Literature DB >> 22219955

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.

Augusto Rivera, Dency José Pacheco, Jaime Ríos-Motta, Michaela Pojarová, Michal Dušek.   

Abstract

In the title compound, C(29)H(42)N(2)O(2), the heterocyclic ring has a twist conformation. The cyclohexane ring adopts a chair conformation. The dihedral angle between the aromatic rings is 32.74 (6)°. The mol-ecular conformation is stabilized by two intramolecular O-H⋯N hydrogen bonds with graph-set motif S(6). The crystal packing is stabilized by C-H⋯O and C-H⋯π inter-actions.

Entities:  

Year:  2011        PMID: 22219955      PMCID: PMC3247337          DOI: 10.1107/S1600536811039171

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


Related literature

For related structures, see: Rivera et al. (2009 ▶, 2010 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶). For hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C29H42N2O2 M = 450.65 Triclinic, a = 6.2383 (2) Å b = 14.2296 (5) Å c = 15.6530 (6) Å α = 105.942 (3)° β = 95.737 (3)° γ = 98.041 (3)° V = 1308.87 (8) Å3 Z = 2 Cu Kα radiation μ = 0.55 mm−1 T = 120 K 0.22 × 0.10 × 0.08 mm

Data collection

Agilent Xcalibur Atlas Gemini Ultra diffractometer Absorption correction: analytical (CrysAlis PRO; Agilent, 2011) ▶ T min = 0.246, T max = 0.581 28373 measured reflections 4676 independent reflections 3632 reflections with I > 2σ(I) R int = 0.139

Refinement

R[F 2 > 2σ(F 2)] = 0.054 wR(F 2) = 0.143 S = 1.01 4676 reflections 304 parameters 2 restraints H-atom parameters constrained Δρmax = 0.21 e Å−3 Δρmin = −0.27 e Å−3 Data collection: CrysAlis PRO (Agilent, 2011 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811039171/bt5652sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811039171/bt5652Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C29H42N2O2Z = 2
Mr = 450.65F(000) = 492
Triclinic, P1Dx = 1.143 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.5418 Å
a = 6.2383 (2) ÅCell parameters from 9605 reflections
b = 14.2296 (5) Åθ = 3.0–67.2°
c = 15.6530 (6) ŵ = 0.55 mm1
α = 105.942 (3)°T = 120 K
β = 95.737 (3)°Prism, colourless
γ = 98.041 (3)°0.22 × 0.10 × 0.08 mm
V = 1308.87 (8) Å3
Agilent Xcalibur Atlas Gemini Ultra diffractometer4676 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source3632 reflections with I > 2σ(I)
mirrorRint = 0.139
Detector resolution: 10.3784 pixels mm-1θmax = 67.3°, θmin = 3.0°
Rotation method data acquisition using ω scansh = −7→7
Absorption correction: analytical (CrysAlis PRO; Agilent, 2011)k = −17→17
Tmin = 0.246, Tmax = 0.581l = −18→18
28373 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.143H-atom parameters constrained
S = 1.01w = 1/[σ2(Fo2) + (0.0802P)2] where P = (Fo2 + 2Fc2)/3
4676 reflections(Δ/σ)max < 0.001
304 parametersΔρmax = 0.21 e Å3
2 restraintsΔρmin = −0.27 e Å3
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically. The isotropic temperature parameters of hydrogen atoms were calculated as 1.2*Ueq of the parent atom. The distance between hydrogen and oxygen atom in hydroxyl group was fixed to the distance 0.87 Å.
xyzUiso*/Ueq
O10.7423 (2)0.60526 (9)0.68014 (9)0.0334 (3)
H1O10.60830.55980.68030.040*
O2−0.2846 (2)0.45402 (10)0.80993 (9)0.0357 (3)
H1O2−0.16760.47210.78650.043*
N10.3185 (2)0.53749 (10)0.67034 (9)0.0253 (3)
N20.1289 (2)0.48505 (10)0.77727 (9)0.0244 (3)
C10.2544 (3)0.57266 (12)0.76055 (11)0.0266 (4)
H1A0.38310.60010.80550.032*
H1B0.16500.62350.76240.032*
C20.1894 (3)0.39934 (12)0.71235 (11)0.0253 (4)
H20.33790.39240.73360.030*
C30.0424 (3)0.29864 (12)0.68838 (11)0.0306 (4)
H3A−0.10590.30350.66700.037*
H3B0.03980.27480.74070.037*
C40.1353 (4)0.22741 (14)0.61467 (13)0.0379 (4)
H4A0.27720.21820.63920.045*
H4B0.03930.16330.59580.045*
C50.1597 (4)0.26467 (14)0.53294 (13)0.0403 (5)
H5A0.01570.26490.50330.048*
H5B0.22950.21950.49080.048*
C60.2954 (3)0.36938 (14)0.55839 (12)0.0363 (4)
H6A0.44580.36830.58030.044*
H6B0.29420.39370.50620.044*
C70.1961 (3)0.43638 (12)0.63083 (11)0.0280 (4)
H70.04690.43940.60680.034*
C80.2926 (3)0.60451 (12)0.61501 (11)0.0276 (4)
H8A0.14750.62160.61560.033*
H8B0.30690.57100.55340.033*
C90.4626 (3)0.69832 (12)0.64956 (11)0.0255 (4)
C100.6796 (3)0.69352 (12)0.67912 (11)0.0263 (4)
C110.8342 (3)0.77961 (13)0.70752 (11)0.0299 (4)
H110.97770.77680.72790.036*
C120.7777 (3)0.87005 (13)0.70595 (11)0.0290 (4)
H120.88420.92700.72540.035*
C130.5642 (3)0.87735 (12)0.67573 (11)0.0268 (4)
C140.4105 (3)0.78981 (12)0.64918 (11)0.0263 (4)
H140.26620.79300.63030.032*
C150.4973 (3)0.97661 (13)0.67471 (12)0.0323 (4)
C160.4002 (4)1.01787 (15)0.76044 (15)0.0449 (5)
H16A0.27710.97080.76360.058*
H16B0.35341.07910.75970.058*
H16C0.50901.02950.81180.058*
C170.3244 (4)0.96239 (14)0.59319 (14)0.0426 (5)
H17A0.19250.92220.59880.055*
H17B0.37830.93020.53930.055*
H17C0.29421.02590.59050.055*
C180.6922 (4)1.05243 (15)0.67086 (17)0.0472 (5)
H18A0.64251.11160.66530.061*
H18B0.76201.02520.62000.061*
H18C0.79481.06820.72490.061*
C190.1725 (3)0.48777 (12)0.87265 (11)0.0260 (4)
H19A0.16120.55290.91060.031*
H19B0.32030.47650.88600.031*
C200.0128 (3)0.41008 (12)0.89290 (11)0.0259 (4)
C21−0.2101 (3)0.39674 (13)0.85995 (11)0.0288 (4)
C22−0.3563 (3)0.32395 (13)0.87683 (12)0.0321 (4)
H22−0.50410.31470.85460.039*
C23−0.2838 (3)0.26467 (13)0.92669 (12)0.0299 (4)
H23−0.38470.21610.93740.036*
C24−0.0639 (3)0.27594 (12)0.96120 (11)0.0269 (4)
C250.0807 (3)0.34982 (12)0.94307 (10)0.0256 (4)
H250.22830.35920.96550.031*
C260.0192 (3)0.20602 (13)1.01118 (11)0.0304 (4)
C27−0.1570 (3)0.16459 (15)1.05918 (13)0.0388 (4)
H27A−0.20920.21851.09830.050*
H27B−0.09580.12601.09380.050*
H27C−0.27630.12331.01550.050*
C280.0852 (4)0.11927 (15)0.94238 (13)0.0417 (5)
H28A0.14500.07670.97290.054*
H28B0.19300.14460.91090.054*
H28C−0.04130.08230.90040.054*
C290.2192 (3)0.25932 (15)1.08137 (12)0.0367 (4)
H29A0.18400.31731.12180.048*
H29B0.33830.27851.05180.048*
H29C0.26090.21551.11450.048*
U11U22U33U12U13U23
O10.0310 (6)0.0344 (6)0.0392 (7)0.0074 (5)0.0080 (5)0.0162 (5)
O20.0280 (6)0.0433 (7)0.0428 (7)0.0066 (5)0.0077 (5)0.0232 (6)
N10.0319 (7)0.0244 (7)0.0210 (7)0.0028 (6)0.0063 (5)0.0091 (5)
N20.0295 (7)0.0236 (7)0.0192 (7)0.0032 (5)0.0046 (5)0.0053 (5)
C10.0319 (8)0.0250 (8)0.0217 (8)0.0031 (7)0.0061 (7)0.0050 (6)
C20.0320 (8)0.0243 (8)0.0193 (8)0.0048 (7)0.0053 (6)0.0052 (6)
C30.0390 (9)0.0276 (8)0.0239 (8)−0.0001 (7)0.0072 (7)0.0071 (7)
C40.0531 (11)0.0270 (9)0.0314 (10)0.0018 (8)0.0096 (8)0.0062 (7)
C50.0603 (13)0.0302 (9)0.0262 (9)0.0008 (9)0.0121 (9)0.0029 (8)
C60.0512 (11)0.0321 (9)0.0246 (9)0.0017 (8)0.0127 (8)0.0071 (7)
C70.0340 (9)0.0264 (8)0.0224 (8)0.0006 (7)0.0044 (7)0.0072 (7)
C80.0319 (8)0.0285 (8)0.0230 (8)0.0009 (7)0.0025 (7)0.0112 (7)
C90.0285 (8)0.0294 (8)0.0191 (8)0.0017 (7)0.0063 (6)0.0086 (6)
C100.0293 (8)0.0320 (9)0.0215 (8)0.0063 (7)0.0099 (6)0.0113 (7)
C110.0262 (8)0.0398 (10)0.0240 (8)0.0024 (7)0.0056 (7)0.0110 (7)
C120.0304 (9)0.0311 (9)0.0224 (8)−0.0026 (7)0.0055 (7)0.0059 (7)
C130.0311 (8)0.0289 (8)0.0200 (8)0.0016 (7)0.0074 (6)0.0069 (6)
C140.0273 (8)0.0308 (8)0.0228 (8)0.0032 (7)0.0059 (6)0.0113 (7)
C150.0366 (9)0.0272 (9)0.0319 (9)0.0033 (7)0.0080 (7)0.0068 (7)
C160.0506 (12)0.0362 (10)0.0434 (11)0.0067 (9)0.0140 (9)0.0024 (9)
C170.0557 (12)0.0296 (9)0.0424 (11)0.0083 (8)−0.0004 (9)0.0126 (8)
C180.0463 (11)0.0354 (10)0.0626 (14)0.0005 (9)0.0120 (10)0.0208 (10)
C190.0285 (8)0.0285 (8)0.0193 (8)0.0031 (6)0.0047 (6)0.0047 (6)
C200.0308 (8)0.0280 (8)0.0179 (7)0.0050 (7)0.0072 (6)0.0039 (6)
C210.0299 (9)0.0331 (9)0.0246 (8)0.0082 (7)0.0072 (7)0.0081 (7)
C220.0273 (8)0.0365 (9)0.0331 (9)0.0044 (7)0.0074 (7)0.0106 (8)
C230.0312 (9)0.0297 (8)0.0278 (9)0.0002 (7)0.0100 (7)0.0075 (7)
C240.0348 (9)0.0275 (8)0.0173 (7)0.0040 (7)0.0078 (7)0.0043 (6)
C250.0285 (8)0.0300 (8)0.0169 (7)0.0032 (7)0.0056 (6)0.0045 (6)
C260.0394 (9)0.0300 (9)0.0222 (8)0.0043 (7)0.0071 (7)0.0083 (7)
C270.0463 (11)0.0394 (10)0.0343 (10)0.0032 (8)0.0105 (8)0.0170 (8)
C280.0588 (13)0.0361 (10)0.0316 (10)0.0154 (9)0.0094 (9)0.0077 (8)
C290.0451 (11)0.0405 (10)0.0261 (9)0.0045 (8)0.0028 (8)0.0147 (8)
O1—C101.370 (2)C13—C151.531 (2)
O1—H1O10.9834C14—H140.9300
O2—C211.370 (2)C15—C181.526 (3)
O2—H1O20.8859C15—C161.530 (3)
N1—C71.465 (2)C15—C171.534 (3)
N1—C81.468 (2)C16—H16A0.9600
N1—C11.478 (2)C16—H16B0.9600
N2—C11.477 (2)C16—H16C0.9600
N2—C21.479 (2)C17—H17A0.9600
N2—C191.479 (2)C17—H17B0.9600
C1—H1A0.9700C17—H17C0.9600
C1—H1B0.9700C18—H18A0.9600
C2—C71.510 (2)C18—H18B0.9600
C2—C31.518 (2)C18—H18C0.9600
C2—H20.9800C19—C201.504 (2)
C3—C41.533 (3)C19—H19A0.9700
C3—H3A0.9700C19—H19B0.9700
C3—H3B0.9700C20—C251.391 (2)
C4—C51.526 (3)C20—C211.402 (2)
C4—H4A0.9700C21—C221.382 (3)
C4—H4B0.9700C22—C231.387 (3)
C5—C61.533 (3)C22—H220.9300
C5—H5A0.9700C23—C241.393 (2)
C5—H5B0.9700C23—H230.9300
C6—C71.514 (3)C24—C251.396 (2)
C6—H6A0.9700C24—C261.537 (2)
C6—H6B0.9700C25—H250.9300
C7—H70.9800C26—C291.531 (3)
C8—C91.514 (2)C26—C271.532 (3)
C8—H8A0.9700C26—C281.534 (3)
C8—H8B0.9700C27—H27A0.9600
C9—C141.387 (2)C27—H27B0.9600
C9—C101.404 (2)C27—H27C0.9600
C10—C111.383 (3)C28—H28A0.9600
C11—C121.387 (3)C28—H28B0.9600
C11—H110.9300C28—H28C0.9600
C12—C131.396 (2)C29—H29A0.9600
C12—H120.9300C29—H29B0.9600
C13—C141.395 (2)C29—H29C0.9600
C10—O1—H1O1106.4C13—C14—H14118.4
C21—O2—H1O2102.7C18—C15—C16108.66 (16)
C7—N1—C8114.76 (13)C18—C15—C13111.78 (15)
C7—N1—C1105.78 (13)C16—C15—C13108.71 (15)
C8—N1—C1113.91 (13)C18—C15—C17108.22 (16)
C1—N2—C2104.36 (12)C16—C15—C17108.85 (17)
C1—N2—C19111.45 (12)C13—C15—C17110.56 (14)
C2—N2—C19115.31 (12)C15—C16—H16A109.5
N2—C1—N1106.28 (12)C15—C16—H16B109.5
N2—C1—H1A110.5H16A—C16—H16B109.5
N1—C1—H1A110.5C15—C16—H16C109.5
N2—C1—H1B110.5H16A—C16—H16C109.5
N1—C1—H1B110.5H16B—C16—H16C109.5
H1A—C1—H1B108.7C15—C17—H17A109.5
N2—C2—C7100.86 (12)C15—C17—H17B109.5
N2—C2—C3119.27 (14)H17A—C17—H17B109.5
C7—C2—C3110.48 (13)C15—C17—H17C109.5
N2—C2—H2108.6H17A—C17—H17C109.5
C7—C2—H2108.6H17B—C17—H17C109.5
C3—C2—H2108.6C15—C18—H18A109.5
C2—C3—C4107.44 (15)C15—C18—H18B109.5
C2—C3—H3A110.2H18A—C18—H18B109.5
C4—C3—H3A110.2C15—C18—H18C109.5
C2—C3—H3B110.2H18A—C18—H18C109.5
C4—C3—H3B110.2H18B—C18—H18C109.5
H3A—C3—H3B108.5N2—C19—C20110.98 (13)
C5—C4—C3112.87 (16)N2—C19—H19A109.4
C5—C4—H4A109.0C20—C19—H19A109.4
C3—C4—H4A109.0N2—C19—H19B109.4
C5—C4—H4B109.0C20—C19—H19B109.4
C3—C4—H4B109.0H19A—C19—H19B108.0
H4A—C4—H4B107.8C25—C20—C21118.67 (16)
C4—C5—C6112.16 (15)C25—C20—C19121.69 (15)
C4—C5—H5A109.2C21—C20—C19119.64 (15)
C6—C5—H5A109.2O2—C21—C22119.48 (15)
C4—C5—H5B109.2O2—C21—C20120.80 (15)
C6—C5—H5B109.2C22—C21—C20119.71 (16)
H5A—C5—H5B107.9C21—C22—C23120.34 (16)
C7—C6—C5108.19 (16)C21—C22—H22119.8
C7—C6—H6A110.1C23—C22—H22119.8
C5—C6—H6A110.1C22—C23—C24121.78 (16)
C7—C6—H6B110.1C22—C23—H23119.1
C5—C6—H6B110.1C24—C23—H23119.1
H6A—C6—H6B108.4C23—C24—C25116.80 (15)
N1—C7—C2101.63 (13)C23—C24—C26121.90 (15)
N1—C7—C6115.78 (15)C25—C24—C26121.16 (15)
C2—C7—C6111.66 (14)C20—C25—C24122.69 (16)
N1—C7—H7109.1C20—C25—H25118.7
C2—C7—H7109.1C24—C25—H25118.7
C6—C7—H7109.1C29—C26—C27108.02 (15)
N1—C8—C9111.07 (13)C29—C26—C28108.58 (16)
N1—C8—H8A109.4C27—C26—C28108.83 (16)
C9—C8—H8A109.4C29—C26—C24111.28 (14)
N1—C8—H8B109.4C27—C26—C24111.77 (15)
C9—C8—H8B109.4C28—C26—C24108.30 (14)
H8A—C8—H8B108.0C26—C27—H27A109.5
C14—C9—C10118.58 (15)C26—C27—H27B109.5
C14—C9—C8121.12 (15)H27A—C27—H27B109.5
C10—C9—C8120.25 (15)C26—C27—H27C109.5
O1—C10—C11119.16 (15)H27A—C27—H27C109.5
O1—C10—C9121.45 (15)H27B—C27—H27C109.5
C11—C10—C9119.38 (15)C26—C28—H28A109.5
C10—C11—C12120.79 (16)C26—C28—H28B109.5
C10—C11—H11119.6H28A—C28—H28B109.5
C12—C11—H11119.6C26—C28—H28C109.5
C11—C12—C13121.37 (15)H28A—C28—H28C109.5
C11—C12—H12119.3H28B—C28—H28C109.5
C13—C12—H12119.3C26—C29—H29A109.5
C14—C13—C12116.71 (15)C26—C29—H29B109.5
C14—C13—C15120.97 (15)H29A—C29—H29B109.5
C12—C13—C15122.28 (15)C26—C29—H29C109.5
C9—C14—C13123.14 (16)H29A—C29—H29C109.5
C9—C14—H14118.4H29B—C29—H29C109.5
Cg3 and Cg4 are the centroids of the C9–C14 and C20–C25 benzene rings, respectively.
D—H···AD—HH···AD···AD—H···A
O1—H1O1···N10.981.772.6585 (18)148
O2—H1O2···N20.891.862.6794 (18)153
C2—H2···O2i0.982.453.367 (18)155
C5—H5B···Cg3ii0.962.873.625 (2)135
C19—H19A···Cg4iii0.962.843.6722 (18)144
Table 1

Hydrogen-bond geometry (Å, °)

Cg3 and Cg4 are the centroids of the C9–C14 and C20–C25 benzene rings, respectively.

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1O1⋯N10.981.772.6585 (18)148
O2—H1O2⋯N20.891.862.6794 (18)153
C2—H2⋯O2i0.982.453.367 (18)155
C5—H5BCg3ii0.962.873.625 (2)135
C19—H19ACg4iii0.962.843.6722 (18)144

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

  2 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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
  2 in total

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