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

Kurawa, M.A.; Adams, C.J.; Orpen, A.G.

doi:10.1107/S1600536808018771

metal-organic compounds

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ISSN: 2056-9890

Volume 64| Part 7| July 2008| Page m969

doi:10.1107/S1600536808018771

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

Mukhtar A. Kurawa,^a Christopher J. Adams ^a and A. Guy Orpen ^a ^*

^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 Cu^II 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 Cu^II 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 ) for [Cu(C₁₂H₁₈N₄)Cl₂(H₂O)₂].

Experimental

Crystal data

[CuCl₂(C₄H₄N₂O)(H₂O)]
M_r = 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 $[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ) 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[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
Δρ_max = 0.73 e Å⁻³
Δρ_min = −0.67 e Å⁻³
Absolute structure: Flack (1983 ), 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	D⋯A	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 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

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

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

checkCIF report

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.

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

	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.

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

Crystal data top

[CuCl₂(C₄H₄N₂O)(H₂O)]	F(000) = 246
M_r = 248.53	D_x = 2.217 Mg m⁻³
Monoclinic, Pn	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P -2yac	Cell parameters from 2806 reflections
a = 9.6104 (4) Å	θ = 2.2–30.0°
b = 3.7942 (2) Å	µ = 3.59 mm⁻¹
c = 10.7375 (4) Å	T = 100 K
β = 107.991 (4)°	Needle, green
V = 372.39 (3) Å³	0.28 × 0.08 × 0.06 mm
Z = 2

Data collection top

Oxford Diffraction Gemini-R Ultra diffractometer	1866 independent reflections
Radiation source: fine-focus sealed tube	1462 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.046
1° wide ω scans	θ_max = 30.1°, θ_min = 2.5°
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007)	h = −13→13
T_min = 0.739, T_max = 0.810	k = −5→5
6373 measured reflections	l = −12→15

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.033	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.098	w = 1/[σ²(F_o²) + (0.0567P)²] where P = (F_o² + 2F_c²)/3
S = 1.01	(Δ/σ)_max < 0.001
1866 reflections	Δρ_max = 0.73 e Å⁻³
106 parameters	Δρ_min = −0.67 e Å⁻³
4 restraints	Absolute structure: Flack (1983), 767 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.03 (2)

Crystal data top

[CuCl₂(C₄H₄N₂O)(H₂O)]	V = 372.39 (3) Å³
M_r = 248.53	Z = 2
Monoclinic, Pn	Mo Kα radiation
a = 9.6104 (4) Å	µ = 3.59 mm⁻¹
b = 3.7942 (2) Å	T = 100 K
c = 10.7375 (4) Å	0.28 × 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)
T_min = 0.739, T_max = 0.810	R_int = 0.046
6373 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.098	Δρ_max = 0.73 e Å⁻³
S = 1.01	Δρ_min = −0.67 e Å⁻³
1866 reflections	Absolute structure: Flack (1983), 767 Friedel pairs
106 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
Cu1	0.12489 (4)	0.17338 (18)	0.33630 (4)	0.01410 (18)
Cl1	0.34639 (14)	0.2487 (4)	0.31142 (14)	0.0148 (3)
Cl2	0.01546 (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	−0.1698	0.3200	0.6298	0.017*
O1	0.0558 (4)	0.4563 (11)	0.5852 (4)	0.0168 (8)
O2	0.2175 (4)	−0.1468 (12)	0.4838 (4)	0.0200 (9)
H2	0.308 (3)	−0.20 (2)	0.511 (7)	0.024*
H1	0.183 (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	−0.0799	0.2394	0.015*
C3	−0.2949 (6)	0.0750 (15)	0.4845 (6)	0.0157 (12)
H3A	−0.3728	0.0450	0.5177	0.019*
C4	−0.3019 (6)	−0.0484 (15)	0.3644 (5)	0.0147 (11)
H4A	−0.3850	−0.1628	0.3120	0.018*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cu1	0.0126 (3)	0.0189 (3)	0.0130 (3)	0.0033 (3)	0.0072 (2)	0.0032 (3)
Cl1	0.0113 (6)	0.0206 (7)	0.0134 (7)	0.0007 (5)	0.0054 (5)	0.0018 (5)
Cl2	0.0147 (5)	0.0155 (7)	0.0137 (6)	0.0025 (5)	0.0053 (5)	0.0039 (6)
N1	0.011 (2)	0.009 (2)	0.017 (2)	−0.0004 (17)	0.0093 (19)	−0.0011 (19)
N2	0.017 (2)	0.019 (2)	0.007 (2)	−0.0019 (18)	0.0043 (17)	−0.0007 (18)
O1	0.0177 (18)	0.017 (2)	0.0130 (18)	−0.0032 (16)	0.0012 (15)	0.0008 (16)
O2	0.0140 (19)	0.028 (3)	0.022 (2)	0.0025 (18)	0.0117 (17)	0.0089 (19)
C1	0.010 (2)	0.015 (3)	0.009 (2)	0.001 (2)	−0.0006 (19)	0.002 (2)
C2	0.013 (2)	0.011 (3)	0.012 (2)	0.006 (2)	0.001 (2)	0.001 (2)
C3	0.023 (3)	0.012 (3)	0.019 (3)	0.004 (2)	0.014 (2)	0.003 (2)
C4	0.015 (3)	0.014 (3)	0.013 (3)	0.002 (2)	0.001 (2)	0.000 (2)

Geometric parameters (Å, º) top

Cu1—O2	1.976 (4)	O1—C1	1.247 (7)
Cu1—N1	2.040 (4)	O2—H2	0.85 (5)
Cu1—Cl1	2.2440 (14)	O2—H1	0.84 (5)
Cu1—Cl2	2.2466 (14)	C2—C4	1.390 (8)
N1—C2	1.316 (7)	C2—H2A	0.9300
N1—C1	1.372 (7)	C3—C4	1.354 (8)
N2—C3	1.335 (7)	C3—H3A	0.9300
N2—C1	1.384 (7)	C4—H4A	0.9300
N2—H2B	0.8600

O2—Cu1—N1	87.87 (17)	H2—O2—H1	104 (7)
O2—Cu1—Cl1	87.99 (12)	O1—C1—N1	124.4 (5)
N1—Cu1—Cl1	168.71 (13)	O1—C1—N2	119.4 (5)
O2—Cu1—Cl2	178.89 (13)	N1—C1—N2	116.2 (5)
N1—Cu1—Cl2	91.22 (14)	N1—C2—C4	124.0 (5)
Cl1—Cu1—Cl2	93.03 (5)	N1—C2—H2A	118.0
C2—N1—C1	119.3 (5)	C4—C2—H2A	118.0
C2—N1—Cu1	122.5 (4)	N2—C3—C4	118.1 (5)
C1—N1—Cu1	118.0 (4)	N2—C3—H3A	120.9
C3—N2—C1	124.8 (5)	C4—C3—H3A	120.9
C3—N2—H2B	117.6	C3—C4—C2	117.6 (5)
C1—N2—H2B	117.6	C3—C4—H4A	121.2
Cu1—O2—H2	125 (5)	C2—C4—H4A	121.2
Cu1—O2—H1	130 (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—O1	179.5 (5)
Cl2—Cu1—N1—C2	68.4 (4)	C3—N2—C1—N1	−1.5 (8)
O2—Cu1—N1—C1	64.2 (4)	C1—N1—C2—C4	−2.8 (8)
Cl1—Cu1—N1—C1	−4.3 (10)	Cu1—N1—C2—C4	172.3 (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—C2	0.9 (8)
Cu1—N1—C1—O1	6.6 (7)	N1—C2—C4—C3	0.7 (8)
C2—N1—C1—N2	3.1 (7)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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−1/2, −y+1, z+1/2; (ii) x+1/2, −y, z+1/2; (iii) x, y−1, z.

Experimental details

Crystal data
Chemical formula	[CuCl₂(C₄H₄N₂O)(H₂O)]
M_r	248.53
Crystal system, space group	Monoclinic, Pn
Temperature (K)	100
a, b, c (Å)	9.6104 (4), 3.7942 (2), 10.7375 (4)
β (°)	107.991 (4)
V (Å³)	372.39 (3)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	3.59
Crystal size (mm)	0.28 × 0.08 × 0.06

Data collection
Diffractometer	Oxford Diffraction Gemini-R Ultra diffractometer
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2007)
T_min, T_max	0.739, 0.810
No. of measured, independent and observed [I > 2σ(I)] reflections	6373, 1866, 1462
R_int	0.046
(sin θ/λ)_max (Å⁻¹)	0.705

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.098, 1.01
No. of reflections	1866
No. of parameters	106
No. of restraints	4
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.73, −0.67
Absolute structure	Flack (1983), 767 Friedel pairs
Absolute structure parameter	0.03 (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—O2	1.976 (4)	Cu1—Cl1	2.2440 (14)
Cu1—N1	2.040 (4)	Cu1—Cl2	2.2466 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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−1/2, −y+1, z+1/2; (ii) x+1/2, −y, z+1/2; (iii) x, y−1, 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

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