Literature DB >> 22412589

6,6'-Dimethyl-2,2'-[1,3-diazinane-1,3-diyl-bis(methyl-ene)]diphenol.

Augusto Rivera, Derly Marcela González, Jaime Ríos-Motta, Karla Fejfarová, Michal Dušek.   

Abstract

In the mol-ecule of the title compound, C(20)H(26)N(2)O(2), the 1,3-diazinane ring adopts a slightly distorted chair conformation and the hy-droxy-benzyl substituents occupy equatorial positions on the n class="Disease">N atoms of the heterocyclic ring. There are two intra-molecular O-H⋯N hydrogen bonds between the N atoms of the 1,3-diazinane ring and the hy-droxy groups of the aromatic rings, with an S(6) set-graph motif. However, the two observed intra-molecular hydrogen-bond distances were different. Considering that both N atoms experience the same chemical environment, it is surprising to see the difference in O⋯N distances [2.6771 (14) and 2.8123 (12) Å]. The crystal structure is further stabilized by a C-H⋯π interaction.

Entities:  

Year:  2012        PMID: 22412589      PMCID: PMC3295478          DOI: 10.1107/S1600536812005284

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


Related literature

For a previous determination of a related structure, see: Rivera et al. (2012 ▶). For a related di-Mannich base, see: Rivera et al. (2009 ▶). 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 n class="Chemical">hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995 ▶). For the background to hydrogen-bond energy in Mannich bases, see: Koll et al. (2006 ▶).

Experimental

Crystal data

C20H26N2O2 M = 326.4 Monoclinic, a = 31.2788 (5) Å b = 9.7215 (1) Å c = 12.4508 (2) Å β = 107.936 (2)° V = 3602.00 (10) Å3 Z = 8 Cu Kα radiation μ = 0.62 mm−1 T = 120 K 0.3 × 0.14 × 0.07 mm

Data collection

Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ▶) T min = 0.615, T max = 1 20724 measured reflections 3210 independent reflections 2750 reflections with I > 3σ(I) R int = 0.031

Refinement

R[F 2 > 2σ(F 2)] = 0.034 wR(F 2) = 0.100 S = 1.61 3210 reflections 224 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.15 e Å−3 Δρmin = −0.14 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/S1600536812005284/nk2137sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812005284/nk2137Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812005284/nk2137Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H26N2O2F(000) = 1408
Mr = 326.4Dx = 1.204 Mg m3
Monoclinic, C2/cCu Kα radiation, λ = 1.5418 Å
Hall symbol: -C 2ycCell parameters from 10886 reflections
a = 31.2788 (5) Åθ = 3.0–67.0°
b = 9.7215 (1) ŵ = 0.62 mm1
c = 12.4508 (2) ÅT = 120 K
β = 107.936 (2)°Prism, colourless
V = 3602.00 (10) Å30.3 × 0.14 × 0.07 mm
Z = 8
Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector3210 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source2750 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.031
Detector resolution: 10.3784 pixels mm-1θmax = 67.1°, θmin = 3.0°
Rotation method data acquisition using ω scansh = −36→37
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)k = −11→11
Tmin = 0.615, Tmax = 1l = −14→13
20724 measured reflections
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.034Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0016I2)
wR(F2) = 0.100(Δ/σ)max = 0.003
S = 1.61Δρmax = 0.15 e Å3
3210 reflectionsΔρmin = −0.14 e Å3
224 parametersExtinction correction: B–C type 1 Lorentzian isotropic (Becker & Coppens, 1974)
0 restraintsExtinction coefficient: 900 (300)
98 constraints
Experimental. CrysAlis PRO (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
O10.06464 (3)0.07051 (9)0.66310 (8)0.0302 (3)
O20.22184 (3)−0.05521 (9)0.85547 (8)0.0307 (3)
N10.09336 (3)−0.12594 (9)0.55120 (8)0.0253 (3)
N20.17352 (3)−0.14744 (9)0.63781 (8)0.0243 (3)
C10.13773 (4)−0.09468 (12)0.54144 (10)0.0246 (4)
C20.08708 (4)−0.27558 (12)0.55476 (12)0.0312 (4)
C30.12437 (4)−0.33754 (12)0.65145 (12)0.0325 (4)
C40.17000 (4)−0.29827 (12)0.64228 (11)0.0287 (4)
C50.05832 (4)−0.06437 (12)0.45500 (11)0.0277 (4)
C60.05613 (4)0.08973 (12)0.46498 (10)0.0251 (4)
C70.05753 (4)0.14970 (12)0.56815 (10)0.0247 (4)
C80.05113 (4)0.29077 (12)0.57775 (11)0.0285 (4)
C90.04476 (4)0.37139 (13)0.48171 (12)0.0329 (4)
C100.04482 (4)0.31518 (13)0.37985 (12)0.0347 (4)
C110.05025 (4)0.17415 (13)0.37139 (11)0.0307 (4)
C120.05171 (5)0.35190 (14)0.68853 (13)0.0404 (5)
C130.21697 (4)−0.10533 (12)0.62478 (10)0.0274 (4)
C140.25656 (4)−0.14837 (11)0.72318 (10)0.0244 (4)
C150.25775 (4)−0.11617 (11)0.83352 (10)0.0239 (4)
C160.29572 (4)−0.14483 (11)0.92540 (10)0.0254 (4)
C170.33194 (4)−0.20947 (11)0.90430 (11)0.0272 (4)
C180.33074 (4)−0.24696 (13)0.79600 (11)0.0291 (4)
C190.29302 (4)−0.21597 (12)0.70615 (11)0.0278 (4)
C200.29665 (5)−0.10650 (14)1.04259 (11)0.0353 (5)
H1a0.140383−0.1343470.4731670.0295*
H1b0.140950.0030830.5362670.0295*
H2a0.087705−0.3155910.4847680.0374*
H2b0.058548−0.2946080.5654530.0374*
H3a0.121489−0.4358940.649720.039*
H3b0.121758−0.305020.721960.039*
H4a0.193116−0.332740.706730.0345*
H4b0.173643−0.3376060.5749060.0345*
H5a0.029635−0.1034890.450480.0332*
H5b0.064148−0.0875480.3858630.0332*
H90.0401930.4685840.486370.0395*
H100.041140.373250.3152610.0416*
H110.0499410.1347350.300460.0368*
H12a0.0332340.2976210.7211320.0605*
H12b0.0819680.3531160.738630.0605*
H12c0.0402860.444190.6768620.0605*
H13a0.217355−0.0073010.61580.0329*
H13b0.219925−0.1437220.5563840.0329*
H170.358424−0.2286170.9661950.0327*
H180.355763−0.2938860.7833510.0349*
H190.292099−0.2416540.6310230.0334*
H20a0.272699−0.1527611.0609760.053*
H20b0.324928−0.1333161.0951010.053*
H20c0.29292−0.0088311.0468160.053*
H10.0756 (5)−0.0090 (18)0.6433 (14)0.0454*
H20.1987 (6)−0.0618 (17)0.7916 (16)0.0461*
U11U22U33U12U13U23
O10.0322 (5)0.0307 (5)0.0310 (5)−0.0004 (3)0.0144 (4)0.0017 (3)
O20.0253 (4)0.0363 (5)0.0309 (5)0.0075 (3)0.0093 (4)−0.0010 (4)
N10.0202 (5)0.0235 (5)0.0300 (6)−0.0009 (4)0.0046 (4)0.0006 (4)
N20.0197 (5)0.0255 (5)0.0262 (5)0.0013 (3)0.0051 (4)0.0026 (4)
C10.0215 (6)0.0258 (6)0.0251 (6)0.0006 (4)0.0051 (5)0.0010 (4)
C20.0264 (6)0.0243 (6)0.0404 (7)−0.0037 (4)0.0068 (5)−0.0013 (5)
C30.0314 (7)0.0241 (6)0.0399 (8)−0.0020 (5)0.0080 (5)0.0042 (5)
C40.0288 (6)0.0253 (6)0.0298 (7)0.0035 (4)0.0057 (5)0.0017 (5)
C50.0206 (6)0.0274 (6)0.0314 (7)−0.0003 (4)0.0025 (5)−0.0023 (5)
C60.0145 (5)0.0290 (6)0.0287 (6)−0.0006 (4)0.0022 (4)−0.0007 (5)
C70.0157 (5)0.0287 (6)0.0295 (7)−0.0018 (4)0.0066 (5)0.0017 (5)
C80.0178 (6)0.0294 (6)0.0386 (7)−0.0017 (4)0.0089 (5)−0.0040 (5)
C90.0226 (6)0.0255 (6)0.0467 (8)0.0003 (4)0.0048 (5)0.0013 (5)
C100.0296 (7)0.0341 (7)0.0348 (7)0.0005 (5)0.0017 (5)0.0087 (5)
C110.0252 (6)0.0355 (7)0.0268 (7)0.0007 (5)0.0016 (5)0.0012 (5)
C120.0392 (8)0.0369 (7)0.0498 (9)0.0007 (5)0.0210 (6)−0.0090 (6)
C130.0225 (6)0.0332 (6)0.0265 (6)0.0010 (5)0.0075 (5)0.0032 (5)
C140.0204 (6)0.0258 (6)0.0267 (6)−0.0002 (4)0.0068 (5)0.0021 (4)
C150.0221 (6)0.0217 (5)0.0291 (6)0.0008 (4)0.0097 (5)0.0010 (4)
C160.0251 (6)0.0226 (6)0.0278 (6)−0.0018 (4)0.0070 (5)0.0010 (4)
C170.0222 (6)0.0265 (6)0.0300 (7)0.0002 (4)0.0037 (5)0.0030 (5)
C180.0222 (6)0.0304 (6)0.0350 (7)0.0038 (5)0.0093 (5)0.0003 (5)
C190.0257 (6)0.0306 (6)0.0285 (7)0.0009 (4)0.0101 (5)−0.0006 (5)
C200.0334 (7)0.0427 (7)0.0278 (7)0.0019 (5)0.0061 (5)−0.0009 (5)
O1—C71.3704 (15)C8—C91.3918 (19)
O1—H10.910 (18)C8—C121.497 (2)
O2—C151.3701 (16)C9—C101.382 (2)
O2—H20.898 (16)C9—H90.96
N1—C11.4619 (16)C10—C111.3895 (18)
N1—C21.4703 (15)C10—H100.96
N1—C51.4784 (14)C11—H110.96
N2—C11.4591 (13)C12—H12a0.96
N2—C41.4727 (15)C12—H12b0.96
N2—C131.4753 (16)C12—H12c0.96
C1—H1a0.96C13—C141.5084 (14)
C1—H1b0.96C13—H13a0.96
C2—C31.5191 (16)C13—H13b0.96
C2—H2a0.96C14—C151.3983 (18)
C2—H2b0.96C14—C191.3879 (18)
C3—C41.515 (2)C15—C161.4000 (14)
C3—H3a0.96C16—C171.3894 (18)
C3—H3b0.96C16—C201.4976 (19)
C4—H4a0.96C17—C181.3861 (19)
C4—H4b0.96C17—H170.96
C5—C61.5066 (16)C18—C191.3861 (15)
C5—H5a0.96C18—H180.96
C5—H5b0.96C19—H190.96
C6—C71.3990 (18)C20—H20a0.96
C6—C111.3903 (18)C20—H20b0.96
C7—C81.3964 (16)C20—H20c0.96
C7—O1—H1102.6 (11)C9—C8—C12121.73 (11)
C15—O2—H2106.3 (13)C8—C9—C10121.71 (12)
C1—N1—C2110.32 (9)C8—C9—H9119.1442
C1—N1—C5109.53 (10)C10—C9—H9119.1447
C2—N1—C5110.63 (8)C9—C10—C11119.64 (13)
C1—N2—C4109.49 (8)C9—C10—H10120.1785
C1—N2—C13108.15 (9)C11—C10—H10120.1783
C4—N2—C13111.25 (9)C6—C11—C10120.44 (13)
N1—C1—N2111.48 (10)C6—C11—H11119.78
N1—C1—H1a109.4714C10—C11—H11119.7804
N1—C1—H1b109.4721C8—C12—H12a109.4711
N2—C1—H1a109.4702C8—C12—H12b109.4722
N2—C1—H1b109.4711C8—C12—H12c109.4711
H1a—C1—H1b107.3846H12a—C12—H12b109.4712
N1—C2—C3109.82 (9)H12a—C12—H12c109.471
N1—C2—H2a109.471H12b—C12—H12c109.4707
N1—C2—H2b109.4726N2—C13—C14112.79 (10)
C3—C2—H2a109.4711N2—C13—H13a109.4717
C3—C2—H2b109.4718N2—C13—H13b109.4711
H2a—C2—H2b109.1181C14—C13—H13a109.4713
C2—C3—C4110.58 (11)C14—C13—H13b109.4711
C2—C3—H3a109.4709H13a—C13—H13b105.9345
C2—C3—H3b109.4706C13—C14—C15120.18 (11)
C4—C3—H3a109.4712C13—C14—C19121.00 (11)
C4—C3—H3b109.4715C15—C14—C19118.79 (10)
H3a—C3—H3b108.3382O2—C15—C14121.16 (9)
N2—C4—C3109.68 (10)O2—C15—C16117.68 (11)
N2—C4—H4a109.4709C14—C15—C16121.16 (11)
N2—C4—H4b109.4709C15—C16—C17118.13 (12)
C3—C4—H4a109.4718C15—C16—C20120.24 (11)
C3—C4—H4b109.4711C17—C16—C20121.63 (10)
H4a—C4—H4b109.2658C16—C17—C18121.56 (10)
N1—C5—C6112.15 (9)C16—C17—H17119.2196
N1—C5—H5a109.4713C18—C17—H17119.2211
N1—C5—H5b109.4705C17—C18—C19119.30 (12)
C6—C5—H5a109.4715C17—C18—H18120.3511
C6—C5—H5b109.4715C19—C18—H18120.3499
H5a—C5—H5b106.6581C14—C19—C18120.99 (12)
C5—C6—C7120.05 (11)C14—C19—H19119.5056
C5—C6—C11121.03 (11)C18—C19—H19119.5079
C7—C6—C11118.83 (11)C16—C20—H20a109.4711
O1—C7—C6120.60 (10)C16—C20—H20b109.4716
O1—C7—C8117.86 (11)C16—C20—H20c109.4707
C6—C7—C8121.54 (11)H20a—C20—H20b109.4715
C7—C8—C9117.77 (12)H20a—C20—H20c109.4703
C7—C8—C12120.50 (12)H20b—C20—H20c109.4722
D—H···AD—HH···AD···AD—H···A
O1—H1···N10.910 (18)1.818 (19)2.6771 (14)156.3 (16)
O2—H2···N20.898 (16)2.013 (18)2.8123 (12)147.6 (17)
C17—H17···Cg2i0.962.733.5577 (14)144
Table 1

Hydrogen-bond geometry (Å, °)

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

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1⋯N10.910 (18)1.818 (19)2.6771 (14)156.3 (16)
O2—H2⋯N20.898 (16)2.013 (18)2.8123 (12)147.6 (17)
C17—H17⋯Cg2i0.962.733.5577 (14)144

Symmetry code: (i) .

  2 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.  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
  2 in total

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