Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807027201/fb2054sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807027201/fb2054Isup2.hkl |
CCDC reference: 258085
Key indicators
- Single-crystal X-ray study
- T = 90 K
- Mean (C-C) = 0.001 Å
- R factor = 0.033
- wR factor = 0.091
- Data-to-parameter ratio = 14.0
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT432_ALERT_2_B Short Inter X...Y Contact O42 .. C21 .. 2.90 Ang.
Alert level C PLAT480_ALERT_4_C Long H...A H-Bond Reported H11A .. O42 .. 2.71 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H11C .. O41 .. 2.63 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H5 .. N3 .. 2.67 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H21C .. O2 .. 2.72 Ang.
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 4 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
The title compound was synthesized by ipso nucleophilic replacement of nitro group from 2,4-dinitro-1-methyl imidazole in methanol-sodium methoxide solution with a yield (ca. 54%). The detailed synthesis will be described elsewhere (Suwiński & Wagner, 2007).
All the hydrogen atoms were discernible in the difference Fourier maps and were freely refined.
The molecule of 1-methyl-2-methoxy-4-nitroimidazole, (I), (Fig. 1, Scheme 1) is almost planar, contrary to its analogue 1-methyl-4-nitro-5-methoxyimidazole, (II), that was determined at 100 K (Kulkarni et al., 1987; CCDC-258086). In (II) the methoxy and and the nitro groups are twisted by 57.55 (14) and by 7.90 (12)°, respectively. These larger twists are obviously concomitant to the steric interactions that have a profound effect on the crystal packing.
In (I), there are weak hydrogen bonds that interconnect molecules into layers (Fig. 2). In (II), on the other hand, the C—H···A interactions (A = O or N) are somewhat stronger (the H···O distances are in the range 2.38 Å - 2.57 Å, H···N is 2.54 Å. Additionally, a π-π interaction with the interplanar distance of 3.275 (2) Å (the distance between the ring centroids is 3.629 (2) Å) is also present in the structure of (II).
This is a part of our studies of intermolecular interactions in 4-nitroimidazole derivatives (e.g. Kubicki, 2004, and references therein). Related literature: Kulkarni et al. (1987); Suwiński & Wagner (2007).
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, 1997); 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.
C5H7N3O3 | F(000) = 328 |
Mr = 157.14 | Dx = 1.539 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5503 reflections |
a = 3.9935 (4) Å | θ = 3–24° |
b = 15.4223 (13) Å | µ = 0.13 mm−1 |
c = 11.1724 (8) Å | T = 90 K |
β = 99.710 (7)° | Prism, colourless |
V = 678.24 (10) Å3 | 0.15 × 0.1 × 0.1 mm |
Z = 4 |
Kuma KM-4 CCD four-circle diffractometer | 1791 independent reflections |
Radiation source: fine-focus sealed tube | 1514 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.019 |
ω scans | θmax = 30.0°, θmin = 3.2° |
Absorption correction: multi-scan (SORTAV; Blessing, 1989) | h = −5→5 |
Tmin = 0.988, Tmax = 0.991 | k = −21→20 |
6537 measured reflections | l = −7→15 |
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)] = 0.033 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.091 | All H-atom parameters refined |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0584P)2 + 0.0288P] where P = (Fo2 + 2Fc2)/3 |
1791 reflections | (Δ/σ)max = 0.001 |
128 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.32 e Å−3 |
0 constraints |
C5H7N3O3 | V = 678.24 (10) Å3 |
Mr = 157.14 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 3.9935 (4) Å | µ = 0.13 mm−1 |
b = 15.4223 (13) Å | T = 90 K |
c = 11.1724 (8) Å | 0.15 × 0.1 × 0.1 mm |
β = 99.710 (7)° |
Kuma KM-4 CCD four-circle diffractometer | 1791 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1989) | 1514 reflections with I > 2σ(I) |
Tmin = 0.988, Tmax = 0.991 | Rint = 0.019 |
6537 measured reflections |
R[F2 > 2σ(F2)] = 0.033 | 0 restraints |
wR(F2) = 0.091 | All H-atom parameters refined |
S = 1.08 | Δρmax = 0.25 e Å−3 |
1791 reflections | Δρmin = −0.32 e Å−3 |
128 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 | 0.9835 (2) | 0.86207 (6) | 0.74562 (7) | 0.01581 (19) | |
C11 | 1.0726 (3) | 0.93772 (7) | 0.82410 (9) | 0.0195 (2) | |
H11A | 0.915 (4) | 0.9850 (9) | 0.8026 (12) | 0.028 (3)* | |
H11B | 1.295 (4) | 0.9564 (10) | 0.8185 (13) | 0.034 (4)* | |
H11C | 1.060 (4) | 0.9218 (11) | 0.9051 (15) | 0.037 (4)* | |
C2 | 1.0365 (2) | 0.85322 (6) | 0.62825 (8) | 0.0154 (2) | |
O2 | 1.19492 (18) | 0.91689 (5) | 0.57922 (6) | 0.01867 (18) | |
C21 | 1.2306 (3) | 0.90098 (7) | 0.45370 (9) | 0.0183 (2) | |
H21A | 1.008 (3) | 0.8990 (9) | 0.4044 (12) | 0.024 (3)* | |
H21B | 1.356 (3) | 0.8470 (9) | 0.4504 (12) | 0.021 (3)* | |
H21C | 1.361 (4) | 0.9506 (10) | 0.4307 (13) | 0.029 (3)* | |
N3 | 0.9215 (2) | 0.78040 (5) | 0.57663 (7) | 0.01595 (19) | |
C4 | 0.7856 (2) | 0.74043 (6) | 0.66772 (8) | 0.0159 (2) | |
N4 | 0.6282 (2) | 0.65768 (6) | 0.64766 (7) | 0.01753 (19) | |
O41 | 0.6293 (2) | 0.62136 (5) | 0.54923 (7) | 0.0250 (2) | |
O42 | 0.49664 (19) | 0.62600 (5) | 0.73091 (7) | 0.02218 (19) | |
C5 | 0.8197 (2) | 0.78822 (6) | 0.77259 (8) | 0.0162 (2) | |
H5 | 0.760 (3) | 0.7775 (9) | 0.8489 (12) | 0.022 (3)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0179 (4) | 0.0188 (4) | 0.0110 (4) | 0.0008 (3) | 0.0032 (3) | −0.0002 (3) |
C11 | 0.0241 (5) | 0.0215 (5) | 0.0130 (5) | −0.0015 (4) | 0.0036 (4) | −0.0034 (4) |
C2 | 0.0159 (4) | 0.0199 (5) | 0.0109 (4) | 0.0023 (3) | 0.0033 (3) | 0.0017 (3) |
O2 | 0.0245 (4) | 0.0205 (4) | 0.0122 (3) | −0.0035 (3) | 0.0065 (3) | −0.0002 (2) |
C21 | 0.0218 (5) | 0.0232 (5) | 0.0107 (4) | −0.0008 (4) | 0.0050 (3) | 0.0006 (3) |
N3 | 0.0180 (4) | 0.0185 (4) | 0.0116 (4) | 0.0011 (3) | 0.0034 (3) | 0.0013 (3) |
C4 | 0.0171 (4) | 0.0187 (4) | 0.0122 (4) | 0.0009 (3) | 0.0031 (3) | 0.0011 (3) |
N4 | 0.0199 (4) | 0.0205 (4) | 0.0125 (4) | 0.0007 (3) | 0.0035 (3) | 0.0004 (3) |
O41 | 0.0360 (4) | 0.0250 (4) | 0.0150 (4) | −0.0049 (3) | 0.0073 (3) | −0.0058 (3) |
O42 | 0.0279 (4) | 0.0240 (4) | 0.0162 (4) | −0.0036 (3) | 0.0082 (3) | 0.0031 (3) |
C5 | 0.0180 (4) | 0.0192 (5) | 0.0117 (4) | 0.0009 (3) | 0.0035 (3) | 0.0013 (3) |
N1—C2 | 1.3699 (12) | C21—H21A | 0.965 (14) |
N1—C5 | 1.3722 (13) | C21—H21B | 0.975 (14) |
N1—C11 | 1.4668 (12) | C21—H21C | 0.984 (15) |
C11—H11A | 0.967 (15) | N3—C4 | 1.3771 (12) |
C11—H11B | 0.946 (17) | C4—C5 | 1.3714 (13) |
C11—H11C | 0.947 (17) | C4—N4 | 1.4234 (13) |
C2—N3 | 1.3097 (13) | N4—O41 | 1.2348 (11) |
C2—O2 | 1.3347 (12) | N4—O42 | 1.2428 (11) |
O2—C21 | 1.4542 (11) | C5—H5 | 0.938 (14) |
C2—N1—C5 | 106.49 (8) | H21A—C21—H21B | 112.4 (11) |
C2—N1—C11 | 126.19 (8) | O2—C21—H21C | 105.2 (8) |
C5—N1—C11 | 127.27 (8) | H21A—C21—H21C | 110.7 (12) |
N1—C11—H11A | 111.6 (8) | H21B—C21—H21C | 110.9 (11) |
N1—C11—H11B | 109.8 (9) | C2—N3—C4 | 102.19 (8) |
H11A—C11—H11B | 109.6 (13) | C5—C4—N3 | 113.33 (9) |
N1—C11—H11C | 108.6 (10) | C5—C4—N4 | 126.43 (9) |
H11A—C11—H11C | 107.2 (13) | N3—C4—N4 | 120.23 (8) |
H11B—C11—H11C | 110.0 (13) | O41—N4—O42 | 123.61 (9) |
N3—C2—O2 | 127.27 (8) | O41—N4—C4 | 118.63 (8) |
N3—C2—N1 | 114.05 (8) | O42—N4—C4 | 117.76 (8) |
O2—C2—N1 | 118.68 (8) | C4—C5—N1 | 103.93 (8) |
C2—O2—C21 | 113.70 (7) | C4—C5—H5 | 132.7 (9) |
O2—C21—H21A | 109.0 (8) | N1—C5—H5 | 123.3 (9) |
O2—C21—H21B | 108.3 (8) | ||
C5—N1—C2—N3 | 0.10 (11) | C2—N3—C4—N4 | 179.52 (8) |
C11—N1—C2—N3 | −177.50 (9) | C5—C4—N4—O41 | −177.26 (9) |
C5—N1—C2—O2 | −179.74 (8) | N3—C4—N4—O41 | 2.98 (13) |
C11—N1—C2—O2 | 2.67 (14) | C5—C4—N4—O42 | 2.78 (14) |
N3—C2—O2—C21 | 1.33 (13) | N3—C4—N4—O42 | −176.99 (8) |
N1—C2—O2—C21 | −178.86 (8) | N3—C4—C5—N1 | 0.34 (11) |
O2—C2—N3—C4 | 179.92 (9) | N4—C4—C5—N1 | −179.44 (9) |
N1—C2—N3—C4 | 0.10 (10) | C2—N1—C5—C4 | −0.25 (10) |
C2—N3—C4—C5 | −0.28 (11) | C11—N1—C5—C4 | 177.31 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
C11—H11A···O42i | 0.967 (15) | 2.713 (15) | 3.6751 (13) | 173.0 (11) |
C11—H11C···O41ii | 0.947 (17) | 2.633 (17) | 3.4342 (13) | 142.6 (12) |
C5—H5···N3ii | 0.938 (14) | 2.670 (14) | 3.5154 (12) | 150.2 (11) |
C21—H21C···O2iii | 0.984 (15) | 2.720 (15) | 3.6841 (13) | 166.5 (11) |
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) x, −y+3/2, z+1/2; (iii) −x+3, −y+2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C5H7N3O3 |
Mr | 157.14 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 90 |
a, b, c (Å) | 3.9935 (4), 15.4223 (13), 11.1724 (8) |
β (°) | 99.710 (7) |
V (Å3) | 678.24 (10) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.15 × 0.1 × 0.1 |
Data collection | |
Diffractometer | Kuma KM-4 CCD four-circle |
Absorption correction | Multi-scan (SORTAV; Blessing, 1989) |
Tmin, Tmax | 0.988, 0.991 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6537, 1791, 1514 |
Rint | 0.019 |
(sin θ/λ)max (Å−1) | 0.704 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.033, 0.091, 1.08 |
No. of reflections | 1791 |
No. of parameters | 128 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.25, −0.32 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2002), CrysAlis CCD, CrysAlis RED (Oxford Diffraction, 2002), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), Stereochemical Workstation Operation Manual (Siemens, 1989), SHELXL97.
D—H···A | D—H | H···A | D···A | D—H···A |
C11—H11A···O42i | 0.967 (15) | 2.713 (15) | 3.6751 (13) | 173.0 (11) |
C11—H11C···O41ii | 0.947 (17) | 2.633 (17) | 3.4342 (13) | 142.6 (12) |
C5—H5···N3ii | 0.938 (14) | 2.670 (14) | 3.5154 (12) | 150.2 (11) |
C21—H21C···O2iii | 0.984 (15) | 2.720 (15) | 3.6841 (13) | 166.5 (11) |
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) x, −y+3/2, z+1/2; (iii) −x+3, −y+2, −z+1. |
The molecule of 1-methyl-2-methoxy-4-nitroimidazole, (I), (Fig. 1, Scheme 1) is almost planar, contrary to its analogue 1-methyl-4-nitro-5-methoxyimidazole, (II), that was determined at 100 K (Kulkarni et al., 1987; CCDC-258086). In (II) the methoxy and and the nitro groups are twisted by 57.55 (14) and by 7.90 (12)°, respectively. These larger twists are obviously concomitant to the steric interactions that have a profound effect on the crystal packing.
In (I), there are weak hydrogen bonds that interconnect molecules into layers (Fig. 2). In (II), on the other hand, the C—H···A interactions (A = O or N) are somewhat stronger (the H···O distances are in the range 2.38 Å - 2.57 Å, H···N is 2.54 Å. Additionally, a π-π interaction with the interplanar distance of 3.275 (2) Å (the distance between the ring centroids is 3.629 (2) Å) is also present in the structure of (II).