Crystal structure of 2,2′-bi­pyrrole

Michaels, C.A.; Zakharov, L.N.; Lamm, A.N.

doi:10.1107/S2056989017013433

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ISSN: 2056-9890

Volume 73| Part 10| October 2017| Pages 1517-1519

https://doi.org/10.1107/S2056989017013433

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Crystal structure of 2,2′-bipyrrole

Christopher A. Michaels,^a Lev N. Zakharov ^b and Ashley N. Lamm ^a ^*

^aDepartment of Chemistry and Biochemistry, Eastern Washington University, Science 226, Cheney, WA 99004, USA, and ^bDepartment of Chemistry, 1253 University of Oregon, Eugene, Oregon 97403, USA
^*Correspondence e-mail: alamm@ewu.edu

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 11 July 2017; accepted 19 September 2017; online 25 September 2017)

The complete molecule of the title compound, C₈H₈N₂, is generated by a crystallographic center of symmetry. In the crystal, short N—H⋯π [H⋯π = 2.499 (19) Å] interactions link the molecules into a herringbone structure.

Keywords: crystal structure; bipyrrole; N—H⋯π interactions; herringbone structure.

CCDC reference: 1575394

1. Chemical context

Bipyrrole, C₈H₈N₂, has been studied extensively over the years: the first reported synthesis was in 1962 (Rapoport & Castagnoli, 1962 ). The bipyrrole core occurs in naturally occurring compounds such as prodigiosin (Wasserman et al., 1960 ). Functionalized bipyrroles have been shown to have anti-cancer activity (Manderville, 2001 ). Corrole rings contain a bipyrrole segment in the macrocycle (Aviv-Harel & Gross, 2009 ). Herein, we report on the crystal structure of the title compound, (I), synthesized by the oxidative coupling of pyrrole.

2. Structural commentary

The complete molecule of (I) is generated by a crystallographic center of symmetry (Fig. 1), and therefore the pyrrole rings are exactly parallel and the N—H groups face in opposite directions. The C2—C3 bond in (I) is 1.4151 (19) Å, versus the equivalent bond in pyrrole, which has a length of 1.423 (3) Å. The double bonds C1=C2 and C3=C4 in (I) are 1.3635 (19) and 1.3767 (17) Å, respectively, versus the double-bond length in pyrrole of 1.357 Å. The shortening of the C2—C3 bond and the lengthening of the adjacent C=C double bonds in (I) compared to pyrrole is consistent with stronger intermolecular interactions (see below).

Figure 1
The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. [Symmetry code: (i) 1 − x, 2 − y, −z.]

3. Supramolecular features

In the crystal of (I), the molecules adopt an edge-to-face orientation: the distance between the N—H group and the centroid of the adjacent pyrrole ring generated by the 2₁ screw axis is 2.499 (19) Å (Table 1). A survey of the Cambridge Crystallographic Database (Groom et al., 2016 ) showed that the average N—H⋯π separation is 2.804 Å and 13 out of 156 interactions (8.3%) had an N—H⋯π interactions shorter than 2.5 Å. The crystal packing in (I) is similar to that of pyrrole, which has the same intermolecular N—H⋯π interactions (Goddard et al., 1997 ). The edge-to-face interaction has been suggested to be a stabilizing factor in protein structures and polypeptides have been observed to have a separation of 2.42 Å from the N—H group to the phenyl ring (Steiner, 1998 ) and calculations corroborate these data (Levitt Perutz, 1988 ). It is notable that the N—H bond of 2,2′-bipyrrole points almost directly at the midpoint of the C2—C3 bond. In the extended structure, the molecules are orientated by edge-to-face interactions generating a herringbone pattern, see Fig. 2.

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the N1/C1–C4 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯Cg1ⁱ	0.907 (16)	2.499 (19)	3.2275 (12)	138.1 (13)
Symmetry code: (i) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 2
View of the N—H⋯π interactions and packing in the title compound.

4. Database survey

There are very few examples of similar compounds available in the literature. Most bipyrroles have carbonyl groups as substituents on the pyrrole ring in which the N—H group forms hydrogen bonds with the oxygen atom of the carbonyl (Okawara et al., 2015 ). So far as we are aware, there are no bipyrrole examples that exhibit the same packing and hydrogen-bonding pattern as the title compound; the closest example is pyrrole itself (Goddard et al., 1997).

5. Synthesis and crystallization

230 µl (3.3 mmol) of pyrrole was added to dichloromethane (10 ml), degassed and cooled to 195 K. Trimethylsilyl bromide (290 µl, 2.2 mmol) and phenyl iodine trifluoracetic acid (477 mg, 1.1 mmol in 1 ml dichloromethane) were added quickly to the cooled reaction. The mixture was stirred for 1 h then extracted with a saturated sodium bicarbonate solution and purified by column chromatography with a pentane/ethyl acetate (1:1) solution. Colourless blocks of (I) were obtained 7 d later by slow evaporation from an ethyl acetate solution.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The H atoms were located in difference maps and refined with isotropic displacement parameters.

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₈N₂
M_r	132.16
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	173
a, b, c (Å)	5.9500 (2), 6.7650 (2), 8.4363 (3)
β (°)	96.746 (2)
V (Å³)	337.22 (2)
Z	2
Radiation type	Cu Kα
μ (mm⁻¹)	0.64
Crystal size (mm)	0.11 × 0.10 × 0.06

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2004 )
T_min, T_max	0.666, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections	1989, 590, 540
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.034, 0.098, 1.08
No. of reflections	590
No. of parameters	62
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.16
Computer programs: APEX2 and SAINT (Bruker, 2004), SHELXS97 and SHELXTL (Sheldrick, 2008 ) and SHELXL2014 (Sheldrick, 2015 ).

Supporting information

CCDC reference: 1575394

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017013433/hb7692sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017013433/hb7692Isup2.hkl

Survey of the Cambridge Database NH-pi bond lengths. DOI: https://doi.org/10.1107/S2056989017013433/hb7692sup3.pdf

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHEXLTL (Sheldrick, 2008).

2,2'-Bipyrrole top

Crystal data top

C₈H₈N₂	F(000) = 140
M_r = 132.16	D_x = 1.302 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54178 Å
a = 5.9500 (2) Å	Cell parameters from 1086 reflections
b = 6.7650 (2) Å	θ = 7.5–66.5°
c = 8.4363 (3) Å	µ = 0.64 mm⁻¹
β = 96.746 (2)°	T = 173 K
V = 337.22 (2) Å³	Cut-block, colorless
Z = 2	0.11 × 0.10 × 0.06 mm

Data collection top

Bruker APEXII CCD diffractometer	540 reflections with I > 2σ(I)
Radiation source: Incoatec IµS	R_int = 0.026
φ and ω scans	θ_max = 66.5°, θ_min = 7.5°
Absorption correction: multi-scan (SADABS; Bruker, 2004)	h = −7→4
T_min = 0.666, T_max = 0.753	k = −7→8
1989 measured reflections	l = −9→10
590 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.034	All H-atom parameters refined
wR(F²) = 0.098	w = 1/[σ²(F_o²) + (0.0657P)² + 0.034P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
590 reflections	Δρ_max = 0.18 e Å⁻³
62 parameters	Δρ_min = −0.16 e Å⁻³
0 restraints

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

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

	x	y	z	U_iso*/U_eq
N1	0.53346 (18)	1.09945 (15)	0.20670 (12)	0.0322 (4)
C1	0.7071 (2)	1.07425 (18)	0.32546 (15)	0.0352 (4)
C2	0.8665 (2)	0.95786 (18)	0.26832 (16)	0.0330 (4)
C3	0.7857 (2)	0.91019 (17)	0.10841 (15)	0.0297 (4)
C4	0.57828 (19)	0.99966 (16)	0.07196 (13)	0.0263 (4)
H1	0.704 (2)	1.135 (2)	0.4292 (17)	0.043 (4)*
H1N	0.407 (2)	1.170 (3)	0.2168 (17)	0.046 (4)*
H2	1.010 (3)	0.916 (2)	0.3269 (19)	0.041 (4)*
H3	0.859 (2)	0.831 (2)	0.0354 (16)	0.039 (4)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0364 (6)	0.0295 (6)	0.0299 (6)	0.0075 (4)	0.0010 (5)	−0.0030 (4)
C1	0.0424 (8)	0.0320 (7)	0.0296 (7)	0.0003 (5)	−0.0028 (6)	−0.0038 (5)
C2	0.0299 (7)	0.0329 (7)	0.0347 (7)	−0.0016 (5)	−0.0023 (5)	0.0043 (5)
C3	0.0278 (7)	0.0307 (7)	0.0312 (7)	0.0005 (5)	0.0055 (5)	0.0021 (5)
C4	0.0306 (6)	0.0217 (6)	0.0270 (6)	−0.0017 (4)	0.0055 (5)	0.0025 (4)

Geometric parameters (Å, º) top

N1—C1	1.3628 (18)	C2—C3	1.4151 (19)
N1—C4	1.3748 (15)	C2—H2	0.979 (16)
N1—H1N	0.907 (16)	C3—C4	1.3767 (17)
C1—C2	1.3635 (19)	C3—H3	0.959 (14)
C1—H1	0.970 (15)	C4—C4ⁱ	1.441 (2)

C1—N1—C4	110.02 (11)	C3—C2—H2	126.4 (9)
C1—N1—H1N	124.3 (9)	C4—C3—C2	107.93 (11)
C4—N1—H1N	125.6 (9)	C4—C3—H3	124.4 (8)
N1—C1—C2	108.12 (11)	C2—C3—H3	127.6 (8)
N1—C1—H1	121.2 (9)	N1—C4—C3	106.69 (11)
C2—C1—H1	130.7 (9)	N1—C4—C4ⁱ	121.74 (13)
C1—C2—C3	107.23 (11)	C3—C4—C4ⁱ	131.57 (13)
C1—C2—H2	126.4 (9)

C4—N1—C1—C2	0.11 (14)	C1—N1—C4—C4ⁱ	179.68 (12)
N1—C1—C2—C3	−0.15 (14)	C2—C3—C4—N1	−0.07 (13)
C1—C2—C3—C4	0.13 (14)	C2—C3—C4—C4ⁱ	−179.73 (15)
C1—N1—C4—C3	−0.03 (13)

Symmetry code: (i) −x+1, −y+2, −z.

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the N1/C1–C4 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···Cg1ⁱⁱ	0.907 (16)	2.499 (19)	3.2275 (12)	138.1 (13)

Symmetry code: (ii) −x+1, y+1/2, −z+1/2.

Acknowledgements

The authors are grateful for the generous support from EWU's Faculty Grants for Research and Creative Works and support from EWU's Department of Chemistry and Biochemistry.

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