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ISSN: 2056-9890

2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethyl 4-fluoro­benzoate

aHEJ 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

(Received 27 January 2012; accepted 13 February 2012; online 3 March 2012)

In the title compound, C13H12FN3O4, the dihedral angle between the benzene and imidazole rings is 32.77 (12)°. In the crystal, mol­ecules are linked into a three-dimensional network by C—H⋯O hydrogen bonds.

Related literature

For biological activities of metronidazole derivatives, see: Atia (2009[Atia, A. J. K. (2009). Molecules, 14, 2431-2446.]); Beena et al. (2009[Beena, Kumar, N., Rohilla, R. K., Roy, N. & Rawat, D. S. (2009). Bioorg. Med. Chem. Lett. 19, 1396-1398.]); Bowden & Izadi (1998[Bowden, K. & Izadi, J. (1998). Il Farmaco, 53, 58-61.]); Dubey et al. (2009[Dubey, S., Jain, V. & Preethi, G. B. (2009). Indian J. Chem. Sect. B, 48, 1571-1576.]); Mao et al. (2009[Mao, W.-J., Lv, P.-C., Shi, L., Li, H.-Q. & Zhu, H.-L. (2009). Bioorg. Med. Chem. 17, 7531-7536.]); Qian et al. (2010[Qian, Y., Zhang, H.-J., Zhang, H., Xu, C., Zhao, J. & Zhu, H.-L. (2010). Bioorg. Med. Chem. 18, 4991-4996.]).

[Scheme 1]

Experimental

Crystal data
  • C13H12FN3O4

  • Mr = 293.26

  • Monoclinic, C c

  • a = 8.9669 (12) Å

  • b = 18.784 (2) Å

  • c = 7.8288 (10) Å

  • β = 99.684 (3)°

  • V = 1299.9 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 273 K

  • 0.50 × 0.29 × 0.16 mm

Data collection
  • Bruker SMART APEX CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.941, Tmax = 0.981

  • 3782 measured reflections

  • 1186 independent reflections

  • 1150 reflections with I > 2σ(I)

  • Rint = 0.022

Refinement
  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 0.088

  • S = 1.06

  • 1186 reflections

  • 192 parameters

  • 2 restraints

  • H-atom parameters constrained

  • Δρmax = 0.15 e Å−3

  • Δρmin = −0.11 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C1—H1A⋯O1i 0.93 2.45 3.378 (3) 172
C2—H2B⋯O3ii 0.93 2.46 3.356 (4) 162
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) [x+{\script{1\over 2}}, y-{\script{1\over 2}}, z].

Data collection: SMART (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL, PARST (Nardelli, 1995[Nardelli, M. (1995). J. Appl. Cryst. 28, 659.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

The title compound is a derivative of well known broad spectrum antibiotic metronidazole, commonly known as Flagyl. A number of metronidazole derivatives have been synthesized to evaluate their biological potentials, such as antibacterial (Atia, 2009; Dubey et al., 2009; Beena et al., 2009; Bowden & Izadi, 1998), anticancer (Qian et al., 2010), and H. pylori urease inhibitors (Mao et al., 2009). These properties of metronidazole derivatives attracted the attention of synthetic and medicinal chemists to further explore their potential against different diseases. In present study, metronidazole ester derivative was prepared in a cost effective manner to evaluate its antiglycation potential.

In the title compound, the benzene (C1–C6) and imidazole (N1/C10/C11/N2/C12) rings are almost planar (Fig. 1) with a dihedral angle of 32.77 (12)° between the mean planes. The bond lengths and angles are within the normal ranges. C1—H1A···O1i and C2—H2B···O3ii hydrogen bonds (symmetry codes as in Table 1) play important roles in stabilizing the crystal structure by forming a three-dimensional network (Fig. 2).

Related literature top

For biological activities of metronidazole derivatives, see: Atia (2009); Beena et al. (2009); Bowden & Izadi (1998); Dubey et al. (2009); Mao et al. (2009); Qian et al. (2010).

Experimental top

The synthesis of title compounds 1 was achieved by reacting metronidazole (171 mg, 1.0 mmole) with 4-fluorobenzoic acid (1.2 equiv.) in the presence of dicyclohexylcarbodiimide (245 mg, 1.2 mmole) and 4-dimethylaminopyridine (0.35 mmole) in dichloromethane (10 ml) at room temperature for 40–45 h. The progress of reaction was monitored by TLC. The reaction was quenched with 20 ml HCl (0.5 M) and then basified with sat.NaHCO3. It was extracted with dichloromethane and evaporated in vacuo to obtain crude product. The mixture of crude product was purified by using silica gel chromatography (EtOAc:hexane, 3.0:7.0 to 7.0:3.0) which afforded compound 1 in 85% yield. Recrystallization from the slow evaporation of dichloromethane afforded pure crystals found suitable for single-crystal X-ray diffraction studies. All chemicals were purchased from Sigma–Aldrich.

Refinement top

H atoms on methyl, methylene and methine groups were positioned geometrically with C—H = 0.96, 0.97 and 0.93 Å, respectively, and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(CH and CH2) and 1.5Ueq(CH3). A rotating group model was applied to the methyl groups. In the absence of significant anomalous scattering effects, 952 Friedel pairs were merged before the final refinement.

Structure description top

The title compound is a derivative of well known broad spectrum antibiotic metronidazole, commonly known as Flagyl. A number of metronidazole derivatives have been synthesized to evaluate their biological potentials, such as antibacterial (Atia, 2009; Dubey et al., 2009; Beena et al., 2009; Bowden & Izadi, 1998), anticancer (Qian et al., 2010), and H. pylori urease inhibitors (Mao et al., 2009). These properties of metronidazole derivatives attracted the attention of synthetic and medicinal chemists to further explore their potential against different diseases. In present study, metronidazole ester derivative was prepared in a cost effective manner to evaluate its antiglycation potential.

In the title compound, the benzene (C1–C6) and imidazole (N1/C10/C11/N2/C12) rings are almost planar (Fig. 1) with a dihedral angle of 32.77 (12)° between the mean planes. The bond lengths and angles are within the normal ranges. C1—H1A···O1i and C2—H2B···O3ii hydrogen bonds (symmetry codes as in Table 1) play important roles in stabilizing the crystal structure by forming a three-dimensional network (Fig. 2).

For biological activities of metronidazole derivatives, see: Atia (2009); Beena et al. (2009); Bowden & Izadi (1998); Dubey et al. (2009); Mao et al. (2009); Qian et al. (2010).

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at 30% probability level.
[Figure 2] Fig. 2. The crystal packing view of the title compound.
2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethyl 4-fluorobenzoate top
Crystal data top
C13H12FN3O4F(000) = 608
Mr = 293.26Dx = 1.498 Mg m3
Monoclinic, CcMo Kα radiation, λ = 0.71073 Å
a = 8.9669 (12) ÅCell parameters from 2305 reflections
b = 18.784 (2) Åθ = 2.6–28.0°
c = 7.8288 (10) ŵ = 0.12 mm1
β = 99.684 (3)°T = 273 K
V = 1299.9 (3) Å3Block, colourless
Z = 40.50 × 0.29 × 0.16 mm
Data collection top
Bruker SMART APEX CCD
diffractometer
1186 independent reflections
Radiation source: fine-focus sealed tube1150 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
ω scansθmax = 25.5°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 1010
Tmin = 0.941, Tmax = 0.981k = 2222
3782 measured reflectionsl = 98
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.088 w = 1/[σ2(Fo2) + (0.0593P)2 + 0.2616P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
1186 reflectionsΔρmax = 0.15 e Å3
192 parametersΔρmin = 0.11 e Å3
2 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0055 (15)
Crystal data top
C13H12FN3O4V = 1299.9 (3) Å3
Mr = 293.26Z = 4
Monoclinic, CcMo Kα radiation
a = 8.9669 (12) ŵ = 0.12 mm1
b = 18.784 (2) ÅT = 273 K
c = 7.8288 (10) Å0.50 × 0.29 × 0.16 mm
β = 99.684 (3)°
Data collection top
Bruker SMART APEX CCD
diffractometer
1186 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
1150 reflections with I > 2σ(I)
Tmin = 0.941, Tmax = 0.981Rint = 0.022
3782 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0322 restraints
wR(F2) = 0.088H-atom parameters constrained
S = 1.06Δρmax = 0.15 e Å3
1186 reflectionsΔρmin = 0.11 e Å3
192 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 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 (Å2) top
xyzUiso*/Ueq
O10.1173 (2)0.24543 (13)0.1523 (3)0.0625 (6)
O20.0800 (2)0.27301 (10)0.0543 (2)0.0534 (5)
O30.0473 (3)0.48885 (12)0.3047 (4)0.0795 (8)
O40.2371 (3)0.50643 (12)0.5096 (4)0.0726 (7)
N10.0456 (2)0.34305 (11)0.3929 (3)0.0405 (5)
N20.1729 (3)0.29745 (13)0.6362 (3)0.0532 (6)
N30.1392 (3)0.46795 (12)0.4283 (3)0.0516 (6)
C10.1985 (3)0.13945 (15)0.0541 (3)0.0454 (6)
H1A0.24960.17410.12620.054*
C20.2552 (3)0.07076 (17)0.0578 (4)0.0539 (7)
H2B0.34420.05870.13120.065*
C30.1764 (3)0.02112 (15)0.0496 (4)0.0533 (7)
C40.0462 (3)0.03555 (17)0.1617 (4)0.0554 (7)
H4A0.00350.00040.23350.066*
C50.0093 (3)0.10470 (15)0.1646 (4)0.0481 (6)
H5A0.09780.11630.23970.058*
C60.0659 (3)0.15675 (14)0.0565 (3)0.0408 (6)
C70.0021 (3)0.22884 (14)0.0609 (3)0.0429 (6)
C80.0198 (4)0.34362 (15)0.0713 (4)0.0569 (7)
H8A0.05140.35540.03230.068*
H8B0.10130.37810.08400.068*
C90.0587 (3)0.34704 (14)0.2269 (4)0.0474 (6)
H9A0.11530.39120.22300.057*
H9B0.13040.30810.22080.057*
C100.1340 (3)0.39608 (14)0.4807 (4)0.0454 (6)
C110.2095 (3)0.36676 (16)0.6288 (4)0.0535 (7)
H11A0.27640.39090.71260.064*
C120.0761 (3)0.28463 (14)0.4928 (4)0.0435 (6)
C130.0081 (4)0.21350 (15)0.4469 (4)0.0579 (8)
H13A0.04720.17980.53530.087*
H13B0.03320.19840.33810.087*
H13C0.09980.21650.43760.087*
F10.2301 (3)0.04671 (11)0.0425 (3)0.0827 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0549 (11)0.0618 (12)0.0642 (14)0.0139 (10)0.0092 (10)0.0027 (11)
O20.0660 (12)0.0480 (11)0.0422 (11)0.0104 (9)0.0022 (9)0.0033 (8)
O30.0938 (17)0.0483 (12)0.0877 (18)0.0064 (12)0.0103 (15)0.0188 (12)
O40.0740 (14)0.0472 (11)0.0926 (18)0.0096 (11)0.0026 (13)0.0116 (12)
N10.0454 (10)0.0358 (10)0.0395 (12)0.0050 (8)0.0048 (9)0.0012 (9)
N20.0660 (14)0.0472 (12)0.0429 (14)0.0034 (11)0.0012 (11)0.0026 (10)
N30.0562 (12)0.0392 (11)0.0598 (15)0.0043 (10)0.0113 (11)0.0010 (11)
C10.0473 (13)0.0508 (14)0.0371 (14)0.0048 (11)0.0039 (11)0.0013 (11)
C20.0525 (15)0.0622 (18)0.0451 (15)0.0134 (13)0.0028 (12)0.0075 (13)
C30.0732 (19)0.0435 (15)0.0463 (17)0.0125 (13)0.0193 (14)0.0061 (12)
C40.0673 (17)0.0485 (14)0.0510 (17)0.0084 (13)0.0119 (14)0.0089 (13)
C50.0475 (13)0.0529 (15)0.0424 (15)0.0014 (11)0.0033 (11)0.0002 (11)
C60.0417 (11)0.0455 (13)0.0359 (14)0.0014 (10)0.0088 (10)0.0009 (10)
C70.0454 (13)0.0484 (15)0.0347 (14)0.0049 (10)0.0064 (10)0.0034 (11)
C80.085 (2)0.0412 (15)0.0427 (16)0.0099 (13)0.0049 (14)0.0064 (11)
C90.0532 (14)0.0419 (13)0.0427 (15)0.0073 (11)0.0049 (11)0.0005 (11)
C100.0480 (12)0.0395 (13)0.0474 (16)0.0047 (10)0.0043 (11)0.0050 (10)
C110.0553 (14)0.0476 (14)0.0531 (17)0.0011 (12)0.0038 (12)0.0071 (13)
C120.0517 (13)0.0381 (12)0.0406 (15)0.0044 (11)0.0079 (11)0.0033 (10)
C130.082 (2)0.0397 (14)0.0501 (18)0.0051 (14)0.0053 (15)0.0026 (13)
F10.1168 (17)0.0497 (11)0.0819 (15)0.0242 (11)0.0175 (13)0.0035 (10)
Geometric parameters (Å, º) top
O1—C71.195 (3)C3—C41.364 (4)
O2—C71.349 (3)C4—C51.390 (4)
O2—C81.447 (3)C4—H4A0.9300
O3—N31.225 (3)C5—C61.391 (4)
O4—N31.229 (4)C5—H5A0.9300
N1—C121.349 (3)C6—C71.483 (3)
N1—C101.382 (3)C8—C91.507 (4)
N1—C91.470 (4)C8—H8A0.9700
N2—C121.321 (4)C8—H8B0.9700
N2—C111.346 (4)C9—H9A0.9700
N3—C101.414 (4)C9—H9B0.9700
C1—C21.385 (4)C10—C111.357 (4)
C1—C61.387 (3)C11—H11A0.9300
C1—H1A0.9300C12—C131.487 (4)
C2—C31.370 (4)C13—H13A0.9600
C2—H2B0.9300C13—H13B0.9600
C3—F11.360 (3)C13—H13C0.9600
C7—O2—C8117.1 (2)O2—C7—C6111.7 (2)
C12—N1—C10104.7 (2)O2—C8—C9110.2 (2)
C12—N1—C9126.2 (2)O2—C8—H8A109.6
C10—N1—C9129.0 (2)C9—C8—H8A109.6
C12—N2—C11105.6 (2)O2—C8—H8B109.6
O3—N3—O4123.2 (3)C9—C8—H8B109.6
O3—N3—C10119.0 (2)H8A—C8—H8B108.1
O4—N3—C10117.8 (3)N1—C9—C8113.4 (2)
C2—C1—C6120.3 (3)N1—C9—H9A108.9
C2—C1—H1A119.9C8—C9—H9A108.9
C6—C1—H1A119.9N1—C9—H9B108.9
C3—C2—C1118.2 (3)C8—C9—H9B108.9
C3—C2—H2B120.9H9A—C9—H9B107.7
C1—C2—H2B120.9C11—C10—N1107.1 (2)
F1—C3—C4118.1 (3)C11—C10—N3126.8 (3)
F1—C3—C2118.1 (3)N1—C10—N3126.0 (2)
C4—C3—C2123.8 (3)N2—C11—C10109.9 (3)
C3—C4—C5117.5 (3)N2—C11—H11A125.1
C3—C4—H4A121.3C10—C11—H11A125.1
C5—C4—H4A121.3N2—C12—N1112.6 (2)
C4—C5—C6120.7 (3)N2—C12—C13123.6 (2)
C4—C5—H5A119.6N1—C12—C13123.8 (3)
C6—C5—H5A119.6C12—C13—H13A109.5
C1—C6—C5119.5 (2)C12—C13—H13B109.5
C1—C6—C7122.3 (2)H13A—C13—H13B109.5
C5—C6—C7118.2 (2)C12—C13—H13C109.5
O1—C7—O2124.0 (2)H13A—C13—H13C109.5
O1—C7—C6124.2 (3)H13B—C13—H13C109.5
C6—C1—C2—C30.3 (4)O2—C8—C9—N170.0 (3)
C1—C2—C3—F1178.3 (2)C12—N1—C10—C111.2 (3)
C1—C2—C3—C40.8 (4)C9—N1—C10—C11179.3 (3)
F1—C3—C4—C5178.4 (3)C12—N1—C10—N3178.8 (3)
C2—C3—C4—C50.6 (4)C9—N1—C10—N31.7 (4)
C3—C4—C5—C60.1 (4)O3—N3—C10—C11168.7 (3)
C2—C1—C6—C50.4 (4)O4—N3—C10—C1111.5 (4)
C2—C1—C6—C7177.9 (2)O3—N3—C10—N18.4 (4)
C4—C5—C6—C10.6 (4)O4—N3—C10—N1171.3 (3)
C4—C5—C6—C7177.8 (2)C12—N2—C11—C100.3 (3)
C8—O2—C7—O12.6 (4)N1—C10—C11—N20.6 (3)
C8—O2—C7—C6175.7 (2)N3—C10—C11—N2178.2 (3)
C1—C6—C7—O1178.7 (3)C11—N2—C12—N11.1 (3)
C5—C6—C7—O10.4 (4)C11—N2—C12—C13179.0 (3)
C1—C6—C7—O20.4 (3)C10—N1—C12—N21.4 (3)
C5—C6—C7—O2177.9 (2)C9—N1—C12—N2179.0 (2)
C7—O2—C8—C999.1 (3)C10—N1—C12—C13178.6 (2)
C12—N1—C9—C899.5 (3)C9—N1—C12—C130.9 (4)
C10—N1—C9—C879.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···O1i0.932.453.378 (3)172
C2—H2B···O3ii0.932.463.356 (4)162
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x+1/2, y1/2, z.

Experimental details

Crystal data
Chemical formulaC13H12FN3O4
Mr293.26
Crystal system, space groupMonoclinic, Cc
Temperature (K)273
a, b, c (Å)8.9669 (12), 18.784 (2), 7.8288 (10)
β (°) 99.684 (3)
V3)1299.9 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.50 × 0.29 × 0.16
Data collection
DiffractometerBruker SMART APEX CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.941, 0.981
No. of measured, independent and
observed [I > 2σ(I)] reflections
3782, 1186, 1150
Rint0.022
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.088, 1.06
No. of reflections1186
No. of parameters192
No. of restraints2
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.15, 0.11

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···O1i0.932.453.378 (3)172
C2—H2B···O3ii0.932.463.356 (4)162
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x+1/2, y1/2, z.
 

References

First citationAtia, A. J. K. (2009). Molecules, 14, 2431–2446.  Web of Science CrossRef PubMed CAS Google Scholar
First citationBeena, Kumar, N., Rohilla, R. K., Roy, N. & Rawat, D. S. (2009). Bioorg. Med. Chem. Lett. 19, 1396–1398.  Web of Science CrossRef PubMed CAS Google Scholar
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