Literature DB >> 22219944

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.

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

Abstract

The title compound, C(25)H(30)N(2)O(6), has the imidazolidine ring in an envelope conformation. There are two intra-molecular O-H⋯N hydrogen-bond inter-actions with graph-set motif S(6). The cyclo-hexane ring adopts a slightly distorted chair conformation. One methyl carboxyl-ate substituent forms a dihedral angle of 12.00 (5)° with the plane of the benzene ring, while the other methyl carboxyl-ate group is almost coplanar, making a dihedral angle of 2.26 (9)°. In the crystal, pairs of inter-molecular C-H⋯O hydrogen bonds form racemic dimers, corresponding to an R(2) (2)(18) graph-set motif. Further weak C-H⋯O inter-actions generate a chain running along the c axis.

Entities:  

Year:  2011        PMID: 22219944      PMCID: PMC3247326          DOI: 10.1107/S1600536811040906

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


Related literature

For related structures, see: Rivera et al. (2011 ▶). 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

C25H30N2O6 M = 454.5 Monoclinic, a = 26.3472 (6) Å b = 9.1432 (1) Å c = 21.6585 (4) Å β = 121.139 (3)° V = 4465.7 (2) Å3 Z = 8 Cu Kα radiation μ = 0.80 mm−1 T = 120 K 0.41 × 0.23 × 0.16 mm

Data collection

Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ▶) T min = 0.853, T max = 1 17421 measured reflections 3970 independent reflections 3309 reflections with I > 3σ(I) R int = 0.028

Refinement

R[F 2 > 2σ(F 2)] = 0.035 wR(F 2) = 0.097 S = 1.54 3970 reflections 304 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.26 e Å−3 Δρmin = −0.18 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/S1600536811040906/bt5658sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811040906/bt5658Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811040906/bt5658Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C25H30N2O6F(000) = 1936
Mr = 454.5Dx = 1.352 Mg m3
Monoclinic, C2/cCu Kα radiation, λ = 1.5418 Å
Hall symbol: -C 2ycCell parameters from 9151 reflections
a = 26.3472 (6) Åθ = 3.4–67.1°
b = 9.1432 (1) ŵ = 0.80 mm1
c = 21.6585 (4) ÅT = 120 K
β = 121.139 (3)°Block, colourless
V = 4465.7 (2) Å30.41 × 0.23 × 0.16 mm
Z = 8
Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector3970 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source3309 reflections with I > 3σ(I)
mirrorRint = 0.028
Detector resolution: 10.3784 pixels mm-1θmax = 67.1°, θmin = 3.9°
Rotation method data acquisition using ω scansh = −31→30
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)k = −10→10
Tmin = 0.853, Tmax = 1l = −24→25
17421 measured reflections
Refinement on F20 constraints
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.097Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
S = 1.54(Δ/σ)max = 0.045
3970 reflectionsΔρmax = 0.26 e Å3
304 parametersΔρmin = −0.18 e Å3
0 restraints
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
O10.25904 (4)0.33029 (11)1.07162 (5)0.0309 (4)
O20.18467 (4)0.18439 (10)1.05612 (5)0.0305 (4)
O30.03275 (4)0.68882 (11)0.84111 (5)0.0269 (4)
O40.01966 (4)0.25644 (10)0.51016 (5)0.0275 (4)
O50.10151 (4)0.15258 (9)0.52210 (5)0.0246 (4)
O60.22213 (4)0.68869 (11)0.72919 (5)0.0281 (4)
N10.11660 (5)0.80792 (11)0.82539 (6)0.0206 (4)
N20.12619 (5)0.80593 (11)0.72269 (6)0.0203 (4)
C10.12226 (6)0.70921 (14)0.77488 (7)0.0229 (5)
C20.12528 (6)0.95764 (13)0.80739 (7)0.0200 (5)
C30.09573 (6)1.07952 (14)0.82484 (7)0.0244 (6)
C40.10153 (7)1.22240 (15)0.79175 (8)0.0282 (6)
C50.07990 (6)1.20809 (15)0.71143 (8)0.0283 (6)
C60.10988 (6)1.08124 (14)0.69607 (7)0.0252 (6)
C70.09940 (6)0.94404 (13)0.72716 (7)0.0203 (5)
C80.15534 (6)0.76766 (14)0.90155 (7)0.0221 (5)
C90.13584 (6)0.62646 (14)0.91905 (6)0.0201 (5)
C100.17667 (6)0.52797 (14)0.96778 (7)0.0209 (5)
C110.15941 (6)0.40115 (14)0.98767 (7)0.0217 (5)
C120.09912 (6)0.37225 (14)0.95701 (7)0.0232 (6)
C130.05745 (6)0.46807 (14)0.90719 (7)0.0234 (6)
C140.07510 (6)0.59530 (14)0.88841 (7)0.0208 (5)
C150.20657 (6)0.30532 (14)1.04216 (7)0.0238 (6)
C160.22831 (7)0.08821 (16)1.11053 (9)0.0354 (7)
C170.09522 (6)0.74531 (14)0.64881 (7)0.0223 (5)
C180.12328 (5)0.60631 (14)0.64261 (7)0.0196 (5)
C190.08850 (6)0.49718 (13)0.59512 (7)0.0193 (5)
C200.11324 (6)0.37195 (13)0.58482 (7)0.0202 (5)
C210.17476 (6)0.35599 (14)0.62305 (7)0.0227 (5)
C220.21021 (6)0.46283 (14)0.67116 (7)0.0243 (5)
C230.18496 (6)0.58707 (14)0.68127 (7)0.0216 (5)
C240.07276 (6)0.25842 (14)0.53542 (7)0.0209 (5)
C250.06444 (6)0.03656 (14)0.47537 (8)0.0280 (6)
H1a0.0874470.6492310.7498280.0275*
H1b0.1580790.6531250.8010010.0275*
H20.1661220.9866130.8356720.024*
H3a0.1149631.09030.8762150.0293*
H3b0.054531.056830.8046440.0293*
H4a0.0796811.29840.7984360.0338*
H4b0.1421661.2537280.8174840.0338*
H5a0.0377111.1941440.6846060.034*
H5b0.0873071.2978280.6944080.034*
H6a0.0921561.0700660.6449020.0302*
H6b0.1517031.099540.7194430.0302*
H70.0569970.9381340.6974210.0244*
H8a0.1550720.8445110.9315810.0265*
H8b0.1953710.7578040.9122490.0265*
H100.2181840.5475190.9885540.0251*
H120.086520.2857320.9704990.0278*
H130.015990.446520.8854110.0281*
H16a0.208870.0042241.1155550.0531*
H16b0.2557370.0572841.0964980.0531*
H16c0.2493660.1391591.1557390.0531*
H17a0.0944720.8171160.6160090.0268*
H17b0.0544770.7270070.6334330.0268*
H190.0461720.5082560.5685870.0232*
H210.1924270.2708040.6159180.0272*
H220.252520.4512480.6977630.0291*
H25a0.088144−0.0304550.4667310.0421*
H25b0.046388−0.0143330.497930.0421*
H25c0.0341080.0772640.4303690.0421*
H30.0529 (8)0.750 (2)0.8286 (10)0.0404*
H60.1986 (8)0.751 (2)0.7320 (10)0.0422*
U11U22U33U12U13U23
O10.0282 (5)0.0290 (5)0.0291 (5)0.0015 (4)0.0104 (4)0.0040 (4)
O20.0339 (5)0.0213 (5)0.0341 (5)0.0023 (4)0.0159 (5)0.0076 (4)
O30.0212 (5)0.0296 (5)0.0295 (5)0.0038 (4)0.0127 (4)0.0069 (4)
O40.0223 (5)0.0260 (5)0.0278 (5)0.0000 (4)0.0085 (4)−0.0035 (4)
O50.0274 (5)0.0199 (5)0.0270 (5)−0.0007 (4)0.0145 (4)−0.0035 (4)
O60.0228 (5)0.0260 (5)0.0319 (5)−0.0039 (4)0.0116 (4)−0.0081 (4)
N10.0240 (5)0.0190 (5)0.0183 (5)−0.0006 (4)0.0107 (5)0.0009 (4)
N20.0236 (5)0.0187 (5)0.0180 (5)0.0017 (4)0.0103 (4)0.0004 (4)
C10.0280 (7)0.0202 (6)0.0213 (6)0.0012 (5)0.0131 (6)0.0010 (5)
C20.0209 (6)0.0179 (6)0.0209 (6)−0.0006 (5)0.0106 (5)0.0013 (5)
C30.0281 (7)0.0239 (7)0.0228 (7)0.0030 (5)0.0144 (6)0.0004 (5)
C40.0368 (8)0.0201 (7)0.0310 (8)0.0052 (6)0.0199 (7)0.0015 (6)
C50.0344 (8)0.0219 (7)0.0297 (7)0.0059 (6)0.0173 (6)0.0062 (6)
C60.0327 (7)0.0226 (7)0.0222 (7)0.0031 (6)0.0156 (6)0.0032 (5)
C70.0202 (6)0.0199 (6)0.0204 (6)0.0027 (5)0.0101 (5)0.0008 (5)
C80.0225 (6)0.0233 (6)0.0182 (6)−0.0015 (5)0.0089 (5)0.0009 (5)
C90.0229 (6)0.0219 (6)0.0168 (6)−0.0020 (5)0.0111 (5)−0.0024 (5)
C100.0218 (6)0.0234 (7)0.0174 (6)−0.0015 (5)0.0099 (5)−0.0028 (5)
C110.0262 (7)0.0198 (6)0.0201 (6)−0.0008 (5)0.0127 (6)−0.0031 (5)
C120.0294 (7)0.0191 (6)0.0253 (7)−0.0019 (5)0.0171 (6)−0.0028 (5)
C130.0228 (7)0.0248 (7)0.0251 (7)−0.0021 (5)0.0141 (6)−0.0035 (5)
C140.0215 (6)0.0232 (6)0.0182 (6)0.0026 (5)0.0106 (5)−0.0010 (5)
C150.0294 (7)0.0210 (7)0.0217 (6)−0.0002 (5)0.0136 (6)−0.0024 (5)
C160.0412 (8)0.0257 (7)0.0366 (8)0.0081 (6)0.0183 (7)0.0110 (6)
C170.0244 (7)0.0228 (7)0.0168 (6)0.0033 (5)0.0087 (5)0.0006 (5)
C180.0230 (6)0.0204 (6)0.0164 (6)0.0018 (5)0.0109 (5)0.0026 (5)
C190.0191 (6)0.0227 (6)0.0162 (6)0.0015 (5)0.0092 (5)0.0040 (5)
C200.0236 (6)0.0202 (6)0.0180 (6)−0.0003 (5)0.0116 (5)0.0035 (5)
C210.0242 (7)0.0194 (6)0.0255 (7)0.0027 (5)0.0137 (6)0.0024 (5)
C220.0193 (6)0.0245 (7)0.0274 (7)0.0011 (5)0.0109 (6)0.0022 (5)
C230.0234 (6)0.0221 (6)0.0190 (6)−0.0035 (5)0.0108 (5)−0.0001 (5)
C240.0258 (7)0.0200 (6)0.0165 (6)0.0030 (5)0.0106 (5)0.0040 (5)
C250.0338 (7)0.0207 (7)0.0276 (7)−0.0019 (6)0.0145 (6)−0.0046 (5)
O1—C151.2075 (17)C7—H70.96
O2—C151.3519 (19)C8—C91.509 (2)
O2—C161.4432 (16)C8—H8a0.96
O3—C141.3578 (14)C8—H8b0.96
O3—H30.90 (2)C9—C101.3812 (16)
O4—C241.2105 (17)C9—C141.4088 (19)
O5—C241.3488 (19)C10—C111.393 (2)
O5—C251.4426 (15)C10—H100.96
O6—C231.3595 (14)C11—C121.394 (2)
O6—H60.87 (2)C11—C151.4791 (16)
N1—C11.484 (2)C12—C131.3828 (16)
N1—C21.4732 (17)C12—H120.96
N1—C81.4686 (15)C13—C141.389 (2)
N2—C11.480 (2)C13—H130.96
N2—C71.4741 (18)C16—H16a0.96
N2—C171.4775 (16)C16—H16b0.96
C1—H1a0.96C16—H16c0.96
C1—H1b0.96C17—C181.511 (2)
C2—C31.515 (2)C17—H17a0.96
C2—C71.5081 (19)C17—H17b0.96
C2—H20.96C18—C191.3850 (16)
C3—C41.535 (2)C18—C231.4021 (18)
C3—H3a0.96C19—C201.391 (2)
C3—H3b0.96C19—H190.96
C4—C51.531 (2)C20—C211.3951 (18)
C4—H4a0.96C20—C241.4763 (16)
C4—H4b0.96C21—C221.3804 (17)
C5—C61.533 (2)C21—H210.96
C5—H5a0.96C22—C231.390 (2)
C5—H5b0.96C22—H220.96
C6—C71.515 (2)C25—H25a0.96
C6—H6a0.96C25—H25b0.96
C6—H6b0.96C25—H25c0.96
C15—O2—C16115.40 (11)C8—C9—C14120.41 (10)
C14—O3—H3103.5 (11)C10—C9—C14118.31 (13)
C24—O5—C25115.23 (11)C9—C10—C11121.95 (13)
C23—O6—H6104.1 (11)C9—C10—H10119.0222
C1—N1—C2106.36 (12)C11—C10—H10119.0236
C1—N1—C8113.53 (10)C10—C11—C12118.98 (11)
C2—N1—C8114.66 (9)C10—C11—C15117.78 (12)
C1—N2—C7103.68 (13)C12—C11—C15123.23 (13)
C1—N2—C17112.66 (10)C11—C12—C13120.07 (14)
C7—N2—C17112.18 (9)C11—C12—H12119.9668
N1—C1—N2105.84 (10)C13—C12—H12119.9653
N1—C1—H1a109.4722C12—C13—C14120.53 (13)
N1—C1—H1b109.4722C12—C13—H13119.7345
N2—C1—H1a109.4704C14—C13—H13119.7351
N2—C1—H1b109.4705O3—C14—C9121.21 (12)
H1a—C1—H1b112.8746O3—C14—C13118.64 (12)
N1—C2—C3116.58 (14)C9—C14—C13120.14 (11)
N1—C2—C7100.87 (10)O1—C15—O2122.75 (11)
N1—C2—H2111.3309O1—C15—C11124.71 (14)
C3—C2—C7111.32 (10)O2—C15—C11112.54 (12)
C3—C2—H2100.891O2—C16—H16a109.472
C7—C2—H2116.5959O2—C16—H16b109.4708
C2—C3—C4108.75 (15)O2—C16—H16c109.4708
C2—C3—H3a109.472H16a—C16—H16b109.4716
C2—C3—H3b109.4708H16a—C16—H16c109.4711
C4—C3—H3a109.4717H16b—C16—H16c109.471
C4—C3—H3b109.471N2—C17—C18112.97 (9)
H3a—C3—H3b110.1798N2—C17—H17a109.4721
C3—C4—C5112.91 (11)N2—C17—H17b109.469
C3—C4—H4a109.4727C18—C17—H17a109.4721
C3—C4—H4b109.4709C18—C17—H17b109.471
C5—C4—H4a109.4714H17a—C17—H17b105.728
C5—C4—H4b109.4703C17—C18—C19120.39 (11)
H4a—C4—H4b105.7947C17—C18—C23121.45 (10)
C4—C5—C6112.36 (11)C19—C18—C23118.06 (13)
C4—C5—H5a109.4713C18—C19—C20121.81 (12)
C4—C5—H5b109.4717C18—C19—H19119.0941
C6—C5—H5a109.4708C20—C19—H19119.0943
C6—C5—H5b109.4712C19—C20—C21119.18 (11)
H5a—C5—H5b106.4244C19—C20—C24118.18 (12)
C5—C6—C7107.28 (15)C21—C20—C24122.60 (13)
C5—C6—H6a109.4711C20—C21—C22119.93 (13)
C5—C6—H6b109.4712C20—C21—H21120.0335
C7—C6—H6a109.4714C22—C21—H21120.0348
C7—C6—H6b109.4712C21—C22—C23120.34 (12)
H6a—C6—H6b111.5736C21—C22—H22119.8287
N2—C7—C2101.53 (9)C23—C22—H22119.8289
N2—C7—C6118.45 (15)O6—C23—C18121.67 (13)
N2—C7—H7109.7793O6—C23—C22117.68 (11)
C2—C7—C6111.47 (10)C18—C23—C22120.66 (11)
C2—C7—H7116.9848O4—C24—O5122.57 (11)
C6—C7—H799.4758O4—C24—C20124.81 (14)
N1—C8—C9111.57 (9)O5—C24—C20112.61 (12)
N1—C8—H8a109.4706O5—C25—H25a109.4719
N1—C8—H8b109.4706O5—C25—H25b109.4705
C9—C8—H8a109.4711O5—C25—H25c109.4708
C9—C8—H8b109.4718H25a—C25—H25b109.4709
H8a—C8—H8b107.2874H25a—C25—H25c109.472
C8—C9—C10121.21 (12)H25b—C25—H25c109.4712
C10—C11—C15—O11.3 (2)C19—C20—C24—O4−10.1 (2)
D—H···AD—HH···AD···AD—H···A
O3—H3···N10.90 (2)1.80 (2)2.6383 (18)154.3 (16)
O6—H6···N20.87 (2)1.88 (2)2.6814 (18)153.0 (18)
C2—H2···O1i0.962.573.414 (2)146
C4—H4b···O1i0.962.583.353 (2)137
C16—H16c···O6ii0.962.593.350 (2)136
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O3—H3⋯N10.90 (2)1.80 (2)2.6383 (18)154.3 (16)
O6—H6⋯N20.87 (2)1.88 (2)2.6814 (18)153.0 (18)
C2—H2⋯O1i0.962.573.414 (2)146
C4—H4b⋯O1i0.962.583.353 (2)137
C16—H16c⋯O6ii0.962.593.350 (2)136

Symmetry codes: (i) ; (ii) .

  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.  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.

Authors:  Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Karla Fejfarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-10-05

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

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