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Acta Crystallogr Sect E Struct Rep Online. 2010 October 1; 66(Pt 10): o2643.
Published online 2010 September 30. doi:  10.1107/S160053681003792X
PMCID: PMC2983180

4,4′-Dichloro-2,2′-[(3aR,7aR/3aS,7aS)-2,3,3a,4,5,6,7,7a-octa­hydro-1H-1,3-benzimidazole-1,3-di­yl)bis­(methyl­ene)]diphenol

Abstract

Mol­ecules of the the title compound, C21H24Cl2N2O2, are located on a twofold rotation axis, which passes through the C atom linking the two N atoms. Two intra­molecular O—H(...)N hydrogen bonds were observed. In the crystal, non-classical inter­molecular C—H(...)O hydrogen bonds link the mol­ecules into chains along the a axis. The crystal studied was a racemic twin.

Related literature

For related structures, see: Rivera et al. (2009 [triangle], 2010 [triangle]). For uses of di-Mannich bases, see: Mitra et al. (2006 [triangle]); Elias et al. (1997 [triangle]). For the anti­malarial activity of di-Mannich bases, see: Shanks & Edstein (2005 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2643-scheme1.jpg

Experimental

Crystal data

  • C21H24Cl2N2O2
  • M r = 407.3
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2643-efi1.jpg
  • a = 5.9529 (2) Å
  • b = 18.3846 (5) Å
  • c = 8.9704 (3) Å
  • V = 981.74 (5) Å3
  • Z = 2
  • Cu Kα radiation
  • μ = 3.11 mm−1
  • T = 120 K
  • 0.36 × 0.21 × 0.12 mm

Data collection

  • Oxford Diffraction Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector
  • Absorption correction: analytical [CrysAlis PRO (Oxford Diffraction, 2009 [triangle]), based on expressions derived by Clark & Reid (1995 [triangle])] T min = 0.518, T max = 0.773
  • 12720 measured reflections
  • 1566 independent reflections
  • 1517 reflections with I > 3σ(I)
  • R int = 0.027

Refinement

  • R[F 2 > 2σ(F 2)] = 0.022
  • wR(F 2) = 0.068
  • S = 1.50
  • 1566 reflections
  • 127 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.11 e Å−3
  • Δρmin = −0.11 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 615 Friedel pairs
  • Flack parameter: 0.32 (1)

Data collection: CrysAlis CCD (Oxford Diffraction, 2009 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2009 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SIR2002 (Burla et al., 2003 [triangle]); program(s) used to refine structure: JANA2006 (Petříček et al., 2006 [triangle]); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 [triangle]); software used to prepare material for publication: JANA2006.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053681003792X/bt5333sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681003792X/bt5333Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We acknowledge the Dirección de Investigaciones Sede Bogotá (DIB) of the Universidad Nacional de Colombia for financial support of this work, the Institutional research plan No. AVOZ10100521 of the Institute of Physics and the project Praemium Academiae of the Academy of Sciences (ASCR).

supplementary crystallographic information

Comment

It is interesting to notice that two types of non-classical intermolecular hydrogen bonds of C—H···O and C—H···Cl were found according to crystallographic data. The molecular structure and atom-numbering scheme for (I) are shown in Fig. 1. Its X-ray structure confirms the presence of intramolecular hydrogen bonds between the phenolic hydroxyl groups and nitrogen atoms [N—H, 1.83 (2) Å), whereas the N···O distances [2.652 (2) Å,] is significantly shorter than the corresponding N···O bond in related structures [2.70 (1) Å]. Furthermore the observed C—O bond length [1.354 (2) Å] is considerably shortened in relation to related structures [1.364 (2) Å] (Rivera et al., 2010) and [1.365 (2) Å] (Rivera et al., 2009). This additional H-bonding does not influence the H—O distance, which shows (as a result of unrestrained refinement) a typical separation of 0.91 (2) Å. Thus, these results indicate an increase in hydrogen-bonding strength due to the presence of chlorine atom. In fact, the presence of the chlorine atom favours the formation of weak intermolecular C—H···O interactions between neighboring molecules, which link them into 1-D extended chains along the a axis and help to stabilize the chain.

The chains are linked along the c direction by C—H···Cl interactions [2.902 (2) Å]. This interaction involves contacts between an apparently electron deficient aromatic C6—H6 and the chlorine atom from a second molecule. The phenyl group in both molecules lies in an orientation which favours hydrogen bond formation.

In the title compound, C21H24Cl2N2O2,the asymmetric unit contains one-half of the molecule, which is related to the other half by a twofold rotation axis [symmetry code: - x, y, -z] passing through C1 (Figure 1). Unlike the related structures Rivera et al. (2010, 2009), the title compound crystallizes in a different crystal system and it has a chiral space group. The compound is a racemic twin and the absolute structure was determined on the basis of that of the starting amine whose stereochemistry is: trans-(rac)-1,2-cyclohexanediamine and the chiral centers were not affected when reacted.

Experimental

Preparation of title compound (I)

A solution of (2R,7R,11S,16S)-1,8,10,17-tetraazapentacyclo[8.8.1.18,17.02,7.011,16] icosane (276 mg, 1.00 mmol) in dioxane (3 ml) and water (4 ml), prepared beforehand following previously described procedures, was added dropwise in a dioxane solution (3 ml) containing two equivalents of p-chlorophenol (257 mg, 2.00 mmol) in a two-necked round-bottomed flask. The mixture was refluxed for about 6 h until precipitation of a colourless solid. The resulting solid was collected by filtration, washed with cool methanol and dried under vacuum (yield 30%, m.p. = 490–492 K). Next, the racemic product (100 mg, 0.246 mmol) was dissolved in 5 ml of a 4:1 mixture of chloroform: methanol. Single crystals of title compound (I) suitable for X-ray analysis were grown by slow evaporation of the solvent at room temperature over a period of about 2 weeks in a preferential crystallization (yield 46%). 1H NMR (CDCl3, 400 MHz): δ 1.29 (4H, m), 1.85 (2H, m), 2.04 (2H, m), 2.34 (2H, m), 3.42 (2H, d, J = 14.0 Hz, ArCH2N), 3.51 (2H, s, NCH2N), 4.14 (2H, d, J = 14.0 Hz, ArCH2N), 6.74 (2H, d, J = 8.8 Hz), 6.92 (2H, s), 7.10 (2H, d, J = 8.8 Hz).

Refinement

All hydrogen atoms were discernible in difference Fourier maps and could be refined to reasonable geometry. According to common practice H atoms attached to C atoms were nevertheless kept in ideal positions during the refinement. The coordinates of the hydroxyl H atom were refined. The isotropic atomic displacement parameters of all hydrogen atoms were set to 1.2*Ueq of the parent atom.

Figures

Fig. 1.
Molecule of the title compound with atom-labeling scheme. Displacement elipsoids are drawn at 50% probability level.
Fig. 2.
Hydrogen bonding of the molecules of the title compound in a direction.

Crystal data

C21H24Cl2N2O2F(000) = 428
Mr = 407.3Dx = 1.378 Mg m3
Orthorhombic, P21212Cu Kα radiation, λ = 1.54184 Å
Hall symbol: P 2 2abCell parameters from 10371 reflections
a = 5.9529 (2) Åθ = 4.8–62.4°
b = 18.3846 (5) ŵ = 3.11 mm1
c = 8.9704 (3) ÅT = 120 K
V = 981.74 (5) Å3Irregular shape, colorless
Z = 20.36 × 0.21 × 0.12 mm

Data collection

Oxford Diffraction Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector1566 independent reflections
Radiation source: X-ray tube1517 reflections with I > 3σ(I)
mirrorRint = 0.027
Detector resolution: 10.3784 pixels mm-1θmax = 62.5°, θmin = 4.8°
Rotation method data acquisition using ω scansh = −6→6
Absorption correction: analytical [CrysAlis PRO (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)]k = −21→20
Tmin = 0.518, Tmax = 0.773l = −10→10
12720 measured reflections

Refinement

Refinement on F2H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.022Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
wR(F2) = 0.068(Δ/σ)max = 0.010
S = 1.50Δρmax = 0.11 e Å3
1566 reflectionsΔρmin = −0.11 e Å3
127 parametersAbsolute structure: Flack (1983), 615 Friedel pairs
0 restraintsFlack parameter: 0.32 (1)
45 constraints

Special details

Experimental. CrysAlisPro, Oxford Diffraction Ltd., Version 1.171.33.51 (release 27-10-2009 CrysAlis171 .NET) Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by Clark & Reid (1995)Physical MeasurementsThe melting point was determined with an Electrothermal apparatus, and it has not been corrected. IR spectrum was recorded as KBr pellets at 292 K on a Perkin-Elmer Paragon FT-IR instrument. NMR spectra were performed in CDCl3 at room temperature on a Bruker AMX 400 Advance spectrometer.
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)

xyzUiso*/Ueq
Cl10.56453 (8)0.22892 (2)0.85004 (4)0.03657 (14)
O10.99889 (19)0.41865 (6)0.41066 (13)0.0278 (3)
N10.59603 (9)0.44360 (5)0.29542 (10)0.0191 (4)
C10.50.50.39535 (12)0.0190 (6)
C20.5511 (3)0.36844 (7)0.34499 (16)0.0207 (4)
C30.6738 (3)0.34996 (7)0.48640 (16)0.0188 (4)
C40.8923 (2)0.37633 (8)0.51184 (18)0.0208 (4)
C51.0043 (3)0.35815 (8)0.64297 (17)0.0260 (5)
C60.9061 (3)0.31220 (8)0.74665 (18)0.0266 (5)
C70.6930 (3)0.28560 (8)0.71952 (17)0.0244 (5)
C80.5774 (3)0.30421 (7)0.59086 (16)0.0204 (4)
C90.5027 (2)0.45884 (7)0.14700 (16)0.0214 (4)
C100.6300 (3)0.43023 (9)0.01323 (18)0.0313 (5)
C110.5134 (3)0.45859 (9)−0.12729 (18)0.0387 (6)
H1a0.3822620.4789810.4544510.0228*
H2a0.3925630.3621220.3598690.0249*
H2b0.5942290.3350340.2678860.0249*
H51.1511370.377670.6617390.0312*
H60.9849630.2990650.8360160.0319*
H80.4293740.2851980.5741250.0245*
H90.3616140.4342590.1346480.0257*
H10a0.6263510.3780210.0136120.0375*
H10b0.7817440.4478390.0160120.0375*
H11a0.3683810.436182−0.1366090.0464*
H11b0.5971310.443924−0.2136540.0464*
H1o0.893 (3)0.4356 (10)0.347 (2)0.0334*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0514 (3)0.0328 (2)0.0254 (2)−0.00039 (19)0.00732 (18)0.00639 (15)
O10.0191 (5)0.0233 (5)0.0410 (6)−0.0026 (4)0.0007 (5)0.0049 (5)
N10.0231 (6)0.0132 (6)0.0208 (6)0.0018 (5)0.0003 (5)0.0012 (5)
C10.0188 (10)0.0153 (9)0.0231 (10)−0.0004 (8)00
C20.0217 (7)0.0140 (6)0.0264 (8)−0.0016 (6)−0.0020 (7)−0.0004 (6)
C30.0200 (7)0.0116 (6)0.0249 (8)0.0028 (6)−0.0009 (6)−0.0019 (6)
C40.0173 (7)0.0150 (6)0.0300 (9)0.0027 (5)0.0017 (6)−0.0035 (6)
C50.0200 (8)0.0239 (7)0.0341 (9)0.0039 (6)−0.0053 (7)−0.0055 (7)
C60.0314 (9)0.0230 (7)0.0253 (8)0.0095 (7)−0.0050 (7)−0.0058 (6)
C70.0339 (9)0.0179 (7)0.0213 (8)0.0045 (7)0.0050 (7)−0.0005 (6)
C80.0204 (7)0.0142 (6)0.0267 (7)0.0010 (6)0.0021 (6)−0.0023 (6)
C90.0246 (8)0.0177 (8)0.0218 (7)0.0029 (5)−0.0014 (6)−0.0014 (6)
C100.0446 (10)0.0239 (8)0.0253 (9)0.0088 (7)0.0027 (8)−0.0020 (7)
C110.0611 (13)0.0322 (10)0.0229 (8)0.0134 (8)−0.0012 (9)−0.0039 (7)

Geometric parameters (Å, °)

Cl1—C71.7441 (16)C5—H50.96
O1—C41.3535 (19)C6—C71.381 (2)
O1—H1o0.91 (2)C6—H60.96
N1—C11.4850 (11)C7—C81.386 (2)
N1—C21.4761 (16)C8—H80.96
N1—C91.4697 (17)C9—C9i1.5138 (19)
C1—H1a0.96C9—C101.514 (2)
C1—H1ai0.96C9—H90.96
C2—C31.503 (2)C10—C111.531 (2)
C2—H2a0.96C10—H10a0.96
C2—H2b0.96C10—H10b0.96
C3—C41.406 (2)C11—C11i1.531 (2)
C3—C81.384 (2)C11—H11a0.96
C4—C51.393 (2)C11—H11b0.96
C5—C61.386 (2)
C4—O1—H1o106.9 (12)C5—C6—H6120.4925
C1—N1—C2113.70 (8)C7—C6—H6120.4933
C1—N1—C9105.56 (8)Cl1—C7—C6119.74 (12)
C2—N1—C9112.50 (9)Cl1—C7—C8119.24 (12)
N1—C1—N1i105.74 (8)C6—C7—C8121.01 (14)
N1—C1—H1a109.4709C3—C8—C7120.52 (14)
N1—C1—H1ai109.4712C3—C8—H8119.7416
N1i—C1—H1a109.4713C7—C8—H8119.7416
N1i—C1—H1ai109.4709N1—C9—C9i101.45 (10)
H1a—C1—H1ai112.9619N1—C9—C10117.56 (12)
N1—C2—C3112.19 (11)N1—C9—H9110.2149
N1—C2—H2a109.4717C9i—C9—C10110.98 (12)
N1—C2—H2b109.4705C9i—C9—H9116.8873
C3—C2—H2a109.4714C10—C9—H9100.538
C3—C2—H2b109.4717C9—C10—C11107.90 (14)
H2a—C2—H2b106.6084C9—C10—H10a109.4715
C2—C3—C4120.58 (13)C9—C10—H10b109.4705
C2—C3—C8120.48 (13)C11—C10—H10a109.4721
C4—C3—C8118.88 (14)C11—C10—H10b109.4708
O1—C4—C3121.52 (14)H10a—C10—H10b110.9991
O1—C4—C5118.68 (13)C10—C11—C11i112.71 (13)
C3—C4—C5119.80 (14)C10—C11—H11a109.4707
C4—C5—C6120.75 (14)C10—C11—H11b109.4709
C4—C5—H5119.6278C11i—C11—H11a109.472
C6—C5—H5119.6266C11i—C11—H11b109.4712
C5—C6—C7119.01 (15)H11a—C11—H11b106.0299
?—?—?—??

Symmetry codes: (i) −x+1, −y+1, z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C1—H1a···O1ii0.952.563.3398 (11)137.58
O1—H1o···N10.91 (2)1.83 (2)2.6515 (13)149.3 (18)

Symmetry codes: (ii) x−1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5333).

References

  • Brandenburg, K. & Putz, H. (2005). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst.36, 1103.
  • Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887–897.
  • Elias, H., Stock, F. & Röhr, C. (1997). Acta Cryst. C53, 862–864.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Mitra, A., Harvey, M. J., Proffitt, M. K., DePue, L. J., Parkin, S. & Atwood, D. A. (2006). J. Organomet. Chem.69, 523–528.
  • Oxford Diffraction (2009). CrysAlis PRO, CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.
  • Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006 Institute of Physics, Praha, Czech Republic.
  • Rivera, A., Quiroga, D., Rios-Motta, J., Carda, J. & Peris, G. (2009). J. Chem. Crystallogr.39, 827–830.
  • Rivera, A., Quiroga, D., Ríos-Motta, J., Dušek, M. & Fejfarová, K. (2010). Acta Cryst. E66, o931. [PMC free article] [PubMed]
  • Shanks, G. D. & Edstein, M. D. (2005). Drugs, 65, 2091–2110. [PubMed]

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