supplementary materials


go2039 scheme

Acta Cryst. (2012). E68, o191-o192    [ doi:10.1107/S1600536811053542 ]

6,6'-Di-tert-butyl-4,4'-dimethoxy-2,2'-[1,3-diazinane-1,3-diylbis(methylene)]diphenol 0.19-hydrate

A. Rivera, D. M. González, J. Ríos-Motta, K. Fejfarová and M. Dusek

Abstract top

In the title hexahydropyrimidine derivative, C28H42N2O4·0.19H2O, the 1,3-diazinane ring has a chair conformation with a diequatorial substitution. The asymmetric unit contains one half-organic molecule and a solvent water molecule with occupany 0.095. The molecule lies on a mirror plane perpendicular to [010] which passes through the C atoms at the 2- and 5-positions of the heterocyclic system. The partially occupied water molecule is also located on this mirror plane. The dihedral angle between the planes of the aromatic rings is 17.71 (3)°. Two intramolecular O-H...N hydrogen bonds with graph-set motif S(6) are present. No remarkable intermolecular contacts exist in the crystal structure.

Comment top

The asymmetric unit (Fig. 1), contains a one symmetry independent half molecule of 2,2'-(dihydropyrimidine-1,3(2H,4H)-diyldimethanediyl)bis(6-tertbutyl-4-methoxyphenol) and a solvent water molecule with occupany 0.095. The molecule lies on a mirror plane perpendicular to [0,1,0] which passes through the central C atom of the heterocyclic system. In Fig. 1 primed atoms were positioned on the other half of the molecules and had symmetry codes (x, 1/2 - y, z). The hexahydropyrimidine ring of the title compound adopts a chair conformation with a diequatorial substitution (Cremer & Pople, 1975) with puckering parameters Q, θ and φ of 0.5891 (10) Å, 3.01 (11)°, 60.0 (18)°. In the molecule of the title compound (Fig. 1), bond lengths (Allen et al., 1987) and angles are normal and comparable to the related structure namely 2,2'-(dihydropyrimidine-1,3(2H,4H)-diyldimethanediyl)bis (6-methylphenol) whose crystallographic data have been deposited at the Cambridge Crystallographic Data Center. The CCDC deposition number is 854735 (Rivera et al.,2012a). However a careful comparison with the values of the corresponding angles and bond distances in the related structure (Rivera,et al. 2012a), indicated that the O1—C6—C7 angle increase by 1.82°. The crystal structure of the title confirms the presence of two O—H···N(1,3-diazinane) hydrogen bond with graph-set motif S(6) (Bernstein et al. 1995) (Table 1). The N···O distance [N1···O1, 2.6735 (10) Å] is shorter in comparison with the values observed in related structure (Rivera, et al. 2012a), showing a slightly increase in hydrogen-bonding strength.

The most obvious difference between the title compound and the related structure (Rivera, et al. 2012a) is the presence of mirror symmetry in the solid state with molecules bisected by mirror planes (the C1 and C2 atoms of the 1,3-diazinane ring lie on the mirror plane). The partially occupied water molecule also is located on this mirror plane. Another important difference is observed in the dihedral angle between the phenyl rings, which is -17.711 (30)° for the title compound and 58.431 (38)° for related structure (Rivera, et al. 2012a). The deviation of the dihedral angle in (I) is probably due to repulsive interactions between the tert-butyl groups.

Fig 2. shows the crystal packing with channels extended along the [1,0,1] axis and accommodating the water molecules. Each channel is composed of two symmetry equivalent positions of the organic molecule. No remarkable intermolecular contacts exist in the presented structure.

Related literature top

For a related structure, see: Rivera et al. (2012a). For the synthesis of the precursor, see: Rivera et al. (2010). For the preparation of the title compound, see: Rivera et al. (2012b). For bond-length data, see: Allen et al. (1987). For puckering parameters, see: Cremer & Pople (1975). For hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995).

Experimental top

The title compound was obtained according to our recently reported methodology (Rivera et al., 2012b), that is, to a stirred solution of 2-tert-butyl-4-methoxy-phenol (2.0 mmol) in 96% ethanol (5 ml) heated under reflux, was added slowly a solution of 1,3,7,9,13,15,19,21-octaazapentacyclo[19.3.1.13,7.19,13.115,19]octacosane prepared according to a previous report (Rivera et al., 2010) (200 mg, 0.54 mmol) in 96% ethanol (5 ml). Upon completion of the addition, the reaction mixture was stirred under reflux for 60 h. Then the reflux was stopped, the solvent was removed on a rotary evaporator under vacuum and the residue obtained was chromatographed on silica gel eluting with benzene/AcOEt (gradient elution with 5% to 20% AcOEt) to afford a solid which was recrystallized in 96% ethanol to provide high quality crystals of the title compound (I), (Yield 27.0%, m.p. 403–404 K).

Refinement top

All hydrogen atoms were discernible in difference Fourier maps and could be refined to reasonable geometry. According to common practice the hydrogen atoms attached to carbons were kept in ideal positions with C–H distance 0.96 Å during the refinement. The methyl H atoms were allowed to rotate freely about the adjacent C—C bonds. The coordinates of the hydrogen atom bonded to oxygen were refined freely. All H atoms were refined with displacement coefficients Uiso(H) set to 1.5Ueq(C, O) for the methyl- and hydroxyl groups and to 1.2Ueq(C) for the CH–, and CH2– groups.

Computing details top

Data collection: CrysAlis PRO (Agilent, 2010); cell refinement: CrysAlis PRO (Agilent, 2010); data reduction: CrysAlis PRO (Agilent, 2010); 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 (Petříček et al., 2006).

Figures top
[Figure 1] Fig. 1. A view of (I) with the numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. The packing of (I), viewed along the [1,0,1] axis.
6,6'-Di-tert-butyl-4,4'-dimethoxy-2,2'-[1,3-diazinane-1,3- diylbis(methylene)]diphenol 0.19-hydrate top
Crystal data top
C28H42N2O4·0.19H2OF(000) = 1029.6
Mr = 473.5Dx = 1.154 Mg m3
Orthorhombic, PnmaCu Kα radiation, λ = 1.5418 Å
Hall symbol: -P 2ac 2nCell parameters from 37659 reflections
a = 8.2265 (1) Åθ = 4.0–67.0°
b = 33.0103 (2) ŵ = 0.61 mm1
c = 10.0322 (5) ÅT = 120 K
V = 2724.34 (14) Å3Block, colourless
Z = 40.42 × 0.36 × 0.30 mm
Data collection top
Agilent Xcalibur
diffractometer with an Atlas (Gemini ultra Cu) detector
2456 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source2353 reflections with I > 3σ(I)
mirrorRint = 0.027
Detector resolution: 10.3784 pixels mm-1θmax = 67.1°, θmin = 4.6°
Rotation method data acquisition using ω scansh = 99
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2010)
k = 3939
Tmin = 0.073, Tmax = 1l = 1111
54017 measured reflections
Refinement top
Refinement on F285 constraints
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.122Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0016I2)
S = 2.64(Δ/σ)max = 0.005
2456 reflectionsΔρmax = 0.17 e Å3
164 parametersΔρmin = 0.14 e Å3
0 restraints
Crystal data top
C28H42N2O4·0.19H2OV = 2724.34 (14) Å3
Mr = 473.5Z = 4
Orthorhombic, PnmaCu Kα radiation
a = 8.2265 (1) ŵ = 0.61 mm1
b = 33.0103 (2) ÅT = 120 K
c = 10.0322 (5) Å0.42 × 0.36 × 0.30 mm
Data collection top
Agilent Xcalibur
diffractometer with an Atlas (Gemini ultra Cu) detector
2456 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2010)
2353 reflections with I > 3σ(I)
Tmin = 0.073, Tmax = 1Rint = 0.027
54017 measured reflectionsθmax = 67.1°
Refinement top
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.122Δρmax = 0.17 e Å3
S = 2.64Δρmin = 0.14 e Å3
2456 reflectionsAbsolute structure: ?
164 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
O10.48228 (8)0.17951 (2)0.02311 (7)0.0238 (2)
O20.18527 (9)0.03041 (2)0.08155 (9)0.0348 (3)
O30.2004 (8)0.250.5283 (7)0.040 (3)*0.185 (6)
N10.20147 (9)0.21389 (2)0.09520 (8)0.0196 (3)
C10.17203 (15)0.250.17490 (13)0.0188 (4)
C20.1074 (2)0.250.10270 (15)0.0302 (4)
C30.08755 (13)0.21221 (2)0.01750 (10)0.0253 (3)
C40.19236 (11)0.17724 (3)0.17868 (10)0.0219 (3)
C50.26169 (12)0.14026 (3)0.11072 (10)0.0196 (3)
C60.40731 (11)0.14256 (3)0.03904 (9)0.0189 (3)
C70.47830 (11)0.10754 (3)0.01656 (9)0.0197 (3)
C80.39696 (12)0.07106 (3)0.00193 (10)0.0226 (3)
C90.25098 (12)0.06858 (3)0.07237 (10)0.0235 (3)
C100.18330 (11)0.10307 (3)0.12733 (10)0.0211 (3)
C110.64179 (11)0.10927 (3)0.09068 (10)0.0214 (3)
C120.63025 (13)0.13705 (3)0.21310 (10)0.0273 (3)
C130.77305 (12)0.12524 (3)0.00455 (10)0.0271 (3)
C140.69608 (13)0.06750 (3)0.13975 (12)0.0323 (3)
C150.04374 (13)0.02586 (3)0.16101 (14)0.0390 (4)
H10.4062 (18)0.1977 (5)0.0432 (14)0.0357*
H1a0.2433040.250.2506660.0225*
H1b0.0614630.250.2054940.0225*
H2a0.2133830.250.1428240.0362*
H2b0.0270770.250.172080.0362*
H3a0.0218130.2108560.0156030.0304*
H3b0.110020.1886340.0704140.0304*
H4a0.0812240.1722040.2027220.0263*
H4b0.2489990.1818580.2609480.0263*
H80.4427010.0467690.0349670.0271*
H100.0833560.1014810.1764540.0253*
H12a0.597440.163670.1855020.041*
H12b0.7344310.1385380.2559380.041*
H12c0.5516680.1263140.2743920.041*
H13a0.7519220.1531860.0246430.0407*
H13b0.7715250.1097110.0854410.0407*
H13c0.8777970.1228260.0368790.0407*
H14a0.7965770.0700490.1876530.0484*
H14b0.7112710.049830.0647750.0484*
H14c0.6144270.0564240.1975960.0484*
H15a0.0100430.0019850.1601560.0585*
H15b0.0671580.0339690.250870.0585*
H15c0.0417340.0425060.1257450.0585*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0244 (4)0.0180 (4)0.0289 (5)0.0026 (3)0.0051 (3)0.0005 (3)
O20.0366 (5)0.0176 (4)0.0502 (6)0.0053 (3)0.0152 (3)0.0021 (3)
N10.0249 (4)0.0159 (4)0.0180 (5)0.0012 (3)0.0013 (3)0.0002 (3)
C10.0219 (6)0.0169 (6)0.0175 (7)00.0009 (5)0
C20.0451 (9)0.0234 (7)0.0220 (8)00.0092 (6)0
C30.0336 (6)0.0185 (5)0.0239 (5)0.0007 (4)0.0056 (4)0.0031 (4)
C40.0271 (5)0.0174 (5)0.0213 (5)0.0011 (3)0.0042 (4)0.0025 (4)
C50.0220 (5)0.0188 (5)0.0180 (5)0.0020 (3)0.0016 (3)0.0024 (3)
C60.0207 (5)0.0183 (5)0.0176 (5)0.0007 (3)0.0023 (4)0.0018 (3)
C70.0203 (5)0.0220 (5)0.0167 (5)0.0022 (3)0.0025 (3)0.0004 (3)
C80.0254 (5)0.0188 (5)0.0236 (5)0.0035 (4)0.0001 (4)0.0011 (4)
C90.0263 (5)0.0181 (5)0.0263 (6)0.0020 (4)0.0001 (4)0.0022 (4)
C100.0205 (5)0.0208 (5)0.0221 (5)0.0007 (3)0.0008 (4)0.0034 (3)
C110.0210 (5)0.0239 (5)0.0195 (5)0.0012 (4)0.0011 (4)0.0010 (4)
C120.0244 (5)0.0374 (5)0.0202 (5)0.0025 (4)0.0024 (4)0.0034 (4)
C130.0199 (5)0.0395 (6)0.0220 (5)0.0003 (4)0.0005 (4)0.0012 (4)
C140.0290 (5)0.0293 (5)0.0386 (7)0.0041 (4)0.0097 (5)0.0059 (4)
C150.0367 (6)0.0233 (5)0.0570 (8)0.0070 (4)0.0153 (5)0.0034 (5)
Geometric parameters (Å, °) top
O1—C61.3762 (11)C7—C81.3899 (13)
O1—H10.890 (15)C7—C111.5379 (13)
O2—C91.3743 (12)C8—C91.3958 (14)
O2—C151.4190 (14)C8—H80.96
N1—C11.4555 (10)C9—C101.3821 (13)
N1—C31.4696 (13)C10—H100.96
N1—C41.4736 (11)C11—C121.5358 (14)
C1—H1a0.96C11—C131.5353 (14)
C1—H1b0.96C11—C141.5306 (14)
C2—C31.5211 (12)C12—H12a0.96
C2—C3i1.5211 (12)C12—H12b0.96
C2—H2a0.96C12—H12c0.96
C2—H2b0.96C13—H13a0.96
C3—H3a0.96C13—H13b0.96
C3—H3b0.96C13—H13c0.96
C4—C51.5100 (12)C14—H14a0.96
C4—H4a0.96C14—H14b0.96
C4—H4b0.96C14—H14c0.96
C5—C61.3993 (13)C15—H15a0.96
C5—C101.3966 (12)C15—H15b0.96
C6—C71.4103 (13)C15—H15c0.96
C6—O1—H1104.8 (10)C7—C8—H8118.9115
C9—O2—C15117.23 (8)C9—C8—H8118.9125
C1—N1—C3110.33 (7)O2—C9—C8115.22 (8)
C1—N1—C4110.60 (8)O2—C9—C10124.76 (9)
C3—N1—C4111.94 (7)C8—C9—C10120.02 (8)
N1—C1—N1i109.94 (10)C5—C10—C9119.37 (9)
N1—C1—H1a109.4711C5—C10—H10120.3163
N1—C1—H1b109.4713C9—C10—H10120.3168
N1i—C1—H1a109.4711C7—C11—C12110.78 (8)
N1i—C1—H1b109.4713C7—C11—C13109.09 (8)
H1a—C1—H1b108.995C7—C11—C14112.16 (8)
C3—C2—C3i110.20 (11)C12—C11—C13109.63 (8)
C3—C2—H2a109.4711C12—C11—C14107.38 (8)
C3—C2—H2b109.4714C13—C11—C14107.72 (8)
C3i—C2—H2a109.4711C11—C12—H12a109.4717
C3i—C2—H2b109.4714C11—C12—H12b109.472
H2a—C2—H2b108.7329C11—C12—H12c109.4713
N1—C3—C2109.43 (9)H12a—C12—H12b109.4696
N1—C3—H3a109.4709H12a—C12—H12c109.4713
N1—C3—H3b109.4712H12b—C12—H12c109.4714
C2—C3—H3a109.4713C11—C13—H13a109.4718
C2—C3—H3b109.4714C11—C13—H13b109.4714
H3a—C3—H3b109.5159C11—C13—H13c109.4712
N1—C4—C5112.83 (8)H13a—C13—H13b109.4709
N1—C4—H4a109.4712H13a—C13—H13c109.4705
N1—C4—H4b109.4728H13b—C13—H13c109.4715
C5—C4—H4a109.4707C11—C14—H14a109.4717
C5—C4—H4b109.4701C11—C14—H14b109.4711
H4a—C4—H4b105.8863C11—C14—H14c109.4716
C4—C5—C6120.76 (8)H14a—C14—H14b109.4711
C4—C5—C10118.83 (8)H14a—C14—H14c109.4707
C6—C5—C10120.29 (8)H14b—C14—H14c109.4712
O1—C6—C5119.44 (8)O2—C15—H15a109.4715
O1—C6—C7119.68 (8)O2—C15—H15b109.4712
C5—C6—C7120.88 (8)O2—C15—H15c109.4719
C6—C7—C8117.26 (8)H15a—C15—H15b109.4706
C6—C7—C11121.53 (8)H15a—C15—H15c109.4704
C8—C7—C11121.18 (8)H15b—C15—H15c109.4716
C7—C8—C9122.18 (8)
C15—O2—C9—C8175.19 (9)O1—C6—C7—C112.32 (13)
C15—O2—C9—C104.54 (15)C5—C6—C7—C80.56 (14)
C3—N1—C1—N1i62.71 (10)C5—C6—C7—C11177.47 (9)
C4—N1—C1—N1i172.88 (8)C6—C7—C8—C90.03 (15)
C1—N1—C3—C258.60 (11)C11—C7—C8—C9178.01 (9)
C4—N1—C3—C2177.78 (8)C6—C7—C11—C1261.16 (11)
C1—N1—C4—C5165.79 (8)C6—C7—C11—C1359.62 (11)
C3—N1—C4—C570.73 (10)C6—C7—C11—C14178.86 (9)
C3i—C2—C3—N154.82 (13)C8—C7—C11—C12120.88 (10)
N1—C4—C5—C643.06 (12)C8—C7—C11—C13118.34 (10)
N1—C4—C5—C10140.83 (9)C8—C7—C11—C140.91 (13)
C4—C5—C6—O14.30 (14)C7—C8—C9—O2179.76 (9)
C4—C5—C6—C7175.48 (9)C7—C8—C9—C100.50 (15)
C10—C5—C6—O1179.64 (9)O2—C9—C10—C5179.80 (10)
C10—C5—C6—C70.58 (14)C8—C9—C10—C50.49 (15)
C4—C5—C10—C9176.10 (9)H1—O1—C6—C516.4 (9)
C6—C5—C10—C90.03 (15)H1—O1—C6—C7163.8 (9)
O1—C6—C7—C8179.65 (8)
Symmetry codes: (i) x, −y+1/2, z.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N10.890 (15)1.843 (15)2.6735 (10)154.6 (14)
C12—H12a···O10.962.363.0103 (12)124.92
C13—H13a···O10.962.382.9943 (12)121.18
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
O1—H1···N10.890 (15)1.843 (15)2.6735 (10)154.6 (14)
Acknowledgements top

We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de la Universidad Nacional de Colombia, for financial support of this work, as well as the Institutional research plan No. AVOZ10100521 of the Institute of Physics and the project Praemium Academiae of the Academy of Sciences of the Czech Republic. DMG acknowledges the Vicerrectoría Académica de la Universidad Nacional de Colombia for a fellowship.

references
References top

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Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.

Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.

Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact, Bonn, Germany.

Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103.

Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.

Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006. Institute of Physics, Prague, Czech Republic.

Rivera, A., Gonzalez, D. M., Ríos-Motta, J., Fejfarova, K. & Dušek, M. (2012a). J. Chem. Crystallogr. In preparation.

Rivera, A., Ríos-Motta, J., Dušek, M. & Jarošová, M. (2010). Acta Cryst. C66, o222–o224.

Rivera, A., Ríos-Motta, J., Trujillo, G. P., González, D. M. & Alcázar, D. (2012b). Synth. Commun. Accepted. (Reference code: ID LSYC-2011-6173)