2-[(1H-Pyrrol-2-yl)meth­yl]-1H-pyrrole

Abstract

In the title compound, C₉H₁₀N₂, the two pyrrole ring planes are twisted by a dihedral angle of 69.07 (16)° and the C—C—C methane angle is 115.1 (2)°. In the crystal, mol­ecules are connected into layers in the bc plane by N—H⋯π inter­actions.

Related literature  

For synthesis of symmetric and non-symmetric porphyrins, see: Shanmugathasan et al. (2000 ▶); Bonifazi et al. (2005 ▶); Fendt et al. (2009 ▶). For their applications as organometallic ligands, see: Ganesan et al. (2001 ▶); Gao et al. (2004 ▶).

Experimental  

Crystal data  

• C₉H₁₀N₂

• M _r = 146.19

• Monoclinic,

• a = 6.048 (3) Å

• b = 7.312 (4) Å

• c = 9.024 (5) Å

• β = 100.78 (1)°

• V = 392.0 (4) ų

• Z = 2

• Mo Kα radiation

• μ = 0.08 mm⁻¹

• T = 153 K

• 0.32 × 0.08 × 0.06 mm

Data collection  

• Rigaku SCX-Mini diffractometer with Mercury 2 CCD

• Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T _min = 0.976, T _max = 0.996

• 4179 measured reflections

• 1786 independent reflections

• 1374 reflections with I > 2σ(I)

• R _int = 0.063

Refinement  

• R[F ² > 2σ(F ²)] = 0.057

• wR(F ²) = 0.132

• S = 1.05

• 1786 reflections

• 100 parameters

• 61 restraints

• H-atom parameters constrained

• Δρ_max = 0.19 e Å⁻³

• Δρ_min = −0.23 e Å⁻³

Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2008 ▶); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXTL/PC (Sheldrick, 2008 ▶); molecular graphics: SHELXTL/PC; software used to prepare material for publication: SHELXL97 (Sheldrick, 2008 ▶).

Supplementary Material

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

Table 1. Hydrogen-bond geometry (Å, °).

Cg1 and Cg2 are the centroids of the N1/C1–C4 and N2/C6–C9 rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯Cg1i	0.88	2.53	3.357 (3)	156
N2—H2N⋯Cg2ii	0.88	2.53	3.363 (3)	159

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

1. Comment

Dipyrromethane (DPM) derivatives have been used as key intermediates in the synthesis of symmetric and non-symmetric porphyrins (Shanmugathasan et al., 2000; Bonifazi et al., 2005; Fendt et al., 2009) and also used as organometallic ligands (Ganesan et al., 2001; Gao et al., 2004). DPMs are typically electron rich and prone to oxidation; this is particularly true in the case of unsubstituted DPMs, which benefit from oxygen-free conditions for isolation and long-term storage. Low temperatures are also beneficial. This sensitivity has made it difficult to obtain unsubstituted dipyrromethanes in the form of X-ray diffraction-grade crystals. Here, we report the crystal structure of 2-(1H-pyrrol-2-ylmethyl)-1H-pyrrole that in crystalline form is stable in air under ambient conditions. The molecular structure of the title compound is shown in Fig. 1. The configuration of two pyrrole ring planes are approximately perpendicular to each other, with the C4—C5—C6 methane angle of 115.1 (2)°.

2. Experimental

For the synthesis of DPM, the solution of paraformaldehyde (0.9 g, 29.97 mmol) in pyrrole (110 ml, 1.58 mol) with InCl₃ (0.3 g, 1.42 mmol) was stirred for 1 h at 70 °C under nitrogen atmosphere. After addition of NaOH (5 pellets), the reaction solution was stirred for 1 h at room temperature and then concentrated under vacuum (20 mmHg) at 70 °C. To the reaction mixture was poured 1 N NaOH solution (100 ml) and ethyl acetate (100 ml), then the organic layer was dried (Na₂SO₄), and distilled to afford DPM (4.37 g, 50% yield) as a dark brown syrup. The crystals of the title compound suitable for X-ray analysis were collected in the form of long needles from the pyrrole-rich distillate after being stored in a freezer for few days.

3. Refinement

H atoms were placed in calculated positions using a riding model with N—H = 0.88 Å and C—H = 0.95 and 0.99 Å for pyrrole and methane H, respectively, and U_iso(H) = 1.2 U_eq(C,N).

Figures

Fig. 1.

The molecular structure of the title compound with 25% probability displacement ellipsoids.

Crystal data

C9H10N2	F(000) = 156
Mr = 146.19	Dx = 1.238 Mg m−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71075 Å
Hall symbol: P 2yb	Cell parameters from 4189 reflections
a = 6.048 (3) Å	θ = 3.0–27.5°
b = 7.312 (4) Å	µ = 0.08 mm−1
c = 9.024 (5) Å	T = 153 K
β = 100.78 (1)°	Needle, colourless
V = 392.0 (4) Å3	0.32 × 0.08 × 0.06 mm
Z = 2

Data collection

Rigaku SCX-Mini with Mercury 2 CCD diffractometer	1786 independent reflections
Radiation source: fine-focus sealed tube	1374 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.063
ω scans	θmax = 27.5°, θmin = 3.4°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −7→7
Tmin = 0.976, Tmax = 0.996	k = −9→9
4179 measured reflections	l = −11→11

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.057	H-atom parameters constrained
wR(F2) = 0.132	w = 1/[σ2(Fo2) + (0.049P)2] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max = 0.001
1786 reflections	Δρmax = 0.19 e Å−3
100 parameters	Δρmin = −0.23 e Å−3
61 restraints	Absolute structure: nd
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. The direction of the twofold screw axis could not be reliably determined.

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

	x	y	z	Uiso*/Ueq
C1	0.2619 (4)	−0.0035 (4)	0.5615 (3)	0.0353 (6)
H1	0.3300	−0.0409	0.6603	0.042*
C2	0.3488 (4)	0.1182 (4)	0.4732 (3)	0.0331 (6)
H2	0.4887	0.1802	0.4991	0.040*
C3	0.1930 (4)	0.1352 (3)	0.3367 (3)	0.0298 (6)
H3	0.2088	0.2109	0.2538	0.036*
C4	0.0136 (4)	0.0222 (4)	0.3451 (2)	0.0284 (5)
C5	−0.2014 (4)	−0.0146 (4)	0.2387 (2)	0.0348 (6)
H5A	−0.3267	0.0374	0.2818	0.042*
H5B	−0.2242	−0.1486	0.2310	0.042*
C6	−0.2144 (4)	0.0606 (3)	0.0837 (3)	0.0301 (6)
C7	−0.3568 (4)	0.1863 (4)	0.0037 (3)	0.0342 (6)
H7	−0.4721	0.2516	0.0396	0.041*
C8	−0.3029 (4)	0.2019 (4)	−0.1402 (3)	0.0362 (6)
H8	−0.3761	0.2785	−0.2195	0.043*
C9	−0.1268 (4)	0.0876 (4)	−0.1462 (2)	0.0367 (6)
H9	−0.0530	0.0711	−0.2294	0.044*
N1	0.0597 (4)	−0.0620 (3)	0.4825 (2)	0.0344 (6)
H1N	−0.0283	−0.1423	0.5153	0.041*
N2	−0.0764 (3)	0.0011 (3)	−0.0094 (2)	0.0336 (5)
H2N	0.0302	−0.0813	0.0148	0.040*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
C1	0.0380 (14)	0.0427 (15)	0.0244 (12)	0.0079 (13)	0.0037 (11)	−0.0002 (12)
C2	0.0322 (13)	0.0322 (14)	0.0356 (13)	−0.0001 (11)	0.0082 (11)	−0.0078 (11)
C3	0.0366 (13)	0.0265 (13)	0.0292 (12)	−0.0002 (10)	0.0135 (11)	0.0000 (10)
C4	0.0349 (12)	0.0269 (13)	0.0249 (11)	0.0027 (10)	0.0096 (10)	0.0001 (9)
C5	0.0311 (12)	0.0358 (14)	0.0388 (14)	−0.0030 (11)	0.0103 (11)	0.0009 (11)
C6	0.0281 (12)	0.0290 (14)	0.0322 (13)	−0.0035 (10)	0.0030 (10)	−0.0048 (10)
C7	0.0248 (13)	0.0328 (14)	0.0438 (15)	0.0010 (11)	0.0031 (11)	0.0001 (11)
C8	0.0343 (14)	0.0296 (14)	0.0394 (14)	−0.0002 (11)	−0.0070 (12)	0.0034 (11)
C9	0.0459 (14)	0.0375 (16)	0.0248 (13)	−0.0032 (13)	0.0016 (11)	−0.0026 (11)
N1	0.0388 (12)	0.0334 (13)	0.0323 (11)	−0.0030 (10)	0.0100 (10)	0.0038 (9)
N2	0.0371 (11)	0.0287 (11)	0.0345 (11)	0.0064 (10)	0.0058 (9)	0.0006 (9)

Geometric parameters (Å, º)

C1—C2	1.363 (4)	C5—H5B	0.9900
C1—N1	1.364 (3)	C6—N2	1.361 (3)
C1—H1	0.9500	C6—C7	1.370 (3)
C2—C3	1.410 (3)	C7—C8	1.402 (3)
C2—H2	0.9500	C7—H7	0.9500
C3—C4	1.377 (3)	C8—C9	1.363 (3)
C3—H3	0.9500	C8—H8	0.9500
C4—N1	1.365 (3)	C9—N2	1.369 (3)
C4—C5	1.490 (3)	C9—H9	0.9500
C5—C6	1.491 (3)	N1—H1N	0.8800
C5—H5A	0.9900	N2—H2N	0.8800
C2—C1—N1	107.8 (2)	N2—C6—C7	106.7 (2)
C2—C1—H1	126.1	N2—C6—C5	122.0 (2)
N1—C1—H1	126.1	C7—C6—C5	131.2 (2)
C1—C2—C3	107.5 (2)	C6—C7—C8	108.1 (2)
C1—C2—H2	126.3	C6—C7—H7	125.9
C3—C2—H2	126.3	C8—C7—H7	125.9
C4—C3—C2	107.7 (2)	C9—C8—C7	107.8 (2)
C4—C3—H3	126.2	C9—C8—H8	126.1
C2—C3—H3	126.2	C7—C8—H8	126.1
N1—C4—C3	107.0 (2)	C8—C9—N2	107.0 (2)
N1—C4—C5	120.6 (2)	C8—C9—H9	126.5
C3—C4—C5	132.4 (2)	N2—C9—H9	126.5
C4—C5—C6	115.1 (2)	C1—N1—C4	110.1 (2)
C4—C5—H5A	108.5	C1—N1—H1N	124.9
C6—C5—H5A	108.5	C4—N1—H1N	124.9
C4—C5—H5B	108.5	C6—N2—C9	110.5 (2)
C6—C5—H5B	108.5	C6—N2—H2N	124.8
H5A—C5—H5B	107.5	C9—N2—H2N	124.8
N1—C1—C2—C3	0.5 (3)	C5—C6—C7—C8	−177.2 (2)
C1—C2—C3—C4	−0.1 (3)	C6—C7—C8—C9	−0.7 (3)
C2—C3—C4—N1	−0.4 (3)	C7—C8—C9—N2	1.1 (3)
C2—C3—C4—C5	178.4 (3)	C2—C1—N1—C4	−0.8 (3)
N1—C4—C5—C6	−170.1 (2)	C3—C4—N1—C1	0.7 (3)
C3—C4—C5—C6	11.2 (4)	C5—C4—N1—C1	−178.3 (2)
C4—C5—C6—N2	64.4 (3)	C7—C6—N2—C9	0.6 (3)
C4—C5—C6—C7	−118.6 (3)	C5—C6—N2—C9	178.2 (2)
N2—C6—C7—C8	0.1 (3)	C8—C9—N2—C6	−1.0 (3)

Hydrogen-bond geometry (Å, º)

Cg1 and Cg2 are the centroids of the N1/C1–C4 and N2/C6–C9 rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···Cg1i	0.88	2.53	3.357 (3)	156
N2—H2N···Cg2ii	0.88	2.53	3.363 (3)	159

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