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cis-Aqua­di­chlorido[pyrimidin-2(1H)-one-κN3]copper(II)

aSchool of Chemistry, University of Bristol, Bristol BS8 1TS, England
*Correspondence e-mail: guy.orpen@bristol.ac.uk

(Received 9 June 2008; accepted 20 June 2008; online 28 June 2008)

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[Crass, J., Baker, A. & Craig, D. (1996). Gazz. Chim. Ital. 126, 765-770.]) for [Cu(C12H18N4)Cl2(H2O)2].

[Scheme 1]

Experimental

Crystal data
  • [CuCl2(C4H4N2O)(H2O)]

  • Mr = 248.53

  • Monoclinic, P n

  • 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[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) Tmin = 0.739, Tmax = 0.810

  • 6373 measured reflections

  • 1866 independent reflections

  • 1462 reflections with I > 2σ(I)

  • Rint = 0.046

Refinement
  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 765 Friedel pairs

  • Flack parameter: 0.03 (2)

Table 1
Selected bond lengths (Å)

Cu1—O2 1.976 (4)
Cu1—N1 2.040 (4)
Cu1—Cl1 2.2440 (14)
Cu1—Cl2 2.2466 (14)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2B⋯Cl1i 0.86 2.51 3.333 (5) 160
O2—H2⋯Cl2ii 0.85 (2) 2.52 (4) 3.279 (4) 149 (7)
O2—H1⋯O1iii 0.84 (2) 1.86 (4) 2.629 (6) 152 (7)
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]; (ii) [x+{\script{1\over 2}}, -y, z+{\script{1\over 2}}]; (iii) x, y-1, z.

Data collection: CrysAlis CCD (Oxford Diffraction, 2007[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2007[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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 top

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).

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular stucture of I with atom labels and 50% probability displacement ellipsoids for non-H atoms.
[Figure 2] 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.
[Figure 3] Fig. 3. ππ stacking of I viewed along the b axis.
cis-Aquadichlorido[pyrimidin-2(1H)-one-κN3]copper(II) top
Crystal data top
[CuCl2(C4H4N2O)(H2O)]F(000) = 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 = 2.2–30.0°
b = 3.7942 (2) ŵ = 3.59 mm1
c = 10.7375 (4) ÅT = 100 K
β = 107.991 (4)°Needle, green
V = 372.39 (3) Å30.28 × 0.08 × 0.06 mm
Z = 2
Data collection top
Oxford Diffraction Gemini-R Ultra
diffractometer
1866 independent reflections
Radiation source: fine-focus sealed tube1462 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
1° wide ω scansθmax = 30.1°, θmin = 2.5°
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2007)
h = 1313
Tmin = 0.739, Tmax = 0.810k = 55
6373 measured reflectionsl = 1215
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.098 w = 1/[σ2(Fo2) + (0.0567P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
1866 reflectionsΔρmax = 0.73 e Å3
106 parametersΔρmin = 0.67 e Å3
4 restraintsAbsolute structure: Flack (1983), 767 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.03 (2)
Crystal data top
[CuCl2(C4H4N2O)(H2O)]V = 372.39 (3) Å3
Mr = 248.53Z = 2
Monoclinic, PnMo Kα radiation
a = 9.6104 (4) ŵ = 3.59 mm1
b = 3.7942 (2) ÅT = 100 K
c = 10.7375 (4) Å0.28 × 0.08 × 0.06 mm
β = 107.991 (4)°
Data collection top
Oxford Diffraction Gemini-R Ultra
diffractometer
1866 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2007)
1462 reflections with I > 2σ(I)
Tmin = 0.739, Tmax = 0.810Rint = 0.046
6373 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.033H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.098Δρmax = 0.73 e Å3
S = 1.01Δρmin = 0.67 e Å3
1866 reflectionsAbsolute structure: Flack (1983), 767 Friedel pairs
106 parametersAbsolute structure parameter: 0.03 (2)
4 restraints
Special details top

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) top
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)
N10.0593 (5)0.1582 (12)0.3924 (5)0.0113 (10)
N20.1732 (5)0.2409 (12)0.5539 (4)0.0141 (9)
H2B0.16980.32000.62980.017*
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*
C10.0520 (6)0.2951 (15)0.5126 (5)0.0120 (11)
C20.1804 (5)0.0019 (14)0.3222 (6)0.0128 (11)
H2A0.18490.07990.23940.015*
C30.2949 (6)0.0750 (15)0.4845 (6)0.0157 (12)
H3A0.37280.04500.51770.019*
C40.3019 (6)0.0484 (15)0.3644 (5)0.0147 (11)
H4A0.38500.16280.31200.018*
Atomic displacement parameters (Å2) top
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, º) top
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—C2111.0 (4)Cu1—N1—C1—N2172.3 (4)
Cl1—Cu1—N1—C2179.5 (5)C3—N2—C1—O1179.5 (5)
Cl2—Cu1—N1—C268.4 (4)C3—N2—C1—N11.5 (8)
O2—Cu1—N1—C164.2 (4)C1—N1—C2—C42.8 (8)
Cl1—Cu1—N1—C14.3 (10)Cu1—N1—C2—C4172.3 (4)
Cl2—Cu1—N1—C1116.4 (4)C1—N2—C3—C40.5 (8)
C2—N1—C1—O1178.0 (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, º) top
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) x1/2, y+1, z+1/2; (ii) x+1/2, y, z+1/2; (iii) x, y1, z.

Experimental details

Crystal data
Chemical formula[CuCl2(C4H4N2O)(H2O)]
Mr248.53
Crystal system, space groupMonoclinic, Pn
Temperature (K)100
a, b, c (Å)9.6104 (4), 3.7942 (2), 10.7375 (4)
β (°) 107.991 (4)
V3)372.39 (3)
Z2
Radiation typeMo Kα
µ (mm1)3.59
Crystal size (mm)0.28 × 0.08 × 0.06
Data collection
DiffractometerOxford Diffraction Gemini-R Ultra
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2007)
Tmin, Tmax0.739, 0.810
No. of measured, independent and
observed [I > 2σ(I)] reflections
6373, 1866, 1462
Rint0.046
(sin θ/λ)max1)0.705
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.098, 1.01
No. of reflections1866
No. of parameters106
No. of restraints4
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.73, 0.67
Absolute structureFlack (1983), 767 Friedel pairs
Absolute structure parameter0.03 (2)

Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Selected bond lengths (Å) top
Cu1—O21.976 (4)Cu1—Cl12.2440 (14)
Cu1—N12.040 (4)Cu1—Cl22.2466 (14)
Hydrogen-bond geometry (Å, º) top
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) x1/2, y+1, z+1/2; (ii) x+1/2, y, z+1/2; (iii) x, y1, z.
 

Acknowledgements

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.

References

First citationCrass, J., Baker, A. & Craig, D. (1996). Gazz. Chim. Ital. 126, 765–770.  CAS Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationOxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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