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organic compounds
Dibenzyl 3,3′,4,4′-tetramethyl-5,5′-(ethynediyl)bis(pyrrole-2-carboxylate)
aDepartment of Chemistry, Louisiana State University, Baton Rouge, LA 70803-1804, USA
*Correspondence e-mail: ffroncz@lsu.edu
The title molecule, C30H28N2O4, has crystallographic twofold rotation symmetry, with the pyrrole planes forming a dihedral angle of 40.49 (4)°. The pyrrole N—H donor and adjacent ester carbonyl acceptor form R22(10) hydrogen-bonded rings about inversion centers, leading to chains of hydrogen-bonded molecules along [001].
Related literature
For background literature, see: Chinchilla & Najera (2007); Black et al. (1999
); Etter (1990
); Vogel (1996
). For related structures, see: Xie et al. (1996
); Weghorn et al. (1995
).
Experimental
Crystal data
|
Data collection
|
Refinement
|
|
Data collection: COLLECT (Nonius, 2000); cell DENZO and SCALEPACK (Otwinowski & Minor, 1997
); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SIR97 (Altomare et al., 1999
); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997
); molecular graphics: ORTEP-3 (Farrugia, 1997
); software used to prepare material for publication: SHELXL97.
Supporting information
https://doi.org/10.1107/S1600536807061739/dn2299sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807061739/dn2299Isup2.hkl
To a 100 ml round bottom flask was added benzyl 5-iodo-3,4-dimethyl-1H-pyrrole-2-carboxylate (2.93 g, 10 mmol) followed by Pd(PPh)2Cl2 (0.7019 g, 0.1 mmol) and CuI (0.191 g 0.1 mmol). The flask was sealed and placed in a dry ice bath under N2. Trimethylsilanyl-ethyne (0.6996 ml, 5 mmol), DBU (8.973 ml, 60 mmol) and water (0.072 ml, 40 molar equiv.) were dissolved in 30 ml of acetonitrile and added to the reaction flask. After the mixture froze in the dry ice bath, the flask was evacuated and N2 gas added. The resulting reaction mixture was allowed to warm slowly to room temperature and was stirred until complete disappearance of the starting material by TLC. The reaction mixture was worked up by adding ethyl acetate (150 ml), and washing the organic layer three times with saline. The organic phase was dried over anhydrous sodium bicarbonate and concentrated under reduced pressure. The crude mixture was purified by flash δ): 11.99 (2H, s, NH), 7.47–7.32 (10H, m, Ar—H), 5.29 (4H, s, CH2), 2.2 (6H, s, CH3), 2.0 (6H, s, CH3). MS (EI) m/z: 480.129 (M+).
using hexane/ethyl acetate (5:1) for elution. The dipyrrole-ethyne (I) was obtained (0.755 g) in 54% yield and recrystallized from dichloromethane to afford colorless crystals. Spectroscopic analysis, 1H NMR (250 MHz, CDCl3, 293 K,H atoms were placed in idealized positions with C—H distances 0.95 - 0.99 Å and thereafter treated as riding. Uiso for H was assigned as 1.2 times Ueq of the attached C atoms (1.5 for methyl). A torsional parameter was refined for each methyl group.
Di(5-benzyloxycarbornyl-3,4-dimethyl-2-pyrrolyl)-ethyne (I) is an important intermediate in the synthesis of porphyrin analogues containing a two-carbon interpyrrolic bridge as in corrphycenes (Vogel, 1996). Compound (I) is also an interesting intermediate in the synthesis of dipyrroles with a two carbon bridge, which have shown selective binding properties to fluoride and other ions (Black et al. 1999). The title compound was prepared via an improved Sonogashira coupling reaction (Chinchilla & Najera, 2007), that took place between benzyl 5-iodo-3,4-dimethyl-1H-pyrrole-2-carboxylate and trimethylsilanyl-ethyne, in the presence of palladium(0) and copper(I) catalysts at room temperature. The exact experimental details are described below.
The structure of the title compound (I), which lies on a crystallographic twofold axis, is shown in Fig 1. The triple-bond distance is 1.2088 (17) Å, and the alkyne bridge is not quite linear, with C4—C5—C5i angle 175.61 (10)° (i = 1 - x, y, 1/2 - z). The pyrrole ring is essentially planar, its five atoms having a mean deviation 0.003 Å from their best plane, with maximum 0.0051 (7) Å for C4. The two pyrrole rings are not coplanar, but form a dihedral angle of 40.49 (4)°. The ester COO group lies nearly in the pyrrole plane, with N1—C1—C6—O2 torsion angle 3.67 (13)°.
The pyrrole N—H group and adjacent ester carbonyl form intermolecular hydrogen bonded rings about inversion centers, having graph-set notation (Etter, 1990) R22(10). Thus, each molecule engages in four hydrogen bonds with two other molecules, forming chains in the [0 0 1] direction, as shown in Fig. 2.
For background literature, see: Chinchilla & Najera (2007); Black et al. (1999); Etter (1990); Vogel (1996). For related structures, see: Xie et al. (1996); Weghorn et al. (1995).
Data collection: COLLECT (Nonius, 2000); cell
DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997). ![]() | Fig. 1. Ellipsoids at the 50% level, with the asymmetric unit labeled. H atoms are represented with arbitrary radius. |
![]() | Fig. 2. View down the twofold axis, showing hydrogen bonding. |
C30H28N2O4 | F(000) = 1016 |
Mr = 480.54 | Dx = 1.283 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 4869 reflections |
a = 19.340 (2) Å | θ = 2.5–33.1° |
b = 9.8955 (10) Å | µ = 0.09 mm−1 |
c = 13.8495 (15) Å | T = 90 K |
β = 110.217 (6)° | Prism, colorless |
V = 2487.2 (5) Å3 | 0.30 × 0.22 × 0.15 mm |
Z = 4 |
Nonius KappaCCD (with Oxford Cryostream) diffractometer | 3948 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.022 |
Graphite monochromator | θmax = 33.2°, θmin = 2.6° |
ω scans with κ offsets | h = −29→29 |
28071 measured reflections | k = −15→15 |
4748 independent reflections | l = −21→21 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.124 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | w = 1/[σ2(Fo2) + (0.067P)2 + 1.378P] where P = (Fo2 + 2Fc2)/3 |
4748 reflections | (Δ/σ)max < 0.001 |
168 parameters | Δρmax = 0.46 e Å−3 |
0 restraints | Δρmin = −0.39 e Å−3 |
C30H28N2O4 | V = 2487.2 (5) Å3 |
Mr = 480.54 | Z = 4 |
Monoclinic, C2/c | Mo Kα radiation |
a = 19.340 (2) Å | µ = 0.09 mm−1 |
b = 9.8955 (10) Å | T = 90 K |
c = 13.8495 (15) Å | 0.30 × 0.22 × 0.15 mm |
β = 110.217 (6)° |
Nonius KappaCCD (with Oxford Cryostream) diffractometer | 3948 reflections with I > 2σ(I) |
28071 measured reflections | Rint = 0.022 |
4748 independent reflections |
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.124 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.46 e Å−3 |
4748 reflections | Δρmin = −0.39 e Å−3 |
168 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.38808 (4) | 0.18151 (7) | 0.63308 (5) | 0.01536 (14) | |
O2 | 0.45716 (4) | 0.03182 (7) | 0.58415 (5) | 0.01670 (14) | |
N1 | 0.46808 (4) | 0.21012 (7) | 0.43512 (5) | 0.01204 (14) | |
H1N | 0.4897 (7) | 0.1328 (14) | 0.4339 (10) | 0.014* | |
C1 | 0.43250 (5) | 0.24465 (9) | 0.50220 (6) | 0.01179 (15) | |
C2 | 0.40633 (5) | 0.37712 (9) | 0.48108 (6) | 0.01253 (15) | |
C3 | 0.42701 (5) | 0.42307 (8) | 0.39832 (6) | 0.01261 (15) | |
C4 | 0.46445 (5) | 0.31725 (8) | 0.37111 (6) | 0.01224 (15) | |
C5 | 0.49073 (5) | 0.31065 (9) | 0.28744 (6) | 0.01342 (15) | |
C6 | 0.42810 (5) | 0.14317 (8) | 0.57551 (6) | 0.01202 (15) | |
C7 | 0.36367 (5) | 0.45910 (9) | 0.53229 (7) | 0.01701 (17) | |
H7A | 0.3974 | 0.5187 | 0.5838 | 0.026* | |
H7B | 0.3389 | 0.3985 | 0.5660 | 0.026* | |
H7C | 0.3268 | 0.5137 | 0.4806 | 0.026* | |
C8 | 0.40864 (6) | 0.55667 (9) | 0.34548 (7) | 0.01793 (17) | |
H8A | 0.4358 | 0.5673 | 0.2979 | 0.027* | |
H8B | 0.4225 | 0.6292 | 0.3968 | 0.027* | |
H8C | 0.3556 | 0.5612 | 0.3071 | 0.027* | |
C9 | 0.37901 (5) | 0.07780 (9) | 0.70202 (7) | 0.01577 (16) | |
H9A | 0.4274 | 0.0553 | 0.7543 | 0.019* | |
H9B | 0.3584 | −0.0052 | 0.6627 | 0.019* | |
C10 | 0.32768 (5) | 0.13018 (9) | 0.75362 (6) | 0.01280 (15) | |
C11 | 0.26606 (5) | 0.20803 (9) | 0.70116 (7) | 0.01592 (16) | |
H11 | 0.2572 | 0.2337 | 0.6318 | 0.019* | |
C12 | 0.21747 (5) | 0.24831 (10) | 0.74984 (8) | 0.01892 (18) | |
H12 | 0.1761 | 0.3027 | 0.7141 | 0.023* | |
C13 | 0.22929 (6) | 0.20909 (11) | 0.85086 (8) | 0.0228 (2) | |
H13 | 0.1954 | 0.2346 | 0.8835 | 0.027* | |
C14 | 0.29082 (6) | 0.13248 (11) | 0.90349 (8) | 0.0235 (2) | |
H14 | 0.2992 | 0.1058 | 0.9725 | 0.028* | |
C15 | 0.34045 (5) | 0.09438 (10) | 0.85570 (7) | 0.01773 (17) | |
H15 | 0.3831 | 0.0438 | 0.8928 | 0.021* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0226 (3) | 0.0130 (3) | 0.0161 (3) | 0.0032 (2) | 0.0138 (2) | 0.0026 (2) |
O2 | 0.0229 (3) | 0.0139 (3) | 0.0171 (3) | 0.0063 (2) | 0.0118 (2) | 0.0028 (2) |
N1 | 0.0154 (3) | 0.0107 (3) | 0.0129 (3) | 0.0023 (2) | 0.0085 (2) | 0.0010 (2) |
C1 | 0.0147 (3) | 0.0117 (3) | 0.0115 (3) | 0.0011 (3) | 0.0077 (3) | −0.0001 (3) |
C2 | 0.0151 (3) | 0.0117 (3) | 0.0128 (3) | 0.0017 (3) | 0.0074 (3) | −0.0004 (3) |
C3 | 0.0151 (4) | 0.0111 (3) | 0.0132 (3) | 0.0015 (3) | 0.0069 (3) | 0.0005 (3) |
C4 | 0.0145 (3) | 0.0119 (3) | 0.0124 (3) | 0.0002 (3) | 0.0073 (3) | 0.0006 (3) |
C5 | 0.0149 (4) | 0.0125 (3) | 0.0147 (3) | 0.0001 (3) | 0.0075 (3) | 0.0000 (3) |
C6 | 0.0142 (3) | 0.0127 (3) | 0.0107 (3) | 0.0010 (3) | 0.0063 (3) | 0.0001 (3) |
C7 | 0.0224 (4) | 0.0148 (4) | 0.0183 (4) | 0.0043 (3) | 0.0127 (3) | −0.0008 (3) |
C8 | 0.0241 (4) | 0.0128 (4) | 0.0192 (4) | 0.0035 (3) | 0.0105 (3) | 0.0038 (3) |
C9 | 0.0220 (4) | 0.0145 (4) | 0.0152 (3) | 0.0034 (3) | 0.0119 (3) | 0.0038 (3) |
C10 | 0.0159 (4) | 0.0120 (3) | 0.0128 (3) | −0.0016 (3) | 0.0080 (3) | −0.0005 (3) |
C11 | 0.0158 (4) | 0.0180 (4) | 0.0145 (3) | −0.0009 (3) | 0.0060 (3) | −0.0004 (3) |
C12 | 0.0155 (4) | 0.0186 (4) | 0.0248 (4) | −0.0006 (3) | 0.0095 (3) | −0.0019 (3) |
C13 | 0.0274 (5) | 0.0211 (4) | 0.0285 (5) | −0.0009 (4) | 0.0209 (4) | −0.0028 (4) |
C14 | 0.0351 (5) | 0.0238 (5) | 0.0190 (4) | 0.0027 (4) | 0.0188 (4) | 0.0021 (4) |
C15 | 0.0240 (4) | 0.0169 (4) | 0.0150 (4) | 0.0026 (3) | 0.0101 (3) | 0.0020 (3) |
O1—C6 | 1.3436 (10) | C8—H8A | 0.9800 |
O1—C9 | 1.4530 (10) | C8—H8B | 0.9800 |
O2—C6 | 1.2240 (10) | C8—H8C | 0.9800 |
N1—C4 | 1.3680 (11) | C9—C10 | 1.5018 (12) |
N1—C1 | 1.3767 (10) | C9—H9A | 0.9900 |
N1—H1N | 0.875 (14) | C9—H9B | 0.9900 |
C1—C2 | 1.3992 (12) | C10—C11 | 1.3940 (12) |
C1—C6 | 1.4514 (11) | C10—C15 | 1.3941 (12) |
C2—C3 | 1.4133 (11) | C11—C12 | 1.3910 (13) |
C2—C7 | 1.4987 (12) | C11—H11 | 0.9500 |
C3—C4 | 1.3969 (12) | C12—C13 | 1.3925 (15) |
C3—C8 | 1.4932 (12) | C12—H12 | 0.9500 |
C4—C5 | 1.4185 (12) | C13—C14 | 1.3866 (16) |
C5—C5i | 1.2088 (17) | C13—H13 | 0.9500 |
C7—H7A | 0.9800 | C14—C15 | 1.3931 (13) |
C7—H7B | 0.9800 | C14—H14 | 0.9500 |
C7—H7C | 0.9800 | C15—H15 | 0.9500 |
C6—O1—C9 | 114.55 (7) | H8A—C8—H8B | 109.5 |
C4—N1—C1 | 108.62 (7) | C3—C8—H8C | 109.5 |
C4—N1—H1N | 125.7 (8) | H8A—C8—H8C | 109.5 |
C1—N1—H1N | 125.7 (8) | H8B—C8—H8C | 109.5 |
N1—C1—C2 | 108.70 (7) | O1—C9—C10 | 108.58 (7) |
N1—C1—C6 | 117.66 (7) | O1—C9—H9A | 110.0 |
C2—C1—C6 | 133.63 (7) | C10—C9—H9A | 110.0 |
C1—C2—C3 | 106.71 (7) | O1—C9—H9B | 110.0 |
C1—C2—C7 | 128.81 (8) | C10—C9—H9B | 110.0 |
C3—C2—C7 | 124.47 (8) | H9A—C9—H9B | 108.4 |
C4—C3—C2 | 107.22 (7) | C11—C10—C15 | 119.27 (8) |
C4—C3—C8 | 126.09 (8) | C11—C10—C9 | 121.96 (7) |
C2—C3—C8 | 126.60 (8) | C15—C10—C9 | 118.70 (8) |
N1—C4—C3 | 108.75 (7) | C12—C11—C10 | 120.32 (8) |
N1—C4—C5 | 122.75 (8) | C12—C11—H11 | 119.8 |
C3—C4—C5 | 128.34 (8) | C10—C11—H11 | 119.8 |
C5i—C5—C4 | 175.61 (10) | C11—C12—C13 | 120.22 (9) |
O2—C6—O1 | 122.38 (8) | C11—C12—H12 | 119.9 |
O2—C6—C1 | 123.73 (8) | C13—C12—H12 | 119.9 |
O1—C6—C1 | 113.89 (7) | C14—C13—C12 | 119.58 (9) |
C2—C7—H7A | 109.5 | C14—C13—H13 | 120.2 |
C2—C7—H7B | 109.5 | C12—C13—H13 | 120.2 |
H7A—C7—H7B | 109.5 | C13—C14—C15 | 120.35 (9) |
C2—C7—H7C | 109.5 | C13—C14—H14 | 119.8 |
H7A—C7—H7C | 109.5 | C15—C14—H14 | 119.8 |
H7B—C7—H7C | 109.5 | C14—C15—C10 | 120.22 (9) |
C3—C8—H8A | 109.5 | C14—C15—H15 | 119.9 |
C3—C8—H8B | 109.5 | C10—C15—H15 | 119.9 |
C4—N1—C1—C2 | −0.61 (10) | C9—O1—C6—C1 | 176.08 (7) |
C4—N1—C1—C6 | 178.33 (7) | N1—C1—C6—O2 | 3.67 (13) |
N1—C1—C2—C3 | 0.08 (10) | C2—C1—C6—O2 | −177.72 (9) |
C6—C1—C2—C3 | −178.63 (9) | N1—C1—C6—O1 | −175.51 (7) |
N1—C1—C2—C7 | 179.36 (9) | C2—C1—C6—O1 | 3.10 (14) |
C6—C1—C2—C7 | 0.65 (16) | C6—O1—C9—C10 | −174.76 (7) |
C1—C2—C3—C4 | 0.47 (10) | O1—C9—C10—C11 | 38.88 (11) |
C7—C2—C3—C4 | −178.85 (8) | O1—C9—C10—C15 | −144.09 (8) |
C1—C2—C3—C8 | 177.24 (9) | C15—C10—C11—C12 | −0.68 (14) |
C7—C2—C3—C8 | −2.09 (14) | C9—C10—C11—C12 | 176.33 (9) |
C1—N1—C4—C3 | 0.92 (10) | C10—C11—C12—C13 | −1.15 (14) |
C1—N1—C4—C5 | −174.76 (8) | C11—C12—C13—C14 | 1.62 (16) |
C2—C3—C4—N1 | −0.86 (10) | C12—C13—C14—C15 | −0.25 (16) |
C8—C3—C4—N1 | −177.64 (8) | C13—C14—C15—C10 | −1.59 (16) |
C2—C3—C4—C5 | 174.51 (8) | C11—C10—C15—C14 | 2.04 (14) |
C8—C3—C4—C5 | −2.28 (15) | C9—C10—C15—C14 | −175.07 (9) |
C9—O1—C6—O2 | −3.12 (12) |
Symmetry code: (i) −x+1, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O2ii | 0.875 (14) | 1.987 (14) | 2.8565 (10) | 172.1 (12) |
Symmetry code: (ii) −x+1, −y, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C30H28N2O4 |
Mr | 480.54 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 90 |
a, b, c (Å) | 19.340 (2), 9.8955 (10), 13.8495 (15) |
β (°) | 110.217 (6) |
V (Å3) | 2487.2 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.30 × 0.22 × 0.15 |
Data collection | |
Diffractometer | Nonius KappaCCD (with Oxford Cryostream) |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 28071, 4748, 3948 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.770 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.124, 1.03 |
No. of reflections | 4748 |
No. of parameters | 168 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.46, −0.39 |
Computer programs: COLLECT (Nonius, 2000), DENZO and SCALEPACK (Otwinowski & Minor, 1997), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O2i | 0.875 (14) | 1.987 (14) | 2.8565 (10) | 172.1 (12) |
Symmetry code: (i) −x+1, −y, −z+1. |
Acknowledgements
The purchase of the diffractometer was made possible by grant No. LEQSF(1999–2000)-ENH-TR-13, administered by the Louisiana Board of Regents.
References
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Di(5-benzyloxycarbornyl-3,4-dimethyl-2-pyrrolyl)-ethyne (I) is an important intermediate in the synthesis of porphyrin analogues containing a two-carbon interpyrrolic bridge as in corrphycenes (Vogel, 1996). Compound (I) is also an interesting intermediate in the synthesis of dipyrroles with a two carbon bridge, which have shown selective binding properties to fluoride and other ions (Black et al. 1999). The title compound was prepared via an improved Sonogashira coupling reaction (Chinchilla & Najera, 2007), that took place between benzyl 5-iodo-3,4-dimethyl-1H-pyrrole-2-carboxylate and trimethylsilanyl-ethyne, in the presence of palladium(0) and copper(I) catalysts at room temperature. The exact experimental details are described below.
The structure of the title compound (I), which lies on a crystallographic twofold axis, is shown in Fig 1. The triple-bond distance is 1.2088 (17) Å, and the alkyne bridge is not quite linear, with C4—C5—C5i angle 175.61 (10)° (i = 1 - x, y, 1/2 - z). The pyrrole ring is essentially planar, its five atoms having a mean deviation 0.003 Å from their best plane, with maximum 0.0051 (7) Å for C4. The two pyrrole rings are not coplanar, but form a dihedral angle of 40.49 (4)°. The ester COO group lies nearly in the pyrrole plane, with N1—C1—C6—O2 torsion angle 3.67 (13)°.
The pyrrole N—H group and adjacent ester carbonyl form intermolecular hydrogen bonded rings about inversion centers, having graph-set notation (Etter, 1990) R22(10). Thus, each molecule engages in four hydrogen bonds with two other molecules, forming chains in the [0 0 1] direction, as shown in Fig. 2.