Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807031455/hb2460sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807031455/hb2460Isup2.hkl |
CCDC reference: 657517
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (C-C) = 0.006 Å
- Disorder in main residue
- R factor = 0.032
- wR factor = 0.087
- Data-to-parameter ratio = 10.8
checkCIF/PLATON results
No syntax errors found
Alert level B CHEMS01_ALERT_1_B The sum formula contains elements in the wrong order. N precedes Cu Sequence must be C, H, then alphabetical. PLAT027_ALERT_3_B _diffrn_reflns_theta_full (too) Low ............ 24.99 Deg. PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low ....... 0.95
Alert level C PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ? PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density .... 2.11 PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 = 3 PLAT301_ALERT_3_C Main Residue Disorder ......................... 8.00 Perc. PLAT366_ALERT_2_C Short? C(sp?)-C(sp?) Bond C8 - C9 ... 1.39 Ang. PLAT366_ALERT_2_C Short? C(sp?)-C(sp?) Bond C8 - C12 ... 1.39 Ang.
Alert level G REFLT03_ALERT_1_G ALERT: Expected hkl max differ from CIF values From the CIF: _diffrn_reflns_theta_max 24.99 From the CIF: _reflns_number_total 1568 From the CIF: _diffrn_reflns_limit_ max hkl 25. 8. 4. From the CIF: _diffrn_reflns_limit_ min hkl -25. -13. -4. TEST1: Expected hkl limits for theta max Calculated maximum hkl 27. 13. 4. Calculated minimum hkl -27. -13. -4. REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 24.99 From the CIF: _reflns_number_total 1568 Count of symmetry unique reflns 993 Completeness (_total/calc) 157.91% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 575 Fraction of Friedel pairs measured 0.579 Are heavy atom types Z>Si present yes PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1
0 ALERT level A = In general: serious problem 3 ALERT level B = Potentially serious problem 6 ALERT level C = Check and explain 3 ALERT level G = General alerts; check 3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 5 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
2-(3-Pyridyl)-1H-benzimidazole was synthesized using a reported procedure (Huang, Zeng & Ng, 2004). A mixture of Cu2(OH)2CO3 (0.110 g, 0.5 mmol), 2-(3-pyridyl)-1H-benzimidazole (0.195 g, 1.0 mmol), aqueous ammonia (25%, 5 ml) and methanol (2 ml) was placed in a 15-ml Teflon-lined bomb. The bomb was heated at 433 K for 80 h and then cooled to room temperature at a rate of 5 K h-1. Pale-yellow needles of (I) were obtained in about 60% yield (based on the ligand). CH&N elemental analysis (calc/found) for C12H8CuN3: C 56.03 (56.09), H 3.14(3.21), N 16.35% (16.28%).
The pyridyl ring is disordered in the atoms at the meta-positions. These were refined as a 50:50 mixture of carbon and nitrogen. The pair of C/N atoms were restrained to the same site and also to have the same Uij values. Hydrogen atoms were placed at calculated positions in the riding model approximation [C—H = 0.93 Å, U(H) = 1.2Ueq(C)].
Imidazolates function as monoanionc µ2-bridging ligands to copper(I) and silver(I), and the resulting compounds are single molecules or linear chains (Huang et al., 2006). The copper derivatives exhibit more complicated structures, and this is brought about by a choice of reaction conditions. Copper compounds with a polygon motif (Huang, Zhang & Chen, 2004) as well as with triple helical chain motifs (Huang et al., 2005) have been synthesized. The title compound is a pyridyl-substituted imidazolate; however, the pyridyl ring does not participate in bonding, so that the copper atom is linked only to the nitrogen atoms of two benzimidazolate anions in a linear geometry.
For the structures of some copper(I) imidazolates, see Huang, Zhang & Chen (2004); Huang et al. (2005, 2006). For the synthesis of the ligand, see Huang, Zeng & Ng (2004).
Data collection: SMART (or APEX2?) (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2007).
Fig. 1. View of a fragment of the chain motif in (I) showing 50% displacement ellipsoids for the non-hydrogen atoms. [Symmetry code (i): 3/2 + x, -1/2 -, z] |
[Cu(C12H8N3)] | F(000) = 520 |
Mr = 257.75 | Dx = 1.774 Mg m−3 |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2n | Cell parameters from 1264 reflections |
a = 22.940 (3) Å | θ = 3.2–27.9° |
b = 11.055 (1) Å | µ = 2.23 mm−1 |
c = 3.8050 (4) Å | T = 295 K |
V = 964.91 (18) Å3 | Rod, light yellow |
Z = 4 | 0.20 × 0.15 × 0.11 mm |
Bruker APEX CCD diffractometer | 1568 independent reflections |
Radiation source: fine-focus sealed tube | 1306 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.020 |
φ and ω scans | θmax = 25.0°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −25→25 |
Tmin = 0.623, Tmax = 0.791 | k = −13→8 |
3566 measured reflections | l = −4→4 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.032 | H-atom parameters constrained |
wR(F2) = 0.087 | w = 1/[σ2(Fo2) + (0.0531P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max = 0.001 |
1568 reflections | Δρmax = 0.48 e Å−3 |
145 parameters | Δρmin = −0.23 e Å−3 |
1 restraint | Absolute structure: Flack (1983), 620 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.04 (4) |
[Cu(C12H8N3)] | V = 964.91 (18) Å3 |
Mr = 257.75 | Z = 4 |
Orthorhombic, Pna21 | Mo Kα radiation |
a = 22.940 (3) Å | µ = 2.23 mm−1 |
b = 11.055 (1) Å | T = 295 K |
c = 3.8050 (4) Å | 0.20 × 0.15 × 0.11 mm |
Bruker APEX CCD diffractometer | 1568 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 1306 reflections with I > 2σ(I) |
Tmin = 0.623, Tmax = 0.791 | Rint = 0.020 |
3566 measured reflections |
R[F2 > 2σ(F2)] = 0.032 | H-atom parameters constrained |
wR(F2) = 0.087 | Δρmax = 0.48 e Å−3 |
S = 1.05 | Δρmin = −0.23 e Å−3 |
1568 reflections | Absolute structure: Flack (1983), 620 Friedel pairs |
145 parameters | Absolute structure parameter: 0.04 (4) |
1 restraint |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
Cu1 | 0.74935 (2) | 0.65062 (4) | 0.5000 (4) | 0.02952 (18) | |
N1 | 0.72737 (15) | 0.8039 (3) | 0.3434 (9) | 0.0286 (8) | |
N2 | 0.72837 (15) | 0.9975 (3) | 0.1567 (9) | 0.0261 (8) | |
N3 | 0.91461 (16) | 1.0027 (4) | 0.3531 (12) | 0.0364 (10) | 0.50 |
C3' | 0.91461 (16) | 1.0027 (4) | 0.3531 (12) | 0.0364 (10) | 0.50 |
H3' | 0.9345 | 1.0707 | 0.4326 | 0.044* | 0.50 |
C1 | 0.67013 (19) | 0.8423 (3) | 0.3150 (12) | 0.0289 (10) | |
C2 | 0.61824 (18) | 0.7842 (3) | 0.3838 (12) | 0.0345 (11) | |
H2 | 0.6177 | 0.7049 | 0.4656 | 0.041* | |
C3 | 0.5674 (2) | 0.8463 (4) | 0.3283 (15) | 0.0393 (12) | |
H3 | 0.5319 | 0.8084 | 0.3725 | 0.047* | |
C4 | 0.5677 (2) | 0.9649 (4) | 0.2074 (12) | 0.0369 (11) | |
H4 | 0.5325 | 1.0050 | 0.1732 | 0.044* | |
C5 | 0.61899 (19) | 1.0236 (4) | 0.1378 (11) | 0.0343 (10) | |
H5 | 0.6191 | 1.1025 | 0.0529 | 0.041* | |
C6 | 0.67062 (17) | 0.9626 (3) | 0.1972 (10) | 0.0259 (9) | |
C7 | 0.76014 (16) | 0.9008 (4) | 0.2484 (11) | 0.0259 (9) | |
C8 | 0.82406 (17) | 0.8993 (4) | 0.2412 (10) | 0.0274 (9) | |
C9 | 0.85672 (19) | 0.9970 (4) | 0.3604 (12) | 0.0371 (11) | |
H9 | 0.8367 | 1.0630 | 0.4518 | 0.045* | |
C10 | 0.9427 (2) | 0.9072 (4) | 0.2275 (14) | 0.0462 (12) | |
H10 | 0.9832 | 0.9092 | 0.2209 | 0.055* | |
C11 | 0.91465 (19) | 0.8052 (4) | 0.1062 (11) | 0.0478 (12) | 0.50 |
H11 | 0.9360 | 0.7402 | 0.0193 | 0.057* | 0.50 |
N11' | 0.91465 (19) | 0.8052 (4) | 0.1062 (11) | 0.0478 (12) | 0.50 |
C12 | 0.85523 (18) | 0.8008 (4) | 0.1152 (10) | 0.0328 (11) | |
H12 | 0.8357 | 0.7321 | 0.0373 | 0.039* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.0323 (3) | 0.0143 (3) | 0.0419 (3) | −0.00030 (17) | −0.00202 (19) | 0.0096 (3) |
N1 | 0.033 (2) | 0.0187 (18) | 0.0344 (18) | 0.0014 (16) | 0.0004 (17) | 0.0056 (17) |
N2 | 0.0297 (19) | 0.0132 (17) | 0.0353 (16) | 0.0004 (15) | −0.0029 (17) | 0.0038 (16) |
N3 | 0.024 (2) | 0.025 (2) | 0.060 (3) | −0.0050 (17) | −0.008 (2) | −0.002 (2) |
C3' | 0.024 (2) | 0.025 (2) | 0.060 (3) | −0.0050 (17) | −0.008 (2) | −0.002 (2) |
C1 | 0.039 (3) | 0.018 (2) | 0.030 (2) | 0.0008 (17) | 0.000 (2) | 0.0029 (19) |
C2 | 0.035 (3) | 0.019 (2) | 0.049 (3) | −0.0057 (18) | 0.000 (2) | 0.0043 (18) |
C3 | 0.033 (3) | 0.036 (3) | 0.048 (3) | −0.012 (2) | −0.006 (2) | 0.006 (2) |
C4 | 0.034 (3) | 0.033 (3) | 0.044 (3) | 0.005 (2) | −0.004 (2) | −0.001 (2) |
C5 | 0.044 (3) | 0.020 (2) | 0.039 (2) | 0.004 (2) | −0.002 (2) | 0.0056 (18) |
C6 | 0.033 (3) | 0.017 (2) | 0.028 (2) | 0.0013 (17) | 0.001 (2) | 0.0042 (18) |
C7 | 0.034 (3) | 0.015 (2) | 0.0283 (17) | −0.0012 (17) | −0.001 (2) | 0.0076 (16) |
C8 | 0.034 (3) | 0.020 (2) | 0.0291 (19) | −0.0012 (19) | 0.002 (2) | 0.0063 (16) |
C9 | 0.045 (3) | 0.021 (2) | 0.046 (2) | 0.001 (2) | −0.002 (2) | 0.003 (2) |
C10 | 0.032 (3) | 0.046 (3) | 0.061 (3) | −0.008 (2) | −0.005 (3) | 0.012 (3) |
C11 | 0.050 (3) | 0.038 (2) | 0.055 (3) | 0.005 (2) | 0.000 (2) | 0.005 (2) |
N11' | 0.050 (3) | 0.038 (2) | 0.055 (3) | 0.005 (2) | 0.000 (2) | 0.005 (2) |
C12 | 0.028 (3) | 0.026 (2) | 0.044 (3) | −0.0018 (18) | −0.001 (2) | 0.0018 (19) |
Cu1—N1 | 1.866 (3) | C3—H3 | 0.9300 |
Cu1—N2i | 1.866 (3) | C4—C5 | 1.370 (5) |
N1—C7 | 1.357 (6) | C4—H4 | 0.9300 |
N1—C1 | 1.384 (5) | C5—C6 | 1.382 (5) |
N2—C7 | 1.340 (5) | C5—H5 | 0.9300 |
N2—C6 | 1.388 (5) | C7—C8 | 1.467 (5) |
N2—Cu1ii | 1.866 (3) | C8—C12 | 1.389 (6) |
N3—C10 | 1.326 (6) | C8—C9 | 1.390 (5) |
N3—C9 | 1.330 (5) | C9—H9 | 0.9300 |
C1—C2 | 1.378 (5) | C10—C11 | 1.378 (6) |
C1—C6 | 1.404 (4) | C10—H10 | 0.9300 |
C2—C3 | 1.371 (6) | C11—C12 | 1.364 (6) |
C2—H2 | 0.9300 | C11—H11 | 0.9300 |
C3—C4 | 1.389 (5) | C12—H12 | 0.9300 |
N1—Cu1—N2i | 179.78 (16) | C6—C5—H5 | 120.9 |
C7—N1—C1 | 105.3 (3) | C5—C6—N2 | 131.6 (4) |
C7—N1—Cu1 | 130.7 (3) | C5—C6—C1 | 120.5 (4) |
C1—N1—Cu1 | 124.0 (3) | N2—C6—C1 | 107.8 (4) |
C7—N2—C6 | 105.6 (3) | N2—C7—N1 | 113.4 (4) |
C7—N2—Cu1ii | 131.1 (3) | N2—C7—C8 | 123.2 (4) |
C6—N2—Cu1ii | 123.3 (3) | N1—C7—C8 | 123.4 (4) |
C10—N3—C9 | 117.1 (4) | C12—C8—C9 | 116.4 (4) |
C2—C1—N1 | 131.5 (4) | C12—C8—C7 | 122.0 (4) |
C2—C1—C6 | 120.6 (4) | C9—C8—C7 | 121.6 (4) |
N1—C1—C6 | 107.9 (4) | N3—C9—C8 | 124.6 (4) |
C3—C2—C1 | 118.2 (4) | N3—C9—H9 | 117.7 |
C3—C2—H2 | 120.9 | C8—C9—H9 | 117.7 |
C1—C2—H2 | 120.9 | N3—C10—C11 | 123.0 (4) |
C2—C3—C4 | 121.3 (4) | N3—C10—H10 | 118.5 |
C2—C3—H3 | 119.4 | C11—C10—H10 | 118.5 |
C4—C3—H3 | 119.4 | C12—C11—C10 | 119.2 (4) |
C5—C4—C3 | 121.1 (4) | C12—C11—H11 | 120.4 |
C5—C4—H4 | 119.5 | C10—C11—H11 | 120.4 |
C3—C4—H4 | 119.5 | C11—C12—C8 | 119.7 (4) |
C4—C5—C6 | 118.3 (4) | C11—C12—H12 | 120.2 |
C4—C5—H5 | 120.9 | C8—C12—H12 | 120.2 |
C7—N1—C1—C2 | −178.5 (5) | Cu1ii—N2—C7—N1 | −178.8 (3) |
Cu1—N1—C1—C2 | −0.7 (7) | C6—N2—C7—C8 | 179.7 (4) |
C7—N1—C1—C6 | 0.8 (5) | Cu1ii—N2—C7—C8 | 0.2 (6) |
Cu1—N1—C1—C6 | 178.6 (3) | C1—N1—C7—N2 | −0.9 (5) |
N1—C1—C2—C3 | −179.7 (5) | Cu1—N1—C7—N2 | −178.6 (3) |
C6—C1—C2—C3 | 1.1 (6) | C1—N1—C7—C8 | −180.0 (4) |
C1—C2—C3—C4 | −0.2 (7) | Cu1—N1—C7—C8 | 2.4 (6) |
C2—C3—C4—C5 | 0.3 (7) | N2—C7—C8—C12 | −137.8 (4) |
C3—C4—C5—C6 | −1.2 (6) | N1—C7—C8—C12 | 41.1 (6) |
C4—C5—C6—N2 | −179.2 (4) | N2—C7—C8—C9 | 42.1 (6) |
C4—C5—C6—C1 | 2.0 (6) | N1—C7—C8—C9 | −138.9 (4) |
C7—N2—C6—C5 | −179.0 (4) | C10—N3—C9—C8 | −1.0 (8) |
Cu1ii—N2—C6—C5 | 0.5 (6) | C12—C8—C9—N3 | 1.7 (7) |
C7—N2—C6—C1 | −0.1 (4) | C7—C8—C9—N3 | −178.2 (4) |
Cu1ii—N2—C6—C1 | 179.4 (3) | C9—N3—C10—C11 | 0.3 (8) |
C2—C1—C6—C5 | −2.0 (6) | N3—C10—C11—C12 | −0.2 (8) |
N1—C1—C6—C5 | 178.6 (4) | C10—C11—C12—C8 | 0.9 (7) |
C2—C1—C6—N2 | 178.9 (4) | C9—C8—C12—C11 | −1.6 (7) |
N1—C1—C6—N2 | −0.4 (4) | C7—C8—C12—C11 | 178.4 (4) |
C6—N2—C7—N1 | 0.7 (5) |
Symmetry codes: (i) −x+3/2, y−1/2, z+1/2; (ii) −x+3/2, y+1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | [Cu(C12H8N3)] |
Mr | 257.75 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 295 |
a, b, c (Å) | 22.940 (3), 11.055 (1), 3.8050 (4) |
V (Å3) | 964.91 (18) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 2.23 |
Crystal size (mm) | 0.20 × 0.15 × 0.11 |
Data collection | |
Diffractometer | Bruker APEX CCD |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.623, 0.791 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3566, 1568, 1306 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.594 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.032, 0.087, 1.05 |
No. of reflections | 1568 |
No. of parameters | 145 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.48, −0.23 |
Absolute structure | Flack (1983), 620 Friedel pairs |
Absolute structure parameter | 0.04 (4) |
Computer programs: SMART (or APEX2?) (Bruker, 2002), SAINT (Bruker, 2002), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), X-SEED (Barbour, 2001), publCIF (Westrip, 2007).
Cu1—N1 | 1.866 (3) | Cu1—N2i | 1.866 (3) |
N1—Cu1—N2i | 179.78 (16) |
Symmetry code: (i) −x+3/2, y−1/2, z+1/2. |
Imidazolates function as monoanionc µ2-bridging ligands to copper(I) and silver(I), and the resulting compounds are single molecules or linear chains (Huang et al., 2006). The copper derivatives exhibit more complicated structures, and this is brought about by a choice of reaction conditions. Copper compounds with a polygon motif (Huang, Zhang & Chen, 2004) as well as with triple helical chain motifs (Huang et al., 2005) have been synthesized. The title compound is a pyridyl-substituted imidazolate; however, the pyridyl ring does not participate in bonding, so that the copper atom is linked only to the nitrogen atoms of two benzimidazolate anions in a linear geometry.