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

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.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.081
• wR factor = 0.278
• Data-to-parameter ratio = 16.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT084_ALERT_3_C High wR2 Value (i.e. > 0.25) ...................       0.28 Report
PLAT260_ALERT_2_C Large Average Ueq of Residue Including        O1      0.113 Check
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............    0.00591 Ang.
PLAT360_ALERT_2_C Short  C(sp3)-C(sp3) Bond  C11      - C12      .       1.41 Ang.
PLAT905_ALERT_3_C Negative K value in the Analysis of Variance ...     -2.785 Report
PLAT978_ALERT_2_C Number C-C Bonds with Positive Residual Density.          0 Info

Alert level G
PLAT005_ALERT_5_G No Embedded Refinement Details Found  in the CIF     Please Do !
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          1 Report
PLAT072_ALERT_2_G SHELXL First  Parameter in WGHT  Unusually Large       0.15 Report
PLAT083_ALERT_2_G SHELXL Second Parameter in WGHT  Unusually Large      16.19 Why ?
PLAT726_ALERT_2_G H...A   Calc     2.13000, Rep     2.12000 Dev...       0.01 Ang.
              H1       -O1              1.555  14.545 ........     #   34 Check
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          2 Note
PLAT909_ALERT_3_G Percentage of I>2sig(I) Data at Theta(Max) Still        35% Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   6 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   7 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   6 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

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Computing details

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)

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) Å^3	Block, colourless
Z = 16	0.32 × 0.28 × 0.26 mm
F(000) = 3488

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

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.081	H-atom parameters constrained
wR(F^2) = 0.278	w = 1/[σ^2(Fo^2) + (0.1517P)^2 + 16.1858P] where P = (Fo^2 + 2Fc^2)/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

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	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*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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—C2^i	1.551 (4)	C11—C12	1.412 (8)
C3—C4	1.518 (4)	C12—H12A	0.9600
C3—C4^i	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—C2^i	111.0 (4)	C11—C10—H10A	108.1
C4^i—C3—C2^i	109.02 (17)	C11—C10—H10B	108.1
C4^i—C3—C2	108.81 (18)	C10—C11—H11A	107.4
C4—C3—C2^i	108.81 (18)	C10—C11—H11B	107.4
C4—C3—C2	109.02 (17)	H11A—C11—H11B	106.9
C4^i—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)	C4^i—C3—C4—N1	44.80 (19)
N1—C4—C5—C6	0.7 (4)	C4^i—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—C2^i	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—C4^i	179.2 (3)	C6—C7—C8—O2	−10.4 (5)
C2—C3—C4—N1	−74.5 (3)	C7—N1—C4—C3	175.5 (2)
C2^i—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)
C2^i—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.

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···O1^ii	0.86	2.12	2.962 (3)	165
C12—H12C···Cg1^iii	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.