A salt from biologically active com­pounds pyridine-2,3-di­carb­oxy­lic (quinolinic) acid and cytosine

Książkiewicz, O.

doi:10.1107/S2053229624009598

A salt from biologically active compounds pyridine-2,3-dicarboxylic (quinolinic) acid and cytosine

Biologically active compounds are highly sought-after materials for developing novel structures applicable to industry. Cytosine and pyridine-2,3-dicarboxylic acid (quinolinic acid) are notably significant environmentally. Cytosine, a pyrimidine derivative, features a six-membered ring with a ketone and an amino group, constituting a fundamental nitrogenous base found in deoxyribonucleic acid (DNA). The present synthesis yielded a salt of dipyridine-2,3-dicarboxylic acid with cytosine, wherein a proton was transferred from a carboxyl group of quinolinic acid to a ring N atom in the cytosine molecule giving the salt 6-amino-2-oxo-2,3-dihydropyrimidin-1-ium 3-carboxypyridine-2-carboxylate, C₄H₆N₃O⁺·C₇H₄NO₄⁻. A Hirshfeld surface analysis was conducted to examine the contribution of contacts within the salt. The structure of the salt was compared to other structures containing quinolinic acid in the Cambridge Structural Database (CSD).

Keywords: crystal structure; cytosine; pyridine-2,3-dicarboxylic acid; hydrogen bond; Hirshfeld surface analysis; nitrogenous base; quinolinic acid.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229624009598/wv3015sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229624009598/wv3015Isup2.hkl Contains datablock I

CCDC reference: 2387832

Computing details top

6-Amino-2-oxo-2,3-dihydropyrimidin-1-ium 3-carboxypyridine-2-carboxylate top

Crystal data top

C₄H₆N₃O⁺·C₇H₄NO₄⁻	F(000) = 576
M_r = 278.23	D_x = 1.676 Mg m⁻³
Monoclinic, P2₁/n	Cu Kα radiation, λ = 1.54184 Å
a = 3.6374 (1) Å	Cell parameters from 6170 reflections
b = 11.3412 (4) Å	θ = 4.2–76.0°
c = 26.7510 (8) Å	µ = 1.16 mm⁻¹
β = 92.162 (3)°	T = 100 K
V = 1102.76 (6) Å³	Needle, colourless
Z = 4	0.45 × 0.03 × 0.02 mm

Data collection top

Rigaku XtaLAB Synergy Dualflex diffractometer with a HyPix detector	2181 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source	2021 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.045
Detector resolution: 10.0000 pixels mm^-1	θ_max = 76.5°, θ_min = 3.3°
ω scans	h = −4→4
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2021)	k = −14→13
T_min = 0.498, T_max = 1.000	l = −30→32
10377 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)] = 0.050	w = 1/[σ²(F_o²) + (0.0427P)² + 1.7012P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.127	(Δ/σ)_max < 0.001
S = 1.14	Δρ_max = 0.38 e Å⁻³
2181 reflections	Δρ_min = −0.26 e Å⁻³
198 parameters	Extinction correction: SHELXL2018 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0024 (5)
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
O3A	0.4919 (5)	0.79064 (15)	0.45863 (6)	0.0239 (4)
O2A	0.6094 (5)	0.60079 (14)	0.65820 (6)	0.0233 (4)
O2B	0.7810 (5)	0.55993 (14)	0.58169 (6)	0.0226 (4)
O1	0.7782 (5)	0.45610 (14)	0.76858 (6)	0.0232 (4)
O3B	0.7046 (5)	0.63242 (14)	0.49696 (6)	0.0236 (4)
H3B	0.724532	0.605880	0.526248	0.035*
N1	0.9615 (5)	0.39974 (17)	0.69187 (7)	0.0176 (4)
N4	0.3371 (5)	0.80471 (17)	0.63457 (7)	0.0198 (4)
N2	1.0591 (6)	0.27708 (17)	0.76082 (7)	0.0211 (4)
N3	1.1454 (6)	0.34897 (19)	0.61351 (7)	0.0217 (4)
C5	0.2680 (6)	0.9002 (2)	0.54065 (8)	0.0181 (5)
H5	0.244847	0.933757	0.508151	0.022*
C1	1.1228 (6)	0.32223 (19)	0.66060 (8)	0.0182 (5)
C9	0.4240 (6)	0.78806 (19)	0.54652 (8)	0.0180 (5)
C6	0.1474 (6)	0.9629 (2)	0.58090 (8)	0.0199 (5)
H6	0.041579	1.039010	0.576732	0.024*
C11	0.5447 (6)	0.7343 (2)	0.49746 (8)	0.0179 (5)
C2	0.9243 (6)	0.3822 (2)	0.74269 (8)	0.0191 (5)
C10	0.6247 (6)	0.6251 (2)	0.61343 (8)	0.0187 (5)
C8	0.4556 (6)	0.7427 (2)	0.59570 (8)	0.0172 (5)
C7	0.1857 (6)	0.9112 (2)	0.62764 (8)	0.0209 (5)
H7	0.101541	0.952883	0.655820	0.025*
C4	1.2603 (6)	0.21507 (19)	0.68180 (9)	0.0205 (5)
H4	1.375181	0.157975	0.661612	0.025*
C3	1.2240 (7)	0.1963 (2)	0.73130 (9)	0.0217 (5)
H3	1.315415	0.125175	0.745830	0.026*
H2	1.058 (8)	0.268 (3)	0.7960 (12)	0.030 (8)*
H3A	1.252 (8)	0.303 (3)	0.5923 (11)	0.028 (8)*
H1	0.861 (9)	0.466 (3)	0.6792 (11)	0.034 (8)*
H3C	1.036 (9)	0.414 (3)	0.6022 (11)	0.034 (8)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O3A	0.0356 (10)	0.0230 (9)	0.0132 (8)	0.0039 (7)	0.0048 (7)	0.0014 (6)
O2A	0.0336 (9)	0.0215 (8)	0.0150 (8)	0.0038 (7)	0.0026 (7)	0.0028 (6)
O2B	0.0341 (9)	0.0179 (8)	0.0160 (8)	0.0042 (7)	0.0044 (7)	0.0010 (6)
O1	0.0306 (9)	0.0224 (8)	0.0168 (8)	0.0048 (7)	0.0060 (7)	−0.0006 (6)
O3B	0.0371 (10)	0.0199 (8)	0.0139 (8)	0.0061 (7)	0.0038 (7)	0.0005 (6)
N1	0.0246 (10)	0.0139 (9)	0.0144 (9)	0.0018 (8)	0.0024 (7)	0.0004 (7)
N4	0.0261 (10)	0.0176 (9)	0.0159 (9)	−0.0016 (8)	0.0026 (8)	−0.0015 (7)
N2	0.0291 (11)	0.0188 (10)	0.0157 (10)	0.0017 (8)	0.0046 (8)	0.0029 (7)
N3	0.0310 (11)	0.0193 (10)	0.0151 (10)	0.0033 (9)	0.0035 (8)	−0.0015 (8)
C5	0.0196 (11)	0.0181 (11)	0.0167 (11)	−0.0025 (9)	0.0002 (8)	0.0012 (8)
C1	0.0214 (11)	0.0165 (11)	0.0168 (11)	−0.0023 (9)	0.0015 (8)	−0.0027 (8)
C9	0.0199 (11)	0.0176 (11)	0.0168 (11)	−0.0038 (9)	0.0025 (8)	−0.0006 (8)
C6	0.0204 (11)	0.0163 (11)	0.0230 (11)	−0.0011 (9)	0.0017 (9)	−0.0006 (9)
C11	0.0198 (11)	0.0182 (11)	0.0157 (10)	−0.0019 (9)	0.0022 (8)	−0.0009 (8)
C2	0.0224 (11)	0.0178 (11)	0.0171 (11)	−0.0012 (9)	0.0026 (9)	0.0005 (8)
C10	0.0218 (11)	0.0172 (11)	0.0171 (11)	−0.0031 (9)	0.0013 (8)	−0.0014 (8)
C8	0.0200 (11)	0.0167 (11)	0.0150 (10)	−0.0032 (9)	0.0021 (8)	−0.0020 (8)
C7	0.0241 (11)	0.0186 (11)	0.0202 (11)	−0.0022 (9)	0.0053 (9)	−0.0040 (9)
C4	0.0234 (11)	0.0148 (10)	0.0234 (12)	0.0015 (9)	0.0033 (9)	−0.0023 (9)
C3	0.0256 (12)	0.0156 (11)	0.0239 (12)	0.0007 (9)	0.0009 (9)	0.0019 (9)

Geometric parameters (Å, º) top

O3A—C11	1.228 (3)	N3—H3A	0.87 (3)
O2A—C10	1.232 (3)	N3—H3C	0.88 (3)
O2B—C10	1.276 (3)	C5—H5	0.9500
O1—C2	1.222 (3)	C5—C9	1.399 (3)
O3B—H3B	0.8400	C5—C6	1.376 (3)
O3B—C11	1.294 (3)	C1—C4	1.424 (3)
N1—C1	1.362 (3)	C9—C11	1.527 (3)
N1—C2	1.385 (3)	C9—C8	1.413 (3)
N1—H1	0.90 (3)	C6—H6	0.9500
N4—C8	1.340 (3)	C6—C7	1.383 (3)
N4—C7	1.338 (3)	C10—C8	1.536 (3)
N2—C2	1.371 (3)	C7—H7	0.9500
N2—C3	1.363 (3)	C4—H4	0.9500
N2—H2	0.95 (3)	C4—C3	1.353 (3)
N3—C1	1.301 (3)	C3—H3	0.9500

C11—O3B—H3B	109.5	C7—C6—H6	121.2
C1—N1—C2	124.8 (2)	O3A—C11—O3B	120.8 (2)
C1—N1—H1	119.3 (19)	O3A—C11—C9	118.6 (2)
C2—N1—H1	115.9 (19)	O3B—C11—C9	120.64 (19)
C7—N4—C8	120.61 (19)	O1—C2—N1	121.2 (2)
C2—N2—H2	115.4 (18)	O1—C2—N2	123.6 (2)
C3—N2—C2	122.6 (2)	N2—C2—N1	115.17 (19)
C3—N2—H2	121.5 (18)	O2A—C10—O2B	123.7 (2)
C1—N3—H3A	122 (2)	O2A—C10—C8	117.54 (19)
C1—N3—H3C	119 (2)	O2B—C10—C8	118.75 (19)
H3A—N3—H3C	119 (3)	N4—C8—C9	120.9 (2)
C9—C5—H5	119.3	N4—C8—C10	110.66 (18)
C6—C5—H5	119.3	C9—C8—C10	128.40 (19)
C6—C5—C9	121.5 (2)	N4—C7—C6	122.3 (2)
N1—C1—C4	117.3 (2)	N4—C7—H7	118.8
N3—C1—N1	119.3 (2)	C6—C7—H7	118.8
N3—C1—C4	123.4 (2)	C1—C4—H4	120.7
C5—C9—C11	113.27 (19)	C3—C4—C1	118.6 (2)
C5—C9—C8	117.0 (2)	C3—C4—H4	120.7
C8—C9—C11	129.7 (2)	N2—C3—H3	119.2
C5—C6—H6	121.2	C4—C3—N2	121.5 (2)
C5—C6—C7	117.7 (2)	C4—C3—H3	119.2

O2A—C10—C8—N4	4.3 (3)	C6—C5—C9—C11	−179.2 (2)
O2A—C10—C8—C9	−177.0 (2)	C6—C5—C9—C8	−0.6 (3)
O2B—C10—C8—N4	−173.8 (2)	C11—C9—C8—N4	178.9 (2)
O2B—C10—C8—C9	4.9 (3)	C11—C9—C8—C10	0.3 (4)
N1—C1—C4—C3	0.0 (3)	C2—N1—C1—N3	−179.3 (2)
N3—C1—C4—C3	179.7 (2)	C2—N1—C1—C4	0.5 (3)
C5—C9—C11—O3A	−1.1 (3)	C2—N2—C3—C4	−0.8 (4)
C5—C9—C11—O3B	177.8 (2)	C8—N4—C7—C6	−0.7 (3)
C5—C9—C8—N4	0.6 (3)	C8—C9—C11—O3A	−179.4 (2)
C5—C9—C8—C10	−177.9 (2)	C8—C9—C11—O3B	−0.5 (4)
C5—C6—C7—N4	0.7 (3)	C7—N4—C8—C9	0.0 (3)
C1—N1—C2—O1	179.5 (2)	C7—N4—C8—C10	178.8 (2)
C1—N1—C2—N2	−1.0 (3)	C3—N2—C2—O1	−179.5 (2)
C1—C4—C3—N2	0.2 (4)	C3—N2—C2—N1	1.1 (3)
C9—C5—C6—C7	0.0 (3)

Selected geometric parameters (Å, °) of crystal structure (I) top

Quinolinic acid		Cytosine
Bond lengths
O2A—C10	1.232 (3)	O1—C2	1.222 (3)
N4—C7	1.338 (3)	N1—C1	1.362 (3)
O2B—C10	1.276 (3)	N1—C2	1.385 (3)
N4—C8	1.340 (3)	N2—C2	1.371 (3)
O3B—C11	1.294 (3)	N2—C3	1.363 (3)
		N3—C1	1.301 (3)

Valence angles
C7—N4—C8	120.61 (19)	C1—N1—C2	124.8 (2)
N4—C7—C6	122.3 (2)	C2—N2—C3	122.6 (2)
N4—C8—C9	120.9 (2)	N1—C1—N3	119.3 (2)
N4—C8—C10	110.66 (18)	N1—C1—N4	117 (1)
O2A—C10—O2B	123.7 (2)	N3—C1—C4	123 (1)
O2A—C10—C8	117.54 (19)	O1—C2—N1	121.2 (2)
O2B—C10—C8	118.75 (19)	O1—C2—N2	123.6 (2)
O3A—C11—O3B	120.8 (2)	N1—C2—N2	115.17 (19)
O3A—C11—C9	118.6 (2)	N2—C3—C4	121.5 (2)
O3B—C11—C9	120.64 (19)	C1—N1—H1	119.3 (19)
C11—O3B—H3B	109.5	C2—N1—H1	115.9 (19)
N4—C7—H7	119	C2—N2—H2	115.4 (18)
		C3—N2—H2	121.5 (18)
		C1—N3—H3A	122 (2)
		C1—N3—H3C	119 (2)
		H3A—N3—H3C	119 (3)
		N2—C3—H3	119

Parameters of selected hydrogen bonds (Å, °) top

D—H···A	D—H	H···A	D···A	D—H···A
Compound (I)
N1—H1···O2A	0.90 (3)	1.86 (3)	2.750 (3)	173 (3)
N2—H2···O2Aⁱ	0.95 (3)	2.35 (3)	3.028 (3)	128 (3)
N2—H2···N4ⁱ	0.95 (3)	1.93 (3)	2.827 (3)	158 (3)
N3—H3A···O3Aⁱⁱ	0.87 (3)	1.99 (3)	2.857 (3)	176 (3)
N3—H3C···O2B	0.89 (3)	1.97 (3)	2.850 (3)	176 (3)
C3—H3···O1ⁱⁱⁱ	0.95	2.46	3.271 (3)	143
C7—H7···O1^iv	0.95	2.49	3.342 (3)	149
O3B—H3B···O2B (intra)	0.84	1.58	2.417 (2)	177

AFUSEC (Elakkiya & Anitha, 2019)
N3—H3C···O2B	0.86	2.03	2.879	172.1
N1—H1···O2A	0.86	2.48	3.331	172.5
O3B—H3B···O2B (intra)	0.82	1.59	2.399	169.2

MICGOX (Chen et al., 2018)
N3—H3C···O2B	0.86	2.09	2.946	172.0
N1—H1···O2A	0.86	1.87	2.712	167.4
O3B—H3B···O2B (intra)	0.82	1.59	2.412	178.0

Symmetry codes: (i) -x+3/2, y-1/2, -z+3/2; (ii) -x+2, -y+1, -z+1; (iii) -x+5/2, y-1/2, -z+3/2; (iv) -x+1/2, y+1/2, -z+3/2.

Parameters of the selected π–π stacking interactions (Å, °) top

π–π stacking interaction	Cg···Cg	PLN1,PLN2	d(Cg···PLN)	Slippage	Symmetry code
Cg(QUI)···Cg(QUI)	3.6372 (12)	0.04 (10)	3.2730 (9), 3.2729 (9)	1.587	x-1, y, z
Cg(QUI)A···Cg(QUI)A	3.6376 (12)	0.04 (10)	3.2731 (9), 3.2731 (9)	1.587	x+1, y, z
Cg(CYT)···Cg(CYT)	3.6375 (13)	0.03 (10)	3.2021 (9), 3.2021 (9)	1.726	x-1, y, z
Cg(CYT)A···Cg(CYT)A	3.6373 (13)	0.03 (10)	3.2020 (9), 3.2020 (9)	1.726	x+1, y, z

Notes: Cg is the centre of gravity of the ring; QUI is quinolinic acid; CYT is cytosine; PLN corresponds to the ring plane calculated by the least-squares method based of the positions of all ring-forming atoms; PLN1,PLN2 is the dihedral angle between neighbouring planes; d(Cg···PLN) is the mean perpendicular distance between Cg and the neighbouring stacking plane; `slippage' is the distance between Cg and d(Cg···PLN); `A' denotes the second molecular stacking of the asymmetric unit.

Selected results of a search of the CSD top

Formula	CSD refcode	Reference
Molecular cocrystals
C₁₂H₈N₄O.C₇H₅NO₄	MEHFOV	Wang et al. (2006)

Cocrystals/salts
C₄H₆N₃⁺.C₇H₄NO₄^-	AFUSEC	Elakkiya & Anitha (2019)
C₄H₈N₃O⁺.C₇H₄NO₄^-	HAHJAF	Matheswari et al. (2021)
C₁₀H₁₀N₂²⁺.2C₇H₄NO₄^-	KOMTIQ	Soleimannejad et al. (2009)
C₁₀H₁₀N₂²⁺.2C₇H₄NO₄^-	KOMTIQ01	Kumaresan et al. (2013)
0.5C₄H₁₂N₂²⁺.C₇H₄NO₄^-	XISREX	Aghabozorg et al. (2008)
C₄H₈N₅⁺.C₇H₄NO₄^-	MICGOX	Chen et al. (2018)
C₁₆H₁₄N₃O⁺.C₇H₄NO₄^-	NUSVIH	Kalita & Baruah (2010)
C₆H₇N₂O⁺.C₇H₄NO₄^-	PAMWIL	Das & Baruah (2011)

Cocrystals/salts/solvates
C₃H₁₂N₂²⁺.C₇H₃NO₄^2-.H₂O	GIHGOU	Manteghi et al. (2007)
CH₇N₄⁺.C₇H₄NO₄^-.H₂O	XADQEB	Packiaraj et al. (2015)
C₆H₁₄N₂²⁺.2C₇H₄NO₄^-.2.17H₂O	NIQQUA	Seethalakshmi et al. (2007)
C₆H₇N₂O⁺.C₇H₄NO₄^-.H₂O	PAMXEI	Das & Baruah (2011)
C₄H₁₂N₂²⁺.C₇H₃NO₄^2-.H₂O	UREZOH	Manteghi et al. (2011)

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A salt from biologically active com­pounds pyridine-2,3-di­carb­oxy­lic (quinolinic) acid and cytosine

Supporting information

A salt from biologically active compounds pyridine-2,3-dicarboxylic (quinolinic) acid and cytosine