Redetermination of bis(2-amino­pyrimidine)­bis(nitrato)copper(II)

The crystal structure of the title compound, [Cu(NO₃)₂(C₄H₅N₃)], at room temperature was reported earlier, but full results were not published. According to the present study at 193 K, the Cu^II atom occupies a special position at an inversion centre and has a distorted octahedral geometry. The basal plane is formed by two N atoms of two 2-amino­pyrimidine mol­ecules and two O atoms of two trans-oriented nitrate anions. The apical positions are occupied by the remaining O atoms of the chelating nitrate groups. The hydrogen bond, formed by an amino group and the uncoordinated pyrimidine N atom of a 2-amino­pyrimidine ligand of the neighbouring mol­ecule of the complex, gives rise to Watson-Crick-type pairwise aggregation of amino­pyrimidine ligands, thus creating infinite chains of mol­ecules of the complex stretching along the [10] direction in the crystal. The chains are further interconnected into layers parallel to the x0z plane, due to additional hydrogen bonds involving the second H atom of the amino group of the 2-amino­pyrimidine ligand and the O atom of the nitrate anion of the neighbouring mol­ecule.

Key indicators

• Single-crystal X-ray study
• T = 193 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.034
• wR factor = 0.100
• Data-to-parameter ratio = 11.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



CELLV_02  Alert C The supplied cell volume s.u. differs from that
          calculated from the cell parameter s.u.'s by > 2
          Calculated cell volume su =      15.04
          Cell volume su given      =      13.00

PLAT_732  Alert C Angle   Calc    90.38(8), Rep    90.37(2) ....       4.00 s.u-Ratio
                     N11  -CU1  -O12     1.555   1.555   1.555


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 2 Alert Level C = Please check

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Computing details

Data collection: CAD-4 Software (Enraf-Nonius, 1985); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL-PC (Sheldrick, 1995); software used to prepare material for publication: SHELXL97.

(I)

Crystal data

[Cu(NO3)2(C4H5N3)]	Z = 1
Mr = 377.78	F(000) = 191
Triclinic, P1	Dx = 1.880 Mg m^−3
a = 5.691 (1) Å	Cu Kα radiation, λ = 1.54180 Å
b = 7.091 (2) Å	Cell parameters from 25 reflections
c = 8.983 (2) Å	θ = 12–27°
α = 81.02 (3)°	µ = 2.82 mm^−1
β = 81.46 (3)°	T = 193 K
γ = 69.51 (3)°	Plate, purple
V = 333.68 (13) Å^3	0.50 × 0.20 × 0.06 mm

Data collection

Enraf-nonius CAD-4 diffractometer	1164 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.042
Graphite monochromator	θmax = 66.9°, θmin = 5.0°
ω–2θ scans	h = −6→6
Absorption correction: ψ scan (North et al., 1968)	k = −8→8
Tmin = 0.580, Tmax = 0.844	l = −10→10
2565 measured reflections	3 standard reflections every 200 reflections
1177 independent reflections	intensity decay: 2.0%

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)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.100	H-atom parameters constrained
S = 0.81	w = 1/[σ^2(Fo^2) + (0.0864P)^2 + 0.6111P] where P = (Fo^2 + 2Fc^2)/3
1177 reflections	(Δ/σ)max < 0.001
106 parameters	Δρmax = 0.59 e Å^−3
0 restraints	Δρmin = −0.51 e Å^−3

Special details

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	0.5000	0.5000	0.5000	0.0186 (2)
N11	0.5748 (4)	0.3868 (3)	0.3024 (2)	0.0202 (4)
C12	0.7395 (4)	0.4280 (4)	0.1862 (3)	0.0213 (5)
N13	0.7939 (4)	0.3443 (3)	0.0557 (2)	0.0258 (5)
C14	0.6782 (6)	0.2166 (4)	0.0410 (3)	0.0317 (6)
H14A	0.7144	0.1566	−0.0485	0.038*
C15	0.5054 (5)	0.1679 (4)	0.1526 (3)	0.0328 (6)
H15A	0.4238	0.0797	0.1391	0.039*
C16	0.4617 (5)	0.2561 (4)	0.2828 (3)	0.0256 (5)
H16A	0.3498	0.2248	0.3609	0.031*
N17	0.8545 (4)	0.5579 (4)	0.1997 (2)	0.0307 (5)
H17A	0.9582	0.5848	0.1267	0.037*
H17B	0.8251	0.6150	0.2814	0.037*
N1	0.1513 (4)	0.8182 (3)	0.3861 (2)	0.0252 (5)
O11	0.3881 (3)	0.7814 (3)	0.3944 (2)	0.0260 (4)
O12	0.0615 (3)	0.6844 (3)	0.4462 (2)	0.0316 (4)
O13	0.0305 (4)	0.9793 (3)	0.3199 (3)	0.0462 (6)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0175 (3)	0.0212 (3)	0.0152 (3)	−0.0044 (2)	−0.00064 (19)	−0.00264 (19)
N11	0.0152 (9)	0.0260 (10)	0.0183 (9)	−0.0059 (8)	−0.0007 (7)	−0.0027 (8)
C12	0.0172 (11)	0.0267 (12)	0.0191 (11)	−0.0056 (9)	−0.0029 (9)	−0.0028 (9)
N13	0.0249 (11)	0.0346 (11)	0.0203 (10)	−0.0125 (9)	0.0007 (8)	−0.0071 (9)
C14	0.0397 (15)	0.0390 (15)	0.0225 (13)	−0.0196 (12)	0.0022 (11)	−0.0111 (11)
C15	0.0368 (15)	0.0407 (15)	0.0302 (14)	−0.0236 (13)	−0.0003 (11)	−0.0093 (12)
C16	0.0235 (12)	0.0307 (13)	0.0239 (12)	−0.0116 (10)	−0.0003 (10)	−0.0027 (10)
N17	0.0332 (12)	0.0467 (14)	0.0213 (10)	−0.0252 (11)	0.0085 (9)	−0.0136 (10)
N1	0.0241 (11)	0.0278 (11)	0.0200 (10)	−0.0028 (9)	−0.0030 (8)	−0.0051 (9)
O11	0.0227 (9)	0.0273 (9)	0.0260 (9)	−0.0067 (7)	−0.0018 (7)	−0.0018 (7)
O12	0.0271 (10)	0.0403 (11)	0.0311 (10)	−0.0145 (8)	−0.0023 (8)	−0.0078 (8)
O13	0.0400 (12)	0.0385 (12)	0.0422 (12)	0.0076 (10)	−0.0126 (10)	0.0066 (10)

Geometric parameters (Å, º)

Cu1—N11^i	1.989 (2)	C14—C15	1.389 (4)
Cu1—N11	1.989 (2)	C14—H14A	0.930
Cu1—O11^i	1.9965 (19)	C15—C16	1.362 (4)
Cu1—O11	1.9965 (19)	C15—H15A	0.930
Cu1—O12	2.459 (2)	C16—H16A	0.930
N11—C16	1.344 (3)	N17—H17A	0.860
N11—C12	1.363 (3)	N17—H17B	0.860
C12—N17	1.332 (3)	N1—O13	1.221 (3)
C12—N13	1.343 (3)	N1—O12	1.245 (3)
N13—C14	1.323 (4)	N1—O11	1.291 (3)
N11^i—Cu1—N11	180.0	N13—C14—H14A	118.4
N11^i—Cu1—O11^i	90.57 (8)	C15—C14—H14A	118.4
N11—Cu1—O11^i	89.43 (8)	C16—C15—C14	116.5 (2)
N11^i—Cu1—O11	89.43 (8)	C16—C15—H15A	121.8
N11—Cu1—O11	90.57 (8)	C14—C15—H15A	121.8
N11—Cu1—O12	90.37 (2)	N11—C16—C15	122.3 (2)
O11^i—Cu1—O11	180.0	N11—C16—H16A	118.9
C16—N11—C12	117.3 (2)	C15—C16—H16A	118.9
C16—N11—Cu1	118.18 (16)	C12—N17—H17A	120.0
C12—N11—Cu1	124.46 (16)	C12—N17—H17B	120.0
N17—C12—N13	117.0 (2)	H17A—N17—H17B	120.0
N17—C12—N11	119.6 (2)	O13—N1—O12	124.2 (2)
N13—C12—N11	123.5 (2)	O13—N1—O11	118.7 (2)
C14—N13—C12	117.2 (2)	O12—N1—O11	117.1 (2)
N13—C14—C15	123.2 (2)	N1—O11—Cu1	103.11 (14)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N17—H17A···N13^ii	0.86	2.12	2.976 (3)	179
N17—H17B···O11	0.86	2.49	3.026 (3)	122
N17—H17B···O12^iii	0.86	2.35	3.037 (3)	137

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