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

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

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.

Related literature

For synthesis of symmetric and non-symmetric porphyrins, see: Shanmugathasan et al. (2000[Shanmugathasan, S., Edwards, C. & Boyle, R. W. (2000). Tetrahedron, 56, 1025-1046.]); Bonifazi et al. (2005[Bonifazi, D., Accorsi, G., Armaroli, N., Song, F., Palkar, A., Echegoyen, L., Scholl, M., Seiler, P., Jaun, B. & Diederich, F. (2005). Helv. Chim. Acta, 88, 1839-1884.]); Fendt et al. (2009[Fendt, L.-A., Stohr, M., Wintjes, N., Enache, M., Jung, T. A. & Diederich, F. (2009). Chem. Eur. J. 15, 11139-11150.]). For their applications as organometallic ligands, see: Ganesan et al. (2001[Ganesan, M., Lalonde, M. P., Gambarotta, S. & Yap, G. P. A. (2001). Organometallics, 20, 2443-2445.]); Gao et al. (2004[Gao, G., Korobkov, I. & Gambarotta, S. (2004). Inorg. Chem. 43, 1108-1115.]).

[Scheme 1]

Experimental

Crystal data
  • C9H10N2

  • Mr = 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.976, Tmax = 0.996

  • 4179 measured reflections

  • 1786 independent reflections

  • 1374 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.19 e Å−3

  • Δρmin = −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 DA D—H⋯A
N1—H1NCg1i 0.88 2.53 3.357 (3) 156
N2—H2NCg2ii 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[Molecular Structure Corporation & Rigaku (2008). CrystalClear. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXTL/PC (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL/PC; software used to prepare material for publication: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


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.

Refinement top

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 Uiso(H) = 1.2 Ueq(C,N).

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
[Figure 1] 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
C9H10N2F(000) = 156
Mr = 146.19Dx = 1.238 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71075 Å
Hall symbol: P 2ybCell parameters from 4189 reflections
a = 6.048 (3) Åθ = 3.0–27.5°
b = 7.312 (4) ŵ = 0.08 mm1
c = 9.024 (5) ÅT = 153 K
β = 100.78 (1)°Needle, colourless
V = 392.0 (4) Å30.32 × 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 tube1374 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.063
ω scansθmax = 27.5°, θmin = 3.4°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 77
Tmin = 0.976, Tmax = 0.996k = 99
4179 measured reflectionsl = 1111
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.057H-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 reflectionsΔρmax = 0.19 e Å3
100 parametersΔρmin = 0.23 e Å3
61 restraintsAbsolute structure: nd
Primary atom site location: structure-invariant direct methods
Crystal data top
C9H10N2V = 392.0 (4) Å3
Mr = 146.19Z = 2
Monoclinic, P21Mo Kα radiation
a = 6.048 (3) ŵ = 0.08 mm1
b = 7.312 (4) ÅT = 153 K
c = 9.024 (5) Å0.32 × 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)
Tmin = 0.976, Tmax = 0.996Rint = 0.063
4179 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.05761 restraints
wR(F2) = 0.132H-atom parameters constrained
S = 1.05Δρmax = 0.19 e Å3
1786 reflectionsΔρmin = 0.23 e Å3
100 parametersAbsolute 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
xyzUiso*/Ueq
C10.2619 (4)0.0035 (4)0.5615 (3)0.0353 (6)
H10.33000.04090.66030.042*
C20.3488 (4)0.1182 (4)0.4732 (3)0.0331 (6)
H20.48870.18020.49910.040*
C30.1930 (4)0.1352 (3)0.3367 (3)0.0298 (6)
H30.20880.21090.25380.036*
C40.0136 (4)0.0222 (4)0.3451 (2)0.0284 (5)
C50.2014 (4)0.0146 (4)0.2387 (2)0.0348 (6)
H5A0.32670.03740.28180.042*
H5B0.22420.14860.23100.042*
C60.2144 (4)0.0606 (3)0.0837 (3)0.0301 (6)
C70.3568 (4)0.1863 (4)0.0037 (3)0.0342 (6)
H70.47210.25160.03960.041*
C80.3029 (4)0.2019 (4)0.1402 (3)0.0362 (6)
H80.37610.27850.21950.043*
C90.1268 (4)0.0876 (4)0.1462 (2)0.0367 (6)
H90.05300.07110.22940.044*
N10.0597 (4)0.0620 (3)0.4825 (2)0.0344 (6)
H1N0.02830.14230.51530.041*
N20.0764 (3)0.0011 (3)0.0094 (2)0.0336 (5)
H2N0.03020.08130.01480.040*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0380 (14)0.0427 (15)0.0244 (12)0.0079 (13)0.0037 (11)0.0002 (12)
C20.0322 (13)0.0322 (14)0.0356 (13)0.0001 (11)0.0082 (11)0.0078 (11)
C30.0366 (13)0.0265 (13)0.0292 (12)0.0002 (10)0.0135 (11)0.0000 (10)
C40.0349 (12)0.0269 (13)0.0249 (11)0.0027 (10)0.0096 (10)0.0001 (9)
C50.0311 (12)0.0358 (14)0.0388 (14)0.0030 (11)0.0103 (11)0.0009 (11)
C60.0281 (12)0.0290 (14)0.0322 (13)0.0035 (10)0.0030 (10)0.0048 (10)
C70.0248 (13)0.0328 (14)0.0438 (15)0.0010 (11)0.0031 (11)0.0001 (11)
C80.0343 (14)0.0296 (14)0.0394 (14)0.0002 (11)0.0070 (12)0.0034 (11)
C90.0459 (14)0.0375 (16)0.0248 (13)0.0032 (13)0.0016 (11)0.0026 (11)
N10.0388 (12)0.0334 (13)0.0323 (11)0.0030 (10)0.0100 (10)0.0038 (9)
N20.0371 (11)0.0287 (11)0.0345 (11)0.0064 (10)0.0058 (9)0.0006 (9)
Geometric parameters (Å, º) top
C1—C21.363 (4)C5—H5B0.9900
C1—N11.364 (3)C6—N21.361 (3)
C1—H10.9500C6—C71.370 (3)
C2—C31.410 (3)C7—C81.402 (3)
C2—H20.9500C7—H70.9500
C3—C41.377 (3)C8—C91.363 (3)
C3—H30.9500C8—H80.9500
C4—N11.365 (3)C9—N21.369 (3)
C4—C51.490 (3)C9—H90.9500
C5—C61.491 (3)N1—H1N0.8800
C5—H5A0.9900N2—H2N0.8800
C2—C1—N1107.8 (2)N2—C6—C7106.7 (2)
C2—C1—H1126.1N2—C6—C5122.0 (2)
N1—C1—H1126.1C7—C6—C5131.2 (2)
C1—C2—C3107.5 (2)C6—C7—C8108.1 (2)
C1—C2—H2126.3C6—C7—H7125.9
C3—C2—H2126.3C8—C7—H7125.9
C4—C3—C2107.7 (2)C9—C8—C7107.8 (2)
C4—C3—H3126.2C9—C8—H8126.1
C2—C3—H3126.2C7—C8—H8126.1
N1—C4—C3107.0 (2)C8—C9—N2107.0 (2)
N1—C4—C5120.6 (2)C8—C9—H9126.5
C3—C4—C5132.4 (2)N2—C9—H9126.5
C4—C5—C6115.1 (2)C1—N1—C4110.1 (2)
C4—C5—H5A108.5C1—N1—H1N124.9
C6—C5—H5A108.5C4—N1—H1N124.9
C4—C5—H5B108.5C6—N2—C9110.5 (2)
C6—C5—H5B108.5C6—N2—H2N124.8
H5A—C5—H5B107.5C9—N2—H2N124.8
N1—C1—C2—C30.5 (3)C5—C6—C7—C8177.2 (2)
C1—C2—C3—C40.1 (3)C6—C7—C8—C90.7 (3)
C2—C3—C4—N10.4 (3)C7—C8—C9—N21.1 (3)
C2—C3—C4—C5178.4 (3)C2—C1—N1—C40.8 (3)
N1—C4—C5—C6170.1 (2)C3—C4—N1—C10.7 (3)
C3—C4—C5—C611.2 (4)C5—C4—N1—C1178.3 (2)
C4—C5—C6—N264.4 (3)C7—C6—N2—C90.6 (3)
C4—C5—C6—C7118.6 (3)C5—C6—N2—C9178.2 (2)
N2—C6—C7—C80.1 (3)C8—C9—N2—C61.0 (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···AD—HH···AD···AD—H···A
N1—H1N···Cg1i0.882.533.357 (3)156
N2—H2N···Cg2ii0.882.533.363 (3)159
Symmetry codes: (i) x, y1/2, z+1; (ii) x, y1/2, 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···AD—HH···AD···AD—H···A
N1—H1N···Cg1i0.882.533.357 (3)156
N2—H2N···Cg2ii0.882.533.363 (3)159
Symmetry codes: (i) x, y1/2, z+1; (ii) x, y1/2, 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.

References

First citationAltomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.  Web of Science CrossRef CAS IUCr Journals
First citationBonifazi, D., Accorsi, G., Armaroli, N., Song, F., Palkar, A., Echegoyen, L., Scholl, M., Seiler, P., Jaun, B. & Diederich, F. (2005). Helv. Chim. Acta, 88, 1839–1884.  Web of Science CSD CrossRef CAS
First citationFendt, L.-A., Stohr, M., Wintjes, N., Enache, M., Jung, T. A. & Diederich, F. (2009). Chem. Eur. J. 15, 11139–11150.  Web of Science CrossRef PubMed CAS
First citationGanesan, M., Lalonde, M. P., Gambarotta, S. & Yap, G. P. A. (2001). Organometallics, 20, 2443–2445.  Web of Science CSD CrossRef CAS
First citationGao, G., Korobkov, I. & Gambarotta, S. (2004). Inorg. Chem. 43, 1108–1115.  Web of Science CSD CrossRef PubMed CAS
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.
First citationMolecular Structure Corporation & Rigaku (2008). CrystalClear. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.
First citationShanmugathasan, S., Edwards, C. & Boyle, R. W. (2000). Tetrahedron, 56, 1025–1046.  Web of Science CrossRef CAS
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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