Cytosinium nitrate

In the title compound, C₄H₆N₃O⁺·NO₃⁻, a two-dimensional network of N—H...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.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.040
• wR factor = 0.112
• Data-to-parameter ratio = 11.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           25.50
         From the CIF: _reflns_number_total               1206
         TEST2: Reflns within _diffrn_reflns_theta_max
         Count of symmetry unique reflns         1337
         Completeness (_total/calc)             90.20%
          Alert C: < 95% complete


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

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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 an equimolar aquous solution of cytosine and nitric acid.

S3. Refinement

All H atoms were then fixed at localized positions. Riding isotropic displacement parameters were used for all H atoms. Owing to the absence of atoms heavier than Si, the Friedel opposites were merged.

Computing details

Data collection: KappaCCD Software (Nonius, 1998); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SIR2002 (Burla et al., 2003); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrujia, 1997) and PLUTON (Spek, 1990 ); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

	Fig. 1. ORTEP-3 (Farrugia, 1997) view of the title compound, showing the immediate hydrogen-bond interaction between the cation and anion.
	Fig. 2. PLATON (Spek, 1990) view of the two dimensional hydrogen-bond network in (I).
	Fig. 3. The layered structure in (I), viewed down the c axis.

(I)

Crystal data

C4H6N3O^+·NO3^−	Z = 2
Mr = 174.13	F(000) = 180
Triclinic, P1	Dx = 1.609 Mg m^−3
Hall symbol: P-1	Mo Kα radiation, λ = 0.71073 Å
a = 6.5300 (2) Å	Cell parameters from 3964 reflections
b = 6.7240 (2) Å	θ = 2.4–25.5°
c = 9.2110 (3) Å	µ = 0.14 mm^−1
α = 71.96 (2)°	T = 293 K
β = 72.84 (3)°	Prism, colorless
γ = 73.75 (3)°	0.6 × 0.25 × 0.15 mm
V = 359.44 (7) Å^3

Data collection

KappaCCD diffractometer	1065 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.033
Graphite monochromator	θmax = 25.5°, θmin = 2.4°
ϕ scans	h = −7→7
3964 measured reflections	k = −8→8
1206 independent reflections	l = −10→11

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.113	H-atom parameters constrained
S = 1.07	w = 1/[σ^2(Fo^2) + (0.0625P)^2 + 0.0661P] where P = (Fo^2 + 2Fc^2)/3
1206 reflections	(Δ/σ)max = 0.001
109 parameters	Δρmax = 0.14 e Å^−3
0 restraints	Δρmin = −0.19 e Å^−3

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 (Ų)

	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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)
C5	0.0573 (9)	0.0288 (7)	0.0457 (10)	−0.0109 (6)	−0.0132 (7)	−0.0126 (6)

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···O1^i	0.86	2.01	2.8553 (18)	169
N1—H1···O2^i	0.86	2.56	3.2285 (18)	135
N8—H8A···O2	0.86	2.08	2.9392 (19)	176
N8—H8B···O1^ii	0.86	2.30	3.0846 (19)	152
N8—H8B···O3^ii	0.86	2.36	3.1513 (19)	153

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