Literature DB >> 22347099

2,2'-[1,3-Diazinane-1,3-diylbis(methyl-ene)]bis-(4-bromo-phenol).

Augusto Rivera, Ginna Paola Trujillo, Jaime Ríos-Motta, Karla Fejfarová, Michal Dušek.   

Abstract

The title compound, C(18)H(20)Br(2)N(2)O(2), the heterocyclic ring adopts a chair conformation. The benzene rings make dihedral angles of 86.84 (10) and 60.73 (10)° with the mean plane of the heterocyclic ring. The dihedral angle between the two benzene rings is 79.77 (10)°. The mol-ecular structure is stabilized by two intra-molecular hydrogen bonds between the phenolic hy-droxy groups and N atoms with graph-set motif S(6). The crystal structure is stabilized by weak C-H⋯π inter-actions.

Entities:  

Year:  2012        PMID: 22347099      PMCID: PMC3275243          DOI: 10.1107/S1600536812001985

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


Related literature

For related structures, see: Rivera et al. (2012 ▶, 2011 ▶). For the synthesis of the precursor, see: Rivera et al. (2010 ▶). For bond-length data, see: Allen et al. (1987 ▶). For Cremer–Pople puckering parameters, see: Cremer & Pople (1975 ▶). For graph-set notation, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C18H20Br2N2O2 M = 456.2 Orthorhombic, a = 5.9602 (3) Å b = 17.2164 (8) Å c = 17.7222 (8) Å V = 1818.53 (15) Å3 Z = 4 Cu Kα radiation μ = 5.76 mm−1 T = 120 K 0.35 × 0.09 × 0.03 mm

Data collection

Agilent Xcalibur with an Atlas (Gemini ultra Cu) detector diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ▶) T min = 0.63, T max = 1 14453 measured reflections 3221 independent reflections 3014 reflections with I > 3σ(I) R int = 0.034

Refinement

R[F 2 > 2σ(F 2)] = 0.023 wR(F 2) = 0.056 S = 1.37 3221 reflections 225 parameters 2 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.27 e Å−3 Δρmin = −0.34 e Å−3 Absolute structure: Flack (1983 ▶), 1894 Friedel pairs Flack parameter: 0.148 (19) 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/S1600536812001985/bx2397sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812001985/bx2397Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812001985/bx2397Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C18H20Br2N2O2F(000) = 912
Mr = 456.2Dx = 1.666 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.5418 Å
Hall symbol: P 2ac 2abCell parameters from 8581 reflections
a = 5.9602 (3) Åθ = 3.6–67.0°
b = 17.2164 (8) ŵ = 5.76 mm1
c = 17.7222 (8) ÅT = 120 K
V = 1818.53 (15) Å3Plate, colourless
Z = 40.35 × 0.09 × 0.03 mm
Agilent Xcalibur with an Atlas (Gemini ultra Cu) detector diffractometer3221 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source3014 reflections with I > 3σ(I)
mirrorRint = 0.034
Detector resolution: 10.3784 pixels mm-1θmax = 67.2°, θmin = 3.6°
Rotation method data acquisition using ω scansh = −7→6
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)k = −20→20
Tmin = 0.63, Tmax = 1l = −21→20
14453 measured reflections
Refinement on F2Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0004I2)
R[F2 > 2σ(F2)] = 0.023(Δ/σ)max = 0.009
wR(F2) = 0.056Δρmax = 0.27 e Å3
S = 1.37Δρmin = −0.34 e Å3
3221 reflectionsExtinction correction: B-C type 1 Lorentzian isotropic (Becker & Coppens, 1974)
225 parametersExtinction coefficient: 360 (70)
2 restraintsAbsolute structure: Flack (1983), 1894 Friedel pairs
74 constraintsFlack parameter: 0.148 (19)
H atoms treated by a mixture of independent and constrained refinement
Experimental. CrysAlisPro (Agilent, 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
Br10.51306 (8)0.332316 (17)1.176266 (16)0.04042 (10)
Br20.49477 (6)0.037552 (13)0.485209 (15)0.03305 (8)
O10.9595 (3)0.38094 (11)0.87498 (12)0.0318 (6)
O20.9653 (3)0.28722 (12)0.66366 (12)0.0326 (6)
N10.5696 (3)0.35867 (12)0.80850 (13)0.0223 (6)
N20.5782 (4)0.36259 (13)0.67419 (14)0.0260 (7)
C10.4884 (6)0.32162 (12)0.74006 (13)0.0251 (7)
C20.4815 (6)0.43895 (13)0.81379 (15)0.0275 (7)
C30.5591 (5)0.48430 (15)0.74549 (19)0.0342 (10)
C40.4950 (7)0.44293 (13)0.67271 (15)0.0339 (8)
C50.5110 (6)0.31139 (12)0.87501 (13)0.0224 (6)
C60.6347 (4)0.33698 (14)0.94497 (16)0.0214 (7)
C70.8526 (4)0.36921 (14)0.94151 (17)0.0251 (8)
C80.9639 (4)0.38989 (13)1.00746 (17)0.0275 (8)
C90.8650 (5)0.37837 (14)1.07713 (18)0.0294 (9)
C100.6495 (5)0.34704 (14)1.08040 (17)0.0264 (8)
C110.5363 (4)0.32626 (13)1.01568 (15)0.0235 (7)
C120.5203 (6)0.32261 (13)0.60354 (14)0.0269 (7)
C130.6347 (4)0.24464 (16)0.59565 (16)0.0246 (8)
C140.8500 (4)0.23092 (16)0.62571 (16)0.0260 (8)
C150.9503 (4)0.15865 (16)0.61723 (16)0.0284 (8)
C160.8460 (5)0.10008 (17)0.57645 (17)0.0286 (8)
C170.6373 (5)0.11513 (16)0.54497 (16)0.0276 (8)
C180.5310 (5)0.18583 (14)0.55486 (14)0.0243 (7)
H1a0.3274690.3235350.739030.0301*
H1b0.5371310.2684770.739040.0301*
H2a0.5379220.4631410.8587610.0329*
H2b0.3205440.4376310.8148560.0329*
H3a0.4925480.535070.7461970.041*
H3b0.7190010.4906580.7474520.041*
H4a0.3346380.4426630.6675240.0406*
H4b0.5594410.4698610.630530.0406*
H5a0.5440720.2578050.8649320.0269*
H5b0.3523060.3143360.8837680.0269*
H81.1110070.4124161.0045890.033*
H90.9436040.391751.1225990.0352*
H110.3886660.3042521.019250.0282*
H12a0.5595370.3549590.5614350.0322*
H12b0.3606790.3157740.600790.0322*
H151.0938830.1490640.6399220.0341*
H160.9165220.0503650.5701660.0343*
H180.3850150.1942730.5334720.0292*
H1o0.868 (5)0.370 (2)0.8398 (15)0.0382*
H2o0.884 (5)0.3266 (14)0.672 (2)0.0391*
U11U22U33U12U13U23
Br10.0547 (2)0.04237 (16)0.02419 (15)−0.0043 (2)0.00098 (18)0.00131 (11)
Br20.04040 (16)0.02472 (13)0.03402 (15)−0.00507 (16)−0.00497 (17)−0.00090 (10)
O10.0236 (11)0.0369 (9)0.0350 (11)−0.0063 (8)0.0030 (8)0.0000 (8)
O20.0303 (11)0.0359 (9)0.0316 (10)−0.0076 (9)−0.0048 (9)−0.0044 (8)
N10.0264 (12)0.0177 (9)0.0227 (11)−0.0022 (7)0.0022 (8)0.0027 (9)
N20.0349 (12)0.0187 (10)0.0243 (12)−0.0034 (8)0.0010 (9)0.0019 (9)
C10.0291 (13)0.0211 (10)0.0250 (12)−0.0045 (14)0.0021 (14)0.0024 (9)
C20.0328 (13)0.0193 (10)0.0303 (13)0.0024 (12)0.0017 (15)0.0003 (9)
C30.049 (2)0.0172 (11)0.0367 (17)−0.0016 (11)0.0032 (13)0.0024 (11)
C40.0483 (15)0.0235 (11)0.0298 (13)0.0023 (16)0.0057 (19)0.0069 (9)
C50.0221 (12)0.0196 (9)0.0256 (11)−0.0050 (13)0.0029 (14)0.0017 (8)
C60.0202 (12)0.0159 (11)0.0281 (14)−0.0005 (10)−0.0020 (10)0.0021 (10)
C70.0229 (13)0.0173 (11)0.0351 (16)0.0026 (10)0.0018 (11)0.0034 (11)
C80.0233 (14)0.0170 (10)0.0421 (15)−0.0023 (10)−0.0081 (12)0.0035 (10)
C90.0354 (15)0.0160 (12)0.0366 (17)0.0013 (11)−0.0112 (12)−0.0026 (11)
C100.0363 (15)0.0165 (12)0.0265 (15)0.0026 (11)0.0004 (11)0.0027 (10)
C110.0248 (14)0.0174 (10)0.0281 (13)0.0036 (10)−0.0006 (11)0.0024 (9)
C120.0306 (14)0.0264 (11)0.0236 (12)0.0002 (13)−0.0007 (14)0.0033 (9)
C130.0252 (13)0.0278 (13)0.0208 (13)−0.0026 (10)0.0011 (11)0.0017 (11)
C140.0221 (13)0.0337 (14)0.0222 (14)−0.0064 (11)−0.0005 (10)0.0021 (12)
C150.0244 (15)0.0355 (13)0.0254 (13)0.0016 (11)−0.0006 (10)0.0023 (11)
C160.0305 (15)0.0295 (14)0.0259 (15)0.0045 (11)0.0012 (11)0.0030 (12)
C170.0284 (14)0.0296 (14)0.0248 (14)−0.0042 (11)0.0028 (11)0.0041 (12)
C180.0221 (14)0.0291 (11)0.0217 (11)−0.0043 (11)−0.0009 (11)0.0052 (9)
Br1—C101.901 (3)C5—H5a0.96
Br2—C171.905 (3)C5—H5b0.96
O1—C71.355 (4)C6—C71.413 (4)
O1—H1o0.85 (3)C6—C111.396 (4)
O2—C141.365 (3)C7—C81.390 (4)
O2—H2o0.85 (3)C8—C91.382 (4)
N1—C11.453 (3)C8—H80.96
N1—C21.481 (3)C9—C101.394 (4)
N1—C51.474 (3)C9—H90.96
N2—C11.465 (3)C10—C111.378 (4)
N2—C41.470 (3)C11—H110.96
N2—C121.470 (3)C12—C131.512 (4)
C1—H1a0.96C12—H12a0.96
C1—H1b0.96C12—H12b0.96
C2—C31.513 (4)C13—C141.410 (4)
C2—H2a0.96C13—C181.389 (4)
C2—H2b0.96C14—C151.388 (4)
C3—C41.522 (4)C15—C161.388 (4)
C3—H3a0.96C15—H150.96
C3—H3b0.96C16—C171.388 (4)
C4—H4a0.96C16—H160.96
C4—H4b0.96C17—C181.383 (4)
C5—C61.508 (4)C18—H180.96
C7—O1—H1o108 (2)C7—C6—C11118.5 (2)
C14—O2—H2o111 (2)O1—C7—C6121.9 (3)
C1—N1—C2110.1 (2)O1—C7—C8118.0 (2)
C1—N1—C5110.24 (19)C6—C7—C8120.2 (3)
C2—N1—C5112.4 (2)C7—C8—C9120.7 (3)
C1—N2—C4110.1 (2)C7—C8—H8119.6439
C1—N2—C12111.6 (2)C9—C8—H8119.6447
C4—N2—C12110.3 (2)C8—C9—C10119.0 (3)
N1—C1—N2109.4 (2)C8—C9—H9120.4851
N1—C1—H1a109.4712C10—C9—H9120.4852
N1—C1—H1b109.4714Br1—C10—C9118.9 (2)
N2—C1—H1a109.4709Br1—C10—C11120.0 (2)
N2—C1—H1b109.4715C9—C10—C11121.1 (3)
H1a—C1—H1b109.5538C6—C11—C10120.5 (2)
N1—C2—C3108.8 (2)C6—C11—H11119.773
N1—C2—H2a109.4711C10—C11—H11119.7736
N1—C2—H2b109.4713N2—C12—C13112.9 (2)
C3—C2—H2a109.4717N2—C12—H12a109.4712
C3—C2—H2b109.471N2—C12—H12b109.4714
H2a—C2—H2b110.1093C13—C12—H12a109.471
C2—C3—C4111.1 (2)C13—C12—H12b109.471
C2—C3—H3a109.4713H12a—C12—H12b105.8417
C2—C3—H3b109.4711C12—C13—C14121.6 (2)
C4—C3—H3a109.4717C12—C13—C18119.6 (2)
C4—C3—H3b109.4711C14—C13—C18118.7 (2)
H3a—C3—H3b107.8053O2—C14—C13121.7 (2)
N2—C4—C3109.9 (2)O2—C14—C15118.2 (2)
N2—C4—H4a109.4721C13—C14—C15120.1 (2)
N2—C4—H4b109.4708C14—C15—C16121.0 (2)
C3—C4—H4a109.4712C14—C15—H15119.5034
C3—C4—H4b109.4711C16—C15—H15119.5043
H4a—C4—H4b109.0337C15—C16—C17118.4 (3)
N1—C5—C6112.3 (2)C15—C16—H16120.817
N1—C5—H5a109.4708C17—C16—H16120.8173
N1—C5—H5b109.4703Br2—C17—C16119.5 (2)
C6—C5—H5a109.4717Br2—C17—C18118.9 (2)
C6—C5—H5b109.4716C16—C17—C18121.6 (3)
H5a—C5—H5b106.4462C13—C18—C17120.2 (3)
C5—C6—C7121.9 (3)C13—C18—H18119.8928
C5—C6—C11119.6 (2)C17—C18—H18119.8919
?—?—?—??
Cg2 is the centroid of the C6–C11 aromatic ring.
D—H···AD—HH···AD···AD—H···A
O1—H1o···N10.85 (3)1.87 (3)2.634 (3)148 (3)
O2—H2o···N20.85 (3)1.92 (3)2.654 (3)144 (3)
.—···......
C11—H11···Cg2i0.962.963.632 (2)128
Table 1

Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C6–C11 aromatic ring.

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1o⋯N10.85 (3)1.87 (3)2.634 (3)148 (3)
O2—H2o⋯N20.85 (3)1.92 (3)2.654 (3)144 (3)
C11—H11⋯Cg2i0.962.963.632 (2)128

Symmetry code: (i) .

  3 in total

1.  Unexpected conformational consequences of weak hydrogen bonds on 1,3,7,9,13,15,19,21-octaazapentacyclo[19.3.1.1(3,7).1(9,13).1(15,19)]octacosane monohydrate.

Authors:  Augusto Rivera; Jaime Ríos-Motta; Michal Dusek; Markéta Jarosová
Journal:  Acta Crystallogr C       Date:  2010-03-27       Impact factor: 1.172

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.  6,6'-Di-tert-butyl-4,4'-dimeth-oxy-2,2'-[1,3-diazinane-1,3-diylbis(methyl-ene)]diphenol 0.19-hydrate.

Authors:  Augusto Rivera; Derly Marcela González; Jaime Ríos-Motta; Karla Fejfarová; Michal Dušek
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-12-21
  3 in total

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