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Acta Crystallogr Sect E Struct Rep Online. 2010 January 1; 66(Pt 1): o223–o224.
Published online 2009 December 24. doi:  10.1107/S1600536809054105
PMCID: PMC2980030

2-[2-(Trimethyl­silyl)eth­yl]isoindoline-1,3-dione

Abstract

In the course of our studies of silicon-containing anti­cancer compounds, the title compound, C13H17NO2Si, was synthesized. The geometrical parameters including the geometry about the Si atom are typical. The mol­ecules form dimers via a weak C—H(...)O inter­action described by the graph set R 2 2(10). The dimers are assembled in rows stacked in the crystallographic b-axis direction via π–π inter­actions with a 3.332 (3) Å separation between the rows.

Related literature

For literature related to drug design see: Bains & Tacke (2003 [triangle]); Bikzhanova et al. (2007 [triangle]); Franz (2007 [triangle]); Franz et al. (2007 [triangle]); Gately & West (2007 [triangle]); Guzei,, Spencer, Zakai & Lynch (2010 [triangle]); Guzei, Spencer & Zakai (2010 [triangle]); Lee et al. (1993 [triangle], 1996 [triangle]); Sen & Roach (1995 [triangle]); Showell & Mills (2003 [triangle]); Tacke & Zilch (1986 [triangle]); Tsuge et al. (1985 [triangle]); Yoon et al. (1991 [triangle], 1992 [triangle], 1997 [triangle]). For a description of the Cambridge Structural Database, see: Allen (2002 [triangle]). Bond distances and angles were confirmed to be typical by a Mogul structural check (Bruno et al., 2002 [triangle]). For graph-set notation, see: Grell et al. (1999 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o223-scheme1.jpg

Experimental

Crystal data

  • C13H17NO2Si
  • M r = 247.37
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o223-efi1.jpg
  • a = 11.562 (5) Å
  • b = 6.411 (2) Å
  • c = 19.445 (8) Å
  • β = 95.176 (14)°
  • V = 1435.5 (10) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.16 mm−1
  • T = 300 K
  • 0.89 × 0.40 × 0.30 mm

Data collection

  • Bruker SMART X2S diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.875, T max = 0.955
  • 9164 measured reflections
  • 2701 independent reflections
  • 1750 reflections with I > 2σ(I)
  • R int = 0.036

Refinement

  • R[F 2 > 2σ(F 2)] = 0.044
  • wR(F 2) = 0.151
  • S = 0.99
  • 2701 reflections
  • 157 parameters
  • H-atom parameters constrained
  • Δρmax = 0.15 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: APEX2 and GIS (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL, OLEX2 (Dolomanov et al., 2009 [triangle]) and FCF_filter (Guzei, 2007 [triangle]); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL, modiCIFer (Guzei, 2007 [triangle]) and publCIF (Westrip, 2010 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809054105/zs2025sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809054105/zs2025Isup2.hkl

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

Acknowledgments

We thank Dr N. J. Hill (UW-Madison) for acquiring the data and Professor R. West (UW-Madison) for his support. We gratefully acknowledge Bruker sponsorship of this publication and also acknowledge grants NIH 1 S10 RRO 8389–01 and NSF CHE-9629688 for providing NMR spectrometers, and grant NSF CHE-9304546 for providing the mass spectrometer for this work.

supplementary crystallographic information

Comment

Sila phthalimides are important intermediates in photochemistry (Lee et al., 1993, 1996; Yoon et al., 1997, 1992, 1991) and organic synthesis (Bikzhanova et al., 2007; Tsuge et al., 1985). We have used methods of organosilicon chemistry (Franz, 2007; Franz et al., 2007; Gately & West, 2007; Tacke & Zilch, 1986; Showell & Mills, 2003) to prepare an array of substituted sila amines (Bikzhanova et al., 2007) and to fine-tune the properties of pharmocological drugs (Bains & Tacke, 2003). Sila phthalimides can be obtained from the respective chlorosilanes (Tsuge et al., 1985) or from alcohols by means of the Misunubu reaction (Sen & Roach, 1995) as in the present case. During our research toward silicon-containing anti-cancer drugs the title compound, (I), was isolated and characterized.

The bond distances and angles of (I) are typical as confirmed by the Mogul structural check (Bruno et al., 2002), and agree well with those for the related compounds 2-(3-(methyldiphenylsilyl)propyl)isoindoline-1,3-dione (Guzei, Spencer, Zakai & Lynch, 2010) and 2-(((4-methoxyphenyl)dimethylsilyl)methyl)isoindoline-1,3-dione (Guzei, Spencer & Zakai, 2010). Specifically, the average Si—C distances of 1.867 (3) Å for compound (I) are statistically similar to the 1.88 (3) Å average for 83 related compounds in the Cambridge Structural Database (Version 1.11, September 2009 release; Allen, 2002). The Si atom has a distorted tetrahedral geometry with angles ranging from 107.87 (11)° to 110.45 (11) °. The phthalate entity is expectedly planar within 0.0083 Å.

The molecules form dimers via a weak C11—H11···O2 interaction with a distance of 3.443 (4) Å and an angle of 155°. The pattern formed can be described in graph set notation as R22(10) (Grell et. al., 1999). The dimers are assembled into rows via weak π-π interactions with a distance of 3.366 (5) Å between atoms C13 in separate dimers. The rows are stacked in the crystallographic b direction.

Experimental

The title compound was obtained via a Mitsunubu reaction as described by Sen and co-workers (Sen & Roach, 1995). To a pre-dried 100 ml round bottom flask was added 2-(trimethylsilyl)ethanol (319 mg, 2.7 mmol). Additionally, potassium phthalimide (512 mg, 3.48 mmol) and triphenyl phosphine (913, 3.48 mmol) were added to the reaction flask. The flask was sealed with a rubber septum, evacuated, and then filled with an inert atmosphere (nitrogen). Subsequently, 30 ml of freshly distilled THF was added to the round bottom flask. In the dark, the flask was then wrapped with aluminium foil and diisopropyl azodicarboxylate (DIAD) was slowly syringed into the reaction flask. This mixture was allowed to stir at room temperature for four hours. Three ml of water was slowly injected into the reaction mixture, and the given suspension was allowed to stir for a few more minutes. The aluminium foil covering the reaction flask was removed and its contents were poured into an extraction flask. The aqueous phase was extracted 3–5 times with hexane and the resultant organic extracts were dried with MgSO4 and filtered. The filtrate was mixed with silica gel and this slurry was dried under reduced pressure. The dry powder was loaded onto a pre-dry packed silica gel column and eluted with a gradient column. The desired material was collected using a 8:2 hexane:ethyl acetate mixture. The compound of interest was dried under reduced pressure and recrystallized from dichloromethane to afford lustrous white needles (0.35 g, 1.41 mmol, 52% yield) for X-ray crystallography. Manipulation of air and moisture sensitive compounds was performed using standard high-vacuum line techniques. All solvents and reagents were obtained from Aldrich. 2-(trimethylsilyl)ethanol was purchased from Gelest. 1H NMR spectra were obtained on a Varian Unity 500 spectrometer, 13C {H} NMR spectra were obtained on a Varian 500 spectrometer operating at 125 MHz, 29Si {H} NMR spectra were obtained on a Varian Unity spectrometer operating at 99 MHz. EI Mass spectra were determined on a Waters (Micromass) AutoSpec mass spectrometer. Melting points were determined on a Mel-Temp Laboratory Device. mp: 48–50°; 1H NMR (500 MHz, CDCl3) δ 0.04 (s, 9H, Si(Me3)3), 0.98 (m, 2H, CH2), 3.69 (m, 2H, CH2), 7.66 (dd, J=5.48, 3.01 Hz, 2H, ArH), 7.79 (dd, J=5.42, 3.06 Hz, 2H, ArH); 13C NMR (125 MHz, CDCl3) δ -1.8 (SiMe), 17.0 (CH2), 34.4 (CH2), 123.0 (CH), 132.3 (CH), 133.7 (CH), 168.2 (CO); 29Si NMR (99 MHz, CDCl3) 0.01 (Si(Me3)3); MS (EI+) m/z (rel. intensity %) 247 (M+, 23), 246 (M-1, 100), 232 (50), 204 (75), 160 (26), 130 (55), 91 (49), 73 (39); HRMS (EI+): calcd. for C13H17NO2Si (M+) 247.1024, found (M-1)+ 246.0945.

Refinement

All H-atoms were placed in idealized locations and refined as riding with appropriate thermal displacement coefficients Uiso(H) = 1.2 or 1.5 times Ueq(bearing atom). The data were collected at room temperature on a Bruker SMART X2S diffractometer in the automated mode and manually processed thereafter.

Figures

Fig. 1.
Molecular structure of (I). The thermal ellipsoids are shown at 30% probability level.

Crystal data

C13H17NO2SiF(000) = 528
Mr = 247.37Dx = 1.145 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2755 reflections
a = 11.562 (5) Åθ = 3.4–23.7°
b = 6.411 (2) ŵ = 0.16 mm1
c = 19.445 (8) ÅT = 300 K
β = 95.176 (14)°Needle, colourless
V = 1435.5 (10) Å30.89 × 0.40 × 0.30 mm
Z = 4

Data collection

Bruker SMART X2S diffractometer2701 independent reflections
Radiation source: micro-focus sealed tube1750 reflections with I > 2σ(I)
doubly curved silicon crystalRint = 0.036
ω scansθmax = 25.7°, θmin = 3.4°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −14→14
Tmin = 0.875, Tmax = 0.955k = −7→7
9164 measured reflectionsl = −23→23

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.151H-atom parameters constrained
S = 0.99w = 1/[σ2(Fo2) + (0.0922P)2 + 0.0229P] where P = (Fo2 + 2Fc2)/3
2701 reflections(Δ/σ)max = 0.010
157 parametersΔρmax = 0.15 e Å3
0 restraintsΔρmin = −0.15 e Å3

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*/Ueq
Si10.90115 (5)0.20211 (9)0.38252 (3)0.0610 (3)
O10.75423 (19)0.2215 (3)0.61648 (12)0.1052 (7)
O20.60178 (16)0.7082 (3)0.46280 (10)0.0929 (6)
N10.68492 (15)0.4340 (3)0.52646 (10)0.0686 (5)
C10.8769 (3)−0.0839 (4)0.38950 (16)0.0987 (9)
H1A0.9213−0.13660.42990.148*
H1B0.9009−0.15220.34920.148*
H1C0.7959−0.11030.39300.148*
C21.0592 (2)0.2585 (5)0.37947 (16)0.1010 (9)
H2A1.10150.20830.42090.152*
H2B1.07050.40630.37570.152*
H2C1.08690.19000.34020.152*
C30.8170 (3)0.3029 (5)0.30296 (15)0.1078 (10)
H3A0.84180.23260.26320.162*
H3B0.83020.45000.29890.162*
H3C0.73570.27780.30580.162*
C40.85121 (18)0.3403 (3)0.45914 (11)0.0615 (6)
H4A0.89760.29240.50010.074*
H4B0.86590.48830.45430.074*
C50.72357 (19)0.3103 (4)0.47001 (13)0.0773 (7)
H5A0.67700.34690.42770.093*
H5B0.71000.16400.47920.093*
C60.7031 (2)0.3775 (4)0.59582 (14)0.0758 (7)
C70.6491 (2)0.5451 (4)0.63477 (13)0.0724 (6)
C80.6418 (3)0.5693 (6)0.70431 (16)0.0995 (9)
H80.67280.47070.73590.119*
C90.5867 (3)0.7459 (7)0.72558 (18)0.1135 (11)
H90.57950.76580.77240.136*
C100.5424 (3)0.8922 (6)0.67926 (19)0.1061 (10)
H100.50591.00920.69550.127*
C110.5502 (2)0.8714 (4)0.60893 (15)0.0847 (8)
H110.52060.97150.57750.102*
C120.60455 (18)0.6934 (4)0.58821 (12)0.0659 (6)
C130.62725 (19)0.6246 (4)0.51808 (13)0.0679 (6)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Si10.0681 (4)0.0500 (4)0.0653 (4)−0.0086 (3)0.0081 (3)−0.0030 (3)
O10.1094 (16)0.0863 (13)0.1218 (16)0.0091 (12)0.0198 (13)0.0246 (12)
O20.0852 (13)0.1100 (14)0.0822 (13)0.0171 (11)−0.0001 (10)0.0038 (10)
N10.0528 (11)0.0727 (12)0.0818 (13)−0.0037 (9)0.0134 (9)−0.0067 (10)
C10.119 (2)0.0547 (15)0.125 (2)−0.0060 (14)0.0245 (19)−0.0052 (15)
C20.0817 (19)0.113 (2)0.113 (2)−0.0169 (17)0.0352 (17)−0.0301 (18)
C30.140 (3)0.100 (2)0.0790 (18)−0.0160 (19)−0.0120 (18)0.0127 (15)
C40.0537 (13)0.0573 (12)0.0731 (14)−0.0078 (10)0.0040 (10)−0.0068 (10)
C50.0557 (14)0.0794 (16)0.0971 (18)−0.0096 (12)0.0096 (13)−0.0228 (13)
C60.0624 (15)0.0761 (16)0.0902 (18)−0.0133 (13)0.0135 (12)0.0076 (14)
C70.0562 (13)0.0845 (16)0.0787 (16)−0.0124 (12)0.0180 (12)0.0012 (13)
C80.088 (2)0.129 (3)0.0849 (19)−0.0080 (18)0.0235 (15)0.0079 (18)
C90.091 (2)0.167 (3)0.086 (2)−0.014 (2)0.0268 (18)−0.025 (2)
C100.078 (2)0.124 (3)0.120 (3)−0.0098 (18)0.0273 (19)−0.045 (2)
C110.0559 (14)0.0910 (18)0.108 (2)−0.0047 (13)0.0119 (13)−0.0201 (16)
C120.0427 (11)0.0765 (15)0.0791 (15)−0.0121 (11)0.0095 (10)−0.0134 (13)
C130.0469 (12)0.0777 (15)0.0789 (16)−0.0061 (11)0.0040 (11)−0.0031 (13)

Geometric parameters (Å, °)

Si1—C11.862 (2)C4—C51.522 (3)
Si1—C21.869 (3)C4—H4A0.9700
Si1—C41.869 (2)C4—H4B0.9700
Si1—C31.867 (3)C5—H5A0.9700
O1—C61.212 (3)C5—H5B0.9700
O2—C131.213 (3)C6—C71.484 (4)
N1—C61.394 (3)C7—C81.371 (4)
N1—C131.395 (3)C7—C121.380 (3)
N1—C51.457 (3)C8—C91.381 (5)
C1—H1A0.9600C8—H80.9300
C1—H1B0.9600C9—C101.367 (5)
C1—H1C0.9600C9—H90.9300
C2—H2A0.9600C10—C111.385 (4)
C2—H2B0.9600C10—H100.9300
C2—H2C0.9600C11—C121.380 (3)
C3—H3A0.9600C11—H110.9300
C3—H3B0.9600C12—C131.479 (3)
C3—H3C0.9600
C1—Si1—C2110.31 (14)H4A—C4—H4B107.5
C1—Si1—C4110.45 (11)N1—C5—C4113.77 (18)
C2—Si1—C4107.87 (11)N1—C5—H5A108.8
C1—Si1—C3109.30 (14)C4—C5—H5A108.8
C2—Si1—C3110.16 (15)N1—C5—H5B108.8
C4—Si1—C3108.73 (14)C4—C5—H5B108.8
C6—N1—C13111.7 (2)H5A—C5—H5B107.7
C6—N1—C5123.9 (2)O1—C6—N1124.2 (3)
C13—N1—C5124.4 (2)O1—C6—C7130.1 (3)
Si1—C1—H1A109.5N1—C6—C7105.8 (2)
Si1—C1—H1B109.5C8—C7—C12121.1 (2)
H1A—C1—H1B109.5C8—C7—C6130.6 (3)
Si1—C1—H1C109.5C12—C7—C6108.3 (2)
H1A—C1—H1C109.5C7—C8—C9117.3 (3)
H1B—C1—H1C109.5C7—C8—H8121.3
Si1—C2—H2A109.5C9—C8—H8121.3
Si1—C2—H2B109.5C10—C9—C8121.4 (3)
H2A—C2—H2B109.5C10—C9—H9119.3
Si1—C2—H2C109.5C8—C9—H9119.3
H2A—C2—H2C109.5C9—C10—C11122.1 (3)
H2B—C2—H2C109.5C9—C10—H10119.0
Si1—C3—H3A109.5C11—C10—H10119.0
Si1—C3—H3B109.5C10—C11—C12116.1 (3)
H3A—C3—H3B109.5C10—C11—H11122.0
Si1—C3—H3C109.5C12—C11—H11122.0
H3A—C3—H3C109.5C11—C12—C7122.1 (2)
H3B—C3—H3C109.5C11—C12—C13129.7 (2)
C5—C4—Si1115.09 (15)C7—C12—C13108.2 (2)
C5—C4—H4A108.5O2—C13—N1124.5 (2)
Si1—C4—H4A108.5O2—C13—C12129.5 (2)
C5—C4—H4B108.5N1—C13—C12106.0 (2)
Si1—C4—H4B108.5
C1—Si1—C4—C5−59.0 (2)C8—C9—C10—C110.1 (5)
C2—Si1—C4—C5−179.61 (18)C9—C10—C11—C120.5 (4)
C3—Si1—C4—C560.9 (2)C10—C11—C12—C7−0.3 (4)
C6—N1—C5—C4−80.8 (3)C10—C11—C12—C13−179.8 (2)
C13—N1—C5—C498.0 (3)C8—C7—C12—C11−0.4 (3)
Si1—C4—C5—N1−174.99 (17)C6—C7—C12—C11−178.9 (2)
C13—N1—C6—O1−177.9 (2)C8—C7—C12—C13179.2 (2)
C5—N1—C6—O11.0 (4)C6—C7—C12—C130.7 (2)
C13—N1—C6—C71.7 (2)C6—N1—C13—O2179.6 (2)
C5—N1—C6—C7−179.43 (18)C5—N1—C13—O20.7 (3)
O1—C6—C7—C8−0.2 (5)C6—N1—C13—C12−1.3 (2)
N1—C6—C7—C8−179.7 (2)C5—N1—C13—C12179.83 (18)
O1—C6—C7—C12178.1 (3)C11—C12—C13—O2−1.0 (4)
N1—C6—C7—C12−1.4 (2)C7—C12—C13—O2179.4 (2)
C12—C7—C8—C91.0 (4)C11—C12—C13—N1179.9 (2)
C6—C7—C8—C9179.1 (3)C7—C12—C13—N10.3 (2)
C7—C8—C9—C10−0.8 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C11—H11···O2i0.932.573.443 (4)156

Symmetry codes: (i) −x+1, −y+2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZS2025).

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