2-Oxo-1,2-dihydro­pyrimidin-3-ium di-μ-chlorido-bis­{dichloridobis[pyrimidin-2(1H)-one-κN ³]cuprate(II)} dihydrate

Abstract

The asymmetric unit of the title compound, (C₄H₅N₂O)₂[Cu₂Cl₆(C₄H₄N₂O)₂]·2H₂O, consists of one cation, one half of a centrosymmetric dianion and one water mol­ecule. The centrosymmetric dianion formed by dimerization in the crystal structure has neutral pyrimidin-2-one ligands coordinated to each copper(II) centre through Cu—N bonds. The Cu atoms each have a distorted trigonal bipyramidal geometry, with the N atom of the pyrimidin-2-one ligand in an axial position, and dimerize by sharing two equatorial Cl atoms. N—H⋯Cl, O—H⋯Cl and N—H⋯O hydrogen bonds connect the anions, cations and water mol­ecules, forming a three-dimensional network.

Related literature

The anion has an essentially similar coordination environment to that of the related compound [{(C₅H₅N)NH₂}CuCl₃]₂ which has 3-amino­pyridinium cations (Blanchette & Willett, 1988 ▶) as the nitro­gen donors and is thus neutral, while the crystal structure of the cation was described by Furberg & Aas (1975 ▶) as its chloride salt.

Experimental

Crystal data

• (C₄H₅N₂O)₂[Cu₂Cl₆(C₄H₄N₂O)₂]·2H₂O

• M _r = 762.22

• Triclinic,

• a = 7.5924 (4) Å

• b = 8.6401 (3) Å

• c = 10.6349 (4) Å

• α = 96.032 (3)°

• β = 100.508 (4)°

• γ = 102.035 (4)°

• V = 663.39 (5) ų

• Z = 1

• Mo Kα radiation

• μ = 2.26 mm⁻¹

• T = 100 (2) K

• 0.41 × 0.18 × 0.15 mm

Data collection

• Oxford Diffraction Gemini R Ultra diffractometer

• Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 ▶) T _min = 0.433, T _max = 0.71

• 14528 measured reflections

• 3902 independent reflections

• 3269 reflections with I > 2σ(I)

• R _int = 0.020

Refinement

• R[F ² > 2σ(F ²)] = 0.024

• wR(F ²) = 0.069

• S = 1.12

• 3902 reflections

• 180 parameters

• 2 restraints

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.49 e Å⁻³

• Δρ_min = −0.57 e Å⁻³

Data collection: CrysAlis CCD (Oxford Diffraction, 2007 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2007 ▶); 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).

Supplementary Material

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

Table 1. Selected bond lengths (Å).

Cu1—N1	1.9989 (12)
Cu1—Cl3	2.2809 (4)
Cu1—Cl1	2.2830 (4)
Cu1—Cl2i	2.3942 (4)
Cu1—Cl2	2.6093 (4)

Symmetry code: (i) .

Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2B⋯Cl1ii	0.86	2.56	3.4143 (14)	171
N3—H3A⋯O3iii	0.86	1.86	2.7099 (18)	168
N4—H2A⋯Cl2iv	0.86	2.30	3.1336 (14)	165
O3—H1⋯Cl1v	0.815 (16)	2.428 (17)	3.2258 (13)	166 (2)
O3—H2⋯Cl3vi	0.844 (17)	2.454 (18)	3.2653 (13)	162 (2)

Symmetry codes: (ii) ; (iii) ; (iv) ; (v) ; (vi) .

supplementary crystallographic information

Comment

N—H···Cl interactions have been extensively used in crystal engineering to design and synthesize materials with desired structures. We sought to further utilize these interactions by reacting 2-hydroxypyrimidine hydrochloride and copper(II) chloride in a 2:1 ratio with the aim of synthesizing [C₄H₅N₂O]₂[CuCl₄]. However, the title compound I was obtained, which crystallizes in the triclinic system with the P1 space group. The copper coordination centres are similar to those described by Blanchette and Willett (1988) in [{(C₅H₅N)NH₂}CuCl₃]₂. The H₂O molecules and the [C₄H₅N₂O]⁺ cations (having both N atoms protonated and the O atoms atom deprotonated) are packed between the anions along the c-axis, the water forming O—H···Cl bridges between the anions while the cations form N—H···Cl and N—H···O bonds with the anions and water molecules respectively (Fig. 2).

For related literature, see Blanchette & Willett (1988) and Furberg & Aas (1975).

Experimental

Copper(II) chloride dihydrate and 2-hydroxypyrimidine hydrochloride in a 1:2 molar ratio were dissolved in concentrated hydrochloric acid solution. The solution was left to evaporate slowly at room temperature and resulted in the formation of green crystals after a few days.

Refinement

H atoms bonded to O atoms were located in the difference map and refined with distance restraints of O—H = 0.84 (2) Å with U_iso(H) = 1.2U_eq(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 U_iso(H) = 1.2 times U_eq(C, N).

Figures

Fig. 1.

The molecular structure of I showing one dimeric dianion, one cation and a molecule of water of crystallization, with atom labels and 50% probability displacement ellipsoids for non-H atoms.

Fig. 2.

Packing of I in the ac plane, with O—H···Cl bridges between the water molecules and the dianions, N—H···O hydrogen bonds between cations and water molecules, and N—H···Cl hydrogen bonds between the anions and cations.

Crystal data

(C4H5N2O)2[Cu2Cl6(C4H4N2O)2]·2H2O	Z = 1
Mr = 762.22	F000 = 382
Triclinic, P1	Dx = 1.908 Mg m−3
a = 7.5924 (4) Å	Mo Kα radiation λ = 0.71073 Å
b = 8.6401 (3) Å	Cell parameters from 10481 reflections
c = 10.6349 (4) Å	θ = 2.4–30.0º
α = 96.032 (3)º	µ = 2.26 mm−1
β = 100.508 (4)º	T = 100 (2) K
γ = 102.035 (4)º	Block, green
V = 663.39 (5) Å3	0.41 × 0.18 × 0.16 mm

Data collection

Oxford Diffraction Gemini-R Ultra diffractometer	3902 independent reflections
Radiation source: fine-focus sealed tube	3269 reflections with I > 2σ(I)
Monochromator: graphite	Rint = 0.020
T = 100(2) K	θmax = 30.1º
ω (1° width) scans	θmin = 2.4º
Absorption correction: multi-scan(CrysAlis RED; Oxford Diffraction, 2007)	h = −10→10
Tmin = 0.433, Tmax = 0.71	k = −12→12
14528 measured reflections	l = −15→15

Refinement

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)] = 0.024	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.069	w = 1/[σ2(Fo2) + (0.0422P)2 + 0.0753P] where P = (Fo2 + 2Fc2)/3
S = 1.12	(Δ/σ)max = 0.002
3902 reflections	Δρmax = 0.49 e Å−3
180 parameters	Δρmin = −0.57 e Å−3
2 restraints	Extinction correction: none
Primary atom site location: structure-invariant direct methods

Special details

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.32.5 (release 08-05-2007 CrysAlis171 .NET) 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	0.07237 (3)	0.45037 (2)	0.848449 (17)	0.01007 (6)
Cl1	−0.06435 (5)	0.63425 (4)	0.75599 (3)	0.01291 (8)
Cl2	0.19396 (5)	0.64570 (4)	1.06611 (3)	0.01065 (8)
Cl3	0.26769 (6)	0.45986 (5)	0.70847 (4)	0.01557 (9)
N1	0.18231 (18)	0.28152 (15)	0.92487 (12)	0.0099 (2)
N2	0.15847 (19)	0.00585 (15)	0.91842 (13)	0.0122 (3)
H2B	0.1020	−0.0912	0.8865	0.015*
N3	0.69462 (19)	0.93935 (16)	0.46681 (12)	0.0124 (3)
H3A	0.7819	1.0237	0.4760	0.015*
N4	0.43187 (19)	0.76169 (16)	0.34665 (13)	0.0137 (3)
H2A	0.3488	0.7298	0.2768	0.016*
O1	0.58355 (18)	0.96484 (15)	0.25699 (12)	0.0204 (3)
O2	−0.02211 (17)	0.10178 (14)	0.76366 (11)	0.0176 (2)
O3	0.93114 (18)	0.22792 (15)	0.49005 (12)	0.0198 (3)
C1	0.0983 (2)	0.12810 (17)	0.86166 (15)	0.0116 (3)
C2	0.3215 (2)	0.30666 (18)	1.02403 (14)	0.0119 (3)
H2C	0.3773	0.4116	1.0619	0.014*
C3	0.3900 (2)	0.18275 (18)	1.07546 (15)	0.0132 (3)
H3B	0.4917	0.2036	1.1436	0.016*
C4	0.3004 (2)	0.03050 (18)	1.02078 (15)	0.0129 (3)
H4A	0.3368	−0.0560	1.0538	0.016*
C5	0.5717 (2)	0.89360 (19)	0.34849 (15)	0.0135 (3)
C6	0.6850 (2)	0.85959 (19)	0.56744 (15)	0.0134 (3)
H6A	0.7744	0.8941	0.6433	0.016*
C7	0.5451 (2)	0.72742 (19)	0.56028 (15)	0.0141 (3)
H7A	0.5372	0.6718	0.6301	0.017*
C8	0.4167 (2)	0.68029 (19)	0.44567 (15)	0.0139 (3)
H8A	0.3194	0.5917	0.4373	0.017*
H1	0.947 (3)	0.268 (3)	0.4257 (19)	0.037 (7)*
H2	1.024 (3)	0.267 (3)	0.551 (2)	0.044 (8)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cu1	0.01130 (11)	0.00927 (9)	0.00972 (10)	0.00265 (7)	0.00141 (7)	0.00270 (7)
Cl1	0.01491 (19)	0.01236 (16)	0.01204 (17)	0.00437 (13)	0.00135 (14)	0.00458 (12)
Cl2	0.01105 (17)	0.00891 (15)	0.01027 (16)	0.00021 (13)	0.00046 (13)	0.00112 (12)
Cl3	0.01575 (19)	0.01618 (18)	0.01615 (18)	0.00296 (14)	0.00692 (14)	0.00377 (14)
N1	0.0118 (6)	0.0074 (5)	0.0097 (6)	0.0012 (5)	0.0015 (5)	0.0009 (4)
N2	0.0136 (7)	0.0069 (5)	0.0160 (6)	0.0012 (5)	0.0042 (5)	0.0008 (5)
N3	0.0102 (6)	0.0135 (6)	0.0123 (6)	0.0010 (5)	0.0007 (5)	0.0024 (5)
N4	0.0115 (6)	0.0165 (6)	0.0101 (6)	0.0018 (5)	−0.0021 (5)	−0.0012 (5)
O1	0.0218 (7)	0.0265 (6)	0.0160 (6)	0.0084 (5)	0.0052 (5)	0.0100 (5)
O2	0.0184 (6)	0.0142 (5)	0.0158 (5)	0.0017 (5)	−0.0033 (5)	−0.0013 (4)
O3	0.0198 (7)	0.0203 (6)	0.0143 (6)	−0.0049 (5)	0.0001 (5)	0.0058 (5)
C1	0.0126 (7)	0.0089 (6)	0.0133 (7)	0.0014 (5)	0.0040 (6)	0.0013 (5)
C2	0.0122 (7)	0.0106 (7)	0.0122 (7)	0.0019 (6)	0.0025 (6)	0.0010 (5)
C3	0.0140 (8)	0.0136 (7)	0.0125 (7)	0.0049 (6)	0.0019 (6)	0.0025 (5)
C4	0.0149 (8)	0.0121 (7)	0.0149 (7)	0.0058 (6)	0.0059 (6)	0.0056 (6)
C5	0.0114 (8)	0.0157 (7)	0.0141 (7)	0.0052 (6)	0.0022 (6)	0.0023 (6)
C6	0.0139 (8)	0.0137 (7)	0.0115 (7)	0.0041 (6)	−0.0005 (6)	0.0009 (5)
C7	0.0160 (8)	0.0139 (7)	0.0119 (7)	0.0028 (6)	0.0022 (6)	0.0030 (5)
C8	0.0121 (8)	0.0128 (7)	0.0158 (7)	0.0020 (6)	0.0030 (6)	−0.0004 (6)

Geometric parameters (Å, °)

Cu1—N1	1.9989 (12)	N4—H2A	0.8600
Cu1—Cl3	2.2809 (4)	O1—C5	1.2119 (19)
Cu1—Cl1	2.2830 (4)	O2—C1	1.221 (2)
Cu1—Cl2i	2.3942 (4)	O3—H1	0.815 (16)
Cu1—Cl2	2.6093 (4)	O3—H2	0.844 (17)
Cl2—Cu1i	2.3942 (4)	C2—C3	1.403 (2)
N1—C2	1.314 (2)	C2—H2C	0.9300
N1—C1	1.3854 (19)	C3—C4	1.361 (2)
N2—C4	1.349 (2)	C3—H3B	0.9300
N2—C1	1.3868 (19)	C4—H4A	0.9300
N2—H2B	0.8600	C6—C7	1.373 (2)
N3—C6	1.337 (2)	C6—H6A	0.9300
N3—C5	1.387 (2)	C7—C8	1.378 (2)
N3—H3A	0.8600	C7—H7A	0.9300
N4—C8	1.335 (2)	C8—H8A	0.9300
N4—C5	1.382 (2)
N1—Cu1—Cl3	88.53 (4)	O2—C1—N1	122.46 (14)
N1—Cu1—Cl1	177.38 (4)	O2—C1—N2	122.11 (14)
Cl3—Cu1—Cl1	91.956 (15)	N1—C1—N2	115.42 (13)
N1—Cu1—Cl2i	88.05 (4)	N1—C2—C3	123.13 (14)
Cl3—Cu1—Cl2i	157.928 (16)	N1—C2—H2C	118.4
Cl1—Cu1—Cl2i	90.538 (15)	C3—C2—H2C	118.4
N1—Cu1—Cl2	91.12 (4)	C4—C3—C2	116.78 (15)
Cl3—Cu1—Cl2	115.984 (15)	C4—C3—H3B	121.6
Cl1—Cu1—Cl2	90.982 (14)	C2—C3—H3B	121.6
Cl2i—Cu1—Cl2	85.883 (14)	N2—C4—C3	119.63 (14)
Cu1i—Cl2—Cu1	94.117 (14)	N2—C4—H4A	120.2
C2—N1—C1	120.92 (13)	C3—C4—H4A	120.2
C2—N1—Cu1	125.69 (10)	O1—C5—N4	123.48 (15)
C1—N1—Cu1	113.38 (10)	O1—C5—N3	123.19 (15)
C4—N2—C1	123.75 (13)	N4—C5—N3	113.30 (13)
C4—N2—H2B	118.1	N3—C6—C7	120.87 (15)
C1—N2—H2B	118.1	N3—C6—H6A	119.6
C6—N3—C5	123.65 (14)	C7—C6—H6A	119.6
C6—N3—H3A	118.2	C6—C7—C8	117.45 (15)
C5—N3—H3A	118.2	C6—C7—H7A	121.3
C8—N4—C5	124.63 (14)	C8—C7—H7A	121.3
C8—N4—H2A	117.7	N4—C8—C7	120.03 (15)
C5—N4—H2A	117.7	N4—C8—H8A	120.0
H1—O3—H2	109 (2)	C7—C8—H8A	120.0
N1—Cu1—Cl2—Cu1i	−87.97 (4)	C4—N2—C1—N1	−6.1 (2)
Cl3—Cu1—Cl2—Cu1i	−176.875 (16)	C1—N1—C2—C3	−2.4 (2)
Cl1—Cu1—Cl2—Cu1i	90.469 (15)	Cu1—N1—C2—C3	178.41 (11)
Cl2i—Cu1—Cl2—Cu1i	0.0	N1—C2—C3—C4	−2.5 (2)
Cl3—Cu1—N1—C2	92.08 (13)	C1—N2—C4—C3	1.5 (2)
Cl2i—Cu1—N1—C2	−109.72 (13)	C2—C3—C4—N2	2.9 (2)
Cl2—Cu1—N1—C2	−23.88 (13)	C8—N4—C5—O1	179.35 (16)
Cl3—Cu1—N1—C1	−87.19 (10)	C8—N4—C5—N3	−2.3 (2)
Cl2i—Cu1—N1—C1	71.00 (10)	C6—N3—C5—O1	−178.50 (16)
Cl2—Cu1—N1—C1	156.84 (10)	C6—N3—C5—N4	3.2 (2)
C2—N1—C1—O2	−174.50 (15)	C5—N3—C6—C7	−2.4 (2)
Cu1—N1—C1—O2	4.8 (2)	N3—C6—C7—C8	0.4 (2)
C2—N1—C1—N2	6.4 (2)	C5—N4—C8—C7	0.7 (2)
Cu1—N1—C1—N2	−174.26 (10)	C6—C7—C8—N4	0.4 (2)
C4—N2—C1—O2	174.79 (15)

Symmetry codes: (i) −x, −y+1, −z+2.

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2B···Cl1ii	0.86	2.56	3.4143 (14)	171
N3—H3A···O3iii	0.86	1.86	2.7099 (18)	168
N4—H2A···Cl2iv	0.86	2.30	3.1336 (14)	165
O3—H1···Cl1v	0.815 (16)	2.428 (17)	3.2258 (13)	166 (2)
O3—H2···Cl3vi	0.844 (17)	2.454 (18)	3.2653 (13)	162 (2)

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