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

Kim, C.-H.; Jeon, Y.-S.; Lynch, V.; Sessler, J.L.; Hwang, K.-J.

doi:10.1107/S1600536813028365

organic compounds

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Volume 69| Part 11| November 2013| Page o1697

doi:10.1107/S1600536813028365

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

Chong-Hyeak Kim,^a Yea-Sel Jeon,^b Vincent Lynch,^c Jonathan L. Sessler ^c ^* and Kwang-Jin Hwang ^b ^*

^aCenter for Chemical Analysis, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 305-600, Republic of Korea, ^bDepartment of Bio and Chemical Engineering, Hongik University at Sejong, 2639 Sejongro, Jochiwon, Sejong 339-701, Republic of Korea, and ^cDepartment of Chemistry, The University of Texas, 105 E. 24th St STOP A5300, Austin, TX 78712-1224, USA
^*Correspondence e-mail: sessler@mail.utexas.edu, kjhwang@hongik.ac.kr

(Received 9 October 2013; accepted 15 October 2013; online 23 October 2013)

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.

CCDC reference: 966627

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, P 2₁
a = 6.048 (3) Å
b = 7.312 (4) Å
c = 9.024 (5) Å
β = 100.78 (1)°
V = 392.0 (4) Å³
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[F² > 2σ(F²)] = 0.057
wR(F²) = 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

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) $[-x, y-{\script{1\over 2}}, -z+1]$ ; (ii) $[-x, y-{\script{1\over 2}}, -z]$ .

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).

Supporting information

CCDC reference: 966627

Crystal structure: contains datablocks hkj, I. DOI: 10.1107/S1600536813028365/tk5264sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813028365/tk5264Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813028365/tk5264Isup3.cml

checkCIF report

Comment top

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)°.

Related literature top

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

Experimental top

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.

Computing details top

Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2008); cell refinement: CrystalClear (Molecular Structure Corporation & Rigaku, 2008); data reduction: CrystalClear (Molecular Structure Corporation & Rigaku, 2008); 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 (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

Fig. 1. The molecular structure of the title compound with 25% probability displacement ellipsoids.

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

Crystal data top

C₉H₁₀N₂	F(000) = 156
M_r = 146.19	D_x = 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 top

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	R_int = 0.063
ω scans	θ_max = 27.5°, θ_min = 3.4°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −7→7
T_min = 0.976, T_max = 0.996	k = −9→9
4179 measured reflections	l = −11→11

Refinement top

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(F_o²) + (0.049P)²] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
1786 reflections	Δρ_max = 0.19 e Å⁻³
100 parameters	Δρ_min = −0.23 e Å⁻³
61 restraints	Absolute structure: nd
Primary atom site location: structure-invariant direct methods

Crystal data top

C₉H₁₀N₂	V = 392.0 (4) Å³
M_r = 146.19	Z = 2
Monoclinic, P2₁	Mo Kα radiation
a = 6.048 (3) Å	µ = 0.08 mm⁻¹
b = 7.312 (4) Å	T = 153 K
c = 9.024 (5) Å	0.32 × 0.08 × 0.06 mm
β = 100.78 (1)°

Data collection top

Rigaku SCX-Mini with Mercury 2 CCD diffractometer	1786 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1374 reflections with I > 2σ(I)
T_min = 0.976, T_max = 0.996	R_int = 0.063
4179 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.057	61 restraints
wR(F²) = 0.132	H-atom parameters constrained
S = 1.05	Δρ_max = 0.19 e Å⁻³
1786 reflections	Δρ_min = −0.23 e Å⁻³
100 parameters	Absolute structure: nd

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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) top

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) top

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.

Hydrogen-bond geometry (Å, º) top

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.

Acknowledgements

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2013R1A1A2012154). The work in Austin was supported by the US National Science Foundation (grant No. CHE-1057904 to JLS and CHE-0741973 for the diffractometer). KJH was on sabbatical leave at the University of Texas, Austin, during 2012.

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CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 69| Part 11| November 2013| Page o1697

doi:10.1107/S1600536813028365

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