metal-organic compounds
2-Oxo-1,2-dihydropyrimidin-3-ium di-μ-chlorido-bis{dichloridobis[pyrimidin-2(1H)-one-κN3]cuprate(II)} dihydrate
aSchool of Chemistry, University of Bristol, Bristol BS8 1TS, England
*Correspondence e-mail: guy.orpen@bristol.ac.uk
The 4H5N2O)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 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.
of the title compound, (CRelated 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 of the cation was described by Furberg & Aas (1975) as its chloride salt.
Experimental
Crystal data
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Refinement
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Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell 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).
Supporting information
10.1107/S1600536808017455/sg2250sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808017455/sg2250Isup2.hkl
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.
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 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).
Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell
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).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. |
(C4H5N2O)2[Cu2Cl6(C4H4N2O)2]·2H2O | Z = 1 |
Mr = 762.22 | F(000) = 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 = 2.4–30.0° |
α = 96.032 (3)° | µ = 2.26 mm−1 |
β = 100.508 (4)° | T = 100 K |
γ = 102.035 (4)° | Block, green |
V = 663.39 (5) Å3 | 0.41 × 0.18 × 0.16 mm |
Oxford Diffraction Gemini-R Ultra diffractometer | 3902 independent reflections |
Radiation source: fine-focus sealed tube | 3269 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.020 |
ω (1° width) scans | θmax = 30.1°, θmin = 2.4° |
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 on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.024 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.069 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | w = 1/[σ2(Fo2) + (0.0422P)2 + 0.0753P] where P = (Fo2 + 2Fc2)/3 |
3902 reflections | (Δ/σ)max = 0.002 |
180 parameters | Δρmax = 0.49 e Å−3 |
2 restraints | Δρmin = −0.57 e Å−3 |
(C4H5N2O)2[Cu2Cl6(C4H4N2O)2]·2H2O | γ = 102.035 (4)° |
Mr = 762.22 | V = 663.39 (5) Å3 |
Triclinic, P1 | Z = 1 |
a = 7.5924 (4) Å | Mo Kα radiation |
b = 8.6401 (3) Å | µ = 2.26 mm−1 |
c = 10.6349 (4) Å | T = 100 K |
α = 96.032 (3)° | 0.41 × 0.18 × 0.16 mm |
β = 100.508 (4)° |
Oxford Diffraction Gemini-R Ultra diffractometer | 3902 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | 3269 reflections with I > 2σ(I) |
Tmin = 0.433, Tmax = 0.71 | Rint = 0.020 |
14528 measured reflections |
R[F2 > 2σ(F2)] = 0.024 | 2 restraints |
wR(F2) = 0.069 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | Δρmax = 0.49 e Å−3 |
3902 reflections | Δρmin = −0.57 e Å−3 |
180 parameters |
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. |
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)* |
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) |
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 code: (i) −x, −y+1, −z+2. |
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 | 0.82 (2) | 2.43 (2) | 3.2258 (13) | 166 (2) |
O3—H2···Cl3vi | 0.84 (2) | 2.45 (2) | 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. |
Experimental details
Crystal data | |
Chemical formula | (C4H5N2O)2[Cu2Cl6(C4H4N2O)2]·2H2O |
Mr | 762.22 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 100 |
a, b, c (Å) | 7.5924 (4), 8.6401 (3), 10.6349 (4) |
α, β, γ (°) | 96.032 (3), 100.508 (4), 102.035 (4) |
V (Å3) | 663.39 (5) |
Z | 1 |
Radiation type | Mo Kα |
µ (mm−1) | 2.26 |
Crystal size (mm) | 0.41 × 0.18 × 0.16 |
Data collection | |
Diffractometer | Oxford Diffraction Gemini-R Ultra diffractometer |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2007) |
Tmin, Tmax | 0.433, 0.71 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 14528, 3902, 3269 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.706 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.024, 0.069, 1.12 |
No. of reflections | 3902 |
No. of parameters | 180 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.49, −0.57 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
Cu1—N1 | 1.9989 (12) | Cu1—Cl2i | 2.3942 (4) |
Cu1—Cl3 | 2.2809 (4) | Cu1—Cl2 | 2.6093 (4) |
Cu1—Cl1 | 2.2830 (4) |
Symmetry code: (i) −x, −y+1, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···Cl1ii | 0.86 | 2.56 | 3.4143 (14) | 170.8 |
N3—H3A···O3iii | 0.86 | 1.86 | 2.7099 (18) | 168.1 |
N4—H2A···Cl2iv | 0.86 | 2.30 | 3.1336 (14) | 164.7 |
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. |
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
Blanchette, J. T. & Willett, R. D. (1988). Inorg. Chem. 27, 843–849. CSD CrossRef CAS Web of Science Google Scholar
Furberg, S. & Aas, J. B. (1975). Acta Chem. Scand. A29, 713–716. CrossRef CAS Web of Science 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
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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).