organic compounds
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
The H-pyrrolo[1,2-a]imidazole, C6H8N2, at 100 K has monoclinic (P21/n) symmetry. The molecule adopts an 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.
of 6,7-dihydro-5Keywords: crystal structure; imidazole derivative; ring puckering analysis.
CCDC reference: 1912032
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; Huang et al., 2017; Wang et al., 2017). 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). 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).
To understand how cations and anions interact in ionic liquids, characterization of the starting materials is important. Towards that end, the H-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.
of 6,7-dihydro-5The molecular structure of imidazole derivative (II) is displayed in Fig. 2. 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 of (II), we compare the fused imidazole moiety of (II) with the imidazole There is no significant difference in bond length of the imidazole moiety of (II) compared to the imidazole (McMullan et al., 1979). However, the C2—N2 (N3—C4 in imidazole; McMullan et al., 1979) bond length of (II) is larger than the same bond found in the imidazole [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 (Dziubek & Katrusiak, 2011). 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 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.
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, Table 1) 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 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 π–π 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 π–π 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 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; Carmona-Negrón et al., 2016). Fig. 3 shows the packing diagram of (II).
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Synthesis and crystallization
The compound was synthesized following a literature procedure with a modification (Kan et al., 2007). 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 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
at 313 K and 1.5 mbar. The crystal under investigation was cut from a larger crystal.Refinement
Crystal data, data collection and structure .
details are summarized in Table 2Structural data
CCDC reference: 1912032
https://doi.org/10.1107/S2414314620006811/wm4129sup1.cif
contains datablock . DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620006811/wm4129Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314620006811/wm4129Isup3.cml
Data collection: CrystalClear (Rigaku, 2008); cell
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).C6H8N2 | F(000) = 232 |
Mr = 108.14 | Dx = 1.279 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 7.908 (7) Å | Cell parameters from 1451 reflections |
b = 7.441 (8) Å | θ = 2.7–27.5° |
c = 9.880 (9) Å | µ = 0.08 mm−1 |
β = 104.91 (3)° | T = 100 K |
V = 561.8 (9) Å3 | Prism, colorless |
Z = 4 | 0.31 × 0.19 × 0.16 mm |
Rigaku AFC-12 with Saturn 724+ CCD diffractometer | 1028 reflections with I > 2σ(I) |
Radiation source: sealed fine focus tube | Rint = 0.036 |
ω–scans | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan (ABSCOR; Higashi, 2001) | h = −6→10 |
Tmin = 0.730, Tmax = 1.00 | k = −6→9 |
2575 measured reflections | l = −12→12 |
1279 independent reflections |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.042 | All 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 reflections | Δρmax = 0.28 e Å−3 |
105 parameters | Δρmin = −0.22 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.35368 (15) | 0.73358 (16) | 0.04868 (12) | 0.0174 (3) | |
C2 | 0.25317 (16) | 0.68855 (17) | −0.08171 (12) | 0.0197 (3) | |
C3 | 0.20769 (14) | 0.96844 (16) | −0.05783 (11) | 0.0156 (3) | |
C4 | 0.17443 (17) | 1.16552 (17) | −0.05457 (13) | 0.0209 (3) | |
C5 | 0.26013 (17) | 1.21318 (18) | 0.10150 (13) | 0.0219 (3) | |
C6 | 0.38632 (16) | 1.05792 (16) | 0.16201 (12) | 0.0183 (3) | |
N1 | 0.32126 (12) | 0.91323 (13) | 0.06209 (9) | 0.0150 (3) | |
N2 | 0.16179 (13) | 0.83657 (14) | −0.14934 (10) | 0.0194 (3) | |
H1 | 0.4341 (18) | 0.6695 (18) | 0.1200 (15) | 0.024 (4)* | |
H2 | 0.2433 (17) | 0.5700 (17) | −0.1276 (14) | 0.023 (4)* | |
H4A | 0.2310 (17) | 1.2310 (17) | −0.1188 (14) | 0.023 (4)* | |
H4B | 0.0496 (19) | 1.1952 (19) | −0.0828 (15) | 0.029 (4)* | |
H5A | 0.3296 (19) | 1.333 (2) | 0.1160 (16) | 0.032 (4)* | |
H5B | 0.167 (2) | 1.2194 (19) | 0.1527 (15) | 0.035 (4)* | |
H6A | 0.5118 (17) | 1.0873 (18) | 0.1648 (13) | 0.022 (3)* | |
H6B | 0.3805 (18) | 1.018 (2) | 0.2585 (15) | 0.036 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0210 (6) | 0.0136 (6) | 0.0166 (6) | −0.0006 (5) | 0.0029 (5) | 0.0022 (5) |
C2 | 0.0246 (6) | 0.0159 (7) | 0.0177 (6) | −0.0034 (5) | 0.0037 (5) | −0.0014 (5) |
C3 | 0.0149 (5) | 0.0193 (6) | 0.0123 (6) | 0.0003 (4) | 0.0029 (4) | 0.0023 (4) |
C4 | 0.0232 (7) | 0.0201 (7) | 0.0199 (6) | 0.0025 (5) | 0.0067 (5) | 0.0036 (5) |
C5 | 0.0255 (7) | 0.0192 (7) | 0.0224 (6) | 0.0004 (5) | 0.0087 (5) | −0.0032 (5) |
C6 | 0.0238 (6) | 0.0178 (6) | 0.0128 (6) | −0.0054 (5) | 0.0038 (4) | −0.0037 (4) |
N1 | 0.0174 (5) | 0.0158 (6) | 0.0111 (5) | −0.0014 (4) | 0.0021 (4) | −0.0001 (4) |
N2 | 0.0207 (5) | 0.0210 (6) | 0.0155 (5) | −0.0017 (4) | 0.0025 (4) | −0.0004 (4) |
C1—C2 | 1.3700 (19) | C4—H4A | 0.993 (14) |
C1—N1 | 1.374 (2) | C4—H4B | 0.980 (15) |
C1—H1 | 0.948 (14) | C5—C6 | 1.543 (2) |
C2—N2 | 1.3905 (18) | C5—H5A | 1.038 (15) |
C2—H2 | 0.986 (13) | C5—H5B | 0.994 (15) |
C3—N2 | 1.3203 (18) | C6—N1 | 1.4619 (17) |
C3—N1 | 1.3533 (17) | C6—H6A | 1.010 (13) |
C3—C4 | 1.492 (2) | C6—H6B | 1.011 (14) |
C4—C5 | 1.557 (2) | ||
C2—C1—N1 | 104.54 (10) | C6—C5—H5A | 108.9 (8) |
C2—C1—H1 | 133.8 (8) | C4—C5—H5A | 114.4 (8) |
N1—C1—H1 | 121.6 (8) | C6—C5—H5B | 109.0 (8) |
C1—C2—N2 | 111.23 (12) | C4—C5—H5B | 108.9 (8) |
C1—C2—H2 | 127.5 (8) | H5A—C5—H5B | 108.9 (12) |
N2—C2—H2 | 121.2 (8) | N1—C6—C5 | 102.10 (11) |
N2—C3—N1 | 112.18 (12) | N1—C6—H6A | 110.5 (7) |
N2—C3—C4 | 136.59 (11) | C5—C6—H6A | 112.4 (8) |
N1—C3—C4 | 111.13 (10) | N1—C6—H6B | 109.0 (9) |
C3—C4—C5 | 102.18 (10) | C5—C6—H6B | 113.8 (9) |
C3—C4—H4A | 111.0 (8) | H6A—C6—H6B | 108.7 (10) |
C5—C4—H4A | 111.6 (8) | C3—N1—C1 | 108.01 (10) |
C3—C4—H4B | 112.7 (8) | C3—N1—C6 | 113.99 (11) |
C5—C4—H4B | 112.4 (8) | C1—N1—C6 | 137.70 (10) |
H4A—C4—H4B | 107.1 (11) | C3—N2—C2 | 104.03 (12) |
C6—C5—C4 | 106.64 (11) | ||
N1—C3—C4—C5 | −10.83 (13) | C4—C3—N1—C6 | −1.63 (13) |
C3—C4—C5—C6 | 18.49 (13) | C5—C6—N1—C3 | 13.39 (12) |
C4—C5—C6—N1 | −19.28 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1···N2 | 0.95 (1) | 2.52 (1) | 3.73 (3) | 150 (1) |
D···A | Distance |
C6-N2 | 3.692 (4) |
C6-C2 | 3.672 (3) |
C6-C3 | 3.620 (3) |
Funding information
The data were collected using instrumentation purchased with funds provided by the National Science Foundation grant No. 0741973.
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