PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o3058–o3059.
Published online 2009 November 11. doi:  10.1107/S1600536809046571
PMCID: PMC2972138

Cytosinium–hydrogen maleate–cytosine (1/1/1)

Abstract

The title organic salt, C4H6N3O+·C4H3O4 ·C4H5N3O, was synthesized from cytosine base and maleic acid. An intra­molecular O—H(...)O hydrogen bond occurs in the hydrogen maleate anion. The crystal packing is stabilized by inter­molecular N—H(...)O, N—H(...)N and C—H(...)O hydrogen bonds, giving rise to a nearly planar two-dimensional network parallel to (101).

Related literature

For background to cytosine, see: Devlin (1986 [triangle]); Johnson & Coghill (1925 [triangle]); Mahan et al. (2004 [triangle]). For the structure of cytosine, see: Barker & Marsh (1964 [triangle]) and for that of cytosine monohydrate, see: Jeffrey & Kinoshita (1963 [triangle]); Swamy et al. (2001 [triangle]). For the stuctures of inorganic cytosinium salts, see: Mandel (1977 [triangle]); Cherouana et al. (2003 [triangle]); Jaskólski (1989 [triangle]); Bagieu-Beucher (1990 [triangle]) and for those of cytosinium salts of organic acids, see: Gdaniec et al. (1989 [triangle]); Smith et al. (2005 [triangle]); Balasubramanian et al. (1996 [triangle]). For the hydrogen maleate anion, see: Madsen & Larsen (1998 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o3058-scheme1.jpg

Experimental

Crystal data

  • C4H6N3O+·C4H3O4 ·C4H5N3O
  • M r = 338.29
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o3058-efi7.jpg
  • a = 27.3226 (5) Å
  • b = 7.3618 (2) Å
  • c = 14.6742 (4) Å
  • β = 93.905 (1)°
  • V = 2944.77 (13) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.13 mm−1
  • T = 298 K
  • 0.3 × 0.15 × 0.1 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: none
  • 3490 measured reflections
  • 3485 independent reflections
  • 2603 reflections with I > 2σ(I)
  • R int = 0.043

Refinement

  • R[F 2 > 2σ(F 2)] = 0.048
  • wR(F 2) = 0.136
  • S = 1.07
  • 3485 reflections
  • 202 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.36 e Å−3
  • Δρmin = −0.23 e Å−3

Data collection: KappaCCD Server Software (Nonius, 1998 [triangle]); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SIR2004 (Burla et al., 2005 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809046571/dn2509sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809046571/dn2509Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We wish to thank Dr M. Giorgi, Faculté des Sciences et Techniques de Saint Jérome, Marseille, France, for providing diffraction facilities and le Centre Universitaire de Khenchela for financial support.

supplementary crystallographic information

Comment

The pyrimidine base, Cytosine, leads to the nucleoside cytidine and its corresponding nucleotide: cytidine 5'-monophosphate. It may be found in very small quantities as a post-modified form, 5-methylcytosine, in certain nucleic acids (Devlin, 1986) such as in tuberculinic acid (Johnson & Coghill, 1925). More recently, 5-fluoro-cytosine (5-FC) has been used as a prodrug in suicide gene therapy of cancer with the crystal structure of bacterial cytosine deaminase (bCD) (Mahan et al., 2004).

The crystal structures of cytosine (Barker & Marsh, 1964) and cytosine monohydrate (Jeffrey & Kinoshita, 1963) were determined many years ago. (Swamy et al., 2001)]. Many inorganic cytosinium salts have been previously synthesized: chloride (Mandel, 1977), nitrate (Cherouana et al., 2003) and dihydrogenphosphate (Jaskólski, 1989; Bagieu-Beucher, 1990). Cytosinium salts of organic acids are also common, the structures of a number of these including trichloroacetate (Gdaniec et al., 1989), Cytosinium 3,5-dinitrosalicylate (Smith, et al., 2005) and hydrogen maleate (Balasubramanian et al., 1996) have been recently reported.

We report here the molecular structure of a novel compound (I) formed from the reaction of cytosine with maleic acid, namely cytosine cytosinium hydrogen maleate. It was prepared in order to extend our study on D—H···A hydrogen bonding in organic systems.

The asymmetric unit in (I) contains a hydrogen maleate anion, a cytosinium cation and a cytosine molecule which are held together by N—H···O and N—H···N hydrogen bonds (Fig. 1; Table 1). As observed in other hydrogen maleate anion, the H atom is roughly in between O1 and O3 (Madsen & Larsen, 1998).

In the crystal packing (Fig.2), cytosine bases and cytosinium cations are linked by N8A–H1N···O7A and N8B–H3N···O7B hydrogen-bonds forming a C(6)R22(8) graph-set motif and yielding infinite chains running parallel to the b axis. These chains are connected through N–H···O and C–H···O hydrogen bonds involving the O2 and O4 atoms of the maleate thus generating R23(10) and R22(7) graph-set motifs (Bernstein et al., 1995) and giving rise to a planar two-dimensionnal network parallel to the (1 0 1) plane (Table 1, Fig. 2).

Experimental

The title compound was prepared by the reaction between cytosine and maleic acid. A colorless prismatic single-cristals were grown after few days of evaporation at room temperature.

Refinement

All H atoms attached to C and N atoms were fixed geometrically and treated as riding with C—H = 0.93 Å and N—H = 0.86 Å with Uiso(H) = 1.2Ueq(C or N). H atom attached to O atom have been freely refined of water molecule were with Uiso(H) = 1.5Ueq(O).

Figures

Fig. 1.
ORTEP view of the asymmetric unit of (I) with the atom labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small spheres of arbitrary radii. Hydrogen bonds are shown as dashed lines.
Fig. 2.
Partial packing view showing the formation of the two dimensionnal network through N-H···O, N-H···N and C-H···O hydrogen bonds. H atoms not involved in hydrogen bondings have been ...

Crystal data

C4H6N3O+·C4H3O4·C4H5N3OF(000) = 1408
Mr = 338.29Dx = 1.526 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
a = 27.3226 (5) ÅCell parameters from 3490 reflections
b = 7.3618 (2) Åθ = 2.8–28.0°
c = 14.6742 (4) ŵ = 0.13 mm1
β = 93.905 (1)°T = 298 K
V = 2944.77 (13) Å3Prism, colourless
Z = 80.3 × 0.15 × 0.1 mm

Data collection

Nonius KappaCCD diffractometer2603 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.043
graphiteθmax = 28.0°, θmin = 2.8°
ω–θ scansh = 0→35
3490 measured reflectionsk = 0→9
3485 independent reflectionsl = −19→19

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.136H atoms treated by a mixture of independent and constrained refinement
S = 1.07w = 1/[σ2(Fo2) + (0.0596P)2 + 1.9669P] where P = (Fo2 + 2Fc2)/3
3485 reflections(Δ/σ)max < 0.001
202 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = −0.23 e Å3

Special details

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. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

xyzUiso*/Ueq
O7B0.33929 (4)1.06422 (15)0.29275 (9)0.0427 (3)
N1B0.40074 (5)0.90020 (18)0.23748 (9)0.0387 (3)
H1B0.41470.99760.21990.046*
N3B0.33603 (5)0.75680 (17)0.30317 (10)0.0356 (3)
H3B0.30850.76160.32810.043*
N8B0.33306 (6)0.44790 (19)0.31458 (11)0.0497 (4)
H8B10.30550.45910.33900.060*
H8B20.34520.34170.30670.060*
C2B0.35779 (6)0.9147 (2)0.27857 (11)0.0345 (3)
C4B0.35667 (6)0.5930 (2)0.28930 (11)0.0377 (4)
C5B0.40201 (6)0.5833 (2)0.24822 (12)0.0428 (4)
H5B0.41710.47220.23900.051*
C6B0.42225 (6)0.7386 (2)0.22325 (12)0.0429 (4)
H6B0.45180.73560.19540.052*
O7A0.23768 (4)0.47389 (15)0.38025 (9)0.0467 (3)
N1A0.17582 (5)0.63603 (19)0.43517 (10)0.0406 (3)
H1A0.16050.53780.44740.049*
N3A0.24320 (5)0.78198 (17)0.37790 (10)0.0366 (3)
N8A0.24807 (6)1.09115 (19)0.37624 (12)0.0508 (4)
H8A10.27571.08100.35190.061*
H8A20.23651.19700.38730.061*
C2A0.21960 (6)0.6237 (2)0.39693 (11)0.0355 (3)
C4A0.22347 (6)0.9448 (2)0.39665 (12)0.0378 (4)
C5A0.17782 (6)0.9546 (2)0.43695 (13)0.0429 (4)
H5A0.16401.06590.45060.051*
C6A0.15542 (6)0.7983 (2)0.45467 (13)0.0433 (4)
H6A0.12540.80080.48080.052*
O10.00023 (4)0.51357 (17)0.62970 (9)0.0448 (3)
O2−0.05080 (5)0.30095 (18)0.67256 (10)0.0541 (4)
O30.07419 (4)0.53110 (16)0.54870 (8)0.0419 (3)
H30.0374 (7)0.532 (3)0.5856 (13)0.063*
O40.12212 (5)0.33885 (18)0.48081 (9)0.054
C10.08607 (6)0.3706 (2)0.52447 (11)0.038
C20.05603 (7)0.2114 (2)0.54876 (14)0.049
H10.06760.10010.52930.059*
C30.01551 (7)0.2018 (2)0.59356 (14)0.0504 (5)
H20.00330.08500.60030.061*
C4−0.01358 (6)0.3478 (2)0.63484 (12)0.0402 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O7B0.0443 (6)0.0235 (6)0.0615 (8)0.0016 (4)0.0113 (5)−0.0015 (5)
N1B0.0405 (7)0.0322 (7)0.0444 (8)−0.0021 (5)0.0104 (6)−0.0013 (6)
N3B0.0351 (7)0.0245 (6)0.0479 (8)0.0008 (5)0.0077 (6)−0.0014 (5)
N8B0.0544 (9)0.0260 (7)0.0704 (10)0.0031 (6)0.0172 (8)0.0006 (7)
C2B0.0369 (8)0.0278 (8)0.0385 (8)0.0007 (6)0.0013 (6)−0.0017 (6)
C4B0.0442 (9)0.0267 (8)0.0419 (9)0.0022 (6)0.0008 (7)−0.0022 (6)
C5B0.0440 (9)0.0352 (9)0.0500 (10)0.0104 (7)0.0084 (8)−0.0028 (7)
C6B0.0408 (9)0.0430 (10)0.0461 (9)0.0061 (7)0.0104 (7)−0.0036 (7)
O7A0.0452 (7)0.0239 (6)0.0724 (8)0.0005 (5)0.0135 (6)−0.0010 (6)
N1A0.0380 (7)0.0313 (7)0.0533 (8)−0.0045 (6)0.0099 (6)−0.0021 (6)
N3A0.0374 (7)0.0215 (6)0.0514 (8)0.0010 (5)0.0061 (6)0.0001 (6)
N8A0.0503 (8)0.0243 (7)0.0793 (11)0.0016 (6)0.0165 (8)−0.0002 (7)
C2A0.0361 (8)0.0259 (8)0.0446 (9)0.0003 (6)0.0029 (7)−0.0001 (6)
C4A0.0392 (8)0.0277 (8)0.0465 (9)0.0027 (6)0.0016 (7)−0.0014 (7)
C5A0.0415 (9)0.0325 (8)0.0550 (10)0.0077 (7)0.0059 (7)−0.0060 (7)
C6A0.0362 (8)0.0433 (10)0.0510 (10)0.0031 (7)0.0082 (7)−0.0062 (8)
O10.0403 (6)0.0392 (7)0.0566 (7)−0.0014 (5)0.0154 (5)−0.0037 (6)
O20.0455 (7)0.0501 (8)0.0694 (9)−0.0055 (6)0.0239 (6)0.0023 (7)
O30.0418 (6)0.0349 (6)0.0506 (7)−0.0033 (5)0.0137 (5)−0.0028 (5)
O40.0520.0460.0670.0000.030−0.006
C10.0370.0380.040−0.0010.0070.000
C20.0530.0310.0670.0020.020−0.002
C30.0526 (10)0.0309 (9)0.0696 (12)−0.0038 (7)0.0179 (9)0.0020 (8)
C40.0367 (8)0.0401 (9)0.0443 (9)−0.0023 (7)0.0067 (7)0.0016 (7)

Geometric parameters (Å, °)

O7B—C2B1.2348 (19)N3A—C2A1.3697 (19)
N1B—C6B1.350 (2)N8A—C4A1.315 (2)
N1B—C2B1.360 (2)N8A—H8A10.8600
N1B—H1B0.8600N8A—H8A20.8600
N3B—C4B1.353 (2)C4A—C5A1.418 (2)
N3B—C2B1.365 (2)C5A—C6A1.337 (2)
N3B—H3B0.8600C5A—H5A0.9300
N8B—C4B1.314 (2)C6A—H6A0.9300
N8B—H8B10.8600O1—C41.281 (2)
N8B—H8B20.8600O1—H31.25 (2)
C4B—C5B1.416 (2)O2—C41.239 (2)
C5B—C6B1.332 (2)O3—C11.282 (2)
C5B—H5B0.9300O3—H31.17 (2)
C6B—H6B0.9300O4—C11.2333 (19)
O7A—C2A1.2398 (19)C1—C21.488 (2)
N1A—C6A1.357 (2)C2—C31.327 (3)
N1A—C2A1.358 (2)C2—H10.9300
N1A—H1A0.8600C3—C41.490 (3)
N3A—C4A1.3503 (19)C3—H20.9300
C6B—N1B—C2B122.40 (14)H8A1—N8A—H8A2120.0
C6B—N1B—H1B118.8O7A—C2A—N1A121.00 (14)
C2B—N1B—H1B118.8O7A—C2A—N3A121.13 (14)
C4B—N3B—C2B121.71 (13)N1A—C2A—N3A117.87 (13)
C4B—N3B—H3B119.1N8A—C4A—N3A117.61 (15)
C2B—N3B—H3B119.1N8A—C4A—C5A122.06 (15)
C4B—N8B—H8B1120.0N3A—C4A—C5A120.33 (15)
C4B—N8B—H8B2120.0C6A—C5A—C4A117.66 (15)
H8B1—N8B—H8B2120.0C6A—C5A—H5A121.2
O7B—C2B—N1B121.34 (14)C4A—C5A—H5A121.2
O7B—C2B—N3B121.59 (14)C5A—C6A—N1A121.10 (15)
N1B—C2B—N3B117.07 (13)C5A—C6A—H6A119.4
N8B—C4B—N3B117.68 (15)N1A—C6A—H6A119.4
N8B—C4B—C5B122.64 (15)C4—O1—H3112.6 (11)
N3B—C4B—C5B119.67 (15)C1—O3—H3111.8 (12)
C6B—C5B—C4B117.72 (15)O4—C1—O3123.04 (15)
C6B—C5B—H5B121.1O4—C1—C2116.62 (16)
C4B—C5B—H5B121.1O3—C1—C2120.34 (14)
C5B—C6B—N1B121.38 (15)C3—C2—C1130.78 (17)
C5B—C6B—H6B119.3C3—C2—H1114.6
N1B—C6B—H6B119.3C1—C2—H1114.6
C6A—N1A—C2A122.13 (14)C2—C3—C4130.43 (16)
C6A—N1A—H1A118.9C2—C3—H2114.8
C2A—N1A—H1A118.9C4—C3—H2114.8
C4A—N3A—C2A120.90 (13)O2—C4—O1123.04 (16)
C4A—N8A—H8A1120.0O2—C4—C3117.21 (16)
C4A—N8A—H8A2120.0O1—C4—C3119.74 (14)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1A—H1A···O40.861.892.7426 (19)174
N1B—H1B···O2i0.861.912.7701 (19)174
N8A—H8A1···O7B0.862.002.8582 (19)178
N8A—H8A2···O7Aii0.862.042.8329 (19)153
N3B—H3B···N3A0.861.982.8370 (19)176
N8B—H8B1···O7A0.861.992.8458 (19)173
N8B—H8B2···O7Biii0.862.062.8491 (18)153
O3—H3···O11.17 (2)1.25 (2)2.4167 (16)173 (2)
C6B—H6B···O1i0.932.503.186 (2)131
C5B—H5B···O2iv0.932.423.330 (2)165
C5A—H5A···O4ii0.932.373.296 (2)175

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2509).

References

  • Bagieu-Beucher, M. (1990). Acta Cryst. C46, 238–240.
  • Balasubramanian, T., Muthiah, P. T. & Robinson, W. T. (1996). Bull. Chem. Soc. Jpn, 69, 2919–2922.
  • Barker, D. L. & Marsh, R. E. (1964). Acta Cryst. 17, 1581–1587.
  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.
  • Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381–388.
  • Cherouana, A., Bouchouit, K., Bendjeddou, L. & Benali-Cherif, N. (2003). Acta Cryst. E59, o983–o985.
  • Devlin, T. M. (1986). Textbook of Biochemistry, 2nd ed., pp. 489–494. New York: McGraw–Hill.
  • Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.
  • Gdaniec, M., Brycki, B. & Szafran, M. (1989). J. Mol. Struct. pp. 57–64.
  • Jaskólski, M. (1989). Acta Cryst. C45, 85–89.
  • Jeffrey, G. A. & Kinoshita, Y. (1963). Acta Cryst. 16, 20–28.
  • Johnson, T. B. & Coghill, R. D. (1925). J. Am. Chem. Soc. 47, 2838–2844.
  • Madsen, D. & Larsen, S. (1998). Acta Cryst. C54, 1507–1511.
  • Mahan, S. D., Ireton, G. C., Stoddard, B. L. & Black, M. E. (2004). Mandel, N. S. (1977). Acta Cryst. B33, 1079–1082.
  • Mandel, N. S. (1977). Acta Cryst. B33, 1079–1082.
  • Nonius (1998). KappaCCD Server Software. Nonius BV, Delft, The Netherlands.
  • Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Smith, G., Wermuth, U. D. & Healy, P. C. (2005). Acta Cryst. E61, o746–o748.
  • Spek, A. L. (2009). Acta Cryst D65, 148–155. [PMC free article] [PubMed]
  • Swamy, K. C. K., Kumaraswamy, S. & Kommana, P. (2001). J. Am. Chem. Soc. 123, 12642–12649. [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography