Literature DB >> 22058915

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.

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

Abstract

In the crystal structure of the title compound, C(21)H(24)I(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 cyclo-hexane ring adopts a chair conformation and the heterocyclic ring to which it is fused has a twisted envelope conformation.

Entities:  

Year:  2011        PMID: 22058915      PMCID: PMC3200707          DOI: 10.1107/S1600536811030054

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


Related literature

For related structures, see: Rivera et al. (2010 ▶, 2011a ▶,b ▶); Merz (2006 ▶).

Experimental

Crystal data

C21H24I2N2O2 M = 590.2 Monoclinic, a = 24.5822 (12) Å b = 6.1121 (3) Å c = 16.5557 (10) Å β = 121.119 (6)° V = 2129.5 (2) Å3 Z = 4 Cu Kα radiation μ = 23.34 mm−1 T = 120 K 0.26 × 0.12 × 0.05 mm

Data collection

Agilent Xcalibur diffractometer with an Atlas (Gemini Ultra Cu) detector Absorption correction: analytical (CrysAlis PRO; Agilent, 2010 ▶) T min = 0.074, T max = 0.424 11449 measured reflections 3650 independent reflections 3397 reflections with I > 3σ(I) R int = 0.062

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.106 S = 1.30 3650 reflections 250 parameters 2 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.85 e Å−3 Δρmin = −0.87 e Å−3 Absolute structure: Flack (1983 ▶), 1566 Friedel pairs Flack parameter: 0.079 (13) Data collection: CrysAlis PRO (Agilent, 2010 ▶); 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 datablock(s) global, I. DOI: 10.1107/S1600536811030054/nc2238sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811030054/nc2238Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811030054/nc2238Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C21H24I2N2O2F(000) = 1144
Mr = 590.2Dx = 1.840 Mg m3
Monoclinic, C2Cu Kα radiation, λ = 1.5418 Å
Hall symbol: C 2yCell parameters from 5885 reflections
a = 24.5822 (12) Åθ = 3.1–67.1°
b = 6.1121 (3) ŵ = 23.34 mm1
c = 16.5557 (10) ÅT = 120 K
β = 121.119 (6)°Prism, colourless
V = 2129.5 (2) Å30.26 × 0.12 × 0.05 mm
Z = 4
Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector3650 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source3397 reflections with I > 3σ(I)
mirrorRint = 0.062
Detector resolution: 10.3784 pixels mm-1θmax = 67.2°, θmin = 3.1°
Rotation method data acquisition using ω scansh = −29→29
Absorption correction: analytical (CrysAlis PRO; Agilent, 2010)k = −7→7
Tmin = 0.074, Tmax = 0.424l = −19→19
11449 measured reflections
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.040Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
wR(F2) = 0.106(Δ/σ)max = 0.038
S = 1.30Δρmax = 0.85 e Å3
3650 reflectionsΔρmin = −0.87 e Å3
250 parametersAbsolute structure: Flack (1983), 1566 Friedel pairs
2 restraintsFlack parameter: 0.079 (13)
91 constraints
Experimental. CrysAlis Pro (Agilent, 2010), Analytical numeric absorption correction using a multifaceted crystal model.
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.The absolute structure was determined on the basis of 1566 Friedel pairs (Flack, 1983),
xyzUiso*/Ueq
I10.40926 (2)0.388850.03435 (3)0.0457 (2)
I20.54564 (3)0.34180 (15)0.67075 (4)0.0621 (3)
O10.2558 (2)0.8312 (10)0.1940 (3)0.040 (2)
O20.2940 (3)−0.1604 (11)0.4035 (4)0.054 (3)
N10.2165 (3)0.4306 (11)0.2051 (4)0.034 (2)
N20.2436 (3)0.2401 (11)0.3459 (4)0.035 (3)
C10.2707 (3)0.3359 (13)0.2912 (4)0.034 (3)
C20.1598 (3)0.3332 (14)0.1992 (4)0.036 (3)
C30.1790 (3)0.3314 (15)0.3014 (5)0.038 (3)
C40.1317 (4)0.2045 (16)0.3154 (6)0.045 (4)
C50.0666 (4)0.314 (2)0.2559 (6)0.061 (5)
C60.0474 (3)0.335 (2)0.1518 (5)0.051 (4)
C70.0975 (4)0.4517 (15)0.1400 (5)0.042 (3)
C80.2198 (3)0.3905 (16)0.1187 (4)0.031 (3)
C90.2733 (3)0.5131 (13)0.1224 (5)0.034 (3)
C100.2890 (4)0.7266 (14)0.1603 (5)0.035 (3)
C110.3386 (3)0.8414 (15)0.1623 (4)0.037 (3)
C120.3732 (4)0.7461 (14)0.1254 (5)0.042 (3)
C130.3568 (4)0.5396 (14)0.0869 (5)0.037 (3)
C140.3084 (3)0.4225 (12)0.0860 (4)0.031 (3)
C150.2835 (4)0.2855 (14)0.4477 (5)0.038 (3)
C160.3459 (4)0.1688 (14)0.4877 (5)0.038 (3)
C170.3489 (4)−0.0472 (14)0.4615 (5)0.042 (4)
C180.4071 (4)−0.1506 (18)0.4971 (6)0.052 (4)
C190.4628 (5)−0.0464 (14)0.5584 (6)0.046 (4)
C200.4608 (4)0.1693 (16)0.5825 (6)0.047 (4)
C210.4035 (4)0.2758 (15)0.5479 (5)0.041 (3)
H1a0.300180.4498070.3274860.041*
H1b0.2896980.2220210.2739890.041*
H20.1501560.1943680.1676350.0427*
H30.1790950.4700590.3287240.046*
H4a0.1442240.2088870.3807350.0534*
H4b0.1293690.0565840.2943650.0534*
H5a0.0677020.4568160.2810370.0736*
H5b0.0351320.230680.2601040.0736*
H6a0.0398280.1924230.1239060.0611*
H6b0.0078880.4129180.1175670.0611*
H7a0.0856230.4470240.0749010.0506*
H7b0.1017310.6000350.1615220.0506*
H8a0.225180.2368210.1130220.0373*
H8b0.1805620.4343850.063910.0373*
H110.3491330.9857490.1888850.0443*
H120.407710.8236320.1270370.05*
H140.2987250.2773910.0601120.0371*
H15a0.2907760.4401170.4573540.0451*
H15b0.262040.2360750.4790590.0451*
H180.408329−0.2983270.4783830.0625*
H190.502706−0.1217140.5843290.0552*
H210.4029930.4252370.5654160.0489*
H1O0.240 (4)0.728 (11)0.209 (7)0.0482*
H2O0.270 (4)−0.059 (13)0.370 (7)0.0643*
U11U22U33U12U13U23
I10.0504 (2)0.0491 (3)0.0454 (2)−0.0022 (2)0.0304 (2)−0.0027 (2)
I20.0572 (3)0.0623 (5)0.0429 (3)0.0124 (3)0.0089 (2)−0.0038 (3)
O10.054 (3)0.030 (3)0.042 (2)−0.003 (2)0.028 (2)−0.001 (2)
O20.090 (4)0.025 (4)0.047 (3)−0.007 (3)0.036 (3)−0.004 (3)
N10.045 (3)0.031 (4)0.029 (3)−0.005 (2)0.021 (2)−0.004 (2)
N20.048 (3)0.032 (4)0.026 (3)−0.007 (3)0.020 (3)−0.003 (2)
C10.045 (3)0.030 (4)0.031 (3)−0.005 (3)0.022 (3)0.000 (3)
C20.045 (3)0.035 (5)0.033 (3)−0.008 (3)0.025 (3)−0.003 (3)
C30.050 (4)0.033 (5)0.034 (3)−0.005 (3)0.024 (3)−0.001 (3)
C40.058 (4)0.046 (5)0.039 (4)−0.011 (4)0.031 (4)0.000 (4)
C50.057 (5)0.088 (9)0.047 (4)−0.008 (5)0.033 (4)−0.001 (5)
C60.042 (4)0.070 (7)0.044 (4)−0.009 (4)0.025 (3)−0.006 (5)
C70.051 (4)0.043 (5)0.034 (4)−0.004 (3)0.022 (3)0.000 (3)
C80.039 (3)0.023 (4)0.026 (3)−0.001 (3)0.013 (2)0.006 (3)
C90.043 (4)0.034 (5)0.022 (3)0.000 (3)0.015 (3)0.007 (3)
C100.041 (4)0.034 (5)0.028 (3)−0.004 (3)0.016 (3)−0.003 (3)
C110.047 (3)0.029 (5)0.029 (3)−0.005 (3)0.016 (3)−0.003 (3)
C120.046 (4)0.040 (5)0.034 (4)−0.006 (3)0.017 (3)0.004 (3)
C130.043 (4)0.040 (5)0.033 (4)−0.001 (3)0.022 (3)−0.001 (3)
C140.046 (3)0.020 (4)0.023 (3)−0.004 (3)0.015 (3)0.000 (3)
C150.059 (4)0.031 (5)0.029 (3)0.005 (3)0.028 (3)0.001 (3)
C160.062 (5)0.025 (4)0.028 (4)0.003 (3)0.024 (4)0.002 (3)
C170.075 (5)0.025 (5)0.033 (4)−0.004 (4)0.034 (4)−0.003 (3)
C180.092 (6)0.028 (6)0.048 (4)0.008 (5)0.044 (4)−0.003 (4)
C190.078 (6)0.031 (5)0.041 (4)0.014 (4)0.039 (4)0.009 (3)
C200.060 (5)0.043 (5)0.034 (4)0.013 (4)0.023 (4)0.009 (4)
C210.063 (5)0.032 (5)0.027 (3)0.006 (3)0.023 (3)0.003 (3)
I1—C132.105 (10)C6—H6b0.96
I2—C202.108 (8)C7—H7a0.96
O1—C101.363 (12)C7—H7b0.96
O1—H1O0.84 (10)C8—C91.488 (12)
O2—C171.372 (10)C8—H8a0.96
O2—H2O0.84 (8)C8—H8b0.96
N1—C11.476 (7)C9—C101.412 (11)
N1—C21.471 (11)C9—C141.396 (13)
N1—C81.494 (11)C10—C111.392 (13)
N2—C11.494 (12)C11—C121.405 (14)
N2—C31.473 (10)C11—H110.96
N2—C151.472 (9)C12—C131.377 (12)
C1—H1a0.96C12—H120.96
C1—H1b0.96C13—C141.383 (12)
C2—C31.503 (11)C14—H140.96
C2—C71.510 (10)C15—C161.501 (12)
C2—H20.96C15—H15a0.96
C3—C41.511 (14)C15—H15b0.96
C3—H30.96C16—C171.404 (12)
C4—C51.532 (12)C16—C211.402 (11)
C4—H4a0.96C17—C181.385 (14)
C4—H4b0.96C18—C191.370 (12)
C5—C61.539 (13)C18—H180.96
C5—H5a0.96C19—C201.385 (13)
C5—H5b0.96C19—H190.96
C6—C71.520 (15)C20—C211.380 (13)
C6—H6a0.96C21—H210.96
C10—O1—H1O104 (7)H7a—C7—H7b110.9091
C17—O2—H2O101 (6)N1—C8—C9111.3 (6)
C1—N1—C2104.8 (6)N1—C8—H8a109.4702
C1—N1—C8113.0 (6)N1—C8—H8b109.4715
C2—N1—C8112.9 (5)C9—C8—H8a109.4718
C1—N2—C3104.6 (6)C9—C8—H8b109.4709
C1—N2—C15112.3 (6)H8a—C8—H8b107.5975
C3—N2—C15114.1 (7)C8—C9—C10121.1 (9)
N1—C1—N2106.1 (6)C8—C9—C14120.8 (7)
N1—C1—H1a109.4714C10—C9—C14118.1 (8)
N1—C1—H1b109.4713O1—C10—C9122.1 (8)
N2—C1—H1a109.472O1—C10—C11117.2 (7)
N2—C1—H1b109.471C9—C10—C11120.7 (9)
H1a—C1—H1b112.6582C10—C11—C12120.0 (8)
N1—C2—C3101.2 (5)C10—C11—H11119.9796
N1—C2—C7117.1 (7)C12—C11—H11119.9777
N1—C2—H2110.6437C11—C12—C13118.9 (9)
C3—C2—C7110.9 (8)C11—C12—H12120.5572
C3—C2—H2116.8819C13—C12—H12120.5582
C7—C2—H2100.8307I1—C13—C12119.8 (7)
N2—C3—C2101.3 (7)I1—C13—C14118.5 (6)
N2—C3—C4116.5 (7)C12—C13—C14121.6 (9)
N2—C3—H3111.0115C9—C14—C13120.7 (7)
C2—C3—C4111.0 (6)C9—C14—H14119.6736
C2—C3—H3116.5093C13—C14—H14119.6733
C4—C3—H3101.3338N2—C15—C16109.9 (8)
C3—C4—C5107.9 (8)N2—C15—H15a109.4717
C3—C4—H4a109.4721N2—C15—H15b109.4717
C3—C4—H4b109.4725C16—C15—H15a109.4703
C5—C4—H4a109.4701C16—C15—H15b109.471
C5—C4—H4b109.47H15a—C15—H15b109.0826
H4a—C4—H4b111.0366C15—C16—C17121.1 (7)
C4—C5—C6111.8 (9)C15—C16—C21121.2 (8)
C4—C5—H5a109.4716C17—C16—C21117.6 (8)
C4—C5—H5b109.4713O2—C17—C16120.0 (8)
C6—C5—H5a109.4709O2—C17—C18119.6 (8)
C6—C5—H5b109.4715C16—C17—C18120.4 (8)
H5a—C5—H5b107.0854C17—C18—C19121.3 (10)
C5—C6—C7112.5 (6)C17—C18—H18119.3262
C5—C6—H6a109.4704C19—C18—H18119.324
C5—C6—H6b109.4702C18—C19—C20119.0 (9)
C7—C6—H6a109.4723C18—C19—H19120.5016
C7—C6—H6b109.4718C20—C19—H19120.5014
H6a—C6—H6b106.2371I2—C20—C19120.4 (7)
C2—C7—C6108.0 (7)I2—C20—C21118.9 (7)
C2—C7—H7a109.4703C19—C20—C21120.7 (8)
C2—C7—H7b109.4705C16—C21—C20120.9 (8)
C6—C7—H7a109.4719C16—C21—H21119.5344
C6—C7—H7b109.4721C20—C21—H21119.5335
?—?—?—??
D—H···AD—HH···AD···AD—H···A
O1—H1O···N10.84 (10)1.90 (7)2.672 (9)152 (11)
O2—H2O···N20.84 (8)1.91 (8)2.686 (9)154 (8)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1O⋯N10.84 (10)1.90 (7)2.672 (9)152 (11)
O2—H2O⋯N20.84 (8)1.91 (8)2.686 (9)154 (8)
  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.  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.  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 in total

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