supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

bh2271 scheme

Acta Cryst. (2010). E66, o566    [ doi:10.1107/S1600536810004459 ]

Dibenzyl 3,3'-diethyl-4,4'-dimethyl-2,2'-methylenebis(pyrrole-5-carboxylate)

H.-J. Kim

Abstract top

In the title compound, C31H34N2O4, the two pyrrole rings are bent around the central methylene C atom, making a dihedral angle of 64.83 (7)°. In the crystal, molecules are linked into dimers via N-H...O=C hydrogen bonds. These dimers are packed through [pi]...[pi] interactions between neighboring pyrrole rings with a separation between the mean planes of symmetry-related pyrrole rings of 3.61 (2) Å and a centroid-centroid distance of 4.33 Å. Parallel phenyl groups in neighboring dimers also exhibit efficient [pi]...[pi] interactions, characterized by an interplane separation of 3.378 (8) Å and a centroid-centroid distance of 3.97 Å.

Comment top

Dipyrrylmethanes have been widely used as versatile precursors in the synthesis of porphyrins (Shanmugathasan et al., 2000), related polypyrrolic macrocycles (Jasat et al., 1997) and pigments (Chen et al., 2000). For the synthesis of novel porphyrins, the title compound was prepared and its crystal structure determined. Related structure of dipyrrylmethanes derivatives were previously reported (Bonnett et al., 1972; Senge et al., 2005; Vega et al., 2003).

The molecular structure of the title compound is shown in Figure 1. The two pyrrole rings are bent with the dihedral angle of 64.83 (7)° around the attached methylene carbon atom C5. As shown in Figure 2, the molecules are linked by paired N—H···O=C hydrogen bonds into dimers in the crystal lattice. The structural parameters for the intermolecular hydrogen bonds resulting in the formation of dimers are given in Table 1. These dimeric units are packed through π···π interactions between neighboring pyrrole rings as well as neighboring phenyl rings as shown in Figure 3. The interplane and a centroid-to-centroid separations between the parallel pyrrole groups are 3.61 (2) and 4.33 Å, respectively. The parallel phenyl groups in neighboring dimers in the crystal also exhibit efficient π···π interactions: interplane separation of 3.378 (8) Å, and centroid-to-centroid distance of 3.973 Å.

Related literature top

For the preparation of the title compound, see: Twyman et al. (1999). For related structures, see: Bonnett et al. (1972); Senge et al. (2005); Vega et al. (2003). For the use of dipyrrylmethanes in organic synthesis, see: Chen et al. (2000) and references cited therein; Jasat et al. (1997); Shanmugathasan et al. (2000).

Experimental top

The title compound was prepared according to the reported procedure (Twyman et al., 1999). Crystals suitable for X-ray crystallographic work were grown by slow vapor diffusion of n-hexane into a toluene solution.

Refinement top

All non-H atoms were refined anisotropically. C-bonded H atoms were placed in geometrically ideal positions and refined as riding to their parent C atoms with C—H bond lengths fixed to 0.99 (methylene) or 0.98 Å (methyl). Displacement parameters were computed as Uiso(H) = 1.2Ueq(carrier C) for methylene groups and Uiso(H) = 1.5Ueq(carrier C) for methyl groups. Atoms H1 and H2, bonded to N1 and N2, were found in a difference map and refined freely (coordinates and displacement parameters).

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT (Bruker, 1998); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing 30 % probability displacement ellipsoids. Hydrogen atoms except for the N—H groups are omitted for clarity.
[Figure 2] Fig. 2. Hydrogen bonded dimer in the crystal of the title compound.
[Figure 3] Fig. 3. Packing diagram for the hydrogen bonded dimers of the title compound in the crystal lattice.
Dibenzyl 3,3'-diethyl-4,4'-dimethyl-2,2'-methylenebis(pyrrole-5-carboxylate) top
Crystal data top
C31H34N2O4F(000) = 1064
Mr = 498.60Dx = 1.211 Mg m−3
Monoclinic, P2/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yacCell parameters from 9928 reflections
a = 14.2002 (9) Åθ = 2.6–24.4°
b = 7.9220 (5) ŵ = 0.08 mm−1
c = 25.0939 (16) ÅT = 162 K
β = 104.373 (3)°Plate, colourless
V = 2734.6 (3) Å30.35 × 0.32 × 0.08 mm
Z = 4
Data collection top
Bruker SMART APEX CCD
diffractometer		6304 independent reflections
Radiation source: fine-focus sealed tube4371 reflections with I > 2σ(I)
graphiteRint = 0.059
φ and ω scansθmax = 27.6°, θmin = 1.5°
Absorption correction: multi-scan
(SADABS; Bruker, 1998)		h = −18→18
Tmin = 0.972, Tmax = 0.993k = −10→10
37570 measured reflectionsl = −31→32
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.136H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.0505P)2 + 0.953P]
where P = (Fo2 + 2Fc2)/3
6304 reflections(Δ/σ)max = 0.001
346 parametersΔρmax = 0.29 e Å−3
0 restraintsΔρmin = −0.26 e Å−3
0 constraints
Crystal data top
C31H34N2O4V = 2734.6 (3) Å3
Mr = 498.60Z = 4
Monoclinic, P2/nMo Kα radiation
a = 14.2002 (9) ŵ = 0.08 mm−1
b = 7.9220 (5) ÅT = 162 K
c = 25.0939 (16) Å0.35 × 0.32 × 0.08 mm
β = 104.373 (3)°
Data collection top
Bruker SMART APEX CCD
diffractometer		6304 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1998)		4371 reflections with I > 2σ(I)
Tmin = 0.972, Tmax = 0.993Rint = 0.059
37570 measured reflectionsθmax = 27.6°
Refinement top
R[F2 > 2σ(F2)] = 0.049H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.136Δρmax = 0.29 e Å−3
S = 1.05Δρmin = −0.26 e Å−3
6304 reflectionsAbsolute structure: ?
346 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.84641 (10)0.85654 (17)0.91775 (6)0.0528 (4)
O20.75643 (10)0.65074 (17)0.86750 (7)0.0603 (4)
O30.76635 (7)0.24675 (15)0.68188 (4)0.0342 (3)
O40.87580 (7)0.18152 (15)0.63406 (4)0.0334 (3)
N10.90073 (10)0.43117 (18)0.88502 (5)0.0310 (3)
H10.8449 (15)0.396 (3)0.8648 (8)0.047 (6)*
N20.90338 (9)0.17664 (17)0.77990 (5)0.0285 (3)
H20.8449 (14)0.204 (2)0.7845 (7)0.045 (5)*
C10.91713 (12)0.5906 (2)0.90767 (7)0.0339 (4)
C21.01355 (12)0.5990 (2)0.93634 (6)0.0348 (4)
C31.05588 (12)0.4413 (2)0.93042 (6)0.0327 (4)
C40.98377 (11)0.3399 (2)0.89853 (6)0.0295 (3)
C50.98552 (12)0.1610 (2)0.87970 (6)0.0319 (4)
H5A0.92830.10100.88630.038*
H5B1.04450.10510.90210.038*
C60.98473 (11)0.1445 (2)0.82008 (6)0.0294 (3)
C71.05896 (11)0.1041 (2)0.79533 (7)0.0315 (4)
C81.01998 (11)0.1126 (2)0.73787 (7)0.0310 (4)
C90.92347 (11)0.1592 (2)0.72921 (6)0.0287 (3)
C101.06422 (14)0.7464 (2)0.96891 (8)0.0461 (5)
H10A1.01610.83180.97230.069*
H10B1.11050.79540.95010.069*
H10C1.09910.70811.00560.069*
C111.07570 (12)0.0804 (3)0.69528 (7)0.0426 (4)
H11A1.05250.15660.66400.064*
H11B1.0659−0.03690.68270.064*
H11C1.14510.10040.71130.064*
C121.16037 (12)0.3931 (3)0.95415 (7)0.0422 (4)
H12A1.16520.26850.95630.051*
H12B1.18150.43790.99210.051*
C131.22892 (14)0.4582 (3)0.92102 (9)0.0538 (5)
H13A1.29520.41990.93800.081*
H13B1.22730.58180.92030.081*
H13C1.20850.41480.88330.081*
C141.16166 (11)0.0618 (2)0.82435 (7)0.0399 (4)
H14A1.17420.10080.86300.048*
H14B1.20610.12430.80670.048*
C151.18485 (14)−0.1252 (3)0.82408 (9)0.0533 (5)
H15A1.2535−0.14340.84250.080*
H15B1.1721−0.16530.78600.080*
H15C1.1440−0.18750.84350.080*
C160.84033 (13)0.7142 (2)0.89944 (8)0.0416 (4)
C170.67700 (17)0.7704 (3)0.85195 (13)0.0862 (9)
H17A0.69560.86440.83060.103*
H17B0.66140.81790.88520.103*
C180.59147 (15)0.6804 (3)0.81813 (9)0.0532 (5)
C190.58054 (18)0.6486 (3)0.76239 (10)0.0682 (7)
H19A0.63010.68280.74530.082*
C200.4995 (2)0.5688 (3)0.73183 (10)0.0717 (7)
H20A0.49370.54820.69390.086*
C210.4286 (2)0.5196 (3)0.75463 (12)0.0751 (8)
H21A0.37280.46460.73280.090*
C220.43577 (19)0.5477 (3)0.80892 (13)0.0766 (8)
H22A0.38500.51350.82500.092*
C230.51800 (19)0.6269 (3)0.84062 (10)0.0637 (6)
H23A0.52340.64450.87870.076*
C240.84815 (11)0.1997 (2)0.68106 (6)0.0276 (3)
C250.80269 (12)0.2219 (2)0.58423 (6)0.0359 (4)
H25A0.78370.34210.58440.043*
H25B0.74410.15140.58140.043*
C260.84675 (12)0.1871 (2)0.53687 (6)0.0324 (4)
C270.81372 (12)0.0548 (2)0.50133 (7)0.0405 (4)
H27A0.7629−0.01560.50690.049*
C280.85450 (14)0.0244 (3)0.45761 (7)0.0478 (5)
H28A0.8312−0.06620.43310.057*
C290.92838 (15)0.1244 (3)0.44945 (7)0.0490 (5)
H29A0.95600.10320.41930.059*
C300.96260 (15)0.2558 (3)0.48502 (8)0.0496 (5)
H30A1.01420.32470.47960.060*
C310.92170 (14)0.2872 (2)0.52860 (7)0.0414 (4)
H31A0.94520.37800.55300.050*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0556 (8)0.0344 (8)0.0696 (9)−0.0040 (6)0.0177 (7)−0.0095 (7)
O20.0426 (8)0.0386 (8)0.0881 (11)0.0093 (6)−0.0059 (7)−0.0128 (7)
O30.0246 (6)0.0458 (7)0.0335 (6)0.0038 (5)0.0095 (5)0.0045 (5)
O40.0264 (6)0.0474 (7)0.0267 (5)0.0018 (5)0.0072 (5)−0.0004 (5)
N10.0286 (7)0.0331 (8)0.0300 (7)−0.0034 (6)0.0047 (6)−0.0023 (6)
N20.0198 (6)0.0365 (8)0.0293 (7)0.0011 (6)0.0067 (5)−0.0012 (6)
C10.0390 (9)0.0325 (9)0.0308 (8)−0.0042 (7)0.0098 (7)−0.0021 (7)
C20.0396 (9)0.0388 (10)0.0255 (8)−0.0079 (8)0.0073 (7)0.0008 (7)
C30.0335 (9)0.0401 (10)0.0227 (7)−0.0062 (7)0.0035 (6)0.0036 (7)
C40.0287 (8)0.0353 (9)0.0241 (7)−0.0025 (7)0.0061 (6)0.0021 (7)
C50.0295 (8)0.0349 (9)0.0297 (8)0.0011 (7)0.0042 (7)0.0040 (7)
C60.0240 (7)0.0305 (9)0.0317 (8)−0.0014 (6)0.0035 (6)−0.0017 (7)
C70.0229 (8)0.0337 (9)0.0365 (9)−0.0017 (7)0.0046 (6)−0.0067 (7)
C80.0220 (7)0.0355 (9)0.0355 (8)−0.0026 (7)0.0073 (6)−0.0065 (7)
C90.0238 (7)0.0340 (9)0.0288 (8)−0.0018 (6)0.0074 (6)−0.0033 (7)
C100.0522 (11)0.0449 (11)0.0387 (10)−0.0128 (9)0.0062 (8)−0.0066 (9)
C110.0289 (9)0.0586 (12)0.0426 (10)0.0007 (8)0.0137 (7)−0.0106 (9)
C120.0365 (10)0.0486 (11)0.0344 (9)−0.0041 (8)−0.0044 (7)0.0032 (8)
C130.0353 (10)0.0589 (13)0.0647 (13)−0.0043 (9)0.0075 (9)0.0014 (11)
C140.0229 (8)0.0482 (11)0.0455 (10)0.0012 (7)0.0026 (7)−0.0091 (9)
C150.0381 (10)0.0506 (12)0.0624 (13)0.0104 (9)−0.0042 (9)−0.0059 (10)
C160.0437 (10)0.0353 (10)0.0461 (10)−0.0035 (8)0.0115 (8)−0.0010 (8)
C170.0564 (14)0.0475 (14)0.133 (2)0.0215 (11)−0.0170 (15)−0.0224 (15)
C180.0521 (12)0.0439 (12)0.0589 (13)0.0229 (10)0.0051 (10)−0.0037 (10)
C190.0650 (15)0.0705 (16)0.0724 (16)0.0287 (13)0.0233 (13)0.0057 (13)
C200.0748 (17)0.0749 (17)0.0536 (13)0.0352 (14)−0.0066 (13)−0.0125 (13)
C210.0650 (16)0.0567 (15)0.089 (2)0.0198 (13)−0.0085 (14)−0.0120 (14)
C220.0667 (16)0.0588 (16)0.108 (2)0.0098 (13)0.0284 (16)0.0136 (16)
C230.0788 (17)0.0564 (14)0.0533 (13)0.0223 (13)0.0112 (12)0.0034 (11)
C240.0241 (7)0.0294 (8)0.0307 (8)−0.0033 (6)0.0096 (6)−0.0001 (7)
C250.0302 (8)0.0458 (10)0.0304 (8)0.0040 (7)0.0053 (7)0.0059 (8)
C260.0316 (8)0.0368 (9)0.0276 (8)0.0038 (7)0.0051 (7)0.0050 (7)
C270.0331 (9)0.0471 (11)0.0364 (9)−0.0033 (8)−0.0005 (7)−0.0010 (8)
C280.0486 (11)0.0553 (12)0.0332 (9)0.0020 (10)−0.0018 (8)−0.0113 (9)
C290.0591 (12)0.0605 (13)0.0285 (9)0.0076 (10)0.0133 (8)−0.0004 (9)
C300.0582 (12)0.0535 (13)0.0430 (10)−0.0070 (10)0.0236 (9)0.0045 (10)
C310.0520 (11)0.0392 (10)0.0353 (9)−0.0073 (8)0.0154 (8)−0.0030 (8)
Geometric parameters (Å, °) top
O1—C161.213 (2)C13—H13A0.9800
O2—C161.356 (2)C13—H13B0.9800
O2—C171.451 (2)C13—H13C0.9800
O3—C241.2249 (18)C14—C151.518 (3)
O4—C241.3400 (18)C14—H14A0.9900
O4—C251.4490 (18)C14—H14B0.9900
N1—C41.352 (2)C15—H15A0.9800
N1—C11.381 (2)C15—H15B0.9800
N1—H10.87 (2)C15—H15C0.9800
N2—C61.356 (2)C17—C181.481 (3)
N2—C91.3778 (19)C17—H17A0.9900
N2—H20.893 (19)C17—H17B0.9900
C1—C21.381 (2)C18—C231.371 (3)
C1—C161.442 (3)C18—C191.391 (3)
C2—C31.410 (3)C19—C201.368 (4)
C2—C101.502 (2)C19—H19A0.9500
C3—C41.388 (2)C20—C211.334 (4)
C3—C121.504 (2)C20—H20A0.9500
C4—C51.496 (2)C21—C221.359 (4)
C5—C61.499 (2)C21—H21A0.9500
C5—H5A0.9900C22—C231.389 (4)
C5—H5B0.9900C22—H22A0.9500
C6—C71.387 (2)C23—H23A0.9500
C7—C81.412 (2)C25—C261.500 (2)
C7—C141.497 (2)C25—H25A0.9900
C8—C91.383 (2)C25—H25B0.9900
C8—C111.501 (2)C26—C271.381 (2)
C9—C241.437 (2)C26—C311.384 (2)
C10—H10A0.9800C27—C281.383 (3)
C10—H10B0.9800C27—H27A0.9500
C10—H10C0.9800C28—C291.370 (3)
C11—H11A0.9800C28—H28A0.9500
C11—H11B0.9800C29—C301.379 (3)
C11—H11C0.9800C29—H29A0.9500
C12—C131.519 (3)C30—C311.382 (2)
C12—H12A0.9900C30—H30A0.9500
C12—H12B0.9900C31—H31A0.9500
C16—O2—C17115.28 (16)C15—C14—H14A108.8
C24—O4—C25115.60 (12)C7—C14—H14B108.8
C4—N1—C1109.76 (14)C15—C14—H14B108.8
C4—N1—H1125.8 (13)H14A—C14—H14B107.7
C1—N1—H1124.5 (13)C14—C15—H15A109.5
C6—N2—C9109.53 (13)C14—C15—H15B109.5
C6—N2—H2126.6 (12)H15A—C15—H15B109.5
C9—N2—H2123.8 (12)C14—C15—H15C109.5
N1—C1—C2107.62 (15)H15A—C15—H15C109.5
N1—C1—C16121.18 (15)H15B—C15—H15C109.5
C2—C1—C16131.20 (16)O1—C16—O2122.53 (17)
C1—C2—C3107.20 (15)O1—C16—C1126.65 (18)
C1—C2—C10126.87 (17)O2—C16—C1110.82 (16)
C3—C2—C10125.92 (16)O2—C17—C18108.16 (17)
C4—C3—C2107.49 (14)O2—C17—H17A110.1
C4—C3—C12126.53 (16)C18—C17—H17A110.1
C2—C3—C12125.98 (15)O2—C17—H17B110.1
N1—C4—C3107.93 (15)C18—C17—H17B110.1
N1—C4—C5120.59 (14)H17A—C17—H17B108.4
C3—C4—C5131.48 (15)C23—C18—C19116.8 (2)
C4—C5—C6113.68 (13)C23—C18—C17120.8 (2)
C4—C5—H5A108.8C19—C18—C17122.3 (2)
C6—C5—H5A108.8C20—C19—C18121.0 (2)
C4—C5—H5B108.8C20—C19—H19A119.5
C6—C5—H5B108.8C18—C19—H19A119.5
H5A—C5—H5B107.7C21—C20—C19120.9 (2)
N2—C6—C7108.19 (14)C21—C20—H20A119.6
N2—C6—C5121.31 (13)C19—C20—H20A119.6
C7—C6—C5130.45 (14)C20—C21—C22120.4 (3)
C6—C7—C8107.30 (13)C20—C21—H21A119.8
C6—C7—C14126.19 (15)C22—C21—H21A119.8
C8—C7—C14126.51 (14)C21—C22—C23119.4 (3)
C9—C8—C7107.16 (13)C21—C22—H22A120.3
C9—C8—C11127.60 (15)C23—C22—H22A120.3
C7—C8—C11125.22 (14)C18—C23—C22121.4 (2)
N2—C9—C8107.80 (13)C18—C23—H23A119.3
N2—C9—C24118.19 (13)C22—C23—H23A119.3
C8—C9—C24133.88 (14)O3—C24—O4122.27 (14)
C2—C10—H10A109.5O3—C24—C9124.37 (14)
C2—C10—H10B109.5O4—C24—C9113.36 (13)
H10A—C10—H10B109.5O4—C25—C26107.03 (13)
C2—C10—H10C109.5O4—C25—H25A110.3
H10A—C10—H10C109.5C26—C25—H25A110.3
H10B—C10—H10C109.5O4—C25—H25B110.3
C8—C11—H11A109.5C26—C25—H25B110.3
C8—C11—H11B109.5H25A—C25—H25B108.6
H11A—C11—H11B109.5C27—C26—C31119.28 (16)
C8—C11—H11C109.5C27—C26—C25120.65 (16)
H11A—C11—H11C109.5C31—C26—C25120.07 (16)
H11B—C11—H11C109.5C26—C27—C28120.15 (17)
C3—C12—C13113.60 (15)C26—C27—H27A119.9
C3—C12—H12A108.8C28—C27—H27A119.9
C13—C12—H12A108.8C29—C28—C27120.34 (18)
C3—C12—H12B108.8C29—C28—H28A119.8
C13—C12—H12B108.8C27—C28—H28A119.8
H12A—C12—H12B107.7C28—C29—C30119.98 (17)
C12—C13—H13A109.5C28—C29—H29A120.0
C12—C13—H13B109.5C30—C29—H29A120.0
H13A—C13—H13B109.5C29—C30—C31119.88 (18)
C12—C13—H13C109.5C29—C30—H30A120.1
H13A—C13—H13C109.5C31—C30—H30A120.1
H13B—C13—H13C109.5C30—C31—C26120.35 (17)
C7—C14—C15113.73 (15)C30—C31—H31A119.8
C7—C14—H14A108.8C26—C31—H31A119.8
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O3i0.87 (2)2.09 (2)2.9334 (18)163.4 (18)
N2—H2···O3i0.89 (2)2.00 (2)2.8610 (17)162.8 (17)
Symmetry codes: (i) −x+3/2, y, −z+3/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O3i0.87 (2)2.09 (2)2.9334 (18)163.4 (18)
N2—H2···O3i0.89 (2)2.00 (2)2.8610 (17)162.8 (17)
Symmetry codes: (i) −x+3/2, y, −z+3/2.
Acknowledgements top

This work was supported by Kumoh National Institute of Technology.

references
References top

Bonnett, R., Hursthouse, M. B. & Neidle, S. (1972). J. Chem. Soc. Perkin Trans. 2, pp. 1335–1340.

Bruker (1998). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, WI, USA.

Chen, J., Burghart, A., Derecskei-Kovacs, A. & Burgess, K. (2000). J. Org. Chem. 65, 2900–2906.

Jasat, A. & Dolphin, D. (1997). Chem. Rev. 97, 2267–2340.

Senge, M. O. (2005). Acta Cryst. E61, o506–o508.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Shanmugathasan, S., Edwards, C. & Boyle, R. W. (2000). Tetrahedron, 56, 1025–1046.

Twyman, L. J. & Sanders, J. K. M. (1999). Tetrahedron Lett. 40, 6681–6684.

Vega, I. E. D., Camiolo, S., Gale, P. A., Hursthouse, M. B. & Light, M. E. (2003). Chem. Commun. pp. 1686–1687.