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Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P21/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)max = 1.12 Å−1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen–Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N—O and C—NO2 exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O—H...N, C—H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S2052520619011272/px5015sup1.cif
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2052520619011272/px5015Isup2.hkl
Contains datablock I

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S2052520619011272/px5015sup3.pdf
Supplementary material

CCDC reference: 1886394

Computing details top

Data collection: Bruker APEX2; cell refinement: Bruker SAINT; data reduction: Bruker SAINT; program(s) used to solve structure: SHELXS2013/1 (Sheldrick, 2008); program(s) used to refine structure: XD2006 (Volkov et al., 2006); molecular graphics: XD2006 (Volkov et al., 2006); software used to prepare material for publication: XD2006 (Volkov et al., 2006).

Metronidazole top
Crystal data top
C6H9N3O3F(000) = 360
Mr = 171.16Dx = 1.492 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 8459 reflections
a = 6.8785 (1) Åθ = 2.8–51.4°
b = 8.6396 (1) ŵ = 0.12 mm1
c = 12.8573 (2) ÅT = 90 K
β = 94.351 (1)°Block, colorless
V = 761.88 (2) Å30.45 × 0.42 × 0.38 mm
Z = 4
Data collection top
Bruker APEX-II CCD
diffractometer
8459 independent reflections
Radiation source: fine-focus sealed tube7409 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
ω scansθmax = 51.4°, θmin = 2.8°
Absorption correction: analytical
SADABS(BRUKER, 2006)
h = 1515
Tmin = 0.705, Tmax = 0.750k = 018
8459 measured reflectionsl = 028
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullPrimary atom site location: structure-invariant direct methods
R[F2 > 2σ(F2)] = 0.032Secondary atom site location: difference Fourier map
wR(F2) = 0.096Hydrogen site location: inferred from neighbouring sites
S = 1.05H atoms treated by a mixture of independent and constrained refinement
8459 reflections w = 1/[σ2(Fo2) + (0.0528P)2 + 0.0396P]
where P = (Fo2 + 2Fc2)/3
145 parameters(Δ/σ)max = 0.002
Special details top

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 > 2sigma(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 (Å2) top
xyzUiso*/Ueq
H20.6492 (12)1.0277 (10)0.1413 (6)0.0239 (18)*
H6B0.6859 (11)1.0814 (9)0.2521 (6)0.0191 (16)*
H5B0.9873 (11)0.9821 (9)0.1992 (6)0.0182 (15)*
H6A0.7972 (12)0.9788 (10)0.3440 (6)0.0232 (17)*
H5A0.9154 (12)0.8111 (10)0.2128 (6)0.0227 (17)*
H30.5741 (16)0.8141 (12)0.3256 (8)0.038 (2)*
H4C0.6413 (14)0.6220 (11)0.1413 (8)0.033 (2)*
H4B0.6552 (14)0.5590 (11)0.0279 (7)0.035 (2)*
H4A0.8431 (15)0.5977 (11)0.1042 (8)0.038 (2)*
N20.78921 (3)0.91339 (2)0.087093 (16)0.01057 (3)
O30.55999 (3)0.87979 (3)0.269883 (17)0.01618 (4)
N30.82263 (3)1.18946 (3)0.034447 (19)0.01301 (3)
N10.65237 (4)0.81923 (3)0.062631 (18)0.01320 (3)
C10.71659 (4)0.78600 (3)0.035743 (19)0.01188 (4)
C20.68468 (4)0.97335 (3)0.076302 (19)0.01226 (4)
C30.76877 (3)1.03302 (3)0.015313 (18)0.01066 (3)
C50.87269 (4)0.91562 (3)0.19572 (2)0.01350 (4)
C60.72842 (5)0.97458 (3)0.27091 (2)0.01492 (4)
O10.80240 (5)1.27862 (3)0.04044 (2)0.02093 (5)
O20.88617 (5)1.22880 (3)0.12263 (2)0.02124 (5)
C40.71365 (5)0.62878 (3)0.08221 (3)0.01834 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N20.01200 (7)0.01087 (6)0.00863 (6)0.00042 (5)0.00059 (5)0.00052 (5)
O30.01664 (8)0.01973 (9)0.01196 (7)0.00067 (6)0.00027 (5)0.00469 (6)
N30.01415 (7)0.01149 (7)0.01339 (7)0.00076 (5)0.00095 (5)0.00097 (5)
N10.01482 (8)0.01402 (8)0.01060 (7)0.00067 (6)0.00022 (5)0.00254 (5)
C10.01339 (8)0.01085 (7)0.01135 (8)0.00060 (6)0.00071 (6)0.00076 (5)
C20.01310 (8)0.01471 (8)0.00884 (7)0.00169 (6)0.00006 (5)0.00002 (6)
C30.01163 (7)0.01083 (7)0.00940 (7)0.00056 (5)0.00001 (5)0.00063 (5)
C50.01423 (8)0.01604 (9)0.00979 (7)0.00065 (7)0.00201 (6)0.00122 (6)
C60.01958 (10)0.01522 (9)0.00990 (8)0.00074 (7)0.00077 (7)0.00030 (6)
O10.03094 (12)0.01369 (8)0.01810 (9)0.00003 (7)0.00144 (8)0.00577 (6)
O20.02953 (12)0.01657 (9)0.01665 (9)0.00693 (8)0.00471 (8)0.00156 (7)
C40.02396 (12)0.01131 (9)0.01971 (11)0.00028 (8)0.00142 (9)0.00133 (7)
Geometric parameters (Å, º) top
N2—C11.3589 (3)C2—C31.3728 (3)
N2—C31.3857 (3)C2—H20.974 (8)
N2—C51.4694 (3)C5—C61.5246 (4)
O3—C61.4180 (4)C5—H5B0.974 (8)
O3—H30.913 (10)C5—H5A0.970 (8)
N3—O21.2316 (3)C6—H6B0.992 (8)
N3—O11.2327 (3)C6—H6A1.020 (8)
N3—C31.4180 (3)C4—H4C0.941 (9)
N1—C11.3389 (3)C4—H4B0.985 (10)
N1—C21.3635 (4)C4—H4A0.952 (11)
C1—C41.4846 (4)
C1—N2—C3105.40 (2)N2—C5—H5B107.9 (5)
C1—N2—C5125.11 (2)C6—C5—H5B109.7 (4)
C3—N2—C5129.49 (2)N2—C5—H5A107.1 (5)
C6—O3—H3108.3 (7)C6—C5—H5A111.6 (5)
O2—N3—O1123.90 (3)H5B—C5—H5A108.0 (7)
O2—N3—C3119.51 (2)O3—C6—C5111.82 (2)
O1—N3—C3116.59 (2)O3—C6—H6B108.0 (4)
C1—N1—C2106.61 (2)C5—C6—H6B110.5 (4)
N1—C1—N2111.60 (2)O3—C6—H6A110.5 (5)
N1—C1—C4124.24 (2)C5—C6—H6A108.5 (4)
N2—C1—C4124.14 (2)H6B—C6—H6A107.4 (7)
N1—C2—C3108.56 (2)C1—C4—H4C114.0 (6)
N1—C2—H2123.3 (5)C1—C4—H4B107.0 (6)
C3—C2—H2128.1 (5)H4C—C4—H4B108.7 (8)
C2—C3—N2107.83 (2)C1—C4—H4A109.7 (6)
C2—C3—N3126.47 (2)H4C—C4—H4A106.4 (8)
N2—C3—N3125.69 (2)H4B—C4—H4A111.1 (8)
N2—C5—C6112.39 (2)
C2—N1—C1—N20.24 (3)C5—N2—C3—C2179.19 (2)
C2—N1—C1—C4178.28 (3)C1—N2—C3—N3179.08 (2)
C3—N2—C1—N10.18 (3)C5—N2—C3—N31.78 (4)
C5—N2—C1—N1179.37 (2)O2—N3—C3—C2175.59 (3)
C3—N2—C1—C4178.34 (3)O1—N3—C3—C24.59 (4)
C5—N2—C1—C40.85 (4)O2—N3—C3—N23.26 (4)
C1—N1—C2—C30.20 (3)O1—N3—C3—N2176.56 (3)
N1—C2—C3—N20.09 (3)C1—N2—C5—C699.64 (3)
N1—C2—C3—N3178.93 (2)C3—N2—C5—C681.37 (3)
C1—N2—C3—C20.05 (3)N2—C5—C6—O360.85 (3)
 

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