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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): m1334.
Published online 2009 October 10. doi:  10.1107/S1600536809040185
PMCID: PMC2971434

Poly[[bis­[μ2-8-ethyl-5-oxo-2-(piperazin-1-yl)-5,8-dihydro­pyrido[2,3-d]pyrimidine-6-carboxyl­ato]cobalt(II)] dihydrate]

Abstract

The title compound, {[Co(C14H16N5O3)2]·2H2O}n or [Co(ppa)2]·2H2O}n, where ppa denotes the 8-ethyl-5-oxo-2-(piperazin-1-yl)-5,8-dihydro­pyrido[2,3-d]pyrimidine-6-carb­ox­yl­ate anion, was synthesized under hydro­thermal conditions. The CoII atom (site symmetry An external file that holds a picture, illustration, etc.
Object name is e-65-m1334-efi1.jpg) exhibits a distorted trans-CoN2O4 octa­hedral geometry defined by two monodentate N-bonded and two bidentate O,O′-bonded ppa anions. The extended two-dimensional structure is a square grid, which is consolidated by N—H(...)O hydrogen bonds. The disordered uncoordinated water mol­ecules occupy cavities within the grid.

Related literature

For the manganese and zinc complexes of the ppa anion, see: Huang et al. (2008 [triangle]); Xu et al. (2009 [triangle]). For background to the medicinal uses of pipemidic acid, see: Mizuki et al. (1996 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-m1334-scheme1.jpg

Experimental

Crystal data

  • [Co(C14H16N5O3)2]·2H2O
  • M r = 699.58
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-m1334-efi2.jpg
  • a = 6.1093 (3) Å
  • b = 21.3690 (11) Å
  • c = 12.5944 (6) Å
  • β = 101.254 (1)°
  • V = 1612.58 (14) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.60 mm−1
  • T = 295 K
  • 0.32 × 0.26 × 0.18 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.832, T max = 0.900
  • 9807 measured reflections
  • 3894 independent reflections
  • 3327 reflections with I > 2σ(I)
  • R int = 0.029

Refinement

  • R[F 2 > 2σ(F 2)] = 0.060
  • wR(F 2) = 0.181
  • S = 1.12
  • 3894 reflections
  • 227 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.77 e Å−3
  • Δρmin = −0.46 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT (Bruker, 1998 [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 I, global. DOI: 10.1107/S1600536809040185/hb5124sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809040185/hb5124Isup2.hkl

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

Acknowledgments

The authors acknowledge financial support from the Foundation for Youth of Heilongjiang Province (grant No. QC07C97).

supplementary crystallographic information

Comment

Pipemidic acid (Hppa, C14H16N5O3, 8-Ethyl-5,8-dihydro-5-oxo-2- (1-piperazinyl)-pyrido(2,3 - d)-pyrimidine-6-carboxylic acid) is member of a class of quinolones used to treat infections (Mizuki et al., 1996). The manganese and cobalt complexes of the ppa anion have been reported (Huang et al., 2008; Xu et al. 2009). The title cobalt(II) complex is reported here(Fig. 1).

The cobalt(II) atom is coordinated by four oxygen atoms and two N atoms from four ppa ligands (two monodentate-N and two O,O-bidentate) to form a square grid propagating in (Fig. 2). The disordered, uncoordinated, water molecules occupy the cavities.

Experimental

A mixture of Co(CH3COO)2.4H2O (0.25 mmol), Hppa (0.5 mmol), sodium hydroxide (1 mmol) and water (12 ml) was stirred for 40 min in air. The mixture was then transferred to a 23 ml Teflon-lined hydrothermal bomb. The bomb was kept at 433 K for 96 h under autogenous pressure. Upon cooling, pink prisms of (I) were obtained from the reaction mixture.

Refinement

The carbon-bound H atoms were positioned geometrically (C—H = 0.93–0.97 Å) and were included in the refinement in the riding model approximation, with U(H) = 1.2Ueq(C). The H on Nitrogen atoms were located in a difference Fourier map, and were refined with a distance restraint of N—H = 0.86 (1) /%A and with Uiso(H) = 1.2Ueq(N).

The water H atoms could not be placed due to this disorder.

Figures

Fig. 1.
The asymmetric unit of (I) expanded to show the metal coordination and polymeric connectivity showing 50% displacement ellipsoids (water molecule O atoms have been omitted for clarity).
Fig. 2.
A view of part of a two-dimensional polymeric sheet in (I) showing the square-grid connectivity (H atoms and water molecule O atoms omitted for clarity).

Crystal data

[Co(C14H16N5O3)2]·2H2OF(000) = 722
Mr = 699.58Dx = 1.433 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4362 reflections
a = 6.1093 (3) Åθ = 2.5–28.2°
b = 21.3690 (11) ŵ = 0.60 mm1
c = 12.5944 (6) ÅT = 295 K
β = 101.254 (1)°Prism, pink
V = 1612.58 (14) Å30.32 × 0.26 × 0.18 mm
Z = 2

Data collection

Bruker SMART CCD diffractometer3894 independent reflections
Radiation source: fine-focus sealed tube3327 reflections with I > 2σ(I)
graphiteRint = 0.029
ω scansθmax = 28.3°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −8→6
Tmin = 0.832, Tmax = 0.900k = −27→28
9807 measured reflectionsl = −15→15

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)] = 0.060Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.181H atoms treated by a mixture of independent and constrained refinement
S = 1.12w = 1/[σ2(Fo2) + (0.0899P)2 + 1.3252P] where P = (Fo2 + 2Fc2)/3
3894 reflections(Δ/σ)max = 0.003
227 parametersΔρmax = 0.77 e Å3
1 restraintΔρmin = −0.46 e Å3

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*/UeqOcc. (<1)
O1W0.669 (4)0.5177 (8)0.5335 (9)0.255 (11)0.50
O2W−0.024 (4)0.5581 (10)0.4291 (11)0.254 (10)0.50
Co10.50000.50000.00000.02469 (18)
O10.6496 (3)0.57810 (9)0.08289 (16)0.0324 (4)
O20.1437 (5)0.51651 (14)0.2499 (2)0.0626 (8)
N10.5101 (5)0.67072 (13)0.3478 (2)0.0487 (7)
N20.7758 (5)0.74617 (12)0.3332 (2)0.0390 (6)
N31.0138 (5)0.73519 (13)0.2023 (2)0.0437 (7)
N41.0250 (4)0.82327 (11)0.3106 (2)0.0362 (6)
C10.2840 (5)0.52788 (13)0.1939 (2)0.0328 (6)
C20.4347 (5)0.58348 (13)0.2241 (2)0.0330 (6)
C30.6059 (4)0.60347 (12)0.1662 (2)0.0275 (5)
C40.7269 (5)0.65898 (13)0.2104 (2)0.0318 (6)
C50.9081 (5)0.68298 (14)0.1695 (3)0.0398 (7)
H50.95660.66030.11550.048*
C60.9339 (5)0.76685 (13)0.2815 (2)0.0334 (6)
C70.6763 (5)0.69244 (13)0.2976 (3)0.0364 (6)
C80.3996 (6)0.61779 (15)0.3104 (3)0.0452 (8)
H80.29050.60360.34670.054*
C90.4470 (8)0.7043 (2)0.4423 (4)0.0646 (12)
H9A0.46930.74890.43510.078*
H9B0.29020.69720.44250.078*
C100.5781 (12)0.6828 (4)0.5417 (5)0.118 (2)
H10A0.54740.63930.55130.177*
H10B0.54170.70650.60060.177*
H10C0.73350.68800.54010.177*
C111.1614 (6)0.85706 (17)0.2461 (3)0.0478 (8)
H11A1.06670.88390.19430.057*
H11B1.23450.82740.20620.057*
C121.3372 (5)0.89675 (15)0.3196 (3)0.0400 (7)
H12A1.44480.86900.36300.048*
H12B1.41620.92160.27470.048*
C131.1106 (5)0.90153 (13)0.4537 (2)0.0330 (6)
H13A1.04240.92930.49890.040*
H13B1.20780.87310.50110.040*
C140.9295 (5)0.86418 (14)0.3823 (3)0.0353 (6)
H14A0.85050.83920.42700.042*
H14B0.82330.89250.33950.042*
N51.2458 (4)0.93890 (10)0.39246 (19)0.0286 (5)
O30.3027 (3)0.49641 (8)0.11147 (17)0.0295 (4)
H5N1.155 (5)0.9660 (14)0.350 (2)0.044*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O1W0.52 (4)0.180 (13)0.073 (8)−0.084 (17)0.063 (13)0.045 (8)
O2W0.35 (2)0.33 (2)0.122 (10)−0.09 (2)0.147 (13)−0.030 (13)
Co10.0276 (3)0.0158 (3)0.0304 (3)−0.00028 (17)0.0050 (2)−0.00242 (17)
O10.0350 (10)0.0243 (9)0.0395 (11)−0.0065 (8)0.0113 (8)−0.0089 (8)
O20.0732 (18)0.0635 (16)0.0631 (17)−0.0401 (15)0.0429 (15)−0.0297 (14)
N10.0630 (18)0.0404 (15)0.0494 (16)−0.0222 (14)0.0271 (14)−0.0189 (12)
N20.0494 (15)0.0296 (12)0.0413 (14)−0.0138 (11)0.0167 (11)−0.0129 (10)
N30.0454 (15)0.0348 (14)0.0556 (16)−0.0152 (12)0.0221 (13)−0.0200 (12)
N40.0390 (13)0.0268 (12)0.0462 (14)−0.0093 (10)0.0169 (11)−0.0132 (10)
C10.0354 (14)0.0250 (13)0.0379 (15)−0.0061 (11)0.0068 (12)−0.0030 (11)
C20.0409 (15)0.0244 (13)0.0343 (14)−0.0074 (11)0.0091 (12)−0.0035 (10)
C30.0309 (13)0.0192 (12)0.0314 (13)−0.0023 (10)0.0034 (10)−0.0024 (10)
C40.0354 (14)0.0241 (12)0.0365 (14)−0.0064 (11)0.0082 (11)−0.0064 (11)
C50.0434 (16)0.0300 (14)0.0498 (18)−0.0102 (12)0.0186 (14)−0.0180 (13)
C60.0338 (14)0.0248 (13)0.0427 (16)−0.0058 (11)0.0097 (12)−0.0087 (11)
C70.0449 (16)0.0269 (13)0.0397 (15)−0.0099 (12)0.0139 (13)−0.0087 (11)
C80.057 (2)0.0352 (16)0.0486 (18)−0.0198 (15)0.0238 (16)−0.0107 (14)
C90.080 (3)0.058 (2)0.065 (3)−0.030 (2)0.035 (2)−0.025 (2)
C100.121 (5)0.155 (7)0.082 (4)−0.025 (5)0.028 (4)−0.020 (4)
C110.055 (2)0.0429 (18)0.0501 (19)−0.0253 (15)0.0221 (16)−0.0187 (15)
C120.0370 (15)0.0326 (15)0.0537 (18)−0.0113 (12)0.0167 (13)−0.0110 (13)
C130.0334 (14)0.0266 (13)0.0402 (15)−0.0067 (11)0.0104 (12)−0.0072 (11)
C140.0290 (13)0.0276 (13)0.0507 (17)−0.0062 (11)0.0114 (12)−0.0119 (12)
N50.0283 (11)0.0208 (10)0.0362 (12)−0.0017 (8)0.0053 (9)−0.0010 (9)
O30.0337 (10)0.0199 (9)0.0353 (11)−0.0035 (7)0.0072 (8)−0.0029 (7)

Geometric parameters (Å, °)

Co1—O3i2.022 (2)C4—C51.405 (4)
Co1—O32.022 (2)C5—H50.9300
Co1—O1i2.0829 (18)C8—H80.9300
Co1—O12.0829 (18)C9—C101.425 (9)
Co1—N5ii2.265 (2)C9—H9A0.9700
Co1—N5iii2.265 (2)C9—H9B0.9700
O1—C31.255 (3)C10—H10A0.9600
O2—C11.235 (4)C10—H10B0.9600
N1—C81.354 (4)C10—H10C0.9600
N1—C71.376 (4)C11—C121.530 (4)
N1—C91.503 (5)C11—H11A0.9700
N2—C71.335 (4)C11—H11B0.9700
N2—C61.341 (4)C12—N51.471 (4)
N3—C51.315 (4)C12—H12A0.9700
N3—C61.371 (4)C12—H12B0.9700
N4—C61.348 (3)C13—N51.471 (3)
N4—C141.459 (3)C13—C141.510 (4)
N4—C111.462 (4)C13—H13A0.9700
C1—O31.261 (3)C13—H13B0.9700
C1—C21.506 (4)C14—H14A0.9700
C2—C81.362 (4)C14—H14B0.9700
C2—C31.451 (4)N5—Co1iv2.265 (2)
C3—C41.450 (4)N5—H5N0.900 (10)
C4—C71.396 (4)
O3i—Co1—O3180.0N1—C8—H8117.2
O3i—Co1—O1i86.86 (7)C2—C8—H8117.2
O3—Co1—O1i93.14 (7)C10—C9—N1110.8 (5)
O3i—Co1—O193.14 (7)C10—C9—H9A109.5
O3—Co1—O186.86 (7)N1—C9—H9A109.5
O1i—Co1—O1180.0C10—C9—H9B109.5
O3i—Co1—N5ii90.28 (8)N1—C9—H9B109.5
O3—Co1—N5ii89.72 (8)H9A—C9—H9B108.1
O1i—Co1—N5ii91.18 (8)C9—C10—H10A109.5
O1—Co1—N5ii88.82 (8)C9—C10—H10B109.5
O3i—Co1—N5iii89.72 (8)H10A—C10—H10B109.5
O3—Co1—N5iii90.28 (8)C9—C10—H10C109.5
O1i—Co1—N5iii88.82 (8)H10A—C10—H10C109.5
O1—Co1—N5iii91.18 (8)H10B—C10—H10C109.5
N5ii—Co1—N5iii180.0N4—C11—C12110.3 (3)
C3—O1—Co1128.37 (17)N4—C11—H11A109.6
C8—N1—C7119.0 (3)C12—C11—H11A109.6
C8—N1—C9119.1 (3)N4—C11—H11B109.6
C7—N1—C9121.9 (3)C12—C11—H11B109.6
C7—N2—C6116.4 (2)H11A—C11—H11B108.1
C5—N3—C6115.1 (3)N5—C12—C11114.2 (3)
C6—N4—C14120.7 (2)N5—C12—H12A108.7
C6—N4—C11122.7 (2)C11—C12—H12A108.7
C14—N4—C11112.8 (2)N5—C12—H12B108.7
O2—C1—O3123.3 (3)C11—C12—H12B108.7
O2—C1—C2118.0 (3)H12A—C12—H12B107.6
O3—C1—C2118.6 (2)N5—C13—C14113.3 (2)
C8—C2—C3118.9 (3)N5—C13—H13A108.9
C8—C2—C1116.3 (3)C14—C13—H13A108.9
C3—C2—C1124.8 (2)N5—C13—H13B108.9
O1—C3—C4119.9 (2)C14—C13—H13B108.9
O1—C3—C2125.8 (2)H13A—C13—H13B107.7
C4—C3—C2114.3 (2)N4—C14—C13110.5 (2)
C7—C4—C5114.4 (2)N4—C14—H14A109.5
C7—C4—C3123.1 (3)C13—C14—H14A109.5
C5—C4—C3122.5 (3)N4—C14—H14B109.5
N3—C5—C4124.7 (3)C13—C14—H14B109.5
N3—C5—H5117.7H14A—C14—H14B108.1
C4—C5—H5117.7C13—N5—C12108.4 (2)
N2—C6—N4117.5 (2)C13—N5—Co1iv112.89 (17)
N2—C6—N3125.7 (3)C12—N5—Co1iv115.23 (17)
N4—C6—N3116.9 (3)C13—N5—H5N108 (2)
N2—C7—N1117.7 (3)C12—N5—H5N107 (2)
N2—C7—C4123.3 (3)Co1iv—N5—H5N105 (2)
N1—C7—C4119.0 (3)C1—O3—Co1135.54 (18)
N1—C8—C2125.6 (3)
O3i—Co1—O1—C3−179.8 (2)C8—N1—C7—N2177.2 (3)
O3—Co1—O1—C30.2 (2)C9—N1—C7—N2−2.4 (5)
N5ii—Co1—O1—C3−89.6 (2)C8—N1—C7—C4−0.5 (5)
N5iii—Co1—O1—C390.4 (2)C9—N1—C7—C4179.9 (4)
O2—C1—C2—C8−1.4 (5)C5—C4—C7—N26.3 (5)
O3—C1—C2—C8176.6 (3)C3—C4—C7—N2−174.7 (3)
O2—C1—C2—C3−179.3 (3)C5—C4—C7—N1−176.2 (3)
O3—C1—C2—C3−1.3 (4)C3—C4—C7—N12.8 (5)
Co1—O1—C3—C4−178.49 (19)C7—N1—C8—C2−1.4 (6)
Co1—O1—C3—C2−0.6 (4)C9—N1—C8—C2178.2 (4)
C8—C2—C3—O1−176.7 (3)C3—C2—C8—N10.9 (6)
C1—C2—C3—O11.2 (5)C1—C2—C8—N1−177.2 (3)
C8—C2—C3—C41.3 (4)C8—N1—C9—C1091.4 (5)
C1—C2—C3—C4179.2 (3)C7—N1—C9—C10−89.0 (5)
O1—C3—C4—C7175.0 (3)C6—N4—C11—C12−149.0 (3)
C2—C3—C4—C7−3.1 (4)C14—N4—C11—C1252.8 (4)
O1—C3—C4—C5−6.0 (4)N4—C11—C12—N5−53.2 (4)
C2—C3—C4—C5175.8 (3)C6—N4—C14—C13146.4 (3)
C6—N3—C5—C4−0.5 (5)C11—N4—C14—C13−54.9 (4)
C7—C4—C5—N3−5.4 (5)N5—C13—C14—N456.7 (3)
C3—C4—C5—N3175.5 (3)C14—C13—N5—C12−55.3 (3)
C7—N2—C6—N4175.2 (3)C14—C13—N5—Co1iv175.84 (18)
C7—N2—C6—N3−5.8 (5)C11—C12—N5—C1353.7 (4)
C14—N4—C6—N2−9.8 (4)C11—C12—N5—Co1iv−178.7 (2)
C11—N4—C6—N2−166.4 (3)O2—C1—O3—Co1178.9 (3)
C14—N4—C6—N3171.1 (3)C2—C1—O3—Co11.0 (4)
C11—N4—C6—N314.5 (5)O1i—Co1—O3—C1179.6 (3)
C5—N3—C6—N26.6 (5)O1—Co1—O3—C1−0.4 (3)
C5—N3—C6—N4−174.4 (3)N5ii—Co1—O3—C188.4 (3)
C6—N2—C7—N1−178.7 (3)N5iii—Co1—O3—C1−91.6 (3)
C6—N2—C7—C4−1.1 (5)

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N5—H5N···O2v0.90 (1)2.28 (1)3.156 (4)165 (3)

Symmetry codes: (v) −x+1, y+1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5124).

References

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