1-(2-Methyl-5-nitro-1H-imidazol-1-yl)propan-2-yl acetate

Abstract

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 R ₂ ²(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.

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  

• C₉H₁₃N₃O₄

• M _r = 227.22

• Monoclinic,

• a = 6.1771 (5) Å

• b = 8.9928 (7) Å

• c = 20.3736 (16) Å

• β = 90.978 (2)°

• V = 1131.58 (16) ų

• Z = 4

• Mo Kα radiation

• μ = 0.11 mm⁻¹

• T = 273 K

• 0.45 × 0.27 × 0.06 mm

Data collection  

• Bruker SMART APEX CCD diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2000 ▶) T _min = 0.954, T _max = 0.994

• 6541 measured reflections

• 2042 independent reflections

• 1567 reflections with I > 2σ(I)

• R _int = 0.025

Refinement  

• R[F ² > 2σ(F ²)] = 0.043

• wR(F ²) = 0.119

• S = 1.02

• 2042 reflections

• 145 parameters

• H-atom parameters constrained

• Δρ_max = 0.20 e Å⁻³

• Δρ_min = −0.12 e Å⁻³

Data collection: SMART (Bruker, 2000 ▶); cell refinement: 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 ▶).

Supplementary Material

CCDC reference: http://scripts.iucr.org/cgi-bin/cr.cgi?rm=csd&csdid=984872

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

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) ; (ii) .

supplementary crystallographic information

1. Comment

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.

2. Experimental

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.

3. Refinement

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 refinement with U_iso(H) = 1.2U_eq(C) for methyl, and U_iso(H) = 1.5_eq(C) for rest of the H atoms.

Figures

Fig. 1.

Fig:1 The molecular structure of title compound I, showing displacement ellipsoids drawn at 50% probability level.

Fig. 2.

Fig: 2 Crystal packing diagram, showing intermolecular hydrogen bonding as dashed lines.

Crystal data

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

Data collection

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

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

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	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*

Atomic displacement parameters (Ų)

	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)

Geometric parameters (Å, º)

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)

Hydrogen-bond geometry (Å, º)

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.