organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 70| Part 1| January 2014| Pages o64-o65

2-(5-Chloro-2-oxoindolin-3-yl­­idene)hydrazinecarbo­thio­amide

aEscola de Quimica e Alimentos, Universidade Federal do Rio Grande, Av. Italia, km 08, Campus Carreiros, 96203-900 Rio Grande-RS, Brazil, and bDepartamento de Quimica, Universidade Federal de Santa Maria, Av. Roraima, Campus, 97105-900 Santa Maria-RS, Brazil
*Correspondence e-mail: vanessa.gervini@gmail.com

(Received 11 November 2013; accepted 9 December 2013; online 14 December 2013)

The title mol­ecule, C9H7ClN4OS, is almost planar, with an r.m.s. deviation of 0.034 (2) Å for the mean plane through all the non-H atoms. Intra­molecular N—H⋯O and N—H⋯N hydrogen bonds form S(6) and S(5) ring motifs, respectively. In the crystal, mol­ecules are assembled into inversion dimers through pairs of co-operative N—H⋯Cl inter­actions. These dimers are connected along the b axis by N—H⋯O and N—H⋯S hydrogen bonds, generating layers parallel to (103). The layers are further connected along the a axis into a three-dimensional network, through weak ππ stacking inter­actions [centroid–centroid distance = 3.849 (2) Å].

Related literature

For the synthesis of the title compound, see: Qasem Ali et al. (2011[Qasem Ali, A., Eltayeb, N. E., Teoh, S. G., Salhin, A. & Fun, H.-K. (2011). Acta Cryst. E67, o3141-o3142.]). For similar hydrazinecarbo­thio­amide crystal structures, see: Bandeira et al. (2013[Bandeira, K. C. T., Bresolin, L., Näther, C., Jess, I. & Oliveira, A. B. (2013). Acta Cryst. E69, o1251-o1252.]); Ali et al. (2012[Ali, A. Q., Eltayeb, N. E., Teoh, S. G., Salhin, A. & Fun, H.-K. (2012). Acta Cryst. E68, o2868-o2869.]); de Oliveira et al. (2012[Oliveira, A. B. de, Silva, C. S., Feitosa, B. R. S., Näther, C. & Jess, I. (2012). Acta Cryst. E68, o2581.]). For the biological activity of isatin and derivatives, see: Cerchiaro & Ferreira (2006[Cerchiaro, G. & Ferreira, A. M. C. (2006). J. Braz. Chem. Soc. 17, 1473-1485.]).

[Scheme 1]

Experimental

Crystal data
  • C9H7ClN4OS

  • Mr = 254.70

  • Monoclinic, P 21 /n

  • a = 5.260 (5) Å

  • b = 15.396 (10) Å

  • c = 13.215 (9) Å

  • β = 96.53 (2)°

  • V = 1063.4 (14) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.54 mm−1

  • T = 173 K

  • 1.27 × 0.38 × 0.35 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.639, Tmax = 0.746

  • 6939 measured reflections

  • 2540 independent reflections

  • 2374 reflections with I > 2σ(I)

  • Rint = 0.014

Refinement
  • R[F2 > 2σ(F2)] = 0.029

  • wR(F2) = 0.084

  • S = 0.81

  • 2540 reflections

  • 161 parameters

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

  • Δρmax = 0.52 e Å−3

  • Δρmin = −0.30 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H21⋯O1 0.865 (18) 2.127 (18) 2.783 (2) 132.2 (15)
N4—H41⋯S1i 0.90 (2) 2.47 (2) 3.354 (2) 169.5 (19)
N1—H11⋯O1ii 0.88 (2) 1.98 (2) 2.848 (2) 169 (2)
N1—H12⋯N3 0.88 (3) 2.15 (3) 2.594 (2) 110 (2)
N1—H12⋯Cl1iii 0.88 (3) 2.62 (3) 3.342 (2) 139 (2)
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+{\script{1\over 2}}]; (iii) -x+2, -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: 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: DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Experimental top

Synthesis and crystallization top

Experimental procedures for synthesis were based on Qasem Ali et al. (2011). Thio­semicarbazide (0.25 g, 2.7 mmol) was mixed to 20 ml of an ethano­lic solution containing 5-chloro­isatin (0.50 g, 2.7 mmol), followed by addition of ten drops of glacial acetic acid. This mixture was maintained under reflux for 4 h, being a yellow precipitated obtained. The product was filtered off under vacuum, yielding 0.38 g (76.2%). Yellow single crystals suitable for X-ray diffraction measurements were grown in ethanol/aceto­nitrile (1:1), adding five drops of pyridine and slow evaporating at room temperature.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 1. H-atoms attached to aromatic C atoms were positioned with idealized geometry and were refined isotropic with Ueq(H) set to 1.2 times of the Ueq(C) using a riding model with C–H = 0.95 Å. H-atoms attached to N atoms were located in difference Fourier maps. Their coordinates and isotropic displacement parameters were refined.

Results and discussion top

Isatin and its derivatives are known for demonstrate biological effects, such as bactericide and fungicide activities (Cerchiaro & Ferreira, 2006). This class of compounds has been characterized through X-ray crystallography: (Ali et al., 2012; de Oliveira et al., 2012; Bandeira et al., 2013). As part of our research, in this paper we describe the synthesis (Qasem Ali et al., 2011) and present the crystal structure determination of 1-(5-Chloro-2-oxoindolin-3-yl­idene)hydrazinecarbo­thio­amide.

The molecular structure of the title compound, C9H7ClN4OS, shows an E conformation about the N2–N3 bond, matching its asymmetric unit (Fig. 1). The molecule is almost planar (Bandeira et al., 2013), with a r.m.s. deviation of 0.034 Å and maximum deviation from the mean plane through non-H atoms observed for the N1 atom (0.0920 (12) Å). Individually, the mean planes defined through non-H atoms of the thio­semicarbazone fragment (S1/C1/N1–N3) and the chloro substituted aromatic ring (C3–C8/Cl1) reveals a dihedral angle of 4.75 (8)°, with maximum deviations of 0.0058 (11) Å and 0.0043 (11) Å, respectively (de Oliveira et al., 2012).

Intra-molecular N1–H12···N3 (2.15 (3) Å) and N2–H21···O1 (2.127 (18) Å) hydrogen bonds are observed, forming S(5) and S(6) ring motifs, respectively. Dimeric species are formed through inter­molecular N3–H12···Cl1i hydrogen bonds with a distance of 2.62 (3) Å (symmetry code: (i) –x + 2, –y + 1, –z) and molecular units being related by crystallographic centers of symmetry. Shorter inter­molecular hydrogen bonding with distances of 2.47 (2) Å (N4–H41···S1ii) and 1.98 (2) Å (N1–H11···O1iii) occur in a R44(8) ring fashion, connecting molecules into a bi-dimensional net parallel to the [103] plane (Fig. 2, symmetry codes: (ii) –x + 1/2, y + 1/2, –z + 1/2; (iii) –x + 1/2, y - 1/2, –z + 1/2). Additional weak ππ stacking inter­actions are verified between adjacent bi-dimensional layers along the a axis, with C2iv···C5v and C9iv···C7v distances of 3.3209 (26) Å and 3.3973 (28) Å, respectively (Fig. 3, symmetry codes: (iv) x + 1/2, –y + 3/2, z + 1/2; (v) x – 1/2, –y + 3/2, z + 1/2). All these bonding features are similar to that described by Bandeira et al. (2013), despite of the different crystal symmetry verified previously.

Related literature top

For the synthesis of the title compound, see: Qasem Ali et al. (2011). For similar hydrazinecarbothioamide crystal structures, see: Bandeira et al. (2013); Ali et al. (2012); de Oliveira et al. (2012). For the biological activity of isatin and derivatives, see: Cerchiaro & Ferreira (2006).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Molecular projection showing the asymmetric unit. Intramolecular hydrogen bonds are represented with dashed lines. Ellipsoid probability: 50%.
[Figure 2] Fig. 2. Bi-dimensional network formed through intermolecular hydrogen bonds, represented with dashed lines. Aromatic hydrogen atoms were omitted for clarity. Symmetry codes: (i) –x + 2, –y + 1, –z; (ii) –x + 1/2, y + 1/2, –z + 1/2; (iii) –x + 1/2, y - 1/2, –z + 1/2.
[Figure 3] Fig. 3. Packing of bidimensional layers through ππ stacking interactions. Aromatic hydrogen atoms were omitted for clarity. Symmetry codes: (iv) x + 1/2, –y + 3/2, z + 1/2; (v) x – 1/2, –y + 3/2, z + 1/2.
2-(5-Chloro-2-oxoindolin-3-ylidene)hydrazinecarbothioamide top
Crystal data top
C9H7ClN4OSZ = 4
Mr = 254.70F(000) = 520
Monoclinic, P21/nDx = 1.591 Mg m3
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 5.260 (5) Åθ = 2.0–28.3°
b = 15.396 (10) ŵ = 0.54 mm1
c = 13.215 (9) ÅT = 173 K
β = 96.53 (2)°Block, yellow
V = 1063.4 (14) Å31.27 × 0.38 × 0.35 mm
Data collection top
Bruker APEXII CCD
diffractometer
2540 independent reflections
Radiation source: fine-focus sealed tube2374 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.014
ϕ and ω scansθmax = 28.3°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 67
Tmin = 0.639, Tmax = 0.746k = 2018
6939 measured reflectionsl = 1717
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)] = 0.029Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.084H atoms treated by a mixture of independent and constrained refinement
S = 0.81 w = 1/[σ2(Fo2) + (0.0594P)2 + 1.1793P]
where P = (Fo2 + 2Fc2)/3
2540 reflections(Δ/σ)max = 0.001
161 parametersΔρmax = 0.52 e Å3
0 restraintsΔρmin = 0.30 e Å3
Crystal data top
C9H7ClN4OSV = 1063.4 (14) Å3
Mr = 254.70Z = 4
Monoclinic, P21/nMo Kα radiation
a = 5.260 (5) ŵ = 0.54 mm1
b = 15.396 (10) ÅT = 173 K
c = 13.215 (9) Å1.27 × 0.38 × 0.35 mm
β = 96.53 (2)°
Data collection top
Bruker APEXII CCD
diffractometer
2540 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
2374 reflections with I > 2σ(I)
Tmin = 0.639, Tmax = 0.746Rint = 0.014
6939 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0290 restraints
wR(F2) = 0.084H atoms treated by a mixture of independent and constrained refinement
S = 0.81Δρmax = 0.52 e Å3
2540 reflectionsΔρmin = 0.30 e Å3
161 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
Cl11.30216 (7)0.60089 (2)0.07671 (3)0.02850 (11)
S10.02044 (6)0.54702 (2)0.36977 (3)0.01934 (10)
O10.35742 (18)0.80256 (6)0.24115 (7)0.0187 (2)
N10.3377 (3)0.47463 (8)0.24996 (11)0.0285 (3)
N20.3459 (2)0.62260 (7)0.25988 (8)0.0162 (2)
N30.5262 (2)0.62044 (7)0.19443 (8)0.0159 (2)
N40.6662 (2)0.83859 (7)0.13477 (8)0.0166 (2)
C10.2444 (2)0.54529 (8)0.28857 (10)0.0163 (2)
C20.6101 (2)0.69327 (8)0.16351 (9)0.0148 (2)
C30.8029 (2)0.70274 (8)0.09346 (9)0.0152 (2)
C40.9460 (2)0.64250 (8)0.04630 (10)0.0173 (2)
H40.92710.58190.05650.021*
C51.1187 (2)0.67488 (9)0.01663 (10)0.0189 (3)
C61.1518 (2)0.76349 (9)0.03214 (10)0.0192 (3)
H61.27280.78290.07530.023*
C80.8326 (2)0.79228 (8)0.07785 (9)0.0152 (2)
C90.5256 (2)0.78350 (8)0.18693 (10)0.0156 (2)
C71.0070 (3)0.82389 (9)0.01575 (10)0.0180 (3)
H71.02740.88450.00610.022*
H210.291 (3)0.6714 (12)0.2814 (13)0.017 (4)*
H410.637 (4)0.8958 (15)0.1304 (16)0.035 (5)*
H110.276 (4)0.4232 (15)0.2616 (16)0.033 (5)*
H120.459 (5)0.4835 (18)0.210 (2)0.054 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.02824 (19)0.0271 (2)0.0332 (2)0.00156 (13)0.01668 (14)0.00782 (13)
S10.02276 (18)0.01321 (17)0.02450 (18)0.00194 (11)0.01337 (13)0.00236 (11)
O10.0228 (5)0.0133 (4)0.0215 (5)0.0022 (3)0.0088 (4)0.0002 (3)
N10.0363 (7)0.0112 (5)0.0437 (8)0.0024 (5)0.0288 (6)0.0028 (5)
N20.0209 (5)0.0099 (5)0.0195 (5)0.0005 (4)0.0093 (4)0.0002 (4)
N30.0180 (5)0.0136 (5)0.0171 (5)0.0003 (4)0.0067 (4)0.0007 (4)
N40.0199 (5)0.0094 (5)0.0216 (5)0.0005 (4)0.0066 (4)0.0016 (4)
C10.0183 (6)0.0117 (6)0.0196 (6)0.0004 (4)0.0051 (5)0.0006 (4)
C20.0169 (5)0.0117 (5)0.0163 (5)0.0010 (4)0.0040 (4)0.0002 (4)
C30.0168 (5)0.0127 (6)0.0165 (5)0.0006 (4)0.0044 (4)0.0016 (4)
C40.0191 (6)0.0132 (6)0.0202 (6)0.0003 (4)0.0050 (5)0.0010 (4)
C50.0184 (6)0.0194 (6)0.0198 (6)0.0011 (5)0.0061 (5)0.0014 (5)
C60.0179 (6)0.0216 (7)0.0191 (6)0.0028 (5)0.0059 (5)0.0018 (5)
C80.0164 (6)0.0132 (6)0.0162 (6)0.0006 (4)0.0024 (4)0.0007 (4)
C90.0190 (6)0.0111 (5)0.0170 (6)0.0004 (4)0.0035 (4)0.0008 (4)
C70.0199 (6)0.0157 (6)0.0187 (6)0.0014 (5)0.0037 (5)0.0036 (4)
Geometric parameters (Å, º) top
Cl1—C51.7417 (16)N4—H410.90 (2)
S1—C11.6816 (17)C2—C31.4561 (19)
O1—C91.2354 (18)C2—C91.5015 (19)
N1—C11.3196 (18)C3—C41.3863 (18)
N1—H110.88 (2)C3—C81.4052 (19)
N1—H120.88 (3)C4—C51.3919 (19)
N2—N31.3548 (17)C4—H40.9500
N2—C11.3753 (17)C5—C61.393 (2)
N2—H210.865 (18)C6—C71.398 (2)
N3—C21.2886 (18)C6—H60.9500
N4—C91.3629 (17)C8—C71.3869 (19)
N4—C81.4108 (17)C7—H70.9500
C1—N1—H11121.0 (14)C3—C4—C5116.98 (13)
C1—N1—H12115.4 (18)C3—C4—H4121.5
H11—N1—H12124 (2)C5—C4—H4121.5
N3—N2—C1118.47 (11)C4—C5—C6122.65 (12)
N3—N2—H21121.0 (12)C4—C5—Cl1118.11 (11)
C1—N2—H21120.5 (12)C6—C5—Cl1119.23 (11)
C2—N3—N2118.11 (11)C5—C6—C7120.06 (12)
C9—N4—C8111.12 (11)C5—C6—H6120.0
C9—N4—H41123.0 (14)C7—C6—H6120.0
C8—N4—H41125.2 (14)C7—C8—C3121.54 (12)
N1—C1—N2115.72 (13)C7—C8—N4129.09 (12)
N1—C1—S1125.31 (10)C3—C8—N4109.36 (11)
N2—C1—S1118.97 (10)O1—C9—N4127.66 (12)
N3—C2—C3125.26 (11)O1—C9—C2126.00 (11)
N3—C2—C9128.28 (12)N4—C9—C2106.33 (11)
C3—C2—C9106.41 (10)C8—C7—C6117.75 (13)
C4—C3—C8121.02 (12)C8—C7—H7121.1
C4—C3—C2132.21 (12)C6—C7—H7121.1
C8—C3—C2106.77 (11)
C1—N2—N3—C2176.25 (12)C4—C3—C8—C70.62 (19)
N3—N2—C1—N11.08 (19)C2—C3—C8—C7178.86 (11)
N3—N2—C1—S1180.00 (9)C4—C3—C8—N4179.71 (11)
N2—N3—C2—C3179.99 (11)C2—C3—C8—N40.23 (14)
N2—N3—C2—C93.0 (2)C9—N4—C8—C7179.50 (12)
N3—C2—C3—C42.3 (2)C9—N4—C8—C30.49 (15)
C9—C2—C3—C4179.81 (13)C8—N4—C9—O1177.55 (12)
N3—C2—C3—C8178.32 (12)C8—N4—C9—C20.97 (14)
C9—C2—C3—C80.79 (14)N3—C2—C9—O10.0 (2)
C8—C3—C4—C50.01 (19)C3—C2—C9—O1177.47 (12)
C2—C3—C4—C5179.33 (13)N3—C2—C9—N4178.51 (13)
C3—C4—C5—C60.6 (2)C3—C2—C9—N41.08 (13)
C3—C4—C5—Cl1179.81 (9)C3—C8—C7—C60.66 (19)
C4—C5—C6—C70.5 (2)N4—C8—C7—C6179.56 (12)
Cl1—C5—C6—C7179.75 (10)C5—C6—C7—C80.11 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H21···O10.865 (18)2.127 (18)2.783 (2)132.2 (15)
N4—H41···S1i0.90 (2)2.47 (2)3.354 (2)169.5 (19)
N1—H11···O1ii0.88 (2)1.98 (2)2.848 (2)169 (2)
N1—H12···N30.88 (3)2.15 (3)2.594 (2)110 (2)
N1—H12···Cl1iii0.88 (3)2.62 (3)3.342 (2)139 (2)
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x+1/2, y1/2, z+1/2; (iii) x+2, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H21···O10.865 (18)2.127 (18)2.783 (2)132.2 (15)
N4—H41···S1i0.90 (2)2.47 (2)3.354 (2)169.5 (19)
N1—H11···O1ii0.88 (2)1.98 (2)2.848 (2)169 (2)
N1—H12···N30.88 (3)2.15 (3)2.594 (2)110 (2)
N1—H12···Cl1iii0.88 (3)2.62 (3)3.342 (2)139 (2)
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x+1/2, y1/2, z+1/2; (iii) x+2, y+1, z.
 

Acknowledgements

We gratefully acknowledge Professor Dr. Manfredo Hörner (Federal University of Santa Maria, Brazil) for his help and support with the X-ray measurements. We also acknowledge financial support through the DECIT/SCTIE-MS-CNPq- FAPERGS-Pronem-# 11/2029–1 and PRONEX-CNPq- FAPERGS projects.

References

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Volume 70| Part 1| January 2014| Pages o64-o65
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