supplementary materials


sj5358 scheme

Acta Cryst. (2013). E69, m598-m599    [ doi:10.1107/S1600536813027499 ]

Aqua­(azido)[N-(pyridin-2-ylcarbon­yl)pyridine-2-carboxamido-[kappa]3N,N',N'']copper(II)

S. Bruda, M. M. Turnbull and J. L. Wikaira

Abstract top

The title compound, [Cu(C12H8N3O2)(N3)(H2O)], was formed by the air oxidation of 2-(amino­meth­yl)pyridine in 95% ethanol in the presence of copper(II) nitrate and sodium azide with condensation of the resulting picolinamide mol­ecules to generate the imide moiety. The CuII ion has a square-pyramidal coordination sphere, the basal plane being occupied by four N atoms [two pyridine (py) N atoms, the imide N atom and an azide N atom] in a nearly planar array [mean deviation = 0.048 (6) Å] with the CuII ion displaced slightly from the plane [0.167 (5) Å] toward the fifth ligand. The apical position is occupied by a coordinating water mol­ecule [Cu-O = 2.319 (4) Å]. The crystal structure is stabilized by hydrogen-bonding inter­actions between the water mol­ecules and carbonyl O atoms. The inversion-related square-pyramidal complex molecules pack base-to-base with long Cu...Npy contact distances of 3.537 (9) Å, preventing coordination of a sixth ligand.

Comment top

We are inter­ested in the design and synthesis of CuII complexes to study magnetostructural relationships in low-dimensional magnetic lattics (Landee and Turnbull, 2013). In this work, a wide variety of heterocyclic amines such as substituted pyrazine and pyridine compounds have been employed both as ligands and as bases. One such compound has been 2-amino­methyl­pyridine (Bruda et al., 2006). We were attempting the preparation of a series of CuII complexes employing the 2-amino­methyl­pyridine molecule as a blocking agent to limit coordination by other species when we encountered the CuII catalyzed air-oxidation and condensation of 2-amino­methyl­pyridine and resulting in situ formation of a CuII nitrate complex of N-(pridin-2-ylcarboyl)pyridine-2-carbamide (bis-picolinimide; bpa) (Turnbull et al., 2013). A similar reaction, in the presence of azide ion, has shown the same oxidation and condensation resulting in the preparation of [(N-(pyridin-2-ylcarboyl)pyridine2-carboxamido)(azido)(aqua)­copper(II)] (1).

Crystals of (1) (Figure 1) were produced via slow crystallization in air of an ethano­lic solution of Cu(NO3)2·3H2O, 2-amino­methyl­pyridine and sodium azide. The CuII ion is coordinated by one bpa anion, one azide anion and a water molecule to generate a nearly square pyramidal, five-coordinate structure. The basal plane is composed of three nitro­gen atoms from the bpa ligand and the coordinated azide ion. The four N-atoms are planar within 0.048 (6) Å and the CuII ion is displaced 0.167 (5) Å out of this plane. The O-atom of the water molecule is located in the apical position [Cu—O = 2.319 (4)Å]. The Addison parameter is 0.053, indicating that the geometry is very close to square pyramidal (Addison et al., 1984).

The pyridine rings in the bpa ligand are virtually planar (mean deviation of constituent atoms = 0.0021 (8) N1-ring; 0.003 (2) N15-ring) and the rings themselves are nearly co-planar (2.5 (1)°). The lattice structure of (1) is supported by hydrogen bonds between the coordinated water molecule (donor) and the carbonyl oxygen atoms (acceptor) of adjacent bpa ligands (see Figure 2, Table 1). The five-coordinate nature of the CuII ion is stabilized by long inter­molecular Cu···N contacts between inversion related molecules [dCu···N15A = 3.537 (9) Å (-x, 2-y, -z)] effectively blocking the basal face of the square pyramidal structure and preventing coordination of a sixth ligand (see Figure 2).

Sahu and co-workers (Sahu et al., 2010) have previously observed the copper catalyzed air-oxidation and condensation of 2-amino­methyl­pyridine to bpa as well as the corresponding reaction for 2-amino­methyl­quinoline. Similar structures have been reported with other inorganic anions replacing the azide ion including halides [Br, (Zhou et al., 2006); F, (Borras et al., 2007)], pseudo halides [OCN, (Dey et al., 2002); SCN, (Madariaga, et al., 1991)] and cyanamide derivatives (Vangdal, et al., 2002; de Gomes et al. 2008)].

Experimental top

Cu(NO3)2.3H2O, ethanol and NaN3 were obtained from VWR Scientific while 2-amino­methyl­pyridine was purchased from Aldrich Chemical. All were used as received.

Synthesis and crystallization top

Cu(NO3)2.3H2O (0.241 g, 1.00 mmol), NaN3 (0.071g, 1.1 mmol) and 2-amino­methyl­pyridine (0.237 g,2.20 mmol) were dissolved in 20 ml of 95% ethanol in a 50 mL beaker and the beaker covered with parafilm with a couple of small holes in the film. Over the course of 2 weeks, blue needle-shaped crystals of (1) formed, which were isolated by filtration to give (1) 0.082 g (23 %).

Refinement top

All H-atoms bound to carbon were placed in calculated positions (C—H = 0.95 Å) and refined using a riding model with Uiso=1.2Ueq (C). Hydrogen atoms bonded to oxygen atoms were located in the difference map and their positions allowed to refine using anti-bumping restraints (0.85 Å for O—H distances) and fixed isotropic U values [Uiso=1.2Ueq (O)].

Related literature top

For magneto structural relationships in CuII complexes, see: Landee & Turnbull (2013). For copper(II)-catalysed air-oxidation of 2-aminomethylpyridine, see: Sahu et al. (2010); Turnbull et al. (2013). For the corresponding dicyanamide complex, see: Vangdal et al. (2002) and for the tricyanomethanide complex, see: de Gomes et al. (2008). For the bromide complex, see: Zhou et al. (2006) and for the fluoride and formate analogues, see: Borras et al. (2007). For the cyanate and thiocyanate complexes, see: Dey et al. (2002) and Madariaga et al. (1991), respectively. For a related 2-aminomethylpyridine structure, see: Bruda et al. (2006). For the Addison parameter as a geometry predictor in coordination complexes, see: Addison et al. (1984).

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008), enCIFer (Allen et al., 2004) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. - Thermal ellipsoid plot (50%) of the molecular unit of (1). Only those H-atoms whose positions were refined are labeled.
[Figure 2] Fig. 2. - Packing diagram of (1) showing hydrogen bonds and short Cu···N intermolecular contacts (dashed lines).
Aqua(azido)[N-(pyridin-2-ylcarbonyl)pyridine-2-carboxamido-κ3N,N',N'']copper(II) top
Crystal data top
[Cu(C12H8N3O2)(N3)(H2O)]Z = 2
Mr = 349.80F(000) = 354
Triclinic, P1Dx = 1.808 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.402 (4) ÅCell parameters from 2526 reflections
b = 8.900 (5) Åθ = 2.9–26.0°
c = 10.606 (6) ŵ = 1.72 mm1
α = 78.186 (9)°T = 168 K
β = 84.118 (8)°Needle, blue
γ = 70.040 (7)°0.28 × 0.06 × 0.03 mm
V = 642.4 (6) Å3
Data collection top
Bruker SMART CCD area-detector
diffractometer
2258 independent reflections
Radiation source: fine-focus sealed tube1837 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.063
φ & ω scansθmax = 25.0°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 88
Tmin = 0.854, Tmax = 1.000k = 910
7577 measured reflectionsl = 1212
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.063Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.105H atoms treated by a mixture of independent and constrained refinement
S = 1.17 w = 1/[σ2(Fo2) + (0.0191P)2 + 2.3778P]
where P = (Fo2 + 2Fc2)/3
2258 reflections(Δ/σ)max = 0.001
205 parametersΔρmax = 0.50 e Å3
2 restraintsΔρmin = 0.69 e Å3
Crystal data top
[Cu(C12H8N3O2)(N3)(H2O)]γ = 70.040 (7)°
Mr = 349.80V = 642.4 (6) Å3
Triclinic, P1Z = 2
a = 7.402 (4) ÅMo Kα radiation
b = 8.900 (5) ŵ = 1.72 mm1
c = 10.606 (6) ÅT = 168 K
α = 78.186 (9)°0.28 × 0.06 × 0.03 mm
β = 84.118 (8)°
Data collection top
Bruker SMART CCD area-detector
diffractometer
2258 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1837 reflections with I > 2σ(I)
Tmin = 0.854, Tmax = 1.000Rint = 0.063
7577 measured reflectionsθmax = 25.0°
Refinement top
R[F2 > 2σ(F2)] = 0.063H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.105Δρmax = 0.50 e Å3
S = 1.17Δρmin = 0.69 e Å3
2258 reflectionsAbsolute structure: ?
205 parametersAbsolute structure parameter: ?
2 restraintsRogers parameter: ?
Special details top

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) top
xyzUiso*/Ueq
Cu0.09830 (10)0.76976 (9)0.14071 (7)0.0155 (2)
N10.0741 (6)0.7152 (5)0.2890 (4)0.0185 (11)
C20.0718 (8)0.7285 (7)0.4124 (5)0.0220 (13)
H20.02060.76910.43610.026*
C30.1984 (8)0.6857 (7)0.5071 (6)0.0247 (14)
H30.19260.69580.59390.030*
C40.3340 (8)0.6274 (7)0.4709 (6)0.0263 (14)
H40.42350.59760.53310.032*
C50.3374 (8)0.6133 (7)0.3427 (5)0.0244 (14)
H50.42910.57380.31670.029*
C60.2058 (7)0.6573 (6)0.2541 (5)0.0169 (12)
C70.2052 (8)0.6497 (6)0.1132 (5)0.0180 (12)
O70.3162 (5)0.5945 (5)0.0733 (4)0.0232 (9)
N80.0714 (6)0.7116 (5)0.0432 (4)0.0164 (10)
C90.0375 (7)0.7206 (6)0.0861 (5)0.0151 (12)
O90.1195 (5)0.6830 (5)0.1644 (4)0.0227 (9)
C100.1237 (7)0.7882 (6)0.1305 (5)0.0163 (12)
C110.1863 (8)0.8111 (6)0.2593 (5)0.0195 (13)
H110.12760.78480.32340.023*
C120.3370 (8)0.8732 (7)0.2914 (5)0.0237 (13)
H120.38300.89010.37830.028*
C130.4194 (8)0.9104 (7)0.1954 (5)0.0228 (13)
H130.52270.95280.21590.027*
C140.3502 (8)0.8853 (7)0.0697 (6)0.0229 (13)
H140.40760.91030.00410.028*
N150.2036 (6)0.8264 (5)0.0380 (4)0.0165 (10)
N160.2400 (7)0.8814 (6)0.2117 (5)0.0241 (12)
N170.2333 (6)0.9146 (6)0.3164 (5)0.0206 (11)
N180.2343 (8)0.9525 (7)0.4143 (5)0.0365 (14)
O10.3387 (5)0.5191 (5)0.1809 (4)0.0217 (9)
H1A0.305 (8)0.455 (6)0.147 (5)0.026*
H1B0.440 (5)0.520 (7)0.138 (5)0.026*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu0.0162 (4)0.0193 (4)0.0141 (4)0.0097 (3)0.0013 (3)0.0040 (3)
N10.018 (3)0.023 (3)0.016 (3)0.008 (2)0.001 (2)0.004 (2)
C20.023 (3)0.029 (3)0.020 (3)0.015 (3)0.004 (3)0.010 (3)
C30.033 (3)0.029 (4)0.015 (3)0.013 (3)0.007 (3)0.007 (3)
C40.027 (3)0.029 (4)0.023 (3)0.014 (3)0.008 (3)0.004 (3)
C50.022 (3)0.031 (4)0.027 (3)0.016 (3)0.005 (3)0.013 (3)
C60.020 (3)0.010 (3)0.018 (3)0.003 (2)0.002 (2)0.002 (2)
C70.020 (3)0.013 (3)0.021 (3)0.005 (2)0.000 (2)0.006 (2)
O70.023 (2)0.028 (2)0.026 (2)0.0158 (19)0.0003 (18)0.0074 (18)
N80.019 (2)0.019 (3)0.016 (3)0.012 (2)0.000 (2)0.004 (2)
C90.016 (3)0.014 (3)0.015 (3)0.005 (2)0.006 (2)0.001 (2)
O90.021 (2)0.028 (2)0.021 (2)0.0119 (18)0.0018 (18)0.0023 (18)
C100.016 (3)0.013 (3)0.019 (3)0.005 (2)0.000 (2)0.001 (2)
C110.021 (3)0.022 (3)0.015 (3)0.007 (3)0.004 (2)0.000 (2)
C120.024 (3)0.029 (3)0.016 (3)0.008 (3)0.005 (2)0.002 (3)
C130.016 (3)0.028 (3)0.025 (3)0.012 (3)0.006 (2)0.000 (3)
C140.020 (3)0.020 (3)0.032 (4)0.011 (3)0.001 (3)0.005 (3)
N150.012 (2)0.020 (3)0.019 (3)0.007 (2)0.0003 (19)0.003 (2)
N160.026 (3)0.034 (3)0.022 (3)0.022 (2)0.001 (2)0.009 (2)
N170.022 (3)0.024 (3)0.020 (3)0.014 (2)0.005 (2)0.001 (2)
N180.044 (3)0.052 (4)0.024 (3)0.026 (3)0.004 (3)0.011 (3)
O10.016 (2)0.025 (2)0.025 (2)0.0093 (18)0.0014 (17)0.0069 (18)
Geometric parameters (Å, º) top
Cu—N161.958 (4)N8—C91.359 (7)
Cu—N81.961 (4)C9—O91.235 (6)
Cu—N152.007 (4)C9—C101.505 (7)
Cu—N12.009 (4)C10—N151.350 (7)
Cu—O12.319 (4)C10—C111.393 (7)
N1—C21.341 (6)C11—C121.390 (7)
N1—C61.359 (6)C11—H110.9500
C2—C31.388 (7)C12—C131.386 (8)
C2—H20.9500C12—H120.9500
C3—C41.393 (8)C13—C141.380 (8)
C3—H30.9500C13—H130.9500
C4—C51.394 (8)C14—N151.344 (6)
C4—H40.9500C14—H140.9500
C5—C61.382 (7)N16—N171.198 (6)
C5—H50.9500N17—N181.157 (6)
C6—C71.509 (7)O1—H1A0.85 (2)
C7—O71.236 (6)O1—H1B0.84 (2)
C7—N81.375 (7)
N16—Cu—N8165.67 (19)N8—C7—C6111.0 (4)
N16—Cu—N1591.65 (19)C9—N8—C7124.6 (4)
N8—Cu—N1580.91 (18)C9—N8—Cu118.2 (3)
N16—Cu—N1103.67 (19)C7—N8—Cu116.9 (3)
N8—Cu—N182.26 (18)O9—C9—N8129.1 (5)
N15—Cu—N1162.45 (16)O9—C9—C10120.3 (5)
N16—Cu—O193.76 (18)N8—C9—C10110.7 (4)
N8—Cu—O198.80 (16)N15—C10—C11121.8 (5)
N15—Cu—O192.89 (16)N15—C10—C9115.9 (4)
N1—Cu—O194.57 (16)C11—C10—C9122.3 (5)
C2—N1—C6119.0 (5)C12—C11—C10118.3 (5)
C2—N1—Cu128.2 (4)C12—C11—H11120.8
C6—N1—Cu112.8 (3)C10—C11—H11120.8
N1—C2—C3122.9 (5)C13—C12—C11119.4 (5)
N1—C2—H2118.5C13—C12—H12120.3
C3—C2—H2118.5C11—C12—H12120.3
C2—C3—C4118.0 (5)C14—C13—C12119.4 (5)
C2—C3—H3121.0C14—C13—H13120.3
C4—C3—H3121.0C12—C13—H13120.3
C3—C4—C5119.4 (5)N15—C14—C13121.6 (5)
C3—C4—H4120.3N15—C14—H14119.2
C5—C4—H4120.3C13—C14—H14119.2
C6—C5—C4119.3 (5)C14—N15—C10119.5 (5)
C6—C5—H5120.4C14—N15—Cu126.3 (4)
C4—C5—H5120.4C10—N15—Cu114.0 (3)
N1—C6—C5121.4 (5)N17—N16—Cu131.4 (4)
N1—C6—C7116.6 (4)N18—N17—N16175.6 (5)
C5—C6—C7122.0 (5)Cu—O1—H1A106 (4)
O7—C7—N8127.9 (5)Cu—O1—H1B112 (4)
O7—C7—C6121.1 (5)H1A—O1—H1B101 (5)
N16—Cu—N1—C29.4 (5)O1—Cu—N8—C787.4 (4)
N8—Cu—N1—C2176.2 (5)C7—N8—C9—O92.8 (9)
N15—Cu—N1—C2159.6 (5)Cu—N8—C9—O9176.3 (4)
O1—Cu—N1—C285.6 (5)C7—N8—C9—C10177.7 (5)
N16—Cu—N1—C6171.0 (4)Cu—N8—C9—C104.1 (6)
N8—Cu—N1—C64.3 (4)O9—C9—C10—N15179.7 (5)
N15—Cu—N1—C620.9 (8)N8—C9—C10—N150.1 (6)
O1—Cu—N1—C694.0 (4)O9—C9—C10—C110.0 (8)
C6—N1—C2—C30.0 (8)N8—C9—C10—C11179.6 (5)
Cu—N1—C2—C3179.5 (4)N15—C10—C11—C120.8 (8)
N1—C2—C3—C40.4 (9)C9—C10—C11—C12179.6 (5)
C2—C3—C4—C50.4 (9)C10—C11—C12—C130.0 (8)
C3—C4—C5—C60.0 (9)C11—C12—C13—C140.1 (8)
C2—N1—C6—C50.5 (8)C12—C13—C14—N150.4 (8)
Cu—N1—C6—C5179.9 (4)C13—C14—N15—C101.1 (8)
C2—N1—C6—C7178.3 (5)C13—C14—N15—Cu175.7 (4)
Cu—N1—C6—C72.1 (6)C11—C10—N15—C141.3 (8)
C4—C5—C6—N10.5 (8)C9—C10—N15—C14179.1 (5)
C4—C5—C6—C7178.2 (5)C11—C10—N15—Cu176.6 (4)
N1—C6—C7—O7177.9 (5)C9—C10—N15—Cu3.8 (6)
C5—C6—C7—O74.3 (8)N16—Cu—N15—C1412.8 (5)
N1—C6—C7—N82.6 (7)N8—Cu—N15—C14179.5 (5)
C5—C6—C7—N8175.2 (5)N1—Cu—N15—C14163.8 (5)
O7—C7—N8—C90.7 (9)O1—Cu—N15—C1481.1 (4)
C6—C7—N8—C9179.9 (5)N16—Cu—N15—C10172.3 (4)
O7—C7—N8—Cu174.3 (4)N8—Cu—N15—C104.6 (4)
C6—C7—N8—Cu6.3 (6)N1—Cu—N15—C1021.3 (8)
N16—Cu—N8—C964.4 (10)O1—Cu—N15—C1093.8 (4)
N15—Cu—N8—C94.9 (4)N8—Cu—N16—N17112.7 (8)
N1—Cu—N8—C9179.9 (4)N15—Cu—N16—N17171.0 (5)
O1—Cu—N8—C986.6 (4)N1—Cu—N16—N170.4 (6)
N16—Cu—N8—C7121.6 (8)O1—Cu—N16—N1796.0 (5)
N15—Cu—N8—C7179.0 (4)Cu—N16—N17—N18171 (7)
N1—Cu—N8—C76.0 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O9i0.85 (2)2.10 (4)2.843 (5)145 (5)
O1—H1B···O7ii0.84 (2)2.13 (3)2.922 (5)157 (5)
O1—H1A···O7i0.85 (2)2.45 (4)3.105 (5)134 (5)
Symmetry codes: (i) x, y+1, z; (ii) x+1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O9i0.85 (2)2.10 (4)2.843 (5)145 (5)
O1—H1B···O7ii0.84 (2)2.13 (3)2.922 (5)157 (5)
O1—H1A···O7i0.85 (2)2.45 (4)3.105 (5)134 (5)
Symmetry codes: (i) x, y+1, z; (ii) x+1, y, z.
references
References top

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