Crystal structure and synthesis of 3-(1H-pyrrol-2-yl)-1-(thio­phen-2-yl)propanone

Gibbons, D.; Emandi, G.; Senge, M.O.

doi:10.1107/S2056989018012331

research communications

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 74| Part 10| October 2018| Pages 1463-1466

https://doi.org/10.1107/S2056989018012331

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Crystal structure and synthesis of 3-(1H-pyrrol-2-yl)-1-(thiophen-2-yl)propanone

Dáire Gibbons,^a ^* Ganapathi Emandi ^a and Mathias O. Senge ^a

^aSchool of Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
^*Correspondence e-mail: gibbondi@tcd.ie

Edited by B. Therrien, University of Neuchâtel, Switzerland (Received 10 August 2018; accepted 30 August 2018; online 21 September 2018)

The title compound, C₁₁H₉NOS, was obtained in an improved yield compared to previous literature methods. The molecule is essentially planar with a maximum deviation of 0.085 Å from the mean plane through all non-H atoms. There is directive intermolecular hydrogen bonding in the form of N—H⋯O hydrogen bonds with a distance of 2.889 (3) Å between the pyrrole amine and the ketone carbonyl O atom. The resulting hydrogen-bonding network defines a ribbon parallel to the a axis. These ribbons form offset stacks along the b axis.

Keywords: crystal structure; thiophene; pyrrole; BODIPY; aza-BODIPY.

CCDC reference: 1864793

1. Chemical context

In nature, pyrroles are often present in tetrapyrrolic ring systems such as heme and chlorophyll. These macrocyclic compounds carry out a multitude of biochemical reactions and are responsible for oxygen transport in the body and harvesting light for food production in plants, respectively. Pyrroles are also widely incorporated in drugs, catalysts and advanced materials (Michlik & Kempe, 2013 ; Estévez et al., 2014 ). The incorporation of pyrroles and thiophenes into boron-dipyrromethene (BODIPY) dyes creates the possibility of long-wavelength absorptions and emissions (Schmidt et al., 2009 ; Zrig et al., 2008 ; Collado et al., 2011 ; Rihn et al., 2009 ; Gresser et al., 2011 ; Ulrich et al., 2007 ; Benniston et al., 2008 ; Goeb & Ziessel, 2008 ). BODIPYs continue to be studied for their potential in fluorescence sensors, photodynamic therapy (PDT) and dye-sensitized solar cells (DSSCs) (Callaghan & Senge, 2018 ; Filatov et al., 2018 ; Boens et al., 2011 , 2012 ; Antina et al., 2017 ; Kamkaew et al., 2013 ; Singh & Gayathri, 2014 ; Loudet & Burgess, 2007 ; Er et al., 2015 ; Kand et al., 2015 ; Cheng et al., 2016 ). Changing the meso-carbon of the BODIPY to a nitrogen atom creates an aza-BODIPY compound. The absorption and emission in an aza-BODIPY is shifted more towards the near infra-red region compared to BODIPY (Lu et al., 2014 ; Balsukuri, et al., 2018 ). Herein, we report the improved synthesis and crystal structure of a previously synthesized ketone (Stark et al., 2016 ) that can be further functionalized to create a sophisticated aza-BODIPY.

2. Structural commentary

The title compound 1 crystallizes in a polar non-centrosymmetric space group (Pna2₁) and is almost planar in its crystalline form (Fig. 1; Table 1) with deviations ranging from −0.059 (3) (C11) to 0.085 Å (C7) from the mean plane of all non-hydrogen atoms. The pyrrole ring (N1/C8–C11) is rotated out of the plane through the ketone and thiophenyl groups (S1/O1/C1–C7) by 4.32 (10)°. The aliphatic chain linking the two ring systems has a trans conformation and the nitrogen atom (N1) of the pyrrole ring is protonated. Atom N1 is oriented opposite to the sulfur atom S1 of the thiophene ring to enable intermolecular hydrogen bonding (Fig. 2). Atom S1 lies on the same side of the molecular backbone as the oxygen of the ketone (O1).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1ⁱ	0.84 (4)	2.06 (4)	2.889 (3)	171 (3)
C6—H6⋯O1ⁱ	0.95	2.50	3.396 (3)	158
Symmetry code: (i) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z]$ .

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

Figure 2
The hydrogen bonding (dashed line) between the amine group and the carbonyl oxygen atom (Table 1

). Displacement ellipsoids are drawn at the 50% probability level.

3. Supramolecular features

Hydrogen bonding dominates the crystal packing of 1 and occurs between the amine group and the carbonyl oxygen (Fig. 2, Table 1), linking the molecules into a head-to-head ribbon-type assembly that extends down the a axis in an alternating X-pattern (Fig. 3). The angle between the alternating molecules in this X-pattern is 88.804 (8)°. The ribbons form offset stacks along the b axis with centroid–centroid distances of 3.9257 (15) Å between the centroids of adjacent pyrrole or thiophene rings and a plane shift distance of 1.89 (3) Å between any two molecules in the three-dimensional crystal structure. C—H⋯O interactions also occur.

Figure 3
View of the X-pattern in the packing, viewed approximately along the a axis. Displacement ellipsoids are drawn at the 50% probability level.

4. Database survey

A search of the Cambridge Structural Database (CSD, version 5.39; Groom et al., 2016 ) gave two structures of aza-BODIPY precursor derivatives of 1 (Table 2). In (E)-1,3-di(thiophen-2-yl)prop-2-en-1-one (LINFET; Li & Su, 1995 ), a thiophene ring replaces the pyrrole ring, yielding a di-thiophene-linked α,β-unsaturated ketone aliphatic chain. LINFET contains two independent molecules in the asymmetric unit. One dithiophene-linked chain is less planar than in 1 (LINFET A) while the other is more planar (LINFET B; Table 2). The deviations from the plane of LINFET A range from −0.127 Å (C5) to 0.233 Å (S1); the deviations in LINFET B are smaller ranging from −0.032 Å for C22 to 0.055 Å for O2. They both exhibit the same trans conformation seen in the title molecule. Non-classical hydrogen bonding exists between a C—H group and the carbonyl oxygen, O1 with a C—H⋯O distance of 3.326 (6) Å. This bonding network results in three separate sheets, parallel to the a-axis. A second non-classical hydrogen-bonding network [C—H⋯O = 2.381 (4) Å] is observed extending along the c-axis direction, generating a staggered ribbon. The combination of these two networks gives rise to a three-dimensional structure.

Table 2
r. m. s. deviations and twist (Å, °) angles

The twist angle is the dihedral angle between the five-membered heterocycle and the keto-aromatic plane.

Compound	r.m.s. deviation	Twist angle
1	0.04 (8)	4.32 (10)
LINFET A^a	0.111 (2)	10.21 (12)
LINFET B^a	0.023 (2)	1.19 (15)
SANRIJ A^b	0.104 (15)	8.98 (4)
SANRIJ B^b	0.122 (20)	9.67 (6)
Notes: (a) Li & Su (1995); (b) Ocak Ískeleli et al. (2005).

(E)-1,3-Di(furan-2-yl)prop-2-en-1-one (SANRIJ; Ocak Ískeleli et al., 2005 ) comprises two furan heterocycles linked by an α,β-unsaturated ketone aliphatic chain. There are also two independent molecules in the asymmetric unit (SANRIJ A and SANRIJ B), both of which are less planar than 1, LINFET A and LINFET B. The largest deviation from the molecular plane is for C17 (0.157 Å) in SANRIJ A and C18 (−0.152 Å) in SANRIJ B. Again, a non-classical hydrogen bonding network exists [C—H⋯O = 2.473 (18) Å] between aryl C—H atoms and the carbonyl oxygen. Each molecule participates in two hydrogen bonds and the network extends in a linear fashion along the b-axis direction, forming a network structure.

5. Synthesis and crystallization

The title compound was synthesized via an elimination unimolecular conjugate base (E1cB) reaction between 2-pyrrole-carbaldehyde (376.87 mg, 3.96 mmol, 1.0 eq.) and 2-acetylthiophene (500 mg, 3.96 mmol, 1.0 eq.) in 1:1 MeOH:H₂O (10 ml) using NaOH (15.85 mg, 396.28 µmol, 0.1 eq.) as a base. The resulting precipitate was filtered and then crystallized using a solution of CHCl₃, layered with hexane to give a single crystal suitable for X-ray diffraction. [C₁₁H₉NOS]: yield 85% m.p 420–430 K.

¹H NMR (CDCl₃, ppm, 400MHz): δ 6.34 (dd, J = 5.9, 2.6 Hz, 1H, =C—H), 6.74 (s, 1H, Ar-H), 7.01 (s, 1H, Ar-H), 7.06–7.10 (d, 1H, Ar-H), 7.15 (t, J = 8.7 Hz, 1H, Ar-H), 7.63 (d, J = 4.9 Hz, 1H, Ar-H), 7.81 (t, 1H, Ar-H), 7.83 (d, J = 10.3 Hz, 1H, =C—H), 9.17 (s, 1H, NH). ¹³C NMR (CDCl₃, ppm, 400 MHz): δ 111.54, 115.16, 123.30, 128.15, 129.16, 131.11, 133.17, 133.98, 145.89, 182.05. HRMS (ESI): m/z calculated for C₁₁H₉NOS: 204.047690 (M + H)⁺. Found: 204.04776.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. H atoms were placed in their expected calculated positions and refined as riding: C—H = 0.95–0.98 Å with U_iso(H) = 1.2 U_eq(C).

Table 3
Experimental details

Crystal data
Chemical formula	C₁₁H₉NOS
M_r	203.25
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	100
a, b, c (Å)	11.1559 (3), 3.9258 (1), 21.6293 (6)
V (Å³)	947.27 (4)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.30
Crystal size (mm)	0.2 × 0.09 × 0.07

Data collection
Diffractometer	Bruker SMART APEXII area detector
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.658, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	25996, 2159, 2070
R_int	0.049
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.082, 1.06
No. of reflections	2159
No. of parameters	131
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.28, −0.17
Absolute structure	Flack x determined using 956 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.00 (4)
Computer programs: APEX3 and SAINT (Bruker, 2016 ), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 1864793

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989018012331/tx2008sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018012331/tx2008Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989018012331/tx2008Isup3.cml

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

3-(1H-Pyrrol-2-yl)-1-(thiophen-2-yl)propanone top

Crystal data top

C₁₁H₉NOS	D_x = 1.425 Mg m⁻³
M_r = 203.25	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna2₁	Cell parameters from 9918 reflections
a = 11.1559 (3) Å	θ = 3.7–27.5°
b = 3.9258 (1) Å	µ = 0.30 mm⁻¹
c = 21.6293 (6) Å	T = 100 K
V = 947.27 (4) Å³	Triangular, yellow
Z = 4	0.2 × 0.09 × 0.07 mm
F(000) = 424

Data collection top

Bruker SMART APEXII area detector diffractometer	2159 independent reflections
Radiation source: standard sealed X-ray tube, Siemens, KFF Mo 2K -90 C	2070 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.049
Detector resolution: 7.9 pixels mm^-1	θ_max = 27.5°, θ_min = 1.9°
ω and φ scans	h = −14→14
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	k = −5→5
T_min = 0.658, T_max = 0.746	l = −27→28
25996 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.032	w = 1/[σ²(F_o²) + (0.0533P)² + 0.3056P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.082	(Δ/σ)_max < 0.001
S = 1.06	Δρ_max = 0.28 e Å⁻³
2159 reflections	Δρ_min = −0.17 e Å⁻³
131 parameters	Absolute structure: Flack x determined using 956 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
1 restraint	Absolute structure parameter: 0.00 (4)
Primary atom site location: dual

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	0.4383 (3)	0.3593 (7)	0.30581 (13)	0.0220 (6)
H1	0.4090	0.2839	0.2669	0.026*
C2	0.5545 (3)	0.3241 (7)	0.32434 (13)	0.0199 (5)
H2	0.6149	0.2208	0.2997	0.024*
C3	0.5754 (2)	0.4580 (6)	0.38425 (12)	0.0146 (5)
H3	0.6510	0.4546	0.4045	0.018*
C4	0.4712 (2)	0.5956 (7)	0.40983 (12)	0.0154 (5)
C5	0.4521 (2)	0.7623 (7)	0.46958 (11)	0.0158 (5)
C6	0.5566 (2)	0.7940 (7)	0.51008 (13)	0.0167 (5)
H6	0.6303	0.6917	0.4983	0.020*
C7	0.5498 (2)	0.9663 (7)	0.56396 (12)	0.0166 (5)
H7	0.4753	1.0719	0.5733	0.020*
C8	0.6436 (2)	1.0055 (7)	0.60829 (13)	0.0160 (5)
C9	0.6393 (2)	1.1517 (7)	0.66686 (12)	0.0183 (5)
H9	0.5713	1.2570	0.6852	0.022*
C10	0.7529 (3)	1.1168 (7)	0.69428 (12)	0.0195 (5)
H10	0.7758	1.1928	0.7343	0.023*
C11	0.8247 (2)	0.9509 (7)	0.65194 (13)	0.0182 (6)
H11	0.9065	0.8924	0.6579	0.022*
N1	0.7588 (2)	0.8850 (6)	0.60020 (11)	0.0179 (5)
H1A	0.787 (3)	0.791 (9)	0.5687 (16)	0.019 (8)*
O1	0.35144 (16)	0.8661 (6)	0.48409 (9)	0.0199 (4)
S1	0.35151 (5)	0.55340 (15)	0.36015 (3)	0.01928 (17)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0338 (15)	0.0180 (12)	0.0144 (12)	−0.0026 (11)	−0.0025 (10)	0.0009 (10)
C2	0.0266 (13)	0.0172 (13)	0.0160 (12)	−0.0001 (10)	0.0048 (10)	−0.0005 (11)
C3	0.0173 (11)	0.0139 (11)	0.0126 (11)	−0.0020 (9)	0.0005 (9)	0.0009 (9)
C4	0.0187 (12)	0.0154 (12)	0.0120 (11)	−0.0046 (9)	−0.0014 (9)	0.0023 (9)
C5	0.0200 (12)	0.0166 (10)	0.0108 (11)	−0.0016 (10)	0.0010 (10)	0.0036 (10)
C6	0.0158 (11)	0.0201 (12)	0.0140 (11)	−0.0006 (10)	−0.0014 (10)	0.0010 (11)
C7	0.0188 (12)	0.0165 (12)	0.0146 (12)	−0.0002 (10)	0.0013 (10)	0.0030 (10)
C8	0.0195 (12)	0.0155 (12)	0.0130 (12)	−0.0010 (10)	0.0007 (9)	0.0016 (9)
C9	0.0244 (13)	0.0168 (12)	0.0138 (12)	0.0011 (10)	0.0017 (10)	−0.0013 (10)
C10	0.0274 (13)	0.0182 (12)	0.0129 (12)	−0.0024 (10)	−0.0025 (10)	−0.0010 (10)
C11	0.0194 (13)	0.0205 (13)	0.0149 (12)	−0.0040 (10)	−0.0010 (10)	0.0006 (10)
N1	0.0191 (11)	0.0218 (11)	0.0129 (11)	−0.0012 (9)	0.0016 (9)	−0.0015 (9)
O1	0.0183 (9)	0.0272 (9)	0.0143 (9)	0.0008 (8)	0.0013 (7)	0.0014 (8)
S1	0.0198 (3)	0.0223 (3)	0.0157 (3)	−0.0019 (2)	−0.0033 (3)	0.0002 (3)

Geometric parameters (Å, º) top

C1—H1	0.9500	C6—C7	1.350 (4)
C1—C2	1.364 (4)	C7—H7	0.9500
C1—S1	1.702 (3)	C7—C8	1.428 (4)
C2—H2	0.9500	C8—C9	1.392 (4)
C2—C3	1.418 (4)	C8—N1	1.381 (3)
C3—H3	0.9500	C9—H9	0.9500
C3—C4	1.397 (4)	C9—C10	1.406 (4)
C4—C5	1.464 (3)	C10—H10	0.9500
C4—S1	1.722 (3)	C10—C11	1.380 (4)
C5—C6	1.463 (3)	C11—H11	0.9500
C5—O1	1.236 (3)	C11—N1	1.364 (4)
C6—H6	0.9500	N1—H1A	0.84 (4)

C2—C1—H1	123.7	C6—C7—C8	126.4 (3)
C2—C1—S1	112.5 (2)	C8—C7—H7	116.8
S1—C1—H1	123.7	C9—C8—C7	129.1 (2)
C1—C2—H2	123.6	N1—C8—C7	124.1 (2)
C1—C2—C3	112.8 (3)	N1—C8—C9	106.8 (2)
C3—C2—H2	123.6	C8—C9—H9	125.9
C2—C3—H3	124.2	C8—C9—C10	108.2 (2)
C4—C3—C2	111.6 (2)	C10—C9—H9	125.9
C4—C3—H3	124.2	C9—C10—H10	126.6
C3—C4—C5	130.0 (2)	C11—C10—C9	106.8 (2)
C3—C4—S1	111.2 (2)	C11—C10—H10	126.6
C5—C4—S1	118.77 (19)	C10—C11—H11	125.6
C6—C5—C4	116.8 (2)	N1—C11—C10	108.7 (2)
O1—C5—C4	120.2 (2)	N1—C11—H11	125.6
O1—C5—C6	122.9 (2)	C8—N1—H1A	127 (2)
C5—C6—H6	119.5	C11—N1—C8	109.4 (2)
C7—C6—C5	121.0 (2)	C11—N1—H1A	124 (2)
C7—C6—H6	119.5	C1—S1—C4	91.90 (14)
C6—C7—H7	116.8

C1—C2—C3—C4	−0.2 (3)	C7—C8—C9—C10	177.3 (3)
C2—C1—S1—C4	0.4 (2)	C7—C8—N1—C11	−177.4 (3)
C2—C3—C4—C5	−179.2 (2)	C8—C9—C10—C11	0.2 (3)
C2—C3—C4—S1	0.5 (3)	C9—C8—N1—C11	0.3 (3)
C3—C4—C5—C6	0.0 (4)	C9—C10—C11—N1	0.0 (3)
C3—C4—C5—O1	−179.5 (3)	C10—C11—N1—C8	−0.2 (3)
C3—C4—S1—C1	−0.5 (2)	N1—C8—C9—C10	−0.3 (3)
C4—C5—C6—C7	175.0 (2)	O1—C5—C6—C7	−5.6 (4)
C5—C4—S1—C1	179.2 (2)	S1—C1—C2—C3	−0.2 (3)
C5—C6—C7—C8	177.7 (2)	S1—C4—C5—C6	−179.67 (19)
C6—C7—C8—C9	−173.4 (3)	S1—C4—C5—O1	0.9 (3)
C6—C7—C8—N1	3.8 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.84 (4)	2.06 (4)	2.889 (3)	171 (3)
C6—H6···O1ⁱ	0.95	2.50	3.396 (3)	158

Symmetry code: (i) x+1/2, −y+3/2, z.

r. m. s. deviations and twist (Å, °) angles top

The twist angle is the dihedral angle between the five-membered heterocycle and the keto-aromatic plane.

Compound	r.m.s. deviation	Twist angle
1	0.04 (8)	4.32 (10)
LINFET A^a	0.111 (2)	10.21 (12)
LINFET B^a	0.023 (2)	1.19 (15)
SANRIJ A^b	0.104 (15)	8.98 (4)
SANRIJ B^b	0.122 (20)	9.67 (6)

Notes: (a) Li & Su (1995); (b) Ocak Ískeleli et al. (2005).

Route mean square (r. m. s.) deviations and twist angles of the two five-membered heterocycles in 1 and the two derivatives known in literature (Li & Su, 1995; Ocak Ískeleli et al., 2005) top

Compound	R. M. S. deviation (Å)	Twist angle (o)
1	0.056	2.87 (11)
2 (First independent molecule)	0.093 (2)	7.15 (6)
Second independent molecule	0.02 (2)	0.20 (15)
3 (First independent molecule)	0.104	8.41 (6)
Second independent molecule	0.122	11.11 (7)

Acknowledgements

Special thanks to Dr. Brendan Twamley for his continued support.

Funding information

This work was supported by a grant from the Science Foundation Ireland (SFI IvP 13/IA/1894, MOS).

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