Synthesis, characterization and supra­molecular analysis for (E)-3-(pyridin-4-yl)acrylic acid

Florez-Muñoz, V.; Guerrero, A.F.; Macias, M.; Illicachi, L.A.; D'Vries, R.

doi:10.1107/S2056989024002627

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ISSN: 2056-9890

Volume 80| Part 4| April 2024| Pages 388-391

https://doi.org/10.1107/S2056989024002627

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Synthesis, characterization and supramolecular analysis for (E)-3-(pyridin-4-yl)acrylic acid

Valentina Florez-Muñoz,^a Andres Felipe Guerrero,^a Mario Macias,^b Luis Alberto Illicachi ^a ^* and Richard D'Vries ^c ^*

^aFacultad de Ciencias Básicas, Universidad Santiago de Cali, Calle 5 No 62-00, Cali, Colombia, ^bCristalografía y Química de Materiales (CrisQuimMat), Facultad de Ciencias, Departamento de Química, Universidad de los Andes, Cra. 1 No 18a-12, Bogotá, Colombia, and ^cFacultad de Ciencias Naturales, Exactas y de la Educación, Departamento de Química, Universidad del Cauca, Calle 5 No 4-70, Popayán, Colombia
^*Correspondence e-mail: luis.illicachi00@usc.edu.co, richard.dvries@unicauca.edu.co

Edited by J. Ellena, Universidade de Sâo Paulo, Brazil (Received 11 March 2024; accepted 19 March 2024; online 26 March 2024)

The title compound, C₈H₇NO₂, crystallizes as prismatic colourless crystals in space group P $[\overline{1}]$ , with one molecule in the asymmetric unit. The pyridine ring is fused to acrylic acid, forming an almost planar structure with an E-configuration about the double bond with a torsion angle of −6.1 (2)°. In the crystal, strong O—H⋯N interactions link the molecules, forming chains along the [101] direction. Weak C—H⋯O interactions link adjacent chains along the [100] direction, generating an R²₂(14) homosynthon. Finally, π–π stacking interactions lead to the formation of the three-dimensional structure. The supramolecular analysis was supported by Hirshfeld surface and two-dimensional fingerprint plot analysis, indicating that the most abundant contacts are associated with H⋯H, O⋯H/H⋯O, N⋯H/H⋯N and C⋯H/H⋯C interactions.

Keywords: crystal structure; (E)-3-(pyridin-4-yl)acrylic acid; supramolecular analysis.

CCDC reference: 2341592

1. Chemical context

Cinnamic acid and its derivatives have been used in several applications related to medicinal chemistry (Deng et al., 2023 ), organic synthesis (Chen et al., 2020 ), and coordination chemistry (Zhou et al., 2016 ). Cinnamic acids are reactive molecules due to possessing an unsaturated carbonyl moiety, which can be considered a Michael acceptor and benzene ring. Both make it possible to modify them, resulting in synthetic cinnamic acid derivatives with a broad range of biological properties, including antibacterial (Ruwizhi & Aderibigbe, 2020 ) antituberculosis (Teixeira et al., 2020 ), antimalarial (Fonte et al., 2023 ), antidiabetic (Adisakwattana, 2017 ; Feng et al., 2022 ), anticancer (Feng et al., 2022), antifungal (Liu et al., 2024 ), Alzheimer's treatment (Drakontaeidi & Pontiki, 2024 ), antioxidant (Nouni et al., 2023 ), and cosmetic (Gunia-Krzyżak et al., 2018 ). Among the various types of cinnamic acids documented, 4-pyridylacrylic acid (4-Hpya) is considered a highly valuable ligand because of several structural characteristics that make it suitable for the construction of coordination compounds. These characteristics include multiple coordination sites, which enable the formation of higher-dimensional structures, and versatile coordination modes to form different structures (Khalfaoui et al., 2021 ). On the other hand, its capacity to function as both a hydrogen-bond donor and acceptor facilitates the creation of intricate hydrogen-bonded networks (Jiao et al., 2007 ; Zhu et al., 2005 ).

2. Structural commentary

The title compound crystallizes in space group P $[\overline{1}]$ with one molecule per asymmetric unit (Fig. 1). The pyridinic ring is fused to acrylic acid, forming an almost planar structure with an E-configuration about the double bond, with a C8—C4—C3—C2 torsion angle of −6.1 (2)°.

Figure 1
The molecule of (E)-3-(pyridin-4-yl)acrylic acid compound with displacement ellipsoids drawn at the 50% probability level.

3. Supramolecular features

In the crystal, strong O1—H1⋯N1 interactions link the molecules, forming chains along the [101] direction (Fig. 2a, Table 1). Adjacent chains are linked along the [100] direction through weak C—H⋯O interactions, generating an R₂²(14) homosynthon (Fig. 2b). Finally, the three-dimensional supramolecular structure is finally formed by slipped π–π stacking interactions (Hunter & Sanders, 1990 ) between the pyridinic rings (N1/C4–C8) with distances of 3.8246 (10) Å, and π–π stacking interactions of the acrylic double bond (C2=C3) of 3.4322 (10)Å (Fig. 2c). An interaction between the nitrogen atom of the pyridinic ring, N1, and the double bond of the acrylic group with a distance of 3.4044 (13) Å is also observed.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯N1ⁱ	0.99 (3)	1.63 (3)	2.6147 (18)	177 (3)
C5—H5⋯O2ⁱⁱ	0.93	2.57	3.336 (2)	140
Symmetry codes: (i) ; (ii) .

Figure 2
Supramolecular interactions in the title compound. (a) O—H⋯N interactions forming chains, (b) two chains joined by C—H⋯O interactions and (c) π–π stacking interactions between the pyridine rings and the acrylic group.

A Hirshfeld surface analysis was performed to confirm, visualise and quantify the supramolecular interactions present in title compound. The Hirshfeld surface mapped over d_norm and 2D fingerprint plots (Spackman & Jayatilaka, 2009 ) were generated using Crystal Explorer 17 (Spackman, et al., 2021 ). Fig. 3 shows the strongest interactions as red spots. These are associated with the donor and acceptor atoms, in this case for the O—H⋯N interaction. The weakest interactions, associated with the C—H⋯O contacts, are shown as white areas. These interactions were quantified through the fingerprint plots, indicating that the most abundant contacts are associated with H⋯H interactions (36.2%) while O⋯H/H⋯O, N⋯H/H⋯N and C⋯H/H⋯C interactions represent 27.8%, 8.7% and 10.7%, respectively. These results show that crystal packing is governed mainly by dispersion and electrostatic interactions.

Figure 3
Hirshfeld surface and fingerprint plot analysis for the title compound.

4. Database survey

A search of the Cambridge Structural Database (Version 2023.3.0; Groom et al., 2016 ) using Conquest (Bruno et al., 2002 ) found seven entries for (E)-3-(pyridin-4-yl)acrylic acid derivative molecules. In all cases, the protonation of the nitrogen atom in the pyridine ring leads to the formation of pyridinium salts. These include halides (Hu, 2010 ; Kole et al., 2010 ), trifluoroacetate (Kole et al., 2010), hydrogen sulfate (Kole et al., 2010), perchlorate and hexafluorophosphate (Kole et al., 2011 ).

5. Synthesis and crystallization

The synthesis of (E)-3-(pyridin-4-yl)acrylic acid compound was performed following the procedure reported by Kudelko et al. (2015 ) for the synthesis of 3-(pyridyl)acrylic acids (Fig. 4). In a 25 mL flat-bottomed flask, 728 mg of malonic acid (0.335 mmol) and 300 mg of 4-pyridincarboxyaldehyde (0.33 5 mmol) were mixed with 2 ml of pyridine. The reaction mixture was refluxed under constant stirring for 3 h. The reaction synthesis was ice-cooled, and then drops of 37% HCl were added until precipitate formation was observed. The obtained solid was separated by filtration and washed with acetone. The solid product was recrystallized by slow water evaporation, giving a colourless crystalline powder and small prismatic crystals in 97.9% yield.

Figure 4
Reaction scheme for obtaining (E)-3-(pyridin-4-yl)acrylic acid.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The O-bound hydrogen atom (H1) was found in electron density maps and freely refined. C-bound hydrogen atoms were positioned geometrically and refined using a riding model [C—H = 0.93 Å, U_iso(H) = 1.2U_eq(C)].

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₇NO₂
M_r	149.15
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	291
a, b, c (Å)	6.6279 (15), 7.3272 (12), 8.2308 (15)
α, β, γ (°)	67.271 (17), 83.403 (17), 73.006 (17)
V (Å³)	352.57 (13)
Z	2
Radiation type	Cu Kα
μ (mm⁻¹)	0.85
Crystal size (mm)	0.09 × 0.06 × 0.05

Data collection
Diffractometer	SuperNova, Dual, Cu at home/near, Atlas
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2021 $[Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.831, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	3635, 1461, 1243
R_int	0.035
(sin θ/λ)_max (Å⁻¹)	0.631

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.153, 1.04
No. of reflections	1461
No. of parameters	104
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.14, −0.27
Computer programs: CrysAlis PRO (Rigaku OD, 2021 $[Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXT (Sheldrick, 2015a ), SHELXL2016/6 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 2341592

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989024002627/ex2082sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024002627/ex2082Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989024002627/ex2082Isup3.cml

checkCIF report

Computing details top

(E)-3-(Pyridin-4-yl)prop-2-enoic acid top

Crystal data top

C₈H₇NO₂	F(000) = 156
M_r = 149.15	D_x = 1.405 Mg m⁻³
Triclinic, P1	Melting point: 553 K
a = 6.6279 (15) Å	Cu Kα radiation, λ = 1.54184 Å
b = 7.3272 (12) Å	Cell parameters from 1657 reflections
c = 8.2308 (15) Å	θ = 6.8–74.9°
α = 67.271 (17)°	µ = 0.85 mm⁻¹
β = 83.403 (17)°	T = 291 K
γ = 73.006 (17)°	Prismatic, colourless
V = 352.57 (13) Å³	0.09 × 0.06 × 0.05 mm
Z = 2

Data collection top

SuperNova, Dual, Cu at home/near, Atlas diffractometer	1461 independent reflections
Radiation source: micro-focus sealed X-ray tube, SuperNova (Cu) X-ray Source	1243 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.035
Detector resolution: 10.6144 pixels mm^-1	θ_max = 76.6°, θ_min = 5.8°
ω scans	h = −8→7
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2021)	k = −8→9
T_min = 0.831, T_max = 1.000	l = −10→10
3635 measured reflections

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) = 0.153	w = 1/[σ²(F_o²) + (0.0977P)² + 0.0215P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max < 0.001
1461 reflections	Δρ_max = 0.14 e Å⁻³
104 parameters	Δρ_min = −0.27 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
O1	0.48195 (18)	0.6974 (2)	0.64537 (15)	0.0609 (4)
O2	0.63738 (19)	0.8136 (2)	0.79722 (16)	0.0669 (4)
C2	0.3116 (2)	0.7317 (2)	0.89960 (18)	0.0484 (4)
H2	0.211812	0.676180	0.879516	0.058*
N1	−0.20475 (19)	0.72846 (17)	1.42131 (15)	0.0504 (4)
C5	0.1186 (2)	0.8159 (2)	1.31387 (18)	0.0490 (4)
H5	0.228403	0.862808	1.329376	0.059*
C4	0.1149 (2)	0.76641 (18)	1.16689 (16)	0.0426 (3)
C7	−0.2089 (2)	0.6805 (2)	1.28079 (19)	0.0507 (4)
H7	−0.320055	0.632669	1.269716	0.061*
C1	0.4937 (2)	0.75386 (19)	0.77647 (17)	0.0477 (4)
C3	0.2868 (2)	0.7884 (2)	1.03649 (18)	0.0456 (3)
H3	0.386535	0.847081	1.051782	0.055*
C8	−0.0552 (2)	0.6991 (2)	1.15114 (18)	0.0483 (4)
H8	−0.065343	0.666782	1.054192	0.058*
C6	−0.0433 (3)	0.7943 (2)	1.43650 (18)	0.0524 (4)
H6	−0.038863	0.827444	1.534078	0.063*
H1	0.600 (4)	0.713 (4)	0.561 (3)	0.099 (8)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0601 (7)	0.0851 (8)	0.0546 (6)	−0.0366 (6)	0.0209 (5)	−0.0374 (5)
O2	0.0631 (7)	0.0930 (9)	0.0644 (7)	−0.0440 (6)	0.0193 (5)	−0.0389 (6)
C2	0.0493 (8)	0.0521 (7)	0.0490 (8)	−0.0225 (6)	0.0125 (6)	−0.0213 (6)
N1	0.0545 (7)	0.0513 (6)	0.0463 (6)	−0.0184 (5)	0.0129 (5)	−0.0197 (5)
C5	0.0523 (8)	0.0528 (7)	0.0489 (7)	−0.0218 (6)	0.0056 (6)	−0.0225 (6)
C4	0.0457 (7)	0.0396 (6)	0.0405 (7)	−0.0122 (5)	0.0055 (5)	−0.0139 (5)
C7	0.0482 (7)	0.0572 (7)	0.0524 (7)	−0.0224 (6)	0.0101 (6)	−0.0233 (6)
C1	0.0508 (7)	0.0488 (7)	0.0451 (7)	−0.0201 (5)	0.0097 (5)	−0.0167 (5)
C3	0.0455 (7)	0.0468 (6)	0.0450 (7)	−0.0168 (5)	0.0058 (5)	−0.0161 (5)
C8	0.0513 (7)	0.0552 (7)	0.0453 (7)	−0.0202 (6)	0.0075 (5)	−0.0240 (5)
C6	0.0621 (9)	0.0553 (7)	0.0458 (7)	−0.0199 (6)	0.0091 (6)	−0.0249 (6)

Geometric parameters (Å, º) top

O1—C1	1.3135 (17)	C5—C4	1.3954 (18)
O1—H1	0.98 (3)	C5—C6	1.386 (2)
O2—C1	1.2110 (19)	C4—C3	1.4729 (19)
C2—H2	0.9300	C4—C8	1.392 (2)
C2—C1	1.4887 (18)	C7—H7	0.9300
C2—C3	1.322 (2)	C7—C8	1.384 (2)
N1—C7	1.3374 (18)	C3—H3	0.9300
N1—C6	1.332 (2)	C8—H8	0.9300
C5—H5	0.9300	C6—H6	0.9300

C1—O1—H1	113.5 (14)	C8—C7—H7	118.6
C1—C2—H2	118.9	O1—C1—C2	112.14 (13)
C3—C2—H2	118.9	O2—C1—O1	124.20 (13)
C3—C2—C1	122.27 (14)	O2—C1—C2	123.65 (13)
C6—N1—C7	117.87 (12)	C2—C3—C4	125.60 (14)
C4—C5—H5	120.4	C2—C3—H3	117.2
C6—C5—H5	120.4	C4—C3—H3	117.2
C6—C5—C4	119.18 (13)	C4—C8—H8	120.2
C5—C4—C3	119.41 (13)	C7—C8—C4	119.52 (12)
C8—C4—C5	117.36 (12)	C7—C8—H8	120.2
C8—C4—C3	123.22 (12)	N1—C6—C5	123.17 (12)
N1—C7—H7	118.6	N1—C6—H6	118.4
N1—C7—C8	122.88 (14)	C5—C6—H6	118.4

N1—C7—C8—C4	1.3 (2)	C3—C2—C1—O2	4.3 (2)
C5—C4—C3—C2	174.27 (12)	C3—C4—C8—C7	179.26 (12)
C5—C4—C8—C7	−1.2 (2)	C8—C4—C3—C2	−6.1 (2)
C4—C5—C6—N1	−0.2 (2)	C6—N1—C7—C8	−0.8 (2)
C7—N1—C6—C5	0.3 (2)	C6—C5—C4—C3	−179.79 (12)
C1—C2—C3—C4	−178.21 (11)	C6—C5—C4—C8	0.6 (2)
C3—C2—C1—O1	−176.96 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1ⁱ	0.99 (3)	1.63 (3)	2.6147 (18)	177 (3)
C5—H5···O2ⁱⁱ	0.93	2.57	3.336 (2)	140

Symmetry codes: (i) x+1, y, z−1; (ii) −x+1, −y+2, −z+2.

Hydrogen bonds and interactions geometry, (Å, °) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1i	0.990 (3)	1.630 (3)	2.61470 (18)	177.0 (3)
C5—H5···O2ii	0.9300	2.5700	3.3360 (2)	140.00
Cp1···Cp1			3.82460 (10)
Cp2···Cp2			3.43220 (10)
N1···Cp1			3.40440 (13)

Funding information

The authors all acknowledge the Universidad Santiago de Cali and Dirección General de Investigaciones for funding this research under call No. 01–2024 and projects 939–621121-3307 and 934–621122-3427. RD acknowledges the Vicerectoria de Investigaciones of Universidad del Cauca for 2024 internal call, project No. ID-6161. MM is grateful for support from the Facultad de Ciencias and Departamento de Química at Universidad de los Andes, Bogotá, Colombia.

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