Literature DB >> 21754901

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.

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

Abstract

In the crystal structure of the title compound, C(21)H(24)F(2)N(2)O(2), the two N atoms of the imidazolidine moiety are linked to the hy-droxy groups by intra-molecular O-H⋯N hydrogen-bonding inter-actions. The crystal studied was a racemic mixture of RR and SS enatiomers. The cyclo-hexane ring adopts a chair conformation and the imidazolidine group to which it is fused has a twisted envelope conformation.

Entities:  

Year:  2011        PMID: 21754901      PMCID: PMC3120376          DOI: 10.1107/S1600536811019763

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


Related literature

For related structures, see: Rivera et al. (2010a ▶,b ▶, 2011 ▶). For uses of di-Mannich bases, see: Mitra et al. (2006 ▶); Elias et al. (1997 ▶). For related quantum-chemical literature, see: Zierkiewicz & Michalska (2003 ▶); Zierkiewicz et al. (2004 ▶).

Experimental

Crystal data

C21H24F2N2O2 M = 374.4 Triclinic, a = 5.4605 (1) Å b = 12.4661 (3) Å c = 14.3363 (4) Å α = 108.053 (3)° β = 91.319 (2)° γ = 97.437 (2)° V = 917.98 (4) Å3 Z = 2 Cu Kα radiation μ = 0.84 mm−1 T = 150 K 0.36 × 0.23 × 0.09 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 = 0.516, T max = 1 15846 measured reflections 3248 independent reflections 2819 reflections with I > 3σ(I) R int = 0.024

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.110 S = 1.95 3248 reflections 250 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.25 e Å−3 Δρmin = −0.23 e Å−3 Data collection: CrysAlis PRO (Oxford Diffraction, 2009 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; 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/S1600536811019763/kj2178sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811019763/kj2178Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811019763/kj2178Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C21H24F2N2O2Z = 2
Mr = 374.4F(000) = 396
Triclinic, P1Dx = 1.354 Mg m3
Hall symbol: -P 1Melting point: 445 K
a = 5.4605 (1) ÅCu Kα radiation, λ = 1.5418 Å
b = 12.4661 (3) ÅCell parameters from 8506 reflections
c = 14.3363 (4) Åθ = 3.3–67°
α = 108.053 (3)°µ = 0.84 mm1
β = 91.319 (2)°T = 150 K
γ = 97.437 (2)°Prism, colourless
V = 917.98 (4) Å30.36 × 0.23 × 0.09 mm
Oxford Diffraction Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector3248 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source2819 reflections with I > 3σ(I)
mirrorRint = 0.024
Detector resolution: 10.3784 pixels mm-1θmax = 67.1°, θmin = 3.3°
Rotation method data acquisition using ω scansh = −6→6
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)k = −14→14
Tmin = 0.516, Tmax = 1l = −17→17
15846 measured reflections
Refinement on F290 constraints
R[F2 > 2σ(F2)] = 0.036H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.110Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
S = 1.95(Δ/σ)max = 0.006
3248 reflectionsΔρmax = 0.25 e Å3
250 parametersΔρmin = −0.23 e Å3
0 restraints
Experimental. CrysAlisPro, Oxford Diffraction (2009), Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.
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
F10.8539 (2)0.55112 (8)0.62051 (7)0.0546 (4)
F2−0.07887 (18)0.52089 (7)0.14954 (7)0.0466 (4)
O10.16405 (19)0.16846 (9)0.53377 (8)0.0378 (4)
O20.43069 (19)0.15534 (9)0.05535 (8)0.0355 (4)
N10.3641 (2)0.10643 (9)0.35698 (7)0.0241 (4)
N20.1999 (2)0.09975 (9)0.20184 (7)0.0239 (4)
C10.3018 (2)0.17945 (11)0.29872 (9)0.0268 (4)
C20.3651 (2)−0.00695 (11)0.28492 (9)0.0240 (4)
C30.1458 (2)−0.01205 (11)0.21678 (9)0.0239 (4)
C40.1213 (3)−0.11590 (11)0.12581 (10)0.0311 (5)
C50.0996 (3)−0.22171 (12)0.15961 (11)0.0358 (5)
C60.3115 (3)−0.21688 (12)0.23326 (11)0.0367 (5)
C70.3397 (3)−0.10836 (12)0.32279 (10)0.0312 (5)
C80.5907 (2)0.15502 (11)0.42136 (9)0.0270 (4)
C90.5514 (2)0.26236 (12)0.50104 (9)0.0267 (4)
C100.3397 (3)0.26295 (12)0.55485 (10)0.0298 (5)
C110.3077 (3)0.35923 (13)0.63185 (10)0.0375 (5)
C120.4816 (3)0.45585 (13)0.65482 (11)0.0404 (5)
C130.6831 (3)0.45507 (13)0.59942 (11)0.0374 (5)
C140.7225 (3)0.36067 (12)0.52322 (10)0.0316 (5)
C15−0.0045 (2)0.13892 (11)0.15950 (9)0.0262 (4)
C160.0880 (2)0.24381 (11)0.13227 (9)0.0244 (4)
C170.3020 (3)0.24648 (12)0.08027 (9)0.0279 (4)
C180.3842 (3)0.34067 (13)0.05171 (10)0.0343 (5)
C190.2565 (3)0.43379 (13)0.07452 (11)0.0363 (5)
C200.0492 (3)0.43006 (12)0.12624 (10)0.0327 (5)
C21−0.0371 (3)0.33780 (11)0.15580 (9)0.0282 (5)
H1a0.4497290.2253990.2904120.0321*
H1b0.1770630.2234660.3296590.0321*
H20.522627−0.0135460.2569340.0288*
H3−0.014925−0.0226580.2410890.0287*
H4a0.266114−0.1127760.0895030.0374*
H4b−0.02548−0.1185460.0865070.0374*
H5a0.095707−0.2885870.1034920.0429*
H5b−0.055536−0.2301870.188560.0429*
H6a0.463729−0.2212710.2009740.0441*
H6b0.284387−0.2827120.2549880.0441*
H7a0.194886−0.1084550.3594830.0375*
H7b0.486083−0.1048890.3626470.0375*
H8a0.7232140.1723230.3831130.0324*
H8b0.6358850.1002960.4508020.0324*
H110.1641570.3585310.6691880.0449*
H120.4619370.5222640.7085180.0484*
H140.866150.3629950.4861290.0379*
H15a−0.1279040.1561610.2064350.0315*
H15b−0.0786380.0795310.1019190.0315*
H180.5304230.3415570.0158940.0411*
H190.3118420.499160.0545860.0435*
H21−0.1824070.3384810.1923160.0338*
H1o0.188 (4)0.1244 (17)0.4743 (16)0.0566*
H2o0.388 (4)0.1166 (17)0.0919 (14)0.0533*
U11U22U33U12U13U23
F10.0699 (7)0.0323 (5)0.0487 (5)−0.0063 (5)−0.0012 (5)0.0002 (4)
F20.0580 (6)0.0287 (5)0.0574 (6)0.0137 (4)0.0065 (4)0.0169 (4)
O10.0320 (6)0.0477 (6)0.0311 (5)0.0010 (5)0.0061 (4)0.0104 (5)
O20.0357 (6)0.0400 (6)0.0377 (6)0.0126 (5)0.0115 (4)0.0187 (5)
N10.0253 (6)0.0246 (6)0.0216 (5)0.0030 (4)−0.0016 (4)0.0067 (4)
N20.0263 (6)0.0227 (5)0.0227 (5)0.0023 (4)−0.0016 (4)0.0079 (4)
C10.0307 (7)0.0248 (6)0.0243 (6)0.0026 (5)−0.0018 (5)0.0077 (5)
C20.0243 (7)0.0240 (7)0.0236 (6)0.0034 (5)0.0025 (5)0.0072 (5)
C30.0237 (7)0.0244 (6)0.0244 (6)0.0018 (5)0.0020 (5)0.0095 (5)
C40.0357 (8)0.0267 (7)0.0279 (7)0.0034 (6)−0.0030 (6)0.0051 (5)
C50.0387 (8)0.0245 (7)0.0404 (8)0.0016 (6)−0.0034 (6)0.0065 (6)
C60.0394 (8)0.0248 (7)0.0470 (9)0.0048 (6)−0.0028 (7)0.0130 (6)
C70.0327 (8)0.0297 (7)0.0344 (7)0.0031 (6)−0.0031 (6)0.0155 (6)
C80.0249 (7)0.0313 (7)0.0230 (6)0.0037 (6)−0.0011 (5)0.0063 (5)
C90.0278 (7)0.0305 (7)0.0212 (6)0.0063 (5)−0.0023 (5)0.0068 (5)
C100.0287 (7)0.0364 (8)0.0255 (6)0.0070 (6)−0.0009 (5)0.0106 (6)
C110.0373 (8)0.0492 (9)0.0266 (7)0.0171 (7)0.0046 (6)0.0085 (6)
C120.0507 (10)0.0369 (8)0.0306 (7)0.0187 (7)−0.0013 (7)0.0018 (6)
C130.0448 (9)0.0291 (7)0.0339 (7)0.0023 (6)−0.0048 (6)0.0056 (6)
C140.0330 (8)0.0332 (7)0.0266 (7)0.0040 (6)−0.0007 (6)0.0072 (6)
C150.0246 (7)0.0282 (7)0.0273 (6)0.0030 (5)−0.0013 (5)0.0114 (5)
C160.0258 (7)0.0272 (7)0.0197 (6)0.0011 (5)−0.0041 (5)0.0080 (5)
C170.0295 (7)0.0315 (7)0.0234 (6)0.0042 (6)−0.0005 (5)0.0099 (5)
C180.0308 (8)0.0423 (8)0.0331 (7)0.0003 (6)0.0026 (6)0.0189 (6)
C190.0409 (9)0.0331 (8)0.0377 (8)−0.0027 (6)−0.0031 (6)0.0188 (6)
C200.0391 (8)0.0259 (7)0.0329 (7)0.0053 (6)−0.0039 (6)0.0094 (6)
C210.0299 (7)0.0294 (7)0.0252 (6)0.0040 (6)−0.0005 (5)0.0088 (5)
F1—C131.3668 (17)C6—H6b0.96
F2—C201.3654 (18)C7—H7a0.96
O1—C101.3682 (17)C7—H7b0.96
O1—H1o0.88 (2)C8—C91.5100 (17)
O2—C171.3706 (18)C8—H8a0.96
O2—H2o0.83 (2)C8—H8b0.96
N1—C11.477 (2)C9—C101.4041 (19)
N1—C21.4704 (15)C9—C141.3873 (19)
N1—C81.4686 (16)C10—C111.3897 (18)
N2—C11.4805 (14)C11—C121.380 (2)
N2—C31.4686 (18)C11—H110.96
N2—C151.4652 (19)C12—C131.371 (2)
C1—H1a0.96C12—H120.96
C1—H1b0.96C13—C141.3799 (18)
C2—C31.5100 (19)C14—H140.96
C2—C71.515 (2)C15—C161.507 (2)
C2—H20.96C15—H15a0.96
C3—C41.5151 (16)C15—H15b0.96
C3—H30.96C16—C171.4032 (19)
C4—C51.532 (2)C16—C211.388 (2)
C4—H4a0.96C17—C181.385 (2)
C4—H4b0.96C18—C191.388 (2)
C5—C61.531 (2)C18—H180.96
C5—H5a0.96C19—C201.371 (2)
C5—H5b0.96C19—H190.96
C6—C71.5369 (17)C20—C211.377 (2)
C6—H6a0.96C21—H210.96
C10—O1—H1o106.9 (13)H7a—C7—H7b111.1929
C17—O2—H2o106.8 (14)N1—C8—C9110.50 (11)
C1—N1—C2105.24 (9)N1—C8—H8a109.471
C1—N1—C8112.56 (10)N1—C8—H8b109.471
C2—N1—C8116.09 (11)C9—C8—H8a109.4713
C1—N2—C3105.27 (10)C9—C8—H8b109.4715
C1—N2—C15113.08 (10)H8a—C8—H8b108.4269
C3—N2—C15116.39 (10)C8—C9—C10119.74 (11)
N1—C1—N2105.37 (10)C8—C9—C14121.22 (12)
N1—C1—H1a109.4709C10—C9—C14119.04 (11)
N1—C1—H1b109.4714O1—C10—C9120.76 (11)
N2—C1—H1a109.4715O1—C10—C11118.91 (13)
N2—C1—H1b109.4707C9—C10—C11120.31 (12)
H1a—C1—H1b113.2798C10—C11—C12120.24 (14)
N1—C2—C3100.30 (10)C10—C11—H11119.8818
N1—C2—C7117.55 (11)C12—C11—H11119.8816
N1—C2—H2111.2215C11—C12—C13118.67 (13)
C3—C2—C7111.58 (10)C11—C12—H12120.6647
C3—C2—H2117.2277C13—C12—H12120.6649
C7—C2—H299.8589F1—C13—C12119.05 (12)
N2—C3—C2100.48 (9)F1—C13—C14118.23 (14)
N2—C3—C4116.86 (11)C12—C13—C14122.72 (14)
N2—C3—H3111.6886C9—C14—C13118.97 (13)
C2—C3—C4112.03 (11)C9—C14—H14120.5126
C2—C3—H3116.5452C13—C14—H14120.5134
C4—C3—H3100.0584N2—C15—C16110.43 (10)
C3—C4—C5107.76 (12)N2—C15—H15a109.4707
C3—C4—H4a109.4714N2—C15—H15b109.4709
C3—C4—H4b109.4705C16—C15—H15a109.4714
C5—C4—H4a109.4712C16—C15—H15b109.4718
C5—C4—H4b109.4712H15a—C15—H15b108.497
H4a—C4—H4b111.1273C15—C16—C17119.77 (12)
C4—C5—C6112.74 (11)C15—C16—C21121.39 (12)
C4—C5—H5a109.4709C17—C16—C21118.82 (13)
C4—C5—H5b109.4714O2—C17—C16120.69 (13)
C6—C5—H5a109.4711O2—C17—C18118.90 (13)
C6—C5—H5b109.4715C16—C17—C18120.40 (14)
H5a—C5—H5b105.995C17—C18—C19120.43 (14)
C5—C6—C7112.66 (13)C17—C18—H18119.7837
C5—C6—H6a109.471C19—C18—H18119.7831
C5—C6—H6b109.4713C18—C19—C20118.30 (15)
C7—C6—H6a109.4711C18—C19—H19120.8492
C7—C6—H6b109.4714C20—C19—H19120.8486
H6a—C6—H6b106.0781F2—C20—C19119.22 (14)
C2—C7—C6107.69 (12)F2—C20—C21118.08 (13)
C2—C7—H7a109.4718C19—C20—C21122.70 (14)
C2—C7—H7b109.4711C16—C21—C20119.33 (13)
C6—C7—H7a109.4711C16—C21—H21120.3339
C6—C7—H7b109.4711C20—C21—H21120.3327
?—?—?—??
D—H···AD—HH···AD···AD—H···A
O1—H1o···N10.88 (2)1.92 (2)2.7105 (15)147.6 (19)
O1—H1o···C80.88 (2)2.37 (2)2.8566 (17)115.3 (15)
O2—H2o···N20.83 (2)1.95 (2)2.6975 (16)148 (2)
O2—H2o···C150.83 (2)2.39 (2)2.8541 (17)116.0 (18)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1o⋯N10.88 (2)1.92 (2)2.7105 (15)147.6 (19)
O2—H2o⋯N20.83 (2)1.95 (2)2.6975 (16)148 (2)
  3 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.  2,2'-[(3aRS,7aRS)-Perhydro-benz-imid-azole-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:  2010-03-27

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

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Michal Dušek; Karla Fejfarová
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-03-02
  3 in total
  3 in total

1.  Di-n-butyl 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:  2011-08-11

2.  4,4'-Diiodo-2,2'-[(3aR,7aR)-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; Karla Fejfarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-08-06

3.  meso-4,4'-Difluoro-2,2'-{[(3aR,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; Monika Kučeraková; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-01-12
  3 in total

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