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Acta Crystallogr Sect E Struct Rep Online. 2008 April 1; 64(Pt 4): m537.
Published online 2008 March 14. doi:  10.1107/S1600536808006521
PMCID: PMC2960974

Bis(2-amino­pyrimidine-κN 1)diaqua­dinitrato-κO2 O,O′-cadmium(II) monohydrate

Abstract

In the title compound, [Cd(NO3)2(C4H5N3)2(H2O)2]·H2O, the Cd atom is seven-coordinated by two 2-amino­pyrimidine mol­ecules, two water mol­ecules, one bidentate nitrate anion and one monodentate nitrate anion. A network of N—H(...)O, N—H(...)N and O—H(...)O hydrogen bonds helps to consolidate the crystal structure.

Related literature

For related literature, see: Cui et al. (2003 [triangle]).

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Object name is e-64-0m537-scheme1.jpg

Experimental

Crystal data

  • [Cd(NO3)2(C4H5N3)2(H2O)2]·H2O
  • M r = 480.69
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m537-efi1.jpg
  • a = 13.451 (2) Å
  • b = 7.8692 (14) Å
  • c = 16.699 (3) Å
  • β = 101.330 (2)°
  • V = 1733.2 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 1.32 mm−1
  • T = 298 (2) K
  • 0.57 × 0.47 × 0.34 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2000 [triangle]) T min = 0.519, T max = 0.662
  • 9748 measured reflections
  • 3771 independent reflections
  • 3209 reflections with I > 2σ(I)
  • R int = 0.046

Refinement

  • R[F 2 > 2σ(F 2)] = 0.029
  • wR(F 2) = 0.079
  • S = 1.04
  • 3771 reflections
  • 236 parameters
  • H-atom parameters constrained
  • Δρmax = 0.83 e Å−3
  • Δρmin = −0.99 e Å−3

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Selected bond lengths (Å)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808006521/hb2693sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808006521/hb2693Isup2.hkl

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

Acknowledgments

The authors thank the National Natural Science Foundation of China (20671073), the National Natural Science Foundation of Shandong, the Science and Technology Foundation of Weifang and Weifang University for research grants.

supplementary crystallographic information

Comment

As part of the ongoing studies (Cui et al., 2003) of the coordination chemistry of Cd(II) ion, we now report the synthesis and structure of the title compound, (I), (Fig. 1).

The Cd atom in (I) is seven-coordinate with two N-donor 2-aminopyrimidine molecules, two water molecules and one bidentate NO3- and one monodentate NO3- ions (Table 1). The coordination polyhedron around Cd is a distorted pengonal bipyramidal with the N atoms in the axial positions [N1—Cd1—N4 = 164.13 (9)°]. The dihedral angle between the aromatic ring planes is 33.76 (17)°.

A network of N—H···O, N—H···N and O—H···O hydrogen bonds (Table 2) helps to establish the structure of (I).

Experimental

A solution of 0.5 mmol C d(NO3)2.4H2O in 10 ml 95% ethanol was added to a solution of 1.0 mmol 2-aminopyrimidine in 10 ml e thanol at room temperature. The mixture was refluxed for 2 h with stirring, then the resulting precipitate was filtered, washed, and dried in vacuo over P4O10 for 48 h. Colourless blocks of (I) were recrystallized from methanol at room temperature.

Refinement

The H atoms were placed geometrically (C—H = 0.93–0.96 Å, O—H = 0.82 Å, N—H = 0.86 Å) and refined as riding with Uiso(H) = 1.2Ueq(carrier) or 1.5Ueq(methyl C). Some short H···H contacts arise from this geometrical placement scheme and the positions of the water H atoms should be regarded as less certain.

Figures

Fig. 1.
The molecular structure of the complex ion in (I) showing 50% displacement ellipsoids for the non-hydrogen atoms. Hydrogen bonds are indicated by double-dashed lines.

Crystal data

[Cd(NO3)2(C4H5N3)2(H2O)2]·H2OF000 = 960
Mr = 480.69Dx = 1.842 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 6206 reflections
a = 13.451 (2) Åθ = 2.6–28.2º
b = 7.8692 (14) ŵ = 1.32 mm1
c = 16.699 (3) ÅT = 298 (2) K
β = 101.330 (2)ºBlock, colourless
V = 1733.2 (5) Å30.57 × 0.47 × 0.34 mm
Z = 4

Data collection

Bruker SMART CCD diffractometer3771 independent reflections
Radiation source: fine-focus sealed tube3209 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.046
T = 298(2) Kθmax = 27.0º
ω scansθmin = 1.5º
Absorption correction: multi-scan(SADABS; Bruker, 2000)h = −16→17
Tmin = 0.519, Tmax = 0.662k = −10→9
9748 measured reflectionsl = −21→17

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.030  w = 1/[σ2(Fo2) + (0.0376P)2 + 0.7065P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.079(Δ/σ)max = 0.001
S = 1.04Δρmax = 0.83 e Å3
3771 reflectionsΔρmin = −0.99 e Å3
236 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0486 (12)
Secondary atom site location: difference Fourier map

Special details

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)

xyzUiso*/Ueq
Cd10.247663 (13)0.03671 (3)0.205049 (12)0.02590 (11)
N10.26466 (19)−0.0114 (4)0.06883 (17)0.0349 (6)
N20.2023 (2)−0.0805 (4)−0.07156 (17)0.0471 (7)
N30.10954 (19)−0.1429 (4)0.02583 (17)0.0441 (7)
H3A0.0637−0.1851−0.01220.053*
H3B0.1010−0.14330.07550.053*
N40.26970 (18)0.0332 (3)0.35116 (16)0.0326 (6)
N50.3562 (2)0.0073 (4)0.49009 (17)0.0452 (7)
N60.4438 (2)−0.0069 (5)0.38605 (19)0.0649 (11)
H6A0.4983−0.02060.42230.078*
H6B0.4468−0.00500.33510.078*
N70.36446 (17)−0.2853 (3)0.22553 (16)0.0343 (6)
N80.10409 (17)0.3297 (3)0.14881 (17)0.0349 (6)
O10.27101 (15)−0.2961 (4)0.21618 (17)0.0569 (7)
O20.40409 (16)−0.1442 (3)0.21968 (15)0.0416 (5)
O30.41920 (17)−0.4123 (3)0.2418 (2)0.0610 (8)
O40.16425 (16)0.3041 (3)0.21572 (16)0.0496 (6)
O50.0921 (2)0.2158 (3)0.09573 (16)0.0580 (7)
O60.0575 (2)0.4627 (3)0.13678 (18)0.0554 (7)
O70.09014 (14)−0.0842 (3)0.19628 (13)0.0323 (5)
H7A0.0430−0.01550.20140.039*
H7B0.0838−0.17320.22360.039*
O80.37736 (15)0.2381 (3)0.21821 (16)0.0471 (6)
H8A0.38660.34450.22460.056*
H8B0.43480.18930.22930.056*
O90.06716 (14)0.8659 (3)0.78566 (13)0.0373 (5)
H9A0.01600.85740.80830.045*
H9B0.05010.92170.74150.045*
C10.1937 (2)−0.0771 (4)0.00777 (19)0.0346 (7)
C20.2866 (3)−0.0177 (5)−0.0896 (2)0.0549 (10)
H20.2937−0.0173−0.14390.066*
C30.3639 (3)0.0467 (5)−0.0314 (3)0.0543 (10)
H30.42340.0880−0.04480.065*
C40.3488 (2)0.0470 (5)0.0473 (2)0.0473 (9)
H40.39990.09020.08800.057*
C50.3540 (2)0.0118 (4)0.40915 (19)0.0347 (7)
C60.2691 (3)0.0261 (5)0.5134 (2)0.0506 (9)
H60.26840.02180.56900.061*
C70.1779 (2)0.0521 (5)0.4590 (2)0.0476 (9)
H70.11720.06700.47680.057*
C80.1826 (2)0.0548 (4)0.3780 (2)0.0390 (8)
H80.12310.07210.33990.047*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cd10.02132 (13)0.02807 (15)0.02691 (14)0.00027 (7)0.00130 (8)−0.00120 (8)
N10.0284 (12)0.0439 (15)0.0309 (14)−0.0010 (11)0.0027 (10)−0.0027 (12)
N20.0498 (16)0.0603 (19)0.0316 (15)−0.0003 (14)0.0091 (12)−0.0078 (15)
N30.0411 (14)0.0565 (19)0.0344 (14)−0.0135 (13)0.0068 (11)−0.0118 (14)
N40.0259 (11)0.0400 (15)0.0300 (13)0.0013 (10)0.0007 (10)−0.0027 (11)
N50.0373 (14)0.068 (2)0.0273 (14)0.0051 (13)−0.0008 (11)−0.0018 (14)
N60.0285 (14)0.135 (3)0.0289 (15)0.0179 (16)−0.0006 (12)0.0009 (18)
N70.0295 (12)0.0305 (14)0.0426 (15)0.0048 (10)0.0067 (10)−0.0004 (12)
N80.0287 (11)0.0337 (14)0.0438 (15)0.0006 (11)0.0109 (11)0.0013 (12)
O10.0241 (10)0.0641 (18)0.083 (2)0.0028 (11)0.0109 (11)0.0149 (15)
O20.0442 (11)0.0270 (12)0.0487 (14)−0.0064 (9)−0.0025 (10)0.0000 (10)
O30.0417 (13)0.0315 (13)0.112 (3)0.0132 (11)0.0204 (14)0.0121 (15)
O40.0369 (11)0.0470 (14)0.0571 (15)0.0023 (10)−0.0096 (10)0.0069 (12)
O50.0936 (19)0.0413 (14)0.0451 (15)−0.0025 (13)0.0288 (14)−0.0077 (12)
O60.0562 (15)0.0451 (15)0.0617 (18)0.0282 (12)0.0039 (13)0.0021 (13)
O70.0255 (9)0.0335 (11)0.0384 (11)0.0016 (8)0.0069 (8)0.0045 (10)
O80.0296 (10)0.0326 (12)0.0763 (18)−0.0078 (9)0.0038 (10)−0.0030 (12)
O90.0358 (10)0.0433 (13)0.0343 (11)0.0034 (9)0.0103 (9)0.0027 (10)
C10.0370 (15)0.0350 (17)0.0305 (15)0.0058 (12)0.0033 (12)−0.0055 (13)
C20.059 (2)0.073 (3)0.0362 (19)0.0019 (19)0.0197 (17)−0.0019 (19)
C30.0426 (19)0.076 (3)0.048 (2)−0.0033 (17)0.0194 (16)−0.001 (2)
C40.0312 (16)0.066 (3)0.044 (2)−0.0030 (15)0.0043 (14)−0.0048 (18)
C50.0278 (14)0.0475 (18)0.0265 (15)0.0022 (13)−0.0005 (12)−0.0014 (14)
C60.050 (2)0.076 (3)0.0254 (16)−0.0004 (18)0.0075 (15)−0.0066 (17)
C70.0344 (16)0.072 (3)0.0373 (18)−0.0029 (15)0.0101 (14)−0.0116 (18)
C80.0235 (14)0.055 (2)0.0368 (17)0.0013 (13)0.0023 (12)−0.0070 (15)

Geometric parameters (Å, °)

Cd1—O72.3009 (19)N7—O31.239 (3)
Cd1—O82.335 (2)N7—O21.244 (3)
Cd1—N12.361 (3)N8—O61.216 (3)
Cd1—N42.399 (3)N8—O51.249 (3)
Cd1—O42.407 (2)N8—O41.260 (3)
Cd1—O22.512 (2)O7—H7A0.8500
Cd1—O12.640 (3)O7—H7B0.8500
N1—C41.335 (4)O8—H8A0.8500
N1—C11.355 (4)O8—H8B0.8501
N2—C21.324 (5)O9—H9A0.8500
N2—C11.353 (4)O9—H9B0.8500
N3—C11.332 (4)C2—C31.373 (6)
N3—H3A0.8600C2—H20.9300
N3—H3B0.8600C3—C41.370 (5)
N4—C81.345 (4)C3—H30.9300
N4—C51.349 (4)C4—H40.9300
N5—C61.315 (4)C6—C71.390 (5)
N5—C51.346 (4)C6—H60.9300
N6—C51.347 (4)C7—C81.366 (5)
N6—H6A0.8600C7—H70.9300
N6—H6B0.8600C8—H80.9300
N7—O11.239 (3)
O7—Cd1—O8161.47 (8)O6—N8—O5120.7 (3)
O7—Cd1—N197.74 (8)O6—N8—O4120.3 (3)
O8—Cd1—N189.28 (9)O5—N8—O4119.0 (3)
O7—Cd1—N489.33 (8)N7—O1—Cd192.53 (19)
O8—Cd1—N488.35 (9)N7—O2—Cd198.61 (16)
N1—Cd1—N4164.13 (9)N8—O4—Cd1107.6 (2)
O7—Cd1—O485.94 (8)Cd1—O7—H7A115.3
O8—Cd1—O475.54 (8)Cd1—O7—H7B119.7
N1—Cd1—O4110.25 (9)H7A—O7—H7B108.3
N4—Cd1—O484.32 (9)Cd1—O8—H8A140.2
O7—Cd1—O2121.01 (7)Cd1—O8—H8B110.1
O8—Cd1—O277.26 (8)H8A—O8—H8B108.3
N1—Cd1—O276.42 (8)H9A—O9—H9B108.8
N4—Cd1—O287.76 (8)N3—C1—N2117.0 (3)
O4—Cd1—O2151.84 (7)N3—C1—N1118.8 (3)
O7—Cd1—O171.92 (7)N2—C1—N1124.2 (3)
O8—Cd1—O1126.19 (7)N2—C2—C3122.7 (4)
N1—Cd1—O182.89 (9)N2—C2—H2118.6
N4—Cd1—O185.87 (9)C3—C2—H2118.6
O4—Cd1—O1155.85 (7)C4—C3—C2116.4 (3)
O2—Cd1—O149.10 (6)C4—C3—H3121.8
C4—N1—C1116.0 (3)C2—C3—H3121.8
C4—N1—Cd1116.9 (2)N1—C4—C3123.4 (3)
C1—N1—Cd1126.8 (2)N1—C4—H4118.3
C2—N2—C1117.2 (3)C3—C4—H4118.3
C1—N3—H3A120.0N5—C5—N6116.1 (3)
C1—N3—H3B120.0N5—C5—N4125.0 (3)
H3A—N3—H3B120.0N6—C5—N4118.9 (3)
C8—N4—C5116.1 (3)N5—C6—C7123.1 (3)
C8—N4—Cd1113.3 (2)N5—C6—H6118.4
C5—N4—Cd1130.5 (2)C7—C6—H6118.4
C6—N5—C5116.7 (3)C8—C7—C6116.3 (3)
C5—N6—H6A120.0C8—C7—H7121.9
C5—N6—H6B120.0C6—C7—H7121.9
H6A—N6—H6B120.0N4—C8—C7122.8 (3)
O1—N7—O3121.1 (3)N4—C8—H8118.6
O1—N7—O2119.4 (3)C7—C8—H8118.6
O3—N7—O2119.5 (2)
O7—Cd1—N1—C4178.2 (2)O8—Cd1—O2—N7172.1 (2)
O8—Cd1—N1—C415.4 (3)N1—Cd1—O2—N7−95.49 (19)
N4—Cd1—N1—C4−66.0 (5)N4—Cd1—O2—N783.32 (19)
O4—Cd1—N1—C489.7 (3)O4—Cd1—O2—N7156.87 (19)
O2—Cd1—N1—C4−61.7 (2)O1—Cd1—O2—N7−3.15 (17)
O1—Cd1—N1—C4−111.3 (2)O6—N8—O4—Cd1−175.1 (2)
O7—Cd1—N1—C15.2 (3)O5—N8—O4—Cd15.9 (3)
O8—Cd1—N1—C1−157.6 (3)O7—Cd1—O4—N8−65.67 (19)
N4—Cd1—N1—C1121.0 (3)O8—Cd1—O4—N8114.8 (2)
O4—Cd1—N1—C1−83.3 (3)N1—Cd1—O4—N831.1 (2)
O2—Cd1—N1—C1125.4 (3)N4—Cd1—O4—N8−155.4 (2)
O1—Cd1—N1—C175.8 (3)O2—Cd1—O4—N8130.22 (19)
O7—Cd1—N4—C8−32.6 (2)O1—Cd1—O4—N8−88.9 (3)
O8—Cd1—N4—C8129.0 (2)C2—N2—C1—N3−178.9 (3)
N1—Cd1—N4—C8−149.4 (3)C2—N2—C1—N11.2 (5)
O4—Cd1—N4—C853.4 (2)C4—N1—C1—N3177.6 (3)
O2—Cd1—N4—C8−153.7 (2)Cd1—N1—C1—N3−9.4 (4)
O1—Cd1—N4—C8−104.5 (2)C4—N1—C1—N2−2.4 (5)
O7—Cd1—N4—C5146.7 (3)Cd1—N1—C1—N2170.6 (2)
O8—Cd1—N4—C5−51.7 (3)C1—N2—C2—C30.9 (6)
N1—Cd1—N4—C529.8 (5)N2—C2—C3—C4−1.5 (6)
O4—Cd1—N4—C5−127.3 (3)C1—N1—C4—C31.7 (5)
O2—Cd1—N4—C525.6 (3)Cd1—N1—C4—C3−172.0 (3)
O1—Cd1—N4—C574.7 (3)C2—C3—C4—N10.1 (6)
O3—N7—O1—Cd1173.5 (3)C6—N5—C5—N6179.7 (4)
O2—N7—O1—Cd1−5.5 (3)C6—N5—C5—N4−0.3 (5)
O7—Cd1—O1—N7−178.1 (2)C8—N4—C5—N51.3 (5)
O8—Cd1—O1—N7−2.6 (2)Cd1—N4—C5—N5−177.9 (2)
N1—Cd1—O1—N781.30 (19)C8—N4—C5—N6−178.6 (3)
N4—Cd1—O1—N7−87.48 (19)Cd1—N4—C5—N62.1 (5)
O4—Cd1—O1—N7−153.7 (2)C5—N5—C6—C7−1.0 (6)
O2—Cd1—O1—N73.13 (17)N5—C6—C7—C81.0 (6)
O1—N7—O2—Cd15.8 (3)C5—N4—C8—C7−1.2 (5)
O3—N7—O2—Cd1−173.2 (3)Cd1—N4—C8—C7178.1 (3)
O7—Cd1—O2—N7−4.5 (2)C6—C7—C8—N40.1 (6)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3A···O5i0.862.293.105 (4)158
N3—H3B···O70.862.102.945 (4)167
N6—H6A···N5ii0.862.203.054 (4)170
N6—H6B···O20.862.192.931 (4)144
N6—H6B···O3iii0.862.523.171 (4)133
O7—H7A···O9iv0.851.942.787 (3)178
O7—H7B···O9v0.851.872.724 (3)178
O8—H8A···O3vi0.851.972.820 (3)176
O8—H8B···O3iii0.852.092.936 (3)176
O9—H9A···O5iv0.852.443.255 (3)162
O9—H9A···O7iv0.852.282.787 (3)119
O9—H9B···O6vii0.851.992.809 (4)161

Symmetry codes: (i) −x, −y, −z; (ii) −x+1, −y, −z+1; (iii) −x+1, y+1/2, −z+1/2; (iv) −x, −y+1, −z+1; (v) x, −y+1/2, z−1/2; (vi) x, y+1, z; (vii) x, −y+3/2, z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB2693).

References

  • Bruker (2000). SMART, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cui, Y., Ngo, L. H., White, P. S. & Lin, W. B. (2003). Inorg. Chem.42, 652–660. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography