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The title compound, [Cu4(C2O4)2(N3)4(C5H9N3)2]·0.9H2O, contains a tetranuclear CuII-based molecule composed of two oxalate-bridged CuII dimers linked through end-on azide ions and related by an inversion center. The tetranuclear unit contains two crystallographically independent CuII ions. One CuII ion coordinates to two N atoms of a histamine mol­ecule, two O atoms of a bridging oxalate ligand, and an N atom of an end-on bridging azide ligand, leading to an elongated square-pyramidal coordination geometry in which the azide ion occupies the axial position. The other CuII ion, which has a square-planar coordination geometry, is coordinated by two O atoms of a bridging oxalate ligand and two N atoms of two different azide ligands, one which is bridging. In the crystal, a two-dimensional network parallel to (010) is formed by N—H...N and N—H...O hydrogen bonds. A partially occupied solvent water mol­ecule refined to an occupancy of 0.447 (5). Two of the azide ligands were refined as disordered over two sets of sites with refined occupancies in the ratios 0.517 (8):0.483 (8) and 0.553 (5):0.447 (5).

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536813013329/lh5597sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536813013329/lh5597Isup2.hkl
Contains datablock I

CCDC reference: 954395

Key indicators

  • Single-crystal X-ray study
  • T = 173 K
  • Mean [sigma](C-C) = 0.004 Å
  • H-atom completeness 91%
  • Disorder in main residue
  • R factor = 0.029
  • wR factor = 0.073
  • Data-to-parameter ratio = 12.1

checkCIF/PLATON results

No syntax errors found



Alert level B PLAT201_ALERT_2_B Isotropic non-H Atoms in Main Residue(s) ....... 2
Alert level C CHEMW01_ALERT_1_C The difference between the given and expected weight for compound is greater 1 mass unit. Check that all hydrogen atoms have been taken into account. PLAT041_ALERT_1_C Calc. and Reported SumFormula Strings Differ ? PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)... ? PLAT077_ALERT_4_C Unitcell contains non-integer number of atoms .. ? PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for N7 PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.1 PLAT350_ALERT_3_C Short C-H (X0.96,N1.08A) C6 - H6A ... 0.84 Ang. PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.600 25 PLAT976_ALERT_2_C Negative Residual Density at 0.93A from N7 . -0.42 eA-3
Alert level G FORMU01_ALERT_2_G There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_site* data. Atom count from _chemical_formula_sum:C14 H19.8 Cu4 N18 O8.9 Atom count from the _atom_site data: C14 H18 Cu4 N18 O8.894 CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected. CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional? From the CIF: _cell_formula_units_Z 1 From the CIF: _chemical_formula_sum C14 H19.8 Cu4 N18 O8.9 TEST: Compare cell contents of formula and atom_site data atom Z*formula cif sites diff C 14.00 14.00 0.00 H 19.80 18.00 1.80 Cu 4.00 4.00 0.00 N 18.00 18.00 0.00 O 8.90 8.89 0.01 PLAT004_ALERT_5_G Info: Polymeric Structure Found with Dimension . 2 PLAT005_ALERT_5_G No _iucr_refine_instructions_details in the CIF ? PLAT007_ALERT_5_G Note: Number of Unrefined Donor-H Atoms ........ 2 PLAT042_ALERT_1_G Calc. and Reported MoietyFormula Strings Differ ? PLAT045_ALERT_1_G Calculated and Reported Z Differ by ............ 2.00 Ratio PLAT154_ALERT_1_G The su's on the Cell Angles are Equal .......... 0.00200 Deg. PLAT164_ALERT_4_G Nr. of Refined C-H H-Atoms in Heavy-Atom Struct. 2 PLAT232_ALERT_2_G Hirshfeld Test Diff (M-X) Cu2 -- N4_c .. 11.6 su PLAT301_ALERT_3_G Note: Main Residue Disorder ................... 18 % PLAT302_ALERT_4_G Note: Anion/Solvent Disorder ................... 100 % PLAT311_ALERT_2_G Isolated Disordered Oxygen Atom (No H's ?) ..... O5 PLAT811_ALERT_5_G No ADDSYM Analysis: Too Many Excluded Atoms .... ! PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L= 0.600 81
0 ALERT level A = Most likely a serious problem - resolve or explain 1 ALERT level B = A potentially serious problem, consider carefully 9 ALERT level C = Check. Ensure it is not caused by an omission or oversight 16 ALERT level G = General information/check it is not something unexpected 8 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 7 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 4 ALERT type 4 Improvement, methodology, query or suggestion 4 ALERT type 5 Informative message, check

Comment top

The title compound is a polynuclear coordination complex involving mixed bridging ligands, both oxalate (Coronado et al. 2003; Pardo et al. 2010; Sun et al., 1997) and azide (Ribas, et al. 1999) anions. The tetrameric unit in the title compound is centrosymmetric (Fig.1), so pairs of equivalent ligands lie trans to each other. Two of the four azide ions within each tetramer are in end-on bridging mode, while the other two are non-bridging but form long N4A–Cu[1-x, 2-y, 1-z] (two-dimensional) bonds of 2.486 (3) Å with CuII ions on neighbouring tetramers and therefore link tetramers along the crystallographic b axis to produce one-dimensional chains (Fig.2). The distance between the two CuII ions linked by this long Cu—N bond is 3.2261 (8) Å.

Related literature top

For background to bridging oxalate and azide ligands, see: Coronado et al. (2003); Ribas et al. (1999); Pardo et al. (2010); Sun et al. (1997).

Experimental top

An aqueous solution (15 ml) of copper(II) nitrate trihydrate (4.0 mmol, 0.97 g) was slowly added to an aqueous solution (50 ml) containing histamine dihydrochloride (4.0 mmol, 0.74 g), sodium oxalate (2.0 mmol, 0.27 g), sodium azide (4.0 mmol, 0.26 g), and sodium hydroxide (8.0 mmol, 0.32 g). The mixture was stirred for 10 minutes and allowed to stand in air. Green platelet crystals were collected after a few days and washed with deionized water and dried in air.

Refinement top

All H atoms were positioned geometrically (C—H = 0.93/1.00 Å) and allowed to ride with Uiso(H)= 1.2/1.5Ueq(C). Methyl H atoms were allowed to rotate around the corresponding C—C.

The N2—N3 and N5—N6 moieties were refined a disordered and each refined in two parts against N2'-N3' and N5'-N6'. A partial water molecule alternates with the N5'-N6' moiety in occupying the same space. The two N9 protons were obtained from a difference Fourier map but did not refine properly thus they were refined in idealized positions and were riding on their parent atom. The N9 proton is refined freely. All disordered parts have properly refined occupancy factors.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with ellipsoids drawn at 30% probability level. Unlabelled atoms are related by the symmetry transofrmation: -x + 1, -y + 1, -z + 1.
[Figure 2] Fig. 2. One-dimensional chain of tetramers of the title compound.
Di-µ-azido-diazidodi-µ-oxalato-dihistaminetetracopper(II) 0.9-hydrate top
Crystal data top
[Cu4(C2O4)2(N3)4(C5H9N3)2]·0.9H2OZ = 1
Mr = 838.62F(000) = 416
Triclinic, P1Dx = 2.137 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.7003 (10) ÅCell parameters from 29 reflections
b = 8.2841 (11) Åθ = 2.0–28.0°
c = 11.8677 (15) ŵ = 3.31 mm1
α = 106.005 (2)°T = 173 K
β = 91.715 (2)°Plate, green
γ = 115.010 (2)°0.12 × 0.11 × 0.04 mm
V = 650.07 (15) Å3
Data collection top
Bruker SMART CCD area-detector
diffractometer
2885 independent reflections
Radiation source: fine-focus sealed tube2442 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.041
ω and ϕ scansθmax = 27.5°, θmin = 1.8°
Absorption correction: integration
[based on measured indexed crystal faces (SHELXTL; Sheldrick, 2008)]
h = 99
Tmin = 0.654, Tmax = 0.877k = 1010
5770 measured reflectionsl = 1515
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)] = 0.029Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.073H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0327P)2 + 0.5471P]
where P = (Fo2 + 2Fc2)/3
2885 reflections(Δ/σ)max < 0.001
238 parametersΔρmax = 0.60 e Å3
0 restraintsΔρmin = 0.56 e Å3
Crystal data top
[Cu4(C2O4)2(N3)4(C5H9N3)2]·0.9H2Oγ = 115.010 (2)°
Mr = 838.62V = 650.07 (15) Å3
Triclinic, P1Z = 1
a = 7.7003 (10) ÅMo Kα radiation
b = 8.2841 (11) ŵ = 3.31 mm1
c = 11.8677 (15) ÅT = 173 K
α = 106.005 (2)°0.12 × 0.11 × 0.04 mm
β = 91.715 (2)°
Data collection top
Bruker SMART CCD area-detector
diffractometer
2885 independent reflections
Absorption correction: integration
[based on measured indexed crystal faces (SHELXTL; Sheldrick, 2008)]
2442 reflections with I > 2σ(I)
Tmin = 0.654, Tmax = 0.877Rint = 0.041
5770 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0290 restraints
wR(F2) = 0.073H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.60 e Å3
2885 reflectionsΔρmin = 0.56 e Å3
238 parameters
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Cu10.10361 (5)0.35821 (5)0.26714 (3)0.0187 (1)
Cu20.45210 (4)0.78190 (4)0.47013 (3)0.0146 (1)
O10.1735 (3)0.3957 (2)0.44160 (16)0.0177 (4)
O20.2983 (3)0.2567 (3)0.24786 (16)0.0196 (4)
O30.4798 (3)0.1874 (3)0.35955 (16)0.0194 (4)
O40.3611 (3)0.3319 (3)0.55217 (16)0.0172 (4)
O50.0013 (8)0.9226 (8)0.3473 (5)0.0304 (14)0.447 (5)
N10.3411 (3)0.6717 (3)0.3003 (2)0.0217 (5)
N20.4238 (7)0.6559 (8)0.2176 (4)0.0181 (11)*0.517 (8)
N30.5044 (9)0.6493 (9)0.1379 (5)0.0389 (17)*0.517 (8)
N2'0.4711 (8)0.7391 (9)0.2413 (5)0.0189 (12)*0.483 (8)
N3'0.5775 (9)0.7833 (9)0.1768 (6)0.0378 (18)*0.483 (8)
N40.2809 (4)0.9047 (3)0.5128 (2)0.0218 (5)
N5'0.1670 (6)0.8882 (5)0.4349 (3)0.0153 (10)0.553 (5)
N6'0.0499 (8)0.8764 (8)0.3687 (5)0.0245 (11)0.553 (5)
N50.2251 (7)0.9251 (7)0.6159 (4)0.0182 (12)0.447 (5)
N60.1813 (7)0.9522 (7)0.7129 (5)0.0228 (13)0.447 (5)
N70.1142 (4)0.4201 (5)0.3030 (2)0.0455 (9)
H7B0.20260.32810.32930.055*
H7C0.06650.53100.36510.055*
H7A0.245 (4)0.240 (4)0.028 (3)0.016 (7)*
N80.0241 (3)0.2683 (3)0.09526 (19)0.0183 (5)
N90.0241 (4)0.1696 (3)0.0948 (2)0.0215 (5)
H90.064 (5)0.142 (5)0.155 (3)0.036 (10)*
C10.3613 (4)0.2501 (3)0.3439 (2)0.0163 (5)
C20.2908 (3)0.3308 (3)0.4554 (2)0.0137 (5)
C30.2212 (4)0.4403 (5)0.2049 (3)0.0296 (7)
H3B0.13150.54580.17950.035*
H3A0.32750.46890.23370.035*
C40.3049 (4)0.2605 (4)0.1001 (2)0.0258 (6)
H4B0.37480.15260.12910.031*
H4A0.40040.26470.04460.031*
C50.1530 (4)0.2306 (4)0.0346 (2)0.0186 (5)
C60.1515 (4)0.1704 (4)0.0830 (3)0.0226 (6)
H6A0.237 (5)0.131 (5)0.143 (3)0.027 (9)*
C70.1261 (4)0.2291 (4)0.0137 (2)0.0205 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.01983 (18)0.02819 (19)0.01006 (17)0.01687 (15)0.00150 (12)0.00048 (13)
Cu20.01364 (16)0.01637 (16)0.01463 (17)0.00709 (13)0.00059 (12)0.00577 (12)
O10.0189 (9)0.0221 (9)0.0142 (9)0.0132 (8)0.0004 (7)0.0024 (7)
O20.0227 (10)0.0281 (10)0.0110 (9)0.0176 (8)0.0011 (7)0.0010 (7)
O30.0239 (10)0.0238 (9)0.0135 (9)0.0169 (8)0.0001 (7)0.0004 (8)
O40.0188 (9)0.0212 (9)0.0140 (9)0.0108 (8)0.0038 (7)0.0058 (7)
O50.026 (3)0.041 (3)0.014 (2)0.009 (2)0.003 (2)0.003 (2)
N10.0218 (12)0.0337 (13)0.0138 (11)0.0166 (10)0.0024 (9)0.0071 (10)
N40.0303 (13)0.0213 (11)0.0163 (11)0.0162 (10)0.0019 (10)0.0030 (9)
N5'0.017 (2)0.0134 (18)0.014 (2)0.0076 (16)0.0051 (16)0.0018 (15)
N6'0.020 (3)0.034 (3)0.023 (3)0.015 (2)0.001 (2)0.010 (2)
N50.018 (3)0.018 (2)0.023 (3)0.012 (2)0.004 (2)0.007 (2)
N60.019 (3)0.025 (3)0.029 (3)0.015 (2)0.006 (2)0.007 (2)
N70.0454 (17)0.089 (2)0.0143 (13)0.0549 (18)0.0038 (12)0.0055 (14)
N80.0199 (11)0.0245 (11)0.0121 (10)0.013 (1)0.0009 (8)0.0034 (9)
N90.0298 (13)0.0263 (12)0.0104 (11)0.0157 (11)0.004 (1)0.0037 (10)
C10.0168 (12)0.0147 (11)0.0140 (12)0.0068 (10)0.0002 (10)0.0003 (10)
C20.0131 (12)0.0117 (11)0.0126 (12)0.0042 (9)0.0007 (9)0.0011 (9)
C30.0287 (16)0.0449 (18)0.0234 (15)0.0297 (15)0.0015 (12)0.0019 (13)
C40.0208 (14)0.0399 (16)0.0176 (14)0.0168 (13)0.0009 (11)0.0053 (12)
C50.0194 (13)0.0202 (12)0.0143 (12)0.0104 (11)0.0042 (10)0.0011 (10)
C60.0252 (15)0.0252 (14)0.0151 (13)0.0127 (12)0.0038 (11)0.0017 (11)
C70.0220 (14)0.0272 (14)0.0155 (13)0.0164 (12)0.0034 (11)0.0029 (11)
Geometric parameters (Å, º) top
Cu1—N81.947 (2)N5'—N6'1.132 (7)
Cu1—N71.977 (2)N5—N61.197 (7)
Cu1—O21.9970 (18)N7—C31.493 (4)
Cu1—O12.0275 (18)N7—H7B0.9200
Cu1—N12.371 (3)N7—H7C0.9200
Cu2—N11.962 (2)N8—C71.322 (3)
Cu2—N41.980 (2)N8—C51.390 (3)
Cu2—O3i1.9915 (18)N9—C71.334 (4)
Cu2—O4i2.0148 (18)N9—C61.366 (4)
O1—C21.258 (3)N9—H90.80 (4)
O2—C11.249 (3)C1—C21.534 (3)
O3—C11.258 (3)C3—C41.516 (4)
O3—Cu2i1.9915 (18)C3—H3B0.9900
O4—C21.251 (3)C3—H3A0.9900
O4—Cu2i2.0148 (18)C4—C51.493 (4)
N1—N21.192 (5)C4—H4B0.9900
N1—N2'1.260 (6)C4—H4A0.9900
N2—N31.149 (7)C5—C61.348 (4)
N2'—N3'1.153 (7)C6—H6A0.84 (3)
N4—N5'1.192 (4)C7—H7A0.88 (3)
N4—N51.300 (5)
N8—Cu1—N795.03 (10)Cu1—N7—H7C107.9
N8—Cu1—O290.05 (8)H7B—N7—H7C107.2
N7—Cu1—O2168.22 (12)C7—N8—C5106.7 (2)
N8—Cu1—O1168.11 (8)C7—N8—Cu1126.94 (19)
N7—Cu1—O189.88 (9)C5—N8—Cu1126.40 (18)
O2—Cu1—O183.23 (7)C7—N9—C6108.3 (2)
N8—Cu1—N1101.85 (9)C7—N9—H9124 (3)
N7—Cu1—N195.97 (12)C6—N9—H9127 (3)
O2—Cu1—N193.37 (8)O2—C1—O3126.8 (2)
O1—Cu1—N188.36 (8)O2—C1—C2117.0 (2)
N1—Cu2—N494.99 (9)O3—C1—C2116.2 (2)
N1—Cu2—O3i162.53 (9)O4—C2—O1126.1 (2)
N4—Cu2—O3i90.34 (8)O4—C2—C1116.7 (2)
N1—Cu2—O4i91.90 (8)O1—C2—C1117.1 (2)
N4—Cu2—O4i173.09 (8)N7—C3—C4110.3 (3)
O3i—Cu2—O4i82.91 (7)N7—C3—H3B109.6
C2—O1—Cu1110.59 (16)C4—C3—H3B109.6
C1—O2—Cu1111.93 (17)N7—C3—H3A109.6
C1—O3—Cu2i112.47 (16)C4—C3—H3A109.6
C2—O4—Cu2i111.66 (16)H3B—C3—H3A108.1
N2—N1—Cu2128.1 (3)C5—C4—C3112.7 (2)
N2'—N1—Cu2109.1 (3)C5—C4—H4B109.0
N2—N1—Cu1102.3 (3)C3—C4—H4B109.0
N2'—N1—Cu1130.6 (3)C5—C4—H4A109.0
Cu2—N1—Cu1107.77 (10)C3—C4—H4A109.0
N3—N2—N1176.5 (6)H4B—C4—H4A107.8
N3'—N2'—N1172.4 (7)C6—C5—N8108.1 (2)
N5'—N4—N5114.0 (3)C6—C5—C4130.8 (2)
N5'—N4—Cu2117.9 (2)N8—C5—C4121.0 (2)
N5—N4—Cu2121.0 (3)C5—C6—N9106.8 (2)
N6'—N5'—N4173.9 (5)C5—C6—H6A132 (2)
N6—N5—N4176.8 (5)N9—C6—H6A121 (2)
C3—N7—Cu1117.6 (2)N8—C7—N9110.1 (2)
C3—N7—H7B107.9N8—C7—H7A125.6 (19)
Cu1—N7—H7B107.9N9—C7—H7A124.4 (19)
C3—N7—H7C107.9
Symmetry code: (i) x+1, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N9—H9···O5ii0.80 (4)2.18 (4)2.861 (6)143 (3)
N9—H9···N6ii0.80 (4)2.59 (4)3.171 (6)130 (3)
N9—H9···N3iii0.80 (4)2.60 (4)3.145 (7)127 (3)
N9—H9···N6iv0.80 (4)2.38 (4)3.108 (6)151 (3)
Symmetry codes: (ii) x, y+1, z; (iii) x+1, y+1, z; (iv) x, y1, z1.

Experimental details

Crystal data
Chemical formula[Cu4(C2O4)2(N3)4(C5H9N3)2]·0.9H2O
Mr838.62
Crystal system, space groupTriclinic, P1
Temperature (K)173
a, b, c (Å)7.7003 (10), 8.2841 (11), 11.8677 (15)
α, β, γ (°)106.005 (2), 91.715 (2), 115.010 (2)
V3)650.07 (15)
Z1
Radiation typeMo Kα
µ (mm1)3.31
Crystal size (mm)0.12 × 0.11 × 0.04
Data collection
DiffractometerBruker SMART CCD area-detector
diffractometer
Absorption correctionIntegration
[based on measured indexed crystal faces (SHELXTL; Sheldrick, 2008)]
Tmin, Tmax0.654, 0.877
No. of measured, independent and
observed [I > 2σ(I)] reflections
5770, 2885, 2442
Rint0.041
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.029, 0.073, 1.03
No. of reflections2885
No. of parameters238
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.60, 0.56

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N9—H9···O5i0.80 (4)2.18 (4)2.861 (6)143 (3)
N9—H9···N6'i0.80 (4)2.59 (4)3.171 (6)130 (3)
N9—H9···N3'ii0.80 (4)2.60 (4)3.145 (7)127 (3)
N9—H9···N6iii0.80 (4)2.38 (4)3.108 (6)151 (3)
Symmetry codes: (i) x, y+1, z; (ii) x+1, y+1, z; (iii) x, y1, z1.
 

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