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Acta Crystallogr Sect E Struct Rep Online. 2009 May 1; 65(Pt 5): o1147–o1148.
Published online 2009 April 30. doi:  10.1107/S1600536809014020
PMCID: PMC2977815

Hydrogen bonding in cytosinium dihydrogen phosphite

Abstract

In the title compound, C4H8N3O4P+·H2PO3 , the cytosine mol­ecule is monoprotonated and the phospho­ric acid is in the monoionized state. Strong hydrogen bonds, dominated by N—H(...)O inter­actions, are responsible for cohesion between the organic and inorganic layers and maintain the stability of this structure.

Related literature

For general background, see: Jeffrey & Saenger (1991 [triangle]); Kabanos et al. (1992 [triangle]); Weber & Craven (1990 [triangle]); Sivanesan et al. (2000 [triangle]). For hydrogen bonds, see: Blessing (1986 [triangle]); Masse & Levy (1991 [triangle]). For related structures, see: Bendheif et al. (2003 [triangle]); Bouchouit et al. (2005 [triangle]); Benali-Cherif, Abouimrane et al. (2002 [triangle]); Benali-Cherif et al. (2007 [triangle]); Benali-Cherif, Benguedouar et al. (2002 [triangle]); Bendjeddou et al. (2003 [triangle]); Cherouana, Benali-Cherif & Bendjeddou (2003 [triangle]); Cherouana, Bouchouit et al. (2003 [triangle]); Messai et al. (2009 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1147-scheme1.jpg

Experimental

Crystal data

  • C4H6N3O+·H2PO3
  • M r = 193.10
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1147-efi1.jpg
  • a = 4.5625 (3) Å
  • b = 6.4739 (4) Å
  • c = 6.5933 (6) Å
  • α = 92.934 (4)°
  • β = 91.236 (4)°
  • γ = 98.627 (5)°
  • V = 192.21 (2) Å3
  • Z = 1
  • Mo Kα radiation
  • μ = 0.34 mm−1
  • T = 293 K
  • 0.1 × 0.1 × 0.1 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: none
  • 1500 measured reflections
  • 1500 independent reflections
  • 1430 reflections with I > 2σ(I)

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.084
  • S = 1.13
  • 1500 reflections
  • 112 parameters
  • 4 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.33 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 580 with Friedel pairs
  • Flack parameter: 0.06 (10)

Data collection: COLLECT (Nonius, 1997–2000 [triangle]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO (Otwinowski & Minor, 1997 [triangle]) 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/S1600536809014020/gw2061sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809014020/gw2061Isup2.hkl

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

Acknowledgments

The authors thank le Centre Universitaire de Khenchela and le Ministére de l’enseignement supérieur et de la Recherche Scientifique–Algeria, via the PNE programme, for financial support.

supplementary crystallographic information

Comment

Studies of metal ion–nucleic acid interactions are of great current interest, since metal ions play a crucial role in the structure and function of nucleic acid and genetic information transfer (Kabanos et al., 1992). Cytosine (6-aminopyrimidin-2-one) is one of the pyrimidines found in deoxyribonucleic acids. It has been the subject of several investigations with the aim of studying the electrostatic properties of its monohydrate form (Weber & Craven, 1990), the relative stabilities of its tautomeric forms and its 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 (Cherouana, Benali-Cherif & Bendjeddou, 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); in particular, 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 hydrogenphosphite (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 (Messai et al., 2009; Benali-Cherif, Abouimrane et al., 2002; Benali-Cherif, Benguedouar et al., 2002; Benali-Cherif et al., 2007).

The asymmetric unit contains one protonated cytosine rings and one hydrogenphosphite anion (Fig. 1). The main feature of the alkyl or aryl ammonium hydrogenphosphite is that the anionic subnetwork is built up through short strong hydrogen bonds (Blessing, 1986) and the organic cations are bonded to the phosphite layers by weaker hydrogen bonds (Masse & Levy, 1991) forming a two-dimensional network of hydrogen bonds (Fig. 2).

The inorganic moiety is a network of H2P O3- tetrahedra, connected by short and strong hydrogen bonds. Inside these chains each H2P O3- group is connected to its two adjacent neighbours by strong hydrogen bonds (O5—H2···O3) to build a two-dimensional network along the c direction. Some similarities may be observed between the present atomic arrangement and the corresponding hydrogenphosphites investigated earlier (Bendheif et al., 2003). cytosine is monoprotonated at atom N3. Some base stacking is retained and hydrogen bonding between cytosine rings, as found cytosinium nitrate (Cherouana, Bouchouit et al., 2003), and cytosinium oxalate monohydrate (Bouchouit et al., 2005) are observed. The pyrimidine ring bond distances are, in general, not signicantly different from those found in cytosine or cytosine monohydrate. Each ring is linked to three nitrate anions by strong N—H···O hydrogen bonds via atoms N1, N3 and N8. The shortest hydrogen bond is observed between the protonated atom N3 of pyrimidine and atom O3 of hydrogenophosphite.

Experimental

The title compound (I) was crystallized from a 1:1 aqueous solution of cytosine [4-aminopyrimidine-2(1H)-one] and phosphorous acid. Yellow crystals grew after a few days, at room temperature and were manually separated for single-crystal X-ray analysis.

Refinement

The title compound crystallizes in the non centrosymmetric space group P1. All non-H atoms were refined with anisotropic atomic displacement parameters. All H atoms were located in Fourier maps; and treated as riding on their parent atoms, with C—H = 0.93 Å, N—H = 0.86 Å, O—H = 0.82 Å, P—H = 1.30 Å, Uiso = 1.2Ueq(C,N,P) and Uiso = 1.5Ueq(O).

Figures

Fig. 1.
ORTEP view of asymmetric unit.
Fig. 2.
PLUTON view down a axis, showing alternate layers of cations and anions stabilized by N—H···O hydrogen bonds.

Crystal data

C4H6N3O+·H2PO3Z = 1
Mr = 193.10F(000) = 100
Triclinic, P1Dx = 1.668 Mg m3
Hall symbol: P 1Mo Kα radiation, λ = 0.71073 Å
a = 4.5625 (3) ÅCell parameters from 739 reflections
b = 6.4739 (4) Åθ = 0.7–27.9°
c = 6.5933 (6) ŵ = 0.34 mm1
α = 92.934 (4)°T = 293 K
β = 91.236 (4)°Cubic, yellow
γ = 98.627 (5)°0.1 × 0.1 × 0.1 mm
V = 192.21 (2) Å3

Data collection

Nonius KappaCCD diffractometer1430 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.0000
horizonally mounted graphite crystalθmax = 28.0°, θmin = 3.2°
Detector resolution: 9 pixels mm-1h = −6→5
CCD rotation images, thick slices scansk = −8→8
1500 measured reflectionsl = −8→8
1500 independent reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.084w = 1/[σ2(Fo2) + (0.0447P)2 + 0.0402P] where P = (Fo2 + 2Fc2)/3
S = 1.13(Δ/σ)max < 0.001
1500 reflectionsΔρmax = 0.25 e Å3
112 parametersΔρmin = −0.33 e Å3
4 restraintsAbsolute structure: Flack (1983), with how many Friedel pairs?
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.06 (10)

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)

xyzUiso*/Ueq
O70.3049 (5)0.5610 (3)1.0498 (3)0.0265 (5)
N10.3442 (5)0.6856 (3)0.7331 (4)0.0213 (5)
H10.24200.78330.76420.026*
N30.5864 (5)0.4107 (3)0.8218 (3)0.0183 (5)
H30.63710.33010.91180.022*
N80.8625 (5)0.2462 (4)0.5932 (4)0.0236 (5)
H70.92270.16520.67930.028*
H80.91800.23120.47010.028*
C20.4021 (5)0.5545 (4)0.8791 (4)0.0177 (5)
C40.6911 (5)0.3898 (4)0.6323 (4)0.0178 (5)
C50.6099 (6)0.5224 (4)0.4837 (4)0.0232 (6)
H50.67110.50940.35070.028*
C60.4412 (6)0.6684 (4)0.5406 (4)0.0228 (6)
H60.39010.75930.44570.027*
P1−0.06174 (7)0.00189 (6)0.08872 (6)0.01852 (18)
O10.1928 (4)0.0549 (3)0.2547 (3)0.0209 (4)
H1A0.35380.06280.20040.031*
O20.0527 (4)−0.0044 (3)−0.1225 (3)0.0222 (4)
O3−0.2857 (4)0.1487 (3)0.1256 (3)0.0214 (4)
H9−0.172 (6)−0.1857 (19)0.137 (5)0.026*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O70.0323 (11)0.0300 (11)0.0203 (11)0.0138 (8)0.0056 (9)0.0032 (8)
N10.0274 (12)0.0176 (11)0.0212 (13)0.0108 (9)−0.0016 (10)0.0023 (9)
N30.0231 (11)0.0198 (11)0.0138 (11)0.0079 (9)−0.0004 (9)0.0043 (8)
N80.0343 (13)0.0234 (11)0.0163 (11)0.0134 (9)0.0058 (10)0.0031 (9)
C20.0175 (13)0.0174 (13)0.0181 (15)0.0036 (10)−0.0010 (10)−0.0007 (10)
C40.0218 (13)0.0166 (12)0.0150 (13)0.0034 (10)−0.0016 (11)−0.0005 (10)
C50.0327 (14)0.0224 (13)0.0165 (13)0.0094 (11)0.0002 (12)0.0042 (10)
C60.0308 (15)0.0188 (13)0.0193 (15)0.0056 (11)−0.0032 (11)0.0033 (10)
P10.0176 (3)0.0189 (3)0.0200 (4)0.0051 (2)0.0016 (2)0.0033 (2)
O10.0142 (8)0.0330 (10)0.0170 (10)0.0066 (7)0.0028 (7)0.0039 (7)
O20.0271 (10)0.0250 (10)0.0174 (10)0.0129 (8)0.0018 (8)0.0008 (8)
O30.0175 (9)0.0255 (10)0.0235 (11)0.0098 (7)0.0024 (8)0.0032 (8)

Geometric parameters (Å, °)

O7—C21.220 (3)C4—C51.414 (4)
N1—C61.358 (4)C5—C61.349 (4)
N1—C21.362 (4)C5—H50.9300
N1—H10.8600C6—H60.9300
N3—C41.354 (3)P1—O21.498 (2)
N3—C21.389 (3)P1—O31.5114 (18)
N3—H30.8600P1—O11.5655 (18)
N8—C41.321 (3)P1—H91.301 (16)
N8—H70.8601O1—H1A0.8200
N8—H80.8600
C6—N1—C2122.8 (2)N3—C4—C5118.4 (2)
C6—N1—H1118.6C6—C5—C4118.1 (3)
C2—N1—H1118.6C6—C5—H5121.0
C4—N3—C2123.8 (2)C4—C5—H5121.0
C4—N3—H3118.1C5—C6—N1121.5 (2)
C2—N3—H3118.1C5—C6—H6119.2
C4—N8—H7126.0N1—C6—H6119.2
C4—N8—H8117.2O2—P1—O3114.99 (10)
H7—N8—H8116.8O2—P1—O1112.60 (10)
O7—C2—N1123.7 (2)O3—P1—O1108.41 (11)
O7—C2—N3121.1 (2)O2—P1—H9110.0 (14)
N1—C2—N3115.2 (2)O3—P1—H9109.9 (13)
N8—C4—N3119.0 (2)O1—P1—H999.9 (14)
N8—C4—C5122.7 (3)P1—O1—H1A109.5
C6—N1—C2—O7−176.3 (2)C2—N3—C4—C50.3 (4)
C6—N1—C2—N34.5 (3)N8—C4—C5—C6−178.0 (3)
C4—N3—C2—O7177.1 (2)N3—C4—C5—C62.4 (4)
C4—N3—C2—N1−3.7 (3)C4—C5—C6—N1−1.7 (4)
C2—N3—C4—N8−179.2 (2)C2—N1—C6—C5−2.0 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.861.862.713 (3)170
O1—H1A···O3ii0.821.752.542 (3)163
N3—H3···O3iii0.861.942.797 (3)175
N8—H7···O2iii0.861.892.750 (3)178
N8—H8···O1ii0.862.293.034 (3)145
N8—H8···O3ii0.862.443.153 (3)141

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GW2061).

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