Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807035301/kj2062sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807035301/kj2062Isup2.hkl |
CCDC reference: 657826
Key indicators
- Single-crystal X-ray study
- T = 100 K
- Mean (C-C) = 0.003 Å
- R factor = 0.034
- wR factor = 0.058
- Data-to-parameter ratio = 9.0
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT432_ALERT_2_B Short Inter X...Y Contact O5 .. C51 .. 2.91 Ang.
Alert level C PLAT230_ALERT_2_C Hirshfeld Test Diff for O42 - N4 .. 5.44 su PLAT390_ALERT_3_C Deviating Methyl C51 X-C-H Bond Angle ...... 102.80 Deg. PLAT391_ALERT_3_C Deviating Methyl C51 H-C-H Bond Angle ...... 117.50 Deg. PLAT480_ALERT_4_C Long H...A H-Bond Reported H16 .. O41 .. 2.69 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H21A .. O5 .. 2.84 Ang.
Alert level G 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 29.26 From the CIF: _reflns_number_total 1739 Count of symmetry unique reflns 1821 Completeness (_total/calc) 95.50% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 3 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
The present work is a part of our study of intermolecular interactions in 4-nitroimidazole derivatives, which started with 1-phenyl-4-nitroimidazole (Kubicki et al., 2001, 2002). A similar packing of 1-aryl-4-nitroimidazoles was described in detail by Kubicki (2004). For related literature, see: Smithen & Hardy (1982).
1.2 g of Sodium was dissolved in 50 ml of dry methanol. To the resulting warm solution, 0.52 g (2 mmol) of 5-bromo-2-methyl-4-nitro-1-phenylimidazole was added and the reaction mixture was stirred at room temperature for 24 h. Afterwards the mixture was neutralized by concentrated HCl to pH 7 and the excess of methanol was removed under vacuum. The residue was treated by 20 ml of water and the organic solid was filtered off, dried then recrystallized from hot methanol to give 0.25 g (54%) of the product.
Friedel pairs were merged by SORTAV (Blessing, 1989). Hydrogen atoms were freely refined, for hydrogen atoms of each methyl group one common isotropic displacement parameter was used.
Nitroimidazoles have been intensively investigated as radiosensitizers of hypoxic tumor cells and as veterinary drugs (Smithen & Hardy, 1982). For some time we have studied weak intermolecular interactions in 4-nitroimidazole derivatives (e.g. Kubicki et al., 2001, 2002).
Similar packing by means of weak C—H···N and C—H···O hydrogen bonds was observed in the crystal structures of (1–4'-methylphenyl)- and (1–4'-methoxyphenyl)-4-nitro-5-methylimidazole (Kubicki, 2004). Interestingly, both these compounds have similar packing modes in spite of crystallizing in different space groups, the former one in the non-centrosymmetric Pna21, and the latter in centrosymmetric P21/c. The title compound is a third example, in still another space group (P212121). All three compounds have also similar unit-cell parameters a, b and c. A comparison of the unit-cell parameters of the title compound determined at 100 K with those determined at room temperature [6.800 (1), 7.527 (1), 23.103 (2)] shows that the compression perpendicular to the imidazole ring planes (i.e. along stack axis, a) is the strongest. That might be related to the lack of π-π interactions in this case, the imidazole planes are parallel but shifted.
The present work is a part of our study of intermolecular interactions in 4-nitroimidazole derivatives, which started with 1-phenyl-4-nitroimidazole (Kubicki et al., 2001, 2002). A similar packing of 1-aryl-4-nitroimidazoles was described in detail by Kubicki (2004). For related literature, see: Smithen & Hardy (1982).
Data collection: CrysAlis CCD (Oxford Diffraction, 2002); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989); software used to prepare material for publication: SHELXL97.
C11H11N3O3 | F(000) = 488 |
Mr = 233.23 | Dx = 1.356 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 4053 reflections |
a = 6.6179 (4) Å | θ = 3–20° |
b = 7.4711 (5) Å | µ = 0.10 mm−1 |
c = 23.1087 (15) Å | T = 100 K |
V = 1142.56 (13) Å3 | Block, colourless |
Z = 4 | 0.2 × 0.2 × 0.05 mm |
Kuma KM4 CCD four-circle diffractometer | 1739 independent reflections |
Radiation source: fine-focus sealed tube | 1210 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.045 |
ω scans | θmax = 29.3°, θmin = 3.2° |
Absorption correction: multi-scan (SORTAV; Blessing, 1989) | h = −8→8 |
Tmin = 0.989, Tmax = 0.989 | k = −9→9 |
7520 measured reflections | l = −26→30 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.034 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.058 | All H-atom parameters refined |
S = 1.00 | w = 1/[σ2(Fo2) + (0.019P)2] where P = (Fo2 + 2Fc2)/3 |
1739 reflections | (Δ/σ)max < 0.001 |
194 parameters | Δρmax = 0.15 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
C11H11N3O3 | V = 1142.56 (13) Å3 |
Mr = 233.23 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 6.6179 (4) Å | µ = 0.10 mm−1 |
b = 7.4711 (5) Å | T = 100 K |
c = 23.1087 (15) Å | 0.2 × 0.2 × 0.05 mm |
Kuma KM4 CCD four-circle diffractometer | 1739 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1989) | 1210 reflections with I > 2σ(I) |
Tmin = 0.989, Tmax = 0.989 | Rint = 0.045 |
7520 measured reflections |
R[F2 > 2σ(F2)] = 0.034 | 0 restraints |
wR(F2) = 0.058 | All H-atom parameters refined |
S = 1.00 | Δρmax = 0.15 e Å−3 |
1739 reflections | Δρmin = −0.24 e Å−3 |
194 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.7905 (3) | 0.35064 (19) | 0.09665 (6) | 0.0177 (3) | |
C11 | 0.7920 (3) | 0.4361 (2) | 0.15235 (8) | 0.0204 (4) | |
C12 | 0.6282 (4) | 0.4126 (3) | 0.18903 (9) | 0.0305 (6) | |
H12 | 0.522 (3) | 0.343 (2) | 0.1755 (8) | 0.025 (6)* | |
C13 | 0.6299 (4) | 0.4964 (4) | 0.24273 (10) | 0.0394 (6) | |
H13 | 0.509 (4) | 0.471 (3) | 0.2681 (9) | 0.056 (8)* | |
C14 | 0.7895 (4) | 0.6040 (3) | 0.25869 (9) | 0.0347 (6) | |
H14 | 0.788 (3) | 0.660 (3) | 0.2980 (9) | 0.039 (6)* | |
C15 | 0.9515 (4) | 0.6282 (3) | 0.22155 (9) | 0.0298 (5) | |
H15 | 1.071 (3) | 0.715 (3) | 0.2320 (8) | 0.039 (6)* | |
C16 | 0.9536 (4) | 0.5429 (3) | 0.16797 (9) | 0.0242 (5) | |
H16 | 1.063 (3) | 0.558 (2) | 0.1431 (9) | 0.031 (6)* | |
C2 | 0.7919 (3) | 0.1686 (2) | 0.08417 (7) | 0.0193 (4) | |
C21 | 0.7984 (4) | 0.0271 (3) | 0.12882 (9) | 0.0279 (5) | |
H21A | 0.859 (4) | −0.080 (3) | 0.1163 (10) | 0.053 (5)* | |
H21B | 0.662 (3) | 0.001 (3) | 0.1402 (10) | 0.053 (5)* | |
H21C | 0.862 (3) | 0.059 (3) | 0.1615 (10) | 0.053 (5)* | |
N3 | 0.7887 (3) | 0.14035 (18) | 0.02801 (6) | 0.0190 (4) | |
C4 | 0.7847 (3) | 0.3083 (2) | 0.00357 (8) | 0.0179 (4) | |
N4 | 0.7881 (3) | 0.3282 (2) | −0.05751 (6) | 0.0230 (4) | |
O41 | 0.7858 (2) | 0.19203 (18) | −0.08821 (5) | 0.0314 (4) | |
O42 | 0.7943 (2) | 0.48142 (18) | −0.07788 (5) | 0.0288 (4) | |
C5 | 0.7861 (3) | 0.4404 (2) | 0.04442 (8) | 0.0184 (4) | |
O5 | 0.7854 (2) | 0.61860 (15) | 0.04423 (5) | 0.0209 (3) | |
C51 | 0.6031 (4) | 0.7009 (3) | 0.02080 (12) | 0.0300 (6) | |
H51A | 0.572 (4) | 0.647 (3) | −0.0184 (10) | 0.054 (4)* | |
H51B | 0.635 (3) | 0.829 (3) | 0.0222 (9) | 0.054 (4)* | |
H51C | 0.502 (4) | 0.678 (3) | 0.0476 (10) | 0.054 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0194 (8) | 0.0163 (8) | 0.0173 (8) | −0.0006 (8) | 0.0005 (8) | −0.0010 (7) |
C11 | 0.0250 (11) | 0.0194 (10) | 0.0169 (9) | 0.0053 (9) | −0.0023 (11) | −0.0022 (8) |
C12 | 0.0266 (13) | 0.0399 (15) | 0.0250 (13) | −0.0019 (11) | 0.0009 (11) | −0.0061 (11) |
C13 | 0.0331 (14) | 0.0573 (17) | 0.0277 (13) | 0.0048 (14) | 0.0067 (11) | −0.0091 (13) |
C14 | 0.0422 (14) | 0.0404 (14) | 0.0215 (11) | 0.0139 (13) | −0.0065 (13) | −0.0107 (10) |
C15 | 0.0379 (14) | 0.0237 (12) | 0.0277 (12) | 0.0033 (12) | −0.0102 (11) | −0.0056 (10) |
C16 | 0.0267 (13) | 0.0232 (12) | 0.0227 (11) | −0.0018 (10) | −0.0012 (10) | 0.0002 (10) |
C2 | 0.0179 (10) | 0.0177 (10) | 0.0224 (10) | −0.0003 (9) | 0.0001 (10) | −0.0015 (8) |
C21 | 0.0374 (14) | 0.0232 (12) | 0.0231 (11) | −0.0020 (13) | −0.0004 (12) | 0.0022 (9) |
N3 | 0.0177 (8) | 0.0186 (8) | 0.0205 (8) | 0.0025 (8) | 0.0005 (8) | −0.0007 (7) |
C4 | 0.0156 (10) | 0.0221 (10) | 0.0162 (9) | −0.0001 (10) | −0.0002 (9) | 0.0003 (8) |
N4 | 0.0183 (9) | 0.0307 (11) | 0.0199 (9) | −0.0010 (9) | −0.0008 (8) | −0.0015 (8) |
O41 | 0.0408 (9) | 0.0326 (8) | 0.0208 (7) | −0.0001 (8) | 0.0004 (8) | −0.0093 (6) |
O42 | 0.0333 (9) | 0.0294 (8) | 0.0237 (7) | −0.0015 (9) | −0.0024 (7) | 0.0078 (6) |
C5 | 0.0156 (10) | 0.0187 (10) | 0.0210 (10) | −0.0019 (9) | 0.0004 (10) | 0.0017 (8) |
O5 | 0.0240 (7) | 0.0145 (7) | 0.0244 (7) | −0.0006 (7) | −0.0045 (7) | 0.0013 (5) |
C51 | 0.0241 (13) | 0.0229 (12) | 0.0430 (15) | 0.0035 (10) | −0.0059 (11) | −0.0010 (12) |
N1—C5 | 1.381 (2) | C2—C21 | 1.478 (3) |
N1—C2 | 1.390 (2) | C21—H21A | 0.94 (2) |
N1—C11 | 1.437 (2) | C21—H21B | 0.96 (2) |
C11—C16 | 1.382 (3) | C21—H21C | 0.90 (2) |
C11—C12 | 1.388 (3) | N3—C4 | 1.376 (2) |
C12—C13 | 1.390 (3) | C4—C5 | 1.366 (2) |
C12—H12 | 0.93 (2) | C4—N4 | 1.419 (2) |
C13—C14 | 1.378 (4) | N4—O42 | 1.2384 (18) |
C13—H13 | 1.01 (2) | N4—O41 | 1.2404 (18) |
C14—C15 | 1.385 (3) | C5—O5 | 1.332 (2) |
C14—H14 | 1.00 (2) | O5—C51 | 1.458 (2) |
C15—C16 | 1.392 (3) | C51—H51A | 1.01 (2) |
C15—H15 | 1.05 (2) | C51—H51B | 0.98 (2) |
C16—H16 | 0.93 (2) | C51—H51C | 0.93 (2) |
C2—N3 | 1.315 (2) | ||
C5—N1—C2 | 107.08 (14) | C2—C21—H21A | 113.9 (14) |
C5—N1—C11 | 124.57 (13) | C2—C21—H21B | 107.9 (14) |
C2—N1—C11 | 128.35 (14) | H21A—C21—H21B | 108 (2) |
C16—C11—C12 | 121.21 (18) | C2—C21—H21C | 114.3 (15) |
C16—C11—N1 | 119.74 (19) | H21A—C21—H21C | 106 (2) |
C12—C11—N1 | 119.04 (19) | H21B—C21—H21C | 105 (2) |
C11—C12—C13 | 118.8 (2) | C2—N3—C4 | 105.01 (15) |
C11—C12—H12 | 117.1 (12) | C5—C4—N3 | 112.03 (15) |
C13—C12—H12 | 124.1 (12) | C5—C4—N4 | 127.70 (16) |
C14—C13—C12 | 120.5 (2) | N3—C4—N4 | 120.21 (16) |
C14—C13—H13 | 124.2 (13) | O42—N4—O41 | 122.75 (14) |
C12—C13—H13 | 115.2 (13) | O42—N4—C4 | 118.39 (15) |
C13—C14—C15 | 120.2 (2) | O41—N4—C4 | 118.86 (16) |
C13—C14—H14 | 118.7 (13) | O5—C5—C4 | 136.08 (17) |
C15—C14—H14 | 121.1 (13) | O5—C5—N1 | 119.24 (15) |
C14—C15—C16 | 119.9 (2) | C4—C5—N1 | 104.68 (14) |
C14—C15—H15 | 121.3 (11) | C5—O5—C51 | 115.18 (17) |
C16—C15—H15 | 118.7 (11) | O5—C51—H51A | 109.3 (14) |
C11—C16—C15 | 119.2 (2) | O5—C51—H51B | 102.7 (14) |
C11—C16—H16 | 120.5 (12) | H51A—C51—H51B | 117.3 (19) |
C15—C16—H16 | 120.2 (13) | O5—C51—H51C | 105.8 (15) |
N3—C2—N1 | 111.20 (15) | H51A—C51—H51C | 112.2 (19) |
N3—C2—C21 | 125.09 (16) | H51B—C51—H51C | 108.4 (19) |
N1—C2—C21 | 123.71 (16) | ||
C5—N1—C11—C16 | −63.6 (3) | C21—C2—N3—C4 | −179.5 (2) |
C2—N1—C11—C16 | 116.7 (2) | C2—N3—C4—C5 | 0.2 (3) |
C5—N1—C11—C12 | 114.9 (2) | C2—N3—C4—N4 | 177.62 (19) |
C2—N1—C11—C12 | −64.7 (3) | C5—C4—N4—O42 | 0.4 (4) |
C16—C11—C12—C13 | −1.1 (3) | N3—C4—N4—O42 | −176.55 (18) |
N1—C11—C12—C13 | −179.62 (19) | C5—C4—N4—O41 | −179.9 (2) |
C11—C12—C13—C14 | 1.4 (4) | N3—C4—N4—O41 | 3.1 (3) |
C12—C13—C14—C15 | −0.7 (4) | N3—C4—C5—O5 | 179.4 (2) |
C13—C14—C15—C16 | −0.3 (3) | N4—C4—C5—O5 | 2.2 (5) |
C12—C11—C16—C15 | 0.1 (3) | N3—C4—C5—N1 | −0.2 (3) |
N1—C11—C16—C15 | 178.63 (17) | N4—C4—C5—N1 | −177.4 (2) |
C14—C15—C16—C11 | 0.6 (3) | C2—N1—C5—O5 | −179.5 (2) |
C5—N1—C2—N3 | 0.0 (2) | C11—N1—C5—O5 | 0.8 (3) |
C11—N1—C2—N3 | 179.7 (2) | C2—N1—C5—C4 | 0.1 (2) |
C5—N1—C2—C21 | 179.4 (2) | C11—N1—C5—C4 | −179.6 (2) |
C11—N1—C2—C21 | −0.9 (4) | C4—C5—O5—C51 | 65.1 (4) |
N1—C2—N3—C4 | −0.1 (2) | N1—C5—O5—C51 | −115.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C51—H51A···O42 | 1.01 (2) | 2.36 (2) | 3.081 (3) | 127.2 (18) |
C12—H12···O41i | 0.93 (2) | 2.567 (19) | 3.343 (3) | 141.6 (15) |
C16—H16···O41ii | 0.93 (2) | 2.69 (2) | 3.363 (3) | 129.5 (15) |
C21—H21A···O5iii | 0.94 (2) | 2.84 (2) | 3.626 (3) | 141.2 (18) |
C51—H51B···N3iv | 0.98 (2) | 2.54 (2) | 3.510 (3) | 168.8 (19) |
Symmetry codes: (i) x−1/2, −y+1/2, −z; (ii) x+1/2, −y+1/2, −z; (iii) x, y−1, z; (iv) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C11H11N3O3 |
Mr | 233.23 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 6.6179 (4), 7.4711 (5), 23.1087 (15) |
V (Å3) | 1142.56 (13) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.2 × 0.2 × 0.05 |
Data collection | |
Diffractometer | Kuma KM4 CCD four-circle |
Absorption correction | Multi-scan (SORTAV; Blessing, 1989) |
Tmin, Tmax | 0.989, 0.989 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7520, 1739, 1210 |
Rint | 0.045 |
(sin θ/λ)max (Å−1) | 0.688 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.058, 1.00 |
No. of reflections | 1739 |
No. of parameters | 194 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.15, −0.24 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2002), CrysAlis CCD, CrysAlis RED (Oxford Diffraction, 2002), SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), Stereochemical Workstation Operation Manual (Siemens, 1989), SHELXL97.
D—H···A | D—H | H···A | D···A | D—H···A |
C51—H51A···O42 | 1.01 (2) | 2.36 (2) | 3.081 (3) | 127.2 (18) |
C12—H12···O41i | 0.93 (2) | 2.567 (19) | 3.343 (3) | 141.6 (15) |
C16—H16···O41ii | 0.93 (2) | 2.69 (2) | 3.363 (3) | 129.5 (15) |
C21—H21A···O5iii | 0.94 (2) | 2.84 (2) | 3.626 (3) | 141.2 (18) |
C51—H51B···N3iv | 0.98 (2) | 2.54 (2) | 3.510 (3) | 168.8 (19) |
Symmetry codes: (i) x−1/2, −y+1/2, −z; (ii) x+1/2, −y+1/2, −z; (iii) x, y−1, z; (iv) x, y+1, z. |
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Nitroimidazoles have been intensively investigated as radiosensitizers of hypoxic tumor cells and as veterinary drugs (Smithen & Hardy, 1982). For some time we have studied weak intermolecular interactions in 4-nitroimidazole derivatives (e.g. Kubicki et al., 2001, 2002).
Similar packing by means of weak C—H···N and C—H···O hydrogen bonds was observed in the crystal structures of (1–4'-methylphenyl)- and (1–4'-methoxyphenyl)-4-nitro-5-methylimidazole (Kubicki, 2004). Interestingly, both these compounds have similar packing modes in spite of crystallizing in different space groups, the former one in the non-centrosymmetric Pna21, and the latter in centrosymmetric P21/c. The title compound is a third example, in still another space group (P212121). All three compounds have also similar unit-cell parameters a, b and c. A comparison of the unit-cell parameters of the title compound determined at 100 K with those determined at room temperature [6.800 (1), 7.527 (1), 23.103 (2)] shows that the compression perpendicular to the imidazole ring planes (i.e. along stack axis, a) is the strongest. That might be related to the lack of π-π interactions in this case, the imidazole planes are parallel but shifted.