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Acta Crystallogr Sect E Struct Rep Online. 2008 July 1; 64(Pt 7): m969.
Published online 2008 June 28. doi:  10.1107/S1600536808018771
PMCID: PMC2961748

cis-Aqua­dichlorido[pyrimidin-2(1H)-one-κN 3]copper(II)

Abstract

In the title compound, [CuCl2(C4H4N2O)(H2O)], the CuII cation is coordinated by two chloride anions, one pyrimidin-2-one N atom and one water mol­ecule, giving a slightly distorted square-planar geometry. In the crystal structure, the pyrimidin-2-one rings stack along the b axis, with an inter­planar distance of 3.306 Å, as do the copper coordination planes (inter­planar spacing = 2.998 Å). The coordination around the Jahn–Teller-distorted CuII ion is completed by long Cu(...)O [3.014 (5) Å] and Cu(...)Cl [3.0194 (15) Å] inter­actions with adjacent mol­ecules involved in this stacking. Several N—H(...)Cl, O—H(...)Cl and O—H(...)O inter­molecular hydrogen bonds form a polar three-dimensional network.

Related literature

A similar coordination environment and geometry about the copper atom was described by Crass et al. (1996 [triangle]) for [Cu(C12H18N4)Cl2(H2O)2].

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Object name is e-64-0m969-scheme1.jpg

Experimental

Crystal data

  • [CuCl2(C4H4N2O)(H2O)]
  • M r = 248.53
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m969-efi1.jpg
  • a = 9.6104 (4) Å
  • b = 3.7942 (2) Å
  • c = 10.7375 (4) Å
  • β = 107.991 (4)°
  • V = 372.39 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 3.59 mm−1
  • T = 100 (2) K
  • 0.28 × 0.08 × 0.06 mm

Data collection

  • Oxford Diffraction Gemini-R Ultra diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 [triangle]) T min = 0.739, T max = 0.810
  • 6373 measured reflections
  • 1866 independent reflections
  • 1462 reflections with I > 2σ(I)
  • R int = 0.046

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 0.098
  • S = 1.01
  • 1866 reflections
  • 106 parameters
  • 4 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.73 e Å−3
  • Δρmin = −0.67 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 765 Friedel pairs
  • Flack parameter: 0.03 (2)

Data collection: CrysAlis CCD (Oxford Diffraction, 2007 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2007 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Selected bond lengths (Å)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808018771/fj2126sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808018771/fj2126Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

MAK thanks Bayero University, Kano, Nigeria, for funding. Oxford Diffraction Ltd are thanked for the loan of an Oxford Gemini-R Ultra diffractometer to the University of Bristol.

supplementary crystallographic information

Comment

Mechanochemistry is a technique currently attracting increasing interest, in part because of its potential to offer an environmentally friendly and sustainable means for solid state synthesis. We sought to broaden the scope of this still relatively under-utilized technique by reacting CuCl2.2H2O and 2-hydroxypyrimidine hydrochloride under mechanochemical conditions to synthesize [C4H5N2O]2[CuCl4]. However, the title compound I was obtained instead, and crystal structure determination at 100 (2) K revealed a square planar molecule in the polar space group Pn. Crass et al. (1996) reported the structure of a related compound [Cu(C12H18N4)Cl2(H2O)2] with a similar type of coordination environment at copper but a different hydrogen bonding network.

Experimental

CuCl2.2H2O and 2-hydroxypyrimidine hydrochloride in a 1:2 molar ratio were ground in an agate mortar. The resulting powder was dissolved in acetonitrile and the solution left to evaporate slowly at room temperature. Green, needle-like crystals of the title compound were obtained after a few days.

Refinement

H atoms bonded to O atom were located in the difference map and refined with distance restraints of O—H = 0.84 (2) Å with Uiso(H) = 1.2Ueq(O). Other H atoms were positioned geometrically and refined using a riding model, with C—H = 0.93 Å and N—H = 0.86 Å, with Uiso(H) = 1.2 times Ueq(C, N).

Figures

Fig. 1.
The molecular stucture of I with atom labels and 50% probability displacement ellipsoids for non-H atoms.
Fig. 2.
Packing of I viewed down the b axis showing the polar packing with various N—H···Cl, O—H···Cl and O—H···O intermolecular hydrogen bonds.
Fig. 3.
π—π stacking of I viewed along the b axis.

Crystal data

[CuCl2(C4H4N2O)(H2O)]F000 = 246
Mr = 248.53Dx = 2.217 Mg m3
Monoclinic, PnMo Kα radiation λ = 0.71073 Å
Hall symbol: P -2yacCell parameters from 2806 reflections
a = 9.6104 (4) Åθ = 2.2–30.0º
b = 3.7942 (2) ŵ = 3.59 mm1
c = 10.7375 (4) ÅT = 100 (2) K
β = 107.991 (4)ºNeedle, green
V = 372.39 (3) Å30.28 × 0.08 × 0.06 mm
Z = 2

Data collection

Oxford Diffraction Gemini-R Ultra diffractometer1866 independent reflections
Radiation source: fine-focus sealed tube1462 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.046
T = 100(2) Kθmax = 30.1º
1° wide ω scansθmin = 2.5º
Absorption correction: multi-scan(CrysAlis RED; Oxford Diffraction, 2007)h = −13→13
Tmin = 0.739, Tmax = 0.810k = −5→5
6373 measured reflectionsl = −12→15

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.033  w = 1/[σ2(Fo2) + (0.0567P)2] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.098(Δ/σ)max < 0.001
S = 1.01Δρmax = 0.73 e Å3
1866 reflectionsΔρmin = −0.67 e Å3
106 parametersExtinction correction: none
4 restraintsAbsolute structure: Flack (1983), 767 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.03 (2)
Secondary atom site location: difference Fourier map

Special details

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.32.5 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 (Å2)

xyzUiso*/Ueq
Cu10.12489 (4)0.17338 (18)0.33630 (4)0.01410 (18)
Cl10.34639 (14)0.2487 (4)0.31142 (14)0.0148 (3)
Cl20.01546 (13)0.5320 (4)0.16807 (13)0.0144 (3)
N1−0.0593 (5)0.1582 (12)0.3924 (5)0.0113 (10)
N2−0.1732 (5)0.2409 (12)0.5539 (4)0.0141 (9)
H2B−0.16980.32000.62980.017*
O10.0558 (4)0.4563 (11)0.5852 (4)0.0168 (8)
O20.2175 (4)−0.1468 (12)0.4838 (4)0.0200 (9)
H20.308 (3)−0.20 (2)0.511 (7)0.024*
H10.183 (7)−0.239 (18)0.539 (5)0.024*
C1−0.0520 (6)0.2951 (15)0.5126 (5)0.0120 (11)
C2−0.1804 (5)0.0019 (14)0.3222 (6)0.0128 (11)
H2A−0.1849−0.07990.23940.015*
C3−0.2949 (6)0.0750 (15)0.4845 (6)0.0157 (12)
H3A−0.37280.04500.51770.019*
C4−0.3019 (6)−0.0484 (15)0.3644 (5)0.0147 (11)
H4A−0.3850−0.16280.31200.018*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cu10.0126 (3)0.0189 (3)0.0130 (3)0.0033 (3)0.0072 (2)0.0032 (3)
Cl10.0113 (6)0.0206 (7)0.0134 (7)0.0007 (5)0.0054 (5)0.0018 (5)
Cl20.0147 (5)0.0155 (7)0.0137 (6)0.0025 (5)0.0053 (5)0.0039 (6)
N10.011 (2)0.009 (2)0.017 (2)−0.0004 (17)0.0093 (19)−0.0011 (19)
N20.017 (2)0.019 (2)0.007 (2)−0.0019 (18)0.0043 (17)−0.0007 (18)
O10.0177 (18)0.017 (2)0.0130 (18)−0.0032 (16)0.0012 (15)0.0008 (16)
O20.0140 (19)0.028 (3)0.022 (2)0.0025 (18)0.0117 (17)0.0089 (19)
C10.010 (2)0.015 (3)0.009 (2)0.001 (2)−0.0006 (19)0.002 (2)
C20.013 (2)0.011 (3)0.012 (2)0.006 (2)0.001 (2)0.001 (2)
C30.023 (3)0.012 (3)0.019 (3)0.004 (2)0.014 (2)0.003 (2)
C40.015 (3)0.014 (3)0.013 (3)0.002 (2)0.001 (2)0.000 (2)

Geometric parameters (Å, °)

Cu1—O21.976 (4)O1—C11.247 (7)
Cu1—N12.040 (4)O2—H20.85 (5)
Cu1—Cl12.2440 (14)O2—H10.84 (5)
Cu1—Cl22.2466 (14)C2—C41.390 (8)
N1—C21.316 (7)C2—H2A0.9300
N1—C11.372 (7)C3—C41.354 (8)
N2—C31.335 (7)C3—H3A0.9300
N2—C11.384 (7)C4—H4A0.9300
N2—H2B0.8600
O2—Cu1—N187.87 (17)H2—O2—H1104 (7)
O2—Cu1—Cl187.99 (12)O1—C1—N1124.4 (5)
N1—Cu1—Cl1168.71 (13)O1—C1—N2119.4 (5)
O2—Cu1—Cl2178.89 (13)N1—C1—N2116.2 (5)
N1—Cu1—Cl291.22 (14)N1—C2—C4124.0 (5)
Cl1—Cu1—Cl293.03 (5)N1—C2—H2A118.0
C2—N1—C1119.3 (5)C4—C2—H2A118.0
C2—N1—Cu1122.5 (4)N2—C3—C4118.1 (5)
C1—N1—Cu1118.0 (4)N2—C3—H3A120.9
C3—N2—C1124.8 (5)C4—C3—H3A120.9
C3—N2—H2B117.6C3—C4—C2117.6 (5)
C1—N2—H2B117.6C3—C4—H4A121.2
Cu1—O2—H2125 (5)C2—C4—H4A121.2
Cu1—O2—H1130 (5)
O2—Cu1—N1—C2−111.0 (4)Cu1—N1—C1—N2−172.3 (4)
Cl1—Cu1—N1—C2−179.5 (5)C3—N2—C1—O1179.5 (5)
Cl2—Cu1—N1—C268.4 (4)C3—N2—C1—N1−1.5 (8)
O2—Cu1—N1—C164.2 (4)C1—N1—C2—C4−2.8 (8)
Cl1—Cu1—N1—C1−4.3 (10)Cu1—N1—C2—C4172.3 (4)
Cl2—Cu1—N1—C1−116.4 (4)C1—N2—C3—C4−0.5 (8)
C2—N1—C1—O1−178.0 (5)N2—C3—C4—C20.9 (8)
Cu1—N1—C1—O16.6 (7)N1—C2—C4—C30.7 (8)
C2—N1—C1—N23.1 (7)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2B···Cl1i0.862.513.333 (5)160
O2—H2···Cl2ii0.85 (2)2.52 (4)3.279 (4)149 (7)
O2—H1···O1iii0.84 (2)1.86 (4)2.629 (6)152 (7)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FJ2126).

References

  • Crass, J., Baker, A. & Craig, D. (1996). Gazz. Chim. Ital.126, 765–770.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography