research communications
H-pyrrole-5-carboxylate)
and Hirshfeld surface analysis of dibutyl 5,5′-(pentane-3,3-diyl)bis(1aCollege of Chemistry, Tianjin Key Laboratory of Structure and Performance for Functional Molecules, Tianjin Normal University, Tianjin 300387, People's Republic of China, and bKey Laboratory of Inorganic–Organic Hybrid Functional Materials Chemistry (Tianjin Normal University), Ministry of Education, Tianjin 300387, People's Republic of China
*Correspondence e-mail: tjyinzm@aliyun.com
The molecular structure of the title compound, C23H34N2O4, has C2 symmetry. In the crystal, interlocked dimers are formed through quadruple N—H⋯O hydrogen bonds between pyrrole N—H groups and carbonyl O atoms.
CCDC reference: 1912079
1. Chemical context
Hydrogen-bonding interactions play an important role in the design of functional assemblies that exhibit a variety of properties and functions (Prins et al., 2001; Steiner, 2002). Pyrrole-2-carboxylate possesses one hydrogen-bond donor (N—Hpyrrole) and one acceptor (C=O), which favour the formation of centrosymmetric dimers with pairs of N—H⋯O hydrogen bonds (Figueira et al., 2015). The dimer motif is structurally similar to classic Watson–Crick nucleotide base-pairs. Calculations have revealed the dimer motif to be a robust supramolecular synthon in crystal engineering (Dubis et al., 2002). In previous work, we have shown a way to use the 2-carbonyl pyrrole dimer as a supramolecular connector to construct hexagonal and grid architectures (Yin et al., 2006). Here, we report the self-assembly of the title compound, via quadruple N—H⋯N hydrogen bonds.
2. Structural commentary
The structure of the title compound is shown in Fig. 1. The contains one half-molecule as it possesses C2 symmetry. In the molecule, the two pyrrole-2-carboxylate groups are both in a syn conformation, with the carbonyl group arranged syn to its adjacent pyrrole NH group. The O1—C8—C7—N1 torsion angle is −8.2 (5)°. The dihedral angle between the pyrrole rings is 72.8 (2)°.
3. Supramolecular features
Pairs of molecules of the title compound form interlocked dimers through four N1—H1⋯O1 hydrogen bonds between the pyrrole carbonyl oxygen atoms and pyrrole NH protons (Table 1, Fig. 2). This type of dimer has also been observed in our previous work (Yin et al., 2007). The dimers are connected into a three-dimensional supramolecular structure through C—H⋯π contacts (Table 1).
4. Hirshfeld surface
A Hirshfeld surface analysis with CrystalExplorer (Turner et al., 2017) was performed to give insights into the important intermolecular interactions. These are normalized by van der Waals radii through a red–white–blue color scheme, where the red spots denote close contacts of molecules. The three-dimensional dnorm surface of the title compound is shown in Fig. 3. The red points represent closer contacts and negative dnorm values on the surface corresponding to the N—H⋯O and C—H⋯π interactions mentioned above. The two-dimensional fingerprint plots in Fig. 4 shown the intermolecular contacts and their percentage distributions on the Hirshfeld surface. H⋯H interactions (74.8%) are present as a major contributor while H⋯O/O⋯H (14.5%), H⋯C/C⋯H (5.4%), C⋯C (2.7%) and H⋯N/N⋯H (0.9%) contacts also give significant contributions to the Hirshfeld surface.
5. Database survey
A search in the Cambridge Structural Database (Groom et al., 2016) returned over 60 entries for dipyrromethane-1,9-dicarbonyl derivatives, including seven entries whose supramolecular structures feature interlocked dimers (ILITAY, Love et al., 2003; ODUMOQ,Yin et al., 2007; PIRJAB, Xie et al., 1994; NIQBAR01, Mahanta et al., 2012; VACRID, Deliomeroglu et al., 2016; PUJMAJ, Kim, 2010 and SAVDUQ, Uppal et al., 2012). In the crystal of PUJMAJ (Kim, 2010), only one of the carbonyl groups is involved in hydrogen bonds with two pyrrole N—H groups.
6. Synthesis and crystallization
n-Butyl alcohol (370 mg, 5 mmol), 2,2′-ditrichlordipyrrolemethane (980 mg, 2 mmol) and triethylamine (0.5 mL) were added to acetonitrile (20 mL), and then the mixture was refluxed for 2h. The solution was evaporated under reduced pressure and the residue was purified by on silica gel (ethyl acetate/petroleum ether = 1:2), affording the title compound (white powder, 672 mg, 71%), m.p. = 388 K. 1H NMR (400 MHz, DMSO-d6); δ 0.64 (t, 6H, J = 7.2 Hz, –CH3), 0.90 (t, 6H, J = 7.2 Hz, –CH3), 1.31–1.41 (m, 4H, –CH2–), 1.58–1.65 (m, 4H, –CH2–), 2.15 (q, 4H, J = 7.2 Hz, Å –CH2–), 4.15 (q, 4H, J = 6.8 Hz, –CH2–), 5.97 (s, 2H, PyCH), 6.66 (s, 2H, PyCH), 11.22 (s, 2H, NH); HRMS (ESI) m/z calculated for C23H34N2O4, (M + H)+ 403.25186; found 403.25224. Crystals suitable for X-ray were obtained by the slow evaporation of a CH3OH solution of the title compound.
7. Refinement
Crystal data, data collection and structure . N—H hydrogen atoms were located from a difference-Fourier map and freely refined. Other H atoms were placed in difference calculated positions (C—H = 0.96 or 0.97 Å) and included in the final cycles of using a riding model, with Uiso(H) = 1.2Ueq(C).
details are summarized in Table 2Supporting information
CCDC reference: 1912079
https://doi.org/10.1107/S205698901900567X/ff2158sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S205698901900567X/ff2158Isup2.hkl
Data collection: SMART (Bruker, 2001); cell
SMART (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS (Sheldrick, 2008); program(s) used to refine structure: SHELXL (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).C23H34N2O4 | Dx = 1.105 Mg m−3 |
Mr = 402.52 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Fddd | Cell parameters from 3608 reflections |
a = 14.358 (6) Å | θ = 2.4–23.4° |
b = 17.333 (7) Å | µ = 0.08 mm−1 |
c = 38.902 (19) Å | T = 296 K |
V = 9681 (7) Å3 | Block, colourless |
Z = 16 | 0.32 × 0.28 × 0.26 mm |
F(000) = 3488 |
Bruker SMART CCD area detector diffractometer | 1501 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
phi and ω scans | θmax = 25.0°, θmin = 1.9° |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −17→16 |
Tmin = 0.822, Tmax = 1.000 | k = −20→18 |
11878 measured reflections | l = −46→44 |
2156 independent reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.081 | H-atom parameters constrained |
wR(F2) = 0.278 | w = 1/[σ2(Fo2) + (0.1517P)2 + 16.1858P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max = 0.002 |
2156 reflections | Δρmax = 0.38 e Å−3 |
134 parameters | Δρmin = −0.34 e Å−3 |
2 restraints |
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 | ||
O1 | 0.68341 (16) | 0.20703 (14) | 0.05576 (7) | 0.0943 (8) | |
O2 | 0.65735 (17) | 0.33467 (14) | 0.05760 (8) | 0.1078 (10) | |
N1 | 0.51592 (15) | 0.18458 (13) | 0.09406 (6) | 0.0673 (7) | |
H1 | 0.5364 | 0.1412 | 0.0865 | 0.081* | |
C1 | 0.2522 (3) | 0.1657 (3) | 0.08110 (13) | 0.1320 (17) | |
H1A | 0.2131 | 0.1822 | 0.0997 | 0.198* | |
H1B | 0.2142 | 0.1459 | 0.0628 | 0.198* | |
H1C | 0.2880 | 0.2087 | 0.0729 | 0.198* | |
C2 | 0.3186 (2) | 0.1018 (2) | 0.09382 (9) | 0.0941 (11) | |
H2A | 0.3591 | 0.0869 | 0.0750 | 0.113* | |
H2B | 0.2819 | 0.0570 | 0.1001 | 0.113* | |
C3 | 0.3798 (3) | 0.1250 | 0.1250 | 0.0756 (11) | |
C4 | 0.44025 (19) | 0.19324 (17) | 0.11502 (7) | 0.0704 (8) | |
C5 | 0.4317 (2) | 0.27091 (19) | 0.12144 (10) | 0.0906 (10) | |
H5 | 0.3864 | 0.2937 | 0.1352 | 0.109* | |
C6 | 0.5026 (3) | 0.31011 (19) | 0.10378 (10) | 0.0919 (10) | |
H6 | 0.5126 | 0.3631 | 0.1036 | 0.110* | |
C7 | 0.5546 (2) | 0.25550 (17) | 0.08689 (8) | 0.0749 (8) | |
C8 | 0.6375 (2) | 0.26101 (19) | 0.06550 (9) | 0.0810 (9) | |
C9 | 0.7383 (3) | 0.3480 (3) | 0.03496 (16) | 0.141 (2) | |
H9A | 0.7953 | 0.3356 | 0.0471 | 0.169* | |
H9B | 0.7342 | 0.3149 | 0.0149 | 0.169* | |
C10 | 0.7401 (4) | 0.4274 (4) | 0.02437 (19) | 0.164 (2) | |
H10A | 0.7967 | 0.4359 | 0.0113 | 0.197* | |
H10B | 0.7440 | 0.4592 | 0.0448 | 0.197* | |
C11 | 0.6604 (5) | 0.4549 (4) | 0.0035 (2) | 0.193 (3) | |
H11A | 0.6551 | 0.4210 | −0.0162 | 0.232* | |
H11B | 0.6045 | 0.4478 | 0.0172 | 0.232* | |
C12 | 0.6597 (7) | 0.5314 (4) | −0.0088 (2) | 0.211 (4) | |
H12A | 0.6611 | 0.5666 | 0.0102 | 0.316* | |
H12B | 0.6042 | 0.5399 | −0.0221 | 0.316* | |
H12C | 0.7133 | 0.5398 | −0.0231 | 0.316* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0756 (14) | 0.0847 (16) | 0.1227 (19) | 0.0097 (12) | 0.0142 (12) | 0.0162 (13) |
O2 | 0.0842 (17) | 0.0826 (16) | 0.157 (2) | 0.0004 (12) | 0.0174 (15) | 0.0302 (14) |
N1 | 0.0571 (13) | 0.0653 (13) | 0.0796 (15) | 0.0047 (10) | −0.0016 (10) | 0.0003 (11) |
C1 | 0.089 (3) | 0.169 (4) | 0.138 (4) | −0.001 (3) | −0.041 (3) | 0.027 (3) |
C2 | 0.072 (2) | 0.116 (3) | 0.095 (2) | −0.0173 (18) | −0.0137 (16) | 0.0109 (19) |
C3 | 0.053 (2) | 0.090 (3) | 0.083 (2) | 0.000 | 0.000 | 0.006 (2) |
C4 | 0.0570 (15) | 0.0767 (18) | 0.0775 (17) | 0.0077 (13) | −0.0020 (12) | 0.0027 (14) |
C5 | 0.084 (2) | 0.083 (2) | 0.104 (2) | 0.0180 (17) | 0.0106 (18) | −0.0065 (18) |
C6 | 0.088 (2) | 0.0640 (18) | 0.124 (3) | 0.0049 (15) | 0.005 (2) | 0.0003 (18) |
C7 | 0.0648 (17) | 0.0672 (17) | 0.093 (2) | 0.0018 (13) | −0.0053 (15) | 0.0099 (14) |
C8 | 0.0659 (18) | 0.0748 (19) | 0.102 (2) | 0.0011 (15) | −0.0014 (16) | 0.0153 (16) |
C9 | 0.075 (2) | 0.129 (3) | 0.219 (6) | −0.003 (2) | 0.039 (3) | 0.043 (4) |
C10 | 0.136 (4) | 0.149 (4) | 0.206 (6) | −0.016 (4) | 0.033 (4) | 0.071 (4) |
C11 | 0.156 (6) | 0.205 (6) | 0.219 (7) | 0.028 (5) | 0.033 (5) | 0.085 (6) |
C12 | 0.276 (11) | 0.175 (5) | 0.182 (6) | 0.040 (7) | 0.051 (6) | 0.036 (5) |
O1—C8 | 1.205 (4) | C5—H5 | 0.9300 |
O2—C8 | 1.344 (4) | C5—C6 | 1.404 (5) |
O2—C9 | 1.477 (5) | C6—H6 | 0.9300 |
N1—H1 | 0.8600 | C6—C7 | 1.372 (5) |
N1—C4 | 1.367 (4) | C7—C8 | 1.456 (5) |
N1—C7 | 1.377 (4) | C9—H9A | 0.9700 |
C1—H1A | 0.9600 | C9—H9B | 0.9700 |
C1—H1B | 0.9600 | C9—C10 | 1.436 (7) |
C1—H1C | 0.9600 | C10—H10A | 0.9700 |
C1—C2 | 1.542 (6) | C10—H10B | 0.9700 |
C2—H2A | 0.9700 | C10—C11 | 1.481 (9) |
C2—H2B | 0.9700 | C11—H11A | 0.9700 |
C2—C3 | 1.551 (4) | C11—H11B | 0.9700 |
C3—C2i | 1.551 (4) | C11—C12 | 1.412 (8) |
C3—C4 | 1.518 (4) | C12—H12A | 0.9600 |
C3—C4i | 1.518 (4) | C12—H12B | 0.9600 |
C4—C5 | 1.375 (4) | C12—H12C | 0.9600 |
C8—O2—C9 | 116.9 (3) | N1—C7—C8 | 120.3 (3) |
C4—N1—H1 | 125.0 | C6—C7—N1 | 107.4 (3) |
C4—N1—C7 | 110.1 (2) | C6—C7—C8 | 132.3 (3) |
C7—N1—H1 | 125.0 | O1—C8—O2 | 123.4 (3) |
H1A—C1—H1B | 109.5 | O1—C8—C7 | 125.1 (3) |
H1A—C1—H1C | 109.5 | O2—C8—C7 | 111.5 (3) |
H1B—C1—H1C | 109.5 | O2—C9—H9A | 109.8 |
C2—C1—H1A | 109.5 | O2—C9—H9B | 109.8 |
C2—C1—H1B | 109.5 | H9A—C9—H9B | 108.2 |
C2—C1—H1C | 109.5 | C10—C9—O2 | 109.6 (4) |
C1—C2—H2A | 108.6 | C10—C9—H9A | 109.8 |
C1—C2—H2B | 108.6 | C10—C9—H9B | 109.8 |
C1—C2—C3 | 114.5 (3) | C9—C10—H10A | 108.1 |
H2A—C2—H2B | 107.6 | C9—C10—H10B | 108.1 |
C3—C2—H2A | 108.6 | C9—C10—C11 | 116.8 (6) |
C3—C2—H2B | 108.6 | H10A—C10—H10B | 107.3 |
C2—C3—C2i | 111.0 (4) | C11—C10—H10A | 108.1 |
C4i—C3—C2i | 109.02 (17) | C11—C10—H10B | 108.1 |
C4i—C3—C2 | 108.81 (18) | C10—C11—H11A | 107.4 |
C4—C3—C2i | 108.81 (18) | C10—C11—H11B | 107.4 |
C4—C3—C2 | 109.02 (17) | H11A—C11—H11B | 106.9 |
C4i—C3—C4 | 110.2 (3) | C12—C11—C10 | 119.7 (8) |
N1—C4—C3 | 121.5 (2) | C12—C11—H11A | 107.4 |
N1—C4—C5 | 106.7 (3) | C12—C11—H11B | 107.4 |
C5—C4—C3 | 131.7 (3) | C11—C12—H12A | 109.5 |
C4—C5—H5 | 125.7 | C11—C12—H12B | 109.5 |
C4—C5—C6 | 108.7 (3) | C11—C12—H12C | 109.5 |
C6—C5—H5 | 125.7 | H12A—C12—H12B | 109.5 |
C5—C6—H6 | 126.4 | H12A—C12—H12C | 109.5 |
C7—C6—C5 | 107.1 (3) | H12B—C12—H12C | 109.5 |
C7—C6—H6 | 126.4 | ||
O2—C9—C10—C11 | −62.9 (8) | C4i—C3—C4—N1 | 44.80 (19) |
N1—C4—C5—C6 | 0.7 (4) | C4i—C3—C4—C5 | −140.2 (4) |
N1—C7—C8—O1 | −8.2 (5) | C4—C5—C6—C7 | −0.5 (4) |
N1—C7—C8—O2 | 171.6 (3) | C5—C6—C7—N1 | 0.1 (4) |
C1—C2—C3—C2i | 59.3 (3) | C5—C6—C7—C8 | −178.0 (3) |
C1—C2—C3—C4 | −60.5 (4) | C6—C7—C8—O1 | 169.8 (4) |
C1—C2—C3—C4i | 179.2 (3) | C6—C7—C8—O2 | −10.4 (5) |
C2—C3—C4—N1 | −74.5 (3) | C7—N1—C4—C3 | 175.5 (2) |
C2i—C3—C4—N1 | 164.3 (3) | C7—N1—C4—C5 | −0.6 (3) |
C2—C3—C4—C5 | 100.5 (4) | C8—O2—C9—C10 | 170.1 (5) |
C2i—C3—C4—C5 | −20.7 (4) | C9—O2—C8—O1 | 1.8 (6) |
C3—C4—C5—C6 | −174.9 (3) | C9—O2—C8—C7 | −178.0 (4) |
C4—N1—C7—C6 | 0.3 (3) | C9—C10—C11—C12 | −177.5 (6) |
C4—N1—C7—C8 | 178.7 (3) |
Symmetry code: (i) x, −y+1/4, −z+1/4. |
Cg1 is the centroid of the N1/C4–C7 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1ii | 0.86 | 2.12 | 2.962 (3) | 165 |
C12—H12C···Cg1iii | 0.96 | 3.21 | 3.944 (3) | 135 |
Symmetry codes: (ii) −x+5/4, −y+1/4, z; (iii) x+1/4, y+1/4, −z. |
Funding information
Funding for this research was provided by: National Natural Science Foundation of China (award No. 21172174).
References
Bruker (2001). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Deliomeroglu, M. K., Lynch, V. M. & Sessler, J. L. (2016). Chem. Sci. 7, 3843–3850. Web of Science CSD CrossRef CAS PubMed Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Dubis, A. T. & Grabowski, S. J. (2002). New J. Chem. 26, 165–169. Web of Science CrossRef CAS Google Scholar
Figueira, C. A., Lopes, P. S., Gomes, C. S. B., Veiros, L. F. & Gomes, P. T. (2015). CrystEngComm, 17, 6406–6419. Web of Science CSD CrossRef CAS Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CrossRef IUCr Journals Google Scholar
Kim, H.-J. (2010). Acta Cryst. E66, o566. Web of Science CSD CrossRef IUCr Journals Google Scholar
Love, J. B., Blake, A. J., Wilson, C., Reid, S. D., Novak, A. & Hitchcock, P. B. (2003). Chem. Commun. pp. 1682–1683. Web of Science CSD CrossRef Google Scholar
Mahanta, S. P., Kumar, B. S., Baskaran, S., Sivasankar, C. & Panda, P. K. (2012). Org. Lett. 14, 548–551. Web of Science CSD CrossRef CAS PubMed Google Scholar
Prins, L. J., Reinhoudt, D. N. & Timmerman, P. (2001). Angew. Chem. Int. Ed. 40, 2382–2426. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Steiner, T. (2002). Angew. Chem. Int. Ed. 41, 48–76. Web of Science CrossRef CAS Google Scholar
Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. Google Scholar
Uppal, T., Hu, X., Fronczek, F. R., Maschek, S., Bobadova-Parvanova, P. & Vicente, M. G. H. (2012). Chem. Eur. J. 18, 3893–3905. Web of Science CSD CrossRef CAS PubMed Google Scholar
Xie, H., Lee, D. A., Senge, M. O. & Smith, K. M. (1994). J. Chem. Soc. Chem. Commun. pp. 791–792. CrossRef Web of Science Google Scholar
Yin, Z. & Li, Z. (2006). Tetrahedron Lett. 47, 7875–7879. Web of Science CSD CrossRef CAS Google Scholar
Yin, Z., Zhang, Y., He, J. & Cheng, J.-P. (2007). Chem. Commun. pp. 2599–2601. Web of Science CSD CrossRef Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.