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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2019 May 3;75(Pt 6):711–713. doi: 10.1107/S205698901900567X

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

Haijing Wang a,b, Zhenming Yin a,b,*
PMCID: PMC6658981  PMID: 31391950

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.

Keywords: dipyrro­methane-di­carboxyl­ate, crystal structure, hydrogen bonding

Abstract

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.

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.graphic file with name e-75-00711-scheme1.jpg

Structural commentary  

The structure of the title compound is shown in Fig. 1 ▸. 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

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

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 ▸).

Table 1. Hydrogen-bond geometry (Å, °).

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

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯O1i 0.86 2.12 2.962 (3) 165
C12—H12C⋯Cg1ii 0.96 3.21 3.944 (3) 135
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Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

Figure 2.

Figure 2

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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 + Inline graphic, −y + Inline graphic, z; (ii) x + Inline graphic, y + Inline graphic − z.]

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 d norm surface of the title compound is shown in Fig. 3 ▸. The red points represent closer contacts and negative d norm 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.

Figure 3.

Figure 3

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The Hirshfeld surface of the title compound mapped over d norm in the range −0.486 to 1.895 a.u. The inter­molecular contacts can be seen in the red regions.

Figure 4.

Figure 4

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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.

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.

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-d 6); 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.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. 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 U iso(H) = 1.2U eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula C23H34N2O4
M r 402.52
Crystal system, space group Orthorhombic, F d d d
Temperature (K) 296
a, b, c (Å) 14.358 (6), 17.333 (7), 38.902 (19)
V (Å3) 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 ▸)
T min, T max 0.822, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 11878, 2156, 1501
R int 0.031
(sin θ/λ)max (Å−1) 0.595
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), 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
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Computer programs: SMART and SAINT (Bruker, 2001 ▸), SHELXS (Sheldrick, 2008 ▸), SHELXL (Sheldrick, 2015 ▸) and OLEX2 (Dolomanov et al., 2009 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698901900567X/ff2158sup1.cif

e-75-00711-sup1.cif (364.9KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698901900567X/ff2158Isup2.hkl

e-75-00711-Isup2.hkl (119.2KB, hkl)

CCDC reference: 1912079

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

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
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Data collection

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
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Refinement

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
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Special details

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

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*
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Atomic displacement parameters (Å2)

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)
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Geometric parameters (Å, º)

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)
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Symmetry code: (i) x, −y+1/4, −z+1/4.

Hydrogen-bond geometry (Å, º)

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
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Symmetry codes: (ii) −x+5/4, −y+1/4, z; (iii) x+1/4, y+1/4, −z.

Funding Statement

This work was funded by National Natural Science Foundation of China grant 21172174.

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698901900567X/ff2158sup1.cif

e-75-00711-sup1.cif (364.9KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698901900567X/ff2158Isup2.hkl

e-75-00711-Isup2.hkl (119.2KB, hkl)

CCDC reference: 1912079

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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