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6,7-Di­hydro-5H-pyrrolo­[1,2-a]imidazole

aMcKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA, and bDepartment of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
*Correspondence e-mail: omorale1@utexas.edu

Edited by M. Weil, Vienna University of Technology, Austria (Received 17 April 2020; accepted 20 May 2020; online 29 May 2020)

The crystal structure of 6,7-di­hydro-5H-pyrrolo­[1,2-a]imidazole, C6H8N2, at 100 K has monoclinic (P21/n) symmetry. The mol­ecule adopts an envelope conformation of the pyrrolidine ring, which might help for the relief torsion tension. The crystal cohesion is achieved by C—H⋯N hydrogen bonds. Inter­estingly, this fused ring system provides protection of the α-C atom (attached to the non-bridging N atom of the imidazole ring), which provides stability that is of inter­est with respect to electrochemical properties as electrolytes for fuel cells and batteries, and electrodeposition.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Ionic liquids have emerged as a promising area in material science because of their tunable properties, allowing them to be used in a wide range of application such as: carbon dioxide capture, fuel cells, nanoparticle stabilization, and many more (Song et al., 2019[Song, T., Avelar Bonilla, G. M., Morales-Collazo, O., Lubben, M. & Brennecke, J. F. (2019). Ind. Eng. Chem. Res. 58, 4997-5007.]; Huang et al., 2017[Huang, K., Song, T., Morales-Collazo, O., Jia, H. & Brennecke, J. F. (2017). J. ECS. 164, F1448-F1459.]; Wang et al., 2017[Wang, J., Morales-Collazo, O. & Wei, A. (2017). ACS Omega, 2, 1287-1294.]). In this context, our group has been working on the synthesis of new cation moieties for ionic liquid designs. From the different chemical entities employed in ionic liquids, imidazolium derivatives are widely used in the field due to their versatility and relatively high stability. Imidazolium ionic liquid research is dominated by fluorine containing anions (Xue et al., 2006[Xue, H., Verma, R. & Shreeve, J. M. (2006). J. Fluor. Chem. 127, 159-176.]). Thus, we intended to explore imidazole derivatives (II) at position 2 of the principal structural component, imidazole (I), in order to decrease its reactivity (Fig. 1[link]).

[Figure 1]
Figure 1
Schematic representation of imidazole (I) with atom numbering and of the title derivative (II).

To understand how cations and anions inter­act in ionic liquids, characterization of the starting materials is important. Towards that end, the crystal structure of 6,7-di­hydro-5H-pyrrolo­[1,2-a]imidazole (II) is presented in order to characterize and establish a structure stability relationship of cyclic imidazole derivative families for imidazolium ionic liquid research applications.

The mol­ecular structure of imidazole derivative (II) is displayed in Fig. 2[link]. We initially envisioned that the electronic and steric effects would be similar to a pyrrole fused to the imidazole moiety and, thus, provide comparison to pyrrolidine below. In order to put into perspective the results found in the mol­ecular and crystal structure of (II), we compare the fused imidazole moiety of (II) with the imidazole crystal structure. There is no significant difference in bond length of the imidazole moiety of (II) compared to the imidazole crystal structure (McMullan et al., 1979[McMullan, R. K., Epstein, J., Ruble, J. R. & Craven, B. M. (1979). Acta Cryst. B35, 688-691.]). However, the C2—N2 (N3—C4 in imidazole; McMullan et al., 1979[McMullan, R. K., Epstein, J., Ruble, J. R. & Craven, B. M. (1979). Acta Cryst. B35, 688-691.]) bond length of (II) is larger than the same bond found in the imidazole crystal structure [1.390 (2) vs1.375 (1) Å]. This bond-length difference might be due to the new substituted imidazole ring system, which can help justify the chemical shifts observed in the 1H-NMR spectrum between (II) and (I) of those hydrogen atoms in C1 and C2 of (II), based on the inductive effects of the substituents. On the other hand, we also compare the pyrrolidine fused ring to the pyrrolidine crystal structure (Dziubek & Katrusiak, 2011[Dziubek, K. F. & Katrusiak, A. (2011). Phys. Chem. Chem. Phys. 13, 15428-15431.]). We found that the major bond length difference occurs between bonds N1—C3 and C3—C4 [1.353 (2) vs 1.457 (2) Å and 1.492 (2) vs 1.528 (2) Å], respectively; only the shortest bond length of pyrrolidine was used due to its symmetry). The C5—C6 bond length was found to be 1.543 (2) Å, which is slightly larger than the one found for pyrrolidine [1.528 (2) Å]. These differences in bond length could be attributed to the new sp2 carbon atom (C3) of (II), which also might be responsible for the differences in bond angles in (II). For example, angles N1—C3—C4 and C6—N1—C3 within the fused ring system are much larger compared to those of the pyrrolidine structure [111.1 (1) vs 107.2 (1) and 113.99 (9) vs 103.37 (1) Å, respectively], but angle N1—C6—C5 [102.10 (9) vs 107.05 (1) Å] becomes smaller. These angle differences, despite being small, can help relieve the ring's stress. Finally, it is important to point out that N1 in pyrrolidine is out of plane (envelope conformation) in order to reduce lone-pair inter­actions, but in (II), this envelope conformation is adopted by C5 as the flap atom where C5 is 0.317 (2) Å out of the plane of the remaining four atoms. Also, the imidazole ring and the planar part of the pyrrolidine ring make a dihedral angle of 3.85 (9)°. By N1 becoming part of the plane, its lone pairs could add new repulsion inter­actions, suggesting why the ring has to adapt to this conformation to avoid repulsions.

[Figure 2]
Figure 2
The mol­ecular structure of (II) showing the atom-labeling scheme. Displacement ellipsoids are scaled to the 50% probability level.

A look into possible inter­molecular hydrogen-bonding inter­actions of (II), we found a value of 3.37 (3) Å between C1⋯N2, indicative of a weak hydrogen bond (Fig. 3[link], Table 1[link]) that leads to the formation of supra­molecular chains extending parallel to [101]. Nevertheless, we believe that the major inter­molecular force contribution to the stabilization of the crystal structure is by aliphatic C—H⋯π inter­actions. We observed how C6 (non-aromatic ring atom) inter­acts with C2i, N2i, and C3i [distances are 3.672 (3), 3.692 (4), and 3.620 (3), respectively; symmetry code: (i) −x + 1, −y + 2, −z). Analyzing the possibility of any ππ inter­actions we determine that due to the reciprocal stacking of the mol­ecules and the offset distance of the aromatic centroids (4.487 Å), we suggest that the possibility of a ππ inter­action between the mol­ecules is not found. We conclude that C—H⋯π inter­actions, although weak compared to a conventional hydrogen bond, could serve together with other inter­molecular forces to impose directionality and order through the crystal lattice. Previously, C—H⋯π inter­actions have been proven to show stability in crystal structures. In fact, it has been suggested that aliphatic–aromatic inter­actions could play a greater stabilization role than aromatic–aromatic inter­actions (Ninković et al., 2016[Ninković, D. B., Vojislavljević-Vasilev, D. Z., Medaković, V. B., Hall, M. B., Brothers, E. N. & Zarić, S. D. (2016). Phys. Chem. Chem. Phys. 18, 25791-25795.]; Carmona-Negrón et al., 2016[Carmona-Negrón, J. A., Cádiz, M. E., Moore, C. E., Rheingold, A. L. & Meléndez, E. (2016). Acta Cryst. E72, 412-416.]). Fig. 3[link] shows the packing diagram of (II).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C1—H1⋯N2 0.95 (1) 2.52 (1) 3.73 (3) 150 (1)
[Figure 3]
Figure 3
Packing diagram for (II) projected along the b axis (A), and the inter­molecular arrangement and distance of (II) found in the crystal structure (B) (a shows the centroid-to-centroid distance, b the centroid-to-atom distance). Hydrogen atoms were omitted for clarity.

Synthesis and crystallization

The compound was synthesized following a literature procedure with a modification (Kan et al., 2007[Kan, H.-C., Tseng, M.-C. & Chu, Y. H. (2007). Tetrahedron, 63, 1644-1653.]). Hydrogen chloride was bubbled into a solution of 4-chloro­butyro­nitrile (10 g, 274 mmol) and methanol (11.65 ml, 288 mmol) in ether (135 ml). The solution was treated with hydrogen chloride at room temperature until saturated. After 24 h of reaction, the white precipitate was washed with ether and dried under vacuum to afford the imidate. 1H NMR (400 MHz, CDCl3) δ 12.51 (s, 1H), 11.60 (s, 1H), 4.26 (s, 3H), 3.57 (t, J = 6.1 Hz, 2H), 2.92 (t, J = 6.6 Hz, 2H), 2.19 (q, J = 6.3 Hz, 2H).

To a solution of the imidate (34 g, 198 mmol) in di­chloro­methane (200 ml), amino­acetaldehyde (20.78 g, 198 mmol) and tri­ethyl­amine (60 g, 593 mmol) were added and heated to 333 K for 2 h to afford the amidine inter­mediary, which was dried under vacuum. The amidine was stirred in formic acid at 353 K for 20 h. Solid sodium bicarbonate was added to the solution to raise the pH to 10. The solution was extracted with di­chloro­methane (3 × 100 ml) and dried over anhydrous Na2SO4. Filtration and evaporation under reduced pressure was followed by sublimation to afford a crystalline solid (12.7 g, 60% yield in two steps); m.p. 338 K; 1H NMR (400 MHz, DMSO-d6) δ 7.02 (d, J = 1.3 Hz, 1H), 6.85 (d, J = 1.3 Hz, 1H), 3.89 (dd, J = 7.6, 6.6 Hz, 2H), 2.66 (m, 2H), 2.44 (m, 2H).

Crystals of the title compound grew as very large, colorless prisms by slow sublimation at 313 K and 1.5 mbar. The crystal under investigation was cut from a larger crystal.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C6H8N2
Mr 108.14
Crystal system, space group Monoclinic, P21/n
Temperature (K) 100
a, b, c (Å) 7.908 (7), 7.441 (8), 9.880 (9)
β (°) 104.91 (3)
V3) 561.8 (9)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.08
Crystal size (mm) 0.31 × 0.19 × 0.16
 
Data collection
Diffractometer Rigaku AFC-12 with Saturn 724+ CCD
Absorption correction Multi-scan (ABSCOR; Higashi, 2001[Higashi, T. (2001). ABSCOR. Rigaku Corporation, Tokyo, Japan.])
Tmin, Tmax 0.730, 1.00
No. of measured, independent and observed [I > 2σ(I)] reflections 2575, 1279, 1028
Rint 0.036
(sin θ/λ)max−1) 0.649
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.123, 1.05
No. of reflections 1279
No. of parameters 105
H-atom treatment All H-atom parameters refined
Δρmax, Δρmin (e Å−3) 0.28, −0.22
Computer programs: CrystalClear (Rigaku, 2008[Rigaku (2008). CrystalClear. Rigaku Americas Corportion, The Woodlands, TX.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. C71, 3-8.]), SHELXL (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. A71, 3-8.]), XP in SHELXTL/PC (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), Mercury Macrae et al., 2020[Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226-235.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data


Computing details top

Data collection: CrystalClear (Rigaku, 2008); cell refinement: CrystalClear (Rigaku, 2008); data reduction: CrystalClear (Rigaku, 2008); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: XP in SHELXTL/PC (Sheldrick, 2008) and Mercury Macrae et al., 2020); software used to prepare material for publication: publCIF (Westrip, 2010).

6,7-Dihydro-5H-pyrrolo[1,2-a]imidazole top
Crystal data top
C6H8N2F(000) = 232
Mr = 108.14Dx = 1.279 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 7.908 (7) ÅCell parameters from 1451 reflections
b = 7.441 (8) Åθ = 2.7–27.5°
c = 9.880 (9) ŵ = 0.08 mm1
β = 104.91 (3)°T = 100 K
V = 561.8 (9) Å3Prism, colorless
Z = 40.31 × 0.19 × 0.16 mm
Data collection top
Rigaku AFC-12 with Saturn 724+ CCD
diffractometer
1028 reflections with I > 2σ(I)
Radiation source: sealed fine focus tubeRint = 0.036
ω–scansθmax = 27.5°, θmin = 3.0°
Absorption correction: multi-scan
(ABSCOR; Higashi, 2001)
h = 610
Tmin = 0.730, Tmax = 1.00k = 69
2575 measured reflectionsl = 1212
1279 independent reflections
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042All H-atom parameters refined
wR(F2) = 0.123 w = 1/[σ2(Fo2) + (0.0797P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
1279 reflectionsΔρmax = 0.28 e Å3
105 parametersΔρmin = 0.22 e Å3
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
xyzUiso*/Ueq
C10.35368 (15)0.73358 (16)0.04868 (12)0.0174 (3)
C20.25317 (16)0.68855 (17)0.08171 (12)0.0197 (3)
C30.20769 (14)0.96844 (16)0.05783 (11)0.0156 (3)
C40.17443 (17)1.16552 (17)0.05457 (13)0.0209 (3)
C50.26013 (17)1.21318 (18)0.10150 (13)0.0219 (3)
C60.38632 (16)1.05792 (16)0.16201 (12)0.0183 (3)
N10.32126 (12)0.91323 (13)0.06209 (9)0.0150 (3)
N20.16179 (13)0.83657 (14)0.14934 (10)0.0194 (3)
H10.4341 (18)0.6695 (18)0.1200 (15)0.024 (4)*
H20.2433 (17)0.5700 (17)0.1276 (14)0.023 (4)*
H4A0.2310 (17)1.2310 (17)0.1188 (14)0.023 (4)*
H4B0.0496 (19)1.1952 (19)0.0828 (15)0.029 (4)*
H5A0.3296 (19)1.333 (2)0.1160 (16)0.032 (4)*
H5B0.167 (2)1.2194 (19)0.1527 (15)0.035 (4)*
H6A0.5118 (17)1.0873 (18)0.1648 (13)0.022 (3)*
H6B0.3805 (18)1.018 (2)0.2585 (15)0.036 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0210 (6)0.0136 (6)0.0166 (6)0.0006 (5)0.0029 (5)0.0022 (5)
C20.0246 (6)0.0159 (7)0.0177 (6)0.0034 (5)0.0037 (5)0.0014 (5)
C30.0149 (5)0.0193 (6)0.0123 (6)0.0003 (4)0.0029 (4)0.0023 (4)
C40.0232 (7)0.0201 (7)0.0199 (6)0.0025 (5)0.0067 (5)0.0036 (5)
C50.0255 (7)0.0192 (7)0.0224 (6)0.0004 (5)0.0087 (5)0.0032 (5)
C60.0238 (6)0.0178 (6)0.0128 (6)0.0054 (5)0.0038 (4)0.0037 (4)
N10.0174 (5)0.0158 (6)0.0111 (5)0.0014 (4)0.0021 (4)0.0001 (4)
N20.0207 (5)0.0210 (6)0.0155 (5)0.0017 (4)0.0025 (4)0.0004 (4)
Geometric parameters (Å, º) top
C1—C21.3700 (19)C4—H4A0.993 (14)
C1—N11.374 (2)C4—H4B0.980 (15)
C1—H10.948 (14)C5—C61.543 (2)
C2—N21.3905 (18)C5—H5A1.038 (15)
C2—H20.986 (13)C5—H5B0.994 (15)
C3—N21.3203 (18)C6—N11.4619 (17)
C3—N11.3533 (17)C6—H6A1.010 (13)
C3—C41.492 (2)C6—H6B1.011 (14)
C4—C51.557 (2)
C2—C1—N1104.54 (10)C6—C5—H5A108.9 (8)
C2—C1—H1133.8 (8)C4—C5—H5A114.4 (8)
N1—C1—H1121.6 (8)C6—C5—H5B109.0 (8)
C1—C2—N2111.23 (12)C4—C5—H5B108.9 (8)
C1—C2—H2127.5 (8)H5A—C5—H5B108.9 (12)
N2—C2—H2121.2 (8)N1—C6—C5102.10 (11)
N2—C3—N1112.18 (12)N1—C6—H6A110.5 (7)
N2—C3—C4136.59 (11)C5—C6—H6A112.4 (8)
N1—C3—C4111.13 (10)N1—C6—H6B109.0 (9)
C3—C4—C5102.18 (10)C5—C6—H6B113.8 (9)
C3—C4—H4A111.0 (8)H6A—C6—H6B108.7 (10)
C5—C4—H4A111.6 (8)C3—N1—C1108.01 (10)
C3—C4—H4B112.7 (8)C3—N1—C6113.99 (11)
C5—C4—H4B112.4 (8)C1—N1—C6137.70 (10)
H4A—C4—H4B107.1 (11)C3—N2—C2104.03 (12)
C6—C5—C4106.64 (11)
N1—C3—C4—C510.83 (13)C4—C3—N1—C61.63 (13)
C3—C4—C5—C618.49 (13)C5—C6—N1—C313.39 (12)
C4—C5—C6—N119.28 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···N20.95 (1)2.52 (1)3.73 (3)150 (1)
Selective Supramolecular interaction of II top
D···ADistance
C6-N23.692 (4)
C6-C23.672 (3)
C6-C33.620 (3)

Funding information

The data were collected using instrumentation purchased with funds provided by the National Science Foundation grant No. 0741973.

References

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