Acta Cryst.(2003). E59, o983±o985 DOI: 10.1107/S160053680301287X Aouatef Cherouanaet al. C4H6N3O+NO3ÿ
o983
organic papers
Acta Crystallographica Section E Structure Reports
Online
ISSN 1600-5368
Cytosinium nitrate
Aouatef Cherouana, Karim Bouchouit, Lamia Bendjeddou and Nourredine Benali-Cherif*
Laboratoire de Chimie MoleÂculaire, du ControÃle, de l'Environnement et des Mesures Physico-Chimiques, Faculte des Sciences, DeÂpartement de Chimie, Universite Mentouri de Constantine, 25000 Constantine, Algeria
Correspondence e-mail: [email protected]
Key indicators
Single-crystal X-ray study T= 293 K
Mean(C±C) = 0.002 AÊ Rfactor = 0.040 wRfactor = 0.112
Data-to-parameter ratio = 11.1
For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.
#2003 International Union of Crystallography Printed in Great Britain ± all rights reserved
In the title compound, C4H6N3O+NO3ÿ, a two-dimensional network of NÐH O hydrogen bonds between the anions and cations generates cytosinium±nitrate parallel layers, linked by enclosed van der Waals interactions. Cytosinium stacking is present, but cytosinium±cytosinium hydrogen bonds are prevented by the presence of planar nitrate anions.
Comment
Analogs of natural purine and pyrimidine nucleosides have proved to be quite effective as antibacterial, antiviral and antitumor agents, due to their roles as enzyme inhibitors and antagonists. Cytosine (6-aminopyrimidin-2-one) is one of the pyrimidines found in deoxyribonucleic acids. It has been the subject of several investigations aiming to study the electro-static properties of its monohydrate form (Weber & Craven, 1990), the relative stabilities of tautomeric forms (Kobayashi, 1998) and hydration effects and hydrogen bonding (Sivanesan
et al., 2000). In several crystal structures of purines and
pyrimidines with inorganic anions, the structural cohesion is assured by strong hydrogen bonds, as was observed in guaninium sulfate monohydrate (Cherouanaet al., 2003) and adeninium perchlorate (Bendjeddou, Cherouana, Berrah & Benali-Cherif, 2003). The potential importance of hydrogen bonding in the structure and function of biomolecules has been well established (Jeffrey & Saenger, 1991); in particular, NÐH O hydrogen bonds are most predominant in deter-mining the formation of secondary structure elements in proteins, base-pairing in nucleic acids and their biomolecular interactions. This structure analysis of cytosinium nitrate (I) was undertaken as part of a more general investigation into the nature of hydrogen bonding between organic bases or amino acids and inorganic acids in their crystalline forms (Benali-Cherif, Abouimrane et al., 2002; Benali-Cherif, Benguedouaret al., 2002; Benali-Cherif, Bendheifet al., 2002; Benali-Cherif, Cherouanaet al., 2002, Cherouanaet al., 2002; Bendjeddou, Cherouana, Dahaouiet al., 2003).
The structure of (I) consists of nitrate ions and proton\-forcelb]ated cytosine rings (Fig. 1) forming a two-dimensional network of hydrogen bonds (Fig. 2). As observed in [cytosineH+]2[PdCl42ÿ] (Kindberg & Amma, 1975) and cytosine hydrochloride (Mandel, 1977), cytosine is
organic papers
o984
Aouatef Cherouanaet al. C4H6N3O+NO3ÿ Acta Cryst.(2003). E59, o983±o985 protonated at atom N3. Some base stacking is retained buthydrogen bonding between cytosine rings, as found in cytosine (Barker & Marsh, 1964), cytosine monohydrate (Jeffrey & Kinoshita, 1963) and cytosine hydrochloride, is completely prevented by the presence of the planar nitrate ions. The protonated cytosine rings are planar, with the greatest devia-tion from the least-squares plane being 0.0057 (17) AÊ for C4; the amino H atoms also lie in this plane. The pyrimidine ring bond distances are, in general, not signi®cantly different from those found in cytosine or cytosine monohydrate. Each ring is linked to three nitrate anions by strong NÐH O hydrogen bondsviaatoms N1, N3 and N8. The shortest hydrogen bond is observed between the protonated atom N3 of pyrimidine and atom O3 of nitrate. As observed in the crystal structure of guaninium dinitrate dihydrate (Bouchouit et al., 2002), the hydrogen-bond system between cations and anions is two-dimensional and generates a succession of parallel layers of cytosinium and nitrate ions perpendicular to their stacking direction (baxis). The shortest interaction ensuring junction of parallel layers is a van der Waals interaction, between atoms C2 and O7 of the cytosinium cations [3.09 (2) AÊ; Fig. 3].
Experimental
Colorless single crystals of cytosinium nitrate were obtained after one week by slow evaporation, at room temperature, of an equimolar aqueous solution of cytosine and nitric acid.
Crystal data
C4H6N3O+NO3ÿ
Mr= 174.13
Triclinic,P1
a= 6.5300 (2) AÊ
b= 6.7240 (2) AÊ
c= 9.2110 (3) AÊ
= 71.96 (2)
= 72.84 (3)
= 73.75 (3)
V= 359.44 (7) AÊ3
Z= 2
Dx= 1.609 Mg mÿ3
MoKradiation Cell parameters from 3964
re¯ections
= 2.4±25.5
= 0.14 mmÿ1
T= 293 (2) K Prism, colorless 0.600.250.15 mm
Data collection
Nonius KappaCCD diffractometer
'scans
Absorption correction: none 3964 measured re¯ections 1206 independent re¯ections 1065 re¯ections withI> 2(I)
Rint= 0.033
max= 25.5
h=ÿ7!7
k=ÿ8!8
l=ÿ10!11
Re®nement
Re®nement onF2
R[F2> 2(F2)] = 0.040
wR(F2) = 0.113
S= 1.07 1206 re¯ections 109 parameters
H-atom parameters constrained
w= 1/[2(F
o2) + (0.0625P)2
+ 0.0661P]
whereP= (Fo2+ 2Fc2)/3
(/)max= 0.001
max= 0.14 e AÊÿ3
min=ÿ0.19 e AÊÿ3
Table 1
Selected geometric parameters (AÊ,).
O1ÐN 1.2483 (17)
O2ÐN 1.2352 (17)
O3ÐN 1.2432 (17)
O7ÐC2 1.2084 (18)
N3ÐC4 1.3510 (19)
N3ÐC2 1.3799 (19)
N1ÐC6 1.355 (2)
N1ÐC2 1.3670 (18)
N8ÐC4 1.310 (2)
C4ÐC5 1.415 (2)
C6ÐC5 1.339 (2)
O2ÐNÐO3 120.97 (12)
O2ÐNÐO1 120.46 (12) O3ÐNÐO1 118.56 (13)
Table 2
Hydrogen-bonding geometry (AÊ,).
DÐH A DÐH H A D A DÐH A
N3ÐH3 O3 0.86 1.99 2.8419 (18) 170
N1ÐH1 O1i 0.86 2.01 2.8553 (18) 169
N1ÐH1 O2i 0.86 2.56 3.2285 (18) 135
N8ÐH8A O2 0.86 2.08 2.9392 (19) 176
N8ÐH8B O1ii 0.86 2.30 3.0846 (19) 152
N8ÐH8B O3ii 0.86 2.36 3.1513 (19) 153
Symmetry codes: (i)x;y;zÿ1; (ii)x;yÿ1;z.
Figure 2
PLATON (Spek, 1990) view of the two-dimensional hydrogen-bond network in (I).
Figure 3
The layered structure in (I), viewed down thecaxis.
Figure 1
All H atoms were located at idealized positions. Riding isotropic displacement parameters were used for all H atoms.
Data collection:KappaCCD Software(Nonius, 1998); cell re®ne-ment: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure:SIR2002 (Burlaet al., 2003); program(s) used to re®ne structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLUTON (Spek, 1990); software used to prepare material for publication:WinGX(Farrugia, 1999).
We thank Drs M. Pierrot and M. Giorgi (LBS±UMR 6517, Faculte des Sciences et Techniques de Saint JeÂroÃme, Avenue Escadrille Normandie Niemen, 13397 Marseille Cedex 20, France) for providing diffraction facilities.
References
Barker, D. L. & Marsh, R. E. (1964).Acta Cryst.17, 1581±1587.
Benali-Cherif, N., Abouimrane, A., Sbai, K., Merazig, H., Cherouana, A. & Bendjeddou, L. (2002).Acta Cryst.E58, o160±o161.
Benali-Cherif, N., Bendheif, L., Merazig, H., Cherouana, A. & Bendjeddou, L. (2002).Phophorus Sulfure Silicon Relat. Elem.178, 411±421.
Benali-Cherif, N., Benguedouar, L., Cherouana, A., Bendjeddou, L. & Merazig, H. (2002).Acta Cryst.E58, o822±o824.
Benali-Cherif, N., Cherouana, A., Bendjeddou, L., Merazig, H., Bendheif, L. & Bouchouit, K. (2002).Acta Cryst.E58, o156±o157.
Bendjeddou, L., Cherouana, A., Berrah, F. & Benali-Cherif, N. (2003).Acta Cryst.E59, o574±o576.
Bendjeddou, L., Cherouana, A., Dahaoui, S., Benali-Cherif, N. & Lecomte, C. (2003).Acta Cryst.E59, o649±o651.
Bouchouit, K., Benali-Cherif, N., Benguedouar, L., Bendheif, L. & Merazig, H. (2002).Acta Cryst.E58, o1397±o1399.
Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003).J. Appl. Cryst.In preparation.
Cherouana, A., Benali-Cherif, N. & Bendjeddou, L. (2003).Acta Cryst.E59, o180±o182.
Cherouana, A., Benali-Cherif, N., Bendjeddou, L. & Merazig, H. (2002).Acta Cryst.E58, o1351±o1353.
Farrugia, L. J. (1997).J. Appl. Cryst.30, 565. Farrugia, L. J. (1999).J. Appl. Cryst.32, 837±838.
Jeffrey, G. A. & Kinoshita, Y. (1963).Acta Cryst.16, 20±28.
Jeffrey, G. A. & Saenger, W. (1991).An Introduction to Hydrogen Bonding, pp. 245±250. Berlin: Springer Verlag.
Kindberg, B. L. & Amma, E. L. (1975).Acta Cryst.B31, 1492±1494. Kobayashi, R. (1998).J. Phys. Chem. A,102, 10813±10817. Mandel, N. S. (1977).Acta Cryst.B33, 1079±1082.
Nonius (1998).KappaCCD 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. (1997).SHELXL97. University of GoÈttingen, Germany. Sivanesan, D., Babu, K., Gadre, S. R., Subramanian, V. & Ramasami, T. (2000).
J. Phys. Chem. A,104, 10887±10894. Spek, A. L. (1990).Acta Cryst.A46, C-34.
Weber, H.-P. & Craven, B. M. (1990).Acta Cryst.B46, 532±538.
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Acta Cryst. (2003). E59, o983–o985
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Acta Cryst. (2003). E59, o983–o985 [doi:10.1107/S160053680301287X]
Cytosinium nitrate
Aouatef Cherouana, Karim Bouchouit, Lamia Bendjeddou and Nourredine Benali-Cherif
S1. Comment
Analogs of natural purine and pyrimidine nucleosides have proved to be quite effective as antibacterial, antiviral and
antitumor agents, due to their roles as enzyme inhibitors and antagonists. Cytosine(6-aminopyrimidine-2-one) is one of
the pyrimidines found in the deoxyribonucleics acids. It has been a subject of several investigations aiming to study the
electrostatic properties of it monohydrate form (Weber & Craven, 1990), the relative stabilities of tautomeric forms
(Kobayashi, 1998) and hydration effects and hydrogen bonding (Sivanesan et al., 2000). In several crystal structures of
purines and pyrimidines with mineral anions, the structural cohesion is assured by strong hydrogen bonds, as was
observed in guaninium sulfate monohydrate (Cherouana at al., 2003) and adeninium perchlorate (Bendjeddou et al.,
2003). The potential importance of hydrogen bonding in the structure and function of biomolecules has been well
established (Jeffrey & Saenger, 1991), particularly N—H···O hydrogen bonds are most predominant in determining the
formation of secondary structure elements in proteins, base-pairing in nucleic acids and their biomolecular interactions.
This structure analysis of cytosinium nitrate (I) was undertaken as part of more general investigation into the nature of
hydrogen bonding between organic bases or amino acids and mineral acids in their crystalline forms (Benali-Cherif,
Abouimrane et al., 2002; Benali-Cherif, Benguedouar et al., 2002; Benali-Cherif, Bendheif et al., 2002; Benali-Cherif,
Cherouana et al., 2002, Cherouana et al., 2002; Bendjeddou et al., 2003). The structure of (I) consists of nitrate ions and
protonated cytosine rings (Fig. 1) forming a two-dimensional network of hydrogen bonds (Fig. 2). As observed in
[cytosine·H+]
2[PdCl42−] (Kindberg & Amma, 1975) and cytosine hydrochloride (Mandel, 1977), cytosine is
monoprotonated at N3 atom. Some base stacking is retained but hydrogen bonding between cytosine rings, as found in
cytosine (Barker & Marsh, 1964), cytosine monohydrate (Jeffrey & Kinoshita, 1963) and cytosine hydrochloride are
completely prevented by the presence of the planar nitrate ions. The protonated cytosine rings are planar, with the
greatest deviation from the least-squares plane being 0.0057 (17) Å for C4, the amine H atoms also lie in this plane. The
pyrimidine ring distances are in general not significantly different from those found in cytosine or cytosine monohydrate.
Each ring is linked to two nitrate anions by strong N—H.·O hydrogen bonds via atoms N3 and N8. The shortest hydrogen
bond is observed between the protonated atom N3 of pyrimidine and atom O3 of nitrate. As observed in the crystal
structure of guaninium dinitrate dihydrate (Bouchouit et al., 2003), the hydrogen-bond system between cations and
anions is two-dimensional and generates a succession of parallel layers of cytosinium and nitrates along their staking
direction (b axis). The junction of these layers exhibits a van der Waals interaction between atoms C2 and O7 of the
cytosinium cations [3.09 (2) Å; Fig. 3].
S2. Experimental
Colorless single crystals of cytosinium nitrate were obtained after one week by slow evaporation, at room temperature, of
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Acta Cryst. (2003). E59, o983–o985 S3. Refinement
All H atoms were then fixed at localized positions. Riding isotropic displacement parameters were used for all H atoms.
[image:5.610.115.488.122.291.2]Owing to the absence of atoms heavier than Si, the Friedel opposites were merged.
Figure 1
ORTEP-3 (Farrugia, 1997) view of the title compound, showing the immediate hydrogen-bond interaction between the
cation and anion.
Figure 2
[image:5.610.126.485.343.597.2]supporting information
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[image:6.610.130.481.74.232.2]Acta Cryst. (2003). E59, o983–o985 Figure 3
The layered structure in (I), viewed down the c axis.
(I)
Crystal data
C4H6N3O+·NO3− Mr = 174.13 Triclinic, P1 Hall symbol: P-1 a = 6.5300 (2) Å b = 6.7240 (2) Å c = 9.2110 (3) Å α = 71.96 (2)° β = 72.84 (3)° γ = 73.75 (3)° V = 359.44 (7) Å3
Z = 2 F(000) = 180 Dx = 1.609 Mg m−3
Mo Kα radiation, λ = 0.71073 Å Cell parameters from 3964 reflections θ = 2.4–25.5°
µ = 0.14 mm−1 T = 293 K Prism, colorless 0.6 × 0.25 × 0.15 mm
Data collection
KappaCCD diffractometer
Radiation source: fine-focus sealed tube Graphite monochromator
φ scans
3964 measured reflections 1206 independent reflections
1065 reflections with I > 2σ(I) Rint = 0.033
θmax = 25.5°, θmin = 2.4° h = −7→7
k = −8→8 l = −10→11
Refinement
Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.040 wR(F2) = 0.113 S = 1.07 1206 reflections 109 parameters 0 restraints
Primary atom site location: structure-invariant direct methods
Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighbouring sites
H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0625P)2 + 0.0661P]
where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001
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Acta Cryst. (2003). E59, o983–o985 Special details
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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)
x y z Uiso*/Ueq
O1 0.2496 (2) 0.59645 (18) 0.70155 (13) 0.0522 (4)
O7 0.2601 (2) 0.64175 (17) 0.06706 (14) 0.0514 (4)
N3 0.2631 (2) 0.33556 (19) 0.26056 (14) 0.0375 (3)
H3 0.2750 0.4001 0.3241 0.045*
O2 0.2593 (2) 0.28692 (18) 0.67381 (15) 0.0561 (4)
N1 0.2401 (2) 0.34027 (19) 0.01434 (15) 0.0390 (3)
H1 0.2352 0.4051 −0.0814 0.047*
O3 0.2460 (2) 0.56423 (19) 0.47820 (13) 0.0538 (4)
N8 0.2566 (2) 0.0355 (2) 0.46429 (16) 0.0453 (4)
H8A 0.2644 0.1087 0.5236 0.054*
H8B 0.2507 −0.0974 0.5019 0.054*
N 0.2525 (2) 0.4804 (2) 0.61792 (14) 0.0383 (3)
C2 0.2551 (2) 0.4538 (2) 0.10955 (18) 0.0368 (4)
C4 0.2537 (2) 0.1266 (2) 0.31673 (18) 0.0359 (4)
C6 0.2327 (3) 0.1300 (3) 0.0642 (2) 0.0415 (4)
H6 0.2231 0.0610 −0.0060 0.050*
C5 0.2389 (3) 0.0185 (2) 0.2118 (2) 0.0424 (4)
H5 0.2336 −0.1257 0.2442 0.051*
Atomic displacement parameters (Å2)
U11 U22 U33 U12 U13 U23
O1 0.0809 (8) 0.0434 (7) 0.0387 (7) −0.0139 (6) −0.0144 (6) −0.0175 (5)
O7 0.0786 (8) 0.0320 (6) 0.0474 (7) −0.0182 (5) −0.0147 (6) −0.0090 (5)
N3 0.0509 (7) 0.0329 (7) 0.0358 (7) −0.0128 (5) −0.0122 (6) −0.0127 (5)
O2 0.0915 (9) 0.0344 (6) 0.0439 (7) −0.0186 (6) −0.0192 (6) −0.0034 (5)
N1 0.0517 (7) 0.0360 (7) 0.0331 (7) −0.0120 (5) −0.0108 (5) −0.0105 (5)
O3 0.0870 (9) 0.0452 (7) 0.0320 (7) −0.0170 (6) −0.0199 (6) −0.0048 (5)
N8 0.0635 (9) 0.0351 (7) 0.0399 (8) −0.0128 (6) −0.0172 (6) −0.0056 (5)
N 0.0468 (7) 0.0362 (7) 0.0319 (7) −0.0092 (5) −0.0075 (5) −0.0092 (5)
C2 0.0425 (8) 0.0327 (8) 0.0380 (8) −0.0101 (6) −0.0084 (6) −0.0115 (6)
C4 0.0378 (7) 0.0315 (7) 0.0394 (9) −0.0066 (5) −0.0099 (6) −0.0097 (6)
C6 0.0500 (9) 0.0363 (8) 0.0455 (9) −0.0094 (6) −0.0113 (7) −0.0192 (6)
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Acta Cryst. (2003). E59, o983–o985 Geometric parameters (Å, º)
O1—N 1.2483 (17) N1—H1 0.8600
O2—N 1.2352 (17) N8—C4 1.310 (2)
O3—N 1.2432 (17) N8—H8A 0.8600
O7—C2 1.2084 (18) N8—H8B 0.8600
N3—C4 1.3510 (19) C4—C5 1.415 (2)
N3—C2 1.3799 (19) C6—C5 1.339 (2)
N3—H3 0.8600 C6—H6 0.9300
N1—C6 1.355 (2) C5—H5 0.9300
N1—C2 1.3670 (18)
C4—N3—C2 125.29 (12) O7—C2—N1 123.60 (13)
C4—N3—H3 117.4 O7—C2—N3 122.19 (13)
C2—N3—H3 117.4 N1—C2—N3 114.21 (12)
C6—N1—C2 122.86 (13) N8—C4—N3 118.85 (13)
C6—N1—H1 118.6 N8—C4—C5 123.60 (14)
C2—N1—H1 118.6 N3—C4—C5 117.55 (13)
C4—N8—H8A 120.0 C5—C6—N1 121.97 (14)
C4—N8—H8B 120.0 C5—C6—H6 119.0
H8A—N8—H8B 120.0 N1—C6—H6 119.0
O2—N—O3 120.97 (12) C6—C5—C4 118.11 (14)
O2—N—O1 120.46 (12) C6—C5—H5 120.9
O3—N—O1 118.56 (13) C4—C5—H5 120.9
Hydrogen-bond geometry (Å, º)
D—H···A D—H H···A D···A D—H···A
N3—H3···O3 0.86 1.99 2.8419 (18) 170
N1—H1···O1i 0.86 2.01 2.8553 (18) 169
N1—H1···O2i 0.86 2.56 3.2285 (18) 135
N8—H8A···O2 0.86 2.08 2.9392 (19) 176
N8—H8B···O1ii 0.86 2.30 3.0846 (19) 152
N8—H8B···O3ii 0.86 2.36 3.1513 (19) 153
