Literature DB >> 21580741

2,2'-[(3aRS,7aRS)-Perhydro-benz-imid-azole-1,3-di-yl)bis-(methyl-ene)]diphenol.

Augusto Rivera, Diego Quiroga, Jaime Ríos-Motta, Michal Dušek, Karla Fejfarová.   

Abstract

The molecular structure of the title compound, C(21)H(26)N(2)O(2), shows two intra-molecular O-H⋯N hydrogen-bonding inter-actions. In the crystal structure, mol-ecular chains are formed along the c axis through weak C-H⋯O inter-actions. Neighbouring chains are weakly associated along the a axis via C-H⋯π inter-actions.

Entities:  

Year:  2010        PMID: 21580741      PMCID: PMC2983906          DOI: 10.1107/S1600536810009918

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

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

Experimental

Crystal data

C21H26N2O2 M = 338.5 Triclinic, 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 ▶) 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 ▶); cell refinement: 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. 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
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
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 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
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.
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*
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)
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
?—?—?—??
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
Table 1

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the C3–C8 and C16–C21 rings, respectively.

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1O⋯N10.85 (2)1.97 (2)2.7096 (14)146 (2)
O2—H2O⋯N20.86 (2)1.91 (2)2.6894 (14)150 (2)
C10—H10a⋯O1i0.962.643.5666 (17)163
C13—H13a⋯O2ii0.962.633.5458 (17)160
C10—H10bCg1iii0.962.943.5885 (13)126
C12—H12bCg2iv0.962.933.7022 (16)139

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

  6 in total

1.  4,4'-Dichloro-2,2'-[(3aR,7aR/3aS,7aS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-1,3-benzimidazole-1,3-di-yl)bis-(methyl-ene)]diphenol.

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Michal Dušek; Karla Fejfarová
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-09-30

2.  4,4'-Difluoro-2,2'-{[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-1,3-benzimidazole-1,3-di-yl]bis-(methyl-ene)]}diphenol.

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Michal Dušek; Karla Fejfarová
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-05-28

3.  4,4'-Di-tert-butyl-2,2'-[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-1,3-benzimidazole-1,3-di-yl)bis-(methyl-ene)]diphenol.

Authors:  Augusto Rivera; Dency José Pacheco; Jaime Ríos-Motta; Michaela Pojarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-10-12

4.  4,4'-Dimeth-oxy-2,2'-{[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-1,3-benzimidazole-1,3-diyl]bis(methyl-ene)}diphenol.

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Karla Fejfarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-08-11

5.  Diethyl 4,4'-dihy-droxy-3,3'-{[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-1,3-benzimidazole-1,3-di-yl]bis-(methyl-ene)}dibenzoate.

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Karla Fejfarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-10-05

6.  Di-n-propyl 4,4'-dihy-droxy-3,3'-{[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-benzimidazole-1,3-di-yl]bis-(methyl-ene)}dibenzoate.

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Karla Fejfarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-09-14
  6 in total

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