organic compounds
1-(2-Methyl-5-nitro-1H-imidazol-1-yl)propan-2-yl acetate
aDepartment of Chemistry, Faculty of Science, Federal Urdu University of Arts, Science and Technology Gulshan-e-Iqbal, Karachi 75300, Pakistan, and bH.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
*Correspondence e-mail: dr.sammer.yousuf@gmail.com
In the title compound, C9H13N3O4, an ester of the anti-infection drug secnidazole, the dihedral angle between the nitroimidazole mean plane (r.m.s. deviation = 0.028 Å) and the pendant acetate group is 43.17 (11)°. In the crystal, inversion dimers linked by pairs of C—H⋯O interactions generate R22(10) loops and further C—H⋯O hydrogen bonds link the dimers into [100] chains. Weak aromatic π–π stacking interactions with a centroid–centroid distance of 3.7623 (11) Å are also observed.
CCDC reference: 984872
Related literature
For background to the antibacterial properties of nitroimidazole and secnidazole-like compounds, see: Mital (2009); Edwards (1993); Crozet et al. (2009). For the crystal structures of related compounds, see: Yousuf et al. (2013); Tao et al. (2008);Zeb et al. (2012).
Experimental
Crystal data
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Data collection: SMART (Bruker, 2000); cell SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL, PARST (Nardelli, 1995) and PLATON (Spek, 2009).
Supporting information
CCDC reference: 984872
10.1107/S1600536814002505/hb7195sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814002505/hb7195Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814002505/hb7195Isup3.cml
The title compound was synthesized by adding acetic anhydride (1.2 ml, 12.70 mmol)to a hot (70 °C) stired solution of secnidazole (2 g m, 10.8 mmol) in pyridine (2 ml) and toluene (10 ml). The reaction mixture was further processed to refluxed for 5 hrs, cooled, treated with water and then organic phase was evaporated to obtain solid product which was recrystallized from chloroform and toluene solution to yield greenish plates in 81% yield. Melting point 346–348 K. 1H NMR (300 MHz, DMSO-d6): δ 8.006 (s, 1 H, imidazole H), 5.162–5.089 (m, 1 H, CH), 4.573–4.322 (m, 2 H, CH2), 3.300 (s, 3 H, CH3), 1.856 (s, 3 H CH3), 1.265–1.244 (d, J=6.3 Hz, 3 H, CH3). 13C NMR (75 MHz, DMSO-d6): δ 169.35 (C=O), 151.52 (N=C), 138.40 (C—NO2), 133.01 (N—CH), 68.64 (O—CH), 49.31 (N—CH2), 20.44 (CH3), 17.11 (CH3), 13.93 (CH3). IR (neat, cm-1): 3434, 3122, 2994, 1732, 1532, 1368, 1140, 1080.
The hydrogen atoms are positioned at their calculated positions geometrically with C—H = 0.9300 Å, 0.9600 Å, 0.9700 Å, 0.9800 Å for aromatic, methyl, methylen, and methin H respectively. These are constrained to ride on their parent atoms during subsequent
with Uiso(H) = 1.2Ueq(C) for methyl, and Uiso(H) = 1.5eq(C) for rest of the H atoms.Data collection: SMART (Bruker, 2000); cell
SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).C9H13N3O4 | F(000) = 480 |
Mr = 227.22 | Dx = 1.334 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 6.1771 (5) Å | Cell parameters from 1751 reflections |
b = 8.9928 (7) Å | θ = 2.5–22.3° |
c = 20.3736 (16) Å | µ = 0.11 mm−1 |
β = 90.978 (2)° | T = 273 K |
V = 1131.58 (16) Å3 | Plate, colourless |
Z = 4 | 0.45 × 0.27 × 0.06 mm |
Bruker SMART APEX CCD diffractometer | 2042 independent reflections |
Radiation source: fine-focus sealed tube | 1567 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.025 |
ω scan | θmax = 25.5°, θmin = 2.0° |
Absorption correction: multi-scan (SADABS; Bruker, 2000) | h = −7→7 |
Tmin = 0.954, Tmax = 0.994 | k = −10→10 |
6541 measured reflections | l = −23→24 |
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)] = 0.043 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.119 | H-atom parameters constrained |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0605P)2 + 0.1628P] where P = (Fo2 + 2Fc2)/3 |
2042 reflections | (Δ/σ)max < 0.001 |
145 parameters | Δρmax = 0.20 e Å−3 |
0 restraints | Δρmin = −0.12 e Å−3 |
C9H13N3O4 | V = 1131.58 (16) Å3 |
Mr = 227.22 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 6.1771 (5) Å | µ = 0.11 mm−1 |
b = 8.9928 (7) Å | T = 273 K |
c = 20.3736 (16) Å | 0.45 × 0.27 × 0.06 mm |
β = 90.978 (2)° |
Bruker SMART APEX CCD diffractometer | 2042 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2000) | 1567 reflections with I > 2σ(I) |
Tmin = 0.954, Tmax = 0.994 | Rint = 0.025 |
6541 measured reflections |
R[F2 > 2σ(F2)] = 0.043 | 0 restraints |
wR(F2) = 0.119 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.20 e Å−3 |
2042 reflections | Δρmin = −0.12 e Å−3 |
145 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 | ||
O1 | 0.9023 (2) | 0.57210 (19) | 0.08857 (8) | 0.0881 (5) | |
O2 | 0.6626 (3) | 0.55701 (17) | 0.16347 (8) | 0.0834 (5) | |
O3 | 0.48247 (17) | 0.11443 (13) | 0.18968 (6) | 0.0498 (3) | |
O4 | 0.8273 (2) | 0.17014 (17) | 0.16857 (8) | 0.0744 (5) | |
N2 | 0.7361 (3) | 0.51890 (17) | 0.11093 (9) | 0.0604 (5) | |
N3 | 0.5484 (3) | 0.2475 (2) | −0.00606 (8) | 0.0658 (5) | |
N1 | 0.4442 (2) | 0.33433 (15) | 0.09081 (7) | 0.0476 (4) | |
C5 | 0.6300 (3) | 0.40876 (19) | 0.07274 (9) | 0.0497 (5) | |
C4 | 0.6890 (3) | 0.3540 (2) | 0.01383 (10) | 0.0599 (5) | |
H4A | 0.8088 | 0.3851 | −0.0095 | 0.072* | |
C2 | 0.4036 (3) | 0.2373 (2) | 0.04109 (10) | 0.0552 (5) | |
C11 | 0.2199 (3) | 0.1309 (3) | 0.03950 (12) | 0.0744 (6) | |
H11A | 0.2237 | 0.0738 | −0.0003 | 0.112* | |
H11B | 0.0859 | 0.1848 | 0.0412 | 0.112* | |
H11C | 0.2312 | 0.0654 | 0.0766 | 0.112* | |
C6 | 0.3239 (3) | 0.3431 (2) | 0.15215 (9) | 0.0517 (5) | |
H6A | 0.1826 | 0.2979 | 0.1455 | 0.062* | |
H6B | 0.3018 | 0.4468 | 0.1633 | 0.062* | |
C7 | 0.4387 (3) | 0.26641 (19) | 0.20886 (9) | 0.0489 (5) | |
H7A | 0.5748 | 0.3178 | 0.2193 | 0.059* | |
C8 | 0.2980 (4) | 0.2624 (2) | 0.26847 (10) | 0.0674 (6) | |
H8A | 0.3741 | 0.2134 | 0.3038 | 0.101* | |
H8B | 0.1670 | 0.2092 | 0.2583 | 0.101* | |
H8C | 0.2633 | 0.3622 | 0.2814 | 0.101* | |
C9 | 0.6837 (3) | 0.0809 (2) | 0.17030 (9) | 0.0514 (5) | |
C10 | 0.7003 (3) | −0.0780 (2) | 0.15128 (12) | 0.0731 (6) | |
H10A | 0.8452 | −0.0989 | 0.1377 | 0.110* | |
H10B | 0.6007 | −0.0982 | 0.1157 | 0.110* | |
H10C | 0.6658 | −0.1395 | 0.1882 | 0.110* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0725 (10) | 0.0951 (12) | 0.0972 (12) | −0.0330 (9) | 0.0186 (9) | −0.0015 (10) |
O2 | 0.1073 (12) | 0.0620 (9) | 0.0817 (11) | −0.0251 (8) | 0.0283 (10) | −0.0176 (8) |
O3 | 0.0430 (6) | 0.0450 (7) | 0.0615 (8) | −0.0013 (5) | 0.0057 (6) | 0.0015 (6) |
O4 | 0.0452 (7) | 0.0801 (10) | 0.0982 (12) | −0.0049 (7) | 0.0122 (7) | 0.0021 (9) |
N2 | 0.0624 (10) | 0.0496 (9) | 0.0693 (12) | −0.0064 (8) | 0.0080 (9) | 0.0057 (8) |
N3 | 0.0700 (11) | 0.0718 (11) | 0.0558 (11) | 0.0022 (9) | 0.0071 (9) | −0.0034 (9) |
N1 | 0.0473 (8) | 0.0420 (7) | 0.0536 (9) | 0.0043 (6) | 0.0056 (7) | 0.0033 (7) |
C5 | 0.0488 (9) | 0.0452 (10) | 0.0551 (12) | 0.0015 (8) | 0.0040 (9) | 0.0065 (8) |
C4 | 0.0565 (11) | 0.0639 (12) | 0.0595 (13) | 0.0037 (10) | 0.0109 (10) | 0.0096 (10) |
C2 | 0.0551 (11) | 0.0536 (11) | 0.0570 (12) | 0.0043 (8) | 0.0002 (9) | −0.0004 (9) |
C11 | 0.0676 (13) | 0.0759 (14) | 0.0794 (16) | −0.0104 (11) | −0.0022 (12) | −0.0129 (12) |
C6 | 0.0461 (9) | 0.0476 (10) | 0.0618 (12) | 0.0042 (8) | 0.0119 (9) | −0.0012 (9) |
C7 | 0.0482 (9) | 0.0444 (9) | 0.0544 (11) | −0.0031 (8) | 0.0073 (8) | −0.0037 (8) |
C8 | 0.0717 (13) | 0.0701 (13) | 0.0609 (13) | −0.0068 (10) | 0.0190 (11) | −0.0045 (10) |
C9 | 0.0445 (9) | 0.0612 (11) | 0.0486 (11) | 0.0040 (9) | 0.0015 (8) | 0.0070 (9) |
C10 | 0.0706 (13) | 0.0668 (13) | 0.0820 (16) | 0.0185 (11) | 0.0043 (12) | −0.0038 (12) |
O1—N2 | 1.2276 (19) | C11—H11B | 0.9600 |
O2—N2 | 1.219 (2) | C11—H11C | 0.9600 |
O3—C9 | 1.3447 (19) | C6—C7 | 1.512 (3) |
O3—C7 | 1.448 (2) | C6—H6A | 0.9700 |
O4—C9 | 1.197 (2) | C6—H6B | 0.9700 |
N2—C5 | 1.414 (2) | C7—C8 | 1.506 (2) |
N3—C2 | 1.327 (2) | C7—H7A | 0.9800 |
N3—C4 | 1.351 (3) | C8—H8A | 0.9600 |
N1—C2 | 1.357 (2) | C8—H8B | 0.9600 |
N1—C5 | 1.384 (2) | C8—H8C | 0.9600 |
N1—C6 | 1.467 (2) | C9—C10 | 1.485 (3) |
C5—C4 | 1.353 (3) | C10—H10A | 0.9600 |
C4—H4A | 0.9300 | C10—H10B | 0.9600 |
C2—C11 | 1.484 (3) | C10—H10C | 0.9600 |
C11—H11A | 0.9600 | ||
C9—O3—C7 | 117.93 (13) | C7—C6—H6A | 109.0 |
O2—N2—O1 | 122.85 (18) | N1—C6—H6B | 109.0 |
O2—N2—C5 | 120.29 (15) | C7—C6—H6B | 109.0 |
O1—N2—C5 | 116.86 (17) | H6A—C6—H6B | 107.8 |
C2—N3—C4 | 105.66 (17) | O3—C7—C8 | 107.95 (14) |
C2—N1—C5 | 104.86 (14) | O3—C7—C6 | 108.15 (14) |
C2—N1—C6 | 125.45 (14) | C8—C7—C6 | 110.95 (15) |
C5—N1—C6 | 129.44 (15) | O3—C7—H7A | 109.9 |
C4—C5—N1 | 107.28 (17) | C8—C7—H7A | 109.9 |
C4—C5—N2 | 127.87 (17) | C6—C7—H7A | 109.9 |
N1—C5—N2 | 124.84 (16) | C7—C8—H8A | 109.5 |
N3—C4—C5 | 110.04 (17) | C7—C8—H8B | 109.5 |
N3—C4—H4A | 125.0 | H8A—C8—H8B | 109.5 |
C5—C4—H4A | 125.0 | C7—C8—H8C | 109.5 |
N3—C2—N1 | 112.15 (17) | H8A—C8—H8C | 109.5 |
N3—C2—C11 | 123.62 (19) | H8B—C8—H8C | 109.5 |
N1—C2—C11 | 124.23 (17) | O4—C9—O3 | 123.20 (17) |
C2—C11—H11A | 109.5 | O4—C9—C10 | 125.65 (18) |
C2—C11—H11B | 109.5 | O3—C9—C10 | 111.14 (16) |
H11A—C11—H11B | 109.5 | C9—C10—H10A | 109.5 |
C2—C11—H11C | 109.5 | C9—C10—H10B | 109.5 |
H11A—C11—H11C | 109.5 | H10A—C10—H10B | 109.5 |
H11B—C11—H11C | 109.5 | C9—C10—H10C | 109.5 |
N1—C6—C7 | 112.86 (13) | H10A—C10—H10C | 109.5 |
N1—C6—H6A | 109.0 | H10B—C10—H10C | 109.5 |
C2—N1—C5—C4 | 0.4 (2) | C5—N1—C2—N3 | −0.6 (2) |
C6—N1—C5—C4 | 174.87 (16) | C6—N1—C2—N3 | −175.27 (16) |
C2—N1—C5—N2 | −178.36 (17) | C5—N1—C2—C11 | 179.00 (18) |
C6—N1—C5—N2 | −3.9 (3) | C6—N1—C2—C11 | 4.3 (3) |
O2—N2—C5—C4 | 179.99 (19) | C2—N1—C6—C7 | 100.0 (2) |
O1—N2—C5—C4 | −0.1 (3) | C5—N1—C6—C7 | −73.4 (2) |
O2—N2—C5—N1 | −1.5 (3) | C9—O3—C7—C8 | −139.19 (17) |
O1—N2—C5—N1 | 178.41 (17) | C9—O3—C7—C6 | 100.71 (17) |
C2—N3—C4—C5 | −0.1 (2) | N1—C6—C7—O3 | −55.09 (18) |
N1—C5—C4—N3 | −0.2 (2) | N1—C6—C7—C8 | −173.30 (14) |
N2—C5—C4—N3 | 178.55 (18) | C7—O3—C9—O4 | 0.4 (3) |
C4—N3—C2—N1 | 0.4 (2) | C7—O3—C9—C10 | −178.99 (16) |
C4—N3—C2—C11 | −179.12 (19) |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—H4A···O1i | 0.93 | 2.45 | 3.369 (2) | 168 |
C6—H6A···O4ii | 0.97 | 2.53 | 3.460 (2) | 161 |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—H4A···O1i | 0.93 | 2.45 | 3.369 (2) | 168 |
C6—H6A···O4ii | 0.97 | 2.53 | 3.460 (2) | 161 |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z. |
Acknowledgements
The authors acknowledge Nabiqasim Pharmaceutical Industries (Pvt) Ltd for financial support during the research work.
References
Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Crozet, M. D., Botta, C., Gasquet, M., Curti, C., Rémusat, V., Hutter, S., Chapelle, O., Azas, N., De Méo, M. & Vanelle, P. (2009). Eur. J. Med. Chem. 44, 653–659. Web of Science CrossRef PubMed CAS Google Scholar
Edwards, D. I. (1993). J. Antimicrob. Chemother. 31, 9–20. CrossRef CAS PubMed Web of Science Google Scholar
Mital, A. (2009). Sci. Pharm. 77, 497–520. CrossRef CAS Google Scholar
Nardelli, M. (1995). J. Appl. Cryst. 28, 659. CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
Tao, X., Yuan, L., Zhang, X.-Q. & Wang, J.-T. (2008). Acta Cryst. E64, o472. Web of Science CSD CrossRef IUCr Journals Google Scholar
Yousuf, S., Khan, K. M., Naz, F., Perveen, S. & Miana, G. A. (2013). Acta Cryst. E69, o552. CSD CrossRef IUCr Journals Google Scholar
Zeb, A., Yousuf, S. & Basha, F. Z. (2012). Acta Cryst. E68, o1218. CSD CrossRef IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
The title compound (I) is an ester derivative of well known 5-nitroimidazole drug i.e secnidazole. The worthwhile use of nitroimidazole derivatives is in the treatment of diseases caused by protozoa and anaerobic bacteria (Mital, 2009). Members of nitroimidazole drugs are pronounced in thier wide-range activities and in addition during their use the rate of resistance in anaerobes is still very low (Edwards, 1993). Antiprotozoal and bactericidal properties of nitroimidazoles are associated with their aromatic nitro group. The Secnidazole like chemotherapeutic agents inhibit the growth of both anaerobic bacteria and some anaerobic protozoa (Crozet et al. 2009).
The structure of the title compound (I) is similar to our previously reported compound 1-(2-Methyl-5-nitro-1H-imidazol-1-yl)acetone with the difference that acetone moiety is replaced by propyl acetate group (C6—C10/O3,O4)(Yousuf et al. 2013);. It also exhibits bond lengths and angles that are of normal range (Yousuf et al. 2013); A three dimensional consolidated architecture is formed by the non-covalent interactions of molecules in the crystal via C4– H4A···O1 [2.45 Å], and C6– H6A···O4 [2.53 Å] hydrogen bonding with R22(10) ring motifs. Possible weak pi-pi interactions (Cg1···Cg1) with minimum centroid-centroid distance of 3.7623 (11) Å are also observed.