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Acta Crystallogr Sect E Struct Rep Online. 2010 April 1; 66(Pt 4): o931.
Published online 2010 March 27. doi:  10.1107/S1600536810009918
PMCID: PMC2983906

2,2′-[(3aRS,7aRS)-Perhydro­benz­imid­azole-1,3-di­yl)bis­(methyl­ene)]diphenol

Abstract

The molecular structure of the title compound, C21H26N2O2, shows two intra­molecular O—H(...)N hydrogen-bonding inter­actions. In the crystal structure, mol­ecular chains are formed along the c axis through weak C—H(...)O inter­actions. Neighbouring chains are weakly associated along the a axis via C—H(...)π inter­actions.

Related literature

For a related structure, see: Rivera et al. (2009 [triangle]). For uses of di-Mannich bases, see Mitra et al. (2006 [triangle]); Elias et al. (1997 [triangle]).

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Object name is e-66-0o931-scheme1.jpg

Experimental

Crystal data

  • C21H26N2O2
  • M r = 338.5
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o931-efi1.jpg
  • a = 5.5177 (1) Å
  • b = 12.0432 (4) Å
  • c = 14.3752 (4) Å
  • α = 69.705 (3)°
  • β = 89.341 (2)°
  • γ = 81.751 (2)°
  • V = 885.92 (5) Å3
  • Z = 2
  • Cu Kα radiation
  • μ = 0.65 mm−1
  • T = 120 K
  • 0.24 × 0.21 × 0.19 mm

Data collection

  • Oxford Diffraction Xcalibur, diffractometer with an Atlas (Gemini ultra Cu) detector
  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009 [triangle]) T min = 0.774, T max = 1.000
  • 11989 measured reflections
  • 3023 independent reflections
  • 2685 reflections with I > 3σ(I)
  • R int = 0.018

Refinement

  • R[F 2 > 2σ(F 2)] = 0.038
  • wR(F 2) = 0.118
  • S = 2.41
  • 3023 reflections
  • 232 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.19 e Å−3

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/S1600536810009918/tk2643sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810009918/tk2643Isup2.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, as well as the Institutional research plan No. AVOZ10100521 of the Institute of Physics and the Praemium Academiae project of the Academy of Sciences (ASCR).

supplementary crystallographic information

Comment

Mannich bases are versatile synthetic intermediates and are used as model systems for the study of intramolecular hydrogen bonding and proton transfer (Mitra et al. 2006; Elias et al. 1997). The presence of these interactions is undoubtedly one of the essential factors contributing to their highly thermodynamic stability. Recently, we used (2R,7R,11S,16S)-1,8,10,17-tetraazapentacyclo[8.8.1.18,17. 02,7.011,16]icosane as precursor for a di-Mannich base (Rivera et al. 2009). The X-ray analysis showed the N lone pairs to be anti-axial and both N atoms to be sufficiently basic to form intramolecular hydrogen bonds. In continuation of our research program on the structure, properties, and reactivity of aminal cages (pre-formed Mannich reagents), we report here the synthesis and crystal structure of the title compound, (I).

Compound (I) features intramolecular hydrogen bonds O—H···N, Fig. 1. The bond lengths are normal and comparable to the corresponding values observed in the related structure of 2,2'-(3aR,7aR/3aS,7aS)-hexahydro-1H-benzo[d]imidazole-1,3(2H)-diyl)-bis(methylene)-bis(4-methyl-phenol) (Rivera et al. 2009).

The crystal packing (Fig 2) displays weak intermolecular C–H···O interactions (Table 1) that link pairs of enantiomers alternately to form a racemic chain along the c axis. Chains are linked along the a direction by C–H···π interactions (Table 1).

Experimental

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 into a dioxane solution (3 ml) containing two equivalents of phenol (188 mg, 2.00 mmol) in a two-necked round-bottomed flask. The mixture was refluxed for about 12 h. The solvent was evaporated under reduced pressure until a sticky residue appeared. The product was purified by chromatography on a silica column, and subjected to gradient elution with benzene:ethyl acetate (yield 21%, M.pt. = 413–414 K). Single crystals of racemic (I) were grown from a CHCl3 solution by slow evaporation of the solvent at room temperature over a period of about 2 weeks.

Refinement

The C-bound H atoms were geometrically placed (C-H = 0.96 Å) and refined as riding with Uiso(H) = 1.2Ueq(C). The positions of the hydroxyl-H atoms were refined with Uiso(H) = 1.2Ueq(O).

Figures

Fig. 1.
The molecular structure of (I), showing the atomic numbering scheme with atomic displacement ellipsoids drawn at the 50% probability level. The dashed lines indicates intramolecular O–H···N hydrogen bonds.
Fig. 2.
Packing diagram for (I) with intermolecular interactions drawn as dashed lines.

Crystal data

C21H26N2O2Z = 2
Mr = 338.5F(000) = 364
Triclinic, P1Dx = 1.268 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.54184 Å
a = 5.5177 (1) ÅCell parameters from 9142 reflections
b = 12.0432 (4) Åθ = 3.3–65.4°
c = 14.3752 (4) ŵ = 0.65 mm1
α = 69.705 (3)°T = 120 K
β = 89.341 (2)°Prism, colorless
γ = 81.751 (2)°0.24 × 0.21 × 0.19 mm
V = 885.92 (5) Å3

Data collection

Oxford Diffraction Xcalibur, diffractometer with an Atlas (Gemini ultra Cu) detector3023 independent reflections
Radiation source: X-ray tube2685 reflections with I > 3σ(I)
mirrorRint = 0.018
Detector resolution: 10.3784 pixels mm-1θmax = 65.8°, θmin = 3.3°
Rotation method data acquisition using ω scansh = −6→6
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)k = −13→13
Tmin = 0.774, Tmax = 1.000l = −16→16
11989 measured reflections

Refinement

Refinement on F298 constraints
R[F2 > 2σ(F2)] = 0.038H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.118Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
S = 2.41(Δ/σ)max = 0.006
3023 reflectionsΔρmax = 0.25 e Å3
232 parametersΔρmin = −0.19 e Å3
0 restraints

Special details

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
O10.55804 (17)0.14020 (9)0.44644 (7)0.0291 (4)
O20.83868 (17)0.18264 (9)−0.03369 (7)0.0305 (4)
N10.79361 (18)0.08554 (9)0.29799 (7)0.0202 (4)
N20.62975 (19)0.10318 (10)0.14258 (7)0.0213 (4)
C10.6914 (2)0.17421 (12)0.20218 (9)0.0226 (5)
C20.9951 (2)0.12344 (12)0.33988 (9)0.0226 (5)
C30.9035 (2)0.23158 (11)0.36752 (9)0.0216 (4)
C40.6882 (2)0.23380 (12)0.42039 (9)0.0227 (4)
C50.6072 (2)0.33136 (12)0.44923 (9)0.0261 (5)
C60.7390 (2)0.42599 (13)0.42654 (10)0.0289 (5)
C70.9518 (2)0.42527 (13)0.37409 (10)0.0289 (5)
C81.0308 (2)0.32828 (12)0.34497 (10)0.0254 (5)
C90.8513 (2)−0.02791 (11)0.27990 (9)0.0210 (4)
C100.8803 (2)−0.14204 (12)0.36961 (9)0.0265 (5)
C110.9041 (3)−0.24770 (13)0.33239 (10)0.0295 (5)
C120.6923 (3)−0.23872 (12)0.26116 (10)0.0295 (5)
C130.6592 (2)−0.11997 (12)0.17294 (10)0.0259 (5)
C140.6331 (2)−0.01887 (11)0.21374 (9)0.0207 (4)
C150.4060 (2)0.15656 (12)0.07972 (9)0.0231 (5)
C160.4414 (2)0.27197 (12)−0.00170 (9)0.0220 (4)
C170.6553 (2)0.27821 (12)−0.05575 (9)0.0242 (5)
C180.6825 (3)0.38203 (13)−0.13478 (10)0.0297 (5)
C190.4978 (3)0.47854 (13)−0.16005 (10)0.0322 (5)
C200.2872 (3)0.47453 (13)−0.10655 (10)0.0321 (5)
C210.2613 (2)0.37168 (13)−0.02762 (10)0.0273 (5)
H1a0.5446920.220780.2130550.0271*
H1b0.8140390.2218180.1699480.0271*
H2a1.1195240.1424330.2920450.0271*
H2b1.0664630.0590260.3977760.0271*
H50.4594270.3329360.4849530.0313*
H60.6831260.4927260.4471910.0347*
H71.0429870.4911740.3582170.0346*
H81.1772550.3280040.3082880.0304*
H91.010365−0.0354870.2530160.0252*
H10a0.737945−0.1428070.4087350.0318*
H10b1.025945−0.1472120.4076890.0318*
H11a0.912941−0.3211130.3880140.0353*
H11b1.056388−0.2525890.3000310.0353*
H12a0.543303−0.2466190.2964770.0354*
H12b0.720963−0.3042890.2370450.0354*
H13a0.800881−0.1162920.1331910.031*
H13b0.513586−0.1139080.1345040.031*
H140.478413−0.0288840.2444250.0249*
H15a0.2739690.1720230.1196980.0277*
H15b0.3617550.101080.0507630.0277*
H180.8294520.386296−0.1714790.0356*
H190.5153680.549372−0.2154240.0386*
H200.1602160.542534−0.1240220.0386*
H210.1158370.3692730.0099090.0328*
H1o0.604 (3)0.0973 (15)0.4118 (12)0.0349*
H2o0.810 (3)0.1344 (15)0.0240 (13)0.0366*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0304 (5)0.0306 (6)0.0309 (6)−0.0103 (4)0.0112 (4)−0.0146 (4)
O20.0248 (5)0.0374 (6)0.0250 (5)−0.0010 (4)0.0063 (4)−0.0072 (4)
N10.0204 (5)0.0221 (6)0.0178 (5)−0.0029 (4)−0.0004 (4)−0.0065 (4)
N20.0215 (6)0.0241 (6)0.0173 (5)−0.0028 (4)−0.0008 (4)−0.0061 (4)
C10.0236 (7)0.0238 (7)0.0200 (7)−0.0034 (5)0.0002 (5)−0.0069 (5)
C20.0198 (6)0.0279 (7)0.0216 (7)−0.0042 (5)0.0002 (5)−0.0101 (5)
C30.0204 (6)0.0270 (7)0.0161 (6)−0.0012 (5)−0.0029 (5)−0.0067 (5)
C40.0230 (6)0.0269 (7)0.0177 (6)−0.0045 (5)−0.0006 (5)−0.0068 (5)
C50.0239 (7)0.0317 (8)0.0231 (7)−0.0014 (5)0.0020 (5)−0.0112 (6)
C60.0321 (7)0.0271 (8)0.0282 (7)0.0006 (6)−0.0014 (6)−0.0124 (6)
C70.0305 (7)0.0278 (7)0.0294 (7)−0.0085 (6)−0.0003 (6)−0.0098 (6)
C80.0215 (7)0.0304 (8)0.0239 (7)−0.0042 (5)0.0012 (5)−0.0089 (6)
C90.0195 (6)0.0251 (7)0.0198 (6)−0.0033 (5)0.0027 (5)−0.0097 (5)
C100.0292 (7)0.0266 (7)0.0214 (7)−0.0021 (6)−0.0025 (5)−0.0061 (6)
C110.0333 (8)0.0239 (7)0.0285 (7)−0.0024 (6)−0.0004 (6)−0.0066 (6)
C120.0320 (8)0.0258 (8)0.0321 (7)−0.0041 (6)0.0000 (6)−0.0118 (6)
C130.0254 (7)0.0292 (7)0.0245 (7)−0.0025 (5)−0.0020 (5)−0.0119 (6)
C140.0193 (6)0.0239 (7)0.0188 (6)−0.0034 (5)0.0033 (5)−0.0071 (5)
C150.0197 (6)0.0295 (7)0.0186 (6)−0.0031 (5)0.0003 (5)−0.0068 (5)
C160.0225 (6)0.0276 (7)0.0160 (6)−0.0050 (5)−0.0022 (5)−0.0073 (5)
C170.0226 (7)0.0315 (8)0.0197 (6)−0.0043 (5)−0.0012 (5)−0.0103 (6)
C180.0279 (7)0.0399 (8)0.0220 (7)−0.0132 (6)0.0034 (5)−0.0086 (6)
C190.0403 (8)0.0296 (8)0.0245 (7)−0.0136 (6)−0.0028 (6)−0.0034 (6)
C200.0354 (8)0.0282 (8)0.0297 (8)−0.0025 (6)−0.0045 (6)−0.0069 (6)
C210.0245 (7)0.0331 (8)0.0241 (7)−0.0029 (6)0.0008 (5)−0.0104 (6)

Geometric parameters (Å, °)

O1—C41.3640 (17)C9—H90.96
O1—H1o0.85 (2)C10—C111.531 (2)
O2—C171.3672 (15)C10—H10a0.96
O2—H2o0.860 (16)C10—H10b0.96
N1—C11.4766 (14)C11—C121.530 (2)
N1—C21.4691 (19)C11—H11a0.96
N1—C91.4682 (19)C11—H11b0.96
N2—C11.476 (2)C12—C131.5360 (17)
N2—C141.4686 (15)C12—H12a0.96
N2—C151.4657 (15)C12—H12b0.96
C1—H1a0.96C13—C141.513 (2)
C1—H1b0.96C13—H13a0.96
C2—C31.508 (2)C13—H13b0.96
C2—H2a0.96C14—H140.96
C2—H2b0.96C15—C161.5112 (17)
C3—C41.4045 (18)C15—H15a0.96
C3—C81.387 (2)C15—H15b0.96
C4—C51.391 (2)C16—C171.4021 (18)
C5—C61.382 (2)C16—C211.3873 (18)
C5—H50.96C17—C181.3932 (17)
C6—C71.388 (2)C18—C191.3774 (19)
C6—H60.96C18—H180.96
C7—C81.385 (2)C19—C201.383 (2)
C7—H70.96C19—H190.96
C8—H80.96C20—C211.3836 (18)
C9—C101.5132 (16)C20—H200.96
C9—C141.5110 (18)C21—H210.96
C4—O1—H1o108.2 (12)H10a—C10—H10b111.0115
C17—O2—H2o106.1 (11)C10—C11—C12112.84 (11)
C1—N1—C2113.14 (10)C10—C11—H11a109.4701
C1—N1—C9105.19 (10)C10—C11—H11b109.4716
C2—N1—C9116.16 (9)C12—C11—H11a109.4715
C1—N2—C14105.33 (9)C12—C11—H11b109.4714
C1—N2—C15113.32 (10)H11a—C11—H11b105.8786
C14—N2—C15116.36 (10)C11—C12—C13112.18 (12)
N1—C1—N2105.37 (10)C11—C12—H12a109.4714
N1—C1—H1a109.4708C11—C12—H12b109.4713
N1—C1—H1b109.4714C13—C12—H12a109.4711
N2—C1—H1a109.4714C13—C12—H12b109.4709
N2—C1—H1b109.4717H12a—C12—H12b106.6143
H1a—C1—H1b113.2791C12—C13—C14108.00 (11)
N1—C2—C3110.68 (10)C12—C13—H13a109.4714
N1—C2—H2a109.4709C12—C13—H13b109.4718
N1—C2—H2b109.4709C14—C13—H13a109.4704
C3—C2—H2a109.4716C14—C13—H13b109.4706
C3—C2—H2b109.4715H13a—C13—H13b110.8996
H2a—C2—H2b108.2321N2—C14—C9100.17 (10)
C2—C3—C4119.73 (12)N2—C14—C13117.53 (10)
C2—C3—C8121.68 (11)N2—C14—H14111.415
C4—C3—C8118.55 (13)C9—C14—C13111.83 (10)
O1—C4—C3121.18 (13)C9—C14—H14117.1568
O1—C4—C5118.71 (12)C13—C14—H1499.6523
C3—C4—C5120.10 (13)N2—C15—C16111.17 (11)
C4—C5—C6120.11 (13)N2—C15—H15a109.4717
C4—C5—H5119.9469N2—C15—H15b109.4711
C6—C5—H5119.9479C16—C15—H15a109.4714
C5—C6—C7120.49 (15)C16—C15—H15b109.4709
C5—C6—H6119.7554H15a—C15—H15b107.7171
C7—C6—H6119.7553C15—C16—C17119.99 (11)
C6—C7—C8119.18 (14)C15—C16—C21121.39 (11)
C6—C7—H7120.41C17—C16—C21118.57 (11)
C8—C7—H7120.4116O2—C17—C16121.12 (10)
C3—C8—C7121.58 (12)O2—C17—C18118.62 (11)
C3—C8—H8119.211C16—C17—C18120.25 (11)
C7—C8—H8119.2111C17—C18—C19119.75 (12)
N1—C9—C10117.23 (11)C17—C18—H18120.1267
N1—C9—C14100.32 (9)C19—C18—H18120.1261
N1—C9—H9111.4609C18—C19—C20120.74 (12)
C10—C9—C14111.72 (11)C18—C19—H19119.6301
C10—C9—H999.994C20—C19—H19119.6303
C14—C9—H9116.9901C19—C20—C21119.43 (12)
C9—C10—C11107.89 (11)C19—C20—H20120.2825
C9—C10—H10a109.4713C21—C20—H20120.2833
C9—C10—H10b109.4707C16—C21—C20121.24 (13)
C11—C10—H10a109.4714C16—C21—H21119.3796
C11—C10—H10b109.4712C20—C21—H21119.3801
?—?—?—??

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the C3–C8 and C16–C21 rings, respectively.
D—H···AD—HH···AD···AD—H···A
O1—H1O···N10.847 (18)1.967 (17)2.7096 (14)145.8 (16)
O2—H2O···N20.860 (18)1.913 (17)2.6894 (14)149.5 (17)
C10—H10a···O1i0.962.643.5666 (17)163
C13—H13a···O2ii0.962.633.5458 (17)160
C10—H10b···Cg1iii0.962.943.5885 (13)126
C12—H12b···Cg2iv0.962.933.7022 (16)139

Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+2, −y, −z; (iii) −x+2, −y, −z+1; (iv) −x+1, −y+1, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2643).

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.
  • Elias, H., Stock, F. & Röhr, C. (1997). Acta Cryst. C53, 862–864.
  • 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 CCD, CrysAlis RED and CrysAlis PRO Oxford Diffraction Ltd, Yarnton, England.
  • Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006 Institute of Physics, Prague, Czech Republic.
  • Rivera, A., Quiroga, D., Rios-Motta, J., Carda, J. & Peris, G. (2009). J. Chem. Crystallogr.39, 827–830.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography