Literature DB >> 22065834

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.

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

Abstract

The title compound, C(23)H(30)N(2)O(4), is a Mannich base useful for studying the effect of an electron-donating phenol substituent on intra-molecular hydrogen bonding. In the mol-ecular structure, the cyclo-hexane ring adopts a chair conformation and the five-membered ring has a twisted envelope conformation. Each meth-oxy group is oriented in the same plane of the respective aromatic ring, showing torsion angles below 11.8 (3)° and bond angles between the meth-oxy group and the aromatic ring of 116.6 (2) and 116.6 (1)°. The structure shows inter-actions between two the N atoms of the heterocyclic ring and the hy-droxy groups by intra-molecular O-H⋯N hydrogen-bonding inter-actions. In the crystal, C-H⋯O inter-actions are observed. The crystal studied was a racemic mixture of RR and SS enanti-omers.

Entities:  

Year:  2011        PMID： 22065834      PMCID： PMC3200725          DOI： 10.1107/S1600536811031436

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 ▶). For the effect of the meth­oxy group on mol­ecular structure, see: Özek et al. (2008 ▶); Ünver et al. (2009 ▶); Jamjah et al. (2011 ▶). For related quantum-chemical literature, see: Konschin (1984 ▶).

Experimental

Crystal data

C23H30N2O4 M = 398.5 Monoclinic, a = 12.7693 (3) Å b = 10.4365 (2) Å c = 16.3229 (4) Å β = 109.579 (3)° V = 2049.53 (9) Å3 Z = 4 Cu Kα radiation μ = 0.71 mm−1 T = 120 K 0.51 × 0.14 × 0.02 mm

Data collection

Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ▶) T min = 0.403, T max = 1 23926 measured reflections 3216 independent reflections 2577 reflections with I > 3σ(I) R int = 0.055

Refinement

R[F 2 > 2σ(F 2)] = 0.037 wR(F 2) = 0.105 S = 1.70 3216 reflections 268 parameters 2 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.19 e Å−3 Δρmin = −0.17 e Å−3 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/S1600536811031436/nr2009sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811031436/nr2009Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811031436/nr2009Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C23H30N2O4F(000) = 856
Mr = 398.5Dx = 1.291 Mg m−3
Monoclinic, P21/nCu Kα radiation, λ = 1.5418 Å
Hall symbol: -P 2ynCell parameters from 11032 reflections
a = 12.7693 (3) Åθ = 3.7–62.6°
b = 10.4365 (2) ŵ = 0.71 mm−1
c = 16.3229 (4) ÅT = 120 K
β = 109.579 (3)°Plate, colourless
V = 2049.53 (9) Å30.51 × 0.14 × 0.02 mm
Z = 4
Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector3216 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source2577 reflections with I > 3σ(I)
mirrorRint = 0.055
Detector resolution: 10.3784 pixels mm-1θmax = 62.7°, θmin = 3.8°
Rotation method data acquisition using ω scansh = −14→14
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)k = −11→11
Tmin = 0.403, Tmax = 1l = −18→18
23926 measured reflections
Refinement on F2114 constraints
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.105Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
S = 1.70(Δ/σ)max = 0.003
3216 reflectionsΔρmax = 0.19 e Å−3
268 parametersΔρmin = −0.17 e Å−3
2 restraints
Experimental. CrysAlisPro (Agilent Technologies, 2010), empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm. 1H NMR (CDCl3, 400 MHz): δ 1.28 (4H, m), 1.84 (2H, m), 2.05 (2H, m), 2.32 (2H, m), 3.40 (2H, d,J = 14.0 Hz, ArCH2N), 3.53 (2H, s, NCH2N), 3.71 (2H, s, ArOCH3), 4.16 (2H, d, J = 14.0 Hz, ArCH2N), 6.51 (2H, d, J= 2.0 Hz), 6.70 (2H, d, J = 8.8 Hz), 6.73 (2H, d, J = 8.8 Hz), 10.05 (2H, bs, ArOH). 13C NMR (CDCl3 , 100 MHz): δ 24.0, 28.9, 55.7, 56.4, 69.1, 75.8, 113.8, 113.9, 116.5, 122.1, 151.1, 152.5.
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
O1−0.00977 (10)0.13997 (12)0.92026 (9)0.0335 (5)
O20.20745 (10)0.49247 (11)1.17311 (8)0.0319 (4)
O30.39277 (11)0.34923 (12)0.73545 (9)0.0364 (5)
O40.68016 (10)0.06056 (12)0.99982 (8)0.0344 (5)
N10.22853 (11)0.21558 (13)0.76675 (9)0.0263 (5)
N20.08623 (12)0.27229 (13)0.82138 (9)0.0254 (5)
C10.20785 (14)0.26197 (17)0.84535 (12)0.0293 (6)
C20.11931 (14)0.17745 (16)0.70585 (11)0.0259 (6)
C30.10493 (15)0.17697 (17)0.61017 (12)0.0320 (7)
C4−0.01711 (15)0.14831 (17)0.55879 (12)0.0338 (7)
C5−0.09725 (15)0.23760 (17)0.58246 (12)0.0321 (7)
C6−0.07651 (15)0.24213 (16)0.68027 (12)0.0302 (7)
C70.04455 (14)0.27539 (16)0.72600 (11)0.0251 (6)
C80.05134 (14)0.37784 (16)0.86593 (11)0.0281 (6)
C90.07705 (13)0.34676 (15)0.96068 (12)0.0252 (6)
C100.04316 (13)0.22793 (16)0.98343 (12)0.0263 (6)
C110.06181 (14)0.19843 (17)1.06953 (12)0.0309 (7)
C120.11433 (14)0.28558 (16)1.13485 (13)0.0295 (6)
C130.15068 (13)0.40195 (16)1.11302 (12)0.0265 (6)
C140.13145 (13)0.43191 (16)1.02638 (11)0.0262 (6)
C150.22791 (16)0.46243 (19)1.26223 (12)0.0359 (7)
C160.31306 (13)0.11383 (16)0.78596 (12)0.0293 (6)
C170.42842 (14)0.16482 (15)0.83063 (11)0.0254 (6)
C180.46432 (15)0.27800 (16)0.80128 (12)0.0284 (6)
C190.57287 (15)0.31821 (17)0.83832 (12)0.0315 (7)
C200.64851 (15)0.24705 (16)0.90374 (12)0.0311 (7)
C210.61355 (14)0.13648 (16)0.93405 (12)0.0281 (6)
C220.50375 (14)0.09762 (16)0.89813 (11)0.0264 (6)
C230.79664 (15)0.0851 (2)1.02718 (14)0.0417 (8)
H1a0.2353210.2003290.891230.0352*
H1b0.2407370.3451160.8606970.0352*
H20.1045040.0891210.7142250.0311*
H3a0.1511090.1115910.5987580.0384*
H3b0.1243880.2595620.5937080.0384*
H4a−0.0290430.1548450.4976620.0405*
H4b−0.0335780.0610820.5686520.0405*
H5a−0.1723130.2107620.5526020.0385*
H5b−0.0911660.3224140.5617380.0385*
H6a−0.1227040.3068650.6923780.0362*
H6b−0.0921140.1597040.6996140.0362*
H70.046430.3611760.7053130.0301*
H8a−0.0270930.3918280.8393020.0337*
H8b0.0896230.4548240.8604710.0337*
H110.0383190.1169811.0845210.0371*
H120.1253630.2654371.1945480.0354*
H140.1561960.5128481.0116930.0314*
H15a0.2696550.5305031.2980340.0539*
H15b0.1584090.4524641.2721940.0539*
H15c0.2694560.3840831.2765430.0539*
H16a0.31020.0719130.7328990.0352*
H16b0.2961880.0498660.8219310.0352*
H190.5964960.3962570.8187130.0378*
H200.7245230.2742970.9277870.0373*
H220.4793740.0224810.9205160.0317*
H23a0.8351560.0233171.0703190.0625*
H23b0.8218870.0788940.9781530.0625*
H23c0.8113040.1696751.0514970.0625*
H10.0129 (19)0.160 (2)0.8762 (13)0.0503*
H30.3253 (14)0.326 (2)0.7320 (16)0.0547*
U11U22U33U12U13U23
O10.0384 (7)0.0312 (7)0.0300 (8)−0.0083 (5)0.0101 (6)−0.0029 (5)
O20.0367 (7)0.0311 (7)0.0269 (7)−0.0039 (5)0.0095 (6)−0.0047 (5)
O30.0392 (7)0.0326 (7)0.0368 (8)0.0016 (6)0.0119 (7)0.0087 (6)
O40.0267 (6)0.0360 (7)0.0362 (8)0.0021 (5)0.0049 (6)0.0024 (5)
N10.0278 (7)0.0249 (7)0.0257 (9)0.0024 (6)0.0081 (7)−0.0016 (6)
N20.0281 (7)0.0249 (7)0.0230 (8)0.0025 (6)0.0083 (7)−0.0009 (6)
C10.0301 (9)0.0305 (10)0.0273 (11)0.0008 (7)0.0095 (8)−0.0027 (7)
C20.0279 (9)0.0235 (9)0.0254 (10)−0.0018 (7)0.0079 (8)0.0000 (7)
C30.0355 (10)0.0329 (10)0.0285 (11)0.0008 (7)0.0118 (9)−0.0011 (8)
C40.0397 (10)0.0321 (10)0.0272 (11)−0.0055 (8)0.0081 (9)−0.0006 (8)
C50.0302 (10)0.0315 (10)0.0298 (11)−0.0055 (7)0.0037 (9)0.0005 (8)
C60.0289 (9)0.0276 (9)0.0333 (11)−0.0005 (7)0.0095 (8)−0.0014 (7)
C70.0299 (9)0.0214 (8)0.0234 (10)−0.0002 (7)0.0082 (8)0.0028 (7)
C80.0331 (9)0.0238 (9)0.0282 (10)0.0043 (7)0.0113 (8)0.0009 (7)
C90.0246 (8)0.0240 (9)0.0286 (10)0.0048 (7)0.0108 (8)0.0006 (7)
C100.0248 (9)0.0255 (9)0.0285 (11)−0.0017 (7)0.0086 (8)−0.0013 (7)
C110.0313 (9)0.0281 (9)0.0343 (11)−0.0031 (7)0.0122 (9)0.0034 (8)
C120.0284 (9)0.0329 (10)0.0279 (11)0.0010 (7)0.0102 (8)0.0024 (8)
C130.0241 (8)0.0286 (9)0.0272 (10)0.0030 (7)0.0091 (8)−0.0039 (7)
C140.0274 (9)0.0210 (8)0.0324 (11)0.0024 (7)0.0130 (8)−0.0003 (7)
C150.0403 (11)0.0391 (11)0.0259 (11)0.0020 (8)0.0080 (9)−0.0047 (8)
C160.0288 (9)0.0246 (9)0.0335 (11)0.0030 (7)0.0091 (8)−0.0011 (7)
C170.0286 (9)0.0237 (9)0.0263 (10)0.0016 (7)0.0125 (8)−0.0043 (7)
C180.0349 (9)0.0259 (9)0.0268 (10)0.0033 (7)0.0137 (8)−0.0001 (7)
C190.0370 (10)0.0270 (9)0.0358 (11)−0.0027 (7)0.0190 (9)−0.0039 (8)
C200.0294 (9)0.0327 (10)0.0337 (11)−0.0038 (7)0.0138 (9)−0.0081 (8)
C210.0301 (9)0.0286 (9)0.0264 (10)0.0029 (7)0.0106 (8)−0.0037 (7)
C220.0305 (9)0.0231 (9)0.0277 (10)0.0013 (7)0.0124 (8)−0.0012 (7)
C230.0282 (9)0.0524 (13)0.0409 (13)0.0044 (9)0.0071 (9)−0.0009 (10)
O1—C101.377 (2)C7—H70.96
O1—H10.89 (2)C8—C91.505 (3)
O2—C131.3797 (19)C8—H8a0.96
O2—C151.424 (2)C8—H8b0.96
O3—C181.373 (2)C9—C101.404 (2)
O3—H30.88 (2)C9—C141.387 (2)
O4—C211.375 (2)C10—C111.379 (3)
O4—C231.426 (2)C11—C121.391 (2)
N1—C11.476 (3)C11—H110.96
N1—C21.4705 (19)C12—C131.389 (3)
N1—C161.471 (2)C12—H120.96
N2—C11.473 (2)C13—C141.388 (3)
N2—C71.467 (2)C14—H140.96
N2—C81.469 (2)C15—H15a0.96
C1—H1a0.96C15—H15b0.96
C1—H1b0.96C15—H15c0.96
C2—C31.510 (3)C16—C171.505 (2)
C2—C71.508 (3)C16—H16a0.96
C2—H20.96C16—H16b0.96
C3—C41.531 (2)C17—C181.408 (3)
C3—H3a0.96C17—C221.386 (2)
C3—H3b0.96C18—C191.379 (2)
C4—C51.526 (3)C19—C201.391 (2)
C4—H4a0.96C19—H190.96
C4—H4b0.96C20—C211.387 (3)
C5—C61.529 (3)C20—H200.96
C5—H5a0.96C21—C221.387 (2)
C5—H5b0.96C22—H220.96
C6—C71.515 (2)C23—H23a0.96
C6—H6a0.96C23—H23b0.96
C6—H6b0.96C23—H23c0.96
C10—O1—H1103.8 (13)C9—C8—H8b109.4712
C13—O2—C15116.64 (14)H8a—C8—H8b108.4897
C18—O3—H3106.3 (15)C8—C9—C10118.81 (14)
C21—O4—C23116.64 (15)C8—C9—C14122.47 (15)
C1—N1—C2105.73 (14)C10—C9—C14118.72 (17)
C1—N1—C16112.57 (13)O1—C10—C9120.55 (16)
C2—N1—C16114.24 (13)O1—C10—C11119.22 (15)
C1—N2—C7105.00 (15)C9—C10—C11120.23 (15)
C1—N2—C8113.02 (13)C10—C11—C12120.62 (17)
C7—N2—C8116.51 (12)C10—C11—H11119.6883
N1—C1—N2105.84 (13)C12—C11—H11119.6884
N1—C1—H1a109.4714C11—C12—C13119.48 (18)
N1—C1—H1b109.4707C11—C12—H12120.2628
N2—C1—H1a109.4711C13—C12—H12120.2617
N2—C1—H1b109.4719O2—C13—C12123.89 (16)
H1a—C1—H1b112.872O2—C13—C14116.21 (15)
N1—C2—C3117.33 (16)C12—C13—C14119.89 (15)
N1—C2—C7101.27 (13)C9—C14—C13121.03 (16)
N1—C2—H2110.5517C9—C14—H14119.4846
C3—C2—C7111.18 (13)C13—C14—H14119.4868
C3—C2—H2100.5211O2—C15—H15a109.4711
C7—C2—H2116.7735O2—C15—H15b109.4712
C2—C3—C4108.40 (17)O2—C15—H15c109.4713
C2—C3—H3a109.471H15a—C15—H15b109.4715
C2—C3—H3b109.4714H15a—C15—H15c109.4714
C4—C3—H3a109.471H15b—C15—H15c109.4709
C4—C3—H3b109.4714N1—C16—C17112.16 (13)
H3a—C3—H3b110.5178N1—C16—H16a109.4712
C3—C4—C5112.81 (15)N1—C16—H16b109.4704
C3—C4—H4a109.4711C17—C16—H16a109.4719
C3—C4—H4b109.4712C17—C16—H16b109.4714
C5—C4—H4a109.4716H16a—C16—H16b106.6446
C5—C4—H4b109.4708C16—C17—C18120.62 (14)
H4a—C4—H4b105.9139C16—C17—C22120.81 (15)
C4—C5—C6112.76 (14)C18—C17—C22118.47 (15)
C4—C5—H5a109.4712O3—C18—C17120.90 (15)
C4—C5—H5b109.471O3—C18—C19119.09 (16)
C6—C5—H5a109.472C17—C18—C19120.02 (15)
C6—C5—H5b109.4709C18—C19—C20120.78 (17)
H5a—C5—H5b105.9654C18—C19—H19119.6089
C5—C6—C7108.22 (17)C20—C19—H19119.6102
C5—C6—H6a109.4719C19—C20—C21119.63 (16)
C5—C6—H6b109.4716C19—C20—H20120.1833
C7—C6—H6a109.4709C21—C20—H20120.1828
C7—C6—H6b109.4705O4—C21—C20124.67 (15)
H6a—C6—H6b110.6899O4—C21—C22115.77 (16)
N2—C7—C2100.68 (12)C20—C21—C22119.55 (15)
N2—C7—C6117.73 (17)C17—C22—C21121.48 (17)
N2—C7—H7110.5362C17—C22—H22119.2602
C2—C7—C6110.69 (14)C21—C22—H22119.2596
C2—C7—H7117.589O4—C23—H23a109.4708
C6—C7—H7100.4929O4—C23—H23b109.4712
N2—C8—C9110.44 (13)O4—C23—H23c109.4711
N2—C8—H8a109.4713H23a—C23—H23b109.4715
N2—C8—H8b109.4709H23a—C23—H23c109.4708
C9—C8—H8a109.471H23b—C23—H23c109.4719
C15—O2—C13—C12−0.5 (3)C1—N1—C16—C17−72.95 (18)
C15—O2—C13—C14−179.80 (16)C2—N1—C16—C17166.44 (14)
C23—O4—C21—C20−11.8 (3)C7—N2—C1—N1−18.92 (16)
C23—O4—C21—C22169.32 (16)C8—N2—C1—N1−146.94 (13)
C2—N1—C1—N2−10.49 (16)C1—N2—C7—C239.95 (16)
C16—N1—C1—N2−135.87 (14)C1—N2—C7—C6160.30 (14)
C1—N1—C2—C3155.91 (15)C8—N2—C7—C2165.82 (14)
C1—N1—C2—C734.74 (16)C8—N2—C7—C6−73.83 (19)
C16—N1—C2—C3−79.74 (18)C1—N2—C8—C9−71.56 (18)
C16—N1—C2—C7159.08 (14)C7—N2—C8—C9166.70 (15)
D—H···AD—HH···AD···AD—H···A
O1—H1···N20.89 (2)1.90 (2)2.709 (2)151.1 (19)
O3—H3···N10.88 (2)1.91 (2)2.706 (2)150.0 (19)
C8—H8A···O2i0.962.553.427 (2)152
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
O1—H1⋯N20.89 (2)1.90 (2)2.709 (2)151.1 (19)
O3—H3⋯N10.88 (2)1.91 (2)2.706 (2)150.0 (19)
C8—H8A⋯O2i0.962.553.427 (2)152

Symmetry code: (i) .

  5 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.  X-ray crystal and computational structural study of (E)-2-[(2-chloro-phenyl)-iminometh-yl]-4-methoxy-phenol.

Authors:  Arzu Ozek; Orhan Büyükgüngör; Ciğdem Albayrak; Mustafa Odabaşoğlu
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-07-23

3.  Spectroscopic study and structure of (E)-2-[(2-chlorobenzylimino)methyl]methoxyphenol.

Authors:  Hüseyin Unver; Mustafa Yildiz; Hava Ozay; Tahsin Nuri Durlu
Journal:  Spectrochim Acta A Mol Biomol Spectrosc       Date:  2009-09-19       Impact factor: 4.098

4.  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

5.  2-tert-Butyl-6-(cyclo-hexyl-imino-meth-yl)-4-meth-oxy-phenol.

Authors:  Roghayieh Jamjah; Mehdi Nekoomanesh; Tayebeh Pourjafar; Gholam Hossein Zohuri; Faramarz Afshartaromi; Behrouz Notash
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-06-22
  5 in total
  1 in total

1.  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.

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Monika Kučeraková; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-06-08
  1 in total

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