research communications
Ethyl 2-amino-1-(4-fluorophenyl)-5-oxo-4,5-dihydro-1H-pyrrole-3-carboxylate: and Hirshfeld surface analysis
aDepartment of Physics, V.V. Nagar, Anand, Gujarat, India, b103, X-Ray Lab, Department of Physics, V.V. Nagar, Anand, Gujarat, India, and cOrganic Synthesis Laboratory, M. G. Science Institute, Ahmedabad, Gujarat, India
*Correspondence e-mail: chintan.jotaniya@gmail.com
In the title molecule, C12H13FN2O3, the central pyrrole ring makes a dihedral angle of 9.2 (3)° with the ethoxy carbonyl moiety whereas the fluorophenyl ring is rotated by 67.6 (2)° from the pyrrole ring. Supramolecular aggregation is due to off-centric π–π stacking interactions involving screw-related pairs of molecules, which are further connected by N—H⋯O and C—H⋯O interactions, forming a sinusoidal pattern along the [001] direction on the bc plane. Three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint plots confirm the contributions of these interactions.
Keywords: crystal structure; halogen-substituted pyrrole derivative; X-ray crystallography; Hirshfeld surface analysis; hydrogen bonding.
CCDC reference: 1555656
1. Chemical context
Pyrrole, an electron-rich five-membered unsaturated ring, and its derivatives are widely used as intermediates in the synthesis of organic compounds, medicines, pharmaceuticals, agrochemicals, perfumes etc. Its derivatives possess a broad spectrum of biological activities. Substitution by a halogen (Cl, Br, F, I) is known to increase the activities of drug molecules and this group of molecules interact with receptors via halogen bonding. Organofluorine compounds display a variety of pharmacological and agro-chemical properties. Specific halogen-bonding interactions are responsible for the supramolecular architecture in halogen-substituted heterocycles. Bearing in mind the importance of pyrrole and the role of halogens, we have synthesized a series of halogen-substituted pyrrole derivatives. Bromo and methoxy derivatives of the title molecule have been reported earlier (Patel et al., 2012, 2013). As a continuation of these studies, the title molecule, with fluorine as one of the substituents, was synthesized and characterized crystallographically and by Hirshfeld surface analysis.
2. Structural commentary
In the title compound, Fig. 1, the F atom is displaced by 0.014 (3) Å from the phenyl ring, facilitating it in to take part in a number of intermolecular interactions. The heterocyclic five-membered pyrrole ring is essentially planar with a maximum displacement of 0.022 (4) Å for atom C3 from its mean plane. The fluorophenyl ring forms a dihedral angle of 67.6 (2)° whereas the mean plane of ethoxy carbonyl tail is inclined at 9.2 (3)° to the central pyrrole ring. The terminal ethoxy carbonyl chain adopts a zigzag extended conformation, as is usually observed in analogous derivatives, with the carbonyl oxygen atom O19 on the same side as the methyl carbon atom C17 [C17—O16—C15—O19 = 5.0 (7)°] and the ethoxy carbon atom C18 in a trans [C15—O16—C17—C18 = 144.6 (5)°] conformation with respect to the pyrrole ring. Bond lengths in the phenyl ring vary from 1.365 (6) to 1.385 (6) Å and the endocyclic angle varies from 118.0 (4) to 122.9 (4)° with an average value of 120.4 (4)°, which coincides exactly with the theoretical value 120° for sp2 hybridization.
The intramolecular N6—H61⋯O19 hydrogen bond involving the carbonyl oxygen atom O19 leads to the formation of a pseudo-six-membered ring with an S(6) graph-set motif.
3. Supramolecular features
In the crystal, two pairs of screw-related molecules are held together by off-centric π–π stacking interactions involving the pyrrole ring and the phenyl ring of a screw-related molecule (−x, + y, − z) [centroid–centroid distance = 4.179 (2) Å, slippage = 2.036 Å, dihedral angle between planes = 5.9 (2)°], forming chains along [010]. The structure contains infinite zigzag chains of screw-related molecules, forming a sinusoidal patterns along [001] on the bc plane as shown in Fig. 2.
The molecular packing features N—H⋯O interactions, which lead to the formation of chains alon [001], and π–π stacking interactions, which link the molecules along [010]. In addition, C—H1⋯O interactions stack the molecules along [100] (Fig. 2, Table 1).
4. Analysis of the Hirshfeld Surfaces
Crystal Explorer 3.1 (Wolff et al., 2012) was used to generate Hirshfeld surfaces mapped over dnorm, de and electrostatic potential for the title compound. The electrostatic potentials were calculated using TONTO (Spackman et al., 2008; Jayatilaka et al., 2005) as integrated in Crystal Explorer and are mapped on Hirshfeld surfaces using the STO-3G basis set at the Hartree–Fock level of theory over a range ±0.10 au as shown in Fig. 3. The positive electrostatic potential (blue region) over the surface indicates a hydrogen-bond donor, whereas the hydrogen-bond acceptors are represented by negative electrostatic potential (red region). The contact distances di and de from the Hirshfeld surface to the nearest atom inside and outside, respectively, enables the analysis of the intermolecular interactions through the mapping of dnorm.
A view of the Hirshfeld surface mapped over dnorm, shape-index and curvedness for the title compound are shown in Fig. 4. Hirshfeld surfaces marked with red regions in dnorm near atoms O7, O19, N6, H62 and H10 reveal the active participation of the respective atoms in intermolecular interactions. The occurrence of N—H⋯O and C—H⋯O interactions is confirmed by analysis of the Hirshfeld surface. N6—H62⋯O19 interactions are shown on the Hirshfeld surface marked with bright-red dotted lines in Fig. 5. Yellow dotted lines mapped on the dnorm Hirshfeld surface in Fig. 6 reveal the presence of C13—H13⋯O7 and C17—H172⋯O19 interactions.
The two-dimensional fingerprint plots (Rohl et al., 2008) for the title molecule are shown in Fig. 7. The inter atomic H⋯H contacts appear as scattered points over the larger part of the plot along with one distinct spike with the highest contribution within the Hirshfeld surface of 44.9% (Fig. 7b), followed by 20.8% for O⋯H/H⋯O contacts, which appear as pairs of adjacent spikes having almost same length. The contributions of H⋯F/F⋯H and C⋯H/H⋯C contacts are 12.8 and 10.4%, respectively. The contribution of C⋯C contacts, i.e. 3.0%, shows the π–π stacking interactions in the compound have a relatively smaller contribution. Apart from these, C⋯O/O⋯C, C⋯N/N⋯C, O⋯F/F⋯O, O⋯N/N⋯O and C⋯F/F⋯C contacts are found, as summarized in Table 2.
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5. Database survey
Two analogous structures, 2-amino-1(4-bromophenyl)-5-oxo-4,5-dihydro-1H-pyrrole-3-carboxylic acid ethyl ester (Patel et al., 2012) and 2-amino-1-(4-methoxyphenyl)-5-oxo-4,5-dihydro-1H-pyrrole-3-carboxylic acid ethyl ester (Patel et al., 2013), in which the fluorophenyl ring of the title compound is replaced by a bromo or methoxyphenyl ring, are reported in the Cambridge Structural Database (Groom et al., 2016).
6. Synthesis and crystallization
In a 50 ml flat-bottom flask, a mixture of dry toluene (15 ml), potassium hydroxide (0.012 mol, 0.672 g) and 18-crown-6 (0.0005 mol, 0.132 g) were prepared. Ethyl cyanoacetate (0.006 mol, 0.6787 g) was then added to this stirred mixture, followed by the portionwise addition of N-(4-fluorophenyl)-2-chloroacetamide (0.005 mol, 1.2425 g) after 5 min. The stirring was continued until the chloroacetamide derivative had been consumed (20 min), monitored TLC (hexane:ethyl acetate 7:3). On completion of the reaction, water (25 ml) was added to the reaction mixture and stirring continued for a further 5 min. This was then taken into a separating funnel and the aqueous phase was neutralized with glacial acetic acid (pH = 7). The phases were separated and the aqueous phase extracted with toluene (10 ml). The combined organic layers were dried over magnesium sulfate and the toluene removed in vacuo to obtain a solid product. The crude product was crystallized from ethanol to obtain 1.42 g (87% yield) of 2-amino-1-(4-fluorophenyl)-oxo-4,5-dihydro-1H-pyrrole-3-carboxylic acid ethyl ester, m.p. 783.24 K. It is more or less soluble in different solvents such as benzene, ethanol, DMF, DMSO, CH2CL2, CHCl3, ethyl acetate but diffraction quality crystal could be grown by the slow evaporation method at room temperature from ethyl acetate only after repeated trials.
7. details
Crystal data, data collection and structure . Carbon-bound H atoms were placed in their calculated positions (C—H = 0.93–0.97 Å) and are included in the in the riding-model approximation, with Uiso(H) set to 1.2Ueq(C).
details are summarized in Table 3Supporting information
CCDC reference: 1555656
https://doi.org/10.1107/S2056989017011628/ds2246sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017011628/ds2246Isup2.hkl
Data collection: APEX2 (Bruker, 2007); cell
SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: publCIF (Westrip, 2010).C13H13FN2O3 | Dx = 1.372 Mg m−3 |
Mr = 264.25 | Melting point: 783.39 K |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 7696 reflections |
a = 5.5357 (16) Å | θ = 1.5–28.2° |
b = 8.548 (2) Å | µ = 0.11 mm−1 |
c = 27.026 (7) Å | T = 273 K |
V = 1278.9 (6) Å3 | Transparent, colourless |
Z = 4 | 0.7 × 0.3 × 0.2 mm |
F(000) = 552 |
Bruker SMART APEX CCD diffractometer | 2975 independent reflections |
Radiation source: SEALED TUBE | 2322 reflections with I > 2Σ(I) |
Graphite monochromator | Rint = 0.032 |
ω–2θ scan | θmax = 28.2°, θmin = 1.5° |
Absorption correction: multi-scan (SADABS; Bruker, 2007) | h = −7→6 |
Tmin = 0.962, Tmax = 0.979 | k = −10→11 |
7696 measured reflections | l = −34→32 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.075 | H-atom parameters constrained |
wR(F2) = 0.148 | Weighting scheme based on measured s.u.'s |
S = 1.18 | (Δ/σ)max = 0.006 |
2975 reflections | Δρmax = 0.23 e Å−3 |
173 parameters | Δρmin = −0.24 e Å−3 |
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell esds are taken into account in the estimation of distances, angles and torsion angles |
x | y | z | Uiso*/Ueq | ||
F14 | 0.0103 (6) | 0.1908 (3) | 0.41628 (9) | 0.0777 (11) | |
O7 | −0.3466 (5) | 0.3868 (3) | 0.20473 (10) | 0.0501 (9) | |
O16 | 0.0782 (6) | 0.1173 (4) | 0.04855 (10) | 0.0675 (11) | |
O19 | 0.3634 (6) | 0.0024 (4) | 0.09592 (11) | 0.0665 (11) | |
N1 | −0.0226 (5) | 0.2174 (3) | 0.21258 (11) | 0.0380 (9) | |
N6 | 0.3131 (6) | 0.0484 (3) | 0.19821 (11) | 0.0449 (10) | |
C2 | −0.1947 (7) | 0.3016 (4) | 0.18607 (14) | 0.0402 (11) | |
C3 | −0.1510 (8) | 0.2676 (4) | 0.13223 (14) | 0.0457 (12) | |
C4 | 0.0711 (7) | 0.1663 (4) | 0.13244 (13) | 0.0403 (11) | |
C5 | 0.1342 (6) | 0.1388 (4) | 0.18000 (13) | 0.0351 (11) | |
C8 | −0.0114 (6) | 0.2105 (4) | 0.26584 (12) | 0.0345 (11) | |
C9 | 0.1786 (7) | 0.2794 (4) | 0.29063 (14) | 0.0420 (12) | |
C10 | 0.1843 (8) | 0.2732 (5) | 0.34181 (15) | 0.0503 (12) | |
C11 | 0.0017 (8) | 0.1985 (5) | 0.36617 (14) | 0.0490 (14) | |
C12 | −0.1879 (8) | 0.1282 (5) | 0.34218 (15) | 0.0527 (16) | |
C13 | −0.1941 (7) | 0.1362 (4) | 0.29129 (14) | 0.0437 (12) | |
C15 | 0.1869 (8) | 0.0873 (5) | 0.09193 (14) | 0.0473 (12) | |
C17 | 0.1672 (12) | 0.0330 (8) | 0.00528 (17) | 0.094 (2) | |
C18 | −0.0234 (14) | −0.0020 (10) | −0.0268 (2) | 0.134 (4) | |
H9 | 0.30124 | 0.32939 | 0.27321 | 0.0506* | |
H10 | 0.31042 | 0.31912 | 0.35929 | 0.0606* | |
H12 | −0.30851 | 0.07676 | 0.35975 | 0.0630* | |
H13 | −0.32196 | 0.09126 | 0.27406 | 0.0526* | |
H31 | −0.12308 | 0.36342 | 0.11386 | 0.0551* | |
H32 | −0.28713 | 0.21277 | 0.11777 | 0.0551* | |
H61 | 0.40656 | −0.00181 | 0.17837 | 0.0539* | |
H62 | 0.33375 | 0.04110 | 0.22967 | 0.0539* | |
H171 | 0.28599 | 0.09643 | −0.01185 | 0.1126* | |
H172 | 0.24516 | −0.06313 | 0.01573 | 0.1126* | |
H181 | 0.03741 | −0.05787 | −0.05497 | 0.2012* | |
H182 | −0.09846 | 0.09335 | −0.03758 | 0.2012* | |
H183 | −0.14019 | −0.06545 | −0.00986 | 0.2012* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F14 | 0.087 (2) | 0.109 (2) | 0.0371 (14) | 0.006 (2) | −0.0004 (14) | 0.0091 (13) |
O7 | 0.0503 (16) | 0.0487 (14) | 0.0512 (16) | 0.0128 (15) | −0.0068 (14) | −0.0092 (12) |
O16 | 0.071 (2) | 0.098 (2) | 0.0334 (15) | 0.011 (2) | −0.0043 (14) | −0.0106 (16) |
O19 | 0.064 (2) | 0.084 (2) | 0.0516 (18) | 0.017 (2) | 0.0054 (15) | −0.0114 (16) |
N1 | 0.0386 (17) | 0.0400 (15) | 0.0355 (17) | 0.0025 (15) | −0.0067 (14) | 0.0008 (13) |
N6 | 0.0452 (19) | 0.0525 (18) | 0.0371 (17) | 0.0057 (17) | 0.0003 (15) | −0.0050 (14) |
C2 | 0.046 (2) | 0.0337 (18) | 0.041 (2) | 0.0002 (19) | −0.0057 (19) | −0.0048 (16) |
C3 | 0.050 (2) | 0.043 (2) | 0.044 (2) | −0.001 (2) | −0.012 (2) | −0.0030 (17) |
C4 | 0.042 (2) | 0.0419 (19) | 0.037 (2) | 0.0004 (17) | −0.0040 (17) | −0.0021 (17) |
C5 | 0.0337 (19) | 0.0340 (17) | 0.0377 (19) | −0.0045 (16) | −0.0009 (16) | −0.0005 (15) |
C8 | 0.034 (2) | 0.0346 (17) | 0.0349 (19) | 0.0072 (17) | 0.0009 (16) | −0.0007 (14) |
C9 | 0.042 (2) | 0.043 (2) | 0.041 (2) | −0.008 (2) | −0.0008 (18) | 0.0053 (16) |
C10 | 0.045 (2) | 0.057 (2) | 0.049 (2) | 0.000 (2) | −0.012 (2) | −0.0007 (19) |
C11 | 0.057 (3) | 0.059 (2) | 0.031 (2) | 0.010 (2) | 0.000 (2) | 0.0080 (18) |
C12 | 0.045 (2) | 0.062 (3) | 0.051 (3) | −0.001 (2) | 0.011 (2) | 0.011 (2) |
C13 | 0.036 (2) | 0.045 (2) | 0.050 (2) | −0.0025 (19) | −0.0008 (18) | −0.0012 (18) |
C15 | 0.048 (2) | 0.052 (2) | 0.042 (2) | −0.006 (2) | −0.0012 (19) | −0.0025 (18) |
C17 | 0.091 (4) | 0.146 (5) | 0.045 (3) | 0.017 (5) | 0.002 (3) | −0.025 (3) |
C18 | 0.108 (6) | 0.205 (8) | 0.090 (4) | 0.009 (6) | −0.017 (4) | −0.078 (5) |
F14—C11 | 1.357 (5) | C9—C10 | 1.385 (6) |
O7—C2 | 1.221 (5) | C10—C11 | 1.365 (6) |
O16—C15 | 1.343 (5) | C11—C12 | 1.372 (6) |
O16—C17 | 1.459 (6) | C12—C13 | 1.378 (6) |
O19—C15 | 1.222 (6) | C17—C18 | 1.398 (9) |
N1—C2 | 1.393 (5) | C3—H31 | 0.9700 |
N1—C5 | 1.407 (4) | C3—H32 | 0.9700 |
N1—C8 | 1.442 (4) | C9—H9 | 0.9300 |
N6—C5 | 1.349 (5) | C10—H10 | 0.9300 |
C2—C3 | 1.503 (5) | C12—H12 | 0.9300 |
C3—C4 | 1.504 (6) | C13—H13 | 0.9300 |
C4—C5 | 1.353 (5) | C17—H171 | 0.9700 |
C4—C15 | 1.437 (5) | C17—H172 | 0.9700 |
N6—H61 | 0.8600 | C18—H181 | 0.9600 |
N6—H62 | 0.8600 | C18—H182 | 0.9600 |
C8—C13 | 1.378 (5) | C18—H183 | 0.9600 |
C8—C9 | 1.379 (5) | ||
C15—O16—C17 | 117.0 (4) | O16—C15—C4 | 112.1 (4) |
C2—N1—C5 | 110.3 (3) | O19—C15—C4 | 124.7 (4) |
C2—N1—C8 | 124.4 (3) | O16—C17—C18 | 110.4 (5) |
C5—N1—C8 | 125.4 (3) | C2—C3—H31 | 111.00 |
O7—C2—N1 | 124.5 (3) | C2—C3—H32 | 111.00 |
O7—C2—C3 | 128.7 (4) | C4—C3—H31 | 111.00 |
N1—C2—C3 | 106.7 (3) | C4—C3—H32 | 111.00 |
C2—C3—C4 | 103.8 (3) | H31—C3—H32 | 109.00 |
C3—C4—C5 | 108.4 (3) | C8—C9—H9 | 120.00 |
C3—C4—C15 | 129.2 (3) | C10—C9—H9 | 120.00 |
C5—C4—C15 | 121.8 (3) | C9—C10—H10 | 121.00 |
N1—C5—N6 | 119.9 (3) | C11—C10—H10 | 121.00 |
N1—C5—C4 | 110.6 (3) | C11—C12—H12 | 121.00 |
N6—C5—C4 | 129.5 (3) | C13—C12—H12 | 121.00 |
C5—N6—H62 | 120.00 | C8—C13—H13 | 120.00 |
H61—N6—H62 | 120.00 | C12—C13—H13 | 120.00 |
C5—N6—H61 | 120.00 | O16—C17—H171 | 110.00 |
C9—C8—C13 | 120.9 (3) | O16—C17—H172 | 110.00 |
N1—C8—C13 | 119.1 (3) | C18—C17—H171 | 110.00 |
N1—C8—C9 | 120.0 (3) | C18—C17—H172 | 110.00 |
C8—C9—C10 | 119.1 (4) | H171—C17—H172 | 108.00 |
C9—C10—C11 | 118.9 (4) | C17—C18—H181 | 109.00 |
F14—C11—C10 | 118.6 (4) | C17—C18—H182 | 109.00 |
F14—C11—C12 | 118.5 (4) | C17—C18—H183 | 109.00 |
C10—C11—C12 | 122.9 (4) | H181—C18—H182 | 109.00 |
C11—C12—C13 | 118.0 (4) | H181—C18—H183 | 109.00 |
C8—C13—C12 | 120.2 (4) | H182—C18—H183 | 109.00 |
O16—C15—O19 | 123.3 (4) | ||
C17—O16—C15—O19 | 5.0 (7) | C3—C4—C5—N6 | 176.4 (3) |
C17—O16—C15—C4 | −174.9 (4) | C15—C4—C5—N1 | −173.6 (3) |
C15—O16—C17—C18 | 144.6 (5) | C15—C4—C5—N6 | 4.7 (6) |
C5—N1—C2—O7 | −176.3 (3) | C3—C4—C15—O16 | 2.6 (6) |
C8—N1—C2—O7 | 4.7 (5) | C3—C4—C5—N1 | −1.9 (4) |
C5—N1—C2—C3 | 2.9 (4) | C3—C4—C15—O19 | −177.3 (4) |
C5—N1—C8—C9 | 69.1 (4) | C5—C4—C15—O16 | 172.5 (4) |
C2—N1—C8—C13 | 67.1 (4) | C5—C4—C15—O19 | −7.4 (7) |
C5—N1—C8—C13 | −111.7 (4) | N1—C8—C9—C10 | 179.2 (3) |
C2—N1—C5—N6 | −179.2 (3) | C13—C8—C9—C10 | 0.0 (5) |
C8—N1—C5—N6 | −0.2 (5) | N1—C8—C13—C12 | −179.9 (3) |
C2—N1—C5—C4 | −0.7 (4) | C9—C8—C13—C12 | −0.7 (5) |
C8—N1—C5—C4 | 178.3 (3) | C8—C9—C10—C11 | 0.2 (6) |
C2—N1—C8—C9 | −112.1 (4) | C9—C10—C11—C12 | 0.3 (7) |
C8—N1—C2—C3 | −176.1 (3) | C9—C10—C11—F14 | 179.0 (4) |
O7—C2—C3—C4 | 175.4 (4) | F14—C11—C12—C13 | −179.7 (4) |
N1—C2—C3—C4 | −3.8 (4) | C10—C11—C12—C13 | −1.0 (7) |
C2—C3—C4—C5 | 3.5 (4) | C11—C12—C13—C8 | 1.2 (6) |
C2—C3—C4—C15 | 174.4 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H61···O19 | 0.86 | 2.2400 | 2.806 (4) | 123 |
N6—H62···O7i | 0.86 | 2.2100 | 2.970 (4) | 147 |
C13—H13···O7ii | 0.93 | 2.6000 | 3.320 (5) | 135 |
C17—H172···O19 | 0.97 | 2.3300 | 2.692 (6) | 101 |
Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x−1, y−1/2, −z+1/2. |
Type of contact | Contribution |
H···H | 44.9 |
O···H/H···O | 20.8 |
H···F/F···H | 12.8 |
C···H/H···C | 10.4 |
C···C | 3.4 |
C···O/O···C | 3.0 |
C···N/N···C | 1.8 |
O···F/F···O | 1.0 |
O···N/N···O | 0.6 |
C···F/F···C | 0.5 |
Acknowledgements
The authors are thankful to the Department of Physics, SPU, for providing the financial support to carry out the work and also to CSMCRI, Bhavnagar, for the data collection.
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