organic compounds
(2-tert-Butyl-5-hydroxymethyl-1,3-dioxan-5-yl)methanol
aCentro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, 22500, Tijuana, B.C., Mexico, and bCentro de Ciencias de la Materia Condensada, Universidad Nacional Autónoma de, México. Km. 107 Carretera Tijuana-Ensenada, Ensenada, BC, CP 22800, Mexico
*Correspondence e-mail: madrigal@tectijuana.mx
In the title compound, C10H20O4, the dioxane ring adopts a chair conformation. The tert-butyl group occupies an equatorial position, and is staggered with respect to the O atoms of the dioxane ring. In the crystal, molecules are connected by O—H⋯O hydrogen-bonds into zigzag chains of R44(8) and R22(12) ring motifs that run parallel to the a axis.
Related literature
For background information on the synthesis and properties of 1,3-dioxanes, see: Anderson (1967); Bailey et al. (1978); Juaristi et al. (1987, 1989); Vázquez-Hernández et al. (2004). For the of a similar compound, see: Zhang et al. (2010).
Experimental
Crystal data
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Data collection
Refinement
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Data collection: XSCANS (Siemens, 1996); cell XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97.
Supporting information
https://doi.org/10.1107/S160053681202541X/pk2419sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053681202541X/pk2419Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S160053681202541X/pk2419Isup3.cml
The synthesis of the title compound included reagents and solvents of reagent grade, which were used without further purification. In a 25 ml round bottom flask provided with a magnetic stirrer, was placed 1.2 g (8.8 mmol) of pentaerythritol, 5 ml of water, 0.01 ml of HCl as catalyst and 0.46 ml (7.35 mmol) of pivalaldehyde. 3 ml of dimethylformamide was then added to complete dissolution of the solid, and the reaction mixture was stirred for 24 h. The precipitate thus formed was filtered and washed with a solution of NaHCO3 (10ml, 3 times) and H2O (10 ml, 3 times). The yield was 41%; melting point: 170–172 °C.
IR(ATR): 3002, 2944, 2969, 2818, 1958, 1479, 1458, 1361, 1166, 1143, 1107, 1038, 1025, 976, 931 cm-1.
1H-NMR (DMSO-d6): δ 4.5 (t, J=5.2 Hz, 1H, OH), 4.45 (t, J=5.2 Hz, 1H, OH), 3.9 (s, 1H, CH), 3.77 (d, J=11.8 Hz, 2H, OCHH), 3.5 (d, J=11.8 Hz, 2H, OCHH), 3.53 (d, J=5.2 Hz, 2H, CH2OH), 3.16 (d, J=5.2 Hz, 2H, CH2OH), 0.8 (s, 9H, C(CH3)3.
13C-NMR (DMSO-d6): 106.5 (OCO), 68.9 (OCH2), 68.1 (CH2OH), 59.7 (CH2OH), 39.0 (C), 34.7 (C(CH3)3, 24.6 (C(CH3)3.
For crystallization, 30 mg of 5,5-dihydroxymethyl-2-tert-butyl-1,3-dioxane compound was placed in a glass vial and 2 ml of dimethyl sulfoxide was added. The solution was allowed to stand at room temperature for seven days and the crystals that formed were separated by filtration.
All H atoms were positioned geometrically and refined using a riding model with C—H = 0.96 Å for -CH3, C—H = 0.97 Å for -CH2- groups and O—H = 0.82 Å. Uiso(H) values were set to 1.2 Ueq(CH2) or 1.5 Ueq(CH3, OH).
The synthesis and conformational studies of several 1,3-dioxanes have been reported in the literature (Vázquez-Hernández et al., 2004; Juaristi et al., 1987, 1989; Bailey et al., 1978). The preparation and some spectroscopic information for the title compound was reported by Anderson et al. (1967).
In our development work, while searching rigid molecules to incorporate fluorophore groups, we synthesized 5,5-dihydroxymethyl-2-tert-butyl-1,3-dioxane as a
In the molecule of C10H20O4 (Scheme 1, Fig. 1), the tert-butyl group occupies an equatorial position, and is staggered with respect to the O atoms of the dioxane ring. The hydroxyl groups act as both hydrogen bond donor and acceptor to neighboring molecules. The hydrogen-bonds (table 1) form zigzag chains of R44(8) and R22(12) ring motifs that run parallel to the a axis (Fig. 2).For background information on the synthesis and properties of 1,3-dioxanes, see: Anderson (1967); Bailey et al. (1978); Juaristi et al. (1987, 1989); Vázquez-Hernández et al. (2004). For the
of a similar compound, see: Zhang et al. (2010).Data collection: XSCANS (Siemens, 1996); cell
XSCANS (Siemens, 1996); data reduction: XSCANS (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C10H20O4 | Z = 2 |
Mr = 204.26 | F(000) = 224 |
Triclinic, P1 | Dx = 1.202 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.8337 (10) Å | Cell parameters from 52 reflections |
b = 6.1408 (9) Å | θ = 5.6–12.5° |
c = 17.941 (3) Å | µ = 0.09 mm−1 |
α = 81.468 (12)° | T = 298 K |
β = 87.335 (14)° | Prismatic, colorless |
γ = 62.606 (13)° | 0.73 × 0.63 × 0.20 mm |
V = 564.16 (15) Å3 |
Siemens P4 diffractometer | 2593 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.013 |
Graphite monochromator | θmax = 30.0°, θmin = 2.3° |
2θ/ω scans | h = 0→8 |
Absorption correction: empirical (using intensity measurements) (XEMP in SHELXTL; Sheldrick, 2008) | k = −7→8 |
Tmin = 0.335, Tmax = 0.466 | l = −25→25 |
3581 measured reflections | 3 standard reflections every 97 reflections |
3283 independent reflections | intensity decay: 5.8% |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.054 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.193 | H-atom parameters constrained |
S = 1.42 | w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3 |
3283 reflections | (Δ/σ)max < 0.001 |
127 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
C10H20O4 | γ = 62.606 (13)° |
Mr = 204.26 | V = 564.16 (15) Å3 |
Triclinic, P1 | Z = 2 |
a = 5.8337 (10) Å | Mo Kα radiation |
b = 6.1408 (9) Å | µ = 0.09 mm−1 |
c = 17.941 (3) Å | T = 298 K |
α = 81.468 (12)° | 0.73 × 0.63 × 0.20 mm |
β = 87.335 (14)° |
Siemens P4 diffractometer | 2593 reflections with I > 2σ(I) |
Absorption correction: empirical (using intensity measurements) (XEMP in SHELXTL; Sheldrick, 2008) | Rint = 0.013 |
Tmin = 0.335, Tmax = 0.466 | 3 standard reflections every 97 reflections |
3581 measured reflections | intensity decay: 5.8% |
3283 independent reflections |
R[F2 > 2σ(F2)] = 0.054 | 0 restraints |
wR(F2) = 0.193 | H-atom parameters constrained |
S = 1.42 | Δρmax = 0.35 e Å−3 |
3283 reflections | Δρmin = −0.29 e Å−3 |
127 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.19141 (17) | 0.04289 (16) | 0.28059 (4) | 0.0416 (2) | |
O2 | −0.01630 (17) | −0.14442 (16) | 0.22771 (4) | 0.0413 (2) | |
O3 | −0.31024 (19) | 0.4084 (2) | 0.08767 (6) | 0.0652 (4) | |
H3A | −0.2724 | 0.4774 | 0.0500 | 0.098* | |
O4 | 0.2736 (2) | 0.3620 (2) | 0.05181 (5) | 0.0572 (3) | |
H4A | 0.4138 | 0.3393 | 0.0675 | 0.086* | |
C1 | 0.1581 (2) | −0.1720 (2) | 0.28510 (6) | 0.0374 (3) | |
H1A | 0.3254 | −0.3144 | 0.2793 | 0.045* | |
C2 | 0.2949 (2) | 0.0938 (2) | 0.21038 (6) | 0.0422 (3) | |
H2A | 0.4652 | −0.0414 | 0.2051 | 0.051* | |
H2B | 0.3125 | 0.2437 | 0.2095 | 0.051* | |
C3 | 0.1194 (2) | 0.12605 (19) | 0.14454 (6) | 0.0336 (2) | |
C4 | 0.0755 (3) | −0.1038 (2) | 0.15426 (6) | 0.0439 (3) | |
H4B | −0.0495 | −0.0829 | 0.1165 | 0.053* | |
H4C | 0.2363 | −0.2477 | 0.1466 | 0.053* | |
C5 | 0.0515 (2) | −0.2160 (2) | 0.36206 (6) | 0.0417 (3) | |
C6 | −0.2078 (3) | 0.0058 (3) | 0.37302 (8) | 0.0546 (3) | |
H6A | −0.3292 | 0.0278 | 0.3347 | 0.082* | |
H6B | −0.1852 | 0.1523 | 0.3694 | 0.082* | |
H6C | −0.2717 | −0.0234 | 0.4218 | 0.082* | |
C7 | 0.2463 (3) | −0.2507 (3) | 0.42305 (8) | 0.0663 (4) | |
H7A | 0.2672 | −0.1033 | 0.4196 | 0.099* | |
H7B | 0.4096 | −0.3887 | 0.4158 | 0.099* | |
H7C | 0.1839 | −0.2816 | 0.4719 | 0.099* | |
C8 | 0.0168 (4) | −0.4500 (3) | 0.36665 (10) | 0.0688 (5) | |
H8A | −0.1058 | −0.4263 | 0.3285 | 0.103* | |
H8B | −0.0452 | −0.4824 | 0.4154 | 0.103* | |
H8C | 0.1796 | −0.5881 | 0.3589 | 0.103* | |
C10 | 0.2505 (3) | 0.1391 (3) | 0.06975 (7) | 0.0467 (3) | |
H10A | 0.4212 | −0.0014 | 0.0720 | 0.056* | |
H10B | 0.1517 | 0.1273 | 0.0299 | 0.056* | |
C9 | −0.1367 (2) | 0.3603 (2) | 0.14803 (7) | 0.0433 (3) | |
H9A | −0.2177 | 0.3427 | 0.1954 | 0.052* | |
H9B | −0.1020 | 0.5009 | 0.1468 | 0.052* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0540 (5) | 0.0534 (5) | 0.0310 (4) | −0.0366 (4) | −0.0015 (3) | −0.0038 (3) |
O2 | 0.0566 (5) | 0.0497 (5) | 0.0326 (4) | −0.0369 (4) | 0.0046 (3) | −0.0080 (3) |
O3 | 0.0482 (5) | 0.0904 (8) | 0.0554 (6) | −0.0377 (5) | −0.0154 (4) | 0.0201 (5) |
O4 | 0.0621 (6) | 0.0766 (7) | 0.0491 (5) | −0.0501 (5) | −0.0003 (4) | 0.0073 (4) |
C1 | 0.0408 (5) | 0.0386 (5) | 0.0343 (5) | −0.0200 (4) | 0.0022 (4) | −0.0036 (4) |
C2 | 0.0432 (6) | 0.0585 (7) | 0.0354 (5) | −0.0339 (5) | −0.0020 (4) | 0.0003 (5) |
C3 | 0.0378 (5) | 0.0412 (5) | 0.0294 (5) | −0.0245 (4) | 0.0032 (4) | −0.0053 (4) |
C4 | 0.0638 (7) | 0.0475 (6) | 0.0339 (5) | −0.0357 (6) | 0.0066 (5) | −0.0119 (4) |
C5 | 0.0498 (6) | 0.0455 (6) | 0.0339 (5) | −0.0264 (5) | 0.0042 (4) | −0.0027 (4) |
C6 | 0.0543 (7) | 0.0636 (8) | 0.0489 (7) | −0.0281 (6) | 0.0139 (6) | −0.0168 (6) |
C7 | 0.0694 (9) | 0.0933 (12) | 0.0373 (6) | −0.0425 (9) | −0.0085 (6) | 0.0083 (7) |
C8 | 0.1062 (13) | 0.0573 (8) | 0.0570 (8) | −0.0518 (9) | 0.0223 (8) | −0.0066 (6) |
C10 | 0.0540 (7) | 0.0600 (7) | 0.0355 (5) | −0.0345 (6) | 0.0090 (5) | −0.0076 (5) |
C9 | 0.0411 (6) | 0.0465 (6) | 0.0426 (6) | −0.0218 (5) | 0.0004 (5) | −0.0012 (4) |
O1—C1 | 1.4100 (13) | C4—H4C | 0.9700 |
O1—C2 | 1.4266 (13) | C5—C6 | 1.529 (2) |
O2—C1 | 1.4181 (14) | C5—C8 | 1.5307 (19) |
O2—C4 | 1.4301 (13) | C5—C7 | 1.5356 (19) |
O3—C9 | 1.4204 (15) | C6—H6A | 0.9600 |
O3—H3A | 0.8200 | C6—H6B | 0.9600 |
O4—C10 | 1.4248 (16) | C6—H6C | 0.9600 |
O4—H4A | 0.8200 | C7—H7A | 0.9600 |
C1—C5 | 1.5267 (15) | C7—H7B | 0.9600 |
C1—H1A | 0.9800 | C7—H7C | 0.9600 |
C2—C3 | 1.5297 (15) | C8—H8A | 0.9600 |
C2—H2A | 0.9700 | C8—H8B | 0.9600 |
C2—H2B | 0.9700 | C8—H8C | 0.9600 |
C3—C10 | 1.5235 (15) | C10—H10A | 0.9700 |
C3—C9 | 1.5314 (16) | C10—H10B | 0.9700 |
C3—C4 | 1.5309 (15) | C9—H9A | 0.9700 |
C4—H4B | 0.9700 | C9—H9B | 0.9700 |
C1—O1—C2 | 112.27 (8) | C6—C5—C7 | 109.52 (12) |
C1—O2—C4 | 111.54 (9) | C8—C5—C7 | 110.10 (12) |
C9—O3—H3A | 109.5 | C5—C6—H6A | 109.5 |
C10—O4—H4A | 109.5 | C5—C6—H6B | 109.5 |
O1—C1—O2 | 110.58 (8) | H6A—C6—H6B | 109.5 |
O1—C1—C5 | 109.07 (9) | C5—C6—H6C | 109.5 |
O2—C1—C5 | 109.32 (9) | H6A—C6—H6C | 109.5 |
O1—C1—H1A | 109.3 | H6B—C6—H6C | 109.5 |
O2—C1—H1A | 109.3 | C5—C7—H7A | 109.5 |
C5—C1—H1A | 109.3 | C5—C7—H7B | 109.5 |
O1—C2—C3 | 110.78 (8) | H7A—C7—H7B | 109.5 |
O1—C2—H2A | 109.5 | C5—C7—H7C | 109.5 |
C3—C2—H2A | 109.5 | H7A—C7—H7C | 109.5 |
O1—C2—H2B | 109.5 | H7B—C7—H7C | 109.5 |
C3—C2—H2B | 109.5 | C5—C8—H8A | 109.5 |
H2A—C2—H2B | 108.1 | C5—C8—H8B | 109.5 |
C10—C3—C2 | 110.54 (9) | H8A—C8—H8B | 109.5 |
C10—C3—C9 | 111.37 (9) | C5—C8—H8C | 109.5 |
C2—C3—C9 | 108.81 (9) | H8A—C8—H8C | 109.5 |
C10—C3—C4 | 108.60 (9) | H8B—C8—H8C | 109.5 |
C2—C3—C4 | 106.80 (9) | O4—C10—C3 | 112.63 (10) |
C9—C3—C4 | 110.62 (9) | O4—C10—H10A | 109.1 |
O2—C4—C3 | 111.25 (9) | C3—C10—H10A | 109.1 |
O2—C4—H4B | 109.4 | O4—C10—H10B | 109.1 |
C3—C4—H4B | 109.4 | C3—C10—H10B | 109.1 |
O2—C4—H4C | 109.4 | H10A—C10—H10B | 107.8 |
C3—C4—H4C | 109.4 | O3—C9—C3 | 112.71 (10) |
H4B—C4—H4C | 108.0 | O3—C9—H9A | 109.0 |
C1—C5—C6 | 110.31 (10) | C3—C9—H9A | 109.0 |
C1—C5—C8 | 108.76 (10) | O3—C9—H9B | 109.0 |
C6—C5—C8 | 109.86 (12) | C3—C9—H9B | 109.0 |
C1—C5—C7 | 108.27 (10) | H9A—C9—H9B | 107.8 |
C2—O1—C1—O2 | −60.72 (11) | O1—C1—C5—C6 | 59.66 (13) |
C2—O1—C1—C5 | 179.03 (9) | O2—C1—C5—C6 | −61.36 (12) |
C4—O2—C1—O1 | 60.20 (11) | O1—C1—C5—C8 | −179.79 (11) |
C4—O2—C1—C5 | −179.71 (8) | O2—C1—C5—C8 | 59.20 (14) |
C1—O1—C2—C3 | 58.43 (12) | O1—C1—C5—C7 | −60.16 (13) |
O1—C2—C3—C10 | −170.96 (9) | O2—C1—C5—C7 | 178.82 (10) |
O1—C2—C3—C9 | 66.45 (12) | C2—C3—C10—O4 | −69.64 (13) |
O1—C2—C3—C4 | −52.99 (12) | C9—C3—C10—O4 | 51.45 (13) |
C1—O2—C4—C3 | −58.05 (13) | C4—C3—C10—O4 | 173.51 (10) |
C10—C3—C4—O2 | 172.44 (9) | C10—C3—C9—O3 | 56.51 (12) |
C2—C3—C4—O2 | 53.21 (13) | C2—C3—C9—O3 | 178.60 (9) |
C9—C3—C4—O2 | −65.05 (12) | C4—C3—C9—O3 | −64.38 (12) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3A···O4i | 0.82 | 1.94 | 2.7346 (14) | 162 |
O4—H4A···O3ii | 0.82 | 1.91 | 2.6878 (15) | 159 |
Symmetry codes: (i) −x, −y+1, −z; (ii) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C10H20O4 |
Mr | 204.26 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 298 |
a, b, c (Å) | 5.8337 (10), 6.1408 (9), 17.941 (3) |
α, β, γ (°) | 81.468 (12), 87.335 (14), 62.606 (13) |
V (Å3) | 564.16 (15) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.73 × 0.63 × 0.20 |
Data collection | |
Diffractometer | Siemens P4 |
Absorption correction | Empirical (using intensity measurements) (XEMP in SHELXTL; Sheldrick, 2008) |
Tmin, Tmax | 0.335, 0.466 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3581, 3283, 2593 |
Rint | 0.013 |
(sin θ/λ)max (Å−1) | 0.703 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.054, 0.193, 1.42 |
No. of reflections | 3283 |
No. of parameters | 127 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.35, −0.29 |
Computer programs: XSCANS (Siemens, 1996), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3A···O4i | 0.82 | 1.94 | 2.7346 (14) | 162.4 |
O4—H4A···O3ii | 0.82 | 1.91 | 2.6878 (15) | 159.3 |
Symmetry codes: (i) −x, −y+1, −z; (ii) x+1, y, z. |
Acknowledgements
Support for this work from the Dirección General de Educación Superior Tecnológica (DGEST) Grant 2574.09P, is gratefully acknowledged.
References
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The synthesis and conformational studies of several 1,3-dioxanes have been reported in the literature (Vázquez-Hernández et al., 2004; Juaristi et al., 1987, 1989; Bailey et al., 1978). The preparation and some spectroscopic information for the title compound was reported by Anderson et al. (1967).
In our development work, while searching rigid molecules to incorporate fluorophore groups, we synthesized 5,5-dihydroxymethyl-2-tert-butyl-1,3-dioxane as a reaction intermediate. In the molecule of C10H20O4 (Scheme 1, Fig. 1), the tert-butyl group occupies an equatorial position, and is staggered with respect to the O atoms of the dioxane ring. The hydroxyl groups act as both hydrogen bond donor and acceptor to neighboring molecules. The hydrogen-bonds (table 1) form zigzag chains of R44(8) and R22(12) ring motifs that run parallel to the a axis (Fig. 2).