Pyridin-1-ium carb­oxy­formate–2-chloro­acetic acid (1/1)

Sadikhova, N.D.; Muradova, F.M.; Guliyeva, N.A.; Hasanov, K.I.; Javadzade, T.A.; Zangrando, E.; Belay, A.N.

doi:10.1107/S2414314624012422

organic compounds

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Volume 10| Part 1| January 2025| x241242

https://doi.org/10.1107/S2414314624012422

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Pyridin-1-ium carboxyformate–2-chloroacetic acid (1/1)

Nurlana D. Sadikhova,^a Farida M. Muradova,^a Narmina A. Guliyeva,^b Khudayar I. Hasanov,^c,^d Tahir A. Javadzade,^e Ennio Zangrando ^f and Alebel N. Belay ^g ^*

^aDepartment of Chemistry, Baku State University, Z. Khalilov Str. 23, AZ 1148, Baku, Azerbaijan, ^bDepartment of Chemical Engineering, Baku Engineering University, Hasan Aliyev, str. 120, Baku, Absheron AZ0101, Azerbaijan, ^cWestern Caspian University, Istiqlaliyyat Street 31, AZ 1001, Baku, Azerbaijan, ^dAzerbaijan Medical University, Scientific Research Centre (SRC), A. Kasumzade, St. 14. AZ 1022, Baku, Azerbaijan, ^eDepartment of Chemistry and Chemical Engineering, Khazar University, Baku, Mahsati st. 41, AZ1096, Baku, Azerbaijan, ^fDepartment of Chemical and Pharmaceutical Sciences, University of Trieste, 34127, Trieste, Italy, and ^gDepartment of Chemistry, Bahir Dar University, PO Box 79, Bahir Dar, Ethiopia
^*Correspondence e-mail: alebel.nibret@bdu.edu.et

(Received 26 November 2024; accepted 24 December 2024; online 3 January 2025)

The asymmetric unit of the title salt co-crystal, C₅H₆N⁺·C₂HO₄⁻·C₂H₃ClO₂, comprises a pyridinium cation, a carboxyformate anion and a 2-chloroacetic acid molecule. In the crystal, the components are connected by hydrogen bonds within a one-dimensional chain in the a-axis direction which incorporates rather short, charge-assisted O—H⋯O hydrogen bonds; the pyridinium-NH group forms bifurcated N—H⋯(O,O) hydrogen bonds of different strength.

Keywords: crystal structure; co-crystal; salt; non-covalent interactions; hydrogen-bonding.

CCDC reference: 2412697

Structure description

Crystal engineering of co-crystals has inspired great interest from researchers in recent times due to their ability to improve functional properties of materials including pharmaceutical active ingredients (Braga et al., 2013 ). The selection of synthons or tectons is an important synthetic step to improve the performance of co-crystals, such as solubility, catalytic activity, dissolution profile, pharmacokinetics and stability (Jlassi et al., 2014 ; Mahmoudi et al., 2017a ,b ). Designing weak intra- or intermolecular interactions and the procedures underlying synthesis constitute the operational part of the crystal engineering endeavour (Abdelhamid et al., 2011 ; Afkhami et al., 2017 ). The use of various types of non-covalent interactions in the design of multi-component co-crystals is based on a complete knowledge of these weak bonds, especially supramolecular synthons (Berry et al., 2017 ; Gurbanov et al., 2018 , 2020 ; Kopylovich et al., 2012a ,b ).

The asymmetric unit of the title compound is shown in Fig. 1. The pyridinium cation, the carboxyformate anion and the chloroacetic acid molecule interact through hydrogen bonds as described below. The C—OH bond lengths for the chloroacetic- and oxalate-bound carboxylate groups, of 1.3215 (19) and 1.3073 (17) Å, respectively, are longer in comparison to the C=O bond lengths, which range from 1.2074 (19) Å (chloroacetic acid) to 1.2653 (17) Å. These observations clearly confirm the positions of the H atoms, which were located in difference-Fourier maps and refined. The C1—Cl1 bond length is 1.7755 (15) Å with this bond being in an eclipsed conformation as the Cl1—C1—C2—O1 torsion angle is −6.4 (2)°. This torsion angle results in a molecular conformation that is close to planar (C_s symmetry) and corresponds to the ground state of the molecule, as confirmed by quantum chemical calculations (Ananyev et al., 2014 ).

Figure 1
Molecular structures of the components of the asymmetric unit, showing the atom-numbering scheme and displacement ellipsoids at the 50% probability level.

In the crystal, the species are connected by hydrogen bonds within a linear one-dimensional chain extending along the a-axis direction (Fig. 2); a space-filling representation is displayed in Fig. 3. The O—H⋯O hydrogen bonds, Table 1, are rather short with O⋯O separations of 2.5834 (14) and 2.6209 (15) Å, while the pyridinium-NH group forms bifurcated N—H⋯(O,O) hydrogen bonds of different strength, with N⋯O distances of 2.7935 (16) and 2.9546 (17) Å. These ribbons interact through non-conventional C—H⋯O hydrogen bonds that consolidate the supramolecular network, Table 1. Within the chain, the pyridinium mean plane forms a dihedral angle of 25.92 (6)° with the adjacent carboxyformate anion, which in turn is twisted by 63.73 (4)° with respect to the mean plane through the chloroacetic acid molecule.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2o⋯O4	0.82 (2)	1.81 (2)	2.6209 (15)	170 (2)
O6—H6o⋯O3ⁱ	0.86 (2)	1.72 (2)	2.5834 (14)	171.8 (19)
N1—H1n⋯O3	0.861 (19)	1.995 (19)	2.7935 (16)	153.8 (17)
N1—H1n⋯O5	0.861 (19)	2.339 (18)	2.9546 (17)	128.7 (15)
C1—H1a⋯O1ⁱⁱ	0.99	2.54	3.4555 (19)	153
C1—H1b⋯O4ⁱⁱⁱ	0.99	2.56	3.3439 (19)	136
C5—H5⋯O6^iv	0.95	2.59	3.3946 (18)	142
C8—H8⋯O1^v	0.95	2.40	3.3400 (19)	172
C9—H9⋯O5	0.95	2.49	3.0356 (19)	116
Symmetry codes: (i) ; (ii) $[-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) ; (iv) ; (v) .

Figure 2
A view of the one-dimensional chain along the a-axis direction and featuring hydrogen bonds shown as blue dashed lines.

Figure 3
Space-filling representation of the one-dimensional chain.

Chloroacetic acid is a strong carboxylic acid with pK_a = 2.7 (Kartrum et al., 1961 ). A search of the Cambridge Structural Database (CSD: version 5.45, March 2024; Groom et al., 2016 ) retrieved 39 hits containing chloroacetic acid. Two polymorphs are known, i.e. the α- (Kanters & Roelofsen, 1976 ) and β-forms (Kanters et al., 1976 ). The α-form has two molecules in the asymmetric unit and has been subjected to a variable temperature study, i.e. in the range from 90 to 210 K (Ananyev et al., 2014). This study shows the Cl—C—C=O torsion angles average 22.33 (5) and 1.30 (5)° in the two independent molecules over the temperature range (Ananyev et al., 2014). Štoček et al. (2022 ) analysed the position of the H atom in the O—H⋯N hydrogen bond of the structure of chloroacetic acid with pyridine-4-carboxamide at ten different temperatures. It is also worth noting the crystal structure of quinolinium 2-carboxylate with 2-chloroacetic acid, a species known to exhibit anti-diabetic activity (Kavitha et al., 2021 ).

Synthesis and crystallization

A mixture of oxalic acid (0.1 mmol), 2-chloroacetic acid (0.1 mmol) and pyridine (0.1 mmol) in methanol (15 ml) was kept for crystallization. The title compound was obtained as a colourless crystals after 2–3 days, yield 87%.

Analysis calculated for C₉H₁₀ClNO₆ (M = 263.63): C 41.00, H 3.82, N 5.31; Found: C 40.89, H 3.77, N 5.29%. ¹H NMR (300 MHz, DMSO) δ 10.50 (1H, NH), 7.45–8.62 (5H, py) and 4.27 (2H, CH₂); OH not observed. ¹³C NMR (75 MHz, DMSO) δ 41.59, 124.44, 137.53, 148.70, 161.49, 168.72 and 169.23. ESI–MS: m/z: 264.58 [M+H]⁺.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The H atoms of the carboxylate and pyridinium ions were refined freely.

Table 2
Experimental details

Crystal data
Chemical formula	C₅H₆N⁺·C₂HO₄⁻·C₂H₃ClO₂
M_r	263.63
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	150
a, b, c (Å)	5.6911 (4), 7.9862 (4), 24.9303 (14)
β (°)	91.008 (3)
V (Å³)	1132.91 (12)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.35
Crystal size (mm)	0.37 × 0.26 × 0.15

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.872, 0.939
No. of measured, independent and observed [I > 2σ(I)] reflections	7091, 2127, 1963
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.611

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.031, 0.082, 1.10
No. of reflections	2127
No. of parameters	163
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.32
Computer programs: APEX4 and SAINT (Bruker, 2012 ), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ) and DIAMOND Brandenburg, 1999 ).

Structural data

CCDC reference: 2412697

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314624012422/tk4114sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314624012422/tk4114Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314624012422/tk4114Isup3.cml

checkCIF report

Computing details top

Pyridin-1-ium carboxyformate–2-chloroacetic acid (1/1) top

Crystal data top

C₅H₆N⁺·C₂HO₄⁻·C₂H₃ClO₂	F(000) = 544
M_r = 263.63	D_x = 1.546 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 5.6911 (4) Å	Cell parameters from 4685 reflections
b = 7.9862 (4) Å	θ = 2.7–25.7°
c = 24.9303 (14) Å	µ = 0.35 mm⁻¹
β = 91.008 (3)°	T = 150 K
V = 1132.91 (12) Å³	Plate, colourless
Z = 4	0.37 × 0.26 × 0.15 mm

Data collection top

Bruker APEXII CCD diffractometer	1963 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.030
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 25.7°, θ_min = 2.7°
T_min = 0.872, T_max = 0.939	h = −4→6
7091 measured reflections	k = −9→9
2127 independent reflections	l = −30→29

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)] = 0.031	Hydrogen site location: mixed
wR(F²) = 0.082	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0367P)² + 0.480P] where P = (F_o² + 2F_c²)/3
2127 reflections	(Δ/σ)_max = 0.001
163 parameters	Δρ_max = 0.19 e Å⁻³
0 restraints	Δρ_min = −0.32 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
Cl1	1.30381 (7)	0.60040 (5)	0.25074 (2)	0.02973 (14)
O1	0.8928 (2)	0.68016 (13)	0.31709 (5)	0.0274 (3)
O2	0.8175 (2)	0.41486 (13)	0.34182 (4)	0.0219 (3)
H2o	0.717 (4)	0.457 (2)	0.3605 (8)	0.033*
O3	0.62947 (17)	0.65703 (12)	0.47108 (4)	0.0177 (2)
O4	0.47024 (18)	0.51382 (13)	0.40178 (4)	0.0202 (2)
O5	0.19134 (18)	0.77629 (14)	0.49141 (5)	0.0259 (3)
O6	0.04269 (18)	0.56931 (13)	0.44029 (4)	0.0193 (2)
H6o	−0.090 (4)	0.608 (2)	0.4516 (8)	0.029*
N1	0.5976 (2)	0.86111 (15)	0.56167 (5)	0.0196 (3)
H1n	0.561 (3)	0.807 (2)	0.5329 (8)	0.024*
C1	1.1476 (3)	0.45380 (19)	0.29004 (6)	0.0211 (3)
H1a	1.091788	0.361048	0.266754	0.025*
H1b	1.255256	0.405946	0.317640	0.025*
C2	0.9388 (3)	0.53258 (18)	0.31738 (6)	0.0183 (3)
C3	0.4606 (2)	0.60253 (16)	0.44239 (6)	0.0146 (3)
C4	0.2140 (2)	0.65877 (17)	0.46095 (5)	0.0152 (3)
C5	0.8036 (3)	0.83223 (19)	0.58675 (6)	0.0222 (3)
H5	0.908910	0.750929	0.573162	0.027*
C6	0.8617 (3)	0.92126 (19)	0.63237 (6)	0.0244 (3)
H6	1.007643	0.902500	0.650458	0.029*
C7	0.7051 (3)	1.03825 (19)	0.65155 (6)	0.0245 (4)
H7	0.743544	1.100904	0.682892	0.029*
C8	0.4919 (3)	1.06414 (18)	0.62502 (6)	0.0236 (3)
H8	0.382242	1.143181	0.638176	0.028*
C9	0.4420 (3)	0.97347 (18)	0.57938 (6)	0.0221 (3)
H9	0.297675	0.990351	0.560428	0.027*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0322 (3)	0.0305 (2)	0.0269 (2)	−0.00243 (17)	0.01274 (18)	−0.00068 (16)
O1	0.0301 (6)	0.0210 (6)	0.0315 (6)	0.0058 (5)	0.0080 (5)	−0.0001 (5)
O2	0.0218 (6)	0.0212 (5)	0.0230 (6)	0.0007 (4)	0.0081 (5)	−0.0047 (4)
O3	0.0113 (5)	0.0204 (5)	0.0212 (5)	0.0000 (4)	−0.0005 (4)	−0.0032 (4)
O4	0.0167 (5)	0.0245 (5)	0.0197 (5)	−0.0009 (4)	0.0043 (4)	−0.0068 (4)
O5	0.0165 (6)	0.0284 (6)	0.0329 (6)	−0.0011 (5)	0.0039 (5)	−0.0153 (5)
O6	0.0100 (5)	0.0251 (5)	0.0229 (6)	−0.0001 (4)	0.0002 (4)	−0.0077 (4)
N1	0.0252 (7)	0.0165 (6)	0.0173 (6)	−0.0043 (5)	0.0025 (5)	−0.0038 (5)
C1	0.0218 (8)	0.0212 (7)	0.0203 (7)	0.0014 (6)	0.0034 (6)	−0.0013 (6)
C2	0.0179 (7)	0.0218 (7)	0.0150 (7)	0.0001 (6)	−0.0013 (6)	−0.0032 (6)
C3	0.0138 (7)	0.0139 (6)	0.0160 (7)	−0.0003 (5)	0.0015 (6)	0.0025 (5)
C4	0.0138 (7)	0.0177 (7)	0.0140 (7)	−0.0004 (5)	0.0002 (5)	0.0008 (5)
C5	0.0220 (8)	0.0182 (7)	0.0265 (8)	0.0016 (6)	0.0055 (6)	−0.0003 (6)
C6	0.0230 (8)	0.0250 (8)	0.0251 (8)	−0.0032 (6)	−0.0014 (7)	0.0009 (6)
C7	0.0336 (9)	0.0203 (7)	0.0198 (8)	−0.0076 (7)	0.0045 (7)	−0.0035 (6)
C8	0.0288 (9)	0.0158 (7)	0.0264 (8)	0.0018 (6)	0.0107 (7)	0.0000 (6)
C9	0.0200 (8)	0.0194 (7)	0.0271 (8)	−0.0009 (6)	0.0011 (6)	0.0035 (6)

Geometric parameters (Å, º) top

Cl1—C1	1.7755 (15)	C1—H1a	0.9900
O1—C2	1.2074 (19)	C1—H1b	0.9900
O2—C2	1.3215 (19)	C3—C4	1.551 (2)
O2—H2o	0.82 (2)	C5—C6	1.377 (2)
O3—C3	1.2653 (17)	C5—H5	0.9500
O4—C3	1.2377 (17)	C6—C7	1.382 (2)
O5—C4	1.2155 (18)	C6—H6	0.9500
O6—C4	1.3073 (17)	C7—C8	1.388 (2)
O6—H6o	0.86 (2)	C7—H7	0.9500
N1—C5	1.339 (2)	C8—C9	1.374 (2)
N1—C9	1.341 (2)	C8—H8	0.9500
N1—H1n	0.861 (19)	C9—H9	0.9500
C1—C2	1.517 (2)

C2—O2—H2o	110.2 (14)	O5—C4—C3	121.09 (13)
C4—O6—H6o	109.1 (13)	O6—C4—C3	113.36 (12)
C5—N1—C9	122.63 (14)	N1—C5—C6	119.49 (14)
C5—N1—H1n	120.0 (12)	N1—C5—H5	120.3
C9—N1—H1n	117.3 (12)	C6—C5—H5	120.3
C2—C1—Cl1	112.23 (10)	C5—C6—C7	119.22 (15)
C2—C1—H1a	109.2	C5—C6—H6	120.4
Cl1—C1—H1a	109.2	C7—C6—H6	120.4
C2—C1—H1b	109.2	C6—C7—C8	119.97 (14)
Cl1—C1—H1b	109.2	C6—C7—H7	120.0
H1a—C1—H1b	107.9	C8—C7—H7	120.0
O1—C2—O2	125.61 (14)	C9—C8—C7	118.84 (14)
O1—C2—C1	125.02 (14)	C9—C8—H8	120.6
O2—C2—C1	109.37 (12)	C7—C8—H8	120.6
O4—C3—O3	127.95 (13)	N1—C9—C8	119.83 (15)
O4—C3—C4	117.59 (12)	N1—C9—H9	120.1
O3—C3—C4	114.44 (12)	C8—C9—H9	120.1
O5—C4—O6	125.55 (13)

Cl1—C1—C2—O1	−6.4 (2)	C9—N1—C5—C6	−0.5 (2)
Cl1—C1—C2—O2	174.23 (10)	N1—C5—C6—C7	0.4 (2)
O4—C3—C4—O5	−161.69 (14)	C5—C6—C7—C8	0.3 (2)
O3—C3—C4—O5	17.27 (19)	C6—C7—C8—C9	−0.9 (2)
O4—C3—C4—O6	17.70 (18)	C5—N1—C9—C8	0.0 (2)
O3—C3—C4—O6	−163.35 (12)	C7—C8—C9—N1	0.7 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2o···O4	0.82 (2)	1.81 (2)	2.6209 (15)	170 (2)
O6—H6o···O3ⁱ	0.86 (2)	1.72 (2)	2.5834 (14)	171.8 (19)
N1—H1n···O3	0.861 (19)	1.995 (19)	2.7935 (16)	153.8 (17)
N1—H1n···O5	0.861 (19)	2.339 (18)	2.9546 (17)	128.7 (15)
C1—H1a···O1ⁱⁱ	0.99	2.54	3.4555 (19)	153
C1—H1b···O4ⁱⁱⁱ	0.99	2.56	3.3439 (19)	136
C5—H5···O6^iv	0.95	2.59	3.3946 (18)	142
C8—H8···O1^v	0.95	2.40	3.3400 (19)	172
C9—H9···O5	0.95	2.49	3.0356 (19)	116

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

Acknowledgements

This work was supported by Baku State University (Azerbaijan), Western Caspian University (Azerbaijan), Azerbaijan Medical University, Baku Engineering University (Azerbaijan) and Khazar University (Azerbaijan).

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