supplementary materials


sj5324 scheme

Acta Cryst. (2013). E69, o1057-o1058    [ doi:10.1107/S1600536813015092 ]

meso-4,4'-Dimethoxy-2,2'-{[(3aR,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-benzimidazole-1,3-diyl]bis(methylene)}diphenol

A. Rivera, D. Quiroga, J. Ríos-Motta, M. Kuceraková and M. Dusek

Abstract top

The title compound, C23H30N2O4, a di-Mannich base derived from 4-methoxyphenol and cis-1,2-diaminecyclohexane, has a perhydrobenzimidazolidine nucleus, in which the cyclohexane ring adopts a chair conformation and the heterocyclic ring has a half-chair conformation with a C-N-C-C torsion angles of -48.14 (15) and -14.57 (16)°. The mean plane of the heterocycle makes dihedral angles of 86.29 (6) and 78.92 (6)° with the pendant benzene rings. The molecular structure of the title compound shows the presence of two interactions between the N atoms of the imidazolidine ring and the hydroxyl groups through intramolecular O-H...N hydrogen bonds with graph-set motif S(6). The unobserved lone pairs of the N atoms are presumed to be disposed in a syn conformation, being only the second example of an exception to the typical `rabbit-ears' effect in 1,2-diamines.

Comment top

Structural features and stereochemistry of 1,1- and 1,2-diamine functionalities play an important role in the potential reactivity of cyclic aminals. We have demonstrated that cyclic aminals are precursors of di-Mannich bases, an interesting family of 1,2-diamines, where the lone pairs usually adopt an anti conformation (Rivera, et al. 2011) to avoid electron pair repulsions (the rabbit-ears effect) (Hutchins et al. 1968). Although a syn conformation is not typical in this kind of compounds, we obtained 4,4'-difluoro-2,2'-{[(3aR,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3-diyl]bis(methylene)}diphenol (Rivera et al., 2013a), one exception of the "rabbit-ears effect" (Hutchins et al., 1968). Here we report the synthesis and crystal structure of the title compound (I).

The molecular structure and atom-numbering scheme for (I) are shown in Fig. 1. The bond lengths are close to normal (Allen et al., 1987). The crystal structure of (I) shows two intramolecular hydrogen bonds with graph-set motif S(6) (Bernstein et al., 1995) (Table 1), where the N···H distances and the N···O distances are shorter (by about 0.06 Å and 0.03 Å, respectively) than the observed values in a related structure (Rivera, et al. 2013a). These results suggest that the electronic character of the< i>para substituent in the aromatic rings does not significantly influence the strength of the intermolecular hydrogen bonds in these compounds.

The cyclohexane ring adopts a chair conformation where the endocyclic C—C—C bond angles are distorted from the normal tetrahedral bond angles in a chair conformation (Geise et al., 1971), since these values are in the range of 110.29 (15)° to 114.50 (14)°. The imidazolidine ring adopts a half chair conformation (Van den Enden & Geise, 1981), where the nitrogen lone pairs are oriented in a syn disposition and the benzyl groups are located in 1,3-diequatorial positions.

The dihedral angle between the aromatic rings is 49.19 (52) °. The C3—C8 and C6—C4 bonds are the longest and the C10—C12 and C19—C22 bond are the shortest in the aromatic rings.

Related literature top

For related structures, see: Rivera et al. (2011, 2013a). For the preparation of the title compound, see: Rivera et al. (2013b). For standard bond lengths, see: Allen et al. (1987). For hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995). For a discussion of the `rabbit-ear' effect in 1,2-diamines, see: Hutchins et al. (1968). For background to this work, see: Van den Enden & Geise (1981); Geise et al. (1971). For the extinction correction, see: Becker & Coppens (1974).

Experimental top

A solution of p-methoxyphenol (2.00 mmol) in dioxane (3 ml) was added dropwise to a stirred solution of (2S,7R,11S,16R)-1,8,10,17-tetraazapentacyclo[8.8.1.1.8,170.2,7011,16]icosane (276 mg, 1.00 mmol) in dioxane (3 ml). The mixture was stirred for 15 min at room temperature and then water (4 ml) was added. The mixture was heated at 313 K during 30 h. After cooling to room temperature, the solvent was removed in vacuo and the crude product was purified by chromatography on a silica column and subjected to gradient elution with light petroleum ether: ethyl acetate (yield 45%, M.p. = 405–406 K). Single crystals of (I) were grown from a CHCl3 solution by slow evaporation of the solvent at room temperature over a period of about 2 weeks.

Refinement top

The hydroxyl hydrogen atoms were found in difference Fourier maps and their coordinates were refined with a distance restraint d(O—H) = 0.926 Å with σ 0.01. All other H atoms atoms were kept in the geometrically correct positions with C—H distance 0.96 A. The isotropic atomic displacement parameters of hydrogen atoms were evaluated as 1.2×Ueq of the parent atom.

Computing details top

Data collection: CrysAlis PRO (Agilent, 2010); cell refinement: CrysAlis PRO (Agilent, 2010); data reduction: CrysAlis PRO (Agilent, 2010); program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis 2007); program(s) used to refine structure: JANA2006 (Petříček et al., 2006); molecular graphics: Diamond (Brandenburg & Putz, 2005); software used to prepare material for publication: JANA2006 (Petříček et al. 2006).

Figures top
[Figure 1] Fig. 1. A perspective view of the title compound. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii. Hydrogen bonds are drawn as dashed lines.
meso-4,4'-Dimethoxy-2,2'-{[(3aR,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-benzimidazole-1,3-diyl]bis(methylene)}diphenol top
Crystal data top
C23H30N2O4F(000) = 856
Mr = 398.5Dx = 1.300 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.5418 Å
Hall symbol: P 2ac 2abCell parameters from 3881 reflections
a = 6.4135 (3) Åθ = 4.2–67.0°
b = 11.4099 (6) ŵ = 0.72 mm1
c = 27.8249 (14) ÅT = 120 K
V = 2036.15 (18) Å3Polygon shape, white
Z = 40.21 × 0.13 × 0.13 mm
Data collection top
Agilent Xcalibur (Atlas, Gemini ultra)
diffractometer
3491 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source3103 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.023
Detector resolution: 10.3784 pixels mm-1θmax = 67.1°, θmin = 3.2°
ω scansh = 74
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2010)
k = 1312
Tmin = 0.341, Tmax = 1l = 3032
5920 measured reflections
Refinement top
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.031Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0016I2)
wR(F2) = 0.080(Δ/σ)max = 0.014
S = 1.13Δρmax = 0.11 e Å3
3491 reflectionsΔρmin = 0.09 e Å3
269 parametersExtinction correction: B-C type 1 Gaussian isotropic (Becker & Coppens, 1974)
1 restraintExtinction coefficient: 1800 (300)
114 constraints
Crystal data top
C23H30N2O4V = 2036.15 (18) Å3
Mr = 398.5Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 6.4135 (3) ŵ = 0.72 mm1
b = 11.4099 (6) ÅT = 120 K
c = 27.8249 (14) Å0.21 × 0.13 × 0.13 mm
Data collection top
Agilent Xcalibur (Atlas, Gemini ultra)
diffractometer
3491 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2010)
3103 reflections with I > 3σ(I)
Tmin = 0.341, Tmax = 1Rint = 0.023
5920 measured reflectionsθmax = 67.1°
Refinement top
R[F2 > 2σ(F2)] = 0.031H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.080Δρmax = 0.11 e Å3
S = 1.13Δρmin = 0.09 e Å3
3491 reflectionsAbsolute structure: ?
269 parametersAbsolute structure parameter: ?
1 restraintRogers parameter: ?
Special details top

Refinement. The refinement was carried out against all reflections. The conventional R-factor is always based on F. The goodness of fit as well as the weighted R-factor are based on F and F2 for refinement carried out on F and F2, respectively. The threshold expression is used only for calculating R-factors etc. and it is not relevant to the choice of reflections for refinement.

The program used for refinement, Jana2006, uses the weighting scheme based on the experimental expectations, see _refine_ls_weighting_details, that does not force S to be one. Therefore the values of S are usually larger than the ones from the SHELX program.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.9143 (2)0.54863 (11)0.19640 (4)0.0301 (4)
O20.5296 (2)0.11931 (11)0.22143 (5)0.0331 (4)
O31.1573 (2)0.56734 (11)0.02995 (4)0.0307 (4)
O40.75546 (19)0.25342 (11)0.08969 (5)0.0323 (4)
N10.6253 (2)0.60135 (11)0.13114 (5)0.0214 (4)
N20.7838 (2)0.63852 (12)0.05764 (5)0.0236 (4)
C10.5156 (3)0.31779 (14)0.18880 (5)0.0235 (5)
C20.6158 (3)0.22830 (15)0.21334 (6)0.0263 (5)
C30.8117 (3)0.44415 (15)0.20127 (6)0.0239 (5)
C40.8426 (3)0.51409 (14)0.01265 (5)0.0227 (4)
C50.7086 (3)0.74987 (14)0.07934 (6)0.0240 (5)
C61.0495 (3)0.49232 (15)0.00056 (6)0.0249 (5)
C70.8898 (3)0.80893 (16)0.10624 (6)0.0291 (5)
C80.6101 (3)0.42686 (14)0.18311 (5)0.0225 (5)
C90.7333 (3)0.62223 (15)0.00643 (6)0.0241 (5)
C101.0459 (3)0.31475 (16)0.04591 (6)0.0299 (5)
C110.4897 (3)0.52615 (15)0.16028 (6)0.0232 (5)
C121.1484 (3)0.39175 (15)0.01597 (6)0.0285 (5)
C130.8412 (3)0.33593 (14)0.05968 (6)0.0253 (5)
C140.7399 (3)0.43469 (14)0.04254 (6)0.0234 (5)
C150.3383 (3)0.09474 (15)0.19795 (7)0.0318 (5)
C160.6655 (3)0.84873 (15)0.17768 (6)0.0296 (5)
C170.6964 (3)0.54281 (14)0.08724 (6)0.0246 (5)
C180.4760 (3)0.79993 (15)0.15171 (6)0.0267 (5)
C190.8144 (3)0.24615 (15)0.23194 (6)0.0277 (5)
C200.8172 (3)0.90189 (16)0.14189 (7)0.0339 (6)
C210.5386 (3)0.26108 (18)0.09885 (7)0.0377 (6)
C220.9116 (3)0.35333 (16)0.22549 (6)0.0273 (5)
C230.5338 (3)0.71070 (14)0.11279 (6)0.0230 (5)
H1c10.3794680.304440.175560.0282*
H1c50.659430.8067830.05660.0288*
H1c70.9697570.7504520.1228420.0349*
H2c70.9836020.8437180.0834470.0349*
H1c90.7779980.6897080.0114080.0289*
H2c90.5852790.6132140.0027860.0289*
H1c101.116460.2459730.0573250.0359*
H1c110.3806640.4947060.1404730.0278*
H2c110.4243730.5722150.1849080.0278*
H1c121.2894710.3757870.0064450.0342*
H1c140.5973070.4486570.0513370.028*
H1c150.2911750.0179190.2068970.0381*
H2c150.2359010.1517530.2072730.0381*
H3c150.3582840.0979240.1637840.0381*
H1c160.6219180.9077190.2001320.0355*
H2c160.7334330.7868930.1950690.0355*
H1c170.5790910.5087860.0709730.0295*
H2c170.8047620.4879850.0950610.0295*
H1c180.3987260.8631340.1375220.0321*
H2c180.3839470.7639890.1745770.0321*
H1c190.8837690.1845330.2491620.0333*
H1c200.9355690.9329310.1587510.0407*
H2c200.7499720.9645030.1248380.0407*
H1c210.497240.1981140.1196560.0453*
H2c210.4634620.2556240.0690840.0453*
H3c210.508010.3346830.1140050.0453*
H1c221.0496750.3651990.2378740.0327*
H1c230.4005140.7015370.0975330.0276*
H1o31.050 (3)0.6060 (18)0.0456 (7)0.0369*
H1o10.834 (3)0.5936 (17)0.1758 (7)0.0361*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0312 (7)0.0281 (7)0.0309 (6)0.0030 (6)0.0068 (5)0.0021 (5)
O20.0438 (7)0.0216 (6)0.0340 (6)0.0000 (6)0.0026 (6)0.0074 (5)
O30.0261 (6)0.0333 (7)0.0328 (6)0.0028 (6)0.0018 (5)0.0048 (5)
O40.0330 (7)0.0310 (7)0.0330 (6)0.0036 (6)0.0062 (5)0.0123 (5)
N10.0260 (7)0.0180 (6)0.0202 (6)0.0011 (6)0.0004 (5)0.0003 (5)
N20.0321 (8)0.0189 (7)0.0197 (6)0.0012 (6)0.0010 (6)0.0011 (5)
C10.0268 (9)0.0236 (9)0.0202 (7)0.0013 (7)0.0010 (7)0.0005 (6)
C20.0346 (10)0.0240 (9)0.0204 (7)0.0042 (8)0.0044 (7)0.0022 (6)
C30.0284 (9)0.0239 (8)0.0194 (7)0.0018 (7)0.0002 (6)0.0010 (6)
C40.0281 (9)0.0227 (8)0.0174 (7)0.0002 (8)0.0035 (7)0.0020 (6)
C50.0348 (9)0.0177 (8)0.0195 (7)0.0026 (8)0.0015 (7)0.0017 (6)
C60.0268 (8)0.0263 (9)0.0217 (7)0.0038 (7)0.0019 (7)0.0006 (6)
C70.0325 (10)0.0258 (9)0.0289 (8)0.0052 (8)0.0034 (7)0.0014 (7)
C80.0269 (9)0.0240 (8)0.0165 (7)0.0029 (7)0.0011 (6)0.0014 (6)
C90.0283 (9)0.0239 (8)0.0201 (7)0.0014 (7)0.0007 (6)0.0011 (6)
C100.0302 (9)0.0242 (9)0.0354 (9)0.0007 (8)0.0105 (8)0.0022 (7)
C110.0240 (8)0.0235 (8)0.0220 (7)0.0001 (7)0.0007 (6)0.0015 (6)
C120.0255 (9)0.0282 (9)0.0319 (8)0.0009 (8)0.0032 (7)0.0037 (7)
C130.0300 (9)0.0223 (8)0.0237 (8)0.0048 (7)0.0062 (7)0.0014 (6)
C140.0242 (8)0.0253 (8)0.0206 (7)0.0013 (7)0.0026 (6)0.0005 (6)
C150.0360 (10)0.0245 (9)0.0349 (9)0.0012 (8)0.0039 (8)0.0040 (7)
C160.0400 (10)0.0239 (8)0.0249 (8)0.0025 (8)0.0039 (8)0.0069 (6)
C170.0313 (9)0.0208 (8)0.0217 (7)0.0035 (7)0.0017 (7)0.0003 (6)
C180.0305 (9)0.0222 (8)0.0274 (8)0.0053 (8)0.0010 (7)0.0010 (7)
C190.0334 (10)0.0275 (9)0.0222 (7)0.0091 (8)0.0003 (7)0.0035 (7)
C200.0425 (11)0.0244 (9)0.0348 (9)0.0045 (9)0.0052 (8)0.0047 (7)
C210.0345 (10)0.0397 (11)0.0389 (10)0.0068 (9)0.0015 (8)0.0152 (8)
C220.0255 (9)0.0341 (9)0.0223 (8)0.0052 (8)0.0024 (7)0.0008 (7)
C230.0248 (9)0.0202 (8)0.0239 (7)0.0020 (7)0.0033 (7)0.0002 (6)
Geometric parameters (Å, º) top
O1—C31.368 (2)C9—H1c90.96
O1—H1o10.93 (2)C9—H2c90.96
O2—C21.380 (2)C10—C121.378 (3)
O2—C151.418 (2)C10—C131.389 (3)
O3—C61.371 (2)C10—H1c100.96
O3—H1o30.93 (2)C11—H1c110.96
O4—C131.373 (2)C11—H2c110.96
O4—C211.417 (2)C12—H1c120.96
N1—C111.466 (2)C13—C141.385 (2)
N1—C171.465 (2)C14—H1c140.96
N1—C231.470 (2)C15—H1c150.96
N2—C51.487 (2)C15—H2c150.96
N2—C91.473 (2)C15—H3c150.96
N2—C171.478 (2)C16—C181.520 (3)
C1—C21.386 (2)C16—C201.519 (3)
C1—C81.393 (2)C16—H1c160.96
C1—H1c10.96C16—H2c160.96
C2—C191.390 (3)C17—H1c170.96
C3—C81.402 (2)C17—H2c170.96
C3—C221.392 (2)C18—C231.532 (2)
C4—C61.399 (3)C18—H1c180.96
C4—C91.515 (2)C18—H2c180.96
C4—C141.395 (2)C19—C221.384 (3)
C5—C71.538 (2)C19—H1c190.96
C5—C231.524 (2)C20—H1c200.96
C5—H1c50.96C20—H2c200.96
C6—C121.390 (2)C21—H1c210.96
C7—C201.525 (3)C21—H2c210.96
C7—H1c70.96C21—H3c210.96
C7—H2c70.96C22—H1c220.96
C8—C111.511 (2)C23—H1c230.96
C3—O1—H1o1106.0 (13)C6—C12—H1c12119.71
C2—O2—C15116.72 (13)C10—C12—H1c12119.71
C6—O3—H1o3101.6 (13)O4—C13—C10115.28 (15)
C13—O4—C21117.40 (14)O4—C13—C14125.39 (16)
C11—N1—C17112.27 (12)C10—C13—C14119.32 (16)
C11—N1—C23116.87 (13)C4—C14—C13120.79 (16)
C17—N1—C23102.81 (12)C4—C14—H1c14119.6
C5—N2—C9115.42 (13)C13—C14—H1c14119.6
C5—N2—C17106.39 (12)O2—C15—H1c15109.47
C9—N2—C17111.24 (13)O2—C15—H2c15109.47
C2—C1—C8120.84 (16)O2—C15—H3c15109.47
C2—C1—H1c1119.58H1c15—C15—H2c15109.47
C8—C1—H1c1119.58H1c15—C15—H3c15109.47
O2—C2—C1123.98 (16)H2c15—C15—H3c15109.47
O2—C2—C19116.01 (15)C18—C16—C20110.30 (14)
C1—C2—C19120.01 (16)C18—C16—H1c16109.47
O1—C3—C8122.03 (15)C18—C16—H2c16109.47
O1—C3—C22118.37 (15)C20—C16—H1c16109.47
C8—C3—C22119.60 (15)C20—C16—H2c16109.47
C6—C4—C9119.44 (14)H1c16—C16—H2c16108.63
C6—C4—C14119.29 (15)N1—C17—N2104.22 (12)
C9—C4—C14121.26 (15)N1—C17—H1c17109.47
N2—C5—C7109.08 (14)N1—C17—H2c17109.47
N2—C5—C23103.65 (13)N2—C17—H1c17109.47
N2—C5—H1c5114.64N2—C17—H2c17109.47
C7—C5—C23112.79 (13)H1c17—C17—H2c17114.25
C7—C5—H1c5105.82C16—C18—C23112.72 (15)
C23—C5—H1c5111.05C16—C18—H1c18109.47
O3—C6—C4121.62 (15)C16—C18—H2c18109.47
O3—C6—C12118.85 (16)C23—C18—H1c18109.47
C4—C6—C12119.52 (16)C23—C18—H2c18109.47
C5—C7—C20113.00 (15)H1c18—C18—H2c18106.02
C5—C7—H1c7109.47C2—C19—C22119.58 (16)
C5—C7—H2c7109.47C2—C19—H1c19120.21
C20—C7—H1c7109.47C22—C19—H1c19120.21
C20—C7—H2c7109.47C7—C20—C16110.14 (15)
H1c7—C7—H2c7105.7C7—C20—H1c20109.47
C1—C8—C3119.06 (15)C7—C20—H2c20109.47
C1—C8—C11119.71 (15)C16—C20—H1c20109.47
C3—C8—C11121.14 (15)C16—C20—H2c20109.47
N2—C9—C4109.87 (13)H1c20—C20—H2c20108.8
N2—C9—H1c9109.47O4—C21—H1c21109.47
N2—C9—H2c9109.47O4—C21—H2c21109.47
C4—C9—H1c9109.47O4—C21—H3c21109.47
C4—C9—H2c9109.47H1c21—C21—H2c21109.47
H1c9—C9—H2c9109.07H1c21—C21—H3c21109.47
C12—C10—C13120.47 (16)H2c21—C21—H3c21109.47
C12—C10—H1c10119.76C3—C22—C19120.89 (16)
C13—C10—H1c10119.76C3—C22—H1c22119.56
N1—C11—C8111.62 (14)C19—C22—H1c22119.56
N1—C11—H1c11109.47N1—C23—C599.62 (13)
N1—C11—H2c11109.47N1—C23—C18114.52 (13)
C8—C11—H1c11109.47N1—C23—H1c23114.61
C8—C11—H2c11109.47C5—C23—C18114.50 (14)
H1c11—C11—H2c11107.24C5—C23—H1c23114.63
C6—C12—C10120.58 (17)C18—C23—H1c2399.77
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H1o3···N20.93 (2)1.78 (2)2.6443 (19)154.4 (19)
O1—H1o1···N10.93 (2)1.83 (2)2.6638 (19)148.8 (18)

Experimental details

Crystal data
Chemical formulaC23H30N2O4
Mr398.5
Crystal system, space groupOrthorhombic, P212121
Temperature (K)120
a, b, c (Å)6.4135 (3), 11.4099 (6), 27.8249 (14)
V3)2036.15 (18)
Z4
Radiation typeCu Kα
µ (mm1)0.72
Crystal size (mm)0.21 × 0.13 × 0.13
Data collection
DiffractometerAgilent Xcalibur (Atlas, Gemini ultra)
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2010)
Tmin, Tmax0.341, 1
No. of measured, independent and
observed [I > 3σ(I)] reflections
5920, 3491, 3103
Rint0.023
(sin θ/λ)max1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.031, 0.080, 1.13
No. of reflections3491
No. of parameters269
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.11, 0.09

Computer programs: CrysAlis PRO (Agilent, 2010), SUPERFLIP (Palatinus & Chapuis 2007), JANA2006 (Petříček et al., 2006), Diamond (Brandenburg & Putz, 2005), JANA2006 (Petříček et al. 2006).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H1o3···N20.93 (2)1.78 (2)2.6443 (19)154.4 (19)
O1—H1o1···N10.93 (2)1.83 (2)2.6638 (19)148.8 (18)
Acknowledgements top

We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de laUniversidad Nacional de Colombia, for financial support of this work and the Praemium Academiae project of the Academy of Sciences of the Czech Republic. DQ acknowledges the Vicerrectoría Académica de la Universidad Nacional de Colombia for a fellowship.

references
References top

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