Crystal structure and Hirshfeld surface analysis of (2E)-1-phenyl-3-(1H-pyrrol-2-yl)propen-1-one

Safarova, A.S.; Khalilov, A.N.; Akkurt, M.; Maharramov, A.M.; Bhattarai, A.; Naghiyev, F.N.; Mamedov, İ.G.

doi:10.1107/S2056989024000495

research communications

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ISSN: 2056-9890

Volume 80| Part 2| February 2024| Pages 191-195

https://doi.org/10.1107/S2056989024000495

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Crystal structure and Hirshfeld surface analysis of (2E)-1-phenyl-3-(1H-pyrrol-2-yl)propen-1-one

Ayten S. Safarova,^a Ali N. Khalilov,^b,^a Mehmet Akkurt,^c Abel M. Maharramov,^a Ajaya Bhattarai,^d ^* Farid N. Naghiyev ^a and İbrahim G. Mamedov ^a

^aDepartment of Chemistry, Baku State University, Z. Khalilov str. 23, AZ1148, Baku, Azerbaijan, ^b`Composite Materials' Scientific Research Center, Azerbaijan State Economic University (UNEC), H. Aliyev str. 135, AZ1063, Baku, Azerbaijan, ^cDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye, and ^dDepartment of Chemistry, M.M.A.M.C. (Tribhuvan University) Biratnagar, Nepal
^*Correspondence e-mail: ajaya.bhattarai@mmamc.tu.edu.np

Edited by B. Therrien, University of Neuchâtel, Switzerland (Received 3 January 2024; accepted 12 January 2024; online 26 January 2024)

The title compound, C₁₃H₁₁NO, adopts an E configuration about the C=C double bond. The pyrrole ring is inclined to the phenyl ring at an angle of 44.94 (8)°. In the crystal, molecules are linked by N—H⋯O hydrogen bonds, forming ribbons parallel to (020) in zigzag C(7) chains along the a axis. These ribbons are connected via C—H⋯π interactions, forming a three-dimensional network. No significant π–π interactions are observed.

Keywords: crystal structure; 1H-pyrrole ring; hydrogen bond; chalcone; Hirshfeld surface analysis.

CCDC reference: 2321201

1. Chemical context

The chemistry of carbo- and heterocyclic aromatic compounds is the most important branch of organic chemistry (Khalilov et al., 2022 ; Akkurt et al., 2023 ). Synthetic organic chemistry is growing tremendously, with recently developed aromatic systems that are designed for various research and commercial purposes (Maharramov et al., 2021 , 2022 ; Erenler et al., 2022 ). Nowadays, five- and six-membered heterocyclic systems find broad applications in different branches of chemistry, as well as coordination chemistry (Gurbanov et al., 2021 ; Mahmoudi et al., 2021 ), drug design and development (Donmez & Turkyılmaz, 2022 ; Askerova, 2022 ), and materials science (Velásquez et al., 2019 ; Afkhami et al., 2019 ). The pyrrole motif is the most widespread five-membered heteroaromatic ring system in nitrogen heterocycles (Mahmoudi et al., 2017 ). It is an essential structural motif present in many natural tetrapyrrole scaffolds of heme and related cofactors (chlorophyll a, heme b, vitamin B12 and factor 430), and other bioactive molecules, like porphobilinogen, nargenicin, prodigiosin, etc. (Walsh et al., 2006 ; Sobhi & Faisal, 2023 ). Chalcones incorporating N-heterocyclic, especially pyrrole, scaffolds with various biological and pharmacological activities, such as antioxidant, antibacterial, antifungal, antileishmanial, anticancer, antitubercular, antimalarial and other properties, have been reviewed recently (Mezgebe et al., 2023 ). In addition, the incorporation of diverse pharmacophore groups in a pyrrole scaffold has led to the development of more desired compounds, such as elopiprazole, lorpiprazole, isamoltane, obatoclax, etc. (Bhardwaj et al., 2015 ; Atalay et al., 2022 ). Thus, in the framework of our studies in heterocyclic chemistry (Naghiyev et al., 2020 , 2021 , 2022 ), we report herein the crystal structure and Hirshfeld surface analysis of the title compound, (2E)-1-phenyl-3-(1H-pyrrol-2-yl)propen-1-one.

2. Structural commentary

The title compound (Fig. 1) shows an E configuration about the C=C double bond. The pyrrole ring (atoms N1/C10–C13) is inclined to the phenyl ring (C1–C6) by 44.94 (8)°, the torsion angles being C5—C6—C7—C8 = −156.04 (13)°, C5—C6—C7—O1 = 22.6 (2)°, C6—C7—C8—C9 = −163.76 (13)°, C7—C8—C9—C10 = −172.34 (13)°, O1—C7—C8—C9 = 17.6 (2)° and C8—C9—C10—C11 = 173.37 (14)°. The geometrical parameters of the the title compound are in agreement with those reported for similar compounds; see the Database survey section.

Figure 1
The molecular structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

3. Supramolecular features and Hirshfeld surface analysis

In the crystal, molecules are linked by N—H⋯O hydrogen bonds, forming ribbons parallel to (020) in zigzag C(7) chains along the a axis (Bernstein et al., 1995 ; Table 1 and Fig. 2). These ribbons are connected via C—H⋯π interactions, forming a three-dimensional network (Table 1 and Fig. 3). No significant π–π interactions are observed.

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the phenyl (C1–C6) and 1H-pyrrole (N1/C10–C13) rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯O1ⁱ	0.872 (17)	2.119 (17)	2.9561 (18)	160.7 (14)
C2—H2⋯Cg1ⁱⁱ	0.93	2.82	3.450 (2)	126
C5—H5⋯Cg1ⁱⁱⁱ	0.93	2.91	3.5233 (19)	124
C9—H9⋯Cg2^iv	0.93	3.00	3.6207 (18)	126
C13—H13⋯Cg2^v	0.93	2.95	3.593 (2)	127
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

Figure 2
View of the N—H⋯O hydrogen bonds of the title compound down the b axis.

Figure 3
View of the C—H⋯π interactions of the title compound in the unit cell.

The Hirshfeld surfaces of the title molecule and the two-dimensional fingerprints were computed with CrystalExplorer17.5 (Spackman et al., 2021 ). The d_norm mappings for the title compound were performed in the range from −0.4746 (red) to +1.2616 (blue) a.u. On the d_norm surfaces, bright-red spots indicate the locations of the N—H⋯O interactions [Table 1 and Figs. 4(a) and 4(b)].

Figure 4
(a) Front and (b) back sides of the three-dimensional Hirshfeld surface of the title compound mapped over d_norm, with a fixed colour scale of −0.4746 to +1.2616 a.u.

The fingerprint plots (Fig. 5) reveal that while H⋯H interactions [Fig. 5(b); 48.4%] make the largest contributions to the surface contacts (Table 1), C⋯H/H⋯C [Fig. 5(c); 31.7%] and O⋯H/H⋯O [Fig. 5(d); 11.3%] contacts are also important. Other less notable interactions are C⋯C (3.7%), N⋯H/H⋯N (3.1%) and O⋯C/C⋯O (1.8%).

Figure 5
The two-dimensional fingerprint plots of the title compound, showing (a) all interactions, and delineated into (b) H⋯H, (c) C⋯H/H⋯C and (d) O⋯H/H⋯O interactions.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.43, last update November 2022; Groom et al., 2016 ) for the `(2E)-1-phenyl-3-(1H-pyrrol-2-yl)prop-2-en-1-one' skeleton of the title compound yielded two hits, namely, 1-(3-chlorophenyl)-3-(3-furyl)prop-2-en-1-one (CSD refcode NUQFOW; Zingales et al., 2015 ) and (E)-3-(2-furyl)-1-phenylprop-2-en-1-one (NOTCUW01; Vázquez-Vuelvas et al., 2015 ). When the positions of the pyrrole and phenyl rings are switched, additional hits are found, namely, 1-(2,4-dimethylfuran-3-yl)-3-phenylprop-2-en-1-one (MISXUL; Khalilov et al., 2023 ), 1-(3-furyl)-3-[3-(trifluoromethyl)phenyl]prop-2-en-1-one (KUDNAA; Bákowicz et al., 2015 ) and (2E)-3-(4-chlorophenyl)-1-(1H-pyrrol-2-yl)prop-2-en-1-one (XIYYOU; Bukhari et al., 2008 ).

In the crystal of NUQFOW, molecules stack along the a axis; however, there are no significant intermolecular interactions present. In the crystal of NOTCUW01, molecules are connected by weak C—H⋯O hydrogen bonds and C—H⋯π interactions, forming ribbons extending along the c axis. In the crystal of MISXUL, pairs of molecules are linked by C—H⋯O hydrogen bonds, forming dimers with R₂²(14) ring motifs. The molecules are connected via C—H⋯π interactions, forming a three-dimensional network. No π–π interactions are observed. In KUDNAA, molecules are linked by intermolecular C—H⋯O interactions, forming zigzag chains with C(5) motifs along the b axis. In addition, molecules are connected by face-to-face π–π stacking interactions [centroid–centroid distances = 3.926 (3) and 3.925 (2) Å] between the opposing benzene and furan rings of the molecules along the c axis. In XIYYOU, intermolecular N—H⋯O hydrogen bonds link the molecules into centrosymmetric R₂²(10) dimers. There are C—H⋯π interactions between the benzene and pyrrole rings and a benzene C—H group. A weak π–π interaction between the pyrrole rings [centroid–centroid distance = 3.8515 (11) Å] further stabilizes the structure. There is also a π-interaction between the pyrrole ring and the carbonyl group, with an O⋯π distance of 3.4825 (18) Å.

5. Synthesis and crystallization

The title compound was synthesized according to a recently reported procedure (Li et al., 2022 ), and colourless crystals were obtained upon recrystallization from an ethanol/water (3:1 v/v) solution.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The C-bound H atoms were placed in calculated positions (0.93 Å) and refined as riding atoms with U_iso(H) = 1.2U_eq(C). The N-bound H atom was located in a difference map and refined with U_iso(H) = 1.2U_eq(N). Three reflections (001, 010 and 020) were omitted in the final cycles of refinement.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₁NO
M_r	197.23
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	293
a, b, c (Å)	5.7855 (16), 7.3347 (19), 12.424 (3)
α, β, γ (°)	106.519 (8), 91.912 (9), 92.326 (9)
V (Å³)	504.5 (2)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.08
Crystal size (mm)	0.12 × 0.11 × 0.10

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.688, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	18072, 2535, 1908
R_int	0.042
(sin θ/λ)_max (Å⁻¹)	0.673

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.108, 1.06
No. of reflections	2535
No. of parameters	139
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.16
Computer programs: APEX2 and SAINT (Bruker, 2007 ), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012 ) and PLATON (Spek, 2020 ).

Supporting information

CCDC reference: 2321201

Crystal structure: contains datablock global. DOI: https://doi.org/10.1107/S2056989024000495/tx2080sup1.cif

Supporting information file. DOI: https://doi.org/10.1107/S2056989024000495/tx2080globalsup2.cml

checkCIF report

Computing details top

(2E)-1-Phenyl-3-(1H-pyrrol-2-yl)propen-1-one top

Crystal data top

C₁₃H₁₁NO	Z = 2
M_r = 197.23	F(000) = 208
Triclinic, P1	D_x = 1.298 Mg m⁻³
a = 5.7855 (16) Å	Mo Kα radiation, λ = 0.71073 Å
b = 7.3347 (19) Å	Cell parameters from 5813 reflections
c = 12.424 (3) Å	θ = 2.9–27.4°
α = 106.519 (8)°	µ = 0.08 mm⁻¹
β = 91.912 (9)°	T = 293 K
γ = 92.326 (9)°	Block, colorless
V = 504.5 (2) Å³	0.12 × 0.11 × 0.10 mm

Data collection top

Bruker APEXII CCD diffractometer	1908 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.042
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 28.6°, θ_min = 2.9°
T_min = 0.688, T_max = 0.746	h = −7→7
18072 measured reflections	k = −9→9
2535 independent reflections	l = −16→16

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.049	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.108	w = 1/[σ²(F_o²) + (0.0348P)² + 0.1277P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max < 0.001
2535 reflections	Δρ_max = 0.18 e Å⁻³
139 parameters	Δρ_min = −0.15 e Å⁻³

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.2761 (2)	0.1954 (2)	0.68844 (12)	0.0384 (3)
H1	0.152580	0.148144	0.636826	0.046*
C2	0.2561 (3)	0.1996 (2)	0.79934 (13)	0.0454 (4)
H2	0.120202	0.152611	0.822105	0.055*
C3	0.4365 (3)	0.2729 (2)	0.87637 (13)	0.0482 (4)
H3	0.421898	0.276227	0.951211	0.058*
C4	0.6386 (3)	0.3416 (2)	0.84307 (13)	0.0455 (4)
H4	0.759276	0.393419	0.895615	0.055*
C5	0.6619 (2)	0.3335 (2)	0.73212 (12)	0.0378 (3)
H5	0.800320	0.376468	0.709453	0.045*
C6	0.4805 (2)	0.26175 (18)	0.65370 (11)	0.0324 (3)
C7	0.5128 (2)	0.25283 (19)	0.53401 (11)	0.0354 (3)
C8	0.3085 (2)	0.2513 (2)	0.46122 (12)	0.0383 (3)
H8	0.168759	0.287979	0.493566	0.046*
C9	0.3176 (2)	0.19850 (19)	0.34947 (11)	0.0357 (3)
H9	0.455504	0.148284	0.321134	0.043*
C10	0.1436 (2)	0.20911 (19)	0.26803 (11)	0.0335 (3)
C11	0.1590 (3)	0.1715 (2)	0.15357 (12)	0.0407 (4)
H11	0.283975	0.120383	0.112231	0.049*
C12	−0.0454 (3)	0.2235 (2)	0.11041 (13)	0.0457 (4)
H12	−0.081206	0.214416	0.035462	0.055*
C13	−0.1829 (3)	0.2901 (2)	0.19837 (13)	0.0436 (4)
H13	−0.330437	0.334068	0.193755	0.052*
N1	−0.0693 (2)	0.28171 (17)	0.29363 (10)	0.0386 (3)
H1N	−0.130 (3)	0.302 (2)	0.3590 (14)	0.046*
O1	0.70997 (17)	0.25046 (16)	0.49928 (8)	0.0496 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0329 (7)	0.0410 (8)	0.0402 (8)	−0.0001 (6)	0.0026 (6)	0.0099 (6)
C2	0.0437 (9)	0.0482 (9)	0.0484 (9)	0.0010 (7)	0.0145 (7)	0.0190 (7)
C3	0.0613 (10)	0.0526 (9)	0.0349 (8)	0.0068 (8)	0.0081 (7)	0.0181 (7)
C4	0.0467 (9)	0.0493 (9)	0.0391 (9)	0.0005 (7)	−0.0068 (7)	0.0115 (7)
C5	0.0338 (7)	0.0404 (8)	0.0402 (8)	0.0016 (6)	0.0029 (6)	0.0128 (6)
C6	0.0320 (7)	0.0324 (7)	0.0331 (7)	0.0059 (5)	0.0044 (6)	0.0089 (5)
C7	0.0335 (7)	0.0379 (7)	0.0349 (7)	0.0053 (6)	0.0059 (6)	0.0096 (6)
C8	0.0315 (7)	0.0474 (8)	0.0371 (8)	0.0078 (6)	0.0052 (6)	0.0127 (6)
C9	0.0328 (7)	0.0373 (7)	0.0380 (8)	0.0013 (6)	0.0052 (6)	0.0120 (6)
C10	0.0320 (7)	0.0354 (7)	0.0334 (7)	−0.0009 (5)	0.0025 (6)	0.0109 (6)
C11	0.0412 (8)	0.0464 (8)	0.0344 (8)	−0.0019 (6)	0.0062 (6)	0.0115 (6)
C12	0.0521 (10)	0.0540 (9)	0.0333 (8)	−0.0052 (7)	−0.0036 (7)	0.0179 (7)
C13	0.0364 (8)	0.0502 (9)	0.0479 (9)	0.0019 (7)	−0.0054 (7)	0.0207 (7)
N1	0.0360 (7)	0.0472 (7)	0.0338 (7)	0.0031 (5)	0.0048 (5)	0.0129 (5)
O1	0.0330 (6)	0.0771 (8)	0.0403 (6)	0.0057 (5)	0.0088 (5)	0.0181 (5)

Geometric parameters (Å, º) top

C1—C2	1.378 (2)	C8—C9	1.3346 (19)
C1—C6	1.3886 (19)	C8—H8	0.9300
C1—H1	0.9300	C9—C10	1.4237 (19)
C2—C3	1.375 (2)	C9—H9	0.9300
C2—H2	0.9300	C10—N1	1.3728 (18)
C3—C4	1.377 (2)	C10—C11	1.3761 (19)
C3—H3	0.9300	C11—C12	1.394 (2)
C4—C5	1.374 (2)	C11—H11	0.9300
C4—H4	0.9300	C12—C13	1.361 (2)
C5—C6	1.3867 (19)	C12—H12	0.9300
C5—H5	0.9300	C13—N1	1.3526 (18)
C6—C7	1.4882 (19)	C13—H13	0.9300
C7—O1	1.2318 (16)	N1—H1N	0.871 (16)
C7—C8	1.462 (2)

C2—C1—C6	120.07 (14)	C9—C8—C7	121.56 (13)
C2—C1—H1	120.0	C9—C8—H8	119.2
C6—C1—H1	120.0	C7—C8—H8	119.2
C3—C2—C1	120.16 (14)	C8—C9—C10	128.38 (13)
C3—C2—H2	119.9	C8—C9—H9	115.8
C1—C2—H2	119.9	C10—C9—H9	115.8
C2—C3—C4	120.20 (14)	N1—C10—C11	106.72 (12)
C2—C3—H3	119.9	N1—C10—C9	124.28 (12)
C4—C3—H3	119.9	C11—C10—C9	128.65 (13)
C5—C4—C3	119.93 (14)	C10—C11—C12	108.08 (13)
C5—C4—H4	120.0	C10—C11—H11	126.0
C3—C4—H4	120.0	C12—C11—H11	126.0
C4—C5—C6	120.48 (13)	C13—C12—C11	107.23 (13)
C4—C5—H5	119.8	C13—C12—H12	126.4
C6—C5—H5	119.8	C11—C12—H12	126.4
C5—C6—C1	119.12 (13)	N1—C13—C12	108.61 (14)
C5—C6—C7	119.03 (12)	N1—C13—H13	125.7
C1—C6—C7	121.83 (12)	C12—C13—H13	125.7
O1—C7—C8	121.73 (13)	C13—N1—C10	109.35 (12)
O1—C7—C6	119.52 (13)	C13—N1—H1N	125.1 (10)
C8—C7—C6	118.74 (12)	C10—N1—H1N	124.9 (10)

C6—C1—C2—C3	1.3 (2)	O1—C7—C8—C9	17.6 (2)
C1—C2—C3—C4	−0.4 (2)	C6—C7—C8—C9	−163.76 (13)
C2—C3—C4—C5	−1.2 (2)	C7—C8—C9—C10	−172.34 (13)
C3—C4—C5—C6	1.9 (2)	C8—C9—C10—N1	1.1 (2)
C4—C5—C6—C1	−1.0 (2)	C8—C9—C10—C11	173.37 (14)
C4—C5—C6—C7	−179.23 (12)	N1—C10—C11—C12	0.50 (16)
C2—C1—C6—C5	−0.7 (2)	C9—C10—C11—C12	−172.82 (13)
C2—C1—C6—C7	177.54 (13)	C10—C11—C12—C13	−0.54 (17)
C5—C6—C7—O1	22.6 (2)	C11—C12—C13—N1	0.37 (17)
C1—C6—C7—O1	−155.56 (14)	C12—C13—N1—C10	−0.06 (16)
C5—C6—C7—C8	−156.04 (13)	C11—C10—N1—C13	−0.27 (15)
C1—C6—C7—C8	25.76 (19)	C9—C10—N1—C13	173.41 (13)

Hydrogen-bond geometry (Å, º) top

Cg1 and Cg2 are the centroids of the (C1–C6) phenyl and (N1/C10–C13) 1H-pyrrole rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O1ⁱ	0.872 (17)	2.119 (17)	2.9561 (18)	160.7 (14)
C2—H2···Cg1ⁱⁱ	0.93	2.82	3.450 (2)	126
C5—H5···Cg1ⁱⁱⁱ	0.93	2.91	3.5233 (19)	124
C9—H9···Cg2^iv	0.93	3.00	3.6207 (18)	126
C13—H13···Cg2^v	0.93	2.95	3.593 (2)	127

Symmetry codes: (i) x−1, y, z; (ii) −x, −y, −z+1; (iii) −x+1, −y+1, −z+1; (iv) −x+1, −y, −z+1; (v) −x, −y+1, −z+1.

Acknowledgements

The contributions of the authors are as follows: conceptualization, IGM, ANK and AMM; methodology, IB and MA; investigation, ASA and FNN; writing (original draft), MA, AB and ANK; writing (review and editing of the manuscript), MA and ANK; visualization, MA, IGM and FNN; funding acquisition, ASA, AB and FNN; resources, AB, ASA and MA; supervision, MA and ANK.

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Volume 80| Part 2| February 2024| Pages 191-195

https://doi.org/10.1107/S2056989024000495

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structure and Hirshfeld surface analysis of (2E)-1-phenyl-3-(1H-pyrrol-2-yl)propen-1-one

1. Chemical context

2. Structural commentary

3. Supra­molecular features and Hirshfeld surface analysis

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

References

research communications

3. Supramolecular features and Hirshfeld surface analysis