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4,4′-Di­bromo-2,2′-{[(3aS,7aS)-2,3,3a,4,5,6,7,7a-octa­hydro-1H-1,3-benzimidazole-1,3-di­yl]bis­­(methyl­­idene)}diphenol

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

(Received 9 February 2011; accepted 21 February 2011; online 2 March 2011)

The cyclo­hexane ring in the title compound, C21H24Br2N2O2, adopts a chair conformation and the five-membered ring to which it is fused has a twisted envelope conformation. The asymmetric unit contains one half-mol­ecule, which is related to the other half by a twofold rotation axis. The two N atoms of the five-membered ring are linked to the hy­droxy groups by intra­molecular O—H⋯N hydrogen bonds. In the crystal, inter­molecular C—H⋯O and C—H⋯π inter­actions occur.

Related literature

For a related structure, see: Rivera et al. (2010[Rivera, A., Quiroga, D., Ríos-Motta, J., Dušek, M. & Fejfarová, K. (2010). Acta Cryst. E66, o2643.]). 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.]).

[Scheme 1]

Experimental

Crystal data
  • C21H24Br2N2O2

  • Mr = 496.2

  • Orthorhombic, P 21 21 2

  • a = 5.9645 (2) Å

  • b = 18.5497 (4) Å

  • c = 9.0494 (2) Å

  • V = 1001.22 (5) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 5.32 mm−1

  • T = 120 K

  • 0.19 × 0.13 × 0.10 mm

Data collection
  • Oxford Diffraction Xcalibur diffractometer with an Atlas detector

  • Absorption correction: analytical (CrysAlis PRO; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD, CrysAlis RED and CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]) Tmin = 0.454, Tmax = 0.678

  • 17493 measured reflections

  • 1749 independent reflections

  • 1739 reflections with I > 3σ(I)

  • Rint = 0.022

Refinement
  • R[F2 > 2σ(F2)] = 0.015

  • wR(F2) = 0.049

  • S = 1.21

  • 1749 reflections

  • 126 parameters

  • 1 restraint

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

  • Δρmax = 0.11 e Å−3

  • Δρmin = −0.12 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 670 Friedel pairs

  • Flack parameter: 0.008 (20)

Table 1
Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C3–C8 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1o⋯N1 0.833 (19) 1.905 (18) 2.6506 (13) 148.3 (19)
C1—H1a⋯O1i 0.96 2.57 3.3351 (11) 137
C8—H8⋯Cg2ii 0.96 2.85 3.5407 (16) 130
C11—H11bCg2iii 0.96 2.86 3.728 (2) 150
Symmetry codes: (i) x-1, y, z; (ii) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z]; (iii) x, y+1, z.

Data collection: CrysAlis CCD (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD, CrysAlis RED and CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD, CrysAlis RED and CrysAlis PRO. 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

The title compound was obtained by reaction of racemic cyclic aminal (2R,7R,11S,16S)-1,8,10,17-tetraazapentacyclo[8.8.1.18,17.02,7.011,16]icosane with p-bromophenol. The molecular structure and atom-numbering scheme for (I) are shown in Fig. 1. Selected angles and bond lengths are listed in Table 1. Its X-ray structure confirms the presence of intramolecular hydrogen bonds between the phenolic hydroxyl groups and nitrogen atoms [N—H, 1.903 (18) Å] that is however by 0.13 Å longer in comparison with related structure (Rivera et al., 2010), whereas the N···O distance [2.6506 (14) Å] is in good agreement with the one found in related structure [2.652 (2) Å]. Similar to this related structure, the observed C—O bond length [1.353 (2) Å] is considerably shortened in relation to other Mannich bases.

In the title compound, C21H24Br2N2O2, 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. The orthorhombic unit cell contains two molecules. Instead, the molecules have identical (S,S)-molecular configuration and its absolute structure was determined with a Flack parameter of 0.01 (2) (Flack, 1983).

Related literature top

For a related structure, see: Rivera et al. (2010). For uses of di-Mannich bases, see: Mitra et al. (2006).

Experimental top

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.

Preparation of 4,4'-Dibromo-2,2'-(3aS,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3- benzimidazole-1,3-diyl)bis(methylene)]diphenol) (I)

A solution of (2R,7R,11S,16S)-1,8,10,17-tetraazapentacyclo[8.8.1.18,17.02,7.011,16]icosane (3) (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-bromophenol (346 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 47%, m.p. = 497–499 K). Next, the crude product (100 mg, 0.202 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 35%). 1H NMR (CDCl3, 400 MHz): δ 1.27 (4H, m), 1.85 (2H, m), 2.05 (2H, m), 2.33 (2H, m), 3.41 (2H, d, J = 14.0 Hz, ArCH2N), 3.51 (2H, s, NCH2N), 4.14 (2H, d, J = 14.0 Hz, ArCH2N), 6.69 (2H, d, J = 8.8 Hz), 7.06 (2H, s), 7.24 (2H, d, J = 8.8 Hz). 13C NMR (CDCl3, 100 MHz): δ 23.9, 28.9, 55.8, 69.1, 75.7, 111.1, 118.1, 123.4, 130.6, 131.8, 156.6.

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 isotropic atomic displacement parameters of hydrogen atoms were evaluated as 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. Ellipsoid plot of the title compound. Displacement ellipsoids are drawn at 50% probability level. [Symmetry codes: (i) 1-x, 1-y, z.]
[Figure 2] Fig. 2. Hydrogen bonding of the molecules of the title compound viewed along c.
4,4'-Dibromo-2,2'-{[(3aS,7aS)-2,3,3a,4,5,6,7,7a-octahydro- 1H-1,3-benzimidazole-1,3-diyl]bis(methylidene)}diphenol top
Crystal data top
C21H24Br2N2O2F(000) = 500
Mr = 496.2Dx = 1.646 Mg m3
Orthorhombic, P21212Cu Kα radiation, λ = 1.54184 Å
Hall symbol: P 2 2abCell parameters from 16248 reflections
a = 5.9645 (2) Åθ = 4.8–66.5°
b = 18.5497 (4) ŵ = 5.32 mm1
c = 9.0494 (2) ÅT = 120 K
V = 1001.22 (5) Å3Prism, colorless
Z = 20.19 × 0.13 × 0.10 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer with an Atlas detector
1749 independent reflections
Radiation source: X-ray tube1739 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.022
Detector resolution: 10.3784 pixels mm-1θmax = 66.8°, θmin = 4.8°
Rotation method data acquisition using ω scansh = 76
Absorption correction: analytical
(CrysAlis PRO; Oxford Diffraction, 2009)
k = 1010
Tmin = 0.454, Tmax = 0.678l = 2121
17493 measured reflections
Refinement top
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.015Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
wR(F2) = 0.049(Δ/σ)max = 0.001
S = 1.21Δρmax = 0.11 e Å3
1749 reflectionsΔρmin = 0.12 e Å3
126 parametersAbsolute structure: Flack (1983), 670 Friedel pairs
1 restraintAbsolute structure parameter: 0.008 (20)
45 constraints
Crystal data top
C21H24Br2N2O2V = 1001.22 (5) Å3
Mr = 496.2Z = 2
Orthorhombic, P21212Cu Kα radiation
a = 5.9645 (2) ŵ = 5.32 mm1
b = 18.5497 (4) ÅT = 120 K
c = 9.0494 (2) Å0.19 × 0.13 × 0.10 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer with an Atlas detector
1749 independent reflections
Absorption correction: analytical
(CrysAlis PRO; Oxford Diffraction, 2009)
1739 reflections with I > 3σ(I)
Tmin = 0.454, Tmax = 0.678Rint = 0.022
17493 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.015H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.049Δρmax = 0.11 e Å3
S = 1.21Δρmin = 0.12 e Å3
1749 reflectionsAbsolute structure: Flack (1983), 670 Friedel pairs
126 parametersAbsolute structure parameter: 0.008 (20)
1 restraint
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
Br10.55638 (3)0.229059 (8)0.146172 (18)0.02610 (7)
O10.99958 (19)0.42005 (6)0.59844 (13)0.0226 (3)
N10.59652 (10)0.44416 (5)0.71146 (11)0.0163 (4)
C10.50.50.61175 (12)0.0154 (6)
C20.5511 (3)0.36959 (8)0.66196 (17)0.0165 (4)
C30.6757 (3)0.35153 (7)0.52184 (17)0.0156 (4)
C40.8947 (3)0.37777 (8)0.49815 (18)0.0174 (4)
C51.0085 (3)0.35992 (9)0.36866 (19)0.0204 (4)
C60.9120 (3)0.31499 (8)0.26478 (18)0.0205 (5)
C70.6975 (3)0.28860 (8)0.29074 (18)0.0180 (4)
C80.5810 (2)0.30615 (8)0.41680 (17)0.0160 (4)
C90.5029 (3)0.45921 (8)0.85825 (17)0.0179 (4)
C100.6319 (3)0.43125 (9)0.99165 (18)0.0268 (5)
C110.5129 (4)0.45880 (10)1.13117 (19)0.0322 (6)
H1a0.3825270.4790080.5533760.0185*
H2a0.393020.3635980.6461780.0198*
H2b0.5935390.3363990.7383870.0198*
H51.1556620.3790870.3514340.0245*
H60.9916270.3022570.1763550.0245*
H80.4334420.2869470.432340.0192*
H90.3624160.4346660.8702960.0214*
H10a0.7824120.4495890.9891850.0322*
H10b0.630820.37950.9911450.0322*
H11a0.59570.4441431.2170410.0386*
H11b0.3677220.436761.1386660.0386*
H1o0.904 (3)0.4361 (12)0.657 (2)0.0272*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.03375 (13)0.02617 (12)0.01839 (12)0.00261 (7)0.00326 (7)0.00361 (7)
O10.0184 (6)0.0183 (5)0.0312 (7)0.0015 (4)0.0002 (5)0.0041 (5)
N10.0203 (7)0.0104 (6)0.0182 (7)0.0013 (5)0.0010 (5)0.0010 (5)
C10.0145 (10)0.0119 (9)0.0197 (10)0.0006 (7)00
C20.0189 (7)0.0107 (7)0.0199 (7)0.0017 (5)0.0040 (7)0.0010 (6)
C30.0185 (7)0.0095 (6)0.0188 (7)0.0034 (6)0.0013 (6)0.0036 (6)
C40.0176 (7)0.0110 (7)0.0236 (8)0.0019 (5)0.0012 (6)0.0012 (6)
C50.0174 (7)0.0167 (7)0.0271 (8)0.0016 (6)0.0032 (6)0.0049 (7)
C60.0229 (9)0.0184 (7)0.0201 (8)0.0063 (6)0.0029 (6)0.0046 (6)
C70.0243 (8)0.0134 (6)0.0165 (8)0.0034 (6)0.0013 (6)0.0005 (6)
C80.0143 (7)0.0119 (7)0.0220 (8)0.0018 (5)0.0021 (6)0.0023 (6)
C90.0215 (8)0.0153 (8)0.0169 (7)0.0023 (5)0.0009 (6)0.0022 (6)
C100.0437 (10)0.0176 (7)0.0191 (8)0.0094 (6)0.0006 (8)0.0008 (7)
C110.0521 (12)0.0251 (10)0.0193 (8)0.0110 (8)0.0014 (9)0.0042 (7)
Geometric parameters (Å, º) top
Br1—C71.9080 (16)C5—H50.96
O1—C41.353 (2)C6—C71.390 (2)
O1—H1o0.84 (2)C6—H60.96
N1—C11.4895 (12)C7—C81.375 (2)
N1—C21.4789 (18)C8—H80.96
N1—C91.4677 (18)C9—C9i1.514 (2)
C1—H1a0.96C9—C101.523 (2)
C1—H1ai0.96C9—H90.96
C2—C31.507 (2)C10—C111.536 (3)
C2—H2a0.96C10—H10a0.96
C2—H2b0.96C10—H10b0.96
C3—C41.410 (2)C11—C11i1.536 (3)
C3—C81.390 (2)C11—H11a0.96
C4—C51.394 (2)C11—H11b0.96
C5—C61.382 (2)
C4—O1—H1o108.6 (14)C5—C6—H6120.6356
C1—N1—C2113.34 (9)C7—C6—H6120.636
C1—N1—C9105.60 (9)Br1—C7—C6119.62 (12)
C2—N1—C9112.48 (10)Br1—C7—C8118.88 (12)
N1—C1—N1i105.43 (9)C6—C7—C8121.48 (15)
N1—C1—H1a109.4713C3—C8—C7120.37 (14)
N1—C1—H1ai109.4712C3—C8—H8119.8142
N1i—C1—H1a109.4712C7—C8—H8119.8142
N1i—C1—H1ai109.4713N1—C9—C9i101.48 (12)
H1a—C1—H1ai113.2317N1—C9—C10117.42 (13)
N1—C2—C3111.86 (12)N1—C9—H9110.1556
N1—C2—H2a109.4713C9i—C9—C10110.62 (13)
N1—C2—H2b109.4715C9i—C9—H9117.0073
C3—C2—H2a109.471C10—C9—H9100.9265
C3—C2—H2b109.4709C9—C10—C11107.74 (15)
H2a—C2—H2b106.9725C9—C10—H10a109.471
C2—C3—C4120.52 (13)C9—C10—H10b109.4714
C2—C3—C8120.64 (14)C11—C10—H10a109.4709
C4—C3—C8118.78 (14)C11—C10—H10b109.4716
O1—C4—C3121.76 (14)H10a—C10—H10b111.1472
O1—C4—C5118.47 (13)C10—C11—C11i112.17 (15)
C3—C4—C5119.78 (14)C10—C11—H11a109.4713
C4—C5—C6120.83 (14)C10—C11—H11b109.4711
C4—C5—H5119.5819C11i—C11—H11a109.4712
C6—C5—H5119.5833C11i—C11—H11b109.4713
C5—C6—C7118.73 (15)H11a—C11—H11b106.632
C2—N1—C1—N1i138.00 (9)O1—C4—C5—C6177.87 (15)
C9—N1—C1—N1i14.44 (9)C3—C4—C5—C61.9 (2)
C1—N1—C2—C368.53 (14)C4—C5—C6—C70.9 (2)
C9—N1—C2—C3171.77 (12)C5—C6—C7—Br1177.93 (12)
C1—N1—C9—C10157.29 (11)C5—C6—C7—C80.1 (2)
C1—N1—C9—C9i36.62 (13)Br1—C7—C8—C3177.66 (11)
C2—N1—C9—C1078.61 (16)C6—C7—C8—C30.4 (2)
C2—N1—C9—C9i160.72 (12)N1—C9—C10—C11175.39 (13)
N1—C2—C3—C437.37 (19)C9i—C9—C10—C1159.64 (18)
N1—C2—C3—C8145.54 (13)N1—C9—C9i—N1i45.12 (14)
C2—C3—C4—O10.5 (2)N1—C9—C9i—C10i170.46 (12)
C2—C3—C4—C5179.31 (14)C10—C9—C9i—N1i170.46 (12)
C8—C3—C4—O1177.62 (14)C10—C9—C9i—C10i64.21 (18)
C8—C3—C4—C52.2 (2)C9—C10—C11—C11i55.1 (2)
C2—C3—C8—C7178.55 (14)C10—C11—C11i—C10i54.8 (2)
C4—C3—C8—C71.4 (2)
Symmetry code: (i) x+1, y+1, z.
Hydrogen-bond geometry (Å, º) top
Cg2 is the centroid of the C3–C8 ring.
D—H···AD—HH···AD···AD—H···A
O1—H1o···N10.833 (19)1.905 (18)2.6506 (13)148.3 (19)
C1—H1a···O1ii0.962.573.3351 (11)137
C8—H8···Cg2iii0.962.853.5407 (16)130
C11—H11b···Cg2iv0.962.863.728 (2)150
Symmetry codes: (ii) x1, y, z; (iii) x1/2, y+3/2, z; (iv) x, y+1, z.

Experimental details

Crystal data
Chemical formulaC21H24Br2N2O2
Mr496.2
Crystal system, space groupOrthorhombic, P21212
Temperature (K)120
a, b, c (Å)5.9645 (2), 18.5497 (4), 9.0494 (2)
V3)1001.22 (5)
Z2
Radiation typeCu Kα
µ (mm1)5.32
Crystal size (mm)0.19 × 0.13 × 0.10
Data collection
DiffractometerOxford Diffraction Xcalibur
diffractometer with an Atlas detector
Absorption correctionAnalytical
(CrysAlis PRO; Oxford Diffraction, 2009)
Tmin, Tmax0.454, 0.678
No. of measured, independent and
observed [I > 3σ(I)] reflections
17493, 1749, 1739
Rint0.022
(sin θ/λ)max1)0.596
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.015, 0.049, 1.21
No. of reflections1749
No. of parameters126
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.11, 0.12
Absolute structureFlack (1983), 670 Friedel pairs
Absolute structure parameter0.008 (20)

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
Cg2 is the centroid of the C3–C8 ring.
D—H···AD—HH···AD···AD—H···A
O1—H1o···N10.833 (19)1.905 (18)2.6506 (13)148.3 (19)
C1—H1a···O1i0.962.573.3351 (11)137
C8—H8···Cg2ii0.962.853.5407 (16)130
C11—H11b···Cg2iii0.962.863.728 (2)150
Symmetry codes: (i) x1, y, z; (ii) x1/2, y+3/2, z; (iii) x, y+1, z.
 

Acknowledgements

We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de La Universidad Nacional de Colombia, for financial support of this work, as well as the Institutional Research Plan No. AVOZ10100521 of the Institute of Physics 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

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First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
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First citationRivera, A., Quiroga, D., Ríos-Motta, J., Dušek, M. & Fejfarová, K. (2010). Acta Cryst. E66, o2643.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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