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Acta Cryst. (2011). E67, m85    [ doi:10.1107/S1600536810051779 ]

{3-[Bis(2-pyridylmethyl-[kappa]N)amino-[kappa]N]propanol}bis(nitrato-[kappa]O)copper(II)

S. R. Rowthu, J. W. Shin, Y. R. Seo and K. S. Min

Abstract top

In the title compound, [Cu(NO3)2(C15H19N3O)], the CuII ion is coordinated by the N atoms of the tetradentate 3-[bis(2-pyridylmethyl)amino]propanol ligand and two O atoms from two monodentate nitrate anions, resulting in a distorted square-pyramidal environment. An intermolecular O-H...O hydrogen-bonding interaction between the free hydroxy group of the ligand and a nitrate O atom of an adjacent complex unit, gives a chain structure which extends across the (101) planes.

Comment top

The preparation and characterization of a large number of polyamine complexes has been done, in order to elucidate the mechanisms of metalloenzymes (Tshuva & Lippard, 2004). Recently, the complexes with bis(2-pyridylmethyl)amine moieties have been widely described (Bebout et al.,1998; Shin et al., 2010) because the tridentate unit is a good candidate for potential biological applications (van Staveren et al., 2002). For example, palladium(II) and platinum(II) complexes with bis(2-pyridylmethyl)amine or its derivatives have been investigated as potential anticancer agents, e.g. cis-platin (Rauterkus et al., 2003). Here, we report the synthesis and crystal structure of five-coordinate Cu(NO3)2 complex with the tetradentate ligand N,N-bis(2-pyridylmethyl)-3-aminopropanol = bdap), the title compound [Cu(bpap)(NO3)2] (I), and the structure is reported here.

In the title compound (Fig. 1), the CuII ion is five-coordinated and exhibits a distorted square pyramidal geometry, the equatorial plane being defined by the three nitrogen atoms of the bdap ligand and one oxygen atom of a nitrate ion. The coordination geometry is completed by the axial coordination of the oxygen atom of the second nitrate anion. The Cu—Leq bond lengths are in the range of 1.965 (4) and 2.093 (3) Å and the Cu—Oax bond length is 2.248 (3) Å. Both nitrate ions are bound in η1-fashion. The bond angles about the copper atom range from 76.95 (12) to 165.48 (15)°. The packing structure involves a strong O—H···O hydrogen bonding interaction between the free hydroxyl group of the bpap ligand and a nitrate O atom of an adjacent complex unit (Table 1), giving a one-dimensional chain structure which extends across the (101) planes in the unit cell (Fig. 2).

Related literature top

Polyamine complexes have been characterized in order to elucidate the mechanisms of metalloenzymes, see: Tshuva & Lippard (2004). For complexes with bis(2-pyridylmethyl)amine ligands, see: Bebout et al. (1998); Shin et al. (2010). Compounds with tridentate units have potential biological applications, see:van Staveren et al. (2002). Palladium(II) and platinum(II) complexes with bis(2-pyridylmethyl)amine or its derivatives have been investigated as potential anticancer agents including cis-platin (Rauterkus et al., 2003). For the preparation of N,N-bis(2-pyridylmethyl)-3-aminopropanol, see: Young et al. (1995).

Experimental top

A MeOH solution (5 ml) of Cu(NO3)2 . 3H2O (47 mg, 0.194 mmol) was added to a MeOH solution (5 ml) of N,N-bis(2-pyridylmethyl)-3-aminopropanol (bpap, 50 mg, 0.194 mmol) (Young et al., 1995). The color changed to blue-green, and the solution was stirred for 10 min at room temperature. Blue-green crystals were obtained by diffusion of diethyl ether into the reaction mixture in methanol and were collected by filtration, washed with diethyl ether, and dried in air (yield: 36 mg, 42%). FTIR (KBr, cm-1): 3399, 1437, 3069, 2970, 2862, 1054, 1608.

Refinement top

All H atoms in the title compound were placed in geometrically idealized positions and constrained to ride on their parent atoms, with C—H distances of 0.95 (ring H atoms) or 0.99 (open chain H atoms) Å and an O—H distance of 0.84 Å, and with Uiso(H) values of 1.2 or 1.5 times Ueq(C,O).

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: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. ORTEP drawing of the title compound with atomic numbering scheme and 30% probability ellipsoids.
[Figure 2] Fig. 2. A view of the title compound showing a one-dimensional chain structure formed by O—H···O hydrogen-bonding interactions.
{3-[Bis(2-pyridylmethyl-κN)amino-κN]propanol}bis(nitrato- κO)copper(II) top
Crystal data top
[Cu(NO3)2(C15H19N3O)]F(000) = 916
Mr = 444.89Dx = 1.657 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2504 reflections
a = 8.3499 (7) Åθ = 2.7–23.6°
b = 14.7703 (12) ŵ = 1.28 mm−1
c = 14.5134 (12) ÅT = 200 K
β = 95.055 (2)°Needle, blue-green
V = 1783.0 (3) Å30.26 × 0.13 × 0.09 mm
Z = 4
Data collection top
Siemens SMART CCD
diffractometer		4412 independent reflections
Radiation source: fine-focus sealed tube2297 reflections with I > 2σ(I)
graphiteRint = 0.078
φ and ω scansθmax = 28.3°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −11→11
Tmin = 0.820, Tmax = 0.892k = −19→18
13134 measured reflectionsl = −17→19
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)] = 0.053Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.151H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.0564P)2]
where P = (Fo2 + 2Fc2)/3
4412 reflections(Δ/σ)max < 0.001
254 parametersΔρmax = 0.78 e Å−3
0 restraintsΔρmin = −0.66 e Å−3
Crystal data top
[Cu(NO3)2(C15H19N3O)]V = 1783.0 (3) Å3
Mr = 444.89Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.3499 (7) ŵ = 1.28 mm−1
b = 14.7703 (12) ÅT = 200 K
c = 14.5134 (12) Å0.26 × 0.13 × 0.09 mm
β = 95.055 (2)°
Data collection top
Siemens SMART CCD
diffractometer		4412 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		2297 reflections with I > 2σ(I)
Tmin = 0.820, Tmax = 0.892Rint = 0.078
13134 measured reflectionsθmax = 28.3°
Refinement top
R[F2 > 2σ(F2)] = 0.053H-atom parameters constrained
wR(F2) = 0.151Δρmax = 0.78 e Å−3
S = 1.03Δρmin = −0.66 e Å−3
4412 reflectionsAbsolute structure: ?
254 parametersFlack parameter: ?
0 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
Cu10.13958 (6)0.34362 (4)0.87320 (4)0.03228 (19)
N1−0.0717 (4)0.3222 (2)0.9189 (2)0.0314 (9)
N20.1137 (4)0.2127 (2)0.8271 (2)0.0336 (9)
N30.3346 (4)0.3396 (2)0.8064 (2)0.0320 (8)
N40.2941 (4)0.3812 (3)1.0535 (2)0.0344 (9)
N50.0028 (5)0.4753 (3)0.7451 (3)0.0464 (11)
O10.2165 (5)0.0185 (3)1.0483 (3)0.0818 (13)
H10.29590.01681.08800.123*
O20.2405 (4)0.4250 (2)0.9813 (2)0.0396 (8)
O30.2729 (4)0.2988 (2)1.0556 (2)0.0539 (10)
O40.3673 (4)0.4229 (3)1.1171 (2)0.0614 (11)
O50.0804 (4)0.4846 (2)0.8229 (2)0.0497 (9)
O6−0.0202 (4)0.3980 (3)0.7120 (2)0.0598 (10)
O7−0.0504 (5)0.5423 (3)0.7013 (3)0.0789 (13)
C1−0.1437 (5)0.3745 (3)0.9779 (3)0.0323 (10)
H1A−0.09270.42900.99920.039*
C2−0.2890 (5)0.3519 (3)1.0086 (3)0.0373 (11)
H2−0.33940.39081.04960.045*
C3−0.3605 (6)0.2721 (3)0.9791 (3)0.0401 (12)
H3−0.45920.25411.00150.048*
C4−0.2894 (5)0.2181 (3)0.9172 (3)0.0382 (11)
H4−0.33840.16300.89570.046*
C5−0.1448 (5)0.2458 (3)0.8868 (3)0.0335 (10)
C6−0.0626 (6)0.1966 (3)0.8132 (3)0.0410 (12)
H6A−0.08490.13090.81650.049*
H6B−0.10460.21860.75130.049*
C70.1975 (6)0.2068 (3)0.7424 (3)0.0427 (12)
H7A0.12290.22380.68840.051*
H7B0.23280.14360.73360.051*
C80.3421 (5)0.2690 (3)0.7485 (3)0.0361 (11)
C90.4694 (6)0.2583 (3)0.6956 (3)0.0451 (13)
H90.47630.20690.65690.054*
C100.5875 (6)0.3244 (3)0.7002 (3)0.0427 (12)
H100.67510.31950.66290.051*
C110.5779 (6)0.3969 (3)0.7584 (3)0.0404 (11)
H110.65790.44270.76160.049*
C120.4513 (5)0.4020 (3)0.8115 (3)0.0341 (10)
H120.44580.45120.85320.041*
C130.1911 (6)0.1521 (3)0.9023 (3)0.0402 (11)
H13A0.14800.16900.96130.048*
H13B0.30790.16500.90890.048*
C140.1684 (6)0.0503 (3)0.8885 (4)0.0543 (14)
H14A0.05360.03480.89100.065*
H14B0.20000.03310.82670.065*
C150.2670 (8)−0.0015 (4)0.9608 (4)0.0659 (17)
H15A0.2553−0.06720.94850.079*
H15B0.38180.01470.95940.079*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.0363 (3)0.0263 (3)0.0347 (3)−0.0016 (2)0.0056 (2)−0.0041 (2)
N10.034 (2)0.026 (2)0.034 (2)−0.0022 (16)0.0002 (17)−0.0023 (15)
N20.035 (2)0.033 (2)0.032 (2)−0.0039 (17)0.0023 (17)−0.0098 (16)
N30.033 (2)0.033 (2)0.030 (2)0.0007 (17)0.0041 (16)0.0008 (16)
N40.037 (2)0.037 (2)0.030 (2)−0.0022 (18)0.0066 (18)−0.0032 (18)
N50.047 (3)0.039 (3)0.054 (3)0.004 (2)0.007 (2)0.010 (2)
O10.091 (3)0.092 (4)0.063 (3)0.022 (3)0.010 (2)0.003 (2)
O20.054 (2)0.0318 (19)0.0322 (18)−0.0032 (15)0.0001 (15)−0.0030 (14)
O30.073 (3)0.030 (2)0.056 (2)−0.0080 (18)−0.0066 (19)0.0031 (17)
O40.082 (3)0.062 (3)0.037 (2)−0.020 (2)−0.0132 (19)−0.0105 (17)
O50.055 (2)0.053 (2)0.040 (2)0.0027 (17)−0.0047 (18)0.0028 (16)
O60.061 (2)0.058 (3)0.059 (2)−0.009 (2)0.0001 (19)−0.001 (2)
O70.099 (3)0.065 (3)0.070 (3)0.025 (2)−0.006 (2)0.034 (2)
C10.033 (3)0.032 (3)0.032 (2)−0.0024 (19)0.007 (2)−0.0065 (19)
C20.041 (3)0.036 (3)0.035 (3)0.006 (2)0.002 (2)−0.003 (2)
C30.037 (3)0.048 (3)0.036 (3)−0.003 (2)0.005 (2)0.004 (2)
C40.042 (3)0.031 (3)0.040 (3)−0.006 (2)−0.003 (2)−0.001 (2)
C50.035 (3)0.033 (3)0.032 (2)0.003 (2)0.000 (2)0.0013 (19)
C60.041 (3)0.036 (3)0.045 (3)−0.002 (2)−0.004 (2)−0.010 (2)
C70.046 (3)0.039 (3)0.043 (3)−0.005 (2)0.005 (2)−0.012 (2)
C80.042 (3)0.033 (3)0.033 (3)0.003 (2)0.003 (2)−0.004 (2)
C90.046 (3)0.052 (3)0.037 (3)0.005 (3)0.007 (2)−0.012 (2)
C100.032 (3)0.055 (4)0.042 (3)0.004 (2)0.008 (2)0.001 (2)
C110.037 (3)0.046 (3)0.038 (3)0.001 (2)0.003 (2)0.006 (2)
C120.039 (3)0.028 (3)0.034 (3)−0.002 (2)−0.001 (2)0.0002 (19)
C130.040 (3)0.034 (3)0.046 (3)0.004 (2)−0.002 (2)−0.004 (2)
C140.066 (4)0.038 (3)0.059 (3)0.001 (3)0.004 (3)−0.002 (2)
C150.091 (5)0.055 (4)0.053 (4)0.021 (3)0.015 (3)0.008 (3)
Geometric parameters (Å, °) top
Cu1—N11.965 (4)C3—H30.9500
Cu1—N31.968 (3)C4—C51.383 (6)
Cu1—N22.051 (3)C4—H40.9500
Cu1—O22.093 (3)C5—C61.507 (6)
Cu1—O52.248 (3)C6—H6A0.9900
N1—C11.335 (5)C6—H6B0.9900
N1—C51.345 (5)C7—C81.514 (6)
N2—C71.469 (5)C7—H7A0.9900
N2—C61.487 (5)C7—H7B0.9900
N2—C131.512 (6)C8—C91.374 (6)
N3—C121.339 (5)C9—C101.385 (6)
N3—C81.343 (5)C9—H90.9500
N4—O41.227 (4)C10—C111.370 (6)
N4—O31.230 (4)C10—H100.9500
N4—O21.279 (4)C11—C121.364 (6)
N5—O71.236 (5)C11—H110.9500
N5—O61.247 (5)C12—H120.9500
N5—O51.259 (5)C13—C141.527 (6)
O1—C151.403 (6)C13—H13A0.9900
O1—H10.8400C13—H13B0.9900
C1—C21.370 (6)C14—C151.487 (7)
C1—H1A0.9500C14—H14A0.9900
C2—C31.373 (6)C14—H14B0.9900
C2—H20.9500C15—H15A0.9900
C3—C41.375 (6)C15—H15B0.9900
N1—Cu1—N3165.48 (15)N2—C6—C5109.5 (4)
N1—Cu1—N283.45 (14)N2—C6—H6A109.8
N3—Cu1—N283.03 (14)C5—C6—H6A109.8
N1—Cu1—O298.85 (13)N2—C6—H6B109.8
N3—Cu1—O295.20 (13)C5—C6—H6B109.8
N2—Cu1—O2144.03 (14)H6A—C6—H6B108.2
N1—Cu1—O594.64 (13)N2—C7—C8110.6 (4)
N3—Cu1—O592.06 (14)N2—C7—H7A109.5
N2—Cu1—O5138.91 (14)C8—C7—H7A109.5
O2—Cu1—O576.95 (12)N2—C7—H7B109.5
C1—N1—C5119.4 (4)C8—C7—H7B109.5
C1—N1—Cu1126.3 (3)H7A—C7—H7B108.1
C5—N1—Cu1114.3 (3)N3—C8—C9121.3 (4)
C7—N2—C6114.5 (4)N3—C8—C7115.2 (4)
C7—N2—C13111.3 (4)C9—C8—C7123.4 (4)
C6—N2—C13111.0 (3)C8—C9—C10118.4 (4)
C7—N2—Cu1106.5 (3)C8—C9—H9120.8
C6—N2—Cu1105.6 (3)C10—C9—H9120.8
C13—N2—Cu1107.2 (3)C11—C10—C9120.0 (4)
C12—N3—C8119.6 (4)C11—C10—H10120.0
C12—N3—Cu1125.6 (3)C9—C10—H10120.0
C8—N3—Cu1114.7 (3)C12—C11—C10118.8 (5)
O4—N4—O3122.8 (4)C12—C11—H11120.6
O4—N4—O2118.5 (4)C10—C11—H11120.6
O3—N4—O2118.6 (4)N3—C12—C11121.8 (4)
O7—N5—O6119.9 (5)N3—C12—H12119.1
O7—N5—O5120.4 (5)C11—C12—H12119.1
O6—N5—O5119.7 (4)N2—C13—C14116.6 (4)
C15—O1—H1109.5N2—C13—H13A108.1
N4—O2—Cu1114.4 (3)C14—C13—H13A108.1
N5—O5—Cu1105.7 (3)N2—C13—H13B108.1
N1—C1—C2122.0 (4)C14—C13—H13B108.1
N1—C1—H1A119.0H13A—C13—H13B107.3
C2—C1—H1A119.0C15—C14—C13111.1 (4)
C1—C2—C3118.7 (4)C15—C14—H14A109.4
C1—C2—H2120.7C13—C14—H14A109.4
C3—C2—H2120.7C15—C14—H14B109.4
C2—C3—C4120.1 (4)C13—C14—H14B109.4
C2—C3—H3119.9H14A—C14—H14B108.0
C4—C3—H3119.9O1—C15—C14109.8 (5)
C3—C4—C5118.4 (4)O1—C15—H15A109.7
C3—C4—H4120.8C14—C15—H15A109.7
C5—C4—H4120.8O1—C15—H15B109.7
N1—C5—C4121.4 (4)C14—C15—H15B109.7
N1—C5—C6115.4 (4)H15A—C15—H15B108.2
C4—C5—C6123.2 (4)
N3—Cu1—N1—C1−171.0 (5)O2—Cu1—O5—N5−179.4 (3)
N2—Cu1—N1—C1167.4 (4)C5—N1—C1—C21.4 (6)
O2—Cu1—N1—C123.7 (4)Cu1—N1—C1—C2−177.4 (3)
O5—Cu1—N1—C1−53.8 (4)N1—C1—C2—C31.4 (7)
N3—Cu1—N1—C510.1 (8)C1—C2—C3—C4−2.4 (7)
N2—Cu1—N1—C5−11.4 (3)C2—C3—C4—C50.8 (7)
O2—Cu1—N1—C5−155.2 (3)C1—N1—C5—C4−3.2 (6)
O5—Cu1—N1—C5127.4 (3)Cu1—N1—C5—C4175.8 (3)
N1—Cu1—N2—C7148.6 (3)C1—N1—C5—C6173.8 (4)
N3—Cu1—N2—C7−26.0 (3)Cu1—N1—C5—C6−7.3 (5)
O2—Cu1—N2—C7−115.3 (3)C3—C4—C5—N12.1 (7)
O5—Cu1—N2—C759.1 (4)C3—C4—C5—C6−174.6 (4)
N1—Cu1—N2—C626.4 (3)C7—N2—C6—C5−152.9 (4)
N3—Cu1—N2—C6−148.3 (3)C13—N2—C6—C579.9 (4)
O2—Cu1—N2—C6122.5 (3)Cu1—N2—C6—C5−36.0 (4)
O5—Cu1—N2—C6−63.1 (3)N1—C5—C6—N230.1 (5)
N1—Cu1—N2—C13−92.1 (3)C4—C5—C6—N2−153.0 (4)
N3—Cu1—N2—C1393.3 (3)C6—N2—C7—C8149.5 (4)
O2—Cu1—N2—C134.0 (4)C13—N2—C7—C8−83.5 (4)
O5—Cu1—N2—C13178.4 (2)Cu1—N2—C7—C833.1 (4)
N1—Cu1—N3—C12169.3 (5)C12—N3—C8—C91.5 (6)
N2—Cu1—N3—C12−169.2 (4)Cu1—N3—C8—C9178.5 (3)
O2—Cu1—N3—C12−25.3 (4)C12—N3—C8—C7−175.2 (4)
O5—Cu1—N3—C1251.7 (3)Cu1—N3—C8—C71.8 (5)
N1—Cu1—N3—C8−7.5 (8)N2—C7—C8—N3−24.4 (6)
N2—Cu1—N3—C814.0 (3)N2—C7—C8—C9159.0 (4)
O2—Cu1—N3—C8157.9 (3)N3—C8—C9—C10−2.8 (7)
O5—Cu1—N3—C8−125.0 (3)C7—C8—C9—C10173.6 (4)
O4—N4—O2—Cu1173.9 (3)C8—C9—C10—C111.8 (7)
O3—N4—O2—Cu1−4.6 (5)C9—C10—C11—C120.4 (7)
N1—Cu1—O2—N479.6 (3)C8—N3—C12—C110.8 (6)
N3—Cu1—O2—N4−96.7 (3)Cu1—N3—C12—C11−175.8 (3)
N2—Cu1—O2—N4−11.4 (4)C10—C11—C12—N3−1.8 (7)
O5—Cu1—O2—N4172.4 (3)C7—N2—C13—C14−71.2 (5)
O7—N5—O5—Cu1177.9 (4)C6—N2—C13—C1457.7 (5)
O6—N5—O5—Cu1−2.2 (5)Cu1—N2—C13—C14172.7 (3)
N1—Cu1—O5—N5−81.4 (3)N2—C13—C14—C15172.9 (4)
N3—Cu1—O5—N585.7 (3)C13—C14—C15—O162.6 (6)
N2—Cu1—O5—N53.9 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O7i0.842.182.961 (6)155
Symmetry codes: (i) x+1/2, −y+1/2, z+1/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O7i0.842.182.961 (6)155
Symmetry codes: (i) x+1/2, −y+1/2, z+1/2.
Acknowledgements top

This work was supported by the Korea Research Foundation (KRF) grant funded by the Korea government (MEST) (No. 2009–0073897). The authors acknowledge the Korea Basic Science Institute for the X-ray data collection.

references
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