organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

3-Nitro-1-(triiso­propyl­silyl)-1H-pyrrole

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aWestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, and bDepartment of Pharmaceutical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, Scotland
*Correspondence e-mail: a.r.kennedy@strath.ac.uk

(Received 29 June 2006; accepted 5 July 2006; online 12 July 2006)

The nitration of 1-(triisopropyl­silyl)-1H-pyrrole leads to a mixture of products following partial acid cleavage of the triisopropyl­silyl protecting group. Structural determination showed the isolated products to be the title compound, C13H24N22O2Si, and 2,4-dinitro­pyrrole. In the solid state, the title compound exists as discrete mol­ecules with only weak C—H⋯nitro hydrogen bonds between them.

Comment

The quest for N-alkyl-substituted pyrroles bearing a nitro group at position three has led us to the use of the cleavable and bulky triisoproplysilyl (TIPS) group. This work is in connection with our research into minor-groove binding compounds (Khalaf et al., 2004[Khalaf, A. I., Ebrahimabadi, A. H., Drummond, A. J., Anthony, N. G., Mackay, S. P., Suckling, C. J. & Waigh, R. D. (2004). Org. Biomol. Chem. 2, 3119-3127.]). These compounds are analogues of naturally occurring distamycin and netropsin, which bind primarily to the adenine-thymine-rich minor groove of DNA. 3-Nitropyrrole (Bray et al., 1990[Bray, B. L., Mathies, P. H., Naef, R., Solas, D. R., Tidwell, T. T., Artis, D. R. & Muchowski, J. M. (1990). J. Org. Chem. 55, 6317-6328.]) was required as a precursor; however, the straightforward nitration of pyrrole favours position two. To prevent the nitration from occurring at position two of the pyrrole, a TIPS protecting group was first attached to the nitro­gen of the pyrrole ring. This led to the nitro group being directed to position three (as anti­cipated), giving rise to the desired product (I) (Fig. 1[link]) in 32% yield. However, during the course of the reaction, and due to the presence of acetic acid, the TIPS group cleaved. The removal of the TIPS group allowed the nitration reaction to occur once again. However, this time it occurred at position two, leading to the formation of the undesired product, 2,4-dinitro­pyrrole (II), in 19% yield.

[Scheme 1]

Despite the large number of substituted pyrroles reported in the Cambridge Structural Database (Version 5.27 with updates to May 2006; Allen, 2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]), a search found only nine relevant 3-nitro derivatives. All of the ring bond lengths and angles (Table 1[link]) of (I)[link] fall within the ranges found for these nine structures, with the exception that in (I)[link] the C2—N1—C5 angle is slightly below the literature range [106.8 (2)° cf. 107.7–110.2°]. This is presumably due to the bulk and inductive effects of the attached TIPS group as no such relevant N-silyl substituent was found in the database. All of the literature nitro groups are approximately coplanar with their pyrrole rings; it can be seen from Table 1[link] that this is also the case for (I)[link].

In the absence of obvious hydrogen-bonding groups, nitro aromatics often display nitro-to-nitro inter­actions of the type described by Wozniak et al. (1994[Wozniak, K., He, H., Klinowski, J., Jones, W. & Grech, E. (1994). J. Phys. Chem. 98, 13755-13765.]); however, none is found in (I)[link]. The only inter­molecular inter­actions of any note are weak C—H⋯O contacts utilizing both sp2 and sp3 CH groups (see Table 2[link]). This can be rationalized as a consequence of the bulky triisopropyl­silyl group, which ensures that the ring systems are widely separated from each other.

[Figure 1]
Figure 1
The mol­ecular structure of (I)[link], with displacement ellipsoids drawn at the 50% probability level.

Experimental

A solution of cupric nitrate trihydrate (2.70 g, 11.2 mmol) in acetic anhydride (20 ml) was cooled to 273 K and 1-(triisopropyl­silyl)-1H-pyrrole (2.50 g, 11.2 mmol) was added dropwise with stirring. The ice bath was removed and stirring was continued for 1 h at room temperature. The reaction mixture was poured slowly over a saturated sodium hydrogen carbonate solution with stirring. After extraction with diethyl ether the organic layer was collected, dried (MgSO4) and the solvent was removed under reduced pressure. The residue was subjected to flash chromatography on silica gel, using ethyl acetate/hexane (1:12) to elute (I)[link]. The solvents were removed under reduced pressure and a slow stream of air was passed over the residue to remove any volatile material. The product was obtained as colourless crystals [0.947 g, 32%; m.p. 325–327 K, literature m.p. 325–327 K (Bray et al., 1990[Bray, B. L., Mathies, P. H., Naef, R., Solas, D. R., Tidwell, T. T., Artis, D. R. & Muchowski, J. M. (1990). J. Org. Chem. 55, 6317-6328.])]. Compound (II) was eluted using ethyl acetate–hexane (1:4). This material was obtained, after the removal of the solvents, as pale-yellow crystals [0.338 g, 19%; m.p. 422–423 K, literature m.p. 423–424 K (Sharnin et al., 1975[Sharnin, G. P., Falyakhov, I. F. & Butovetskii, D. N. (1975). Khim. Geterotsikl. Soedin. 5, 655-658 Chem. Heteocycl. Compd (Engl. Transl.), 11, 571-573.])].

Crystal data
  • C13H24N2O2Si

  • Mr = 268.43

  • Monoclinic, P 21 /n

  • a = 9.6924 (5) Å

  • b = 15.9437 (10) Å

  • c = 10.1267 (6) Å

  • β = 95.089 (4)°

  • V = 1558.74 (16) Å3

  • Z = 4

  • Dx = 1.144 Mg m−3

  • Mo Kα radiation

  • μ = 0.15 mm−1

  • T = 123 (2) K

  • Cut fragment, colourless

  • 0.30 × 0.12 × 0.08 mm

Data collection
  • Nonius KappaCCD diffractometer

  • ω and φ scans

  • Absorption correction: none

  • 13088 measured reflections

  • 3060 independent reflections

  • 1685 reflections with I > 2σ(I)

  • Rint = 0.108

  • θmax = 26.0°

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.059

  • wR(F2) = 0.123

  • S = 1.01

  • 3060 reflections

  • 169 parameters

  • H-atom parameters constrained

  • w = 1/[σ2(Fo2) + (0.0471P)2 + 0.0035P] where P = (Fo2 + 2Fc2)/3

  • (Δ/σ)max = 0.001

  • Δρmax = 0.34 e Å−3

  • Δρmin = −0.36 e Å−3

Table 1
Selected geometric parameters (Å, °)

Si1—N1 1.805 (2)
N1—C2 1.365 (3)
N1—C5 1.395 (3)
C2—C3 1.365 (3)
C3—C4 1.410 (4)
C4—C5 1.358 (4)
C2—N1—C5 106.8 (2)
C3—C2—N1 108.4 (2)
C2—C3—C4 109.1 (2)
C5—C4—C3 105.3 (2)
C4—C5—N1 110.3 (2)
O1—N2—C3—C2 −0.5 (4)
O2—N2—C3—C2 178.9 (2)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C5—H5⋯O2i 0.95 2.47 3.403 (4) 166
C10—H10⋯O1ii 1.00 2.55 3.245 (4) 126
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) -x+1, -y, -z.

All H atoms were positioned geometrically, C—H = 0.95 (Csp2), 0.98 (CH3) or 1.00 Å (Csp3), and refined using a riding model [Uiso(H) = 1.5Ueq(C) for CH3 and 1.2Ueq(C) for all others].

Data collection: COLLECT (Hooft, 1988[Hooft, R. (1988). COLLECT. Nonius BV, Delft, The Netherlands.]) and DENZO (Otwin­owski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp 307-326. New York: Academic Press.]); cell refinement: DENZO and COLLECT; data reduction: DENZO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); molecular graphics: ORTEPII (Johnson, 1976[Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: SHELXL97.

Supporting information


Computing details top

Data collection: COLLECT (Hooft, 1988) and DENZO (Otwinowski & Minor, 1997); cell refinement: DENZO and COLLECT; data reduction: DENZO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97.

3-Nitro-1-(triisopropylsilyl)-1H-pyrrole top
Crystal data top
C13H24N2O2SiF(000) = 584
Mr = 268.43Dx = 1.144 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 9.6924 (5) ÅCell parameters from 3020 reflections
b = 15.9437 (10) Åθ = 1.0–26.1°
c = 10.1267 (6) ŵ = 0.15 mm1
β = 95.089 (4)°T = 123 K
V = 1558.74 (16) Å3Cut fragment, colourless
Z = 40.30 × 0.12 × 0.08 mm
Data collection top
Nonius KappaCCD
diffractometer
1685 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.108
Graphite monochromatorθmax = 26.0°, θmin = 2.4°
ω and φ scansh = 1111
13088 measured reflectionsk = 1919
3060 independent reflectionsl = 1212
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.123H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0471P)2 + 0.0035P]
where P = (Fo2 + 2Fc2)/3
3060 reflections(Δ/σ)max = 0.001
169 parametersΔρmax = 0.34 e Å3
0 restraintsΔρmin = 0.36 e Å3
Special details top

Experimental. A solution of cupric nitrate trihydrate (2.70 g, 11.2 mmol) in acetic anhydride (20 ml) was cooled to 273 K and 1-(triisopropylsilyl)-1H-pyrrole (2.50 g, 11.2 mmol) was added dropwise with stirring. The ice bath was removed and stirring was continued for 1 h at room temperature. The reaction mixture was poured slowly over a saturated sodium hydrogen carbonate solution with stirring. After extraction with ether the organic layer was collected, dried (MgSO4) and the solvent was removed under reduced pressure. The residue was subjected to flash chromatography on silica gel, using ethyl acetate/hexane (1:12) to elute (I). The solvents were removed under reduced pressure and a slow stream of air was passed over it to remove any volatile material. The product was obtained as colourless crystals [0.947 g, 32%; m.p. 325–327 K, literature m.p. 325–327 K (Bray et al., 1990)]. 1H NMR (DMSO-d6): δ 7.88 (1H, dd, J = 2.6, 5.4 Hz), 6.88 (1H, dd, J = 3.9, 7.8 Hz), 6.67 (1H, dd, J = 3.9, 6.4 Hz), 1.05–0.86 (21H, m). IR (KBr): 1550, 1330, 1240 cm-1. Compound (II) was eluted using ethyl acetate–hexane (1:4). This material was obtained, after the removal of the solvents, as pale-yellow crystals [0.338 g, 19%; m.p. 422–423 K, literature m.p. 423–424 K (Sharnin et al., 1975)]. 1H NMR (DMSO-d6): δ 14.4 (1H, br), 8.26 (1H, d, J = 2.9 Hz), 7.71 (1H, d, J = 2.9 Hz). IR (KBr): 3195, 3153, 1554, 1488, 1347, 1239, 1124, 1080, 957, 846, 815, 751 cm-1.

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) top
xyzUiso*/Ueq
Si10.84500 (8)0.11350 (5)0.27816 (7)0.0205 (2)
O10.5558 (2)0.07380 (14)0.21907 (19)0.0418 (6)
O20.6482 (2)0.17835 (13)0.31778 (19)0.0346 (6)
N10.8022 (2)0.15042 (14)0.1111 (2)0.0215 (6)
N20.6353 (2)0.13427 (17)0.2192 (2)0.0287 (6)
C20.7113 (3)0.11329 (18)0.0182 (3)0.0217 (7)
H20.65430.06620.03260.026*
C30.7160 (3)0.15521 (17)0.0989 (3)0.0211 (7)
C40.8127 (3)0.22120 (18)0.0811 (3)0.0252 (7)
H40.83690.26050.14560.030*
C50.8639 (3)0.21657 (18)0.0480 (3)0.0249 (7)
H50.93210.25310.08930.030*
C60.9494 (3)0.03860 (18)0.1823 (3)0.0342 (8)
H6A0.92180.01960.09170.051*
H6B0.87140.06750.21770.051*
H6C1.02800.07720.18140.051*
C70.9916 (3)0.03755 (17)0.2703 (3)0.0220 (7)
H71.01500.01590.36220.026*
C81.1233 (3)0.07824 (19)0.2257 (3)0.0327 (8)
H8A1.19600.03570.22330.049*
H8B1.15470.12260.28830.049*
H8C1.10330.10240.13710.049*
C90.5574 (3)0.11509 (19)0.3264 (3)0.0314 (8)
H9A0.47390.08040.32650.047*
H9B0.54950.15180.24850.047*
H9C0.56730.14930.40700.047*
C100.6848 (3)0.05834 (17)0.3218 (3)0.0216 (7)
H100.66100.01730.24870.026*
C110.7071 (3)0.00593 (18)0.4497 (3)0.0309 (8)
H11A0.72440.04340.52600.046*
H11B0.78690.03130.44420.046*
H11C0.62420.02770.46020.046*
C120.7990 (3)0.28032 (18)0.3786 (3)0.0412 (9)
H12A0.72330.26350.43090.062*
H12B0.76180.29320.28780.062*
H12C0.84480.33010.41860.062*
C130.9040 (3)0.20860 (17)0.3765 (3)0.0239 (7)
H130.98390.23180.33220.029*
C140.9625 (3)0.18556 (18)0.5188 (3)0.0323 (8)
H14A1.00430.23540.56270.049*
H14B1.03300.14170.51520.049*
H14C0.88730.16500.56880.049*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Si10.0208 (4)0.0213 (5)0.0190 (4)0.0002 (4)0.0003 (3)0.0005 (4)
O10.0396 (14)0.0471 (15)0.0365 (13)0.0144 (12)0.0085 (10)0.0055 (12)
O20.0399 (13)0.0426 (14)0.0211 (12)0.0074 (11)0.0013 (10)0.0046 (11)
N10.0226 (14)0.0214 (14)0.0201 (13)0.0030 (11)0.0001 (11)0.0005 (11)
N20.0252 (15)0.0341 (17)0.0266 (16)0.0064 (13)0.0012 (12)0.0037 (14)
C20.0213 (15)0.0185 (16)0.0252 (17)0.0006 (13)0.0016 (13)0.0001 (14)
C30.0181 (15)0.0250 (17)0.0196 (16)0.0021 (14)0.0016 (13)0.0022 (14)
C40.0249 (17)0.0266 (18)0.0240 (17)0.0008 (14)0.0016 (13)0.0089 (14)
C50.0255 (17)0.0221 (17)0.0265 (18)0.0072 (14)0.0013 (13)0.0022 (14)
C60.0292 (18)0.032 (2)0.0413 (19)0.0012 (15)0.0048 (15)0.0053 (16)
C70.0214 (16)0.0232 (18)0.0212 (16)0.0009 (13)0.0003 (13)0.0001 (13)
C80.0249 (18)0.0315 (18)0.042 (2)0.0011 (15)0.0029 (15)0.0052 (16)
C90.0233 (17)0.037 (2)0.0343 (18)0.0037 (15)0.0059 (13)0.0060 (16)
C100.0232 (16)0.0233 (17)0.0185 (16)0.0003 (14)0.0026 (12)0.0014 (13)
C110.0304 (17)0.0294 (19)0.0334 (18)0.0001 (15)0.0063 (14)0.0045 (15)
C120.051 (2)0.0266 (19)0.045 (2)0.0056 (17)0.0019 (17)0.0090 (17)
C130.0276 (17)0.0208 (17)0.0238 (16)0.0011 (14)0.0046 (13)0.0000 (14)
C140.0415 (19)0.0307 (19)0.0240 (17)0.0020 (15)0.0016 (15)0.0024 (15)
Geometric parameters (Å, º) top
Si1—N11.805 (2)C8—H8A0.9800
Si1—C101.871 (3)C8—H8B0.9800
Si1—C71.874 (3)C8—H8C0.9800
Si1—C131.876 (3)C9—C101.535 (4)
O1—N21.234 (3)C9—H9A0.9800
O2—N21.237 (3)C9—H9B0.9800
N1—C21.365 (3)C9—H9C0.9800
N1—C51.395 (3)C10—C111.540 (4)
N2—C31.428 (3)C10—H101.0000
C2—C31.365 (3)C11—H11A0.9800
C2—H20.9500C11—H11B0.9800
C3—C41.410 (4)C11—H11C0.9800
C4—C51.358 (4)C12—C131.532 (4)
C4—H40.9500C12—H12A0.9800
C5—H50.9500C12—H12B0.9800
C6—C71.540 (4)C12—H12C0.9800
C6—H6A0.9800C13—C141.545 (4)
C6—H6B0.9800C13—H131.0000
C6—H6C0.9800C14—H14A0.9800
C7—C81.535 (3)C14—H14B0.9800
C7—H71.0000C14—H14C0.9800
N1—Si1—C10104.37 (11)C7—C8—H8C109.5
N1—Si1—C7106.44 (11)H8A—C8—H8C109.5
C10—Si1—C7110.77 (12)H8B—C8—H8C109.5
N1—Si1—C13105.56 (11)C10—C9—H9A109.5
C10—Si1—C13118.35 (12)C10—C9—H9B109.5
C7—Si1—C13110.39 (12)H9A—C9—H9B109.5
C2—N1—C5106.8 (2)C10—C9—H9C109.5
C2—N1—Si1125.80 (18)H9A—C9—H9C109.5
C5—N1—Si1127.14 (18)H9B—C9—H9C109.5
O1—N2—O2123.5 (2)C9—C10—C11110.4 (2)
O1—N2—C3118.5 (2)C9—C10—Si1114.63 (19)
O2—N2—C3118.0 (3)C11—C10—Si1113.34 (18)
C3—C2—N1108.4 (2)C9—C10—H10105.9
C3—C2—H2125.8C11—C10—H10105.9
N1—C2—H2125.8Si1—C10—H10105.9
C2—C3—C4109.1 (2)C10—C11—H11A109.5
C2—C3—N2124.6 (3)C10—C11—H11B109.5
C4—C3—N2126.3 (3)H11A—C11—H11B109.5
C5—C4—C3105.3 (2)C10—C11—H11C109.5
C5—C4—H4127.3H11A—C11—H11C109.5
C3—C4—H4127.3H11B—C11—H11C109.5
C4—C5—N1110.3 (2)C13—C12—H12A109.5
C4—C5—H5124.9C13—C12—H12B109.5
N1—C5—H5124.9H12A—C12—H12B109.5
C7—C6—H6A109.5C13—C12—H12C109.5
C7—C6—H6B109.5H12A—C12—H12C109.5
H6A—C6—H6B109.5H12B—C12—H12C109.5
C7—C6—H6C109.5C12—C13—C14110.7 (2)
H6A—C6—H6C109.5C12—C13—Si1116.03 (19)
H6B—C6—H6C109.5C14—C13—Si1111.87 (19)
C8—C7—C6110.4 (2)C12—C13—H13105.8
C8—C7—Si1113.14 (19)C14—C13—H13105.8
C6—C7—Si1111.76 (18)Si1—C13—H13105.8
C8—C7—H7107.1C13—C14—H14A109.5
C6—C7—H7107.1C13—C14—H14B109.5
Si1—C7—H7107.1H14A—C14—H14B109.5
C7—C8—H8A109.5C13—C14—H14C109.5
C7—C8—H8B109.5H14A—C14—H14C109.5
H8A—C8—H8B109.5H14B—C14—H14C109.5
C10—Si1—N1—C229.4 (2)N1—Si1—C7—C863.3 (2)
C7—Si1—N1—C287.8 (2)C10—Si1—C7—C8176.16 (18)
C13—Si1—N1—C2154.9 (2)C13—Si1—C7—C850.8 (2)
C10—Si1—N1—C5157.3 (2)N1—Si1—C7—C662.1 (2)
C7—Si1—N1—C585.5 (2)C10—Si1—C7—C650.8 (2)
C13—Si1—N1—C531.8 (2)C13—Si1—C7—C6176.13 (18)
C5—N1—C2—C30.2 (3)N1—Si1—C10—C964.0 (2)
Si1—N1—C2—C3174.65 (18)C7—Si1—C10—C9178.14 (19)
N1—C2—C3—C40.0 (3)C13—Si1—C10—C953.0 (2)
N1—C2—C3—N2179.8 (2)N1—Si1—C10—C11168.10 (19)
O1—N2—C3—C20.5 (4)C7—Si1—C10—C1153.9 (2)
O2—N2—C3—C2178.9 (2)C13—Si1—C10—C1175.0 (2)
O1—N2—C3—C4179.3 (3)N1—Si1—C13—C1259.0 (2)
O2—N2—C3—C41.3 (4)C10—Si1—C13—C1257.3 (2)
C2—C3—C4—C50.2 (3)C7—Si1—C13—C12173.6 (2)
N2—C3—C4—C5179.6 (2)N1—Si1—C13—C14172.69 (18)
C3—C4—C5—N10.3 (3)C10—Si1—C13—C1471.0 (2)
C2—N1—C5—C40.3 (3)C7—Si1—C13—C1458.1 (2)
Si1—N1—C5—C4174.66 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5···O2i0.952.473.403 (4)166
C10—H10···O1ii1.002.553.245 (4)126
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x+1, y, z.
 

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