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organic compounds
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
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 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
|
|
Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2008); cell 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
10.1107/S1600536813028365/tk5264sup1.cif
contains datablocks hkj, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536813028365/tk5264Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536813028365/tk5264Isup3.cml
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.
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).
Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2008); cell
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). ![]() | Fig. 1. The molecular structure of the title compound with 25% probability displacement ellipsoids. |
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 |
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 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 |
C9H10N2 | V = 392.0 (4) Å3 |
Mr = 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)° |
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 = 0.996 | Rint = 0.063 |
4179 measured reflections |
R[F2 > 2σ(F2)] = 0.057 | 61 restraints |
wR(F2) = 0.132 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.19 e Å−3 |
1786 reflections | Δρmin = −0.23 e Å−3 |
100 parameters | Absolute structure: nd |
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. |
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* |
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) |
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) |
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. |
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.
References
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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)°.