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Crystal structure of ethyl 4-(2,4-di­chloro­phen­yl)-2-methyl-4H-benzo[4,5]thia­zolo[3,2-a]pyrimidine-3-carboxyl­ate

aCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, bInstitution of Excellence, University of Mysore, Manasagangotri, Mysore 570 006, India, and cDepartment of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570 006, India
*Correspondence e-mail: gunaunom@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 7 April 2015; accepted 8 April 2015; online 15 April 2015)

In the title compound, C20H16Cl2N2O2S, the pyrimidine ring has a screw-boat conformation. The attached di­chloro­phenyl ring is twisted at an angle of 89.29 (13)° with respect to the pyrimidine ring mean plane. The benzo­thia­zole group is approximately planar (r.m.s. deviation = 0.008 Å) and inclined to the pyrimidine ring mean plane by 3.04 (10)°. The carboxyl­ate group assumes an extended conformation with respect to the pyrimidine ring, which can be seen from the O=C—O—C torsion angle of 3.2 (4) °. In the crystal, mol­ecules are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming slabs lying parallel to (100).

1. Related literature

For general background and literature on the biological properties of pyrimidine derivatives, see: Kumar et al. (2002[Kumar, A., Sinha, S. & Chauhan, P. M. (2002). Bioorg. Med. Chem. Lett. 12, 667-669.]; Baraldi et al. (2002[Baraldi, P. G., Pavani, M. G., Nuñez, M. del C., Brigidi, P., Vitali, B., Gambari, R. & Romagnoli, R. (2002). Bioorg. Med. Chem. 10, 449-456.]); Nasr & Gineinah (2002[Nasr, M. N. & Gineinah, M. M. (2002). Arch. Pharm. Pharm. Med. Chem. 335, 289-295.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C20H16Cl2N2O2S

  • Mr = 419.31

  • Monoclinic, C 2/c

  • a = 38.654 (8) Å

  • b = 11.787 (3) Å

  • c = 8.774 (2) Å

  • β = 102.415 (14)°

  • V = 3904.1 (15) Å3

  • Z = 8

  • Cu Kα radiation

  • μ = 4.14 mm−1

  • T = 296 K

  • 0.30 × 0.27 × 0.25 mm

2.2. Data collection

  • Bruker SMART APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.370, Tmax = 0.424

  • 10089 measured reflections

  • 3114 independent reflections

  • 2519 reflections with I > 2σ(I)

  • Rint = 0.042

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.047

  • wR(F2) = 0.139

  • S = 1.04

  • 3114 reflections

  • 246 parameters

  • H-atom parameters constrained

  • Δρmax = 0.36 e Å−3

  • Δρmin = −0.31 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C5—H5⋯N1i 0.93 2.59 3.515 (4) 176
C16—H16⋯O24ii 0.93 2.53 3.180 (4) 128
Symmetry codes: (i) [-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [x, -y+2, z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. 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: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Structural commentary top

Many pyrimidine derivatives are reported to have anti-bacterial, anti-tumor and anti-viral activities (Kumar et al., 2012; Baraldi et al., 2002; Nasr et al., 2002). In view of their important properties we synthesized the title compound and report herein on its crystal structure.

The molecular structure of the title compound is shown in Fig. 1. The pyrimidine ring [N1/C13/C12/C11/N10/C2] has a screw-boat conformation and its mean plane is inclined to the planar benzo­thia­zole group [S3/C2/N10/C4—C9; r.m.s. deviation = 0.008 Å] by 3.04 (10) °. The di­chloro­phenyl ring [C15—C20] is twisted at an angle of 89.29 (13) ° with respect to the pyrimidine ring mean plane. The carboxyl­ate group assumes an extended conformation with respect to the pyrimidine ring, which can be seen from the torsion angle O24—C23—O25—C26 = 3.2 (4) °.

In the crystal, molecules are linked via C—H···O and C—H···N hydrogen bonds forming slabs lying parallel to (100); see Table 1 and Fig. 2.

Synthesis and crystallization top

A mixture of 2,4-di­chloro benzaldehyde was treated with ethyl aceto­acetate and 2-amino­benzo­thia­zole in the presence of ammonium acetate in ethanol. The mixture was gently warmed in a water bath at 353 K until the colour changed and it was then kept aside overnight at room temperature. The completion of reaction was monitored by TLC. The solid obtained was separated and purified by means of column chromatography using hexane and ethyl acetate as eluent. The sample was recrystallized using a 1:1 mixture of ethanol and THF, yielding yellow block-like crystals.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were positioned geometrically and allowed to ride on their parent atoms: C—H = 0.93-0.98 Å with Uiso(H) = 1.5Ueq(C) for methyl H atoms and 1.2Ueq(C) for other H atoms.

Related literature top

For general background and literature on the biological properties of pyrimidine derivatives, see: Kumar et al. (2002; Baraldi et al. (2002); Nasr & Gineinah (2002).

Structure description top

Many pyrimidine derivatives are reported to have anti-bacterial, anti-tumor and anti-viral activities (Kumar et al., 2012; Baraldi et al., 2002; Nasr et al., 2002). In view of their important properties we synthesized the title compound and report herein on its crystal structure.

The molecular structure of the title compound is shown in Fig. 1. The pyrimidine ring [N1/C13/C12/C11/N10/C2] has a screw-boat conformation and its mean plane is inclined to the planar benzo­thia­zole group [S3/C2/N10/C4—C9; r.m.s. deviation = 0.008 Å] by 3.04 (10) °. The di­chloro­phenyl ring [C15—C20] is twisted at an angle of 89.29 (13) ° with respect to the pyrimidine ring mean plane. The carboxyl­ate group assumes an extended conformation with respect to the pyrimidine ring, which can be seen from the torsion angle O24—C23—O25—C26 = 3.2 (4) °.

In the crystal, molecules are linked via C—H···O and C—H···N hydrogen bonds forming slabs lying parallel to (100); see Table 1 and Fig. 2.

For general background and literature on the biological properties of pyrimidine derivatives, see: Kumar et al. (2002; Baraldi et al. (2002); Nasr & Gineinah (2002).

Synthesis and crystallization top

A mixture of 2,4-di­chloro benzaldehyde was treated with ethyl aceto­acetate and 2-amino­benzo­thia­zole in the presence of ammonium acetate in ethanol. The mixture was gently warmed in a water bath at 353 K until the colour changed and it was then kept aside overnight at room temperature. The completion of reaction was monitored by TLC. The solid obtained was separated and purified by means of column chromatography using hexane and ethyl acetate as eluent. The sample was recrystallized using a 1:1 mixture of ethanol and THF, yielding yellow block-like crystals.

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were positioned geometrically and allowed to ride on their parent atoms: C—H = 0.93-0.98 Å with Uiso(H) = 1.5Ueq(C) for methyl H atoms and 1.2Ueq(C) for other H atoms.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. The crystal packing of the molecules viewed down the c axis.
Ethyl 4-(2,4-dichlorophenyl)-2-methyl-4H-benzo[4,5]thiazolo[3,2-a]pyrimidine-3-carboxylate top
Crystal data top
C20H16Cl2N2O2SF(000) = 1728
Mr = 419.31Dx = 1.427 Mg m3
Monoclinic, C2/cCu Kα radiation, λ = 1.54178 Å
Hall symbol: -C 2ycCell parameters from 3114 reflections
a = 38.654 (8) Åθ = 5.1–64.1°
b = 11.787 (3) ŵ = 4.14 mm1
c = 8.774 (2) ÅT = 296 K
β = 102.415 (14)°Block, yellow
V = 3904.1 (15) Å30.30 × 0.27 × 0.25 mm
Z = 8
Data collection top
Bruker SMART APEXII CCD
diffractometer
3114 independent reflections
Radiation source: fine-focus sealed tube2519 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.042
ω and φ scansθmax = 64.1°, θmin = 5.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 4344
Tmin = 0.370, Tmax = 0.424k = 1212
10089 measured reflectionsl = 109
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)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.139H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0772P)2 + 2.6744P]
where P = (Fo2 + 2Fc2)/3
3114 reflections(Δ/σ)max < 0.001
246 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
C20H16Cl2N2O2SV = 3904.1 (15) Å3
Mr = 419.31Z = 8
Monoclinic, C2/cCu Kα radiation
a = 38.654 (8) ŵ = 4.14 mm1
b = 11.787 (3) ÅT = 296 K
c = 8.774 (2) Å0.30 × 0.27 × 0.25 mm
β = 102.415 (14)°
Data collection top
Bruker SMART APEXII CCD
diffractometer
3114 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
2519 reflections with I > 2σ(I)
Tmin = 0.370, Tmax = 0.424Rint = 0.042
10089 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.139H-atom parameters constrained
S = 1.04Δρmax = 0.36 e Å3
3114 reflectionsΔρmin = 0.31 e Å3
246 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
N10.29291 (6)0.8365 (2)0.6499 (3)0.0540 (6)
C20.29669 (6)0.7278 (2)0.6518 (3)0.0450 (6)
S30.267722 (17)0.63964 (6)0.72345 (9)0.0552 (3)
C40.28999 (6)0.5193 (2)0.6806 (3)0.0446 (6)
C50.28233 (7)0.4079 (2)0.7057 (3)0.0520 (7)
H50.26310.38910.74880.062*
C60.30359 (8)0.3250 (3)0.6658 (4)0.0561 (7)
H60.29900.24920.68320.067*
C70.33195 (8)0.3533 (2)0.5997 (4)0.0560 (7)
H70.34600.29580.57300.067*
C80.33984 (7)0.4649 (2)0.5723 (3)0.0484 (7)
H80.35890.48310.52760.058*
C90.31847 (6)0.5488 (2)0.6136 (3)0.0406 (6)
N100.32157 (5)0.66662 (18)0.5982 (2)0.0417 (5)
C110.35145 (6)0.7226 (2)0.5479 (3)0.0411 (6)
H110.35370.69080.44740.049*
C120.34297 (7)0.8489 (2)0.5275 (3)0.0463 (6)
C130.31608 (7)0.8979 (2)0.5811 (3)0.0513 (7)
C140.30725 (9)1.0217 (3)0.5713 (4)0.0694 (9)
H14A0.32631.06380.63450.104*
H14B0.28591.03440.60840.104*
H14C0.30381.04640.46490.104*
C150.38581 (6)0.7024 (2)0.6676 (3)0.0409 (6)
C160.38873 (7)0.7454 (2)0.8175 (3)0.0472 (6)
H160.36950.78360.84170.057*
C170.41907 (8)0.7332 (3)0.9307 (4)0.0608 (8)
H170.42050.76301.03000.073*
C180.44751 (8)0.6758 (3)0.8946 (4)0.0627 (8)
C190.44582 (7)0.6332 (3)0.7486 (4)0.0612 (8)
H190.46510.59530.72510.073*
C200.41531 (7)0.6470 (2)0.6369 (3)0.0491 (7)
Cl210.41503 (2)0.59197 (7)0.45153 (10)0.0706 (3)
Cl220.48585 (3)0.65809 (11)1.03772 (14)0.1075 (4)
C230.36748 (8)0.9170 (3)0.4592 (3)0.0556 (7)
O240.36870 (7)1.0189 (2)0.4524 (3)0.0880 (8)
O250.39033 (6)0.8507 (2)0.4043 (3)0.0734 (7)
C260.41805 (13)0.9061 (4)0.3433 (5)0.1021 (15)
H26A0.40880.97540.29030.122*
H26B0.42530.85680.26740.122*
C270.44862 (13)0.9328 (5)0.4666 (8)0.134 (2)
H27A0.44160.98360.54000.201*
H27B0.46650.96820.42210.201*
H27C0.45790.86420.51900.201*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0535 (13)0.0408 (15)0.0701 (16)0.0048 (10)0.0185 (12)0.0012 (11)
C20.0429 (13)0.0401 (17)0.0513 (15)0.0021 (11)0.0086 (11)0.0025 (12)
S30.0456 (4)0.0476 (5)0.0771 (5)0.0017 (3)0.0239 (3)0.0002 (3)
C40.0394 (12)0.0424 (17)0.0512 (15)0.0019 (11)0.0077 (11)0.0004 (12)
C50.0495 (15)0.0455 (18)0.0619 (17)0.0077 (13)0.0142 (13)0.0038 (13)
C60.0656 (18)0.0351 (16)0.0682 (19)0.0063 (13)0.0155 (15)0.0017 (13)
C70.0608 (17)0.0400 (18)0.0682 (19)0.0019 (13)0.0163 (15)0.0035 (14)
C80.0491 (14)0.0408 (17)0.0574 (17)0.0014 (12)0.0162 (12)0.0049 (13)
C90.0420 (13)0.0351 (15)0.0429 (14)0.0045 (11)0.0050 (11)0.0022 (11)
N100.0421 (11)0.0343 (13)0.0502 (12)0.0013 (9)0.0136 (10)0.0016 (9)
C110.0462 (13)0.0366 (15)0.0432 (14)0.0043 (11)0.0154 (11)0.0037 (11)
C120.0538 (15)0.0379 (16)0.0450 (15)0.0023 (11)0.0058 (12)0.0034 (11)
C130.0560 (16)0.0381 (16)0.0563 (17)0.0024 (12)0.0044 (13)0.0004 (12)
C140.075 (2)0.0404 (19)0.092 (2)0.0083 (15)0.0153 (18)0.0044 (16)
C150.0456 (13)0.0315 (14)0.0479 (14)0.0041 (11)0.0152 (11)0.0003 (11)
C160.0526 (14)0.0401 (16)0.0513 (15)0.0009 (12)0.0165 (12)0.0034 (12)
C170.0724 (19)0.057 (2)0.0495 (17)0.0046 (16)0.0048 (15)0.0073 (14)
C180.0493 (16)0.063 (2)0.070 (2)0.0035 (15)0.0002 (14)0.0069 (16)
C190.0433 (15)0.057 (2)0.085 (2)0.0012 (13)0.0171 (15)0.0003 (17)
C200.0490 (14)0.0414 (16)0.0623 (17)0.0040 (12)0.0241 (13)0.0068 (13)
Cl210.0700 (5)0.0747 (6)0.0771 (5)0.0009 (4)0.0375 (4)0.0252 (4)
Cl220.0677 (6)0.1307 (10)0.1058 (8)0.0037 (6)0.0221 (5)0.0064 (7)
C230.0678 (18)0.048 (2)0.0501 (17)0.0049 (14)0.0103 (14)0.0078 (13)
O240.0960 (18)0.0479 (16)0.127 (2)0.0077 (12)0.0385 (16)0.0245 (14)
O250.0905 (16)0.0654 (16)0.0767 (15)0.0168 (12)0.0455 (13)0.0005 (11)
C260.126 (3)0.104 (3)0.098 (3)0.039 (3)0.071 (3)0.006 (2)
C270.088 (3)0.143 (5)0.182 (6)0.025 (3)0.050 (4)0.008 (4)
Geometric parameters (Å, º) top
N1—C21.290 (4)C14—H14A0.9600
N1—C131.387 (4)C14—H14B0.9600
C2—N101.364 (3)C14—H14C0.9600
C2—S31.741 (3)C15—C201.390 (3)
S3—C41.741 (3)C15—C161.392 (4)
C4—C51.375 (4)C16—C171.372 (4)
C4—C91.399 (3)C16—H160.9300
C5—C61.369 (4)C17—C181.384 (4)
C5—H50.9300C17—H170.9300
C6—C71.387 (4)C18—C191.365 (5)
C6—H60.9300C18—Cl221.737 (3)
C7—C81.383 (4)C19—C201.371 (4)
C7—H70.9300C19—H190.9300
C8—C91.385 (4)C20—Cl211.748 (3)
C8—H80.9300C23—O241.204 (4)
C9—N101.403 (3)C23—O251.343 (4)
N10—C111.478 (3)O25—C261.452 (4)
C11—C151.524 (3)C26—C271.455 (7)
C11—C121.527 (4)C26—H26A0.9700
C11—H110.9800C26—H26B0.9700
C12—C131.358 (4)C27—H27A0.9600
C12—C231.465 (4)C27—H27B0.9600
C13—C141.497 (4)C27—H27C0.9600
C2—N1—C13116.2 (2)C13—C14—H14B109.5
N1—C2—N10127.4 (2)H14A—C14—H14B109.5
N1—C2—S3121.2 (2)C13—C14—H14C109.5
N10—C2—S3111.4 (2)H14A—C14—H14C109.5
C4—S3—C291.26 (12)H14B—C14—H14C109.5
C5—C4—C9121.3 (2)C20—C15—C16116.8 (2)
C5—C4—S3127.6 (2)C20—C15—C11124.7 (2)
C9—C4—S3111.0 (2)C16—C15—C11118.4 (2)
C6—C5—C4118.6 (3)C17—C16—C15121.9 (3)
C6—C5—H5120.7C17—C16—H16119.0
C4—C5—H5120.7C15—C16—H16119.0
C5—C6—C7120.5 (3)C16—C17—C18118.9 (3)
C5—C6—H6119.8C16—C17—H17120.6
C7—C6—H6119.7C18—C17—H17120.6
C8—C7—C6121.6 (3)C19—C18—C17121.0 (3)
C8—C7—H7119.2C19—C18—Cl22119.7 (3)
C6—C7—H7119.2C17—C18—Cl22119.3 (3)
C7—C8—C9117.9 (3)C18—C19—C20119.2 (3)
C7—C8—H8121.1C18—C19—H19120.4
C9—C8—H8121.1C20—C19—H19120.4
C8—C9—C4120.0 (2)C19—C20—C15122.2 (3)
C8—C9—N10127.8 (2)C19—C20—Cl21117.0 (2)
C4—C9—N10112.2 (2)C15—C20—Cl21120.9 (2)
C2—N10—C9114.1 (2)O24—C23—O25121.8 (3)
C2—N10—C11121.4 (2)O24—C23—C12127.0 (3)
C9—N10—C11124.0 (2)O25—C23—C12111.2 (3)
N10—C11—C15110.2 (2)C23—O25—C26117.7 (3)
N10—C11—C12108.0 (2)O25—C26—C27111.6 (4)
C15—C11—C12111.5 (2)O25—C26—H26A109.3
N10—C11—H11109.0C27—C26—H26A109.3
C15—C11—H11109.0O25—C26—H26B109.3
C12—C11—H11109.0C27—C26—H26B109.3
C13—C12—C23121.3 (3)H26A—C26—H26B108.0
C13—C12—C11122.4 (2)C26—C27—H27A109.5
C23—C12—C11116.1 (2)C26—C27—H27B109.5
C12—C13—N1122.9 (3)H27A—C27—H27B109.5
C12—C13—C14125.2 (3)C26—C27—H27C109.5
N1—C13—C14111.9 (3)H27A—C27—H27C109.5
C13—C14—H14A109.5H27B—C27—H27C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5···N1i0.932.593.515 (4)176
C16—H16···O24ii0.932.533.180 (4)128
Symmetry codes: (i) x+1/2, y1/2, z+3/2; (ii) x, y+2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5···N1i0.932.593.515 (4)176
C16—H16···O24ii0.932.533.180 (4)128
Symmetry codes: (i) x+1/2, y1/2, z+3/2; (ii) x, y+2, z+1/2.
 

Acknowledgements

The authors are thankful to the Institution of Excellence, University of Mysore, for providing the single-crystal X-ray diffraction facility.

References

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