Literature DB >> 22219864

Diethyl 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.

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

Abstract

The heterocyclic ring in the title compound, C(27)H(34)N(2)O(6), has an envelope conformation on one of the bridgehead C atoms [Q(2) = 0.4487 (19) Å and ϕ = 291.3 (2)°]. Two strong intra-molecular O-H⋯N hydrogen bonds stabilize the mol-ecular conformation. The benzoate groups differ in the relative orientations of the ethyl groups, as quanti-fied by the values of the C-O-C-C torsion angles of -86.5 (2) and -178.97 (17)°. The carbonyl groups are nearly coplanar with the benzene rings, forming C-C-C-O torsion angles of 0.9 (3) and 3.4 (3)°. The crystal structure is stabilized by weak inter-molecular C-H⋯O inter-actions.

Entities:  

Year:  2011        PMID: 22219864      PMCID: PMC3247559          DOI: 10.1107/S1600536811039559

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


Related literature

For related structures, see: Rivera et al. (2010 ▶, 2011 ▶). For the background to this work, see: Van den Enden & Geise (1981 ▶); Geise et al. (1971 ▶). For the synthesis of the precursor, see: Murray-Rust & Riddell (1975 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶). For hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C27H34N2O6 M = 482.6 Triclinic, a = 8.1132 (4) Å b = 10.9796 (7) Å c = 15.2450 (8) Å α = 89.580 (5)° β = 81.028 (4)° γ = 70.028 (5)° V = 1259.19 (13) Å3 Z = 2 Cu Kα radiation μ = 0.73 mm−1 T = 120 K 0.46 × 0.18 × 0.11 mm

Data collection

Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ▶) T min = 0.752, T max = 1 11294 measured reflections 4430 independent reflections 3313 reflections with I > 3σ(I) R int = 0.034

Refinement

R[F 2 > 2σ(F 2)] = 0.043 wR(F 2) = 0.111 S = 1.64 4430 reflections 323 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.47 e Å−3 Δρmin = −0.24 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/S1600536811039559/bt5654sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811039559/bt5654Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811039559/bt5654Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C27H34N2O6Z = 2
Mr = 482.6F(000) = 516
Triclinic, P1Dx = 1.272 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.5418 Å
a = 8.1132 (4) ÅCell parameters from 4486 reflections
b = 10.9796 (7) Åθ = 2.9–67.1°
c = 15.2450 (8) ŵ = 0.73 mm1
α = 89.580 (5)°T = 120 K
β = 81.028 (4)°Block, colourless
γ = 70.028 (5)°0.46 × 0.18 × 0.11 mm
V = 1259.19 (13) Å3
Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector4430 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source3313 reflections with I > 3σ(I)
mirrorRint = 0.034
Detector resolution: 10.3784 pixels mm-1θmax = 67.2°, θmin = 2.9°
Rotation method data acquisition using ω scansh = −8→9
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)k = −13→12
Tmin = 0.752, Tmax = 1l = −18→18
11294 measured reflections
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.043Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0009I2]
wR(F2) = 0.111(Δ/σ)max = 0.005
S = 1.64Δρmax = 0.47 e Å3
4430 reflectionsΔρmin = −0.24 e Å3
323 parametersExtinction correction: B-C type 1 Lorentzian isotropic (Becker & Coppens, 1974)
0 restraintsExtinction coefficient: 900 (200)
130 constraints
Experimental. CrysAlisPro (Agilent Technologies, 2010) 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
O10.80490 (18)0.62458 (15)−0.09060 (10)0.0383 (6)
O20.86246 (17)0.80304 (15)−0.05677 (10)0.0363 (6)
O30.16819 (17)0.90030 (14)0.22196 (9)0.0305 (5)
O40.88617 (18)0.26784 (14)0.50761 (10)0.0336 (5)
O51.05002 (16)0.09728 (14)0.41510 (9)0.0289 (5)
O60.35533 (18)0.23291 (15)0.24830 (10)0.0327 (6)
N10.16240 (18)0.65935 (16)0.21904 (10)0.0230 (6)
N20.20550 (18)0.47944 (15)0.31013 (10)0.0223 (5)
C10.2970 (2)0.5617 (2)0.26184 (14)0.0301 (7)
C2−0.0010 (2)0.62702 (18)0.23985 (12)0.0215 (6)
C30.0186 (2)0.56664 (18)0.32802 (12)0.0212 (6)
C4−0.1214 (2)0.5040 (2)0.35509 (13)0.0251 (7)
C5−0.3031 (2)0.6115 (2)0.36049 (13)0.0284 (7)
C6−0.3246 (2)0.6841 (2)0.27465 (13)0.0289 (7)
C7−0.1753 (2)0.7398 (2)0.24635 (13)0.0263 (7)
C80.2195 (2)0.66840 (19)0.12354 (13)0.0247 (7)
C90.3493 (2)0.74075 (18)0.10787 (12)0.0220 (6)
C100.5003 (2)0.69903 (19)0.04363 (13)0.0237 (7)
C110.6112 (2)0.77285 (19)0.02585 (12)0.0237 (7)
C120.5683 (2)0.89060 (19)0.07296 (12)0.0243 (7)
C130.4197 (2)0.93306 (19)0.13820 (13)0.0252 (7)
C140.3118 (2)0.85782 (19)0.15638 (12)0.0235 (7)
C150.7677 (2)0.7236 (2)−0.04577 (13)0.0281 (7)
C161.0021 (3)0.7736 (2)−0.13485 (16)0.0406 (9)
C171.1722 (3)0.6775 (3)−0.11692 (17)0.0510 (11)
C180.2807 (2)0.42669 (18)0.38978 (13)0.0234 (6)
C190.4584 (2)0.31872 (18)0.36541 (12)0.0216 (6)
C200.5969 (2)0.30589 (19)0.41223 (12)0.0226 (6)
C210.7585 (2)0.20349 (18)0.39261 (12)0.0223 (6)
C220.7816 (2)0.11224 (19)0.32436 (13)0.0248 (7)
C230.6454 (2)0.1236 (2)0.27718 (13)0.0275 (7)
C240.4850 (2)0.22611 (19)0.29689 (13)0.0239 (7)
C250.9003 (2)0.19539 (18)0.44524 (13)0.0233 (7)
C261.2010 (2)0.0805 (2)0.45986 (14)0.0289 (7)
C271.3504 (2)−0.0335 (2)0.41217 (14)0.0335 (8)
H1a0.3909960.5094760.2170220.0361*
H1b0.3391670.604550.3033870.0361*
H2−0.0097210.5731150.1927560.0257*
H3−0.0021720.6241780.3788530.0255*
H4a−0.1097050.4388540.3105720.0301*
H4b−0.1090340.4686380.4124730.0301*
H5a−0.3953710.5748810.3741160.034*
H5b−0.3198890.6719050.4091180.034*
H6a−0.3260410.6265260.2279010.0346*
H6b−0.4375130.7532030.2825480.0346*
H7a−0.1863380.7759930.1891460.0316*
H7b−0.1801830.8028460.2909010.0316*
H8a0.1175250.7120730.0962220.0296*
H8b0.2741730.5827410.0958790.0296*
H100.5292840.6181780.0107540.0285*
H120.6423660.9425960.0600720.0292*
H130.3908891.0140690.1708410.0302*
H16a0.9636790.740749−0.1831660.0488*
H16b1.0210280.852032−0.1537320.0488*
H17a1.2621120.665384−0.1683450.0765*
H17b1.2082070.708856−0.0671320.0765*
H17c1.1560020.596333−0.1036940.0765*
H18a0.1995410.3942520.4268760.0281*
H18b0.2953010.4947970.4234470.0281*
H200.5810290.3688160.4590720.0271*
H220.8922950.0415230.3102080.0298*
H230.661590.0603220.2305160.033*
H26a1.1725410.0609670.5206340.0347*
H26b1.2336980.1566810.4544380.0347*
H27a1.31469−0.1084410.4142480.0503*
H27b1.378537−0.0141120.3513440.0503*
H27c1.453165−0.0505790.4405050.0503*
H3o0.139 (3)0.829 (3)0.2311 (15)0.0366*
H6o0.280 (3)0.316 (3)0.2587 (16)0.0393*
U11U22U33U12U13U23
O10.0355 (8)0.0382 (9)0.0379 (9)−0.0156 (7)0.0104 (6)−0.0086 (7)
O20.0280 (7)0.0358 (9)0.0439 (9)−0.0156 (6)0.0079 (6)−0.0004 (7)
O30.0272 (7)0.0266 (8)0.0324 (8)−0.0073 (6)0.0060 (6)−0.0034 (6)
O40.0325 (8)0.0300 (8)0.0357 (8)−0.0042 (6)−0.0127 (6)−0.0063 (7)
O50.0199 (7)0.0305 (8)0.0329 (8)−0.0025 (6)−0.0080 (5)−0.0027 (6)
O60.0278 (7)0.0283 (8)0.0416 (9)−0.0046 (6)−0.0155 (6)−0.0064 (7)
N10.0175 (7)0.0280 (9)0.0235 (8)−0.0080 (6)−0.0031 (6)0.0047 (7)
N20.0173 (7)0.0239 (9)0.0238 (8)−0.0047 (6)−0.0034 (6)0.0040 (7)
C10.0193 (9)0.0345 (12)0.0359 (12)−0.0084 (8)−0.0055 (8)0.0115 (9)
C20.0175 (9)0.0246 (10)0.0230 (10)−0.0082 (7)−0.0035 (7)0.0022 (8)
C30.0174 (9)0.0221 (10)0.0216 (9)−0.0039 (7)−0.0024 (7)−0.0009 (8)
C40.0203 (9)0.0296 (11)0.0262 (10)−0.0101 (8)−0.0027 (7)0.0042 (8)
C50.0193 (9)0.0357 (12)0.0294 (11)−0.0098 (8)−0.0015 (8)0.0025 (9)
C60.0173 (9)0.0362 (12)0.0305 (11)−0.0058 (8)−0.0044 (8)0.0024 (9)
C70.0216 (9)0.0290 (11)0.0255 (10)−0.0048 (8)−0.0042 (8)0.0045 (8)
C80.0244 (9)0.0255 (10)0.0230 (10)−0.0089 (8)0.0002 (7)0.0004 (8)
C90.0223 (9)0.0228 (10)0.0209 (9)−0.0077 (7)−0.0041 (7)0.0038 (8)
C100.0247 (9)0.0232 (10)0.0224 (10)−0.0073 (8)−0.0034 (7)0.0012 (8)
C110.0229 (9)0.0273 (10)0.0214 (10)−0.0091 (8)−0.0044 (7)0.0033 (8)
C120.0258 (10)0.0250 (10)0.0250 (10)−0.0108 (8)−0.0081 (8)0.0068 (8)
C130.0284 (10)0.0218 (10)0.0253 (10)−0.0075 (8)−0.0073 (8)0.0015 (8)
C140.0217 (9)0.0226 (10)0.0222 (10)−0.0032 (7)−0.0021 (7)0.0026 (8)
C150.0262 (10)0.0305 (11)0.0283 (11)−0.0117 (8)−0.0022 (8)0.0041 (9)
C160.0318 (11)0.0473 (14)0.0405 (13)−0.0171 (10)0.0093 (9)0.0016 (11)
C170.0365 (13)0.0683 (19)0.0445 (15)−0.0167 (12)0.0008 (11)0.0037 (13)
C180.0220 (9)0.0233 (10)0.0226 (10)−0.0051 (7)−0.0032 (7)0.0020 (8)
C190.0211 (9)0.0209 (10)0.0222 (9)−0.0066 (7)−0.0027 (7)0.0030 (8)
C200.0239 (9)0.0214 (10)0.0209 (9)−0.0071 (7)−0.0010 (7)0.0000 (8)
C210.0219 (9)0.0218 (10)0.0226 (10)−0.0075 (7)−0.0018 (7)0.0038 (8)
C220.0208 (9)0.0226 (10)0.0275 (10)−0.0039 (8)−0.0017 (8)−0.0013 (8)
C230.0273 (10)0.0247 (11)0.0288 (11)−0.0070 (8)−0.0038 (8)−0.0049 (8)
C240.0219 (9)0.0234 (10)0.0279 (10)−0.0089 (8)−0.0064 (8)0.0010 (8)
C250.0229 (9)0.0207 (10)0.0256 (10)−0.0069 (8)−0.0037 (8)0.0032 (8)
C260.0235 (10)0.0298 (11)0.0353 (11)−0.0081 (8)−0.0130 (8)0.0056 (9)
C270.0217 (10)0.0369 (12)0.0396 (12)−0.0064 (8)−0.0067 (9)0.0036 (10)
O1—C151.209 (3)C8—H8b0.96
O2—C151.340 (3)C9—C101.385 (2)
O2—C161.463 (3)C9—C141.403 (3)
O3—C141.359 (2)C10—C111.400 (3)
O3—H3o0.89 (3)C10—H100.96
O4—C251.210 (3)C11—C121.392 (3)
O5—C251.3364 (19)C11—C151.485 (2)
O5—C261.451 (3)C12—C131.382 (2)
O6—C241.360 (3)C12—H120.96
O6—H6o0.91 (2)C13—C141.393 (3)
N1—C11.476 (2)C13—H130.96
N1—C21.474 (3)C16—C171.487 (3)
N1—C81.471 (2)C16—H16a0.96
N2—C11.479 (3)C16—H16b0.96
N2—C31.474 (2)C17—H17a0.96
N2—C181.470 (2)C17—H17b0.96
C1—H1a0.96C17—H17c0.96
C1—H1b0.96C18—C191.514 (2)
C2—C31.501 (3)C18—H18a0.96
C2—C71.518 (2)C18—H18b0.96
C2—H20.96C19—C201.390 (3)
C3—C41.522 (3)C19—C241.402 (3)
C3—H30.96C20—C211.396 (2)
C4—C51.533 (2)C20—H200.96
C4—H4a0.96C21—C221.396 (3)
C4—H4b0.96C21—C251.481 (3)
C5—C61.529 (3)C22—C231.380 (3)
C5—H5a0.96C22—H220.96
C5—H5b0.96C23—C241.391 (2)
C6—C71.539 (3)C23—H230.96
C6—H6a0.96C26—C271.505 (2)
C6—H6b0.96C26—H26a0.96
C7—H7a0.96C26—H26b0.96
C7—H7b0.96C27—H27a0.96
C8—C91.512 (3)C27—H27b0.96
C8—H8a0.96C27—H27c0.96
C15—O2—C16116.06 (17)C10—C11—C15117.93 (18)
C14—O3—H3o102.3 (13)C12—C11—C15122.6 (2)
C25—O5—C26117.08 (16)C11—C12—C13120.4 (2)
C24—O6—H6o103.4 (18)C11—C12—H12119.8207
C1—N1—C2105.79 (16)C13—C12—H12119.8195
C1—N1—C8113.67 (13)C12—C13—C14119.71 (19)
C2—N1—C8114.09 (16)C12—C13—H13120.1478
C1—N2—C3102.83 (14)C14—C13—H13120.1472
C1—N2—C18112.75 (16)O3—C14—C9120.36 (19)
C3—N2—C18114.62 (13)O3—C14—C13118.70 (18)
N1—C1—N2106.30 (15)C9—C14—C13120.94 (16)
N1—C1—H1a109.4712O1—C15—O2123.33 (17)
N1—C1—H1b109.4709O1—C15—C11124.4 (2)
N2—C1—H1a109.4716O2—C15—C11112.25 (18)
N2—C1—H1b109.4715O2—C16—C17112.13 (19)
H1a—C1—H1b112.4688O2—C16—H16a109.4709
N1—C2—C3101.91 (15)O2—C16—H16b109.4712
N1—C2—C7116.25 (17)C17—C16—H16a109.4713
N1—C2—H2110.6306C17—C16—H16b109.4715
C3—C2—C7110.74 (14)H16a—C16—H16b106.6803
C3—C2—H2116.1453C16—C17—H17a109.4706
C7—C2—H2101.7775C16—C17—H17b109.471
N2—C3—C2100.86 (13)C16—C17—H17c109.4713
N2—C3—C4116.93 (16)H17a—C17—H17b109.4711
N2—C3—H3110.9593H17a—C17—H17c109.4713
C2—C3—C4110.85 (17)H17b—C17—H17c109.4722
C2—C3—H3117.026N2—C18—C19111.38 (14)
C4—C3—H3100.9923N2—C18—H18a109.4715
C3—C4—C5106.90 (17)N2—C18—H18b109.4713
C3—C4—H4a109.4713C19—C18—H18a109.4707
C3—C4—H4b109.4714C19—C18—H18b109.4714
C5—C4—H4a109.4711H18a—C18—H18b107.4978
C5—C4—H4b109.471C18—C19—C20121.07 (17)
H4a—C4—H4b111.9296C18—C19—C24120.63 (17)
C4—C5—C6112.75 (15)C20—C19—C24118.26 (15)
C4—C5—H5a109.4716C19—C20—C21121.41 (18)
C4—C5—H5b109.4711C19—C20—H20119.2941
C6—C5—H5a109.4709C21—C20—H20119.2942
C6—C5—H5b109.4716C20—C21—C22119.27 (18)
H5a—C5—H5b105.9755C20—C21—C25118.64 (17)
C5—C6—C7112.22 (17)C22—C21—C25122.08 (15)
C5—C6—H6a109.4716C21—C22—C23120.05 (15)
C5—C6—H6b109.4709C21—C22—H22119.9737
C7—C6—H6a109.4709C23—C22—H22119.9726
C7—C6—H6b109.4708C22—C23—C24120.36 (19)
H6a—C6—H6b106.5811C22—C23—H23119.8209
C2—C7—C6106.70 (17)C24—C23—H23119.8211
C2—C7—H7a109.4713O6—C24—C19121.35 (14)
C2—C7—H7b109.4711O6—C24—C23118.01 (18)
C6—C7—H7a109.4719C19—C24—C23120.64 (19)
C6—C7—H7b109.4712O4—C25—O5123.08 (18)
H7a—C7—H7b112.1028O4—C25—C21125.33 (15)
N1—C8—C9111.39 (17)O5—C25—C21111.58 (16)
N1—C8—H8a109.4707O5—C26—C27106.08 (17)
N1—C8—H8b109.4706O5—C26—H26a109.4715
C9—C8—H8a109.4718O5—C26—H26b109.4715
C9—C8—H8b109.4714C27—C26—H26a109.4715
H8a—C8—H8b107.4817C27—C26—H26b109.4709
C8—C9—C10122.19 (18)H26a—C26—H26b112.6645
C8—C9—C14119.30 (15)C26—C27—H27a109.4704
C10—C9—C14118.4 (2)C26—C27—H27b109.4712
C9—C10—C11121.07 (19)C26—C27—H27c109.4714
C9—C10—H10119.4657H27a—C27—H27b109.4716
C11—C10—H10119.4663H27a—C27—H27c109.4708
C10—C11—C12119.46 (16)H27b—C27—H27c109.4719
N1—C2—C3—N2−45.57 (16)C20—C21—C25—O43.4 (3)
C7—C2—C3—C465.6 (2)C15—O2—C16—C17−86.5 (2)
C10—C11—C15—O10.9 (3)C25—O5—C26—C27−178.97 (17)
D—H···AD—HH···AD···AD—H···A
O3—H3o···N10.89 (3)1.82 (3)2.663 (2)156.9 (19)
O6—H6o···N20.91 (2)1.82 (3)2.669 (2)154 (3)
C2—H2···O1i0.962.583.362 (2)138
C3—H3···O4ii0.962.573.436 (2)151
C8—H8b···O1i0.962.573.336 (2)137
C22—H22···O3iii0.962.443.351 (2)159
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O3—H3o⋯N10.89 (3)1.82 (3)2.663 (2)156.9 (19)
O6—H6o⋯N20.91 (2)1.82 (3)2.669 (2)154 (3)
C2—H2⋯O1i0.962.583.362 (2)138
C3—H3⋯O4ii0.962.573.436 (2)151
C8—H8b⋯O1i0.962.573.336 (2)137
C22—H22⋯O3iii0.962.443.351 (2)159

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

  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.  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.  Di-n-propyl 4,4'-dihy-droxy-3,3'-{[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octa-hydro-1H-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:  2011-09-14
  3 in total
  1 in total

1.  Dimethyl 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:  2011-10-12
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.