(2-Aminopyrimidine-κN¹)aqua(pyridine-2,6-di­carboxylato-κ³O²,N,O⁶)copper(II): X-ray and DFT calculated structure

In the title compound, [Cu(C₇H₃N₂O₄)(C₄H₅N₂)(H₂O)], (I), pyridine-2,6-di­car­box­ylate (pydc²⁻), 2-aminopyrimidine and aqua ligands coordinate the Cu^II centre through two N atoms, two carboxylate O atoms and one water O atom, respectively, to give a nominally distorted square-pyramidal coordination geometry, a common arrangement for copper complexes containing the pydc²⁻ ligand. Because of the presence of Cu...X_bridged contacts (X = N or O) between adjacent molecules in the crystal structures of (I) and three analogous previously reported compounds, and the corresponding uncertainty about the effective coordination number of the Cu^II centre, density functional theory (DFT) calculations were used to elucidate the degree of covalency in these contacts. The calculated Wiberg and Mayer bond-order indices reveal that the Cu...O contact can be considered as a coordination bond, whereas the amine group forming a Cu...N contact is not an effective participant in the coordination environment.

S1. Experimental

S1.1. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1.

S2. Results and discussion

Computing details

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures

(2-Aminopyrimidine-κN¹)aqua(pyridine-2,6-dicarboxylato-κ³O²,N,O⁶)copper(II)

Crystal data

[Cu(C7H3N2O4)(C4H5N2)(H2O)]	Z = 2
Mr = 341.77	F(000) = 346
Triclinic, P1	Dx = 1.867 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.4376 (4) Å	Cell parameters from 4000 reflections
b = 8.0321 (4) Å	θ = 2.8–28.8°
c = 11.4220 (6) Å	µ = 1.83 mm^−1
α = 80.980 (4)°	T = 294 K
β = 87.261 (4)°	Prism, blue
γ = 64.488 (5)°	0.26 × 0.17 × 0.10 mm
V = 608.05 (5) Å^3

Data collection

Agilent Xcalibur Eos diffractometer	2797 independent reflections
Radiation source: Enhance (Mo) X-ray Source	2377 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
Detector resolution: 16.1544 pixels mm^-1	θmax = 28.8°, θmin = 2.8°
ω scans	h = −9→10
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)	k = −10→10
Tmin = 0.913, Tmax = 1.000	l = −15→15
8678 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.031	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0336P)^2 + 0.2457P] where P = (Fo^2 + 2Fc^2)/3
2797 reflections	(Δ/σ)max = 0.001
198 parameters	Δρmax = 0.37 e Å^−3
0 restraints	Δρmin = −0.30 e Å^−3

Special details

Experimental. Absorption correction: CrysAlisPro, Agilent Technologies, Version 1.171.35.4 Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) 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	0.58382 (4)	0.63364 (4)	0.27226 (2)	0.02800 (10)
N1	0.4559 (3)	0.4729 (2)	0.26850 (16)	0.0240 (4)
O1	0.7374 (2)	0.4895 (2)	0.14170 (15)	0.0368 (4)
O2	0.7335 (3)	0.2913 (2)	0.02734 (15)	0.0379 (4)
C1	0.6719 (3)	0.3808 (3)	0.1090 (2)	0.0274 (5)
C2	0.5024 (3)	0.3669 (3)	0.18306 (19)	0.0241 (4)
C3	0.4001 (4)	0.2635 (3)	0.1699 (2)	0.0328 (5)
H3A	0.4314	0.1891	0.1104	0.039*
C4	0.2490 (4)	0.2737 (3)	0.2479 (2)	0.0368 (6)
H4A	0.1762	0.2065	0.2401	0.044*
C5	0.2041 (3)	0.3827 (3)	0.3377 (2)	0.0319 (5)
H5A	0.1036	0.3882	0.3908	0.038*
C6	0.3134 (3)	0.4824 (3)	0.34576 (19)	0.0235 (4)
C7	0.2921 (3)	0.6128 (3)	0.4336 (2)	0.0266 (5)
O3	0.3991 (2)	0.7031 (2)	0.40966 (14)	0.0308 (4)
O4	0.1818 (2)	0.6234 (2)	0.51765 (15)	0.0377 (4)
N11	0.7311 (3)	0.7845 (3)	0.29023 (16)	0.0255 (4)
N12	0.9146 (3)	0.7348 (3)	0.1188 (2)	0.0397 (5)
H12A	1.000 (4)	0.751 (4)	0.077 (3)	0.040 (8)*
H12B	0.868 (4)	0.659 (4)	0.105 (3)	0.050 (8)*
C12	0.8681 (3)	0.8129 (3)	0.2162 (2)	0.0262 (5)
N13	0.9603 (3)	0.9186 (3)	0.23718 (18)	0.0321 (4)
C14	0.9059 (3)	1.0040 (3)	0.3312 (2)	0.0327 (5)
H14A	0.9664	1.0790	0.3459	0.039*
C15	0.7651 (3)	0.9885 (3)	0.4086 (2)	0.0337 (5)
H15A	0.7270	1.0527	0.4733	0.040*
C16	0.6844 (3)	0.8733 (3)	0.3851 (2)	0.0312 (5)
H16A	0.5923	0.8555	0.4374	0.037*
O1W	0.3478 (2)	0.8782 (2)	0.14239 (15)	0.0374 (4)
H1W	0.2332	0.9035	0.1683	0.049*
H2W	0.3575	0.8362	0.0818	0.049*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.03005 (16)	0.03724 (17)	0.02993 (17)	−0.02393 (13)	0.01428 (11)	−0.01781 (12)
N1	0.0244 (9)	0.0274 (9)	0.0243 (9)	−0.0143 (8)	0.0062 (7)	−0.0074 (8)
O1	0.0409 (9)	0.0491 (10)	0.0401 (10)	−0.0335 (8)	0.0211 (8)	−0.0258 (8)
O2	0.0448 (10)	0.0495 (10)	0.0340 (9)	−0.0297 (9)	0.0193 (8)	−0.0240 (8)
C1	0.0307 (11)	0.0325 (12)	0.0255 (11)	−0.0184 (10)	0.0086 (9)	−0.0106 (9)
C2	0.0266 (10)	0.0267 (11)	0.0232 (11)	−0.0147 (9)	0.0046 (9)	−0.0070 (9)
C3	0.0398 (13)	0.0354 (13)	0.0332 (13)	−0.0235 (11)	0.0070 (10)	−0.0130 (10)
C4	0.0416 (13)	0.0414 (14)	0.0445 (15)	−0.0323 (12)	0.0106 (11)	−0.0138 (12)
C5	0.0305 (12)	0.0359 (12)	0.0359 (13)	−0.0207 (10)	0.0098 (10)	−0.0071 (10)
C6	0.0231 (10)	0.0258 (10)	0.0240 (11)	−0.0127 (9)	0.0062 (8)	−0.0055 (9)
C7	0.0226 (10)	0.0321 (12)	0.0272 (12)	−0.0127 (9)	0.0059 (9)	−0.0090 (9)
O3	0.0326 (8)	0.0402 (9)	0.0313 (9)	−0.0235 (7)	0.0134 (7)	−0.0178 (7)
O4	0.0352 (9)	0.0501 (10)	0.0366 (10)	−0.0243 (8)	0.0192 (8)	−0.0189 (8)
N11	0.0249 (9)	0.0323 (10)	0.0262 (10)	−0.0175 (8)	0.0071 (7)	−0.0106 (8)
N12	0.0474 (13)	0.0593 (15)	0.0342 (12)	−0.0409 (12)	0.0210 (10)	−0.0209 (11)
C12	0.0230 (10)	0.0312 (11)	0.0272 (12)	−0.0141 (9)	0.0032 (9)	−0.0055 (9)
N13	0.0305 (10)	0.0393 (11)	0.0361 (11)	−0.0231 (9)	0.0075 (8)	−0.0101 (9)
C14	0.0315 (12)	0.0340 (12)	0.0414 (14)	−0.0205 (10)	0.0030 (10)	−0.0116 (11)
C15	0.0331 (12)	0.0389 (13)	0.0371 (14)	−0.0192 (11)	0.0064 (10)	−0.0185 (11)
C16	0.0286 (11)	0.0406 (13)	0.0317 (13)	−0.0194 (10)	0.0098 (10)	−0.0145 (10)
O1W	0.0408 (9)	0.0459 (10)	0.0360 (10)	−0.0260 (8)	0.0061 (8)	−0.0153 (8)

Geometric parameters (Å, º)

Cu1—N1	1.9112 (17)	C6—C7	1.516 (3)
Cu1—N11	1.9880 (17)	C7—O4	1.222 (3)
Cu1—O3	2.0175 (15)	C7—O3	1.284 (3)
Cu1—O1	2.0267 (16)	N11—C16	1.340 (3)
Cu1—O1W	2.3465 (17)	N11—C12	1.365 (3)
N1—C6	1.331 (3)	N12—C12	1.321 (3)
N1—C2	1.331 (3)	N12—H12A	0.82 (3)
O1—C1	1.275 (3)	N12—H12B	0.85 (3)
O2—C1	1.218 (3)	C12—N13	1.352 (3)
C1—C2	1.519 (3)	N13—C14	1.319 (3)
C2—C3	1.374 (3)	C14—C15	1.372 (3)
C3—C4	1.383 (3)	C14—H14A	0.9300
C3—H3A	0.9300	C15—C16	1.364 (3)
C4—C5	1.388 (3)	C15—H15A	0.9300
C4—H4A	0.9300	C16—H16A	0.9300
C5—C6	1.379 (3)	O1W—H1W	0.8368
C5—H5A	0.9300	O1W—H2W	0.8029
N1—Cu1—N11	174.43 (8)	N1—C6—C5	120.0 (2)
N1—Cu1—O3	80.07 (7)	N1—C6—C7	111.80 (17)
N11—Cu1—O3	98.26 (7)	C5—C6—C7	128.22 (19)
N1—Cu1—O1	79.79 (7)	O4—C7—O3	126.3 (2)
N11—Cu1—O1	101.38 (7)	O4—C7—C6	120.16 (19)
O3—Cu1—O1	159.40 (6)	O3—C7—C6	113.59 (18)
N1—Cu1—O1W	93.49 (7)	C7—O3—Cu1	115.69 (14)
N11—Cu1—O1W	91.85 (7)	C16—N11—C12	116.53 (18)
O3—Cu1—O1W	91.03 (6)	C16—N11—Cu1	115.40 (14)
O1—Cu1—O1W	94.48 (7)	C12—N11—Cu1	128.03 (15)
C6—N1—C2	122.75 (18)	C12—N12—H12A	117.5 (19)
C6—N1—Cu1	118.48 (14)	C12—N12—H12B	121 (2)
C2—N1—Cu1	118.55 (14)	H12A—N12—H12B	121 (3)
C1—O1—Cu1	115.47 (14)	N12—C12—N13	117.5 (2)
O2—C1—O1	126.1 (2)	N12—C12—N11	119.3 (2)
O2—C1—C2	119.90 (19)	N13—C12—N11	123.2 (2)
O1—C1—C2	113.96 (18)	C14—N13—C12	117.3 (2)
N1—C2—C3	120.5 (2)	N13—C14—C15	123.6 (2)
N1—C2—C1	111.58 (17)	N13—C14—H14A	118.2
C3—C2—C1	127.9 (2)	C15—C14—H14A	118.2
C2—C3—C4	117.8 (2)	C16—C15—C14	116.0 (2)
C2—C3—H3A	121.1	C16—C15—H15A	122.0
C4—C3—H3A	121.1	C14—C15—H15A	122.0
C3—C4—C5	121.1 (2)	N11—C16—C15	123.3 (2)
C3—C4—H4A	119.4	N11—C16—H16A	118.4
C5—C4—H4A	119.4	C15—C16—H16A	118.4
C6—C5—C4	117.9 (2)	Cu1—O1W—H1W	109.7
C6—C5—H5A	121.1	Cu1—O1W—H2W	104.5
C4—C5—H5A	121.1	H1W—O1W—H2W	108.5

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N12—H12A···O2^i	0.82 (3)	2.19 (3)	2.984 (3)	164 (3)
N12—H12B···O1	0.85 (3)	1.98 (3)	2.780 (3)	157 (3)
O1W—H1W···N13^ii	0.84	2.10	2.931 (2)	170
O1W—H2W···O2^iii	0.80	2.03	2.761 (2)	150

Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) −x+1, −y+1, −z.