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Crystal structure and Hirshfeld surface analysis of di­butyl 5,5′-(pentane-3,3-diyl)bis­(1H-pyrrole-5-carboxylate)

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aCollege 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

Edited by K. Fejfarova, Institute of Biotechnology CAS, Czech Republic (Received 22 March 2019; accepted 25 April 2019; online 3 May 2019)

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.

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[Prins, L. J., Reinhoudt, D. N. & Timmerman, P. (2001). Angew. Chem. Int. Ed. 40, 2382-2426.]; Steiner, 2002[Steiner, T. (2002). Angew. Chem. Int. Ed. 41, 48-76.]). 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[Figueira, C. A., Lopes, P. S., Gomes, C. S. B., Veiros, L. F. & Gomes, P. T. (2015). CrystEngComm, 17, 6406-6419.]). 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[Dubis, A. T. & Grabowski, S. J. (2002). New J. Chem. 26, 165-169.]). 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[Yin, Z. & Li, Z. (2006). Tetrahedron Lett. 47, 7875-7879.]). Here, we report the self-assembly of the title compound, via quadruple N—H⋯N hydrogen bonds.

[Scheme 1]

2. Structural commentary

The structure of the title compound is shown in Fig. 1[link]. The asymmetric unit 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)°.

[Figure 1]
Figure 1
ORTEP diagram for the title compound, with displacement ellipsoids drawn at the 30% probability level. [Symmetry code: (A) x, [1 \over 4] − y, [1 \over 4] − z.]

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[link], Fig. 2[link]). This type of dimer has also been observed in our previous work (Yin et al., 2007[Yin, Z., Zhang, Y., He, J. & Cheng, J.-P. (2007). Chem. Commun. pp. 2599-2601.]). The dimers are connected into a three-dimensional supra­molecular structure through C—H⋯π contacts (Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the N1/C4–C7 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O1i 0.86 2.12 2.962 (3) 165
C12—H12CCg1ii 0.96 3.21 3.944 (3) 135
Symmetry codes: (i) [-x+{\script{5\over 4}}, -y+{\script{1\over 4}}, z]; (ii) [x+{\script{1\over 4}}, y+{\script{1\over 4}}, -z].
[Figure 2]
Figure 2
Part of the crystal packing showing mol­ecules linked by N—H⋯O hydrogen bonds (red dashed lines) and C—H⋯π contacts (green dashed lines). [Symmetry codes: (i) −x + [{5\over 4}], −y + [{1\over 4}], z; (ii) x + [{1\over 4}], y + [{1\over 4}] − z.]

4. Hirshfeld surface

A Hirshfeld surface analysis with CrystalExplorer (Turner et al., 2017[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.]) 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[link]. 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[link] 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.

[Figure 3]
Figure 3
The Hirshfeld surface of the title compound mapped over dnorm in the range −0.486 to 1.895 a.u. The inter­molecular contacts can be seen in the red regions.
[Figure 4]
Figure 4
The two-dimensional fingerprint plots of title compound: (a) all contacts; (b) H⋯H, (c) H⋯O/O⋯H, (d) H⋯C/C⋯H, (e) H⋯N/N⋯H and (f) C⋯C.

5. Database survey

A search in the Cambridge Structural Database (Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) returned over 60 entries for dipyrro­methane-1,9-dicarb­onyl derivatives, including seven entries whose supra­molecular structures feature inter­locked dimers (ILITAY, Love et al., 2003[Love, J. B., Blake, A. J., Wilson, C., Reid, S. D., Novak, A. & Hitchcock, P. B. (2003). Chem. Commun. pp. 1682-1683.]; ODUMOQ,Yin et al., 2007[Yin, Z., Zhang, Y., He, J. & Cheng, J.-P. (2007). Chem. Commun. pp. 2599-2601.]; PIRJAB, Xie et al., 1994[Xie, H., Lee, D. A., Senge, M. O. & Smith, K. M. (1994). J. Chem. Soc. Chem. Commun. pp. 791-792.]; NIQBAR01, Mahanta et al., 2012[Mahanta, S. P., Kumar, B. S., Baskaran, S., Sivasankar, C. & Panda, P. K. (2012). Org. Lett. 14, 548-551.]; VACRID, Deliomeroglu et al., 2016[Deliomeroglu, M. K., Lynch, V. M. & Sessler, J. L. (2016). Chem. Sci. 7, 3843-3850.]; PUJMAJ, Kim, 2010[Kim, H.-J. (2010). Acta Cryst. E66, o566.] and SAVDUQ, Uppal et al., 2012[Uppal, T., Hu, X., Fronczek, F. R., Maschek, S., Bobadova-Parvanova, P. & Vicente, M. G. H. (2012). Chem. Eur. J. 18, 3893-3905.]). In the crystal of PUJMAJ (Kim, 2010[Kim, H.-J. (2010). Acta Cryst. E66, o566.]), 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 column chromatography 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 diffraction analysis were obtained by the slow evaporation of a CH3OH solution of the title compound.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. 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 refinement using a riding model, with Uiso(H) = 1.2Ueq(C).

Table 2
Experimental details

Crystal data
Chemical formula C23H34N2O4
Mr 402.52
Crystal system, space group Orthorhombic, Fddd
Temperature (K) 296
a, b, c (Å) 14.358 (6), 17.333 (7), 38.902 (19)
V3) 9681 (7)
Z 16
Radiation type Mo Kα
μ (mm−1) 0.08
Crystal size (mm) 0.32 × 0.28 × 0.26
 
Data collection
Diffractometer Bruker SMART CCD area detector
Absorption correction Multi-scan (SADABS; Bruker, 2001[Bruker (2001). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.822, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 11878, 2156, 1501
Rint 0.031
(sin θ/λ)max−1) 0.595
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.081, 0.278, 1.05
No. of reflections 2156
No. of parameters 134
No. of restraints 2
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.38, −0.34
Computer programs: SMART and SAINT (Bruker, 2001[Bruker (2001). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information


Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: 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).

Dibutyl 5,5'-(pentane-3,3-diyl)bis(1H-pyrrole-5-carboxylate) top
Crystal data top
C23H34N2O4Dx = 1.105 Mg m3
Mr = 402.52Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, FdddCell parameters from 3608 reflections
a = 14.358 (6) Åθ = 2.4–23.4°
b = 17.333 (7) ŵ = 0.08 mm1
c = 38.902 (19) ÅT = 296 K
V = 9681 (7) Å3Block, colourless
Z = 160.32 × 0.28 × 0.26 mm
F(000) = 3488
Data collection top
Bruker SMART CCD area detector
diffractometer
1501 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.031
phi and ω scansθmax = 25.0°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 1716
Tmin = 0.822, Tmax = 1.000k = 2018
11878 measured reflectionsl = 4644
2156 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.081H-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 reflectionsΔρmax = 0.38 e Å3
134 parametersΔρmin = 0.34 e Å3
2 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
xyzUiso*/Ueq
O10.68341 (16)0.20703 (14)0.05576 (7)0.0943 (8)
O20.65735 (17)0.33467 (14)0.05760 (8)0.1078 (10)
N10.51592 (15)0.18458 (13)0.09406 (6)0.0673 (7)
H10.53640.14120.08650.081*
C10.2522 (3)0.1657 (3)0.08110 (13)0.1320 (17)
H1A0.21310.18220.09970.198*
H1B0.21420.14590.06280.198*
H1C0.28800.20870.07290.198*
C20.3186 (2)0.1018 (2)0.09382 (9)0.0941 (11)
H2A0.35910.08690.07500.113*
H2B0.28190.05700.10010.113*
C30.3798 (3)0.12500.12500.0756 (11)
C40.44025 (19)0.19324 (17)0.11502 (7)0.0704 (8)
C50.4317 (2)0.27091 (19)0.12144 (10)0.0906 (10)
H50.38640.29370.13520.109*
C60.5026 (3)0.31011 (19)0.10378 (10)0.0919 (10)
H60.51260.36310.10360.110*
C70.5546 (2)0.25550 (17)0.08689 (8)0.0749 (8)
C80.6375 (2)0.26101 (19)0.06550 (9)0.0810 (9)
C90.7383 (3)0.3480 (3)0.03496 (16)0.141 (2)
H9A0.79530.33560.04710.169*
H9B0.73420.31490.01490.169*
C100.7401 (4)0.4274 (4)0.02437 (19)0.164 (2)
H10A0.79670.43590.01130.197*
H10B0.74400.45920.04480.197*
C110.6604 (5)0.4549 (4)0.0035 (2)0.193 (3)
H11A0.65510.42100.01620.232*
H11B0.60450.44780.01720.232*
C120.6597 (7)0.5314 (4)0.0088 (2)0.211 (4)
H12A0.66110.56660.01020.316*
H12B0.60420.53990.02210.316*
H12C0.71330.53980.02310.316*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0756 (14)0.0847 (16)0.1227 (19)0.0097 (12)0.0142 (12)0.0162 (13)
O20.0842 (17)0.0826 (16)0.157 (2)0.0004 (12)0.0174 (15)0.0302 (14)
N10.0571 (13)0.0653 (13)0.0796 (15)0.0047 (10)0.0016 (10)0.0003 (11)
C10.089 (3)0.169 (4)0.138 (4)0.001 (3)0.041 (3)0.027 (3)
C20.072 (2)0.116 (3)0.095 (2)0.0173 (18)0.0137 (16)0.0109 (19)
C30.053 (2)0.090 (3)0.083 (2)0.0000.0000.006 (2)
C40.0570 (15)0.0767 (18)0.0775 (17)0.0077 (13)0.0020 (12)0.0027 (14)
C50.084 (2)0.083 (2)0.104 (2)0.0180 (17)0.0106 (18)0.0065 (18)
C60.088 (2)0.0640 (18)0.124 (3)0.0049 (15)0.005 (2)0.0003 (18)
C70.0648 (17)0.0672 (17)0.093 (2)0.0018 (13)0.0053 (15)0.0099 (14)
C80.0659 (18)0.0748 (19)0.102 (2)0.0011 (15)0.0014 (16)0.0153 (16)
C90.075 (2)0.129 (3)0.219 (6)0.003 (2)0.039 (3)0.043 (4)
C100.136 (4)0.149 (4)0.206 (6)0.016 (4)0.033 (4)0.071 (4)
C110.156 (6)0.205 (6)0.219 (7)0.028 (5)0.033 (5)0.085 (6)
C120.276 (11)0.175 (5)0.182 (6)0.040 (7)0.051 (6)0.036 (5)
Geometric parameters (Å, º) top
O1—C81.205 (4)C5—H50.9300
O2—C81.344 (4)C5—C61.404 (5)
O2—C91.477 (5)C6—H60.9300
N1—H10.8600C6—C71.372 (5)
N1—C41.367 (4)C7—C81.456 (5)
N1—C71.377 (4)C9—H9A0.9700
C1—H1A0.9600C9—H9B0.9700
C1—H1B0.9600C9—C101.436 (7)
C1—H1C0.9600C10—H10A0.9700
C1—C21.542 (6)C10—H10B0.9700
C2—H2A0.9700C10—C111.481 (9)
C2—H2B0.9700C11—H11A0.9700
C2—C31.551 (4)C11—H11B0.9700
C3—C2i1.551 (4)C11—C121.412 (8)
C3—C41.518 (4)C12—H12A0.9600
C3—C4i1.518 (4)C12—H12B0.9600
C4—C51.375 (4)C12—H12C0.9600
C8—O2—C9116.9 (3)N1—C7—C8120.3 (3)
C4—N1—H1125.0C6—C7—N1107.4 (3)
C4—N1—C7110.1 (2)C6—C7—C8132.3 (3)
C7—N1—H1125.0O1—C8—O2123.4 (3)
H1A—C1—H1B109.5O1—C8—C7125.1 (3)
H1A—C1—H1C109.5O2—C8—C7111.5 (3)
H1B—C1—H1C109.5O2—C9—H9A109.8
C2—C1—H1A109.5O2—C9—H9B109.8
C2—C1—H1B109.5H9A—C9—H9B108.2
C2—C1—H1C109.5C10—C9—O2109.6 (4)
C1—C2—H2A108.6C10—C9—H9A109.8
C1—C2—H2B108.6C10—C9—H9B109.8
C1—C2—C3114.5 (3)C9—C10—H10A108.1
H2A—C2—H2B107.6C9—C10—H10B108.1
C3—C2—H2A108.6C9—C10—C11116.8 (6)
C3—C2—H2B108.6H10A—C10—H10B107.3
C2—C3—C2i111.0 (4)C11—C10—H10A108.1
C4i—C3—C2i109.02 (17)C11—C10—H10B108.1
C4i—C3—C2108.81 (18)C10—C11—H11A107.4
C4—C3—C2i108.81 (18)C10—C11—H11B107.4
C4—C3—C2109.02 (17)H11A—C11—H11B106.9
C4i—C3—C4110.2 (3)C12—C11—C10119.7 (8)
N1—C4—C3121.5 (2)C12—C11—H11A107.4
N1—C4—C5106.7 (3)C12—C11—H11B107.4
C5—C4—C3131.7 (3)C11—C12—H12A109.5
C4—C5—H5125.7C11—C12—H12B109.5
C4—C5—C6108.7 (3)C11—C12—H12C109.5
C6—C5—H5125.7H12A—C12—H12B109.5
C5—C6—H6126.4H12A—C12—H12C109.5
C7—C6—C5107.1 (3)H12B—C12—H12C109.5
C7—C6—H6126.4
O2—C9—C10—C1162.9 (8)C4i—C3—C4—N144.80 (19)
N1—C4—C5—C60.7 (4)C4i—C3—C4—C5140.2 (4)
N1—C7—C8—O18.2 (5)C4—C5—C6—C70.5 (4)
N1—C7—C8—O2171.6 (3)C5—C6—C7—N10.1 (4)
C1—C2—C3—C2i59.3 (3)C5—C6—C7—C8178.0 (3)
C1—C2—C3—C460.5 (4)C6—C7—C8—O1169.8 (4)
C1—C2—C3—C4i179.2 (3)C6—C7—C8—O210.4 (5)
C2—C3—C4—N174.5 (3)C7—N1—C4—C3175.5 (2)
C2i—C3—C4—N1164.3 (3)C7—N1—C4—C50.6 (3)
C2—C3—C4—C5100.5 (4)C8—O2—C9—C10170.1 (5)
C2i—C3—C4—C520.7 (4)C9—O2—C8—O11.8 (6)
C3—C4—C5—C6174.9 (3)C9—O2—C8—C7178.0 (4)
C4—N1—C7—C60.3 (3)C9—C10—C11—C12177.5 (6)
C4—N1—C7—C8178.7 (3)
Symmetry code: (i) x, y+1/4, z+1/4.
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the N1/C4–C7 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1···O1ii0.862.122.962 (3)165
C12—H12C···Cg1iii0.963.213.944 (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).

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