a = 7.7355 (1) Å	θ = 2.7–29.9°
b = 13.2772 (2) Å	µ = 1.80 mm^−1
c = 12.4147 (2) Å	T = 296 K
β = 104.333 (2)°	Prism, blue
V = 1235.37 (3) Å^3	0.30 × 0.24 × 0.12 mm
Z = 4

Data collection

Kuma KM-4 CCD diffractometer	2688 independent reflections
Radiation source: CX-Mo12x0.4-S Seifert Mo tube	2438 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.010
Detector resolution: 8.2356 pixels mm^-1	θmax = 27.0°, θmin = 2.8°
ω scans	h = −9→9
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006)	k = −16→16
Tmin = 0.596, Tmax = 0.814	l = −15→15
13400 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: structure-invariant direct methods
R[F^2 > 2σ(F^2)] = 0.022	Hydrogen site location: difference Fourier map
wR(F^2) = 0.062	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0337P)^2 + 0.5556P] where P = (Fo^2 + 2Fc^2)/3
2688 reflections	(Δ/σ)max = 0.001
197 parameters	Δρmax = 0.36 e Å^−3
0 restraints	Δρmin = −0.29 e Å^−3

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Cu1	0.91871 (2)	0.79729 (1)	0.46233 (2)	0.0278 (1)
O1	0.82820 (17)	0.72202 (9)	0.32210 (10)	0.0361 (4)
O2	0.99275 (16)	0.85784 (10)	0.60908 (10)	0.0371 (4)
O3	0.9346 (2)	0.89120 (13)	0.77194 (12)	0.0595 (5)
O4	0.68592 (16)	0.74097 (9)	0.54645 (10)	0.0340 (3)
O5	0.72887 (15)	0.89632 (9)	0.41005 (11)	0.0354 (4)
O6	0.43811 (17)	0.92043 (12)	0.35059 (12)	0.0495 (4)
O7	1.1011 (3)	0.90533 (14)	0.39538 (19)	0.0637 (7)
N1	1.08345 (18)	0.67767 (10)	0.49316 (11)	0.0279 (4)
N2	0.8586 (2)	0.58362 (13)	0.22552 (13)	0.0368 (5)
C1	0.9078 (2)	0.64115 (12)	0.31296 (13)	0.0280 (4)
C2	1.0604 (2)	0.61205 (12)	0.40834 (13)	0.0268 (4)
C3	1.1611 (2)	0.52483 (13)	0.41424 (15)	0.0343 (5)
C4	1.2872 (2)	0.50461 (14)	0.51251 (16)	0.0391 (6)
C5	1.3100 (2)	0.57096 (14)	0.60005 (16)	0.0393 (5)
C6	1.2065 (2)	0.65726 (13)	0.58795 (14)	0.0336 (5)
C7	0.8996 (2)	0.84925 (13)	0.68138 (14)	0.0354 (5)
C8	0.7381 (3)	0.7809 (2)	0.65578 (16)	0.0530 (7)
C9	0.5314 (2)	0.78558 (15)	0.47609 (16)	0.0393 (6)
C10	0.5693 (2)	0.87439 (13)	0.40789 (14)	0.0327 (5)
H1	0.758 (3)	0.5959 (17)	0.1771 (19)	0.045 (6)*
H2	0.913 (3)	0.5324 (19)	0.2210 (18)	0.042 (6)*
H3	1.14450	0.48120	0.35400	0.0410*
H4	1.35600	0.44640	0.51920	0.0470*
H5	1.39390	0.55800	0.66640	0.0470*
H6	1.22250	0.70230	0.64690	0.0400*
H8A	0.76150	0.72500	0.70770	0.0640*
H8B	0.63800	0.81820	0.66980	0.0640*
H9A	0.45340	0.80800	0.52160	0.0470*
H9B	0.46780	0.73450	0.42570	0.0470*
H71	1.187 (4)	0.906 (2)	0.383 (2)	0.064 (9)*
H72	1.072 (4)	0.958 (3)	0.398 (3)	0.091 (12)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0264 (1)	0.0288 (1)	0.0271 (1)	0.0030 (1)	0.0047 (1)	−0.0014 (1)
O1	0.0380 (7)	0.0355 (6)	0.0293 (6)	0.0073 (5)	−0.0018 (5)	−0.0024 (5)
O2	0.0359 (6)	0.0421 (7)	0.0321 (6)	−0.0048 (5)	0.0061 (5)	−0.0076 (5)
O3	0.0683 (10)	0.0699 (10)	0.0408 (8)	−0.0023 (8)	0.0146 (7)	−0.0230 (7)
O4	0.0342 (6)	0.0335 (6)	0.0326 (6)	−0.0013 (5)	0.0053 (5)	0.0042 (5)
O5	0.0277 (6)	0.0325 (6)	0.0473 (7)	0.0038 (5)	0.0116 (5)	0.0102 (5)
O6	0.0296 (6)	0.0592 (9)	0.0576 (8)	0.0065 (6)	0.0071 (6)	0.0241 (7)
O7	0.0475 (10)	0.0430 (9)	0.1135 (16)	0.0028 (7)	0.0446 (10)	0.0180 (9)
N1	0.0264 (7)	0.0295 (7)	0.0270 (7)	0.0000 (5)	0.0051 (5)	0.0013 (5)
N2	0.0400 (9)	0.0366 (8)	0.0308 (7)	0.0006 (7)	0.0033 (7)	−0.0056 (6)
C1	0.0285 (8)	0.0306 (8)	0.0257 (7)	−0.0023 (6)	0.0085 (6)	0.0014 (6)
C2	0.0253 (7)	0.0293 (7)	0.0271 (7)	−0.0025 (6)	0.0088 (6)	0.0016 (6)
C3	0.0333 (9)	0.0318 (8)	0.0402 (9)	0.0009 (7)	0.0139 (7)	−0.0022 (7)
C4	0.0310 (9)	0.0328 (9)	0.0537 (11)	0.0064 (7)	0.0109 (8)	0.0085 (8)
C5	0.0310 (9)	0.0413 (10)	0.0405 (9)	0.0015 (7)	−0.0007 (7)	0.0107 (8)
C6	0.0317 (8)	0.0354 (9)	0.0299 (8)	−0.0013 (7)	0.0006 (7)	0.0015 (7)
C7	0.0384 (9)	0.0347 (9)	0.0314 (8)	0.0075 (7)	0.0057 (7)	−0.0031 (7)
C8	0.0476 (12)	0.0834 (16)	0.0287 (9)	−0.0130 (11)	0.0110 (8)	0.0006 (10)
C9	0.0289 (9)	0.0457 (10)	0.0419 (10)	−0.0035 (7)	0.0060 (7)	0.0116 (8)
C10	0.0295 (8)	0.0356 (8)	0.0330 (8)	0.0013 (7)	0.0077 (7)	0.0034 (7)

Geometric parameters (Å, º)

Cu1—O1	1.9789 (12)	N2—H1	0.87 (2)
Cu1—O2	1.9435 (12)	N2—H2	0.81 (2)
Cu1—O4	2.4132 (13)	C1—C2	1.501 (2)
Cu1—O5	1.9582 (12)	C2—C3	1.387 (2)
Cu1—O7	2.306 (2)	C3—C4	1.387 (3)
Cu1—N1	2.0128 (14)	C4—C5	1.376 (3)
O1—C1	1.257 (2)	C5—C6	1.385 (2)
O2—C7	1.288 (2)	C7—C8	1.513 (3)
O3—C7	1.223 (2)	C9—C10	1.522 (3)
O4—C8	1.420 (2)	C3—H3	0.93
O4—C9	1.423 (2)	C4—H4	0.93
O5—C10	1.262 (2)	C5—H5	0.93
O6—C10	1.246 (2)	C6—H6	0.93
O7—H71	0.72 (3)	C8—H8A	0.97
O7—H72	0.74 (4)	C8—H8B	0.97
N1—C2	1.344 (2)	C9—H9A	0.97
N1—C6	1.345 (2)	C9—H9B	0.97
N2—C1	1.305 (2)
O1—Cu1—O2	172.55 (5)	N1—C2—C3	122.40 (15)
O1—Cu1—O4	94.87 (5)	C1—C2—C3	125.32 (15)
O1—Cu1—O5	88.54 (5)	N1—C2—C1	112.15 (14)
O1—Cu1—O7	96.42 (7)	C2—C3—C4	118.13 (16)
O1—Cu1—N1	80.69 (5)	C3—C4—C5	119.71 (16)
O2—Cu1—O4	78.51 (5)	C4—C5—C6	119.11 (17)
O2—Cu1—O5	93.20 (5)	N1—C6—C5	121.77 (16)
O2—Cu1—O7	90.91 (7)	O2—C7—O3	124.44 (16)
O2—Cu1—N1	97.03 (5)	O2—C7—C8	118.83 (15)
O4—Cu1—O5	76.87 (5)	O3—C7—C8	116.71 (16)
O4—Cu1—O7	159.59 (6)	O4—C8—C7	116.71 (17)
O4—Cu1—N1	100.27 (5)	O4—C9—C10	114.56 (13)
O5—Cu1—O7	86.47 (7)	O6—C10—C9	117.13 (15)
O5—Cu1—N1	168.63 (5)	O5—C10—O6	123.58 (16)
O7—Cu1—N1	98.30 (7)	O5—C10—C9	119.28 (15)
Cu1—O1—C1	115.87 (11)	C2—C3—H3	121
Cu1—O2—C7	122.07 (11)	C4—C3—H3	121
Cu1—O4—C8	103.42 (12)	C3—C4—H4	120
Cu1—O4—C9	102.05 (9)	C5—C4—H4	120
C8—O4—C9	115.36 (15)	C4—C5—H5	120
Cu1—O5—C10	120.09 (11)	C6—C5—H5	120
Cu1—O7—H72	111 (3)	N1—C6—H6	119
H71—O7—H72	108 (3)	C5—C6—H6	119
Cu1—O7—H71	140 (2)	O4—C8—H8A	108
C2—N1—C6	118.86 (14)	O4—C8—H8B	108
Cu1—N1—C2	114.05 (11)	C7—C8—H8A	108
Cu1—N1—C6	127.08 (11)	C7—C8—H8B	108
C1—N2—H2	120.0 (16)	H8A—C8—H8B	107
H1—N2—H2	120 (2)	O4—C9—H9A	109
C1—N2—H1	119.4 (15)	O4—C9—H9B	109
N2—C1—C2	121.08 (15)	C10—C9—H9A	109
O1—C1—N2	121.79 (15)	C10—C9—H9B	109
O1—C1—C2	117.12 (14)	H9A—C9—H9B	108
O4—Cu1—O1—C1	−101.07 (12)	Cu1—O1—C1—N2	178.58 (13)
O5—Cu1—O1—C1	−177.75 (12)	Cu1—O1—C1—C2	−0.16 (18)
O7—Cu1—O1—C1	95.97 (13)	Cu1—O2—C7—O3	−175.11 (14)
N1—Cu1—O1—C1	−1.43 (12)	Cu1—O2—C7—C8	6.6 (2)
O4—Cu1—O2—C7	−2.54 (13)	Cu1—O4—C8—C7	5.4 (2)
O5—Cu1—O2—C7	73.36 (13)	C9—O4—C8—C7	−105.2 (2)
O7—Cu1—O2—C7	159.88 (14)	Cu1—O4—C9—C10	−20.20 (16)
N1—Cu1—O2—C7	−101.65 (13)	C8—O4—C9—C10	91.13 (19)
O1—Cu1—O4—C8	174.68 (12)	Cu1—O5—C10—O6	−160.48 (14)
O1—Cu1—O4—C9	−65.25 (11)	Cu1—O5—C10—C9	18.0 (2)
O2—Cu1—O4—C8	−1.89 (12)	Cu1—N1—C2—C1	−3.65 (17)
O2—Cu1—O4—C9	118.18 (11)	Cu1—N1—C2—C3	−179.72 (13)
O5—Cu1—O4—C8	−97.97 (13)	C6—N1—C2—C1	174.91 (14)
O5—Cu1—O4—C9	22.11 (10)	C6—N1—C2—C3	−1.2 (2)
O7—Cu1—O4—C8	−61.9 (2)	Cu1—N1—C6—C5	178.63 (12)
O7—Cu1—O4—C9	58.2 (2)	C2—N1—C6—C5	0.3 (2)
N1—Cu1—O4—C8	93.28 (13)	O1—C1—C2—N1	2.6 (2)
N1—Cu1—O4—C9	−146.65 (10)	O1—C1—C2—C3	178.53 (16)
O1—Cu1—O5—C10	72.95 (13)	N2—C1—C2—N1	−176.16 (15)
O2—Cu1—O5—C10	−99.81 (13)	N2—C1—C2—C3	−0.2 (3)
O4—Cu1—O5—C10	−22.39 (12)	N1—C2—C3—C4	1.3 (2)
O7—Cu1—O5—C10	169.48 (14)	C1—C2—C3—C4	−174.25 (15)
O1—Cu1—N1—C2	2.90 (11)	C2—C3—C4—C5	−0.5 (2)
O1—Cu1—N1—C6	−175.52 (15)	C3—C4—C5—C6	−0.3 (3)
O2—Cu1—N1—C2	175.73 (11)	C4—C5—C6—N1	0.4 (3)
O2—Cu1—N1—C6	−2.69 (15)	O2—C7—C8—O4	−8.3 (3)
O4—Cu1—N1—C2	96.20 (11)	O3—C7—C8—O4	173.30 (18)
O4—Cu1—N1—C6	−82.22 (14)	O4—C9—C10—O5	6.2 (2)
O7—Cu1—N1—C2	−92.31 (12)	O4—C9—C10—O6	−175.28 (15)
O7—Cu1—N1—C6	89.28 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H1···O2^i	0.87 (2)	2.11 (2)	2.946 (2)	161 (2)
N2—H2···O5^ii	0.81 (2)	2.50 (2)	2.985 (2)	120 (2)
N2—H2···O6^ii	0.81 (2)	2.20 (2)	2.966 (2)	158 (2)
O7—H71···O6^iii	0.72 (3)	2.09 (3)	2.804 (3)	175 (3)
O7—H72···O2^iv	0.74 (4)	2.49 (4)	3.225 (2)	171 (4)
C3—H3···O6^ii	0.93	2.59	3.474 (2)	159
C5—H5···O3^v	0.93	2.60	3.251 (2)	128
C6—H6···O1^vi	0.93	2.35	3.248 (2)	162
C9—H9B···O3^i	0.97	2.50	3.399 (3)	154

Symmetry codes: (i) x−1/2, −y+3/2, z−1/2; (ii) −x+3/2, y−1/2, −z+1/2; (iii) x+1, y, z; (iv) −x+2, −y+2, −z+1; (v) −x+5/2, y−1/2, −z+3/2; (vi) x+1/2, −y+3/2, z+1/2.