Bis(acetato-κO)triaqua­cadmium 2-amino-4,6-dimethyl­pyrimidine tetra­solvate dihydrate

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...O_COO 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.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.004 Å
• Disorder in main residue
• R factor = 0.052
• wR factor = 0.145
• Data-to-parameter ratio = 18.4

checkCIF/PLATON results

No syntax errors found



Alert level B
ABSTM02_ALERT_3_B  The ratio of expected to reported Tmax/Tmin(RR') is < 0.75
            Tmin and Tmax reported:      0.567     0.903
            Tmin(prime) and Tmax expected:      0.767     0.901
            RR(prime) =      0.737
            Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_B Tmax/Tmin Range Test RR' too Large .............       0.73

Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.96
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        O1W
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        Cd1
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.27
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.15
PLAT301_ALERT_3_C Main Residue  Disorder .........................       3.00 Perc.
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          9
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          3
              C6 H9 N3

Alert level G
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          6

   0 ALERT level A = In general: serious problem
   2 ALERT level B = Potentially serious problem
   8 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   4 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

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

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).

S2. Experimental

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.

S3. Refinement

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

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

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

Crystal data

[Cd(C2H3O2)2(H2O)3]·4C6H9N3·2H2O	F(000) = 848
Mr = 813.22	Dx = 1.455 Mg m^−3
Monoclinic, P2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yc	Cell parameters from 3660 reflections
a = 19.287 (1) Å	θ = 2.9–27.5°
b = 6.7697 (4) Å	µ = 0.65 mm^−1
c = 14.2238 (4) Å	T = 295 K
β = 91.444 (1)°	Block, colorless
V = 1856.56 (16) Å^3	0.40 × 0.20 × 0.16 mm
Z = 2

Data collection

Bruker APEX CCD diffractometer	4386 independent reflections
Radiation source: fine-focus sealed tube	3794 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.053
φ and ω scans	θmax = 28.2°, θmin = 1.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −24→25
Tmin = 0.567, Tmax = 0.903	k = −8→8
13020 measured reflections	l = −15→18

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.145	H-atom parameters constrained
S = 1.11	w = 1/[σ^2(Fo^2) + (0.0786P)^2] where P = (Fo^2 + 2Fc^2)/3
4386 reflections	(Δ/σ)max = 0.001
238 parameters	Δρmax = 0.88 e Å^−3
6 restraints	Δρmin = −0.62 e Å^−3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Cd1	0.5000	0.83464 (7)	0.2500	0.03522 (16)	0.856 (2)
Cd1'	0.5000	0.6668 (5)	0.2500	0.0545 (12)	0.144 (2)
O1	0.44455 (12)	0.8964 (4)	0.37992 (17)	0.0488 (6)
O2	0.45034 (12)	0.5760 (4)	0.37344 (17)	0.0508 (6)
O1w	0.40361 (12)	0.7807 (6)	0.15998 (19)	0.0725 (10)
H1w1	0.3597	0.7741	0.1660	0.087*
H1w2	0.4116	0.7753	0.1013	0.087*
O2w	0.5000	1.2162 (7)	0.2500	0.0726 (12)
H2w1	0.4831	1.2922	0.2920	0.087*
O3w	0.41291 (12)	0.7615 (4)	−0.02930 (18)	0.0499 (6)
H3w1	0.4292	0.8643	−0.0557	0.060*
H3w2	0.4306	0.6557	−0.0509	0.060*
N1	0.25822 (12)	0.7573 (4)	0.15794 (19)	0.0381 (6)
N2	0.15315 (13)	0.7540 (5)	0.06446 (19)	0.0413 (6)
N3	0.25850 (14)	0.7558 (6)	−0.0040 (2)	0.0568 (9)
H3N1	0.2369	0.7547	−0.0577	0.068*
H3N2	0.3031	0.7570	−0.0013	0.068*
N4	0.18959 (12)	0.7447 (4)	−0.19967 (18)	0.0374 (6)
N5	0.09175 (13)	0.7455 (5)	−0.3069 (2)	0.0426 (6)
N6	0.07806 (14)	0.7472 (6)	−0.1467 (2)	0.0537 (8)
H6N1	0.0339	0.7478	−0.1565	0.064*
H6N2	0.0949	0.7475	−0.0901	0.064*
C1	0.43394 (16)	0.7257 (6)	0.4143 (2)	0.0433 (8)
C2	0.4002 (2)	0.7178 (7)	0.5091 (3)	0.0613 (10)
H2A	0.3568	0.6487	0.5032	0.092*
H2B	0.3921	0.8498	0.5310	0.092*
H2C	0.4302	0.6500	0.5532	0.092*
C3	0.22286 (15)	0.7559 (5)	0.0748 (2)	0.0376 (7)
C4	0.22067 (15)	0.7571 (5)	0.2354 (2)	0.0383 (7)
C5	0.14889 (16)	0.7550 (6)	0.2313 (2)	0.0452 (8)
H5	0.1230	0.7541	0.2856	0.054*
C6	0.11762 (15)	0.7543 (6)	0.1434 (3)	0.0440 (8)
C7	0.25937 (18)	0.7567 (6)	0.3288 (2)	0.0479 (8)
H7A	0.2491	0.6374	0.3621	0.072*
H7B	0.2453	0.8686	0.3651	0.072*
H7C	0.3083	0.7639	0.3185	0.072*
C8	0.03971 (17)	0.7526 (9)	0.1313 (3)	0.0714 (13)
H8A	0.0273	0.7562	0.0655	0.107*
H8B	0.0207	0.8660	0.1619	0.107*
H8C	0.0215	0.6345	0.1588	0.107*
C9	0.12098 (15)	0.7459 (5)	−0.2201 (2)	0.0359 (6)
C10	0.13499 (17)	0.7441 (6)	−0.3780 (2)	0.0452 (8)
C11	0.20641 (17)	0.7422 (6)	−0.3641 (2)	0.0453 (8)
H11	0.2361	0.7409	−0.4145	0.054*
C12	0.23172 (15)	0.7423 (5)	−0.2725 (2)	0.0389 (7)
C13	0.1036 (2)	0.7431 (9)	−0.4754 (3)	0.0721 (13)
H13A	0.0591	0.6794	−0.4748	0.108*
H13B	0.1335	0.6728	−0.5167	0.108*
H13C	0.0980	0.8766	−0.4972	0.108*
C14	0.30850 (16)	0.7406 (6)	−0.2523 (3)	0.0500 (9)
H14A	0.3287	0.8597	−0.2759	0.075*
H14B	0.3289	0.6286	−0.2824	0.075*
H14C	0.3170	0.7325	−0.1856	0.075*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cd1	0.02966 (19)	0.0508 (3)	0.0253 (2)	0.000	0.00195 (13)	0.000
Cd1'	0.0625 (18)	0.069 (3)	0.0324 (15)	0.000	0.0009 (11)	0.000
O1	0.0517 (12)	0.0571 (15)	0.0379 (13)	0.0050 (11)	0.0090 (10)	0.0006 (11)
O2	0.0545 (13)	0.0566 (16)	0.0419 (13)	−0.0019 (12)	0.0081 (11)	−0.0023 (12)
O1w	0.0333 (12)	0.148 (3)	0.0359 (15)	−0.0059 (14)	0.0006 (11)	−0.0090 (16)
O2w	0.087 (3)	0.078 (3)	0.055 (3)	0.000	0.027 (2)	0.000
O3w	0.0531 (13)	0.0574 (15)	0.0396 (14)	−0.0016 (11)	0.0077 (11)	0.0011 (11)
N1	0.0328 (12)	0.0482 (16)	0.0333 (14)	−0.0005 (10)	−0.0039 (11)	−0.0001 (11)
N2	0.0345 (12)	0.0579 (17)	0.0314 (14)	0.0002 (11)	−0.0023 (11)	−0.0005 (12)
N3	0.0355 (14)	0.104 (3)	0.0309 (15)	0.0007 (15)	0.0006 (12)	0.0001 (16)
N4	0.0347 (12)	0.0457 (15)	0.0318 (14)	0.0000 (10)	−0.0014 (11)	0.0003 (11)
N5	0.0349 (12)	0.0547 (18)	0.0380 (15)	−0.0006 (11)	−0.0030 (11)	0.0006 (12)
N6	0.0380 (14)	0.086 (2)	0.0374 (17)	−0.0002 (14)	0.0036 (13)	0.0009 (15)
C1	0.0323 (14)	0.067 (2)	0.0305 (16)	−0.0023 (14)	0.0029 (12)	0.0035 (15)
C2	0.061 (2)	0.086 (3)	0.037 (2)	−0.002 (2)	0.0163 (18)	0.0017 (19)
C3	0.0350 (14)	0.0467 (18)	0.0310 (16)	−0.0012 (12)	−0.0025 (12)	−0.0001 (13)
C4	0.0378 (15)	0.0460 (18)	0.0309 (16)	0.0001 (12)	−0.0018 (13)	0.0004 (13)
C5	0.0357 (15)	0.066 (2)	0.0342 (17)	−0.0004 (14)	0.0036 (14)	−0.0015 (15)
C6	0.0311 (14)	0.059 (2)	0.0412 (19)	0.0010 (13)	−0.0031 (13)	0.0003 (15)
C7	0.0461 (17)	0.065 (2)	0.0317 (17)	0.0006 (15)	−0.0072 (14)	−0.0021 (15)
C8	0.0298 (16)	0.135 (4)	0.050 (2)	−0.002 (2)	0.0001 (16)	0.001 (2)
C9	0.0352 (14)	0.0381 (16)	0.0344 (16)	−0.0014 (11)	−0.0004 (12)	−0.0009 (12)
C10	0.0423 (16)	0.057 (2)	0.0358 (18)	−0.0003 (14)	−0.0073 (14)	−0.0005 (15)
C11	0.0412 (16)	0.061 (2)	0.0333 (17)	0.0005 (14)	0.0031 (14)	−0.0018 (15)
C12	0.0340 (14)	0.0457 (18)	0.0367 (17)	−0.0013 (12)	−0.0008 (13)	−0.0005 (13)
C13	0.059 (2)	0.121 (4)	0.035 (2)	0.002 (2)	−0.0132 (18)	0.001 (2)
C14	0.0323 (14)	0.071 (3)	0.046 (2)	0.0003 (14)	0.0012 (14)	0.0011 (17)

Geometric parameters (Å, º)

Cd1—O1	2.198 (2)	N5—C9	1.345 (4)
Cd1—O1^i	2.198 (2)	N6—C9	1.348 (4)
Cd1—O2	2.674 (2)	N6—H6N1	0.8600
Cd1—O2^i	2.674 (2)	N6—H6N2	0.8600
Cd1—O1w	2.260 (3)	C1—C2	1.513 (5)
Cd1—O1w^i	2.260 (3)	C2—H2A	0.9600
Cd1—O2w	2.583 (5)	C2—H2B	0.9600
Cd1'—O2^i	2.113 (3)	C2—H2C	0.9600
Cd1'—O2	2.113 (3)	C4—C5	1.384 (4)
Cd1'—O1w^i	2.360 (3)	C4—C7	1.507 (4)
Cd1'—O1w	2.360 (3)	C5—C6	1.375 (5)
Cd1'—C1	2.719 (3)	C5—H5	0.9300
Cd1'—C1^i	2.719 (3)	C6—C8	1.508 (4)
C1—O1	1.274 (5)	C7—H7A	0.9600
C1—O2	1.214 (5)	C7—H7B	0.9600
O1w—H1w1	0.85	C7—H7C	0.9600
O1w—H1w2	0.85	C8—H8A	0.9600
O2w—H2w1	0.86	C8—H8B	0.9600
O3w—H3w1	0.85	C8—H8C	0.9600
O3w—H3w2	0.85	C10—C11	1.387 (5)
N1—C4	1.334 (4)	C10—C13	1.499 (5)
N1—C3	1.350 (4)	C11—C12	1.379 (5)
N2—C6	1.330 (4)	C11—H11	0.9300
N2—C3	1.349 (4)	C12—C14	1.502 (4)
N3—C3	1.330 (4)	C13—H13A	0.9600
N3—H3N1	0.8600	C13—H13B	0.9600
N3—H3N2	0.8600	C13—H13C	0.9600
N4—C12	1.332 (4)	C14—H14A	0.9600
N4—C9	1.348 (4)	C14—H14B	0.9600
N5—C10	1.326 (4)	C14—H14C	0.9600
Cd1'—Cd1—O1	100.96 (7)	H2B—C2—H2C	109.5
Cd1'—Cd1—O1^i	100.96 (7)	N3—C3—N2	116.3 (3)
O1—Cd1—O1^i	158.07 (15)	N3—C3—N1	118.6 (3)
Cd1'—Cd1—O1w^i	80.71 (11)	N2—C3—N1	125.2 (3)
O1—Cd1—O1w^i	88.00 (9)	N1—C4—C5	121.9 (3)
O1^i—Cd1—O1w^i	95.53 (9)	N1—C4—C7	117.4 (3)
O1—Cd1—O1w	95.53 (9)	C5—C4—C7	120.6 (3)
O1^i—Cd1—O1w	88.00 (9)	C6—C5—C4	117.0 (3)
O1w^i—Cd1—O1w	161.4 (2)	C6—C5—H5	121.5
O1—Cd1—O2w	79.04 (7)	C4—C5—H5	121.5
O1^i—Cd1—O2w	79.04 (7)	N2—C6—C5	123.0 (3)
O1w^i—Cd1—O2w	99.29 (11)	N2—C6—C8	115.9 (3)
O1w—Cd1—O2w	99.29 (11)	C5—C6—C8	121.1 (3)
O2^i—Cd1'—O2	146.2 (2)	C4—C7—H7A	109.5
O2^i—Cd1'—O1w^i	100.29 (9)	C4—C7—H7B	109.5
O2—Cd1'—O1w^i	90.67 (9)	H7A—C7—H7B	109.5
O2^i—Cd1'—O1w	90.67 (9)	C4—C7—H7C	109.5
O2—Cd1'—O1w	100.29 (9)	H7A—C7—H7C	109.5
O1w^i—Cd1'—O1w	141.9 (3)	H7B—C7—H7C	109.5
C1—O1—Cd1	103.7 (2)	C6—C8—H8A	109.5
C1—O2—Cd1'	106.5 (3)	C6—C8—H8B	109.5
Cd1—O1w—H1w1	139.0	H8A—C8—H8B	109.5
Cd1'—O1w—H1w1	134.2	C6—C8—H8C	109.5
Cd1—O1w—H1w2	113.3	H8A—C8—H8C	109.5
Cd1'—O1w—H1w2	111.0	H8B—C8—H8C	109.5
H1w1—O1w—H1w2	107.5	N5—C9—N4	125.8 (3)
Cd1—O2w—H2w1	126.8	N5—C9—N6	117.4 (3)
H3w1—O3w—H3w2	111.8	N4—C9—N6	116.9 (3)
C4—N1—C3	116.8 (3)	N5—C10—C11	122.2 (3)
C6—N2—C3	116.2 (3)	N5—C10—C13	117.2 (3)
C3—N3—H3N1	120.0	C11—C10—C13	120.6 (3)
C3—N3—H3N2	120.0	C12—C11—C10	117.5 (3)
H3N1—N3—H3N2	120.0	C12—C11—H11	121.3
C12—N4—C9	116.6 (3)	C10—C11—H11	121.3
C10—N5—C9	116.3 (3)	N4—C12—C11	121.7 (3)
C9—N6—H6N1	120.0	N4—C12—C14	118.0 (3)
C9—N6—H6N2	120.0	C11—C12—C14	120.3 (3)
H6N1—N6—H6N2	120.0	C10—C13—H13A	109.5
O2—C1—O1	121.8 (3)	C10—C13—H13B	109.5
O2—C1—C2	121.4 (4)	H13A—C13—H13B	109.5
O1—C1—C2	116.8 (3)	C10—C13—H13C	109.5
O2—C1—Cd1'	48.15 (19)	H13A—C13—H13C	109.5
O1—C1—Cd1'	73.72 (19)	H13B—C13—H13C	109.5
C2—C1—Cd1'	169.2 (3)	C12—C14—H14A	109.5
C1—C2—H2A	109.5	C12—C14—H14B	109.5
C1—C2—H2B	109.5	H14A—C14—H14B	109.5
H2A—C2—H2B	109.5	C12—C14—H14C	109.5
C1—C2—H2C	109.5	H14A—C14—H14C	109.5
H2A—C2—H2C	109.5	H14B—C14—H14C	109.5
O1^i—Cd1—O1—C1	−176.9 (2)	C7—C4—C5—C6	−179.6 (3)
O1w^i—Cd1—O1—C1	−77.0 (2)	C3—N2—C6—C5	−0.5 (6)
O1w—Cd1—O1—C1	84.7 (2)	C3—N2—C6—C8	179.9 (4)
O2w—Cd1—O1—C1	−176.9 (2)	C4—C5—C6—N2	0.5 (6)
O2^i—Cd1'—O2—C1	180.0 (2)	C4—C5—C6—C8	−179.8 (4)
O1w^i—Cd1'—O2—C1	70.2 (2)	C10—N5—C9—N4	−0.1 (5)
O1w—Cd1'—O2—C1	−73.1 (3)	C10—N5—C9—N6	180.0 (3)
Cd1'—O2—C1—O1	2.9 (4)	C12—N4—C9—N5	−0.2 (5)
Cd1'—O2—C1—C2	−176.8 (3)	C12—N4—C9—N6	179.7 (3)
Cd1—O1—C1—O2	−3.6 (4)	C9—N5—C10—C11	0.3 (5)
Cd1—O1—C1—C2	176.1 (2)	C9—N5—C10—C13	179.9 (4)
C6—N2—C3—N3	−179.9 (4)	N5—C10—C11—C12	−0.2 (6)
C6—N2—C3—N1	0.2 (5)	C13—C10—C11—C12	−179.7 (4)
C4—N1—C3—N3	−179.9 (3)	C9—N4—C12—C11	0.4 (5)
C4—N1—C3—N2	−0.1 (5)	C9—N4—C12—C14	−179.9 (3)
C3—N1—C4—C5	0.1 (5)	C10—C11—C12—N4	−0.2 (6)
C3—N1—C4—C7	179.4 (3)	C10—C11—C12—C14	−179.9 (3)
N1—C4—C5—C6	−0.3 (6)

Symmetry code: (i) −x+1, y, −z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1w—H1w1···N1	0.85	1.96	2.808 (3)	171
O1w—H1w2···O3w	0.85	1.86	2.706 (4)	170
O2w—H2w1···O2^ii	0.86	2.34	3.165 (5)	162
O3w—H3w1···O1^iii	0.85	1.89	2.728 (4)	167
O3w—H3w2···O2^iv	0.85	1.95	2.776 (4)	164
N3—H3n1···N4	0.86	2.20	3.055 (4)	176
N3—H3n2···O3w	0.86	2.17	3.009 (4)	167
N6—H6n1···N5^v	0.86	2.47	3.324 (4)	177
N6—H6n2···N2	0.86	2.44	3.302 (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.