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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): m647–m648.
Published online 2010 May 15. doi:  10.1107/S1600536810016843
PMCID: PMC2979663

(2-Amino­pyrimidine-κN 1)diaqua(pyridine-2,6-dicarboxyl­ato-κ3 O 2,N,O 6)­nickel(II) monohydrate

Abstract

The reaction of Ni(NO3)2·6H2O with pyridine-2,6-dicarboxylic acid, NaOH and 2-amino­pyrimidine in aqueous solution leads to the formation of the title complex, [Ni(C7H3NO4)(C4H5N3)(H2O)2]·H2O. The NiII ion is coordinated by one N and two O atoms of the tridentate chelating pyridine-2,6-dicarboxyl­ate anion, one heterocyclic N atom of the 2-amino­pyrimidine ligand, and two water mol­ecules. The resulting geometry for the [NiN2O4] coordination environment can be described as distorted octa­hedral. One uncoord­inated water mol­ecule completes the asymmetric unit. Extensive O—H(...)O and N—H(...)O hydrogen-bonding inter­actions between the NH2 group of 2-amino­pyrimidine, carboxyl­ate groups, and coordinated and uncoordinated water mol­ecules contribute to the formation of a three-dimensional supra­molecular structure.

Related literature

For transition metal complexes with 2-amino­pyrimidine, see: Ponticelli et al. (1999 [triangle]); Prince et al. (2003 [triangle]); Lee et al. (2003 [triangle]); Masaki et al. (2002 [triangle]). For related structures, see: Tabatabaee et al. (2008 [triangle]); Tabatabaee, Aghabozorg et al. (2009 [triangle]); Tabatabaee, Masoodpour et al. (2009 [triangle]); Tabatabaee, Sharif et al. (2009 [triangle]); Altin et al. (2004 [triangle]); Aghabozorg et al. (2007 [triangle], 2008 [triangle]); Li et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0m647-scheme1.jpg

Experimental

Crystal data

  • [Ni(C7H3NO4)(C4H5N3)(H2O)2]·H2O
  • M r = 372.97
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0m647-efi5.jpg
  • a = 9.6073 (8) Å
  • b = 10.2038 (10) Å
  • c = 14.6095 (15) Å
  • β = 102.677 (2)°
  • V = 1397.3 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 1.44 mm−1
  • T = 120 K
  • 0.24 × 0.22 × 0.15 mm

Data collection

  • Bruker SMART 1000 CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 1998 [triangle]) T min = 0.717, T max = 0.810
  • 12010 measured reflections
  • 2725 independent reflections
  • 2396 reflections with I > 2σ(I)
  • R int = 0.029

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.163
  • S = 1.01
  • 2725 reflections
  • 208 parameters
  • H-atom parameters constrained
  • Δρmax = 0.65 e Å−3
  • Δρmin = −0.51 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT-Plus (Bruker, 1998 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810016843/bh2281sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810016843/bh2281Isup2.hkl

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

Acknowledgments

The author is grateful to Islamic Azad University, Yazd Branch, for the support of this work.

supplementary crystallographic information

Comment

Pyrimidine derivatives possess considerable biological activity and have been widely used in medicinal and industrial applications. The complexing ability of 2-aminopyrimidine derivatives with transition metal ions is of great interest. Several transition metal complexes of 2-aminopyrimidine with halide salts, MX2 (M= Pt, Pd, Cu, Mn, Co and Ni), have been synthesized and their crystal structures reported (Ponticelli et al., 1999; Prince et al., 2003; Lee et al., 2003; Masaki et al., 2002).

In continuation of our recent works on aminopyrimidine derivatives and hydrothermal synthesis of complexes (Tabatabaee et al., 2008; Tabatabaee, Aghabozorg et al., 2009; Tabatabaee, Masoodpour et al., 2009; Tabatabaee, Sharif et al., 2009), in this communication we wish to report our results on the synthesis and characterization of the first complex of NiII with pyridine-2,6-dicarboxylic acid (pydcH2) and neutral 2-aminopyrimidine (amp), under hydrothermal conditions.

The title compound consists of [Ni(amp)(pydc)(H2O)2] and one uncoordinated water molecule (Fig. 1). The metal ion is hexacoordinated by nitrogen atom N1 and two oxygen atoms O1 and O3 of the pydc2– fragment, which acts as a tridentate ligand, two oxygen atoms of two coordinated water molecules (O1W and O2W) and heterocyclic nitrogen atom of amp (N2). N1 and N2 atoms occupy the axial positions (shortest coordination bond lengths), while oxygen atoms form the equatorial plane. The crystal structure of a four-coordinated CuII complex with pyridine-2,6-dicarboxylate and 2-aminopyrimidine, formulated [Cu(amp)(pydc)].3H2O has been reported by Altin et al. (Altin et al., 2004). Cu2+ ion in [Cu(amp)(pydc)] is four-coordinated with a pydc2– tridentate ligand and N atom from 2-aminopyrimidine. In the title complex, N1—Ni1—N2 angle is deviated by 1.06° from linearity. The dihedral angle between the mean planes of the pyridine and pyrimidine rings is 18.5 (1)°, indicating that pyridine and pyrimidine ligands are almost parallel to each other. Ni—N distances of 1.975 (4) and 2.062 (4) Å and Ni—O distances [Ni1—O1W: 2.070 (4), Ni1—O2W: 2.076 (4), Ni1—O1: 2.117 (3) and Ni1—O7: 2.136 (4) Å] are consistent with the corresponding data reported in the literature (Aghabozorg et al., 2007; Li et al., 2007). According to bond lengths, bond angles and torsion angles, arrangement of the six donor atoms around Ni1 is distorted octahedral.

The extensive O—H···O, N—H···O hydrogen bonding interactions (Table 1) between complex and uncoordinated water molecule (Fig. 2) play an important role in stabilizing the crystal (Aghabozorg et al., 2008; Tabatabaee, Aghabozorg et al., 2009; Tabatabaee, Masoodpour et al., 2009; Tabatabaee, Sharif et al., 2009) and the formation of a three dimensional supramolecular crystal structure (Fig. 3).

Experimental

Pyridine-2,6-dicarboxylic acid (0.167 g, 1 mmol) was dissolved in 10 ml of deionized water containing 0.08 g (2 mmol) of NaOH, and stirred for 30 min. at room temperature. A water solution of Ni(NO3)2.6H2O (0.29 g, 1 mmol) and 2-aminopyrimidine (0.095 g, 1 mmol) were added to the pyridine-2,6-dicarboxylic acid solution. Reaction mixture was placed in a Parr-Teflon lined stainless steel vessel. It was sealed and heated to 403 K for 8 h. Blue crystals of the complex were obtained upon slow cooling (Yield: 88%).

Refinement

The H atoms bonded to O and N atoms were found in a difference map and normalized to distances of 0.86 and 0.85 Å, and positions of other H atoms were calculated. All hydrogen atoms were refined in isotropic approximation using a riding model, with Uiso(H) parameters equal to 1.5 Ueq(Oi), 1.2 Ueq(Ni) and 1.2 Ueq(Ci), where U(Xi) are the equivalent thermal parameters of the atoms to which the corresponding H atoms are bonded.

Figures

Fig. 1.
ORTEP-like view (30% probability level) of the title compound. The angle between the least-squares planes (N1/C2/C3/C4/C5/C6) and (N2/N3/N4/C8/C9/C10/C11) is 18.5 (1)°.
Fig. 2.
Fragment of hydrogen bonds (shown with dashed lines) in the title compound. Symmetry transformations used to generate equivalent atoms: #A x, y+1, z; #B -x+1, -y, -z; #C -x+1, -y+1, -z; #D x, -y+1/2, z-1/2; #E x+1, y, z; #F -x+1, y-1/2, -z+1/2.
Fig. 3.
Fragment of crystal packing (view along crystallographic axes c). Only H atoms involved in hydrogen bonding are depicted. Hydrogen bonds are shown with dashed lines.

Crystal data

[Ni(C7H3NO4)(C4H5N3)(H2O)2]·H2OF(000) = 768
Mr = 372.97Dx = 1.773 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 896 reflections
a = 9.6073 (8) Åθ = 2.9–25.0°
b = 10.2038 (10) ŵ = 1.44 mm1
c = 14.6095 (15) ÅT = 120 K
β = 102.677 (2)°Prism, blue
V = 1397.3 (2) Å30.24 × 0.22 × 0.15 mm
Z = 4

Data collection

Bruker SMART 1000 CCD area-detector diffractometer2725 independent reflections
Radiation source: fine-focus sealed tube2396 reflections with I > 2σ(I)
graphiteRint = 0.029
[var phi] and ω scansθmax = 26.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 1998)h = −11→11
Tmin = 0.717, Tmax = 0.810k = −12→12
12010 measured reflectionsl = −18→17

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)] = 0.056Hydrogen site location: mixed
wR(F2) = 0.163H-atom parameters constrained
S = 1.01w = 1/[σ2(Fo2) + (0.07P)2 + 9.P] where P = (Fo2 + 2Fc2)/3
2725 reflections(Δ/σ)max < 0.001
208 parametersΔρmax = 0.65 e Å3
0 restraintsΔρmin = −0.51 e Å3
0 constraints

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
Ni10.71391 (7)0.20931 (6)0.07096 (4)0.0268 (2)
N10.7944 (4)0.0931 (3)0.1775 (2)0.0212 (8)
N20.6262 (5)0.3303 (4)−0.0398 (3)0.0364 (11)
N30.5712 (6)0.5362 (6)−0.1177 (3)0.0574 (17)
N40.7236 (6)0.5244 (4)0.0275 (3)0.0451 (13)
H4B0.76780.48120.07580.054*
H4C0.73320.60800.02540.054*
O10.7779 (4)0.3446 (3)0.1821 (2)0.0328 (8)
O20.8528 (5)0.3529 (3)0.3379 (2)0.0395 (9)
O30.6800 (4)0.0198 (4)0.0080 (2)0.0328 (8)
O40.7485 (7)−0.1853 (4)0.0367 (3)0.0740 (18)
C10.8233 (6)0.2929 (4)0.2627 (3)0.0289 (11)
C20.8404 (5)0.1458 (4)0.2621 (3)0.0229 (9)
C30.8944 (5)0.0683 (5)0.3388 (3)0.0290 (10)
H3A0.92720.10480.39790.035*
C40.8982 (6)−0.0660 (5)0.3249 (4)0.0376 (12)
H4A0.9347−0.12100.37530.045*
C50.8481 (7)−0.1188 (5)0.2367 (4)0.0394 (13)
H5A0.8490−0.20880.22720.047*
C60.7967 (5)−0.0346 (4)0.1630 (3)0.0271 (10)
C70.7374 (5)−0.0716 (5)0.0620 (3)0.0307 (11)
C80.6402 (7)0.4615 (6)−0.0441 (3)0.0416 (15)
C90.5438 (7)0.2718 (7)−0.1134 (4)0.0497 (17)
H9A0.53430.1812−0.11210.060*
C100.4716 (7)0.3385 (8)−0.1914 (4)0.060 (2)
H10A0.41430.2962−0.24240.072*
C110.4907 (8)0.4728 (8)−0.1885 (4)0.068 (3)
H11A0.44360.5216−0.23970.082*
O1W0.5159 (4)0.2003 (4)0.1048 (2)0.0419 (10)
H10.47220.15490.05850.063*
H20.47210.26930.11480.063*
O2W0.9039 (4)0.2190 (3)0.0257 (2)0.0266 (7)
H30.88940.1987−0.03200.040*
H40.97530.18350.06190.040*
O3W0.1432 (4)0.1177 (3)0.1323 (2)0.0320 (8)
H50.14650.03510.14020.048*
H60.19220.12480.09070.048*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Ni10.0394 (4)0.0241 (3)0.0137 (3)0.0101 (3)−0.0012 (2)−0.0018 (2)
N10.0236 (19)0.0191 (18)0.0180 (17)0.0013 (14)−0.0016 (14)−0.0012 (14)
N20.057 (3)0.038 (2)0.0124 (18)0.029 (2)0.0047 (18)−0.0002 (16)
N30.080 (4)0.071 (4)0.028 (3)0.056 (3)0.028 (3)0.027 (3)
N40.087 (4)0.024 (2)0.029 (2)0.020 (2)0.023 (2)0.0073 (18)
O10.062 (2)0.0211 (16)0.0139 (15)0.0066 (16)0.0060 (15)0.0004 (13)
O20.081 (3)0.0207 (17)0.0148 (16)−0.0061 (17)0.0053 (16)−0.0018 (13)
O30.0317 (18)0.041 (2)0.0225 (16)0.0007 (15)0.0000 (14)−0.0072 (15)
O40.174 (6)0.021 (2)0.031 (2)−0.021 (3)0.029 (3)−0.0078 (17)
C10.048 (3)0.017 (2)0.019 (2)−0.004 (2)0.001 (2)0.0006 (17)
C20.028 (2)0.019 (2)0.020 (2)−0.0006 (17)0.0011 (17)−0.0022 (17)
C30.040 (3)0.027 (2)0.017 (2)0.003 (2)0.0000 (19)0.0004 (18)
C40.060 (4)0.024 (2)0.028 (3)0.013 (2)0.009 (2)0.010 (2)
C50.071 (4)0.020 (2)0.031 (3)0.003 (2)0.018 (3)0.000 (2)
C60.036 (3)0.019 (2)0.027 (2)−0.0036 (19)0.0095 (19)−0.0023 (18)
C70.038 (3)0.028 (2)0.029 (2)−0.013 (2)0.014 (2)−0.007 (2)
C80.067 (4)0.043 (3)0.020 (2)0.038 (3)0.020 (2)0.012 (2)
C90.059 (4)0.066 (4)0.019 (2)0.039 (3)−0.002 (2)−0.007 (2)
C100.052 (4)0.111 (6)0.017 (2)0.056 (4)0.005 (2)−0.002 (3)
C110.082 (5)0.107 (6)0.021 (3)0.077 (5)0.023 (3)0.025 (3)
O1W0.041 (2)0.067 (3)0.0181 (16)0.0300 (19)0.0075 (15)0.0021 (16)
O2W0.043 (2)0.0210 (16)0.0131 (14)0.0062 (14)−0.0003 (13)−0.0016 (12)
O3W0.047 (2)0.0229 (17)0.0244 (16)0.0005 (15)0.0040 (15)0.0003 (13)

Geometric parameters (Å, °)

Ni1—N11.975 (4)C2—C31.377 (6)
Ni1—N22.062 (4)C3—C41.388 (7)
Ni1—O1W2.070 (4)C3—H3A0.9300
Ni1—O2W2.076 (4)C4—C51.382 (7)
Ni1—O12.117 (3)C4—H4A0.9300
Ni1—O32.136 (4)C5—C61.381 (7)
N1—C61.321 (6)C5—H5A0.9300
N1—C21.330 (5)C6—C71.509 (6)
N2—C91.329 (7)C9—C101.377 (8)
N2—C81.348 (8)C9—H9A0.9300
N3—C111.317 (10)C10—C111.382 (12)
N3—C81.365 (6)C10—H10A0.9300
N4—C81.334 (8)C11—H11A0.9300
N4—H4B0.8600O1W—H10.8500
N4—H4C0.8600O1W—H20.8499
O1—C11.278 (5)O2W—H30.8500
O2—C11.235 (6)O2W—H40.8500
O3—C71.267 (6)O3W—H50.8500
O4—C71.230 (6)O3W—H60.8500
C1—C21.510 (6)
N1—Ni1—N2178.94 (18)C2—C3—H3A121.1
N1—Ni1—O1W90.35 (15)C4—C3—H3A121.1
N2—Ni1—O1W88.59 (17)C5—C4—C3120.4 (5)
N1—Ni1—O2W93.46 (14)C5—C4—H4A119.8
N2—Ni1—O2W87.59 (16)C3—C4—H4A119.8
O1W—Ni1—O2W175.37 (12)C6—C5—C4118.5 (5)
N1—Ni1—O177.84 (13)C6—C5—H5A120.8
N2—Ni1—O1102.19 (15)C4—C5—H5A120.8
O1W—Ni1—O188.48 (15)N1—C6—C5120.2 (4)
O2W—Ni1—O194.88 (13)N1—C6—C7112.9 (4)
N1—Ni1—O378.02 (13)C5—C6—C7126.9 (4)
N2—Ni1—O3101.92 (15)O4—C7—O3124.2 (5)
O1W—Ni1—O390.07 (15)O4—C7—C6119.4 (5)
O2W—Ni1—O388.15 (13)O3—C7—C6116.4 (4)
O1—Ni1—O3155.80 (13)N4—C8—N2119.3 (4)
C6—N1—C2122.3 (4)N4—C8—N3117.0 (6)
C6—N1—Ni1118.9 (3)N2—C8—N3123.7 (6)
C2—N1—Ni1118.8 (3)N2—C9—C10123.4 (7)
C9—N2—C8117.1 (5)N2—C9—H9A118.3
C9—N2—Ni1115.7 (4)C10—C9—H9A118.3
C8—N2—Ni1127.1 (4)C9—C10—C11115.1 (6)
C11—N3—C8116.4 (6)C9—C10—H10A122.4
C8—N4—H4B120.0C11—C10—H10A122.4
C8—N4—H4C120.0N3—C11—C10124.2 (5)
H4B—N4—H4C120.0N3—C11—H11A117.9
C1—O1—Ni1114.9 (3)C10—C11—H11A117.9
C7—O3—Ni1113.2 (3)Ni1—O1W—H198.9
O2—C1—O1125.5 (4)Ni1—O1W—H2121.3
O2—C1—C2119.6 (4)H1—O1W—H2114.3
O1—C1—C2114.8 (4)Ni1—O2W—H3109.9
N1—C2—C3120.9 (4)Ni1—O2W—H4115.4
N1—C2—C1113.2 (4)H3—O2W—H4116.5
C3—C2—C1126.0 (4)H5—O3W—H699.9
C2—C3—C4117.7 (4)
O1W—Ni1—N1—C692.7 (4)O2—C1—C2—N1175.1 (5)
O2W—Ni1—N1—C6−84.7 (4)O1—C1—C2—N1−5.0 (6)
O1—Ni1—N1—C6−179.0 (4)O2—C1—C2—C3−3.6 (8)
O3—Ni1—N1—C62.7 (3)O1—C1—C2—C3176.3 (5)
O1W—Ni1—N1—C2−85.3 (3)N1—C2—C3—C4−0.4 (7)
O2W—Ni1—N1—C297.3 (3)C1—C2—C3—C4178.2 (5)
O1—Ni1—N1—C23.0 (3)C2—C3—C4—C5−0.5 (8)
O3—Ni1—N1—C2−175.3 (4)C3—C4—C5—C61.1 (9)
O1W—Ni1—N2—C9−75.1 (4)C2—N1—C6—C50.0 (7)
O2W—Ni1—N2—C9102.3 (4)Ni1—N1—C6—C5−177.9 (4)
O1—Ni1—N2—C9−163.2 (4)C2—N1—C6—C7179.2 (4)
O3—Ni1—N2—C914.7 (4)Ni1—N1—C6—C71.3 (5)
O1W—Ni1—N2—C8102.8 (5)C4—C5—C6—N1−0.8 (8)
O2W—Ni1—N2—C8−79.8 (5)C4—C5—C6—C7−179.9 (5)
O1—Ni1—N2—C814.7 (5)Ni1—O3—C7—O4−169.6 (5)
O3—Ni1—N2—C8−167.4 (4)Ni1—O3—C7—C69.5 (5)
N1—Ni1—O1—C1−5.9 (4)N1—C6—C7—O4171.6 (5)
N2—Ni1—O1—C1173.0 (4)C5—C6—C7—O4−9.3 (8)
O1W—Ni1—O1—C184.8 (4)N1—C6—C7—O3−7.5 (6)
O2W—Ni1—O1—C1−98.4 (4)C5—C6—C7—O3171.6 (5)
O3—Ni1—O1—C1−2.0 (6)C9—N2—C8—N4−179.0 (5)
N1—Ni1—O3—C7−6.9 (3)Ni1—N2—C8—N43.2 (7)
N2—Ni1—O3—C7174.2 (3)C9—N2—C8—N32.3 (8)
O1W—Ni1—O3—C7−97.2 (3)Ni1—N2—C8—N3−175.6 (4)
O2W—Ni1—O3—C787.1 (3)C11—N3—C8—N4179.1 (5)
O1—Ni1—O3—C7−10.7 (6)C11—N3—C8—N2−2.1 (8)
Ni1—O1—C1—O2−172.6 (5)C8—N2—C9—C10−1.2 (9)
Ni1—O1—C1—C27.4 (6)Ni1—N2—C9—C10176.9 (5)
C6—N1—C2—C30.6 (7)N2—C9—C10—C110.0 (9)
Ni1—N1—C2—C3178.6 (4)C8—N3—C11—C100.8 (9)
C6—N1—C2—C1−178.1 (4)C9—C10—C11—N30.2 (9)
Ni1—N1—C2—C1−0.2 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N4—H4B···O10.862.072.867 (5)153
N4—H4C···O4i0.862.122.973 (6)173
O1W—H1···O4ii0.852.292.906 (7)130
O1W—H1···O3ii0.852.373.152 (5)152
O1W—H2···N3iii0.852.032.835 (7)158
O2W—H3···O2iv0.851.932.777 (4)178
O2W—H4···O3Wv0.851.842.685 (5)173
O3W—H5···O2vi0.851.892.736 (4)177
O3W—H6···O4ii0.852.152.964 (6)159
O3W—H6···O3ii0.852.563.253 (5)140

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BH2281).

References

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