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

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ISSN: 2056-9890

Ethyl 2-(3-phenyl­thio­ureido)-5,6-di­hydro-4H-cyclo­penta­[b]thio­phene-3-carboxyl­ate

aLaboratório de Síntese e Vetorização de Moléculas Bioativas, Universidade Estadual da Paraíba, 58020-540 João Pessoa, PB, Brazil, bLaboratório de Síntese e Planejamento de Fármacos, Departamento de Antibióticos, Universidade Federal de Pernambuco, 50670-910 Recife, PE, Brazil, and cDepartamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo – USP, 13560-970 São Carlos, SP, Brazil
*Correspondence e-mail: casimone@ifsc.usp.br

(Received 4 June 2012; accepted 30 June 2012; online 7 July 2012)

In the title compound, C17H18N2O2S2, the angle between the mean plane defined by the atoms of the 5,6-dihydro-4H-cyclo­penta­[b]thio­phene moiety (r.m.s. deviation = 0.19 Å) and the phenyl ring is 72.8°(2). The mol­ecular conformation is stabilized by an intra­molecular N—H⋯O inter­action, which generates an S(6) ring motif. In the crystal, pairs of N—H⋯S hydrogen bonds link the mol­ecules to form inversion dimers with an R22(8) ring motif.

Related literature

For background to 2-amino­thio­phene derivatives, see: Puterová et al. (2010[Puterová, Z., Krutošíková, A. & Végh, D. (2010). Arkivoc, i, 209-246.]). For the biological activity of 2-ureido- and 2-thio­ureido-thio­phene-3-carboxyl­ate derivatives, see: Arhin et al. (2006[Arhin, F., et al. (2006). Bioorg. Med. Chem. 14, 5812-5832.]); Saeed et al. (2010[Saeed, S., Rashid, N., Ali, M., Hussain, R. & Jones, P. (2010). Eur. J. Chem. 1, 221-227.]). For the synthesis of 2-amino­thio­phenes, see: Gewald et al. (1966[Gewald, K., Schinke, E. & Bottcher, H. (1966). Chem. Ber. 99, 99-100.]). For a related structure, see: Larson & Simonsen (1988[Larson, S. B. & Simonsen, S. H. (1988). Acta Cryst. C44, 2035-2037.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C17H18N2O2S2

  • Mr = 346.45

  • Triclinic, [P \overline 1]

  • a = 5.0755 (2) Å

  • b = 12.5088 (6) Å

  • c = 13.3304 (5) Å

  • α = 90.562 (3)°

  • β = 95.711 (3)°

  • γ = 94.378 (2)°

  • V = 839.61 (6) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.33 mm−1

  • T = 295 K

  • 0.32 × 0.17 × 0.11 mm

Data collection
  • Nonius KappaCCD diffractometer

  • 9172 measured reflections

  • 3876 independent reflections

  • 2727 reflections with I > 2σ(I)

  • Rint = 0.041

Refinement
  • R[F2 > 2σ(F2)] = 0.045

  • wR(F2) = 0.129

  • S = 1.04

  • 3876 reflections

  • 208 parameters

  • H-atom parameters constrained

  • Δρmax = 0.28 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯S1i 0.86 2.61 3.415 (2) 157
N1—H1⋯O1 0.86 2.04 2.719 (2) 136
Symmetry code: (i) -x+1, -y, -z+1.

Data collection: COLLECT (Nonius, 1997[Nonius (1997). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) and SCALEPACK; 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, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

The various uses and applications of 2-amino thiophene derivatives have been well documented (Puterová et al., 2010). Amongst these appplications, 2-thioureido-thiophene derivatives presents antifungal (Saeed et al., 2010) and antibacterial activities (Arhin et al., 2006). In this work, we report the structure of the title compound prepared by the condensation of 2-amino-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carbonitrile with phenyl isothiocyanate.

The angle between the least-squares plane defined by the atoms of the 5,6-dihydro-4H-cyclopenta[b]thiophene moiety (rms deviation=0.19 Å) and the phenyl rings is 72.8°(2). There is an intramolecular N—H···O interaction giving an S(6) ring motif. In the crystal N—H···S hydrogen-bond interactions link the molecules into pairs giving an R22(8) motif which extends parallel to the plane (120). (Table 2, Fig.2).

Related literature top

For background to 2-aminothiophene derivatives, see: Puterová et al. (2010). For the biological activity of 2-ureido- and 2-thioureido-thiophene-3-carboxylate derivatives, see: Arhin et al. (2006); Saeed et al. (2010). For the synthesis of 2-aminothiophenes, see: Gewald et al.(1966). For a related structure, see: Larson & Simonsen (1988). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Experimental top

Equimolar amounts of 2-amino-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carbonitrile (4.19 mmol) and phenyl isothiocyanate (4.19 mmol) were heated under reflux for 16 h, in the presence of dry toluene (10 ml), and 5 drops of trietylamine. The solid product formed was collected by filtration, washed with ethyl acetate (3 x 10 ml) and crystallized from absolute etanol, affording the title compound as pale yellow crystals (1.07 g, 74%), M.p. 185–187 °C. Crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation at room temperature of a solution of the pure title compound in absolute ethanol. NMR 1H (400 MHz, CDCl3)δ: 1.25 (t, 3H, J = 6.4 Hz), 2.28 (d, 2H, J = 6.0 Hz), 2.76–2.81 (m, 4H), 4.20 (d, 2H, J = 6.0 Hz), 7.24 (s, 1H), 7.39 (d, 2H, J = 6.8 Hz), 7.48 (d, 2H, J = 7.2 Hz), 11.00 (bs, 1H); 11.58 (bs, 1H).

Refinement top

All H atoms attached to C atoms and N atom were fixed geometrically and treated as riding with C—H = 0.93 Å (aromatic) or 0.97 Å (methylene) and N—H = 0.86 Å with Uiso(H) = 1.2Ueq(C or N).The maximum and minimum residual electron density peaks were located 0.60 and 0.82 Å, from the C2 and S2 atoms respectively.

Structure description top

The various uses and applications of 2-amino thiophene derivatives have been well documented (Puterová et al., 2010). Amongst these appplications, 2-thioureido-thiophene derivatives presents antifungal (Saeed et al., 2010) and antibacterial activities (Arhin et al., 2006). In this work, we report the structure of the title compound prepared by the condensation of 2-amino-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carbonitrile with phenyl isothiocyanate.

The angle between the least-squares plane defined by the atoms of the 5,6-dihydro-4H-cyclopenta[b]thiophene moiety (rms deviation=0.19 Å) and the phenyl rings is 72.8°(2). There is an intramolecular N—H···O interaction giving an S(6) ring motif. In the crystal N—H···S hydrogen-bond interactions link the molecules into pairs giving an R22(8) motif which extends parallel to the plane (120). (Table 2, Fig.2).

For background to 2-aminothiophene derivatives, see: Puterová et al. (2010). For the biological activity of 2-ureido- and 2-thioureido-thiophene-3-carboxylate derivatives, see: Arhin et al. (2006); Saeed et al. (2010). For the synthesis of 2-aminothiophenes, see: Gewald et al.(1966). For a related structure, see: Larson & Simonsen (1988). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Computing details top

Data collection: COLLECT (Nonius, 1997); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); 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, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. Projection of C17H18N2O2S2, with 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. View of the packing along c axis.
Ethyl 2-(3-phenylthioureido)-5,6-dihydro-4H- cyclopenta[b]thiophene-3-carboxylate top
Crystal data top
C17H18N2O2S2Z = 2
Mr = 346.45F(000) = 364
Triclinic, P1Dx = 1.370 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.0755 (2) ÅCell parameters from 5829 reflections
b = 12.5088 (6) Åθ = 2.6–27.5°
c = 13.3304 (5) ŵ = 0.33 mm1
α = 90.562 (3)°T = 295 K
β = 95.711 (3)°Prism, yellow
γ = 94.378 (2)°0.32 × 0.17 × 0.11 mm
V = 839.61 (6) Å3
Data collection top
Nonius KappaCCD
diffractometer
2727 reflections with I > 2σ(I)
Radiation source: Enraf Nonius FR590Rint = 0.041
Horizonally mounted graphite crystal monochromatorθmax = 27.5°, θmin = 3.1°
Detector resolution: 9 pixels mm-1h = 56
CCD rotation images,thick slices scansk = 1616
9172 measured reflectionsl = 1717
3876 independent 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)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.129H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0607P)2 + 0.2145P]
where P = (Fo2 + 2Fc2)/3
3876 reflections(Δ/σ)max = 0.001
208 parametersΔρmax = 0.28 e Å3
0 restraintsΔρmin = 0.25 e Å3
Crystal data top
C17H18N2O2S2γ = 94.378 (2)°
Mr = 346.45V = 839.61 (6) Å3
Triclinic, P1Z = 2
a = 5.0755 (2) ÅMo Kα radiation
b = 12.5088 (6) ŵ = 0.33 mm1
c = 13.3304 (5) ÅT = 295 K
α = 90.562 (3)°0.32 × 0.17 × 0.11 mm
β = 95.711 (3)°
Data collection top
Nonius KappaCCD
diffractometer
2727 reflections with I > 2σ(I)
9172 measured reflectionsRint = 0.041
3876 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0450 restraints
wR(F2) = 0.129H-atom parameters constrained
S = 1.04Δρmax = 0.28 e Å3
3876 reflectionsΔρmin = 0.25 e Å3
208 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
S10.55314 (12)0.02072 (4)0.67471 (4)0.05884 (19)
S20.35795 (11)0.09492 (4)0.87171 (4)0.05360 (17)
O20.2636 (3)0.37540 (12)0.83065 (10)0.0528 (4)
O10.1299 (3)0.33086 (13)0.68141 (10)0.0607 (4)
N10.2196 (3)0.17647 (13)0.68280 (11)0.0469 (4)
H10.13180.22290.64940.056*
N20.3310 (4)0.13297 (14)0.52705 (13)0.0582 (5)
H20.39990.08960.48850.070*
C10.1968 (4)0.17638 (15)0.78532 (14)0.0423 (4)
C90.1970 (4)0.21777 (16)0.47921 (14)0.0487 (5)
C100.3005 (4)0.32279 (17)0.49491 (15)0.0536 (5)
H100.45510.33840.53770.064*
C20.0363 (4)0.24425 (15)0.83011 (13)0.0425 (4)
C40.0737 (4)0.2761 (2)1.02319 (15)0.0566 (5)
H4A0.26590.26601.01340.068*
H4B0.02080.35211.03130.068*
C80.3604 (4)0.11405 (15)0.62679 (15)0.0466 (4)
C60.2245 (5)0.1327 (2)1.07959 (16)0.0670 (6)
H6A0.40380.14751.11170.080*
H6B0.16200.05971.09340.080*
C110.1727 (5)0.40396 (19)0.44669 (17)0.0635 (6)
H110.24080.47480.45730.076*
C150.1225 (4)0.31881 (16)0.77266 (14)0.0459 (4)
C30.0489 (4)0.22821 (16)0.93666 (14)0.0468 (4)
C160.4291 (5)0.45183 (19)0.77988 (16)0.0573 (5)
H16A0.56130.41520.73130.069*
H16B0.32180.50360.74460.069*
C70.2103 (4)0.15241 (18)0.96808 (15)0.0533 (5)
C130.1550 (5)0.2766 (3)0.36669 (18)0.0747 (7)
H130.30810.26140.32290.090*
C140.0298 (5)0.1938 (2)0.41490 (17)0.0635 (6)
H140.09790.12300.40400.076*
C120.0536 (5)0.3809 (2)0.38337 (18)0.0704 (7)
H120.13950.43620.35140.084*
C170.5609 (5)0.5069 (2)0.85914 (18)0.0677 (6)
H17A0.67270.55840.82820.102*
H17B0.42800.54280.90670.102*
H17C0.66650.45480.89340.102*
C50.0370 (7)0.2135 (3)1.11409 (18)0.0839 (8)
H5A0.10790.17581.14480.101*
H5B0.13280.26281.16400.101*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0707 (4)0.0530 (3)0.0557 (3)0.0257 (3)0.0055 (3)0.0062 (2)
S20.0602 (3)0.0550 (3)0.0490 (3)0.0214 (2)0.0087 (2)0.0070 (2)
O20.0585 (8)0.0617 (9)0.0428 (7)0.0272 (7)0.0098 (6)0.0028 (6)
O10.0755 (10)0.0716 (10)0.0404 (7)0.0340 (8)0.0104 (7)0.0052 (7)
N10.0571 (10)0.0472 (9)0.0395 (8)0.0183 (7)0.0090 (7)0.0002 (7)
N20.0839 (13)0.0522 (10)0.0443 (9)0.0294 (9)0.0165 (9)0.0042 (7)
C10.0445 (10)0.0414 (9)0.0419 (9)0.0075 (8)0.0061 (8)0.0001 (7)
C90.0612 (12)0.0511 (11)0.0376 (9)0.0169 (9)0.0151 (9)0.0015 (8)
C100.0628 (12)0.0535 (12)0.0462 (11)0.0113 (10)0.0092 (9)0.0018 (9)
C20.0430 (9)0.0469 (10)0.0388 (9)0.0080 (8)0.0062 (7)0.0016 (7)
C40.0593 (12)0.0712 (14)0.0419 (10)0.0127 (11)0.0123 (9)0.0014 (9)
C80.0542 (11)0.0401 (10)0.0469 (10)0.0080 (8)0.0100 (9)0.0062 (8)
C60.0708 (14)0.0866 (17)0.0461 (11)0.0164 (13)0.0095 (11)0.0156 (11)
C110.0840 (16)0.0557 (13)0.0551 (12)0.0173 (12)0.0192 (12)0.0064 (10)
C150.0472 (10)0.0495 (11)0.0431 (10)0.0119 (8)0.0094 (8)0.0015 (8)
C30.0480 (10)0.0530 (11)0.0401 (10)0.0066 (9)0.0062 (8)0.0001 (8)
C160.0640 (13)0.0641 (13)0.0481 (11)0.0295 (11)0.0071 (10)0.0053 (9)
C70.0558 (12)0.0611 (13)0.0453 (10)0.0139 (10)0.0089 (9)0.0065 (9)
C130.0649 (15)0.108 (2)0.0526 (13)0.0221 (15)0.0002 (11)0.0051 (13)
C140.0652 (14)0.0703 (15)0.0556 (13)0.0062 (12)0.0090 (11)0.0085 (11)
C120.0844 (17)0.0814 (18)0.0520 (13)0.0384 (14)0.0141 (12)0.0134 (12)
C170.0762 (15)0.0731 (15)0.0578 (13)0.0338 (13)0.0067 (11)0.0080 (11)
C50.109 (2)0.103 (2)0.0471 (13)0.0402 (18)0.0182 (14)0.0121 (13)
Geometric parameters (Å, º) top
S1—C81.671 (2)C4—H4B0.9700
S2—C71.728 (2)C6—C71.505 (3)
S2—C11.7310 (19)C6—C51.537 (4)
O2—C151.337 (2)C6—H6A0.9700
O2—C161.449 (2)C6—H6B0.9700
O1—C151.224 (2)C11—C121.366 (4)
N1—C81.363 (2)C11—H110.9300
N1—C11.383 (2)C3—C71.343 (3)
N1—H10.8600C16—C171.495 (3)
N2—C81.348 (3)C16—H16A0.9700
N2—C91.425 (3)C16—H16B0.9700
N2—H20.8600C13—C121.374 (4)
C1—C21.391 (3)C13—C141.386 (4)
C9—C141.377 (3)C13—H130.9300
C9—C101.383 (3)C14—H140.9300
C10—C111.377 (3)C12—H120.9300
C10—H100.9300C17—H17A0.9600
C2—C31.432 (3)C17—H17B0.9600
C2—C151.453 (3)C17—H17C0.9600
C4—C31.504 (3)C5—H5A0.9700
C4—C51.532 (3)C5—H5B0.9700
C4—H4A0.9700
C7—S2—C190.32 (9)C10—C11—H11119.9
C15—O2—C16116.57 (15)O1—C15—O2122.23 (17)
C8—N1—C1129.72 (17)O1—C15—C2125.21 (17)
C8—N1—H1115.1O2—C15—C2112.56 (16)
C1—N1—H1115.1C7—C3—C2112.96 (18)
C8—N2—C9126.40 (16)C7—C3—C4111.40 (18)
C8—N2—H2116.8C2—C3—C4135.63 (18)
C9—N2—H2116.8O2—C16—C17107.08 (17)
N1—C1—C2122.14 (17)O2—C16—H16A110.3
N1—C1—S2125.40 (14)C17—C16—H16A110.3
C2—C1—S2112.45 (14)O2—C16—H16B110.3
C14—C9—C10120.6 (2)C17—C16—H16B110.3
C14—C9—N2119.4 (2)H16A—C16—H16B108.6
C10—C9—N2119.87 (19)C3—C7—C6114.13 (19)
C11—C10—C9119.5 (2)C3—C7—S2113.40 (16)
C11—C10—H10120.3C6—C7—S2132.46 (17)
C9—C10—H10120.3C12—C13—C14120.2 (2)
C1—C2—C3110.87 (17)C12—C13—H13119.9
C1—C2—C15122.59 (16)C14—C13—H13119.9
C3—C2—C15126.54 (17)C9—C14—C13119.1 (2)
C3—C4—C5103.25 (18)C9—C14—H14120.5
C3—C4—H4A111.1C13—C14—H14120.5
C5—C4—H4A111.1C11—C12—C13120.4 (2)
C3—C4—H4B111.1C11—C12—H12119.8
C5—C4—H4B111.1C13—C12—H12119.8
H4A—C4—H4B109.1C16—C17—H17A109.5
N2—C8—N1114.24 (17)C16—C17—H17B109.5
N2—C8—S1121.58 (14)H17A—C17—H17B109.5
N1—C8—S1124.18 (15)C16—C17—H17C109.5
C7—C6—C5101.64 (19)H17A—C17—H17C109.5
C7—C6—H6A111.4H17B—C17—H17C109.5
C5—C6—H6A111.4C4—C5—C6109.55 (19)
C7—C6—H6B111.4C4—C5—H5A109.8
C5—C6—H6B111.4C6—C5—H5A109.8
H6A—C6—H6B109.3C4—C5—H5B109.8
C12—C11—C10120.3 (2)C6—C5—H5B109.8
C12—C11—H11119.9H5A—C5—H5B108.2
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···S1i0.862.613.415 (2)157
N1—H1···O10.862.042.719 (2)136
Symmetry code: (i) x+1, y, z+1.

Experimental details

Crystal data
Chemical formulaC17H18N2O2S2
Mr346.45
Crystal system, space groupTriclinic, P1
Temperature (K)295
a, b, c (Å)5.0755 (2), 12.5088 (6), 13.3304 (5)
α, β, γ (°)90.562 (3), 95.711 (3), 94.378 (2)
V3)839.61 (6)
Z2
Radiation typeMo Kα
µ (mm1)0.33
Crystal size (mm)0.32 × 0.17 × 0.11
Data collection
DiffractometerNonius KappaCCD
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
9172, 3876, 2727
Rint0.041
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.129, 1.04
No. of reflections3876
No. of parameters208
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.28, 0.25

Computer programs: COLLECT (Nonius, 1997), DENZO and SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···S1i0.862.613.415 (2)157
N1—H1···O10.862.042.719 (2)136
Symmetry code: (i) x+1, y, z+1.
 

Acknowledgements

This work has received partial support from CNPq, CAPES, FACEPE and FINEP. CADS thanks the Instituto de Física de São Carlos — USP for allowing the use of the KappaCCD diffractometer.

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