Literature DB >> 24046631

meso-4,4'-Dimeth-oxy-2,2'-{[(3aR,7aS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-benz-imidazole-1,3-di-yl]bis-(methyl-ene)}diphenol.

Augusto Rivera1, Diego Quiroga, Jaime Ríos-Motta, Monika Kučeraková, Michal Dušek.   

Abstract

The title compound, C23H30N2O4, a di-Mannich base derived from 4-meth-oxy-phenol and cis-1,2-di-amine-cyclo-hexane, has a perhydro-benzimidazolidine nucleus, in which the cyclo-hexane ring adopts a chair conformation and the heterocyclic ring has a half-chair conformation with a C-N-C-C torsion angles of -48.14 (15) and -14.57 (16)°. The mean plane of the heterocycle makes dihedral angles of 86.29 (6) and 78.92 (6)° with the pendant benzene rings. The mol-ecular structure of the title compound shows the presence of two inter-actions between the N atoms of the imidazolidine ring and the hydroxyl groups through intra-molecular O-H⋯N hydrogen bonds with graph-set motif S(6). The unobserved lone pairs of the N atoms are presumed to be disposed in a syn conformation, being only the second example of an exception to the typical 'rabbit-ears' effect in 1,2-di-amines.

Entities:  

Year:  2013        PMID: 24046631      PMCID: PMC3772488          DOI: 10.1107/S1600536813015092

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


Related literature

For related structures, see: Rivera et al. (2011 ▶, 2013a ▶). For the preparation of the title compound, see: Rivera et al. (2013b ▶). For standard bond lengths, see: Allen et al. (1987 ▶). For hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995 ▶). For a discussion of the ‘rabbit-ear’ effect in 1,2-di­amines, see: Hutchins et al. (1968 ▶). For background to this work, see: Van den Enden & Geise (1981 ▶); Geise et al. (1971 ▶). For the extinction correction, see: Becker & Coppens (1974 ▶).

Experimental

Crystal data

C23H30N2O4 M = 398.5 Orthorhombic, a = 6.4135 (3) Å b = 11.4099 (6) Å c = 27.8249 (14) Å V = 2036.15 (18) Å3 Z = 4 Cu Kα radiation μ = 0.72 mm−1 T = 120 K 0.21 × 0.13 × 0.13 mm

Data collection

Agilent Xcalibur (Atlas, Gemini ultra) diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ▶) T min = 0.341, T max = 1 5920 measured reflections 3491 independent reflections 3103 reflections with I > 3σ(I) R int = 0.023

Refinement

R[F 2 > 2σ(F 2)] = 0.031 wR(F 2) = 0.080 S = 1.13 3491 reflections 269 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.11 e Å−3 Δρmin = −0.09 e Å−3 Data collection: CrysAlis PRO (Agilent, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis 2007 ▶); 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 datablock(s) global, I. DOI: 10.1107/S1600536813015092/sj5324sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813015092/sj5324Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C23H30N2O4F(000) = 856
Mr = 398.5Dx = 1.300 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.5418 Å
Hall symbol: P 2ac 2abCell parameters from 3881 reflections
a = 6.4135 (3) Åθ = 4.2–67.0°
b = 11.4099 (6) ŵ = 0.72 mm1
c = 27.8249 (14) ÅT = 120 K
V = 2036.15 (18) Å3Polygon shape, white
Z = 40.21 × 0.13 × 0.13 mm
Agilent Xcalibur (Atlas, Gemini ultra) diffractometer3491 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source3103 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.023
Detector resolution: 10.3784 pixels mm-1θmax = 67.1°, θmin = 3.2°
ω scansh = −7→4
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)k = −13→12
Tmin = 0.341, Tmax = 1l = −30→32
5920 measured reflections
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.031Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0016I2)
wR(F2) = 0.080(Δ/σ)max = 0.014
S = 1.13Δρmax = 0.11 e Å3
3491 reflectionsΔρmin = −0.09 e Å3
269 parametersExtinction correction: B-C type 1 Gaussian isotropic (Becker & Coppens, 1974)
1 restraintExtinction coefficient: 1800 (300)
114 constraints
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
O10.9143 (2)0.54863 (11)0.19640 (4)0.0301 (4)
O20.5296 (2)0.11931 (11)0.22143 (5)0.0331 (4)
O31.1573 (2)0.56734 (11)0.02995 (4)0.0307 (4)
O40.75546 (19)0.25342 (11)−0.08969 (5)0.0323 (4)
N10.6253 (2)0.60135 (11)0.13114 (5)0.0214 (4)
N20.7838 (2)0.63852 (12)0.05764 (5)0.0236 (4)
C10.5156 (3)0.31779 (14)0.18880 (5)0.0235 (5)
C20.6158 (3)0.22830 (15)0.21334 (6)0.0263 (5)
C30.8117 (3)0.44415 (15)0.20127 (6)0.0239 (5)
C40.8426 (3)0.51409 (14)−0.01265 (5)0.0227 (4)
C50.7086 (3)0.74987 (14)0.07934 (6)0.0240 (5)
C61.0495 (3)0.49232 (15)0.00056 (6)0.0249 (5)
C70.8898 (3)0.80893 (16)0.10624 (6)0.0291 (5)
C80.6101 (3)0.42686 (14)0.18311 (5)0.0225 (5)
C90.7333 (3)0.62223 (15)0.00643 (6)0.0241 (5)
C101.0459 (3)0.31475 (16)−0.04591 (6)0.0299 (5)
C110.4897 (3)0.52615 (15)0.16028 (6)0.0232 (5)
C121.1484 (3)0.39175 (15)−0.01597 (6)0.0285 (5)
C130.8412 (3)0.33593 (14)−0.05968 (6)0.0253 (5)
C140.7399 (3)0.43469 (14)−0.04254 (6)0.0234 (5)
C150.3383 (3)0.09474 (15)0.19795 (7)0.0318 (5)
C160.6655 (3)0.84873 (15)0.17768 (6)0.0296 (5)
C170.6964 (3)0.54281 (14)0.08724 (6)0.0246 (5)
C180.4760 (3)0.79993 (15)0.15171 (6)0.0267 (5)
C190.8144 (3)0.24615 (15)0.23194 (6)0.0277 (5)
C200.8172 (3)0.90189 (16)0.14189 (7)0.0339 (6)
C210.5386 (3)0.26108 (18)−0.09885 (7)0.0377 (6)
C220.9116 (3)0.35333 (16)0.22549 (6)0.0273 (5)
C230.5338 (3)0.71070 (14)0.11279 (6)0.0230 (5)
H1c10.3794680.304440.175560.0282*
H1c50.659430.8067830.05660.0288*
H1c70.9697570.7504520.1228420.0349*
H2c70.9836020.8437180.0834470.0349*
H1c90.7779980.689708−0.0114080.0289*
H2c90.5852790.6132140.0027860.0289*
H1c101.116460.245973−0.0573250.0359*
H1c110.3806640.4947060.1404730.0278*
H2c110.4243730.5722150.1849080.0278*
H1c121.2894710.375787−0.0064450.0342*
H1c140.5973070.448657−0.0513370.028*
H1c150.2911750.0179190.2068970.0381*
H2c150.2359010.1517530.2072730.0381*
H3c150.3582840.0979240.1637840.0381*
H1c160.6219180.9077190.2001320.0355*
H2c160.7334330.7868930.1950690.0355*
H1c170.5790910.5087860.0709730.0295*
H2c170.8047620.4879850.0950610.0295*
H1c180.3987260.8631340.1375220.0321*
H2c180.3839470.7639890.1745770.0321*
H1c190.8837690.1845330.2491620.0333*
H1c200.9355690.9329310.1587510.0407*
H2c200.7499720.9645030.1248380.0407*
H1c210.497240.198114−0.1196560.0453*
H2c210.4634620.255624−0.0690840.0453*
H3c210.508010.334683−0.1140050.0453*
H1c221.0496750.3651990.2378740.0327*
H1c230.4005140.7015370.0975330.0276*
H1o31.050 (3)0.6060 (18)0.0456 (7)0.0369*
H1o10.834 (3)0.5936 (17)0.1758 (7)0.0361*
U11U22U33U12U13U23
O10.0312 (7)0.0281 (7)0.0309 (6)−0.0030 (6)−0.0068 (5)0.0021 (5)
O20.0438 (7)0.0216 (6)0.0340 (6)0.0000 (6)−0.0026 (6)0.0074 (5)
O30.0261 (6)0.0333 (7)0.0328 (6)−0.0028 (6)−0.0018 (5)−0.0048 (5)
O40.0330 (7)0.0310 (7)0.0330 (6)−0.0036 (6)0.0062 (5)−0.0123 (5)
N10.0260 (7)0.0180 (6)0.0202 (6)0.0011 (6)0.0004 (5)−0.0003 (5)
N20.0321 (8)0.0189 (7)0.0197 (6)0.0012 (6)−0.0010 (6)−0.0011 (5)
C10.0268 (9)0.0236 (9)0.0202 (7)0.0013 (7)0.0010 (7)0.0005 (6)
C20.0346 (10)0.0240 (9)0.0204 (7)0.0042 (8)0.0044 (7)0.0022 (6)
C30.0284 (9)0.0239 (8)0.0194 (7)0.0018 (7)−0.0002 (6)−0.0010 (6)
C40.0281 (9)0.0227 (8)0.0174 (7)0.0002 (8)0.0035 (7)0.0020 (6)
C50.0348 (9)0.0177 (8)0.0195 (7)0.0026 (8)−0.0015 (7)0.0017 (6)
C60.0268 (8)0.0263 (9)0.0217 (7)−0.0038 (7)0.0019 (7)0.0006 (6)
C70.0325 (10)0.0258 (9)0.0289 (8)−0.0052 (8)0.0034 (7)−0.0014 (7)
C80.0269 (9)0.0240 (8)0.0165 (7)0.0029 (7)0.0011 (6)−0.0014 (6)
C90.0283 (9)0.0239 (8)0.0201 (7)0.0014 (7)−0.0007 (6)0.0011 (6)
C100.0302 (9)0.0242 (9)0.0354 (9)0.0007 (8)0.0105 (8)−0.0022 (7)
C110.0240 (8)0.0235 (8)0.0220 (7)0.0001 (7)−0.0007 (6)0.0015 (6)
C120.0255 (9)0.0282 (9)0.0319 (8)0.0009 (8)0.0032 (7)0.0037 (7)
C130.0300 (9)0.0223 (8)0.0237 (8)−0.0048 (7)0.0062 (7)−0.0014 (6)
C140.0242 (8)0.0253 (8)0.0206 (7)−0.0013 (7)0.0026 (6)0.0005 (6)
C150.0360 (10)0.0245 (9)0.0349 (9)−0.0012 (8)0.0039 (8)0.0040 (7)
C160.0400 (10)0.0239 (8)0.0249 (8)0.0025 (8)−0.0039 (8)−0.0069 (6)
C170.0313 (9)0.0208 (8)0.0217 (7)0.0035 (7)0.0017 (7)−0.0003 (6)
C180.0305 (9)0.0222 (8)0.0274 (8)0.0053 (8)0.0010 (7)−0.0010 (7)
C190.0334 (10)0.0275 (9)0.0222 (7)0.0091 (8)0.0003 (7)0.0035 (7)
C200.0425 (11)0.0244 (9)0.0348 (9)−0.0045 (9)−0.0052 (8)−0.0047 (7)
C210.0345 (10)0.0397 (11)0.0389 (10)−0.0068 (9)0.0015 (8)−0.0152 (8)
C220.0255 (9)0.0341 (9)0.0223 (8)0.0052 (8)−0.0024 (7)0.0008 (7)
C230.0248 (9)0.0202 (8)0.0239 (7)0.0020 (7)−0.0033 (7)0.0002 (6)
O1—C31.368 (2)C9—H1c90.96
O1—H1o10.93 (2)C9—H2c90.96
O2—C21.380 (2)C10—C121.378 (3)
O2—C151.418 (2)C10—C131.389 (3)
O3—C61.371 (2)C10—H1c100.96
O3—H1o30.93 (2)C11—H1c110.96
O4—C131.373 (2)C11—H2c110.96
O4—C211.417 (2)C12—H1c120.96
N1—C111.466 (2)C13—C141.385 (2)
N1—C171.465 (2)C14—H1c140.96
N1—C231.470 (2)C15—H1c150.96
N2—C51.487 (2)C15—H2c150.96
N2—C91.473 (2)C15—H3c150.96
N2—C171.478 (2)C16—C181.520 (3)
C1—C21.386 (2)C16—C201.519 (3)
C1—C81.393 (2)C16—H1c160.96
C1—H1c10.96C16—H2c160.96
C2—C191.390 (3)C17—H1c170.96
C3—C81.402 (2)C17—H2c170.96
C3—C221.392 (2)C18—C231.532 (2)
C4—C61.399 (3)C18—H1c180.96
C4—C91.515 (2)C18—H2c180.96
C4—C141.395 (2)C19—C221.384 (3)
C5—C71.538 (2)C19—H1c190.96
C5—C231.524 (2)C20—H1c200.96
C5—H1c50.96C20—H2c200.96
C6—C121.390 (2)C21—H1c210.96
C7—C201.525 (3)C21—H2c210.96
C7—H1c70.96C21—H3c210.96
C7—H2c70.96C22—H1c220.96
C8—C111.511 (2)C23—H1c230.96
C3—O1—H1o1106.0 (13)C6—C12—H1c12119.71
C2—O2—C15116.72 (13)C10—C12—H1c12119.71
C6—O3—H1o3101.6 (13)O4—C13—C10115.28 (15)
C13—O4—C21117.40 (14)O4—C13—C14125.39 (16)
C11—N1—C17112.27 (12)C10—C13—C14119.32 (16)
C11—N1—C23116.87 (13)C4—C14—C13120.79 (16)
C17—N1—C23102.81 (12)C4—C14—H1c14119.6
C5—N2—C9115.42 (13)C13—C14—H1c14119.6
C5—N2—C17106.39 (12)O2—C15—H1c15109.47
C9—N2—C17111.24 (13)O2—C15—H2c15109.47
C2—C1—C8120.84 (16)O2—C15—H3c15109.47
C2—C1—H1c1119.58H1c15—C15—H2c15109.47
C8—C1—H1c1119.58H1c15—C15—H3c15109.47
O2—C2—C1123.98 (16)H2c15—C15—H3c15109.47
O2—C2—C19116.01 (15)C18—C16—C20110.30 (14)
C1—C2—C19120.01 (16)C18—C16—H1c16109.47
O1—C3—C8122.03 (15)C18—C16—H2c16109.47
O1—C3—C22118.37 (15)C20—C16—H1c16109.47
C8—C3—C22119.60 (15)C20—C16—H2c16109.47
C6—C4—C9119.44 (14)H1c16—C16—H2c16108.63
C6—C4—C14119.29 (15)N1—C17—N2104.22 (12)
C9—C4—C14121.26 (15)N1—C17—H1c17109.47
N2—C5—C7109.08 (14)N1—C17—H2c17109.47
N2—C5—C23103.65 (13)N2—C17—H1c17109.47
N2—C5—H1c5114.64N2—C17—H2c17109.47
C7—C5—C23112.79 (13)H1c17—C17—H2c17114.25
C7—C5—H1c5105.82C16—C18—C23112.72 (15)
C23—C5—H1c5111.05C16—C18—H1c18109.47
O3—C6—C4121.62 (15)C16—C18—H2c18109.47
O3—C6—C12118.85 (16)C23—C18—H1c18109.47
C4—C6—C12119.52 (16)C23—C18—H2c18109.47
C5—C7—C20113.00 (15)H1c18—C18—H2c18106.02
C5—C7—H1c7109.47C2—C19—C22119.58 (16)
C5—C7—H2c7109.47C2—C19—H1c19120.21
C20—C7—H1c7109.47C22—C19—H1c19120.21
C20—C7—H2c7109.47C7—C20—C16110.14 (15)
H1c7—C7—H2c7105.7C7—C20—H1c20109.47
C1—C8—C3119.06 (15)C7—C20—H2c20109.47
C1—C8—C11119.71 (15)C16—C20—H1c20109.47
C3—C8—C11121.14 (15)C16—C20—H2c20109.47
N2—C9—C4109.87 (13)H1c20—C20—H2c20108.8
N2—C9—H1c9109.47O4—C21—H1c21109.47
N2—C9—H2c9109.47O4—C21—H2c21109.47
C4—C9—H1c9109.47O4—C21—H3c21109.47
C4—C9—H2c9109.47H1c21—C21—H2c21109.47
H1c9—C9—H2c9109.07H1c21—C21—H3c21109.47
C12—C10—C13120.47 (16)H2c21—C21—H3c21109.47
C12—C10—H1c10119.76C3—C22—C19120.89 (16)
C13—C10—H1c10119.76C3—C22—H1c22119.56
N1—C11—C8111.62 (14)C19—C22—H1c22119.56
N1—C11—H1c11109.47N1—C23—C599.62 (13)
N1—C11—H2c11109.47N1—C23—C18114.52 (13)
C8—C11—H1c11109.47N1—C23—H1c23114.61
C8—C11—H2c11109.47C5—C23—C18114.50 (14)
H1c11—C11—H2c11107.24C5—C23—H1c23114.63
C6—C12—C10120.58 (17)C18—C23—H1c2399.77
D—H···AD—HH···AD···AD—H···A
O3—H1o3···N20.93 (2)1.78 (2)2.6443 (19)154.4 (19)
O1—H1o1···N10.93 (2)1.83 (2)2.6638 (19)148.8 (18)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O3—H1o3⋯N20.93 (2)1.78 (2)2.6443 (19)154.4 (19)
O1—H1o1⋯N10.93 (2)1.83 (2)2.6638 (19)148.8 (18)
  2 in total

1.  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

2.  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
  2 in total

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