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Acta Crystallogr Sect E Struct Rep Online. 2008 June 1; 64(Pt 6): o1174.
Published online 2008 May 30. doi:  10.1107/S1600536808015444
PMCID: PMC2961358

tert-Butyl­dimethyl­silanol hemihydrate

Abstract

The crystal structure of the title compound, C6H16OSi·0.5H2O, reveals an asymmetric unit containing two mol­ecules of the silanol and a single water mol­ecule. There is evidence of hydrogen bonding between the three mol­ecules in the asymmetric unit. The H atoms of the silanol OH groups and the water H atoms are each disordered equally over two positions.

Related literature

For related literature, see: Krall et al. (2005 [triangle]); Lickiss et al. (1995 [triangle]); Mansfeld, Schürmann & Mehring (2005 [triangle]); Mansfeld, Mehring & Schürmann (2005 [triangle]); McGeary et al. (1991 [triangle]); Veith et al. (2006 [triangle]); Barry & Rutledge (2008 [triangle]); Görbitz (1999 [triangle]).

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Object name is e-64-o1174-scheme1.jpg

Experimental

Crystal data

  • C6H16OSi·0.5H2O
  • M r = 141.29
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1174-efi1.jpg
  • a = 7.7078 (18) Å
  • b = 22.119 (5) Å
  • c = 11.058 (3) Å
  • β = 90.307 (4)°
  • V = 1885.2 (8) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.19 mm−1
  • T = 100 (2) K
  • 1.00 × 1.00 × 0.80 mm

Data collection

  • Bruker SMART APEX detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2000 [triangle]) T min = 0.519, T max = 0.865
  • 15971 measured reflections
  • 4093 independent reflections
  • 3529 reflections with I > 2σ(I)
  • R int = 0.054

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.149
  • S = 1.05
  • 4093 reflections
  • 181 parameters
  • 6 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.55 e Å−3
  • Δρmin = −0.49 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT (Bruker, 2001 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808015444/kj2088sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808015444/kj2088Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the Irish Research Council for Science, Engineering and Technology for an Embark Award postgraduate scholarship to SMB, the Centre for Synthesis & Chemical Biology (CSCB) funded by the Irish Higher Education Authority (HEA) through the Programme for Research in Third-Level Institutions (PRTLI) for financial support, and Professor Cameron Kepert for helpful advice.

supplementary crystallographic information

Comment

The stucture of the title compound tert-butyldimethylsilanol hemihydrate is shown below (Fig. 1, 2); dimensions are available in the archived CIF. This compound has previously been characterized by gas-phase electron diffraction of both the free silanol and its hemihydrate (Lickiss et al., 1995). It has also been structurally characterized within lanthanoid complexes (McGeary et al., 1991) and in recent structures of complexes with several main group and transition metals (for examples see Mansfeld, Mehring & Schürmann, 2005; Mansfeld, Schürmann & Mehring, 2005, Veith et al., 2006). However direct crystallographic characterization of the silanol has hitherto remained elusive.

tert-Butyldimethylsilanol hemihydrate was isolated in crystalline form during the synthesis of biomimetic ligands for iron-mediated hydrocarbon oxidation (Krall et al., 2005, Barry & Rutledge, 2008). The title compound was obtained as the side product of reactions to prepare a compound incorporating the tert-butyldimethylsilyl ether as a protecting group (2-(bromomethyl)-6-((tert-butyldimethylsilyloxy)methyl)pyridine).

The assymetric unit contains two molecules of the silanol and one water molecule, linked by hydrogen bonding. The hydrogen atoms of the water molecule and the silanol O—H groups are disordered between two alternative occupancies (Fig. 2).

Experimental

The title compound crystallized serendipitously as colourless needles from a sample of the silyl ether 2-(bromomethyl)-6-((tert-butyldimethylsilyloxy)methyl)pyridine (isolated as an oil from a pentane:ether solvent mixture), upon standing at room temperature for several weeks.

Large crystals of the silanol were obtained (1.00 × 1.00 × 0.80 mm) and data was collected from a crystal at the upper size limit of the beam used. Moreover, the crystals of tert-butyldimethylsilanol hemihydrate that have been isolated exhibit remarkably low density (0.996 g cm-3), a property that may be linked to the high volitility of this compound.

Refinement

A full sphere of the reciprocal space was scanned by [var phi]-ω scans. Hydrogen atoms of the silanol molecules were added at calculated positions and refined using a riding model. C–H distances were assumed to be 0.98 Å, O–H distances to be 0.84 Å. The water protons were located in the difference Fourier map. The distance of these protons to the oxygen atom was restrained to be 0.84 Å using the DFIX command. In the same way the H–O–H angles were restrained to be 114°, the value to which a preliminary refinement of one component converged. Uiso(H) = 1.5 Ueq(carrier) for all H atoms.

The site occupation factor of the disordered hydrogen atoms was fixed to 0.5. Attempts to refine the occupation factors were unsuccessful. However, electron densities in the difference Fourier map suggest a fairly even distribution between the two disordered parts.

Discrepancies between the expected and reported values of the maximum and minimum transmission (Tmax/Tmin) are thought to have arisen from the large size of the crystal relative to the beam, and because the crystal mount has given rise to some absorption during data collection. However this is not thought to impact significantly on the dataset given that there is an almost fourfold redundancy with the collection of a full sphere, and the capacity of SADABS to handle data collected from large crystals (Görbitz, 1999, Sheldrick, 2000).

Figures

Fig. 1.
The molecular structure of the title compound with atom labels and thermal ellipsoids drawn on the 50% probability level. Carbon atoms are shown in grey, the silicon in black and the oxygen in blue.
Fig. 2.
View of two adjacent silanols and a bridging water showing the disorder that is present (Part 1 black bonds, Part 2 brown bonds); thermal ellipsoids are drawn on the 50% probabibility level.

Crystal data

C6H16OSi·0.5H2OF000 = 632
Mr = 141.29Dx = 0.996 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
a = 7.7078 (18) ÅCell parameters from 5333 reflections
b = 22.119 (5) Åθ = 2.6–29.4º
c = 11.058 (3) ŵ = 0.19 mm1
β = 90.307 (4)ºT = 100 (2) K
V = 1885.2 (8) Å3Block, colourless
Z = 81.00 × 1.00 × 0.80 mm

Data collection

Bruker SMART APEX detector diffractometer4093 independent reflections
Radiation source: fine-focus sealed tube3529 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.054
T = 100(2) Kθmax = 27.0º
[var phi] and ω scansθmin = 0.9º
Absorption correction: multi-scan(SADABS; Sheldrick, 2000)h = −9→9
Tmin = 0.519, Tmax = 0.865k = −28→28
15971 measured reflectionsl = −14→14

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.055H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.149  w = 1/[σ2(Fo2) + (0.0859P)2 + 1.0972P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.040
4093 reflectionsΔρmax = 0.55 e Å3
181 parametersΔρmin = −0.49 e Å3
6 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/UeqOcc. (<1)
Si10.08637 (10)0.59717 (3)1.24126 (7)0.01975 (18)
O10.0393 (3)0.56062 (9)1.1151 (2)0.0313 (5)
H1O1−0.05090.53991.12510.047*0.50
H2O10.13140.54881.08250.047*0.50
C10.0225 (5)0.55098 (15)1.3734 (3)0.0408 (8)
H1A−0.10010.53981.36600.061*
H1B0.04000.57441.44770.061*
H1C0.09370.51431.37660.061*
C20.3243 (4)0.60908 (15)1.2437 (3)0.0350 (7)
H2A0.38340.56991.24010.052*
H2B0.35750.63011.31840.052*
H2C0.35800.63361.17380.052*
C3−0.0367 (4)0.67096 (12)1.2379 (2)0.0227 (5)
C4−0.0021 (5)0.70679 (15)1.3542 (3)0.0385 (8)
H4A0.12240.71511.36160.058*
H4B−0.04050.68311.42400.058*
H4C−0.06610.74511.35120.058*
C50.0191 (6)0.70852 (15)1.1297 (3)0.0471 (10)
H5A−0.04530.74671.12880.071*
H5B−0.00510.68611.05500.071*
H5C0.14370.71691.13550.071*
C6−0.2315 (4)0.65768 (16)1.2285 (3)0.0425 (8)
H6A−0.26770.63361.29840.064*
H6B−0.25530.63511.15410.064*
H6C−0.29610.69581.22710.064*
Si20.41635 (10)0.62186 (3)0.80713 (7)0.02124 (19)
O20.4716 (3)0.56071 (10)0.8832 (2)0.0345 (5)
H1O20.57800.56190.89960.052*0.50
H2O20.39310.53460.87610.052*0.50
C70.4726 (5)0.68968 (15)0.8981 (3)0.0402 (8)
H7A0.39940.69110.97030.060*
H7B0.45310.72610.84960.060*
H7C0.59480.68760.92250.060*
C80.1783 (4)0.61756 (15)0.7803 (3)0.0381 (8)
H8A0.15090.58050.73560.057*
H8B0.14070.65280.73320.057*
H8C0.11790.61720.85810.057*
C90.5397 (4)0.62185 (11)0.6618 (2)0.0226 (6)
C100.4979 (5)0.56497 (14)0.5889 (3)0.0379 (8)
H10A0.56570.56500.51420.057*
H10B0.37390.56430.56900.057*
H10C0.52740.52910.63690.057*
C110.7347 (4)0.62329 (15)0.6898 (3)0.0375 (8)
H11A0.76540.58860.74070.056*
H11B0.76340.66080.73250.056*
H11C0.79980.62140.61400.056*
C120.4920 (5)0.67741 (14)0.5854 (3)0.0364 (7)
H12A0.52090.71430.63030.055*
H12B0.36730.67690.56740.055*
H12C0.55720.67660.50960.055*
O30.2501 (2)0.48396 (9)0.99424 (19)0.0261 (4)
H1O30.190 (7)0.503 (2)1.043 (5)0.039*0.50
H2O30.316 (7)0.506 (2)0.956 (5)0.039*0.50
H3O30.327 (6)0.464 (2)1.026 (6)0.039*0.50
H4O30.172 (6)0.464 (2)0.963 (6)0.039*0.50

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Si10.0189 (3)0.0196 (3)0.0207 (3)−0.0005 (3)−0.0001 (3)0.0000 (3)
O10.0248 (11)0.0336 (12)0.0354 (11)−0.0016 (8)0.0018 (9)−0.0151 (9)
C10.050 (2)0.0316 (17)0.0408 (18)0.0045 (14)0.0121 (16)0.0115 (14)
C20.0251 (16)0.0441 (18)0.0357 (17)0.0006 (13)−0.0040 (13)−0.0035 (14)
C30.0275 (14)0.0209 (13)0.0198 (12)−0.0004 (10)0.0043 (10)−0.0001 (10)
C40.055 (2)0.0293 (16)0.0317 (16)−0.0003 (14)0.0047 (15)−0.0066 (13)
C50.077 (3)0.0299 (17)0.0342 (17)0.0152 (17)0.0179 (18)0.0108 (14)
C60.0287 (17)0.0419 (18)0.057 (2)0.0116 (14)−0.0020 (15)−0.0126 (16)
Si20.0187 (4)0.0208 (3)0.0242 (4)−0.0002 (3)−0.0008 (3)0.0022 (3)
O20.0254 (11)0.0366 (12)0.0415 (12)0.0014 (9)0.0020 (10)0.0170 (10)
C70.053 (2)0.0360 (17)0.0315 (16)−0.0072 (15)0.0082 (15)−0.0135 (14)
C80.0212 (15)0.0394 (18)0.054 (2)0.0025 (12)−0.0009 (14)0.0073 (15)
C90.0282 (14)0.0184 (12)0.0211 (13)0.0008 (10)0.0008 (11)−0.0017 (10)
C100.053 (2)0.0259 (16)0.0349 (17)0.0045 (14)−0.0021 (15)−0.0099 (13)
C110.0272 (16)0.0475 (19)0.0379 (17)−0.0007 (13)0.0123 (14)0.0009 (14)
C120.055 (2)0.0263 (15)0.0279 (15)0.0023 (14)0.0011 (15)0.0053 (12)
O30.0188 (11)0.0259 (10)0.0334 (11)0.0004 (8)−0.0024 (9)−0.0003 (9)

Geometric parameters (Å, °)

Si1—O11.651 (2)Si2—C81.859 (3)
Si1—C11.852 (3)Si2—C91.871 (3)
Si1—C21.853 (3)O2—H1O20.8400
Si1—C31.888 (3)O2—H2O20.8400
O1—H1O10.8400C7—H7A0.9800
O1—H2O10.8400C7—H7B0.9800
C1—H1A0.9800C7—H7C0.9800
C1—H1B0.9800C8—H8A0.9800
C1—H1C0.9800C8—H8B0.9800
C2—H2A0.9800C8—H8C0.9800
C2—H2B0.9800C9—C101.528 (4)
C2—H2C0.9800C9—C111.533 (4)
C3—C51.521 (4)C9—C121.535 (4)
C3—C41.532 (4)C10—H10A0.9800
C3—C61.533 (4)C10—H10B0.9800
C4—H4A0.9800C10—H10C0.9800
C4—H4B0.9800C11—H11A0.9800
C4—H4C0.9800C11—H11B0.9800
C5—H5A0.9800C11—H11C0.9800
C5—H5B0.9800C12—H12A0.9800
C5—H5C0.9800C12—H12B0.9800
C6—H6A0.9800C12—H12C0.9800
C6—H6B0.9800O3—H1O30.824 (19)
C6—H6C0.9800O3—H2O30.82 (2)
Si2—O21.648 (2)O3—H3O30.822 (19)
Si2—C71.856 (3)O3—H4O30.815 (19)
O1—Si1—C1109.79 (15)O2—Si2—C9107.90 (12)
O1—Si1—C2107.15 (13)C7—Si2—C9110.33 (14)
C1—Si1—C2109.53 (17)C8—Si2—C9111.62 (16)
O1—Si1—C3107.38 (12)Si2—O2—H1O2109.5
C1—Si1—C3110.88 (14)Si2—O2—H2O2109.5
C2—Si1—C3112.00 (14)Si2—C7—H7A109.5
Si1—O1—H1O1109.5Si2—C7—H7B109.5
Si1—O1—H2O1109.5H7A—C7—H7B109.5
Si1—C1—H1A109.5Si2—C7—H7C109.5
Si1—C1—H1B109.5H7A—C7—H7C109.5
H1A—C1—H1B109.5H7B—C7—H7C109.5
Si1—C1—H1C109.5Si2—C8—H8A109.5
H1A—C1—H1C109.5Si2—C8—H8B109.5
H1B—C1—H1C109.5H8A—C8—H8B109.5
Si1—C2—H2A109.5Si2—C8—H8C109.5
Si1—C2—H2B109.5H8A—C8—H8C109.5
H2A—C2—H2B109.5H8B—C8—H8C109.5
Si1—C2—H2C109.5C10—C9—C11109.1 (3)
H2A—C2—H2C109.5C10—C9—C12108.6 (3)
H2B—C2—H2C109.5C11—C9—C12109.0 (3)
C5—C3—C4109.2 (2)C10—C9—Si2110.3 (2)
C5—C3—C6109.4 (3)C11—C9—Si2109.2 (2)
C4—C3—C6108.8 (3)C12—C9—Si2110.6 (2)
C5—C3—Si1110.1 (2)C9—C10—H10A109.5
C4—C3—Si1110.2 (2)C9—C10—H10B109.5
C6—C3—Si1109.13 (19)H10A—C10—H10B109.5
C3—C4—H4A109.5C9—C10—H10C109.5
C3—C4—H4B109.5H10A—C10—H10C109.5
H4A—C4—H4B109.5H10B—C10—H10C109.5
C3—C4—H4C109.5C9—C11—H11A109.5
H4A—C4—H4C109.5C9—C11—H11B109.5
H4B—C4—H4C109.5H11A—C11—H11B109.5
C3—C5—H5A109.5C9—C11—H11C109.5
C3—C5—H5B109.5H11A—C11—H11C109.5
H5A—C5—H5B109.5H11B—C11—H11C109.5
C3—C5—H5C109.5C9—C12—H12A109.5
H5A—C5—H5C109.5C9—C12—H12B109.5
H5B—C5—H5C109.5H12A—C12—H12B109.5
C3—C6—H6A109.5C9—C12—H12C109.5
C3—C6—H6B109.5H12A—C12—H12C109.5
H6A—C6—H6B109.5H12B—C12—H12C109.5
C3—C6—H6C109.5H1O3—O3—H2O3113 (4)
H6A—C6—H6C109.5H1O3—O3—H3O3113 (7)
H6B—C6—H6C109.5H2O3—O3—H3O395 (6)
O2—Si2—C7109.13 (16)H1O3—O3—H4O398 (7)
O2—Si2—C8106.94 (13)H2O3—O3—H4O3123 (7)
C7—Si2—C8110.79 (16)H3O3—O3—H4O3115 (4)
O1—Si1—C3—C5−60.8 (2)O2—Si2—C9—C1059.0 (2)
C1—Si1—C3—C5179.3 (2)C7—Si2—C9—C10178.1 (2)
C2—Si1—C3—C556.6 (3)C8—Si2—C9—C10−58.3 (2)
O1—Si1—C3—C4178.8 (2)O2—Si2—C9—C11−60.9 (2)
C1—Si1—C3—C458.8 (3)C7—Si2—C9—C1158.3 (2)
C2—Si1—C3—C4−63.9 (2)C8—Si2—C9—C11−178.1 (2)
O1—Si1—C3—C659.4 (2)O2—Si2—C9—C12179.1 (2)
C1—Si1—C3—C6−60.6 (3)C7—Si2—C9—C12−61.7 (3)
C2—Si1—C3—C6176.7 (2)C8—Si2—C9—C1261.9 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1O1···O3i0.842.092.717 (3)131
O1—H2O1···O30.841.962.706 (3)147
O2—H1O2···O3ii0.842.042.718 (3)138
O2—H2O2···O30.842.052.707 (3)135
O3—H1O3···O10.824 (19)1.91 (3)2.706 (3)163 (6)
O3—H4O3···O1i0.815 (19)1.92 (2)2.717 (3)164 (6)
O3—H2O3···O20.82 (2)1.89 (2)2.707 (3)173 (6)
O3—H3O3···O2ii0.822 (19)1.92 (2)2.718 (3)164 (6)

Symmetry codes: (i) −x, −y+1, −z+2; (ii) −x+1, −y+1, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: KJ2088).

References

  • Barry, S. M. & Rutledge, P. J. (2008). In preparation.
  • Bruker (2001). SAINT and SMART Bruker AXS Inc., Madison, Wisconsin, USA.
  • Görbitz, C. H. (1999). Acta Cryst. B55, 1090–1098. [PubMed]
  • Krall, J. A., Rutledge, P. J. & Baldwin, J. E. (2005). Tetrahedron, 61, 137–143.
  • Lickiss, P. D., Clipston, N. L., Rankin, D. W. H. & Robertson, H. E. (1995). J. Mol. Struct.344, 111–116.
  • Mansfeld, D., Mehring, M. & Schürmann, M. (2005). Angew. Chem. Int. Ed.44, 245–249. [PubMed]
  • Mansfeld, D., Schürmann, M. & Mehring, M. (2005). Appl. Organomet. Chem.19, 1185–1188.
  • McGeary, M. J., Coan, P. S., Folting, K., Streib, W. E. & Caulton, K. G. (1991). Inorg. Chem.30, 1723–1735.
  • Sheldrick, C. M. (2000). SADABS Bruker AXS Inc., Madison, Wisconson, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Veith, M., Freres, J., Huch, V. & Zimmer, M. (2006). Organometallics, 25, 1875–1880.

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