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ISSN: 2056-9890

N-Cyclo­hexyl-2-(5-fluoro-1H-indol-3-yl)-2-oxoacetamide

aSchool of Pharmacy, Tianjin Medical University, Tianjin 300070, People's Republic of China, bMedical College of Chinese People's Armed Police Forces, Tianjin 300162, People's Republic of China, and cTianjin Key Laboratory for Biomarkers of Occupational, and Environmental Hazards, Tianjin 300162, People's Republic of China
*Correspondence e-mail: tjch2010@yahoo.cn

(Received 17 June 2011; accepted 21 June 2011; online 30 June 2011)

In title compound, C16H17FN2O2, the cyclo­hexane ring adopts a chair conformation.. The crystal packing is stabilized by weak ππ stacking inter­actions [centroid–centroid distance = 3.503 (5) Å] and inter­molecular C—H⋯O, N—H⋯O and N—H⋯F hydrogen-bond inter­actions.

Related literature

For the biological activity of the title compound and its deriv­atives, see: Souli et al. (2008[Souli, E., Machluf, M., Morgenstern, A., Sabo, E. & Yannai, S. (2008). Food Chem. Toxicol. 46, 863-870.]); Chai et al. (2006[Chai, H. F., Zhao, Y. F., Zhao, C. S. & Gong, P. (2006). Bioorg. Med. Chem. 14, 911-917.]); Radwan et al. (2007[Radwan, M. A. A., Ragab, E. A., Sabry, N. M. & El-Shenawy, S. M. (2007). Bioorg. Med. Chem. 15, 3832-3841.]); Karthikeyan et al. (2009[Karthikeyan, S. V., Perumal, S., Shetty, K. A., Yogeeswari, P. & Sriram, D. (2009). Bioorg. Med. Chem. Lett. 19, 3006-3009.]). For the preparation, see: Bacher et al. (2001[Bacher, G., Nickel, B., Emig, P., Vanhoefer, U., Seeber, S., Shandra, A., Klenner, T. & Becker, T. (2001). Cancer Res. 61, 392-399.]). For bond-length and angle data for similar structures, see: Liu et al. (2011[Liu, J., Liu, Y.-F., Zhang, S., Gao, Y. & Chen, H. (2011). Acta Cryst. E67, o288.]); Sonar et al. (2006[Sonar, V. N., Parkin, S. & Crooks, P. A. (2006). Acta Cryst. E62, o3744-o3746.]).

[Scheme 1]

Experimental

Crystal data
  • C16H17FN2O2

  • Mr = 288.32

  • Monoclinic, P 21 /c

  • a = 11.5065 (15) Å

  • b = 9.7666 (12) Å

  • c = 12.3139 (16) Å

  • β = 96.639 (5)°

  • V = 1374.5 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 113 K

  • 0.20 × 0.16 × 0.12 mm

Data collection
  • Rigaku Saturn CCD area-detector diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005[Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.980, Tmax = 0.988

  • 18432 measured reflections

  • 3717 independent reflections

  • 3007 reflections with I > 2σ(I)

  • Rint = 0.035

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.098

  • S = 1.04

  • 3717 reflections

  • 198 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.27 e Å−3

  • Δρmin = −0.28 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯F1i 0.905 (13) 2.275 (13) 3.1234 (11) 156.1 (11)
N1—H1⋯O2ii 0.939 (14) 1.863 (14) 2.7786 (11) 164.5 (13)
C8—H8⋯O1iii 0.95 2.31 3.0586 (12) 136
Symmetry codes: (i) [-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [-x, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) [x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}].

Data collection: CrystalClear (Rigaku, 2005[Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; 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.

Supporting information


Comment top

Indole and their derivatives are well known as substances with biologically activity such as anti-cancer (Souli et al., 2008), anti-virus(Chai et al., 2006), anti-tubercular (Karthikeyan et al., 2009), and anti-inflammatory (Radwan et al., 2007). In recent years, our recent study is paying attention to synthesize different kinds of indole derivatives with improved bioactivities. In this paper, we reported the crystal structure of title compound.

In title compound, C16H17FN2O2, bond lengths and angles are normal and in good agreement with those reported previously (Liu et al., 2011; Sonar, et al., 2006). The cyclohexane ring (C11—C16) adopts a chair conformation. ππ interactions are indicated by the short distance (Cg1···Cg2 distance of 3.503 (5) Å, symmetry code: -x,1 - y,-z) between the centroids of the pyrrole ring (N1/C1/C6—C8) (Cg1) and benzene ring C1—C6 (Cg2) (Table 1). There are weaker C—H···O N—H···F and N—H···O intermolecular interactions, which stabilized the structure (Table 1)

Related literature top

For the biological activity of the title compound and its derivatives, see: Souli et al. (2008); Chai et al. (2006); Radwan et al. (2007); Karthikeyan et al. (2009). For the preparation, see: Bacher et al. (2001). For bond-length and angle data for similar structures, see: Liu et al. (2011); Sonar et al. (2006).

Experimental top

The target compound was synthesized by two steps. Oxalyl chloride was added dropwise to 5-fluorine indole in dry ether. 5-fluorine indole-3-yl-glyoxyl chloride which was the crude product, cyclohexane, two drops of triethylamine were in dry dichloromethane. The reaction mixture was washed with water and dried over Na2SO4 and concentrated in vacuo (Bacher et al., 2001). The residue was resolved in a methanol solution. Slow evaporation over two week at room temperature gave light-white crystals suitable for X-ray analysis.

Refinement top

All C H atoms were found on difference maps, with C—H = 0.95–1.00 Å and H atoms bonded N were refined freely with N—H = 0.90 and 0.94 Å and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq(C) for aryl and methylene H atoms.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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).

Figures top
[Figure 1] Fig. 1. View of the title compound, with displacement ellipsoids drawn at the 40% probability level.
N-Cyclohexyl-2-(5-fluoro-1H-indol-3-yl)-2-oxoacetamide top
Crystal data top
C16H17FN2O2F(000) = 608
Mr = 288.32Dx = 1.393 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5346 reflections
a = 11.5065 (15) Åθ = 1.7–29.1°
b = 9.7666 (12) ŵ = 0.10 mm1
c = 12.3139 (16) ÅT = 113 K
β = 96.639 (5)°Prism, colorless
V = 1374.5 (3) Å30.20 × 0.16 × 0.12 mm
Z = 4
Data collection top
Rigaku Saturn CCD area-detector
diffractometer
3717 independent reflections
Radiation source: rotating anode3007 reflections with I > 2σ(I)
Multilayer monochromatorRint = 0.035
Detector resolution: 14.63 pixels mm-1θmax = 29.2°, θmin = 2.7°
ω and ϕ scansh = 1515
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
k = 1213
Tmin = 0.980, Tmax = 0.988l = 1616
18432 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.098H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0605P)2]
where P = (Fo2 + 2Fc2)/3
3717 reflections(Δ/σ)max = 0.001
198 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = 0.28 e Å3
Crystal data top
C16H17FN2O2V = 1374.5 (3) Å3
Mr = 288.32Z = 4
Monoclinic, P21/cMo Kα radiation
a = 11.5065 (15) ŵ = 0.10 mm1
b = 9.7666 (12) ÅT = 113 K
c = 12.3139 (16) Å0.20 × 0.16 × 0.12 mm
β = 96.639 (5)°
Data collection top
Rigaku Saturn CCD area-detector
diffractometer
3717 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
3007 reflections with I > 2σ(I)
Tmin = 0.980, Tmax = 0.988Rint = 0.035
18432 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0370 restraints
wR(F2) = 0.098H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.27 e Å3
3717 reflectionsΔρmin = 0.28 e Å3
198 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
F10.25500 (5)1.05586 (6)0.22558 (5)0.02199 (16)
O10.03563 (6)0.68310 (7)0.38752 (6)0.01933 (17)
O20.10442 (6)0.59789 (7)0.66261 (6)0.01922 (17)
N10.11616 (7)0.93484 (9)0.65153 (7)0.01534 (18)
N20.18874 (7)0.53328 (8)0.51269 (7)0.01509 (18)
C10.16319 (8)0.97805 (10)0.54839 (8)0.0138 (2)
C20.24187 (9)1.08328 (10)0.51989 (8)0.0164 (2)
H2A0.27371.13640.57390.020*
C30.27217 (8)1.10769 (10)0.40949 (8)0.0167 (2)
H30.32551.17880.38590.020*
C40.22354 (9)1.02687 (10)0.33359 (8)0.0156 (2)
C50.14663 (8)0.92118 (9)0.35915 (8)0.0140 (2)
H50.11620.86820.30420.017*
C60.11544 (8)0.89560 (9)0.47050 (8)0.01231 (19)
C70.03768 (8)0.79970 (10)0.53188 (7)0.01268 (19)
C80.04120 (8)0.83109 (9)0.64156 (8)0.0141 (2)
H80.00300.78580.70090.017*
C90.03360 (8)0.69899 (10)0.48630 (7)0.01308 (19)
C100.11288 (8)0.60472 (9)0.56399 (8)0.0135 (2)
C110.26943 (8)0.43341 (10)0.56915 (8)0.0150 (2)
H110.22310.37000.61120.018*
C120.36197 (9)0.50230 (11)0.64966 (9)0.0204 (2)
H12A0.32350.55620.70340.024*
H12B0.40920.56570.60990.024*
C130.44143 (10)0.39422 (12)0.70913 (9)0.0249 (3)
H13A0.50250.43990.75970.030*
H13B0.39480.33520.75300.030*
C140.49948 (9)0.30599 (11)0.62842 (9)0.0229 (2)
H14A0.55380.36320.59120.028*
H14B0.54570.23280.66880.028*
C150.40945 (9)0.24164 (10)0.54345 (9)0.0205 (2)
H15A0.36300.17350.57950.025*
H15B0.45030.19300.48840.025*
C160.32700 (8)0.34877 (10)0.48594 (8)0.0168 (2)
H16A0.37160.41000.44180.020*
H16B0.26590.30240.43580.020*
H10.1231 (12)0.9799 (14)0.7178 (12)0.043 (4)*
H20.1848 (11)0.5448 (12)0.4395 (11)0.027 (3)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0241 (3)0.0273 (3)0.0137 (3)0.0058 (3)0.0016 (2)0.0056 (2)
O10.0251 (4)0.0224 (4)0.0100 (3)0.0067 (3)0.0000 (3)0.0008 (3)
O20.0269 (4)0.0197 (4)0.0110 (3)0.0042 (3)0.0019 (3)0.0041 (3)
N10.0181 (4)0.0177 (4)0.0103 (4)0.0015 (3)0.0018 (3)0.0032 (3)
N20.0171 (4)0.0157 (4)0.0121 (4)0.0022 (3)0.0002 (3)0.0017 (3)
C10.0145 (4)0.0148 (5)0.0118 (4)0.0030 (4)0.0008 (3)0.0013 (3)
C20.0154 (5)0.0157 (5)0.0187 (5)0.0010 (4)0.0035 (4)0.0036 (4)
C30.0141 (5)0.0144 (5)0.0214 (5)0.0009 (4)0.0011 (4)0.0006 (4)
C40.0160 (5)0.0179 (5)0.0123 (5)0.0020 (4)0.0013 (3)0.0023 (4)
C50.0153 (5)0.0148 (5)0.0119 (5)0.0015 (4)0.0013 (3)0.0011 (3)
C60.0129 (4)0.0124 (4)0.0116 (4)0.0022 (4)0.0014 (3)0.0004 (3)
C70.0143 (4)0.0132 (4)0.0102 (4)0.0028 (4)0.0002 (3)0.0004 (3)
C80.0154 (4)0.0150 (5)0.0116 (5)0.0027 (4)0.0006 (3)0.0001 (3)
C90.0149 (4)0.0136 (4)0.0102 (4)0.0024 (4)0.0006 (3)0.0005 (3)
C100.0162 (5)0.0116 (4)0.0122 (4)0.0025 (4)0.0000 (3)0.0007 (3)
C110.0148 (5)0.0143 (5)0.0154 (5)0.0006 (4)0.0010 (4)0.0022 (4)
C120.0193 (5)0.0202 (5)0.0200 (5)0.0004 (4)0.0041 (4)0.0017 (4)
C130.0211 (5)0.0283 (6)0.0230 (6)0.0024 (5)0.0071 (4)0.0016 (4)
C140.0163 (5)0.0217 (5)0.0295 (6)0.0023 (4)0.0027 (4)0.0053 (4)
C150.0173 (5)0.0164 (5)0.0277 (6)0.0010 (4)0.0020 (4)0.0012 (4)
C160.0154 (5)0.0162 (5)0.0185 (5)0.0009 (4)0.0007 (4)0.0003 (4)
Geometric parameters (Å, º) top
F1—C41.3671 (11)C7—C91.4358 (14)
O1—C91.2291 (11)C8—H80.9500
O2—C101.2313 (12)C9—C101.5470 (13)
N1—C81.3454 (13)C11—C121.5249 (14)
N1—C11.3874 (12)C11—C161.5261 (14)
N1—H10.939 (14)C11—H111.0000
N2—C101.3324 (13)C12—C131.5270 (14)
N2—C111.4655 (12)C12—H12A0.9900
N2—H20.905 (13)C12—H12B0.9900
C1—C21.3877 (14)C13—C141.5265 (16)
C1—C61.4113 (13)C13—H13A0.9900
C2—C31.3846 (14)C13—H13B0.9900
C2—H2A0.9500C14—C151.5206 (14)
C3—C41.3895 (14)C14—H14A0.9900
C3—H30.9500C14—H14B0.9900
C4—C51.3723 (14)C15—C161.5300 (13)
C5—C61.3992 (13)C15—H15A0.9900
C5—H50.9500C15—H15B0.9900
C6—C71.4466 (13)C16—H16A0.9900
C7—C81.3901 (13)C16—H16B0.9900
C8—N1—C1109.38 (8)N2—C11—C12111.79 (8)
C8—N1—H1123.5 (9)N2—C11—C16110.02 (8)
C1—N1—H1126.2 (9)C12—C11—C16110.54 (8)
C10—N2—C11122.51 (8)N2—C11—H11108.1
C10—N2—H2116.5 (8)C12—C11—H11108.1
C11—N2—H2120.8 (8)C16—C11—H11108.1
N1—C1—C2129.11 (9)C11—C12—C13109.95 (8)
N1—C1—C6107.90 (9)C11—C12—H12A109.7
C2—C1—C6122.99 (9)C13—C12—H12A109.7
C3—C2—C1117.30 (9)C11—C12—H12B109.7
C3—C2—H2A121.3C13—C12—H12B109.7
C1—C2—H2A121.3H12A—C12—H12B108.2
C2—C3—C4119.17 (9)C14—C13—C12111.15 (9)
C2—C3—H3120.4C14—C13—H13A109.4
C4—C3—H3120.4C12—C13—H13A109.4
F1—C4—C5118.04 (9)C14—C13—H13B109.4
F1—C4—C3117.05 (9)C12—C13—H13B109.4
C5—C4—C3124.91 (9)H13A—C13—H13B108.0
C4—C5—C6116.40 (9)C15—C14—C13111.51 (8)
C4—C5—H5121.8C15—C14—H14A109.3
C6—C5—H5121.8C13—C14—H14A109.3
C5—C6—C1119.23 (9)C15—C14—H14B109.3
C5—C6—C7134.48 (9)C13—C14—H14B109.3
C1—C6—C7106.27 (8)H14A—C14—H14B108.0
C8—C7—C9127.81 (9)C14—C15—C16111.87 (8)
C8—C7—C6106.20 (8)C14—C15—H15A109.2
C9—C7—C6125.88 (8)C16—C15—H15A109.2
N1—C8—C7110.23 (8)C14—C15—H15B109.2
N1—C8—H8124.9C16—C15—H15B109.2
C7—C8—H8124.9H15A—C15—H15B107.9
O1—C9—C7123.40 (9)C11—C16—C15110.71 (8)
O1—C9—C10117.35 (8)C11—C16—H16A109.5
C7—C9—C10119.25 (8)C15—C16—H16A109.5
O2—C10—N2124.75 (9)C11—C16—H16B109.5
O2—C10—C9122.28 (8)C15—C16—H16B109.5
N2—C10—C9112.97 (8)H16A—C16—H16B108.1
C8—N1—C1—C2178.59 (10)C6—C7—C8—N11.51 (10)
C8—N1—C1—C60.56 (11)C8—C7—C9—O1175.91 (9)
N1—C1—C2—C3178.08 (9)C6—C7—C9—O10.28 (16)
C6—C1—C2—C30.96 (14)C8—C7—C9—C103.92 (15)
C1—C2—C3—C40.18 (14)C6—C7—C9—C10179.56 (8)
C2—C3—C4—F1179.24 (8)C11—N2—C10—O22.07 (15)
C2—C3—C4—C50.59 (15)C11—N2—C10—C9177.56 (8)
F1—C4—C5—C6179.28 (8)O1—C9—C10—O2168.77 (9)
C3—C4—C5—C60.55 (15)C7—C9—C10—O211.39 (14)
C4—C5—C6—C10.23 (13)O1—C9—C10—N210.87 (12)
C4—C5—C6—C7178.32 (10)C7—C9—C10—N2168.98 (9)
N1—C1—C6—C5178.22 (8)C10—N2—C11—C1268.08 (12)
C2—C1—C6—C51.00 (14)C10—N2—C11—C16168.70 (8)
N1—C1—C6—C70.37 (10)N2—C11—C12—C13178.16 (8)
C2—C1—C6—C7179.58 (9)C16—C11—C12—C1358.92 (11)
C5—C6—C7—C8177.15 (10)C11—C12—C13—C1457.56 (12)
C1—C6—C7—C81.12 (10)C12—C13—C14—C1554.88 (12)
C5—C6—C7—C90.74 (17)C13—C14—C15—C1653.30 (12)
C1—C6—C7—C9177.53 (9)N2—C11—C16—C15178.68 (8)
C1—N1—C8—C71.32 (11)C12—C11—C16—C1557.37 (11)
C9—C7—C8—N1177.83 (9)C14—C15—C16—C1154.54 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···F1i0.905 (13)2.275 (13)3.1234 (11)156.1 (11)
N1—H1···O2ii0.939 (14)1.863 (14)2.7786 (11)164.5 (13)
C8—H8···O1iii0.952.313.0586 (12)136
Symmetry codes: (i) x, y1/2, z+1/2; (ii) x, y+1/2, z+3/2; (iii) x, y+3/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC16H17FN2O2
Mr288.32
Crystal system, space groupMonoclinic, P21/c
Temperature (K)113
a, b, c (Å)11.5065 (15), 9.7666 (12), 12.3139 (16)
β (°) 96.639 (5)
V3)1374.5 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.20 × 0.16 × 0.12
Data collection
DiffractometerRigaku Saturn CCD area-detector
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.980, 0.988
No. of measured, independent and
observed [I > 2σ(I)] reflections
18432, 3717, 3007
Rint0.035
(sin θ/λ)max1)0.687
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.098, 1.04
No. of reflections3717
No. of parameters198
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.27, 0.28

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···F1i0.905 (13)2.275 (13)3.1234 (11)156.1 (11)
N1—H1···O2ii0.939 (14)1.863 (14)2.7786 (11)164.5 (13)
C8—H8···O1iii0.952.313.0586 (12)135.8
Symmetry codes: (i) x, y1/2, z+1/2; (ii) x, y+1/2, z+3/2; (iii) x, y+3/2, z+1/2.
 

Acknowledgements

This work was supported by the National Natural Science Foundation of China (No. 30873363), the Program of the Science Foundation of Tianjin (08JCYBJC070000) and the Major Program of the Science Foundation of Tianjin (09ZCKFSH01700).

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