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Acta Cryst. (2007). E63, m1523-m1524    [ doi:10.1107/S1600536807020545 ]

Bis(acetato-[kappa]O)triaquacadmium 2-amino-4,6-dimethylpyrimidine tetrasolvate dihydrate

H. Fang and S. W. Ng

Abstract top

The Cd atom (site symmetry 2) in the title compound, [Cd(C2H3O2)2(H2O)3]·4C6H9N3·2H2O, adopts a trigonal-bipyramidal coordination geometry but it tends towards a distorted pentagonal bipyramid owing to two long [2.674 (2) Å] Cd...OCOO interactions from the asymmetrically coordinated acetate anions. The neutral metal complex, uncoordinated water molecules and N-heterocycles engage in O-H...O, O-H...N, N-H...O and N-H...N hydrogen-bonding interactions, forming a three-dimensional network.

Comment top

Cadmium acetate forms adducts with nitrogen-donor ligands and among the known crystal structures of such materials are the bis(4-aminophenyl)methane (Wang et al., 2004), 2,2'-bipyridine (Ye et al., 2000) and diethylnicotinamide (Sergienko et al., 1980) adducts.

The title compound, (I), the product of the reaction of cadmium acetate with 2-amino-4,6-pyrimidine, has the N-heterocycle engaging instead in an outer-sphere type of coordination (i.e. interacting indirectly through hydrogen bonds). Compound (I) consists of a triaquadiacetatocadmium molecule (Cd site symmetry 2) along with an uncoordinated water molecule and two N-heterocycles (Fig. 1). The cadmium atom is five-coordinate, but the geometry is distorted towards a pentagonal bipyramid owing to two long Cd···O interactions (Table 1). Hydrogen bonds link the three entities into a three-dimensional network motif (Table 2).

Related literature top

For chemically related materials arising from cadmium acetate which contain cadmium coordinated by N-donor ligands, see: Wang et al. (2004); Ye et al. (2000); Sergienko et al. (1980). For details of the preparation, see: Xue et al. (1993).

Experimental top

2-Amino-4,6-dimethylpyrimidine was synthesized according to a literature procedure (Xue et al., 1993). This heterocycle (0.12 g, 1 mmol) was added to an aqueous solution (20 ml) of cadmium acetate dihydrate (0.27 g, 1 mmol). The solution was filtered and then set aside for the growth of crystals. Block-shaped crystals of (I) were harvested after a week.

Refinement top

The cadmium atom, which lies on a twofold rotation axis, is disordered over two positions, the disorder refining to a 0.856 (2):0.144 (2) ratio. The vibration of the minor component was restrained to be nearly isotropic. The minor component is then covalently bonded to O2, and the distortion of geometry arises from the proximity of the O1 atom. The carbon- and nitrogen-bound H atoms were treated as riding; the methyl groups were rotated to fit the electron density. The H atoms of the water molecules were placed in chemically sensible positions on the basis of hydrogen bonding interactions, but they were not refined.

Computing details top

Data collection: SMART (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2007).

Figures top
[Figure 1] Fig. 1. The formula unit of (I). Displacement ellipsoids are shown at the 50% probability level (arbitrary spheres for the H atoms. Symmetry code (i): 1 + x, 1 - y, 1/2 + z. The minor disorder component is not shown.
Bis(acetato-κO)triaquacadmium dihydrate 2-amino-4,6-dimethylpyrimidine tetrasolvate dihydrate top
Crystal data top
[Cd(C2H3O2)2(H2O)3]·4C6H9N3·2H2OF(000) = 848
Mr = 813.22Dx = 1.455 Mg m−3
Monoclinic, P2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ycCell parameters from 3660 reflections
a = 19.287 (1) Åθ = 2.9–27.5°
b = 6.7697 (4) ŵ = 0.65 mm−1
c = 14.2238 (4) ÅT = 295 K
β = 91.444 (1)°Block, colorless
V = 1856.56 (16) Å30.40 × 0.20 × 0.16 mm
Z = 2
Data collection top
Bruker APEX CCD
diffractometer		4386 independent reflections
Radiation source: fine-focus sealed tube3794 reflections with I > 2σ(I)
graphiteRint = 0.053
φ and ω scansθmax = 28.2°, θmin = 1.1°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −24→25
Tmin = 0.567, Tmax = 0.903k = −8→8
13020 measured reflectionsl = −15→18
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.145H-atom parameters constrained
S = 1.11 w = 1/[σ2(Fo2) + (0.0786P)2]
where P = (Fo2 + 2Fc2)/3
4386 reflections(Δ/σ)max = 0.001
238 parametersΔρmax = 0.88 e Å−3
6 restraintsΔρmin = −0.62 e Å−3
Crystal data top
[Cd(C2H3O2)2(H2O)3]·4C6H9N3·2H2OV = 1856.56 (16) Å3
Mr = 813.22Z = 2
Monoclinic, P2/cMo Kα radiation
a = 19.287 (1) ŵ = 0.65 mm−1
b = 6.7697 (4) ÅT = 295 K
c = 14.2238 (4) Å0.40 × 0.20 × 0.16 mm
β = 91.444 (1)°
Data collection top
Bruker APEX CCD
diffractometer		4386 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		3794 reflections with I > 2σ(I)
Tmin = 0.567, Tmax = 0.903Rint = 0.053
13020 measured reflectionsθmax = 28.2°
Refinement top
R[F2 > 2σ(F2)] = 0.052H-atom parameters constrained
wR(F2) = 0.145Δρmax = 0.88 e Å−3
S = 1.11Δρmin = −0.62 e Å−3
4386 reflectionsAbsolute structure: ?
238 parametersFlack parameter: ?
6 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Cd10.50000.83464 (7)0.25000.03522 (16)0.856 (2)
Cd1'0.50000.6668 (5)0.25000.0545 (12)0.144 (2)
O10.44455 (12)0.8964 (4)0.37992 (17)0.0488 (6)
O20.45034 (12)0.5760 (4)0.37344 (17)0.0508 (6)
O1w0.40361 (12)0.7807 (6)0.15998 (19)0.0725 (10)
H1w10.35970.77410.16600.087*
H1w20.41160.77530.10130.087*
O2w0.50001.2162 (7)0.25000.0726 (12)
H2w10.48311.29220.29200.087*
O3w0.41291 (12)0.7615 (4)−0.02930 (18)0.0499 (6)
H3w10.42920.8643−0.05570.060*
H3w20.43060.6557−0.05090.060*
N10.25822 (12)0.7573 (4)0.15794 (19)0.0381 (6)
N20.15315 (13)0.7540 (5)0.06446 (19)0.0413 (6)
N30.25850 (14)0.7558 (6)−0.0040 (2)0.0568 (9)
H3N10.23690.7547−0.05770.068*
H3N20.30310.7570−0.00130.068*
N40.18959 (12)0.7447 (4)−0.19967 (18)0.0374 (6)
N50.09175 (13)0.7455 (5)−0.3069 (2)0.0426 (6)
N60.07806 (14)0.7472 (6)−0.1467 (2)0.0537 (8)
H6N10.03390.7478−0.15650.064*
H6N20.09490.7475−0.09010.064*
C10.43394 (16)0.7257 (6)0.4143 (2)0.0433 (8)
C20.4002 (2)0.7178 (7)0.5091 (3)0.0613 (10)
H2A0.35680.64870.50320.092*
H2B0.39210.84980.53100.092*
H2C0.43020.65000.55320.092*
C30.22286 (15)0.7559 (5)0.0748 (2)0.0376 (7)
C40.22067 (15)0.7571 (5)0.2354 (2)0.0383 (7)
C50.14889 (16)0.7550 (6)0.2313 (2)0.0452 (8)
H50.12300.75410.28560.054*
C60.11762 (15)0.7543 (6)0.1434 (3)0.0440 (8)
C70.25937 (18)0.7567 (6)0.3288 (2)0.0479 (8)
H7A0.24910.63740.36210.072*
H7B0.24530.86860.36510.072*
H7C0.30830.76390.31850.072*
C80.03971 (17)0.7526 (9)0.1313 (3)0.0714 (13)
H8A0.02730.75620.06550.107*
H8B0.02070.86600.16190.107*
H8C0.02150.63450.15880.107*
C90.12098 (15)0.7459 (5)−0.2201 (2)0.0359 (6)
C100.13499 (17)0.7441 (6)−0.3780 (2)0.0452 (8)
C110.20641 (17)0.7422 (6)−0.3641 (2)0.0453 (8)
H110.23610.7409−0.41450.054*
C120.23172 (15)0.7423 (5)−0.2725 (2)0.0389 (7)
C130.1036 (2)0.7431 (9)−0.4754 (3)0.0721 (13)
H13A0.05910.6794−0.47480.108*
H13B0.13350.6728−0.51670.108*
H13C0.09800.8766−0.49720.108*
C140.30850 (16)0.7406 (6)−0.2523 (3)0.0500 (9)
H14A0.32870.8597−0.27590.075*
H14B0.32890.6286−0.28240.075*
H14C0.31700.7325−0.18560.075*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cd10.02966 (19)0.0508 (3)0.0253 (2)0.0000.00195 (13)0.000
Cd1'0.0625 (18)0.069 (3)0.0324 (15)0.0000.0009 (11)0.000
O10.0517 (12)0.0571 (15)0.0379 (13)0.0050 (11)0.0090 (10)0.0006 (11)
O20.0545 (13)0.0566 (16)0.0419 (13)−0.0019 (12)0.0081 (11)−0.0023 (12)
O1w0.0333 (12)0.148 (3)0.0359 (15)−0.0059 (14)0.0006 (11)−0.0090 (16)
O2w0.087 (3)0.078 (3)0.055 (3)0.0000.027 (2)0.000
O3w0.0531 (13)0.0574 (15)0.0396 (14)−0.0016 (11)0.0077 (11)0.0011 (11)
N10.0328 (12)0.0482 (16)0.0333 (14)−0.0005 (10)−0.0039 (11)−0.0001 (11)
N20.0345 (12)0.0579 (17)0.0314 (14)0.0002 (11)−0.0023 (11)−0.0005 (12)
N30.0355 (14)0.104 (3)0.0309 (15)0.0007 (15)0.0006 (12)0.0001 (16)
N40.0347 (12)0.0457 (15)0.0318 (14)0.0000 (10)−0.0014 (11)0.0003 (11)
N50.0349 (12)0.0547 (18)0.0380 (15)−0.0006 (11)−0.0030 (11)0.0006 (12)
N60.0380 (14)0.086 (2)0.0374 (17)−0.0002 (14)0.0036 (13)0.0009 (15)
C10.0323 (14)0.067 (2)0.0305 (16)−0.0023 (14)0.0029 (12)0.0035 (15)
C20.061 (2)0.086 (3)0.037 (2)−0.002 (2)0.0163 (18)0.0017 (19)
C30.0350 (14)0.0467 (18)0.0310 (16)−0.0012 (12)−0.0025 (12)−0.0001 (13)
C40.0378 (15)0.0460 (18)0.0309 (16)0.0001 (12)−0.0018 (13)0.0004 (13)
C50.0357 (15)0.066 (2)0.0342 (17)−0.0004 (14)0.0036 (14)−0.0015 (15)
C60.0311 (14)0.059 (2)0.0412 (19)0.0010 (13)−0.0031 (13)0.0003 (15)
C70.0461 (17)0.065 (2)0.0317 (17)0.0006 (15)−0.0072 (14)−0.0021 (15)
C80.0298 (16)0.135 (4)0.050 (2)−0.002 (2)0.0001 (16)0.001 (2)
C90.0352 (14)0.0381 (16)0.0344 (16)−0.0014 (11)−0.0004 (12)−0.0009 (12)
C100.0423 (16)0.057 (2)0.0358 (18)−0.0003 (14)−0.0073 (14)−0.0005 (15)
C110.0412 (16)0.061 (2)0.0333 (17)0.0005 (14)0.0031 (14)−0.0018 (15)
C120.0340 (14)0.0457 (18)0.0367 (17)−0.0013 (12)−0.0008 (13)−0.0005 (13)
C130.059 (2)0.121 (4)0.035 (2)0.002 (2)−0.0132 (18)0.001 (2)
C140.0323 (14)0.071 (3)0.046 (2)0.0003 (14)0.0012 (14)0.0011 (17)
Geometric parameters (Å, °) top
Cd1—O12.198 (2)N5—C91.345 (4)
Cd1—O1i2.198 (2)N6—C91.348 (4)
Cd1—O22.674 (2)N6—H6N10.8600
Cd1—O2i2.674 (2)N6—H6N20.8600
Cd1—O1w2.260 (3)C1—C21.513 (5)
Cd1—O1wi2.260 (3)C2—H2A0.9600
Cd1—O2w2.583 (5)C2—H2B0.9600
Cd1'—O2i2.113 (3)C2—H2C0.9600
Cd1'—O22.113 (3)C4—C51.384 (4)
Cd1'—O1wi2.360 (3)C4—C71.507 (4)
Cd1'—O1w2.360 (3)C5—C61.375 (5)
Cd1'—C12.719 (3)C5—H50.9300
Cd1'—C1i2.719 (3)C6—C81.508 (4)
C1—O11.274 (5)C7—H7A0.9600
C1—O21.214 (5)C7—H7B0.9600
O1w—H1w10.85C7—H7C0.9600
O1w—H1w20.85C8—H8A0.9600
O2w—H2w10.86C8—H8B0.9600
O3w—H3w10.85C8—H8C0.9600
O3w—H3w20.85C10—C111.387 (5)
N1—C41.334 (4)C10—C131.499 (5)
N1—C31.350 (4)C11—C121.379 (5)
N2—C61.330 (4)C11—H110.9300
N2—C31.349 (4)C12—C141.502 (4)
N3—C31.330 (4)C13—H13A0.9600
N3—H3N10.8600C13—H13B0.9600
N3—H3N20.8600C13—H13C0.9600
N4—C121.332 (4)C14—H14A0.9600
N4—C91.348 (4)C14—H14B0.9600
N5—C101.326 (4)C14—H14C0.9600
Cd1'—Cd1—O1100.96 (7)H2B—C2—H2C109.5
Cd1'—Cd1—O1i100.96 (7)N3—C3—N2116.3 (3)
O1—Cd1—O1i158.07 (15)N3—C3—N1118.6 (3)
Cd1'—Cd1—O1wi80.71 (11)N2—C3—N1125.2 (3)
O1—Cd1—O1wi88.00 (9)N1—C4—C5121.9 (3)
O1i—Cd1—O1wi95.53 (9)N1—C4—C7117.4 (3)
O1—Cd1—O1w95.53 (9)C5—C4—C7120.6 (3)
O1i—Cd1—O1w88.00 (9)C6—C5—C4117.0 (3)
O1wi—Cd1—O1w161.4 (2)C6—C5—H5121.5
O1—Cd1—O2w79.04 (7)C4—C5—H5121.5
O1i—Cd1—O2w79.04 (7)N2—C6—C5123.0 (3)
O1wi—Cd1—O2w99.29 (11)N2—C6—C8115.9 (3)
O1w—Cd1—O2w99.29 (11)C5—C6—C8121.1 (3)
O2i—Cd1'—O2146.2 (2)C4—C7—H7A109.5
O2i—Cd1'—O1wi100.29 (9)C4—C7—H7B109.5
O2—Cd1'—O1wi90.67 (9)H7A—C7—H7B109.5
O2i—Cd1'—O1w90.67 (9)C4—C7—H7C109.5
O2—Cd1'—O1w100.29 (9)H7A—C7—H7C109.5
O1wi—Cd1'—O1w141.9 (3)H7B—C7—H7C109.5
C1—O1—Cd1103.7 (2)C6—C8—H8A109.5
C1—O2—Cd1'106.5 (3)C6—C8—H8B109.5
Cd1—O1w—H1w1139.0H8A—C8—H8B109.5
Cd1'—O1w—H1w1134.2C6—C8—H8C109.5
Cd1—O1w—H1w2113.3H8A—C8—H8C109.5
Cd1'—O1w—H1w2111.0H8B—C8—H8C109.5
H1w1—O1w—H1w2107.5N5—C9—N4125.8 (3)
Cd1—O2w—H2w1126.8N5—C9—N6117.4 (3)
H3w1—O3w—H3w2111.8N4—C9—N6116.9 (3)
C4—N1—C3116.8 (3)N5—C10—C11122.2 (3)
C6—N2—C3116.2 (3)N5—C10—C13117.2 (3)
C3—N3—H3N1120.0C11—C10—C13120.6 (3)
C3—N3—H3N2120.0C12—C11—C10117.5 (3)
H3N1—N3—H3N2120.0C12—C11—H11121.3
C12—N4—C9116.6 (3)C10—C11—H11121.3
C10—N5—C9116.3 (3)N4—C12—C11121.7 (3)
C9—N6—H6N1120.0N4—C12—C14118.0 (3)
C9—N6—H6N2120.0C11—C12—C14120.3 (3)
H6N1—N6—H6N2120.0C10—C13—H13A109.5
O2—C1—O1121.8 (3)C10—C13—H13B109.5
O2—C1—C2121.4 (4)H13A—C13—H13B109.5
O1—C1—C2116.8 (3)C10—C13—H13C109.5
O2—C1—Cd1'48.15 (19)H13A—C13—H13C109.5
O1—C1—Cd1'73.72 (19)H13B—C13—H13C109.5
C2—C1—Cd1'169.2 (3)C12—C14—H14A109.5
C1—C2—H2A109.5C12—C14—H14B109.5
C1—C2—H2B109.5H14A—C14—H14B109.5
H2A—C2—H2B109.5C12—C14—H14C109.5
C1—C2—H2C109.5H14A—C14—H14C109.5
H2A—C2—H2C109.5H14B—C14—H14C109.5
O1i—Cd1—O1—C1−176.9 (2)C7—C4—C5—C6−179.6 (3)
O1wi—Cd1—O1—C1−77.0 (2)C3—N2—C6—C5−0.5 (6)
O1w—Cd1—O1—C184.7 (2)C3—N2—C6—C8179.9 (4)
O2w—Cd1—O1—C1−176.9 (2)C4—C5—C6—N20.5 (6)
O2i—Cd1'—O2—C1180.0 (2)C4—C5—C6—C8−179.8 (4)
O1wi—Cd1'—O2—C170.2 (2)C10—N5—C9—N4−0.1 (5)
O1w—Cd1'—O2—C1−73.1 (3)C10—N5—C9—N6180.0 (3)
Cd1'—O2—C1—O12.9 (4)C12—N4—C9—N5−0.2 (5)
Cd1'—O2—C1—C2−176.8 (3)C12—N4—C9—N6179.7 (3)
Cd1—O1—C1—O2−3.6 (4)C9—N5—C10—C110.3 (5)
Cd1—O1—C1—C2176.1 (2)C9—N5—C10—C13179.9 (4)
C6—N2—C3—N3−179.9 (4)N5—C10—C11—C12−0.2 (6)
C6—N2—C3—N10.2 (5)C13—C10—C11—C12−179.7 (4)
C4—N1—C3—N3−179.9 (3)C9—N4—C12—C110.4 (5)
C4—N1—C3—N2−0.1 (5)C9—N4—C12—C14−179.9 (3)
C3—N1—C4—C50.1 (5)C10—C11—C12—N4−0.2 (6)
C3—N1—C4—C7179.4 (3)C10—C11—C12—C14−179.9 (3)
N1—C4—C5—C6−0.3 (6)
Symmetry codes: (i) −x+1, y, −z+1/2.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1w—H1w1···N10.851.962.808 (3)171
O1w—H1w2···O3w0.851.862.706 (4)170
O2w—H2w1···O2ii0.862.343.165 (5)162
O3w—H3w1···O1iii0.851.892.728 (4)167
O3w—H3w2···O2iv0.851.952.776 (4)164
N3—H3n1···N40.862.203.055 (4)176
N3—H3n2···O3w0.862.173.009 (4)167
N6—H6n1···N5v0.862.473.324 (4)177
N6—H6n2···N20.862.443.302 (4)175
Symmetry codes: (ii) x, y+1, z; (iii) x, −y+2, z−1/2; (iv) x, −y+1, z−1/2; (v) −x, y, −z−1/2.
Table 1
Selected geometric parameters (Å) top
Cd1—O12.198 (2)Cd1—O2w2.583 (5)
Cd1—O22.674 (2)C1—O11.274 (5)
Cd1—O1w2.260 (3)C1—O21.214 (5)
Table 2
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1w—H1w1···N10.851.962.808 (3)171
O1w—H1w2···O3w0.851.862.706 (4)170
O2w—H2w1···O2i0.862.343.165 (5)162
O3w—H3w1···O1ii0.851.892.728 (4)167
O3w—H3w2···O2iii0.851.952.776 (4)164
N3—H3n1···N40.862.203.055 (4)176
N3—H3n2···O3w0.862.173.009 (4)167
N6—H6n1···N5iv0.862.473.324 (4)177
N6—H6n2···N20.862.443.302 (4)175
Symmetry codes: (i) x, y+1, z; (ii) x, −y+2, z−1/2; (iii) x, −y+1, z−1/2; (iv) −x, y, −z−1/2.
Acknowledgements top

The authors thank Wuhan Polytechnic University and the University of Malaya for supporting this study.

references
References top

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