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

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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

aDepartamento de Química, Universidad Nacional de Colombia, Bogotá, AA 14490, Colombia, and bInstitute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
*Correspondence e-mail: ariverau@unal.edu.co

(Received 20 August 2010; accepted 22 September 2010; online 30 September 2010)

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[Rivera, A., Quiroga, D., Rios-Motta, J., Carda, J. & Peris, G. (2009). J. Chem. Crystallogr. 39, 827-830.], 2010[Rivera, A., Quiroga, D., Ríos-Motta, J., Dušek, M. & Fejfarová, K. (2010). Acta Cryst. E66, o931.]). For uses of di-Mannich bases, see: Mitra et al. (2006[Mitra, A., Harvey, M. J., Proffitt, M. K., DePue, L. J., Parkin, S. & Atwood, D. A. (2006). J. Organomet. Chem. 69, 523-528.]); Elias et al. (1997[Elias, H., Stock, F. & Röhr, C. (1997). Acta Cryst. C53, 862-864.]). For the anti­malarial activity of di-Mannich bases, see: Shanks & Edstein (2005[Shanks, G. D. & Edstein, M. D. (2005). Drugs, 65, 2091-2110.]).

[Scheme 1]

Experimental

Crystal data
  • C21H24Cl2N2O2

  • Mr = 407.3

  • Orthorhombic, P 21 21 2

  • 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[Oxford Diffraction (2009). CrysAlis PRO, CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]), based on expressions derived by Clark & Reid (1995[Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897.])] Tmin = 0.518, Tmax = 0.773

  • 12720 measured reflections

  • 1566 independent reflections

  • 1517 reflections with I > 3σ(I)

  • Rint = 0.027

Refinement
  • R[F2 > 2σ(F2)] = 0.022

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 615 Friedel pairs

  • Flack parameter: 0.32 (1)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C1—H1a⋯O1i 0.95 2.56 3.3398 (11) 137.58
O1—H1o⋯N1 0.91 (2) 1.83 (2) 2.6515 (13) 149.3 (18)
Symmetry code: (i) x-1, y, z.

Data collection: CrysAlis CCD (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO, CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO, CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); data reduction: CrysAlis RED; program(s) used to solve structure: SIR2002 (Burla et al., 2003[Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103.]); program(s) used to refine structure: JANA2006 (Petříček et al., 2006[Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006. Institute of Physics, Praha, Czech Republic.]); molecular graphics: DIAMOND (Brandenburg & Putz, 2005[Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: JANA2006.

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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 top

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.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SIR2002 (Burla et al., 2003); 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. Molecule of the title compound with atom-labeling scheme. Displacement elipsoids are drawn at 50% probability level.
[Figure 2] Fig. 2. Hydrogen bonding of the molecules of the title compound in a direction.
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 top
Crystal data top
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 top
Oxford Diffraction Xcalibur
diffractometer with an Atlas (Gemini ultra Cu) detector
1566 independent reflections
Radiation source: X-ray tube1517 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.027
Detector resolution: 10.3784 pixels mm-1θmax = 62.5°, θmin = 4.8°
Rotation method data acquisition using ω scansh = 66
Absorption correction: analytical
[CrysAlis PRO (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)]
k = 2120
Tmin = 0.518, Tmax = 0.773l = 1010
12720 measured reflections
Refinement top
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 restraintsAbsolute structure parameter: 0.32 (1)
45 constraints
Crystal data top
C21H24Cl2N2O2V = 981.74 (5) Å3
Mr = 407.3Z = 2
Orthorhombic, P21212Cu Kα radiation
a = 5.9529 (2) ŵ = 3.11 mm1
b = 18.3846 (5) ÅT = 120 K
c = 8.9704 (3) Å0.36 × 0.21 × 0.12 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer with an Atlas (Gemini ultra Cu) detector
1566 independent reflections
Absorption correction: analytical
[CrysAlis PRO (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)]
1517 reflections with I > 3σ(I)
Tmin = 0.518, Tmax = 0.773Rint = 0.027
12720 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.022H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.068Δρmax = 0.11 e Å3
S = 1.50Δρmin = 0.11 e Å3
1566 reflectionsAbsolute structure: Flack (1983), 615 Friedel pairs
127 parametersAbsolute structure parameter: 0.32 (1)
0 restraints
Special details top

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 Measurements

The 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) top
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*
H11a0.3683810.4361820.1366090.0464*
H11b0.5971310.4439240.2136540.0464*
H1o0.893 (3)0.4356 (10)0.347 (2)0.0334*
Atomic displacement parameters (Å2) top
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, º) top
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 code: (i) x+1, y+1, z.
Hydrogen-bond geometry (Å, º) top
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 code: (ii) x1, y, z.

Experimental details

Crystal data
Chemical formulaC21H24Cl2N2O2
Mr407.3
Crystal system, space groupOrthorhombic, P21212
Temperature (K)120
a, b, c (Å)5.9529 (2), 18.3846 (5), 8.9704 (3)
V3)981.74 (5)
Z2
Radiation typeCu Kα
µ (mm1)3.11
Crystal size (mm)0.36 × 0.21 × 0.12
Data collection
DiffractometerOxford Diffraction Xcalibur
diffractometer with an Atlas (Gemini ultra Cu) detector
Absorption correctionAnalytical
[CrysAlis PRO (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)]
Tmin, Tmax0.518, 0.773
No. of measured, independent and
observed [I > 3σ(I)] reflections
12720, 1566, 1517
Rint0.027
(sin θ/λ)max1)0.575
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.022, 0.068, 1.50
No. of reflections1566
No. of parameters127
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.11, 0.11
Absolute structureFlack (1983), 615 Friedel pairs
Absolute structure parameter0.32 (1)

Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SIR2002 (Burla et al., 2003), JANA2006 (Petříček et al., 2006), DIAMOND (Brandenburg & Putz, 2005).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1a···O1i0.952.563.3398 (11)137.58
O1—H1o···N10.91 (2)1.83 (2)2.6515 (13)149.3 (18)
Symmetry code: (i) x1, y, z.
 

Acknowledgements

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).

References

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First citationRivera, A., Quiroga, D., Ríos-Motta, J., Dušek, M. & Fejfarová, K. (2010). Acta Cryst. E66, o931.  Web of Science CrossRef IUCr Journals Google Scholar
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