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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): m680.
Published online 2010 May 22. doi:  10.1107/S1600536810017770
PMCID: PMC2979429

[(Z)-1-Amino-2-cyano-2-(4,6-di-2-pyridyl­pyrimidin-2-yl)ethenolato]chlorido(N,N-dimethyl­formamide-κO)zinc(II)

Abstract

In the title complex, [Zn(C17H11N6O)Cl(C3H7NO)], the ZnII atom has a distorted square-pyramidal coordination formed by one Cl, two O and two N atoms. In the crystal structure, inter­molecular N—H(...)Cl hydrogen bonds link mol­ecules into centrosymmetric dimers, which are further assembled by π–π inter­actions [centroid–centroid distances = 3.809 (3) and 3.834 (3) Å] into layers parallel to the ab plane. The crystal packing exhibits also weak inter­molecular C—H(...)Cl inter­actions.

Related literature

For general background concerning the self-assembly of metal complexes with organic ligands, see: Chi et al. (2008 [triangle]); Patroniak et al. (2005 [triangle]); Kovbasyuk et al. (2005 [triangle]). For related structures, see: Preston & Kennard (1969 [triangle]); Jian et al. (2004 [triangle]); Patroniak et al. (2003 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0m680-scheme1.jpg

Experimental

Crystal data

  • [Zn(C17H11N6O)Cl(C3H7NO)]
  • M r = 489.23
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0m680-efi1.jpg
  • a = 8.5610 (17) Å
  • b = 11.250 (2) Å
  • c = 12.259 (3) Å
  • α = 110.70 (3)°
  • β = 91.36 (3)°
  • γ = 101.37 (3)°
  • V = 1077.1 (4) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 1.30 mm−1
  • T = 295 K
  • 0.20 × 0.17 × 0.15 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • 10564 measured reflections
  • 4863 independent reflections
  • 4214 reflections with I > 2σ(I)
  • R int = 0.026
  • 3 standard reflections every 100 reflections intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.049
  • wR(F 2) = 0.167
  • S = 1.09
  • 4863 reflections
  • 284 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 1.58 e Å−3
  • Δρmin = −0.58 e Å−3

Data collection: CAD-4 Software (Enraf–Nonius, 1989 [triangle]); cell refinement: CAD-4 Software; data reduction: NRCVAX (Gabe et al., 1989 [triangle]); 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: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810017770/cv2708sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810017770/cv2708Isup2.hkl

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

Acknowledgments

This work was supported financially by the Doctoral Fund of Shandaong Province (grant No. 2007BS04046), People’s Republic of China.

supplementary crystallographic information

Comment

Recently, self-assembly of specially designed metal complexes have attracted intense attention due to their fascinating molecular structures and crystal-packing motifs (Chi et al., 2008). Several metal complexes with ligands containig heterocyclic pyrimidine and pyridine units have been studied previously to explore the role of hydrogen bonding in supramolecular assemblies (Patroniak et al., 2005; Kovbasyuk et al., 2005). Herein, we report the crystal structure of the title compound (I).

In (I) (Fig. 1), the zinc(II) ion is coordinated by one O anion and two N atoms of (Z)-3-amino-2-(4,6-di(pyridin-2-yl)pyrimidin-2-yl)-3- hydroxyacrylonitrile ligand, one O atom from DMF (DMF = N,N-dimethylformamide) and one Cl- anion, forming a distorted square-pyramidal geometry. The Zn—Cl distance of 2.2956 (12)Å is longer than the value of 2.212 (4) Å in ZnCl2(2,9-dimethyl-1,10-phenanthroline) (Preston et al., 1969) and 2.209 (1)Å in ZnCl2(C6H4N3CH2COPh)2 (Jian et al., 2004). The Zn—O bond lengths of 1.996 (3) and 2.066 (2)Å, respectively, are shorter than those reported previously (Patroniak et al., 2003). The Zn—N bond lengths are 2.103 (3) and 2.106 (2) Å, respectively, which are in disagreement with the corresponding five-coordination Zn—N distances found in similar compounds (Patroniak et al., 2003; Chi et al., 2008 ). The N3—Zn1—N4 bite angle is 77.58 (10)°, which is narrower than that in {Zn[4,6-bis(2-pyridyl)-2-aminopyrimidine](OOCCH3)2} [78.40 (7)°, Chi et al., 2008].

The five-membered chelate ring N3/C8/C9/N4/Zn1 (P1) is fairly planar, the deviation of atom Zn1 from the weighted least-squares plane N3/C8/C9/N4 is 0.079 Å. The dihedral angles formed by P1 with the planes N3/C14/C15/C17/O1/Zn1(P2), N2/C6—C8/N3/C14(P3), N4/C9—C13(P4) and N1/C1—C5(P5) are 16.67, 9.93, 5.02 and 19.49°, respectively. The dihedral angles formed by P3 with P4 and P5 are 5.61 and 16.55°, respectively. The dihedral angle between P2 and P4 is 14.55°.

In the crystal structure, intermolecular N—H···Cl hydrogen bonds (Table 2) link molecules into centrosymmetric dimers, which are further assembled by π-π interactions (Table 1) into layers parallel to ab plane. The crystal packing exhibits also weak intermolecular C—H···Cl interactions (Table 2).

Experimental

The title complex was prepared by the reaction of (Z)-3-amino-2-(4,6-di(pyridin-2-yl)pyrimidin-2-yl)-3-\ hydroxyacrylonitrile (3.16 g, 10 mmol) with Zinc dichloride (1.36 g, 10 mmol) in water solution at 353 K for four hours. Single crystals suitable for x-ray measurements were obtained by recrystallization from DMF at room temperature.

Refinement

All H atoms, except H1, were fixed geometrically and allowed to ride on their attached atoms, with C—H distances constrained to 0.93-0.96Å, N—H = 0.86 Å, and with Uiso(H) = 1.2-1.5Ueq (C, N). Atom H1 was located on a difference map and refined isotropically.

Figures

Fig. 1.
The structure of the title compound showing 50% probability displacement ellipsoids and the atom-numbering scheme.

Crystal data

[Zn(C17H11N6O)Cl(C3H7NO)]Z = 2
Mr = 489.23F(000) = 500
Triclinic, P1Dx = 1.509 Mg m3
Hall symbol: -p 1Mo Kα radiation, λ = 0.71073 Å
a = 8.5610 (17) ÅCell parameters from 25 reflections
b = 11.250 (2) Åθ = 4–14°
c = 12.259 (3) ŵ = 1.30 mm1
α = 110.70 (3)°T = 295 K
β = 91.36 (3)°Block, red
γ = 101.37 (3)°0.20 × 0.17 × 0.15 mm
V = 1077.1 (4) Å3

Data collection

Enraf–Nonius CAD-4 diffractometerRint = 0.026
Radiation source: fine-focus sealed tubeθmax = 27.5°, θmin = 3.0°
graphiteh = −10→11
ω scansk = −14→14
10564 measured reflectionsl = −15→15
4863 independent reflections3 standard reflections every 100 reflections
4214 reflections with I > 2σ(I) intensity decay: none

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.167H atoms treated by a mixture of independent and constrained refinement
S = 1.09w = 1/[σ2(Fo2) + (0.1038P)2 + 0.732P] where P = (Fo2 + 2Fc2)/3
4863 reflections(Δ/σ)max = 0.001
284 parametersΔρmax = 1.58 e Å3
0 restraintsΔρmin = −0.58 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
Zn10.33598 (4)0.22665 (3)0.92885 (3)0.03870 (16)
Cl10.17317 (10)0.36222 (8)1.02298 (8)0.0497 (2)
O10.5618 (3)0.3196 (3)0.9911 (2)0.0511 (6)
O20.3716 (3)0.2649 (3)0.7773 (2)0.0542 (6)
N10.3389 (4)−0.0424 (3)1.3640 (3)0.0566 (8)
N20.4266 (4)0.0756 (3)1.2026 (3)0.0496 (7)
N30.3565 (3)0.1094 (2)1.0273 (2)0.0328 (5)
N40.1814 (3)0.0487 (3)0.8275 (2)0.0401 (6)
N50.7321 (5)0.3459 (4)1.3637 (3)0.0727 (10)
N60.7680 (4)0.4302 (3)1.1244 (3)0.0591 (8)
H6A0.80200.47361.08110.071*
H6B0.82090.44621.19040.071*
N70.4824 (4)0.3814 (3)0.6721 (3)0.0499 (7)
C10.3016 (6)−0.0996 (5)1.4418 (4)0.0646 (11)
H1B0.3465−0.05511.51890.078*
C20.2027 (5)−0.2183 (5)1.4156 (4)0.0628 (10)
H2B0.1794−0.25301.47330.075*
C30.1376 (6)−0.2861 (5)1.3011 (4)0.0655 (11)
H3A0.0698−0.36791.27990.079*
C40.1749 (5)−0.2300 (4)1.2179 (4)0.0562 (9)
H4A0.1348−0.27461.13970.067*
C50.2727 (4)−0.1070 (3)1.2534 (3)0.0417 (7)
C60.3068 (4)−0.0356 (3)1.1717 (3)0.0375 (6)
C70.2136 (4)−0.0771 (3)1.0636 (3)0.0377 (6)
H7A0.1342−0.15331.03860.045*
C80.2430 (3)−0.0020 (3)0.9955 (2)0.0344 (6)
C90.1483 (3)−0.0380 (3)0.8802 (2)0.0358 (6)
C100.0349 (4)−0.1544 (3)0.8286 (3)0.0460 (7)
H10A0.0137−0.21410.86580.055*
C11−0.0458 (5)−0.1798 (4)0.7204 (3)0.0538 (9)
H11A−0.1233−0.25620.68500.065*
C12−0.0105 (4)−0.0919 (4)0.6666 (3)0.0526 (8)
H12A−0.0620−0.10850.59340.063*
C130.1019 (4)0.0213 (4)0.7218 (3)0.0483 (8)
H13A0.12420.08150.68520.058*
C140.4514 (3)0.1485 (3)1.1287 (2)0.0354 (6)
C150.5791 (4)0.2644 (3)1.1610 (3)0.0385 (6)
C160.6641 (4)0.3068 (3)1.2730 (3)0.0448 (7)
C170.6313 (4)0.3365 (3)1.0886 (3)0.0392 (6)
C180.4729 (4)0.3546 (4)0.7681 (3)0.0460 (7)
C190.3704 (7)0.3062 (5)0.5696 (4)0.0831 (15)
H19A0.29530.24050.58580.125*
H19B0.42750.26550.50530.125*
H19C0.31400.36270.54960.125*
C200.6072 (6)0.4868 (4)0.6641 (4)0.0608 (10)
H20A0.67420.52850.73700.091*
H20B0.55830.54930.64780.091*
H20C0.67090.45160.60220.091*
H10.546 (5)0.406 (4)0.831 (4)0.056 (11)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Zn10.0394 (2)0.0427 (2)0.0365 (2)0.00096 (15)0.00087 (14)0.02205 (16)
Cl10.0495 (5)0.0453 (4)0.0573 (5)0.0067 (3)0.0090 (4)0.0242 (4)
O10.0415 (12)0.0654 (16)0.0501 (13)−0.0046 (11)−0.0003 (10)0.0344 (12)
O20.0582 (15)0.0631 (16)0.0436 (13)−0.0035 (12)0.0051 (11)0.0313 (12)
N10.068 (2)0.0629 (19)0.0421 (15)0.0026 (15)−0.0026 (14)0.0297 (14)
N20.0516 (16)0.0552 (17)0.0468 (15)0.0107 (13)0.0047 (12)0.0251 (13)
N30.0365 (12)0.0333 (11)0.0290 (11)0.0053 (9)0.0033 (9)0.0130 (9)
N40.0424 (13)0.0445 (14)0.0350 (13)0.0048 (11)0.0015 (10)0.0191 (11)
N50.074 (2)0.079 (3)0.055 (2)−0.0010 (19)−0.0158 (17)0.0238 (18)
N60.0483 (17)0.0606 (19)0.067 (2)−0.0140 (14)−0.0101 (14)0.0364 (16)
N70.0607 (18)0.0525 (16)0.0411 (14)0.0061 (13)0.0101 (13)0.0257 (12)
C10.079 (3)0.077 (3)0.046 (2)0.009 (2)0.0025 (18)0.0359 (19)
C20.068 (2)0.080 (3)0.063 (2)0.018 (2)0.0154 (19)0.052 (2)
C30.070 (3)0.063 (2)0.073 (3)−0.003 (2)0.000 (2)0.046 (2)
C40.063 (2)0.056 (2)0.055 (2)−0.0007 (17)−0.0042 (17)0.0341 (17)
C50.0447 (16)0.0456 (17)0.0432 (16)0.0119 (13)0.0056 (12)0.0253 (13)
C60.0407 (15)0.0404 (15)0.0376 (15)0.0112 (12)0.0084 (12)0.0202 (12)
C70.0402 (15)0.0362 (14)0.0373 (14)0.0037 (11)0.0035 (11)0.0169 (12)
C80.0369 (14)0.0351 (14)0.0325 (13)0.0080 (11)0.0044 (11)0.0137 (11)
C90.0342 (14)0.0401 (15)0.0333 (14)0.0081 (11)0.0044 (11)0.0138 (11)
C100.0490 (18)0.0418 (16)0.0439 (17)0.0021 (13)−0.0014 (13)0.0164 (13)
C110.0513 (19)0.0502 (19)0.0464 (18)−0.0023 (15)−0.0069 (15)0.0092 (15)
C120.0515 (19)0.062 (2)0.0381 (17)0.0084 (16)−0.0079 (14)0.0143 (15)
C130.0515 (19)0.057 (2)0.0364 (16)0.0049 (15)−0.0040 (13)0.0217 (14)
C140.0358 (14)0.0375 (14)0.0354 (14)0.0085 (11)0.0046 (11)0.0161 (11)
C150.0376 (14)0.0402 (15)0.0376 (15)0.0041 (12)0.0004 (11)0.0164 (12)
C160.0436 (17)0.0468 (17)0.0401 (17)0.0031 (13)−0.0038 (13)0.0153 (13)
C170.0332 (14)0.0401 (15)0.0434 (16)0.0045 (11)0.0018 (11)0.0163 (13)
C180.0488 (18)0.0525 (19)0.0398 (16)0.0079 (15)0.0064 (13)0.0223 (14)
C190.110 (4)0.086 (3)0.048 (2)−0.009 (3)−0.012 (2)0.036 (2)
C200.075 (3)0.058 (2)0.061 (2)0.0138 (19)0.027 (2)0.0358 (18)

Geometric parameters (Å, °)

Zn1—O11.996 (3)C3—H3A0.9300
Zn1—O22.066 (2)C4—C51.380 (5)
Zn1—N42.103 (3)C4—H4A0.9300
Zn1—N32.106 (2)C5—C61.491 (4)
Zn1—Cl12.2956 (12)C6—C71.406 (4)
O1—C171.256 (4)C7—C81.378 (4)
O2—C181.234 (4)C7—H7A0.9300
N1—C11.338 (5)C8—C91.493 (4)
N1—C51.339 (5)C9—C101.394 (4)
N2—C61.378 (4)C10—C111.388 (5)
N2—C141.416 (4)C10—H10A0.9300
N3—C81.350 (4)C11—C121.362 (6)
N3—C141.350 (4)C11—H11A0.9300
N4—C91.339 (4)C12—C131.372 (5)
N4—C131.353 (4)C12—H12A0.9300
N5—C161.136 (5)C13—H13A0.9300
N6—C171.355 (4)C14—C151.451 (4)
N6—H6A0.8600C15—C161.413 (4)
N6—H6B0.8600C15—C171.426 (4)
N7—C181.314 (4)C18—H10.91 (4)
N7—C191.444 (6)C19—H19A0.9600
N7—C201.465 (5)C19—H19B0.9600
C1—C21.357 (6)C19—H19C0.9600
C1—H1B0.9300C20—H20A0.9600
C2—C31.379 (6)C20—H20B0.9600
C2—H2B0.9300C20—H20C0.9600
C3—C41.389 (5)
Cg1···Cg1i3.809 (3)Cg1···Cg2ii3.834 (3)
O1—Zn1—O289.37 (11)C8—C7—H7A120.9
O1—Zn1—N4146.12 (12)C6—C7—H7A120.9
O2—Zn1—N488.67 (11)N3—C8—C7123.4 (3)
O1—Zn1—N387.29 (10)N3—C8—C9114.8 (3)
O2—Zn1—N3149.32 (11)C7—C8—C9121.8 (3)
N4—Zn1—N377.58 (10)N4—C9—C10121.5 (3)
O1—Zn1—Cl1107.51 (9)N4—C9—C8115.4 (3)
O2—Zn1—Cl1103.78 (9)C10—C9—C8123.1 (3)
N4—Zn1—Cl1105.79 (8)C11—C10—C9118.8 (3)
N3—Zn1—Cl1106.30 (7)C11—C10—H10A120.6
C17—O1—Zn1126.9 (2)C9—C10—H10A120.6
C18—O2—Zn1125.8 (2)C12—C11—C10119.5 (3)
C1—N1—C5117.3 (3)C12—C11—H11A120.3
C6—N2—C14120.6 (3)C10—C11—H11A120.3
C8—N3—C14119.3 (2)C11—C12—C13119.2 (3)
C8—N3—Zn1114.61 (19)C11—C12—H12A120.4
C14—N3—Zn1124.8 (2)C13—C12—H12A120.4
C9—N4—C13118.6 (3)N4—C13—C12122.5 (3)
C9—N4—Zn1115.2 (2)N4—C13—H13A118.8
C13—N4—Zn1125.8 (2)C12—C13—H13A118.8
C17—N6—H6A120.0N3—C14—N2119.8 (3)
C17—N6—H6B120.0N3—C14—C15119.9 (3)
H6A—N6—H6B120.0N2—C14—C15120.3 (3)
C18—N7—C19120.9 (3)C16—C15—C17116.8 (3)
C18—N7—C20121.7 (3)C16—C15—C14117.0 (3)
C19—N7—C20117.4 (3)C17—C15—C14126.1 (3)
N1—C1—C2124.4 (4)N5—C16—C15177.3 (4)
N1—C1—H1B117.8O1—C17—N6115.8 (3)
C2—C1—H1B117.8O1—C17—C15125.4 (3)
C1—C2—C3118.3 (4)N6—C17—C15118.9 (3)
C1—C2—H2B120.9O2—C18—N7123.6 (3)
C3—C2—H2B120.9O2—C18—H1119 (3)
C2—C3—C4118.8 (4)N7—C18—H1117 (3)
C2—C3—H3A120.6N7—C19—H19A109.5
C4—C3—H3A120.6N7—C19—H19B109.5
C5—C4—C3118.8 (4)H19A—C19—H19B109.5
C5—C4—H4A120.6N7—C19—H19C109.5
C3—C4—H4A120.6H19A—C19—H19C109.5
N1—C5—C4122.3 (3)H19B—C19—H19C109.5
N1—C5—C6115.6 (3)N7—C20—H20A109.5
C4—C5—C6122.0 (3)N7—C20—H20B109.5
N2—C6—C7118.5 (3)H20A—C20—H20B109.5
N2—C6—C5120.6 (3)N7—C20—H20C109.5
C7—C6—C5120.8 (3)H20A—C20—H20C109.5
C8—C7—C6118.3 (3)H20B—C20—H20C109.5

Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+2, −y+2, −z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N6—H6A···Cl1iii0.862.573.396 (4)161
C10—H10A···Cl1iv0.932.803.670 (4)156

Symmetry codes: (iii) −x+1, −y+1, −z+2; (iv) −x, −y, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2708).

References

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  • Jian, F., Xiao, H. & Sun, P. (2004). Acta Cryst. E60, m38–m39.
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