organic compounds
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
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 The 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). For uses of di-Mannich bases, see: Mitra et al. (2006).
Experimental
Crystal data
|
Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED; 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.
Supporting information
10.1107/S1600536811006489/ng5118sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811006489/ng5118Isup2.hkl
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.
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
The isotropic atomic displacement parameters of hydrogen atoms were evaluated as 1.2*Ueq of the parent atom.Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell
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).C21H24Br2N2O2 | F(000) = 500 |
Mr = 496.2 | Dx = 1.646 Mg m−3 |
Orthorhombic, P21212 | Cu Kα radiation, λ = 1.54184 Å |
Hall symbol: P 2 2ab | Cell parameters from 16248 reflections |
a = 5.9645 (2) Å | θ = 4.8–66.5° |
b = 18.5497 (4) Å | µ = 5.32 mm−1 |
c = 9.0494 (2) Å | T = 120 K |
V = 1001.22 (5) Å3 | Prism, colorless |
Z = 2 | 0.19 × 0.13 × 0.10 mm |
Oxford Diffraction Xcalibur diffractometer with an Atlas detector | 1749 independent reflections |
Radiation source: X-ray tube | 1739 reflections with I > 3σ(I) |
Mirror monochromator | Rint = 0.022 |
Detector resolution: 10.3784 pixels mm-1 | θmax = 66.8°, θmin = 4.8° |
Rotation method data acquisition using ω scans | h = −7→6 |
Absorption correction: analytical (CrysAlis PRO; Oxford Diffraction, 2009) | k = −10→10 |
Tmin = 0.454, Tmax = 0.678 | l = −21→21 |
17493 measured reflections |
Refinement on F2 | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.015 | Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2] |
wR(F2) = 0.049 | (Δ/σ)max = 0.001 |
S = 1.21 | Δρmax = 0.11 e Å−3 |
1749 reflections | Δρmin = −0.12 e Å−3 |
126 parameters | Absolute structure: Flack (1983), 670 Friedel pairs |
1 restraint | Absolute structure parameter: 0.008 (20) |
45 constraints |
C21H24Br2N2O2 | V = 1001.22 (5) Å3 |
Mr = 496.2 | Z = 2 |
Orthorhombic, P21212 | Cu Kα radiation |
a = 5.9645 (2) Å | µ = 5.32 mm−1 |
b = 18.5497 (4) Å | T = 120 K |
c = 9.0494 (2) Å | 0.19 × 0.13 × 0.10 mm |
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 = 0.678 | Rint = 0.022 |
17493 measured reflections |
R[F2 > 2σ(F2)] = 0.015 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.049 | Δρmax = 0.11 e Å−3 |
S = 1.21 | Δρmin = −0.12 e Å−3 |
1749 reflections | Absolute structure: Flack (1983), 670 Friedel pairs |
126 parameters | Absolute structure parameter: 0.008 (20) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | ||
Br1 | 0.55638 (3) | 0.229059 (8) | 0.146172 (18) | 0.02610 (7) | |
O1 | 0.99958 (19) | 0.42005 (6) | 0.59844 (13) | 0.0226 (3) | |
N1 | 0.59652 (10) | 0.44416 (5) | 0.71146 (11) | 0.0163 (4) | |
C1 | 0.5 | 0.5 | 0.61175 (12) | 0.0154 (6) | |
C2 | 0.5511 (3) | 0.36959 (8) | 0.66196 (17) | 0.0165 (4) | |
C3 | 0.6757 (3) | 0.35153 (7) | 0.52184 (17) | 0.0156 (4) | |
C4 | 0.8947 (3) | 0.37777 (8) | 0.49815 (18) | 0.0174 (4) | |
C5 | 1.0085 (3) | 0.35992 (9) | 0.36866 (19) | 0.0204 (4) | |
C6 | 0.9120 (3) | 0.31499 (8) | 0.26478 (18) | 0.0205 (5) | |
C7 | 0.6975 (3) | 0.28860 (8) | 0.29074 (18) | 0.0180 (4) | |
C8 | 0.5810 (2) | 0.30615 (8) | 0.41680 (17) | 0.0160 (4) | |
C9 | 0.5029 (3) | 0.45921 (8) | 0.85825 (17) | 0.0179 (4) | |
C10 | 0.6319 (3) | 0.43125 (9) | 0.99165 (18) | 0.0268 (5) | |
C11 | 0.5129 (4) | 0.45880 (10) | 1.13117 (19) | 0.0322 (6) | |
H1a | 0.382527 | 0.479008 | 0.553376 | 0.0185* | |
H2a | 0.39302 | 0.363598 | 0.646178 | 0.0198* | |
H2b | 0.593539 | 0.336399 | 0.738387 | 0.0198* | |
H5 | 1.155662 | 0.379087 | 0.351434 | 0.0245* | |
H6 | 0.991627 | 0.302257 | 0.176355 | 0.0245* | |
H8 | 0.433442 | 0.286947 | 0.43234 | 0.0192* | |
H9 | 0.362416 | 0.434666 | 0.870296 | 0.0214* | |
H10a | 0.782412 | 0.449589 | 0.989185 | 0.0322* | |
H10b | 0.63082 | 0.3795 | 0.991145 | 0.0322* | |
H11a | 0.5957 | 0.444143 | 1.217041 | 0.0386* | |
H11b | 0.367722 | 0.43676 | 1.138666 | 0.0386* | |
H1o | 0.904 (3) | 0.4361 (12) | 0.657 (2) | 0.0272* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.03375 (13) | 0.02617 (12) | 0.01839 (12) | −0.00261 (7) | −0.00326 (7) | −0.00361 (7) |
O1 | 0.0184 (6) | 0.0183 (5) | 0.0312 (7) | −0.0015 (4) | −0.0002 (5) | −0.0041 (5) |
N1 | 0.0203 (7) | 0.0104 (6) | 0.0182 (7) | 0.0013 (5) | 0.0010 (5) | −0.0010 (5) |
C1 | 0.0145 (10) | 0.0119 (9) | 0.0197 (10) | 0.0006 (7) | 0 | 0 |
C2 | 0.0189 (7) | 0.0107 (7) | 0.0199 (7) | −0.0017 (5) | 0.0040 (7) | −0.0010 (6) |
C3 | 0.0185 (7) | 0.0095 (6) | 0.0188 (7) | 0.0034 (6) | 0.0013 (6) | 0.0036 (6) |
C4 | 0.0176 (7) | 0.0110 (7) | 0.0236 (8) | 0.0019 (5) | −0.0012 (6) | 0.0012 (6) |
C5 | 0.0174 (7) | 0.0167 (7) | 0.0271 (8) | 0.0016 (6) | 0.0032 (6) | 0.0049 (7) |
C6 | 0.0229 (9) | 0.0184 (7) | 0.0201 (8) | 0.0063 (6) | 0.0029 (6) | 0.0046 (6) |
C7 | 0.0243 (8) | 0.0134 (6) | 0.0165 (8) | 0.0034 (6) | −0.0013 (6) | 0.0005 (6) |
C8 | 0.0143 (7) | 0.0119 (7) | 0.0220 (8) | 0.0018 (5) | −0.0021 (6) | 0.0023 (6) |
C9 | 0.0215 (8) | 0.0153 (8) | 0.0169 (7) | 0.0023 (5) | 0.0009 (6) | 0.0022 (6) |
C10 | 0.0437 (10) | 0.0176 (7) | 0.0191 (8) | 0.0094 (6) | −0.0006 (8) | 0.0008 (7) |
C11 | 0.0521 (12) | 0.0251 (10) | 0.0193 (8) | 0.0110 (8) | 0.0014 (9) | 0.0042 (7) |
Br1—C7 | 1.9080 (16) | C5—H5 | 0.96 |
O1—C4 | 1.353 (2) | C6—C7 | 1.390 (2) |
O1—H1o | 0.84 (2) | C6—H6 | 0.96 |
N1—C1 | 1.4895 (12) | C7—C8 | 1.375 (2) |
N1—C2 | 1.4789 (18) | C8—H8 | 0.96 |
N1—C9 | 1.4677 (18) | C9—C9i | 1.514 (2) |
C1—H1a | 0.96 | C9—C10 | 1.523 (2) |
C1—H1ai | 0.96 | C9—H9 | 0.96 |
C2—C3 | 1.507 (2) | C10—C11 | 1.536 (3) |
C2—H2a | 0.96 | C10—H10a | 0.96 |
C2—H2b | 0.96 | C10—H10b | 0.96 |
C3—C4 | 1.410 (2) | C11—C11i | 1.536 (3) |
C3—C8 | 1.390 (2) | C11—H11a | 0.96 |
C4—C5 | 1.394 (2) | C11—H11b | 0.96 |
C5—C6 | 1.382 (2) | ||
C4—O1—H1o | 108.6 (14) | C5—C6—H6 | 120.6356 |
C1—N1—C2 | 113.34 (9) | C7—C6—H6 | 120.636 |
C1—N1—C9 | 105.60 (9) | Br1—C7—C6 | 119.62 (12) |
C2—N1—C9 | 112.48 (10) | Br1—C7—C8 | 118.88 (12) |
N1—C1—N1i | 105.43 (9) | C6—C7—C8 | 121.48 (15) |
N1—C1—H1a | 109.4713 | C3—C8—C7 | 120.37 (14) |
N1—C1—H1ai | 109.4712 | C3—C8—H8 | 119.8142 |
N1i—C1—H1a | 109.4712 | C7—C8—H8 | 119.8142 |
N1i—C1—H1ai | 109.4713 | N1—C9—C9i | 101.48 (12) |
H1a—C1—H1ai | 113.2317 | N1—C9—C10 | 117.42 (13) |
N1—C2—C3 | 111.86 (12) | N1—C9—H9 | 110.1556 |
N1—C2—H2a | 109.4713 | C9i—C9—C10 | 110.62 (13) |
N1—C2—H2b | 109.4715 | C9i—C9—H9 | 117.0073 |
C3—C2—H2a | 109.471 | C10—C9—H9 | 100.9265 |
C3—C2—H2b | 109.4709 | C9—C10—C11 | 107.74 (15) |
H2a—C2—H2b | 106.9725 | C9—C10—H10a | 109.471 |
C2—C3—C4 | 120.52 (13) | C9—C10—H10b | 109.4714 |
C2—C3—C8 | 120.64 (14) | C11—C10—H10a | 109.4709 |
C4—C3—C8 | 118.78 (14) | C11—C10—H10b | 109.4716 |
O1—C4—C3 | 121.76 (14) | H10a—C10—H10b | 111.1472 |
O1—C4—C5 | 118.47 (13) | C10—C11—C11i | 112.17 (15) |
C3—C4—C5 | 119.78 (14) | C10—C11—H11a | 109.4713 |
C4—C5—C6 | 120.83 (14) | C10—C11—H11b | 109.4711 |
C4—C5—H5 | 119.5819 | C11i—C11—H11a | 109.4712 |
C6—C5—H5 | 119.5833 | C11i—C11—H11b | 109.4713 |
C5—C6—C7 | 118.73 (15) | H11a—C11—H11b | 106.632 |
C2—N1—C1—N1i | 138.00 (9) | O1—C4—C5—C6 | 177.87 (15) |
C9—N1—C1—N1i | 14.44 (9) | C3—C4—C5—C6 | −1.9 (2) |
C1—N1—C2—C3 | 68.53 (14) | C4—C5—C6—C7 | 0.9 (2) |
C9—N1—C2—C3 | −171.77 (12) | C5—C6—C7—Br1 | 177.93 (12) |
C1—N1—C9—C10 | −157.29 (11) | C5—C6—C7—C8 | −0.1 (2) |
C1—N1—C9—C9i | −36.62 (13) | Br1—C7—C8—C3 | −177.66 (11) |
C2—N1—C9—C10 | 78.61 (16) | C6—C7—C8—C3 | 0.4 (2) |
C2—N1—C9—C9i | −160.72 (12) | N1—C9—C10—C11 | 175.39 (13) |
N1—C2—C3—C4 | 37.37 (19) | C9i—C9—C10—C11 | 59.64 (18) |
N1—C2—C3—C8 | −145.54 (13) | N1—C9—C9i—N1i | 45.12 (14) |
C2—C3—C4—O1 | −0.5 (2) | N1—C9—C9i—C10i | 170.46 (12) |
C2—C3—C4—C5 | 179.31 (14) | C10—C9—C9i—N1i | 170.46 (12) |
C8—C3—C4—O1 | −177.62 (14) | C10—C9—C9i—C10i | −64.21 (18) |
C8—C3—C4—C5 | 2.2 (2) | C9—C10—C11—C11i | −55.1 (2) |
C2—C3—C8—C7 | −178.55 (14) | C10—C11—C11i—C10i | 54.8 (2) |
C4—C3—C8—C7 | −1.4 (2) |
Symmetry code: (i) −x+1, −y+1, z. |
Cg2 is the centroid of the C3–C8 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1o···N1 | 0.833 (19) | 1.905 (18) | 2.6506 (13) | 148.3 (19) |
C1—H1a···O1ii | 0.96 | 2.57 | 3.3351 (11) | 137 |
C8—H8···Cg2iii | 0.96 | 2.85 | 3.5407 (16) | 130 |
C11—H11b···Cg2iv | 0.96 | 2.86 | 3.728 (2) | 150 |
Symmetry codes: (ii) x−1, y, z; (iii) x−1/2, −y+3/2, −z; (iv) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C21H24Br2N2O2 |
Mr | 496.2 |
Crystal system, space group | Orthorhombic, P21212 |
Temperature (K) | 120 |
a, b, c (Å) | 5.9645 (2), 18.5497 (4), 9.0494 (2) |
V (Å3) | 1001.22 (5) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 5.32 |
Crystal size (mm) | 0.19 × 0.13 × 0.10 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur diffractometer with an Atlas detector |
Absorption correction | Analytical (CrysAlis PRO; Oxford Diffraction, 2009) |
Tmin, Tmax | 0.454, 0.678 |
No. of measured, independent and observed [I > 3σ(I)] reflections | 17493, 1749, 1739 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.596 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.015, 0.049, 1.21 |
No. of reflections | 1749 |
No. of parameters | 126 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.11, −0.12 |
Absolute structure | Flack (1983), 670 Friedel pairs |
Absolute structure parameter | 0.008 (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).
Cg2 is the centroid of the C3–C8 ring. |
D—H···A | D—H | H···A | D···A | 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—H11b···Cg2iii | 0.96 | 2.86 | 3.728 (2) | 150 |
Symmetry codes: (i) x−1, y, z; (ii) x−1/2, −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
Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103. CrossRef IUCr Journals Google Scholar
Flack, H. D. (1983). Acta Cryst. A39, 876–881. CrossRef CAS Web of Science IUCr Journals Google Scholar
Mitra, A., Harvey, M. J., Proffitt, M. K., DePue, L. J., Parkin, S. & Atwood, D. A. (2006). J. Organomet. Chem. 69, 523–528. Web of Science CSD CrossRef Google Scholar
Oxford Diffraction (2009). CrysAlis CCD, CrysAlis RED and CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England. Google Scholar
Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006. Institute of Physics, Praha, Czech Republic. Google Scholar
Rivera, A., Quiroga, D., Ríos-Motta, J., Dušek, M. & Fejfarová, K. (2010). Acta Cryst. E66, o2643. Web of Science CSD CrossRef IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).