(Z)-1-Benzoyl-5-benzyl­idene-2-hydroxy-4-oxo-4,5-di­hydro-1H-pyrrole-3-carbo­nitrile

Onami, Y.; Siddaraju, B.P.; Anilkumar, H.G.; Yathirajan, H.S.; Haraguchi, T.; Akitsu, T.

doi:10.1107/S2414314619002207

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 4| Part 2| February 2019| x190220

https://doi.org/10.1107/S2414314619002207

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(Z)-1-Benzoyl-5-benzylidene-2-hydroxy-4-oxo-4,5-dihydro-1H-pyrrole-3-carbonitrile

Yuika Onami,^a Budanur P. Siddaraju,^b Haleyur G. Anilkumar,^c Hemmige S. Yathirajan,^d Tomoyuki Haraguchi ^a and Takashiro Akitsu ^a ^*

^aDepartment of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan, ^bDepartment of Chemistry, Cauvery Institute of Technology, Mandya-571402, India, ^cDepartment of Chemistry, PESIT University, Bangalore-560085, India, and ^dDepartment of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore-570 006, India
^*Correspondence e-mail: akitsu2@rs.tus.ac.jp

Edited by E. V. Boldyreva, Russian Academy of Sciences, Russia (Received 29 January 2019; accepted 11 February 2019; online 22 February 2019)

The title compound, C₁₉H₁₂N₂O₃, obtained as an intermediate in the synthesis of a pyrrole derivative, is composed of a five-membered heterocycle with substituted groups via double or triple bonds as well as single bonds, without an asymmetric carbon atom. An intramolecular O—H⋯O link occurs. In the crystal, O—H⋯N hydrogen bonds link the molecules.

Keywords: crystal structure; pyrrole; heterocycle; phenyl group; chiral crystallization.

CCDC reference: 1896436

Structure description

Pyrrole is widely known as a biologically active scaffold, which possesses a diverse nature of activities (Tzankova et al., 2018 ). Pyrrole derivatives are biologically active and attract attention for the synthesis of new medicinal products (Guo et al., 2015 ); Mokrov et al., 2015 ). Here we report the crystal structure of (Z)-1-benzoyl-5-benzylidene-2-hydroxy-4-oxo-4,5-dihydro-1H-pyrrole-3-carbonitrile, which crystallizes in a chiral space group despite there being no apparent chiral moiety in the molecule (Koshima & Matsuura, 1998 ; Matsuura & Koshima, 2005 ).

The molecular structure of the title compound (Fig. 1) is composed of a planar [maximum deviation of 0.051 (3) Å for atom C12] five-membered (N1/C8/C9/C11/C12) pyrrole ring in the usual geometry (Gainsford et al., 2013 ) and two phenyl rings (C1–C6 and C14–19) arranged approximately parallel to each other [dihedral angle = 15.2 (2)°; torsion angles N1—C12—C13—C14 = 2.9 (6) and C12—N1—C7—C6 = 23.0 (5)°]. Pyrroles can incorporate various types of substituent groups (Sun et al., 2014 ; Polindara-García & Miranda, 2012 ) and in this compound all five atoms in the pyrrole ring are substituted. An intramolecular hydrogen bond (O2—H2⋯O1; Table 1) is observed.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯O1	0.82	2.10	2.769 (4)	138
O2—H2⋯N2ⁱ	0.82	2.52	3.074 (5)	126
Symmetry code: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ .

Figure 1
The title compound with 50% probability ellipsoids for non-hydrogen atoms.

In the crystal, O2—H2⋯N2ⁱ hydrogen bonds (Fig. 2 and Table 1) link the molecules. In addition, the almost planar moieties of the molecules, namely the phenyl and pyrrole rings, afford a helical step-like conformation with neighboring molecules aligned along the b-axis direction (Fig. 3).

Figure 2
Arrangement of molecules along the b-axis direction.

Figure 3
Hydrogen bonds (dashed lines) in the title structure.

A similar compound 4-methyl-5-(4-nitrobenzylidene)-2-oxo-2,5-dihydro-1H-pyrrole-3-carbonitrile (Gainsford et al., 2013) has already been reported and has a similar structure to the title compound. Narasegowda et al. (2005 ) reported a case of chiral crystallization in space group P2₁2₁2₁, the same space group as the title compound. In contrast, our recent examples of chiral crystals composed of achiral molecules both crystallize in space group P2₁ (Yagi et al., 2018 ; Yamazaki et al., 2018 ). To the best of our knowledge, this is the first crystal structure reported for chiral crystallization of a pyrrole of this type.

Synthesis and crystallization

The title compound was obtained as an intermediate in the synthesis of pyrrole derivatives, namely treatment of 1-acetyl-2-amino-4-oxo-4,5-dihydro-1H-pyrrole-3-carbonitrile, benzaldehyde and benzoyl chloride. X-ray quality crystals were obtained from slow evaporation of a methanol solution.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. Since it is very difficult to determine the absolute structure reliably with Mo radiation, the choice of the absolute structure is arbitrary.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₉H₁₂N₂O₃
M_r	316.31
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	296
a, b, c (Å)	10.432 (2), 11.297 (2), 12.688 (2)
V (Å³)	1495.3 (5)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.10
Crystal size (mm)	0.58 × 0.27 × 0.17

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2001 )
T_min, T_max	0.55, 0.97
No. of measured, independent and observed [I > 2σ(I)] reflections	8161, 3341, 3139
R_int	0.085
(sin θ/λ)_max (Å⁻¹)	0.651

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.071, 0.173, 1.08
No. of reflections	3341
No. of parameters	218
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.41, −0.46
Computer programs: APEX2 and SAINT (Bruker, 2014 ), SHELXT2014 (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012 ), Mercury (Macrae et al., 2008 ), SHELXTL (Sheldrick, 2008 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1896436

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314619002207/eb4001sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314619002207/eb4001Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314619002207/eb4001Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and publCIF (Westrip, 2010).

(Z)-1-benzoyl-5-benzylidene-2-hydroxy-4-oxo-4,5-dihydro-1H-pyrrole-3-carbonitrile top

Crystal data top

C₁₉H₁₂N₂O₃	D_x = 1.405 Mg m⁻³
M_r = 316.31	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 5372 reflections
a = 10.432 (2) Å	θ = 2.4–27.5°
b = 11.297 (2) Å	µ = 0.10 mm⁻¹
c = 12.688 (2) Å	T = 296 K
V = 1495.3 (5) Å³	Prism, yellow
Z = 4	0.58 × 0.27 × 0.17 mm
F(000) = 656

Data collection top

Bruker APEXII CCD diffractometer	3341 independent reflections
Radiation source: fine-focus sealed tube	3139 reflections with I > 2σ(I)
Detector resolution: 8.3333 pixels mm^-1	R_int = 0.085
φ and ω scans	θ_max = 27.6°, θ_min = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −13→8
T_min = 0.55, T_max = 0.97	k = −14→13
8161 measured reflections	l = −16→16

Refinement top

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)] = 0.071	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.173	H-atom parameters constrained
S = 1.08	w = 1/[σ²(F_o²) + (0.0946P)² + 0.6486P] where P = (F_o² + 2F_c²)/3
3341 reflections	(Δ/σ)_max < 0.001
218 parameters	Δρ_max = 0.41 e Å⁻³
0 restraints	Δρ_min = −0.46 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.

Refinement. All H atoms were located on difference Fourier maps. The C-bound H atoms were constrained using a riding model [C—H = 0.95 Å and U_iso(H) = 1.2U_eq(C) for aromatic H atoms, C—H = 0.98 Å and U_iso(H) = 1.5U_eq(C) for the methyl H atom] The N-bound H atoms were constrained using a riding model [O—H = 0.82 Å and U_iso(H) = 1.2U_eq(O) for amine H atoms]

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.3806 (2)	0.7264 (2)	0.58946 (17)	0.0230 (5)
O3	0.7778 (2)	0.5105 (3)	0.84556 (18)	0.0268 (6)
O2	0.6352 (3)	0.7026 (3)	0.5317 (2)	0.0357 (7)
H2	0.5601	0.7133	0.5151	0.054*
N1	0.5311 (3)	0.6322 (3)	0.6886 (2)	0.0179 (6)
N2	0.9763 (3)	0.6243 (3)	0.6021 (2)	0.0299 (7)
C7	0.4168 (3)	0.6986 (3)	0.6766 (2)	0.0177 (7)
C11	0.7122 (3)	0.5563 (3)	0.7764 (2)	0.0191 (7)
C12	0.5681 (3)	0.5634 (3)	0.7786 (2)	0.0176 (6)
C9	0.7491 (3)	0.6073 (3)	0.6772 (3)	0.0194 (7)
C6	0.3488 (3)	0.7375 (3)	0.7744 (2)	0.0184 (6)
C8	0.6403 (3)	0.6502 (3)	0.6251 (2)	0.0173 (6)
C14	0.3553 (3)	0.4793 (3)	0.8357 (3)	0.0209 (7)
C13	0.4949 (3)	0.5000 (3)	0.8427 (2)	0.0192 (7)
H13	0.5366	0.4641	0.8991	0.023*
C10	0.8740 (3)	0.6158 (3)	0.6366 (2)	0.0208 (7)
C1	0.4160 (4)	0.7778 (3)	0.8625 (3)	0.0223 (7)
H1	0.5051	0.7748	0.8639	0.027*
C5	0.2156 (3)	0.7417 (3)	0.7713 (3)	0.0238 (7)
H5	0.1715	0.7168	0.7116	0.029*
C15	0.2784 (4)	0.4872 (4)	0.9260 (3)	0.0263 (8)
H15	0.3152	0.5032	0.9912	0.032*
C19	0.2982 (4)	0.4502 (3)	0.7397 (3)	0.0251 (7)
H19	0.3486	0.4436	0.6796	0.03*
C4	0.1494 (4)	0.7839 (4)	0.8589 (3)	0.0305 (9)
H4	0.0602	0.7845	0.8587	0.037*
C18	0.1670 (4)	0.4310 (4)	0.7329 (3)	0.0320 (9)
H18	0.1304	0.4099	0.6688	0.038*
C16	0.1462 (4)	0.4711 (4)	0.9175 (3)	0.0321 (9)
H16	0.0952	0.4791	0.9771	0.039*
C2	0.3483 (4)	0.8226 (4)	0.9484 (3)	0.0317 (9)
H2A	0.3923	0.8509	1.0069	0.038*
C17	0.0900 (4)	0.4435 (4)	0.8225 (3)	0.0340 (9)
H17	0.0017	0.4333	0.8179	0.041*
C3	0.2154 (5)	0.8251 (4)	0.9467 (3)	0.0351 (9)
H3	0.1704	0.8543	1.0043	0.042*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0245 (12)	0.0301 (13)	0.0143 (11)	0.0031 (11)	−0.0006 (9)	0.0009 (10)
O3	0.0228 (12)	0.0379 (15)	0.0197 (11)	0.0048 (12)	−0.0034 (9)	0.0032 (11)
O2	0.0334 (15)	0.0454 (18)	0.0284 (14)	0.0018 (15)	0.0022 (12)	0.0046 (13)
N1	0.0189 (14)	0.0198 (13)	0.0150 (13)	0.0002 (12)	0.0016 (9)	0.0027 (11)
N2	0.0217 (15)	0.0419 (19)	0.0261 (15)	0.0021 (15)	0.0026 (12)	0.0079 (15)
C7	0.0208 (16)	0.0175 (14)	0.0147 (14)	−0.0004 (13)	0.0002 (11)	−0.0002 (12)
C11	0.0195 (15)	0.0215 (15)	0.0162 (15)	0.0009 (13)	−0.0010 (12)	−0.0024 (12)
C12	0.0190 (15)	0.0194 (15)	0.0144 (14)	0.0037 (13)	−0.0016 (11)	−0.0011 (12)
C9	0.0185 (16)	0.0221 (16)	0.0178 (15)	0.0008 (13)	0.0001 (11)	−0.0026 (13)
C6	0.0230 (15)	0.0156 (14)	0.0165 (15)	0.0017 (13)	0.0023 (11)	0.0021 (11)
C8	0.0194 (15)	0.0188 (14)	0.0138 (14)	−0.0011 (12)	0.0019 (12)	−0.0025 (11)
C14	0.0234 (17)	0.0173 (15)	0.0219 (15)	0.0004 (13)	0.0014 (12)	0.0063 (12)
C13	0.0223 (16)	0.0206 (16)	0.0148 (14)	0.0025 (13)	0.0001 (11)	0.0034 (13)
C10	0.0219 (16)	0.0245 (17)	0.0161 (14)	0.0010 (14)	−0.0006 (12)	0.0013 (12)
C1	0.0279 (18)	0.0195 (15)	0.0195 (16)	0.0005 (14)	−0.0005 (12)	−0.0021 (13)
C5	0.0249 (17)	0.0248 (16)	0.0215 (17)	0.0068 (15)	0.0017 (12)	0.0051 (13)
C15	0.0261 (18)	0.0316 (19)	0.0211 (16)	0.0025 (16)	0.0030 (13)	0.0091 (14)
C19	0.0297 (18)	0.0216 (16)	0.0240 (17)	−0.0021 (15)	0.0028 (13)	0.0036 (14)
C4	0.0267 (18)	0.036 (2)	0.0292 (18)	0.0116 (16)	0.0082 (14)	0.0073 (16)
C18	0.0297 (19)	0.0320 (19)	0.034 (2)	−0.0049 (17)	−0.0045 (15)	0.0045 (16)
C16	0.0242 (19)	0.037 (2)	0.035 (2)	0.0035 (17)	0.0097 (14)	0.0155 (17)
C2	0.047 (2)	0.0283 (18)	0.0201 (17)	0.0029 (19)	0.0030 (16)	−0.0051 (14)
C17	0.0204 (18)	0.032 (2)	0.050 (2)	−0.0048 (17)	0.0012 (15)	0.0140 (19)
C3	0.046 (2)	0.034 (2)	0.0249 (18)	0.012 (2)	0.0153 (16)	−0.0001 (16)

Geometric parameters (Å, º) top

O1—C7	1.211 (4)	C13—H13	0.93
O3—C11	1.228 (4)	C1—C2	1.394 (5)
O2—C8	1.326 (4)	C1—H1	0.93
O2—H2	0.82	C5—C4	1.393 (5)
N1—C8	1.410 (4)	C5—H5	0.93
N1—C7	1.416 (4)	C15—C16	1.395 (6)
N1—C12	1.434 (4)	C15—H15	0.93
N2—C10	1.157 (5)	C19—C18	1.388 (6)
C7—C6	1.495 (4)	C19—H19	0.93
C11—C9	1.436 (4)	C4—C3	1.390 (6)
C11—C12	1.506 (4)	C4—H4	0.93
C12—C13	1.326 (5)	C18—C17	1.400 (6)
C9—C8	1.401 (5)	C18—H18	0.93
C9—C10	1.405 (5)	C16—C17	1.376 (6)
C6—C5	1.391 (5)	C16—H16	0.93
C6—C1	1.396 (5)	C2—C3	1.387 (6)
C14—C19	1.395 (5)	C2—H2A	0.93
C14—C15	1.401 (5)	C17—H17	0.93
C14—C13	1.478 (5)	C3—H3	0.93

C8—O2—H2	109.5	C2—C1—H1	120.3
C8—N1—C7	122.9 (3)	C6—C1—H1	120.3
C8—N1—C12	108.4 (3)	C6—C5—C4	119.0 (3)
C7—N1—C12	126.8 (3)	C6—C5—H5	120.5
O1—C7—N1	119.9 (3)	C4—C5—H5	120.5
O1—C7—C6	122.2 (3)	C16—C15—C14	119.6 (4)
N1—C7—C6	117.8 (3)	C16—C15—H15	120.2
O3—C11—C9	130.2 (3)	C14—C15—H15	120.2
O3—C11—C12	124.5 (3)	C18—C19—C14	120.8 (3)
C9—C11—C12	105.2 (3)	C18—C19—H19	119.6
C13—C12—N1	128.8 (3)	C14—C19—H19	119.6
C13—C12—C11	123.9 (3)	C3—C4—C5	120.6 (4)
N1—C12—C11	106.4 (3)	C3—C4—H4	119.7
C8—C9—C10	123.7 (3)	C5—C4—H4	119.7
C8—C9—C11	109.6 (3)	C19—C18—C17	120.0 (4)
C10—C9—C11	126.7 (3)	C19—C18—H18	120.0
C5—C6—C1	120.9 (3)	C17—C18—H18	120.0
C5—C6—C7	117.4 (3)	C17—C16—C15	121.3 (4)
C1—C6—C7	121.5 (3)	C17—C16—H16	119.4
O2—C8—C9	127.5 (3)	C15—C16—H16	119.4
O2—C8—N1	122.9 (3)	C3—C2—C1	120.1 (4)
C9—C8—N1	109.6 (3)	C3—C2—H2A	119.9
C19—C14—C15	119.0 (3)	C1—C2—H2A	119.9
C19—C14—C13	120.7 (3)	C16—C17—C18	119.3 (3)
C15—C14—C13	120.3 (3)	C16—C17—H17	120.4
C12—C13—C14	128.0 (3)	C18—C17—H17	120.4
C12—C13—H13	116.0	C2—C3—C4	120.1 (4)
C14—C13—H13	116.0	C2—C3—H3	120.0
N2—C10—C9	178.9 (4)	C4—C3—H3	120.0
C2—C1—C6	119.4 (3)

C8—N1—C7—O1	37.5 (5)	C7—N1—C8—O2	−20.6 (5)
C12—N1—C7—O1	−160.3 (3)	C12—N1—C8—O2	174.4 (3)
C8—N1—C7—C6	−139.2 (3)	C7—N1—C8—C9	158.1 (3)
C12—N1—C7—C6	23.0 (5)	C12—N1—C8—C9	−6.9 (4)
C8—N1—C12—C13	−160.3 (3)	N1—C12—C13—C14	2.9 (6)
C7—N1—C12—C13	35.5 (5)	C11—C12—C13—C14	−164.8 (3)
C8—N1—C12—C11	9.1 (3)	C19—C14—C13—C12	45.2 (6)
C7—N1—C12—C11	−155.2 (3)	C15—C14—C13—C12	−135.6 (4)
O3—C11—C12—C13	−15.1 (5)	C5—C6—C1—C2	0.2 (5)
C9—C11—C12—C13	162.1 (3)	C7—C6—C1—C2	174.5 (3)
O3—C11—C12—N1	174.9 (3)	C1—C6—C5—C4	−1.8 (5)
C9—C11—C12—N1	−7.9 (3)	C7—C6—C5—C4	−176.4 (3)
O3—C11—C9—C8	−179.2 (3)	C19—C14—C15—C16	−2.7 (5)
C12—C11—C9—C8	3.9 (4)	C13—C14—C15—C16	178.0 (4)
O3—C11—C9—C10	0.1 (6)	C15—C14—C19—C18	0.9 (6)
C12—C11—C9—C10	−176.9 (3)	C13—C14—C19—C18	−179.8 (3)
O1—C7—C6—C5	37.8 (5)	C6—C5—C4—C3	2.3 (6)
N1—C7—C6—C5	−145.5 (3)	C14—C19—C18—C17	1.5 (6)
O1—C7—C6—C1	−136.7 (4)	C14—C15—C16—C17	2.2 (6)
N1—C7—C6—C1	39.9 (4)	C6—C1—C2—C3	1.1 (6)
C10—C9—C8—O2	1.1 (6)	C15—C16—C17—C18	0.2 (6)
C11—C9—C8—O2	−179.7 (3)	C19—C18—C17—C16	−2.1 (6)
C10—C9—C8—N1	−177.6 (3)	C1—C2—C3—C4	−0.6 (6)
C11—C9—C8—N1	1.7 (4)	C5—C4—C3—C2	−1.1 (6)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···O1	0.82	2.10	2.769 (4)	138
O2—H2···N2ⁱ	0.82	2.52	3.074 (5)	126

Symmetry code: (i) x−1/2, −y+3/2, −z+1.

Acknowledgements

BPS thanks Cauvery Institute of Technology for basic research facilities.

Funding information

Funding for this research was provided under award No. F.18-1/2011 (BSR) UGC–BSR Faculty Fellowship to H. S. Yathirajan).

References

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