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Acta Crystallogr Sect E Struct Rep Online. 2010 February 1; 66(Pt 2): o393.
Published online 2010 January 16. doi:  10.1107/S1600536809054269
PMCID: PMC2979789

4,4-Bis(1H-pyrrol-2-yl)penta­nol

Abstract

The title achiral compound, C13H18N2O, crystallized in the chiral monoclinic space group P21. The pyrrole rings are inclined to one another by 62.30 (11)°, and the propanol chain is in an extended conformation. In the crystal, the two pyrrole NH groups are involved in inter­molecular N—H(...)O hydrogen bonds, leading to the formation of a helical arrangement propagating along the b axis. An inter­esting feature of the crystal structure is the absence of any conventional hydrogen bonds involving the hydr­oxy H atom. There is, however, a weak inter­molecular O—H(...)π inter­action involving one of the pyrrole rings.

Related literature

For substituted calix[4]pyrroles, see: Gale et al. (1998 [triangle]); Sessler & Davis (2001 [triangle]); Sessler et al. (2003 [triangle]). For the crystal structures of similar compounds, see: Warriner et al. (2003 [triangle]); Maeda et al. (2007 [triangle]); Sobral et al. (2003 [triangle]). For details of hydrogen-bonding graph-set analysis, see: Bernstein et al. (1995 [triangle]). For a description of the Cambridge Structural Database, see: Allen (2002 [triangle]).

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Object name is e-66-0o393-scheme1.jpg

Experimental

Crystal data

  • C13H18N2O
  • M r = 218.29
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o393-efi1.jpg
  • a = 8.4721 (15) Å
  • b = 8.2111 (9) Å
  • c = 8.7120 (15) Å
  • β = 101.530 (14)°
  • V = 593.82 (16) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 173 K
  • 0.45 × 0.45 × 0.40 mm

Data collection

  • Stoe IPDS-2 diffractometer
  • 6119 measured reflections
  • 1701 independent reflections
  • 1518 reflections with I > 2σ(I)
  • R int = 0.032

Refinement

  • R[F 2 > 2σ(F 2)] = 0.030
  • wR(F 2) = 0.077
  • S = 0.97
  • 1701 reflections
  • 159 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.19 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: X-AREA (Stoe & Cie, 2009 [triangle]); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2009 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809054269/is2505sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809054269/is2505Isup2.hkl

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

Acknowledgments

HSE is grateful to the XRD Application LAB, Microsystems Technology Division, Swiss Center for Electronics and Microtechnology, Neuchâtel, for access to the X-ray diffraction equipment.

supplementary crystallographic information

Comment

The title compound (systematic name: 4,4-di(1H-pyrrol-2-yl)pentan-1-ol) was prepared as a building block for the formation of substituted calix[4]pyrroles. The latter have been shown to form extremely interesting host–guest complexes with various anions (Gale et al., 1998; Sessler and Davis, 2001; Sessler et al., 2003).

The structure of the title compound is shown in Fig. 1, and the geometrical parameters are given in the Supplementary Information and the archived CIF. This achiral compound crystallized in the chiral monoclinic space group P21. The bond lengths and angles are similar to those observed in 5 similar 1,1-bis(2-pyrrolyl)ethane compounds in the Cambridge Crystal Structure Database (CSD, V5.30, last update Sep. 2009; Allen et al., 2002). These include the (3,4,5-tribromo-2-pyrrolyl) derivative (Warriner et al., 2003; AJARIM), the o-, m- and p-pyridyl derivaties (Maeda et al., 2007; CIGKIN, CIGKEJ, CIGKAF, respectively) and the phenyl derivative (Sobral et al., 2003; JADHUS), all of which crystallized as racemates.

In the title compound the pyrrole ring mean-planes are inclined to one another by 62.30 (11)°, and the propanol chain is in the extended conformation. In the 5 compounds located in the CSD this angle varies between 68.5 to 89.6 °.

In the crystal the molecules are linked by conventional N—H···N intermolecular hydrogen bonds leading to the formation of helical chains propagating along the b axis (Fig. 2 and Table 1). The basic unitary hydrogen bonding graph set can be described by an R23(16) ring, while the basic binary graph set is a C(8) chain. This gives an extended notation of C(8)[R23(16)] (Bernstein et al., 1995). A fuller hydrogen bonding graph set analysis can be obtained using the program Mercury (Macrea et al., 2006).

An O—H···π interaction is also observed in the crystal structure (Fig. 2 and Table 1). It can be considered either to involve the C7═C8 bond (centroid = Cg1) with an O—H···π angle of ca 135°, or a weaker interaction involving the pyrrole ring (N2/C5—C8; centroid = Cg2), with an O—H···π angle of only ca 114° [these data were obtained using the program Mercury (Macrae et al., 2006)].

Experimental

A mixture of 3-acetylpropanol (10 ml, 98.6 mmol) and pyrrole (50 ml, 0.720 mol) were stirred for 5 min and then trifluoro acetic acid [TFA] (0.74 ml, 9.6 mmol, 0.097 equiv.) was added. The whole mixture was stirred foran additional 5 min and then quenched with aqueous NaOH (0.1 N, 30 ml). The mixture was extracted with CH2Cl2 (50 ml × 2) and the organic layer dried (Na2SO4). The solvent was removed in vacuo and the remaining oil crystallized with dichloromethane (20 ml). The colourless block-like crystals obtained were washed with 2-propanol [m.p. 372 K; Yield 14.1 g (65.3%)]. 1H NMR (CDCl3) δ 7.85 (bs, 2H, N—H), 6.63–6.61 (ddd, J = 2.7 Hz,2.7 Hz, 1.6 Hz, 2H, pyrrolic-H1–8), 6.15–6.13 (ddd, J = 3.3 Hz, 2.7 Hz, 1.6 Hz, 2H, pyrrolic-H2–7), 6.10–6.08 (ddd, J = 3.3 Hz, 1.6 Hz,1.6 Hz, 2H, pyrrolic-H3–6), 3.61–3.57 (td, J = 6 Hz, 5 Hz, 2H, –O—CH212), 2.07–2.03 (m, 2H, –CH210–), 1.59 (s, 3H, –CH313), 1.51–1.43 (m, 2H,-CH211–), 1.24–1.20 (t, J = 5 Hz, 1H, –OH); 13C NMR (CDCl3)δ 137.97 (C4–5), 117.15 (C1–5), 107.92 (C2–7),104.77 (C3–6), 63.26 (C12), 39.04 (C9), 37.35 (C10),28.01 (C11), 26.62 (C13). MS calcd. for C13H18N2O 218.14, found 217.13 (M—H+).

Refinement

In the final cycles of refinement, in the absence of significant anomalous scattering effects, 1239 Friedel pairs were merged and Δf " set to zero. The OH and NH H-atoms, located in a difference electron-density map, were freely refined: O—H = 0.83 (3) Å; N—H = 0.88 (2) - 0.90 (2) Å. The C-bound H-atoms were included in calculated positions and treated as riding atoms: C—H = 0.95, 0.99 and 0.98 Å for CH, CH2 and CH3 H-atoms, respectively, with Uiso(H) = k × Ueq(C), where k = 1.2 for CH and CH2 H-atoms, and 1.5 for CH3 H-atoms.

Figures

Fig. 1.
A view of the molecular structure of the title compound, with the displacement ellipsoids drawn at the 50% probability level.
Fig. 2.
A view, along the c axis, of the crystal packing of the title compound. The N—H···O hydrogen bonds are shown as dotted cyan lines and the O—H···π interactions as dotted black lines ...

Crystal data

C13H18N2OF(000) = 236
Mr = 218.29Dx = 1.221 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 5671 reflections
a = 8.4721 (15) Åθ = 2.4–29.6°
b = 8.2111 (9) ŵ = 0.08 mm1
c = 8.7120 (15) ÅT = 173 K
β = 101.530 (14)°Block, colourless
V = 593.82 (16) Å30.45 × 0.45 × 0.40 mm
Z = 2

Data collection

Stoe IPDS-2 diffractometer1518 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.032
graphiteθmax = 29.2°, θmin = 2.4°
[var phi] ans ω scansh = −10→11
6119 measured reflectionsk = −11→11
1701 independent reflectionsl = −11→11

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.077w = 1/[σ2(Fo2) + (0.0571P)2] where P = (Fo2 + 2Fc2)/3
S = 0.97(Δ/σ)max < 0.001
1701 reflectionsΔρmax = 0.19 e Å3
159 parametersΔρmin = −0.16 e Å3
1 restraintExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.108 (11)

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
Refinement. In the final cycles of refinement, in the absence of significant anomalous scattering effects, 1239 Friedel pairs were merged and Δf " set to zero. The OH and NH hydrogen atoms were located in difference electron-density maps and were freely refined. The C-bound H-atoms were included in calculated positions and treated as riding.

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

xyzUiso*/Ueq
O10.41371 (13)1.28786 (14)0.88057 (13)0.0300 (3)
N10.24737 (14)0.55996 (17)0.99568 (13)0.0244 (3)
N20.48148 (15)0.66563 (17)0.79634 (16)0.0281 (3)
C10.18516 (15)0.69959 (18)0.92203 (15)0.0220 (3)
C20.12554 (18)0.7921 (2)1.02911 (17)0.0293 (4)
C30.15673 (18)0.7047 (2)1.17356 (17)0.0318 (4)
C40.23207 (17)0.5631 (2)1.14900 (16)0.0286 (4)
C50.33030 (17)0.64998 (19)0.70462 (15)0.0248 (4)
C60.3443 (2)0.5545 (3)0.57848 (18)0.0409 (5)
C70.5085 (3)0.5108 (3)0.5947 (2)0.0518 (7)
C80.5900 (2)0.5804 (3)0.7302 (2)0.0419 (6)
C90.18427 (16)0.72822 (17)0.74921 (15)0.0221 (3)
C100.17922 (17)0.91270 (19)0.71418 (16)0.0244 (4)
C110.32247 (16)1.01255 (19)0.79998 (16)0.0248 (4)
C120.2876 (2)1.1921 (2)0.7865 (2)0.0398 (5)
C130.03085 (19)0.6525 (2)0.65082 (18)0.0349 (4)
H1N0.297 (2)0.482 (3)0.955 (2)0.037 (5)*
H1O0.485 (4)1.307 (4)0.823 (3)0.073 (9)*
H20.073500.894801.010500.0350*
H2N0.504 (2)0.709 (3)0.893 (2)0.034 (5)*
H30.129900.738901.269300.0380*
H40.267600.481101.225000.0340*
H60.259100.523300.495300.0490*
H70.553600.445400.524500.0620*
H80.702300.571200.771300.0500*
H10A0.171200.927600.600100.0290*
H10B0.079800.958000.740900.0290*
H11A0.347100.981100.911900.0300*
H11B0.418300.988100.755100.0300*
H12A0.274801.225400.675500.0480*
H12B0.184701.214300.820100.0480*
H13A−0.064100.701300.680900.0520*
H13B0.031000.534800.669400.0520*
H13C0.027800.673300.539500.0520*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0322 (5)0.0208 (6)0.0362 (5)−0.0021 (4)0.0048 (4)−0.0009 (4)
N10.0277 (6)0.0221 (6)0.0244 (5)−0.0005 (5)0.0073 (4)0.0010 (5)
N20.0256 (5)0.0262 (7)0.0345 (6)0.0036 (5)0.0106 (5)0.0033 (5)
C10.0204 (5)0.0215 (7)0.0239 (6)−0.0020 (5)0.0043 (4)0.0001 (5)
C20.0302 (7)0.0289 (8)0.0307 (7)0.0036 (6)0.0108 (5)−0.0001 (6)
C30.0331 (7)0.0384 (9)0.0262 (6)−0.0018 (7)0.0118 (5)−0.0011 (6)
C40.0299 (7)0.0320 (8)0.0249 (6)−0.0035 (6)0.0078 (5)0.0046 (6)
C50.0321 (7)0.0208 (7)0.0224 (6)0.0019 (6)0.0073 (5)0.0027 (5)
C60.0604 (11)0.0407 (10)0.0228 (6)0.0155 (9)0.0113 (6)0.0012 (6)
C70.0729 (13)0.0529 (13)0.0382 (9)0.0297 (11)0.0318 (9)0.0085 (9)
C80.0396 (8)0.0425 (11)0.0505 (10)0.0156 (8)0.0257 (7)0.0153 (8)
C90.0231 (6)0.0217 (7)0.0206 (5)−0.0018 (5)0.0025 (4)−0.0003 (5)
C100.0245 (6)0.0230 (7)0.0243 (6)0.0015 (5)0.0016 (5)0.0018 (5)
C110.0241 (6)0.0200 (7)0.0290 (6)0.0013 (5)0.0025 (5)0.0026 (5)
C120.0364 (8)0.0217 (9)0.0537 (10)0.0023 (7)−0.0094 (7)−0.0004 (7)
C130.0336 (7)0.0372 (9)0.0303 (7)−0.0103 (7)−0.0021 (5)−0.0021 (7)

Geometric parameters (Å, °)

O1—C121.443 (2)C10—C111.530 (2)
O1—H1O0.87 (3)C11—C121.504 (2)
N1—C11.367 (2)C2—H20.9500
N1—C41.3678 (18)C3—H30.9500
N2—C81.371 (2)C4—H40.9500
N2—C51.3735 (19)C6—H60.9500
N1—H1N0.88 (2)C7—H70.9500
N2—H2N0.899 (19)C8—H80.9500
C1—C91.5224 (18)C10—H10A0.9900
C1—C21.375 (2)C10—H10B0.9900
C2—C31.427 (2)C11—H11A0.9900
C3—C41.364 (2)C11—H11B0.9900
C5—C61.374 (2)C12—H12A0.9900
C5—C91.512 (2)C12—H12B0.9900
C6—C71.416 (3)C13—H13A0.9800
C7—C81.368 (3)C13—H13B0.9800
C9—C101.544 (2)C13—H13C0.9800
C9—C131.538 (2)
C12—O1—H1O106.9 (19)C4—C3—H3126.00
C1—N1—C4109.86 (13)N1—C4—H4126.00
C5—N2—C8109.48 (13)C3—C4—H4126.00
C4—N1—H1N123.7 (13)C5—C6—H6126.00
C1—N1—H1N126.3 (13)C7—C6—H6126.00
C5—N2—H2N125.5 (11)C6—C7—H7126.00
C8—N2—H2N124.2 (12)C8—C7—H7126.00
N1—C1—C2107.72 (12)N2—C8—H8126.00
N1—C1—C9121.26 (12)C7—C8—H8126.00
C2—C1—C9130.98 (13)C9—C10—H10A108.00
C1—C2—C3106.99 (14)C9—C10—H10B108.00
C2—C3—C4107.48 (13)C11—C10—H10A108.00
N1—C4—C3107.94 (13)C11—C10—H10B108.00
N2—C5—C6107.40 (14)H10A—C10—H10B107.00
N2—C5—C9121.77 (12)C10—C11—H11A109.00
C6—C5—C9130.82 (13)C10—C11—H11B109.00
C5—C6—C7107.75 (15)C12—C11—H11A109.00
C6—C7—C8107.25 (18)C12—C11—H11B109.00
N2—C8—C7108.11 (17)H11A—C11—H11B108.00
C1—C9—C10109.96 (11)O1—C12—H12A109.00
C1—C9—C5110.24 (11)O1—C12—H12B109.00
C5—C9—C10110.97 (12)C11—C12—H12A109.00
C5—C9—C13109.20 (12)C11—C12—H12B109.00
C1—C9—C13108.99 (11)H12A—C12—H12B108.00
C10—C9—C13107.43 (11)C9—C13—H13A109.00
C9—C10—C11116.18 (12)C9—C13—H13B109.00
C10—C11—C12111.28 (12)C9—C13—H13C109.00
O1—C12—C11112.24 (13)H13A—C13—H13B109.00
C1—C2—H2127.00H13A—C13—H13C109.00
C3—C2—H2126.00H13B—C13—H13C110.00
C2—C3—H3126.00
C4—N1—C1—C2−1.41 (16)N2—C5—C6—C70.2 (2)
C4—N1—C1—C9−179.27 (12)C9—C5—C6—C7−178.96 (17)
C1—N1—C4—C31.08 (17)N2—C5—C9—C1−45.13 (18)
C8—N2—C5—C6−0.4 (2)N2—C5—C9—C1076.94 (16)
C8—N2—C5—C9178.81 (15)N2—C5—C9—C13−164.83 (14)
C5—N2—C8—C70.5 (2)C6—C5—C9—C1133.92 (18)
N1—C1—C2—C31.17 (17)C6—C5—C9—C10−104.0 (2)
C9—C1—C2—C3178.74 (14)C6—C5—C9—C1314.2 (2)
N1—C1—C9—C5−32.86 (18)C5—C6—C7—C80.1 (2)
N1—C1—C9—C10−155.52 (13)C6—C7—C8—N2−0.4 (3)
N1—C1—C9—C1386.97 (15)C1—C9—C10—C1161.87 (15)
C2—C1—C9—C5149.85 (15)C5—C9—C10—C11−60.36 (15)
C2—C1—C9—C1027.2 (2)C13—C9—C10—C11−179.65 (12)
C2—C1—C9—C13−90.32 (18)C9—C10—C11—C12−166.90 (12)
C1—C2—C3—C4−0.53 (18)C10—C11—C12—O1173.65 (12)
C2—C3—C4—N1−0.33 (17)

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the C7═C8 bond and the N2/C5–C8 pyrrole ring, respectively.
D—H···AD—HH···AD···AD—H···A
N1—H1N···O1i0.88 (2)2.05 (2)2.9238 (18)174.3 (19)
N2—H2N···O1ii0.90 (2)2.06 (2)2.9529 (18)171.5 (19)
O1—H1O···Cg1iii0.87 (3)2.533.20135
O1—H1O···Cg2iii0.87 (3)2.643.10114

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2505).

References

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