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ISSN: 2056-9890

(E)-N′-(2,4,5-Tri­fluoro­benzyl­­idene)isonicotinohydrazide monohydrate

aSchool of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my

(Received 2 February 2010; accepted 4 February 2010; online 10 February 2010)

In the Schiff base mol­ecule of the title compound, C13H8F3N3O·H2O, the benzene ring and the pyridine ring are nearly coplanar, making a dihedral angle of 6.64 (7)°. The mol­ecule exists in an E configuration with respect to the C=N double bond. In the crystal structure, mol­ecules are linked via the water mol­ecules into two-dimensional planes parallel to the ab plane through inter­molecular N—H⋯O, O—H⋯O O—H⋯N and C—H⋯O hydrogen bonds.

Related literature

For applications of isoniazid (isonicotinylhydrazine) derivatives, see: Janin (2007[Janin, Y. L. (2007). Bioorg. Med. Chem. 15, 2479-2513.]); Maccari et al. (2005[Maccari, R., Ottana, R. & Vigorita, M. G. (2005). Bioorg. Med. Chem. Lett. 15, 2509-2513.]); Slayden & Barry (2000[Slayden, R. A. & Barry, C. E. (2000). Microbes Infect. 2, 659-669.]); Kahwa et al. (1986[Kahwa, I. A., Selbin, J., Hsieh, T. C.-Y. & Laine, R. A. (1986). Inorg. Chim. Acta. 118, 179-185.]). For the preparation of the title compound, see: Lourenco et al. (2008[Lourenco, M. C. S., Ferreira, M. L., de Souza, M. V. N., Peralta, M. A., Vasconcelos, T. R. A. & Henriques, M. G. M. O. (2008). Eur. J. Med. Chem. 43, 1344-1347.]). For related structures, see: Naveenkumar et al. (2009[Naveenkumar, H. S., Sadikun, A., Ibrahim, P., Loh, W.-S. & Fun, H.-K. (2009). Acta Cryst. E65, o2540-o2541.], 2010[Naveenkumar, H. S., Sadikun, A., Ibrahim, P., Quah, C. K. & Fun, H.-K. (2010). Acta Cryst. E66, o291.]); Shi (2005[Shi, J. (2005). Acta Cryst. E61, o3933-o3934.]).

[Scheme 1]

Experimental

Crystal data
  • C13H8F3N3O·H2O

  • Mr = 297.24

  • Triclinic, [P \overline 1]

  • a = 4.9241 (1) Å

  • b = 6.3915 (1) Å

  • c = 21.3387 (2) Å

  • α = 88.616 (1)°

  • β = 86.556 (1)°

  • γ = 76.056 (1)°

  • V = 650.58 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.13 mm−1

  • T = 296 K

  • 0.32 × 0.32 × 0.13 mm

Data collection
  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.958, Tmax = 0.984

  • 14710 measured reflections

  • 4024 independent reflections

  • 2730 reflections with I > 2σ(I)

  • Rint = 0.022

Refinement
  • R[F2 > 2σ(F2)] = 0.046

  • wR(F2) = 0.146

  • S = 1.05

  • 4024 reflections

  • 230 parameters

  • All H-atom parameters refined

  • Δρmax = 0.27 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H1N2⋯O1W 0.883 (19) 1.921 (19) 2.7910 (13) 168.1 (16)
O1W—H1W1⋯O1i 0.79 (2) 2.03 (2) 2.8263 (17) 176.3 (18)
O1W—H2W1⋯O1ii 0.84 (2) 2.19 (2) 2.9670 (17) 155 (2)
O1W—H2W1⋯N1ii 0.84 (2) 2.47 (2) 3.1024 (14) 133.7 (19)
C7—H7A⋯O1W 0.967 (13) 2.492 (14) 3.2576 (16) 135.9 (12)
C13—H13A⋯O1W 0.963 (19) 2.427 (18) 3.3308 (19) 156.2 (14)
Symmetry codes: (i) x+1, y-1, z; (ii) x, y-1, z.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

In the search for new biologically active compounds, isoniazid (isonicotinylhydrazine) derivatives have been found to possess potential tuberculostatic activity (Janin, 2007; Maccari et al., 2005; Slayden & Barry, 2000). As part of our current work on the synthesis of (E)-N'-substituted isonicotinohydrazide derivatives, in this paper we present the crystal structure of the title compound, (I).

The asymmetric unit consists of one Schiff base molecule and one water molecule (Fig. 1). The geometric parameters are comparable to those related structures (Naveenkumar et al., 2009, 2010; Shi, 2005). The molecule is nearly coplanar with a dihedral angle between the benzene ring and the pyridine ring of 6.64 (7)°. The molecule exists in an E configuration with respect to the C7=N1 double bond. In the crystal structure, the water molecules link the molecules into two-dimensional planes parallel to the ab plane through intermolecular N–H···O, O–H···O O–H···N and C–H···O hydrogen bonds (Fig. 2, Table 1).

Related literature top

For applications of isoniazid (isonicotinylhydrazine) derivatives, see: Janin (2007); Maccari et al. (2005); Slayden & Barry (2000); Kahwa et al. (1986). For the preparation of the title compound, see: Lourenco et al. (2008). For related structures, see: Naveenkumar et al. (2009, 2010); Shi (2005).

Experimental top

The isoniazid derivative was prepared following a procedure reported by Lourenco et al., (2008). 2,4,5-triflurobenzaldehyde (1.0 eq) was added to isoniazid (1.0 eq) in ethanol/water. After stirring for 1-3 h at room temperature, the resulting mixture was concentrated under reduced pressure. The residue was purified by washing with cold ethanol and diethyl ether to give the pure derivative. Colourless single crystals suitable for X-ray analysis were obtained by re-crystallization from methanol.

Refinement top

All hydrogen atoms were located from the difference Fourier map and refined freely.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) with atom labels and 50% probability ellipsoids for non-H atoms.
[Figure 2] Fig. 2. The crystal packing of (I), viewed down the a axis, showing the molecules are linked into 2-dimensional planes parallel to the ab plane. Intermolecular hydrogen bonds are shown as dashed lines.
(E)-N'-(2,4,5-Trifluorobenzylidene)isonicotinohydrazide monohydrate top
Crystal data top
C13H8F3N3O·H2OZ = 2
Mr = 297.24F(000) = 304
Triclinic, P1Dx = 1.517 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 4.9241 (1) ÅCell parameters from 6031 reflections
b = 6.3915 (1) Åθ = 2.9–30.8°
c = 21.3387 (2) ŵ = 0.13 mm1
α = 88.616 (1)°T = 296 K
β = 86.556 (1)°Plate, colourless
γ = 76.056 (1)°0.32 × 0.32 × 0.13 mm
V = 650.58 (2) Å3
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
4024 independent reflections
Radiation source: fine-focus sealed tube2730 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
ϕ and ω scansθmax = 30.8°, θmin = 2.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 67
Tmin = 0.958, Tmax = 0.984k = 99
14710 measured reflectionsl = 3029
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)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.146All H-atom parameters refined
S = 1.05 w = 1/[σ2(Fo2) + (0.0764P)2 + 0.0515P]
where P = (Fo2 + 2Fc2)/3
4024 reflections(Δ/σ)max < 0.001
230 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = 0.22 e Å3
Crystal data top
C13H8F3N3O·H2Oγ = 76.056 (1)°
Mr = 297.24V = 650.58 (2) Å3
Triclinic, P1Z = 2
a = 4.9241 (1) ÅMo Kα radiation
b = 6.3915 (1) ŵ = 0.13 mm1
c = 21.3387 (2) ÅT = 296 K
α = 88.616 (1)°0.32 × 0.32 × 0.13 mm
β = 86.556 (1)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
4024 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
2730 reflections with I > 2σ(I)
Tmin = 0.958, Tmax = 0.984Rint = 0.022
14710 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0460 restraints
wR(F2) = 0.146All H-atom parameters refined
S = 1.05Δρmax = 0.27 e Å3
4024 reflectionsΔρmin = 0.22 e Å3
230 parameters
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 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
F11.20930 (18)0.63383 (14)0.34682 (4)0.0667 (3)
F21.2581 (2)1.19398 (18)0.48033 (4)0.0824 (3)
F30.8111 (2)1.44958 (15)0.42966 (5)0.0834 (3)
O10.1646 (2)1.24750 (13)0.19113 (5)0.0552 (3)
N10.5532 (2)1.00798 (15)0.25981 (4)0.0386 (2)
N20.4249 (2)0.91747 (15)0.21550 (4)0.0377 (2)
N30.1882 (3)0.7926 (2)0.04246 (6)0.0592 (3)
C11.1071 (3)0.8366 (2)0.36730 (6)0.0431 (3)
C21.2389 (3)0.9080 (3)0.41488 (6)0.0532 (3)
C31.1375 (3)1.1151 (3)0.43436 (6)0.0533 (3)
C40.9082 (3)1.2479 (2)0.40781 (6)0.0520 (3)
C50.7792 (3)1.1753 (2)0.36057 (6)0.0465 (3)
C60.8779 (2)0.96531 (19)0.33900 (5)0.0381 (3)
C70.7429 (2)0.87952 (19)0.28944 (5)0.0391 (3)
C80.2279 (2)1.05161 (17)0.18276 (5)0.0381 (3)
C90.0888 (2)0.95209 (18)0.13457 (5)0.0381 (3)
C100.1271 (3)1.0858 (2)0.10359 (6)0.0469 (3)
C110.2587 (3)0.9994 (3)0.05883 (6)0.0549 (3)
C120.0208 (4)0.6670 (3)0.07203 (7)0.0645 (4)
C130.1642 (3)0.7368 (2)0.11825 (7)0.0555 (4)
O1W0.6042 (3)0.46898 (15)0.22162 (5)0.0567 (3)
H2A1.388 (4)0.807 (3)0.4315 (9)0.079 (5)*
H5A0.619 (4)1.275 (3)0.3436 (8)0.069 (5)*
H7A0.798 (3)0.727 (2)0.2805 (7)0.054 (4)*
H10A0.178 (3)1.237 (3)0.1110 (7)0.061 (4)*
H11A0.398 (4)1.092 (3)0.0388 (8)0.069 (5)*
H12A0.087 (4)0.519 (3)0.0585 (9)0.084 (6)*
H13A0.316 (4)0.636 (3)0.1371 (8)0.073 (5)*
H1N20.479 (3)0.776 (3)0.2116 (8)0.067 (5)*
H1W10.759 (4)0.402 (3)0.2127 (8)0.071 (6)*
H2W10.499 (4)0.384 (4)0.2232 (10)0.099 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0610 (5)0.0571 (5)0.0724 (6)0.0110 (4)0.0253 (4)0.0153 (4)
F20.0779 (6)0.1120 (8)0.0649 (6)0.0278 (6)0.0330 (5)0.0306 (5)
F30.0999 (8)0.0612 (5)0.0897 (7)0.0114 (5)0.0295 (6)0.0347 (5)
O10.0565 (6)0.0337 (4)0.0772 (6)0.0068 (4)0.0346 (5)0.0034 (4)
N10.0405 (5)0.0378 (5)0.0402 (5)0.0114 (4)0.0145 (4)0.0050 (4)
N20.0408 (5)0.0331 (5)0.0412 (5)0.0087 (4)0.0177 (4)0.0039 (4)
N30.0653 (8)0.0712 (8)0.0501 (6)0.0285 (6)0.0241 (5)0.0041 (6)
C10.0381 (6)0.0491 (7)0.0410 (6)0.0062 (5)0.0103 (5)0.0040 (5)
C20.0407 (7)0.0730 (9)0.0446 (7)0.0073 (6)0.0172 (5)0.0031 (6)
C30.0490 (7)0.0758 (9)0.0409 (6)0.0220 (7)0.0140 (5)0.0131 (6)
C40.0593 (8)0.0503 (7)0.0499 (7)0.0161 (6)0.0125 (6)0.0129 (5)
C50.0492 (7)0.0431 (6)0.0480 (7)0.0086 (5)0.0183 (5)0.0049 (5)
C60.0377 (6)0.0422 (6)0.0367 (5)0.0119 (4)0.0110 (4)0.0020 (4)
C70.0411 (6)0.0361 (5)0.0415 (6)0.0091 (4)0.0139 (5)0.0039 (4)
C80.0372 (6)0.0355 (5)0.0442 (6)0.0107 (4)0.0138 (5)0.0013 (4)
C90.0378 (6)0.0433 (6)0.0375 (6)0.0153 (5)0.0126 (4)0.0005 (4)
C100.0449 (7)0.0509 (7)0.0451 (7)0.0084 (5)0.0161 (5)0.0017 (5)
C110.0484 (7)0.0724 (9)0.0459 (7)0.0138 (7)0.0216 (6)0.0011 (6)
C120.0858 (11)0.0528 (8)0.0630 (9)0.0250 (8)0.0335 (8)0.0060 (7)
C130.0671 (9)0.0427 (7)0.0603 (8)0.0132 (6)0.0322 (7)0.0036 (6)
O1W0.0608 (7)0.0322 (4)0.0771 (7)0.0067 (4)0.0194 (5)0.0063 (4)
Geometric parameters (Å, º) top
F1—C11.3454 (15)C5—C61.3922 (17)
F2—C31.3445 (13)C5—H5A0.969 (18)
F3—C41.3463 (16)C6—C71.4660 (14)
O1—C81.2299 (13)C7—H7A0.965 (15)
N1—C71.2737 (15)C8—C91.5025 (14)
N1—N21.3791 (11)C9—C131.3835 (17)
N2—C81.3477 (14)C9—C101.3843 (17)
N2—H1N20.881 (18)C10—C111.3821 (17)
N3—C121.326 (2)C10—H10A0.953 (16)
N3—C111.3324 (19)C11—H11A0.911 (19)
C1—C21.3800 (17)C12—C131.3882 (17)
C1—C61.3877 (16)C12—H12A0.966 (19)
C2—C31.363 (2)C13—H13A0.963 (18)
C2—H2A0.93 (2)O1W—H1W10.79 (2)
C3—C41.381 (2)O1W—H2W10.83 (2)
C4—C51.3699 (16)
C7—N1—N2116.55 (9)N1—C7—C6118.93 (10)
C8—N2—N1117.36 (9)N1—C7—H7A121.8 (9)
C8—N2—H1N2126.2 (11)C6—C7—H7A119.2 (9)
N1—N2—H1N2116.5 (11)O1—C8—N2122.04 (9)
C12—N3—C11116.24 (11)O1—C8—C9120.84 (10)
F1—C1—C2118.25 (11)N2—C8—C9117.12 (9)
F1—C1—C6118.70 (10)C13—C9—C10117.67 (10)
C2—C1—C6123.04 (12)C13—C9—C8124.60 (10)
C3—C2—C1117.80 (12)C10—C9—C8117.72 (10)
C3—C2—H2A126.1 (11)C11—C10—C9119.15 (12)
C1—C2—H2A116.1 (11)C11—C10—H10A119.8 (9)
F2—C3—C2120.48 (12)C9—C10—H10A121.0 (9)
F2—C3—C4118.53 (13)N3—C11—C10123.93 (13)
C2—C3—C4120.99 (11)N3—C11—H11A119.1 (11)
F3—C4—C5120.41 (12)C10—C11—H11A116.9 (11)
F3—C4—C3118.89 (11)N3—C12—C13124.42 (14)
C5—C4—C3120.70 (12)N3—C12—H12A117.9 (11)
C4—C5—C6120.06 (12)C13—C12—H12A117.5 (11)
C4—C5—H5A117.3 (10)C9—C13—C12118.58 (13)
C6—C5—H5A122.7 (10)C9—C13—H13A121.8 (10)
C1—C6—C5117.41 (10)C12—C13—H13A119.6 (10)
C1—C6—C7120.67 (11)H1W1—O1W—H2W1108.0 (19)
C5—C6—C7121.89 (10)
C7—N1—N2—C8178.64 (11)N2—N1—C7—C6177.37 (10)
F1—C1—C2—C3178.60 (12)C1—C6—C7—N1172.44 (12)
C6—C1—C2—C30.2 (2)C5—C6—C7—N19.12 (19)
C1—C2—C3—F2179.70 (12)N1—N2—C8—O10.66 (18)
C1—C2—C3—C40.8 (2)N1—N2—C8—C9179.99 (9)
F2—C3—C4—F31.2 (2)O1—C8—C9—C13174.03 (13)
C2—C3—C4—F3178.33 (14)N2—C8—C9—C135.32 (19)
F2—C3—C4—C5179.61 (13)O1—C8—C9—C104.90 (18)
C2—C3—C4—C50.8 (2)N2—C8—C9—C10175.74 (11)
F3—C4—C5—C6178.86 (13)C13—C9—C10—C110.8 (2)
C3—C4—C5—C60.3 (2)C8—C9—C10—C11179.78 (12)
F1—C1—C6—C5179.11 (12)C12—N3—C11—C100.3 (2)
C2—C1—C6—C50.3 (2)C9—C10—C11—N31.0 (2)
F1—C1—C6—C72.38 (18)C11—N3—C12—C130.7 (3)
C2—C1—C6—C7178.84 (12)C10—C9—C13—C120.1 (2)
C4—C5—C6—C10.3 (2)C8—C9—C13—C12178.85 (13)
C4—C5—C6—C7178.75 (12)N3—C12—C13—C90.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N2···O1W0.883 (19)1.921 (19)2.7910 (13)168.1 (16)
O1W—H1W1···O1i0.79 (2)2.03 (2)2.8263 (17)176.3 (18)
O1W—H2W1···O1ii0.84 (2)2.19 (2)2.9670 (17)155 (2)
O1W—H2W1···N1ii0.84 (2)2.47 (2)3.1024 (14)133.7 (19)
C7—H7A···O1W0.967 (13)2.492 (14)3.2576 (16)135.9 (12)
C13—H13A···O1W0.963 (19)2.427 (18)3.3308 (19)156.2 (14)
Symmetry codes: (i) x+1, y1, z; (ii) x, y1, z.

Experimental details

Crystal data
Chemical formulaC13H8F3N3O·H2O
Mr297.24
Crystal system, space groupTriclinic, P1
Temperature (K)296
a, b, c (Å)4.9241 (1), 6.3915 (1), 21.3387 (2)
α, β, γ (°)88.616 (1), 86.556 (1), 76.056 (1)
V3)650.58 (2)
Z2
Radiation typeMo Kα
µ (mm1)0.13
Crystal size (mm)0.32 × 0.32 × 0.13
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.958, 0.984
No. of measured, independent and
observed [I > 2σ(I)] reflections
14710, 4024, 2730
Rint0.022
(sin θ/λ)max1)0.721
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.046, 0.146, 1.05
No. of reflections4024
No. of parameters230
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.27, 0.22

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N2···O1W0.883 (19)1.921 (19)2.7910 (13)168.1 (16)
O1W—H1W1···O1i0.79 (2)2.03 (2)2.8263 (17)176.3 (18)
O1W—H2W1···O1ii0.84 (2)2.19 (2)2.9670 (17)155 (2)
O1W—H2W1···N1ii0.84 (2)2.47 (2)3.1024 (14)133.7 (19)
C7—H7A···O1W0.967 (13)2.492 (14)3.2576 (16)135.9 (12)
C13—H13A···O1W0.963 (19)2.427 (18)3.3308 (19)156.2 (14)
Symmetry codes: (i) x+1, y1, z; (ii) x, y1, z.
 

Footnotes

Additional Correspondence author: amirin@usm.my.

§Thomson Reuters ResearcherID: A-5523-2009.

Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

This research was supported by Universiti Sains Malaysia (USM) under the University Research Grant (1001/PFARMASI/815005). HSNK and CSY each thank USM for the award of a USM Fellowship. HKF and CSY thank USM for the Research University Golden Goose Grant (1001/PFIZIK/811012).

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