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The asymmetric unit of the racemic title compound, C7H10ClN3O3·0.5H2O, has two independent mol­ecules of ornidazole. The crystal structure is formed via inter­molecular hydrogen bonds involving the water mol­ecules.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807045680/rk2037sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807045680/rk2037Isup2.hkl
Contains datablock I

CCDC reference: 667270

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.045
  • wR factor = 0.146
  • Data-to-parameter ratio = 18.1

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ? PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ? PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............ 0.50 Ratio PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C11 PLAT417_ALERT_2_C Short Inter D-H..H-D H21 .. H701 .. 2.11 Ang.
Alert level G PLAT793_ALERT_1_G Check the Absolute Configuration of C12 = ... R PLAT793_ALERT_1_G Check the Absolute Configuration of C22 = ... S
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 2 ALERT level G = General alerts; check 5 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 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

5–Nitroimidazoles are a well–established group of antiprotozoan and antibacterial agents. 1–(2–Hydroxy–3–chloropropyl)–2–methyl–5–nitroimidazole (ornidazole) is a member of the nitroimidazole group so it is used for the treatment of susceptible protozoal infections and prophylaxis of anaerobic bacterial infections. Due to its antimicrobial activity it inhibits the growth of both anaerobic bacteria and certain anaerobic protozoa such as Trichomonas vaginalis, Entamoeba histolytica and Giardia lamblia (López Nigro et al., 2003). The asymmetric unit have two independent molecules of ornidazole with the different chirality - C12 atom is R and C22 atom is S absolute configuration. The crystal structure of the title compound is formed by the system of intermolecular hydrogen bonds, which involve the water molecules.

Related literature top

For related literature, see: López Nigro et al. (2003).

Experimental top

1–(2-Hydroxy–3–chloropropyl)–2-methyl–5–nitroimidazole was recrystallized from C5H5OH/H2O (1:1) to give the ornidazole hemihydrate. Diffraction quality crystal was obtained by slow evaporation of at room temperature.

Refinement top

The H atoms on the oxygen were located in a difference Fourier map and the other H atoms were placed in calculated posistion with C—H = 0.96–0.98 Å. All H atoms included in the final cycles of refinement as riding mode, with Uiso(H) = 1.2Ueq of the carrier atoms.

Structure description top

5–Nitroimidazoles are a well–established group of antiprotozoan and antibacterial agents. 1–(2–Hydroxy–3–chloropropyl)–2–methyl–5–nitroimidazole (ornidazole) is a member of the nitroimidazole group so it is used for the treatment of susceptible protozoal infections and prophylaxis of anaerobic bacterial infections. Due to its antimicrobial activity it inhibits the growth of both anaerobic bacteria and certain anaerobic protozoa such as Trichomonas vaginalis, Entamoeba histolytica and Giardia lamblia (López Nigro et al., 2003). The asymmetric unit have two independent molecules of ornidazole with the different chirality - C12 atom is R and C22 atom is S absolute configuration. The crystal structure of the title compound is formed by the system of intermolecular hydrogen bonds, which involve the water molecules.

For related literature, see: López Nigro et al. (2003).

Computing details top

Data collection: PROCESS-AUTO (Rigaku/MSC & Rigaku, 2004); cell refinement: PROCESS-AUTO (Rigaku/MSC & Rigaku, 2004); data reduction: CrystalStructure (Rigaku/MSC & Rigaku, 2004); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: CrystalStructure (Rigaku/MSC & Rigaku, 2004).

Figures top
[Figure 1] Fig. 1. The ORTEP view of the title complex with the numbering scheme. The displacement ellipsoids are drawn with the 50% probability level.
[Figure 2] Fig. 2. View of the two crystallographically independent molecules linked by hydrogen bonds.
[Figure 3] Fig. 3. Unit cell packing of the title compound.
Ornidazole hemihydrate top
Crystal data top
C7H10ClN3O3·0.5H2OF(000) = 1904.00
Mr = 228.64Dx = 1.462 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71075 Å
Hall symbol: -C 2ycCell parameters from 14509 reflections
a = 23.202 (8) Åθ = 3.1–27.5°
b = 8.289 (2) ŵ = 0.36 mm1
c = 22.270 (7) ÅT = 298 K
β = 103.996 (14)°Block, colourless
V = 4156 (2) Å30.31 × 0.28 × 0.25 mm
Z = 16
Data collection top
Rigaku R-AXIS RAPID
diffractometer
3287 reflections with F2 > 2σ(F2)
Detector resolution: 10.00 pixels mm-1Rint = 0.026
ω scansθmax = 27.5°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 3030
Tmin = 0.890, Tmax = 0.914k = 109
18814 measured reflectionsl = 2828
4755 independent reflections
Refinement top
Refinement on F2H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.045 w = 1/[0.002Fo2 + σ(Fo2)]/(4Fo2)
wR(F2) = 0.146(Δ/σ)max < 0.001
S = 1.01Δρmax = 0.59 e Å3
4755 reflectionsΔρmin = 0.62 e Å3
263 parametersExtinction correction: Larson, A. C. (1970). Crystallographic Computing, edited by F. R. Ahmed, pp. 291–294. Copenhagen: Munksgaard.
0 restraintsExtinction coefficient: 94 (36)
Crystal data top
C7H10ClN3O3·0.5H2OV = 4156 (2) Å3
Mr = 228.64Z = 16
Monoclinic, C2/cMo Kα radiation
a = 23.202 (8) ŵ = 0.36 mm1
b = 8.289 (2) ÅT = 298 K
c = 22.270 (7) Å0.31 × 0.28 × 0.25 mm
β = 103.996 (14)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer
4755 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
3287 reflections with F2 > 2σ(F2)
Tmin = 0.890, Tmax = 0.914Rint = 0.026
18814 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0450 restraints
wR(F2) = 0.146H-atom parameters constrained
S = 1.01Δρmax = 0.59 e Å3
4755 reflectionsΔρmin = 0.62 e Å3
263 parameters
Special details top

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 using all reflections. The weighted R–factor (wR) and goodness of fit (S) are based on F2. R–factor (gt) are based on F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R–factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.51877 (3)0.54256 (8)0.64516 (4)0.0940 (2)
Cl20.36375 (4)1.26213 (8)0.21447 (4)0.0870 (2)
O70.12252 (6)0.44528 (16)0.43419 (6)0.0487 (3)
O110.38555 (6)0.74189 (13)0.52290 (6)0.0433 (3)
O120.43759 (6)0.28657 (19)0.48376 (8)0.0615 (4)
O130.37775 (9)0.1710 (2)0.40646 (9)0.0889 (6)
O210.43764 (6)0.9665 (2)0.18369 (6)0.0604 (4)
O220.31344 (9)0.6537 (2)0.19209 (8)0.0759 (5)
O230.25133 (9)0.5497 (2)0.23892 (10)0.0952 (7)
N110.33913 (6)0.42982 (16)0.51646 (6)0.0347 (3)
N120.24678 (6)0.42340 (19)0.45819 (8)0.0454 (4)
N130.38789 (8)0.2606 (2)0.45115 (8)0.0508 (4)
N210.38473 (6)0.75918 (17)0.30684 (6)0.0384 (3)
N220.36136 (8)0.7319 (2)0.39693 (8)0.0484 (4)
N230.29640 (8)0.6258 (2)0.23892 (9)0.0590 (5)
C110.46743 (8)0.6864 (2)0.60469 (10)0.0475 (5)
C120.42434 (8)0.6139 (2)0.54889 (8)0.0374 (4)
C130.38913 (6)0.4751 (2)0.56720 (8)0.0368 (4)
C140.33813 (8)0.3374 (2)0.46472 (8)0.0388 (4)
C150.28143 (9)0.3346 (2)0.43015 (9)0.0438 (4)
C160.28216 (8)0.4799 (2)0.51017 (8)0.0378 (4)
C170.26214 (9)0.5812 (2)0.55585 (10)0.0501 (5)
C210.39930 (12)1.0974 (2)0.26126 (11)0.0650 (7)
C220.39831 (9)0.9501 (2)0.22289 (9)0.0496 (5)
C230.41990 (8)0.8002 (2)0.26236 (9)0.0459 (5)
C240.33042 (8)0.6820 (2)0.29689 (9)0.0438 (4)
C250.31703 (9)0.6678 (2)0.35252 (10)0.0506 (5)
C260.40150 (8)0.7856 (2)0.36831 (8)0.0388 (4)
C270.45826 (9)0.8620 (2)0.40072 (9)0.0519 (5)
H110.37810.73120.48040.052*
H210.41230.96020.14240.074*
H1110.44500.72970.63260.057*
H1120.48920.77280.59080.057*
H1220.44600.57620.51890.045*
H1310.37420.50780.60240.044*
H1320.41510.38270.57850.044*
H1510.26840.27990.39290.053*
H1710.22060.60480.54090.060*
H1720.26840.52440.59450.060*
H1730.28430.68000.56190.060*
H2110.44021.12620.28020.078*
H2120.37861.07570.29330.078*
H2210.35790.93170.19780.060*
H2310.46060.81910.28520.055*
H2320.41870.70910.23470.055*
H2510.28260.62130.35920.061*
H2710.45990.87000.44410.062*
H2720.49090.79750.39500.062*
H2730.46080.96790.38410.062*
H7010.11470.54760.44900.058*
H7020.16370.43860.43800.058*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0725 (4)0.0614 (3)0.1148 (6)0.0113 (3)0.0424 (4)0.0073 (3)
Cl20.1094 (5)0.0701 (4)0.0873 (5)0.0288 (3)0.0349 (4)0.0337 (3)
O70.0426 (7)0.0498 (7)0.0506 (7)0.0022 (5)0.0053 (5)0.0054 (5)
O110.0546 (7)0.0402 (6)0.0349 (6)0.0055 (5)0.0103 (5)0.0015 (5)
O120.0428 (7)0.0742 (9)0.0691 (10)0.0090 (7)0.0168 (7)0.0120 (8)
O130.0853 (12)0.1008 (13)0.0805 (12)0.0155 (10)0.0200 (10)0.0501 (11)
O210.0479 (7)0.0967 (11)0.0396 (7)0.0034 (7)0.0165 (6)0.0138 (7)
O220.0980 (13)0.0804 (11)0.0395 (8)0.0058 (9)0.0024 (8)0.0063 (7)
O230.0642 (11)0.1136 (15)0.0996 (15)0.0259 (11)0.0042 (10)0.0344 (12)
N110.0328 (7)0.0361 (6)0.0346 (7)0.0018 (5)0.0069 (5)0.0001 (5)
N120.0355 (7)0.0486 (8)0.0483 (9)0.0001 (6)0.0025 (6)0.0026 (7)
N130.0540 (10)0.0498 (9)0.0506 (9)0.0072 (7)0.0167 (8)0.0085 (7)
N210.0413 (7)0.0424 (7)0.0313 (7)0.0063 (6)0.0083 (5)0.0046 (5)
N220.0544 (9)0.0546 (9)0.0376 (8)0.0031 (7)0.0134 (7)0.0078 (7)
N230.0562 (11)0.0573 (10)0.0544 (11)0.0027 (9)0.0046 (8)0.0087 (8)
C110.0412 (9)0.0422 (9)0.0540 (11)0.0029 (7)0.0015 (8)0.0085 (8)
C120.0368 (8)0.0372 (8)0.0383 (9)0.0032 (7)0.0093 (7)0.0038 (7)
C130.0361 (8)0.0416 (8)0.0310 (8)0.0013 (7)0.0047 (6)0.0005 (6)
C140.0429 (9)0.0363 (8)0.0372 (9)0.0008 (7)0.0097 (7)0.0023 (6)
C150.0480 (10)0.0429 (9)0.0365 (9)0.0042 (8)0.0024 (7)0.0026 (7)
C160.0342 (8)0.0371 (8)0.0416 (9)0.0024 (7)0.0084 (7)0.0046 (7)
C170.0457 (10)0.0535 (10)0.0532 (11)0.0095 (8)0.0160 (9)0.0003 (8)
C210.0857 (17)0.0616 (12)0.0488 (12)0.0138 (12)0.0181 (11)0.0135 (10)
C220.0488 (10)0.0629 (11)0.0405 (10)0.0081 (9)0.0177 (8)0.0127 (8)
C230.0440 (10)0.0590 (11)0.0365 (9)0.0114 (8)0.0135 (7)0.0057 (8)
C240.0420 (9)0.0460 (9)0.0411 (10)0.0029 (7)0.0055 (7)0.0017 (7)
C250.0481 (11)0.0520 (10)0.0519 (11)0.0038 (9)0.0124 (9)0.0058 (8)
C260.0431 (9)0.0397 (8)0.0328 (8)0.0065 (7)0.0077 (7)0.0048 (6)
C270.0492 (11)0.0606 (11)0.0417 (10)0.0022 (9)0.0027 (8)0.0016 (8)
Geometric parameters (Å, º) top
Cl1—C111.7702 (19)C22—C231.534 (2)
Cl2—C211.793 (2)C24—C251.353 (3)
O11—C121.421 (2)C26—C271.482 (2)
O12—N131.224 (2)O7—H7010.944
O13—N131.218 (2)O7—H7020.940
O21—C221.414 (2)O11—H110.925
O22—N231.223 (2)O21—H210.965
O23—N231.221 (2)C11—H1110.970
N11—C131.4593 (19)C11—H1120.970
N11—C141.379 (2)C12—H1220.980
N11—C161.360 (2)C13—H1310.970
N12—C151.350 (2)C13—H1320.970
N12—C161.332 (2)C15—H1510.930
N13—C141.414 (2)C17—H1710.960
N21—C231.468 (2)C17—H1720.960
N21—C241.383 (2)C17—H1730.960
N21—C261.347 (2)C21—H2110.970
N22—C251.351 (2)C21—H2120.970
N22—C261.326 (2)C22—H2210.980
N23—C241.419 (2)C23—H2310.970
C11—C121.518 (2)C23—H2320.970
C12—C131.522 (2)C25—H2510.930
C14—C151.354 (2)C27—H2710.960
C16—C171.478 (2)C27—H2720.960
C21—C221.488 (3)C27—H2730.960
C13—N11—C14129.75 (14)Cl1—C11—H112108.8
C13—N11—C16124.89 (14)C12—C11—H111108.8
C14—N11—C16105.31 (13)C12—C11—H112108.8
C15—N12—C16106.46 (15)H111—C11—H112109.5
O12—N13—O13124.1 (2)O11—C12—H122109.8
O12—N13—C14119.65 (16)C11—C12—H122109.8
O13—N13—C14116.28 (17)C13—C12—H122109.8
C23—N21—C24129.28 (15)N11—C13—H131109.0
C23—N21—C26125.24 (15)N11—C13—H132109.0
C24—N21—C26105.43 (16)C12—C13—H131109.0
C25—N22—C26106.19 (17)C12—C13—H132109.0
O22—N23—O23123.43 (19)H131—C13—H132109.5
O22—N23—C24119.36 (18)N12—C15—H151125.3
O23—N23—C24117.2 (2)C14—C15—H151125.3
Cl1—C11—C12112.27 (13)C16—C17—H171109.5
O11—C12—C11105.34 (13)C16—C17—H172109.5
O11—C12—C13110.20 (14)C16—C17—H173109.5
C11—C12—C13111.70 (15)H171—C17—H172109.5
N11—C13—C12111.38 (13)H171—C17—H173109.5
N11—C14—N13125.40 (14)H172—C17—H173109.5
N11—C14—C15107.59 (16)Cl2—C21—H211109.2
N13—C14—C15127.01 (16)Cl2—C21—H212109.2
N12—C15—C14109.45 (16)C22—C21—H211109.2
N11—C16—N12111.18 (16)C22—C21—H212109.2
N11—C16—C17124.20 (14)H211—C21—H212109.5
N12—C16—C17124.61 (16)O21—C22—H221109.6
Cl2—C21—C22110.50 (15)C21—C22—H221109.6
O21—C22—C21110.69 (18)C23—C22—H221109.6
O21—C22—C23105.16 (16)N21—C23—H231108.2
C21—C22—C23112.22 (16)N21—C23—H232108.2
N21—C23—C22114.63 (16)C22—C23—H231108.2
N21—C24—N23125.63 (18)C22—C23—H232108.2
N21—C24—C25107.19 (15)H231—C23—H232109.5
N23—C24—C25127.17 (18)N22—C25—H251125.3
N22—C25—C24109.48 (18)C24—C25—H251125.3
N21—C26—N22111.71 (15)C26—C27—H271109.5
N21—C26—C27124.64 (18)C26—C27—H272109.5
N22—C26—C27123.64 (16)C26—C27—H273109.5
H701—O7—H702107.3H271—C27—H272109.5
C12—O11—H11106.7H271—C27—H273109.5
C22—O21—H21104.3H272—C27—H273109.5
Cl1—C11—H111108.8
C13—N11—C14—N132.1 (2)C24—N21—C26—N220.6 (2)
C13—N11—C14—C15177.86 (16)C24—N21—C26—C27178.17 (17)
C14—N11—C13—C1279.1 (2)C26—N21—C24—N23178.00 (17)
C13—N11—C16—N12177.80 (15)C26—N21—C24—C250.8 (2)
C13—N11—C16—C173.4 (2)C25—N22—C26—N210.2 (2)
C16—N11—C13—C1297.8 (2)C25—N22—C26—C27178.59 (17)
C14—N11—C16—N120.24 (19)C26—N22—C25—C240.3 (2)
C14—N11—C16—C17179.06 (17)O22—N23—C24—N214.4 (2)
C16—N11—C14—N13179.52 (17)O22—N23—C24—C25177.1 (2)
C16—N11—C14—C150.46 (19)O23—N23—C24—N21174.86 (19)
C15—N12—C16—N110.07 (19)O23—N23—C24—C253.6 (3)
C15—N12—C16—C17178.74 (18)Cl1—C11—C12—O11178.33 (13)
C16—N12—C15—C140.4 (2)Cl1—C11—C12—C1358.69 (19)
O12—N13—C14—N117.1 (2)O11—C12—C13—N1150.51 (19)
O12—N13—C14—C15172.92 (19)C11—C12—C13—N11167.24 (14)
O13—N13—C14—N11173.08 (18)N11—C14—C15—N120.5 (2)
O13—N13—C14—C156.9 (2)N13—C14—C15—N12179.46 (17)
C23—N21—C24—N230.5 (3)Cl2—C21—C22—O2171.3 (2)
C23—N21—C24—C25178.28 (17)Cl2—C21—C22—C23171.55 (15)
C24—N21—C23—C2278.6 (2)O21—C22—C23—N21179.62 (14)
C23—N21—C26—N22178.24 (16)C21—C22—C23—N2160.0 (2)
C23—N21—C26—C270.5 (2)N21—C24—C25—N220.7 (2)
C26—N21—C23—C22104.36 (19)N23—C24—C25—N22178.05 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H701···O11i0.941.852.7854 (17)169
O7—H702···N120.941.872.808 (2)172
O11—H11···N220.931.802.726 (2)174
O21—H21···O7ii0.971.712.6643 (18)171
Symmetry codes: (i) x+1/2, y+3/2, z+1; (ii) x+1/2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC7H10ClN3O3·0.5H2O
Mr228.64
Crystal system, space groupMonoclinic, C2/c
Temperature (K)298
a, b, c (Å)23.202 (8), 8.289 (2), 22.270 (7)
β (°) 103.996 (14)
V3)4156 (2)
Z16
Radiation typeMo Kα
µ (mm1)0.36
Crystal size (mm)0.31 × 0.28 × 0.25
Data collection
DiffractometerRigaku R-AXIS RAPID
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.890, 0.914
No. of measured, independent and
observed [F2 > 2σ(F2)] reflections
18814, 4755, 3287
Rint0.026
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.146, 1.01
No. of reflections4755
No. of parameters263
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.59, 0.62

Computer programs: PROCESS-AUTO (Rigaku/MSC & Rigaku, 2004), CrystalStructure (Rigaku/MSC & Rigaku, 2004), SIR97 (Altomare et al., 1999), CRYSTALS (Betteridge et al., 2003), ORTEP-3 for Windows (Farrugia, 1997).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H701···O11i0.9441.8542.7854 (17)168.7
O7—H702···N120.9401.8742.808 (2)171.6
O11—H11···N220.9251.8042.726 (2)174.1
O21—H21···O7ii0.9651.7072.6643 (18)171.1
Symmetry codes: (i) x+1/2, y+3/2, z+1; (ii) x+1/2, y+1/2, z+1/2.
 

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