organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 65| Part 5| May 2009| Pages o1147-o1148

Hydrogen bonding in cytosinium di­hydrogen phosphite

aLaboratoire des Structures, Propriétés et Interactions Inter Atomiques, (LASPI2A), Centre Universitaire de Khenchela, 40000 Khenchela, Algeria, and bUniversité Claude Bernard Lyon 1, Laboratoire des Multimatériaux et Interfaces UMR 5615, 69622 Villeurbanne Cedex, France
*Correspondence e-mail: benalicherif@hotmail.com

(Received 27 February 2009; accepted 14 April 2009; online 30 April 2009)

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[Jeffrey, G. A. & Saenger, W. (1991). Hydrogen Bonding in Biological Structures. Berlin, Heidelberg, New York: Springer Verlag. ]); Kabanos et al. (1992[Kabanos, T. A., Keramidas, A. D., Mentzafos, D., Russo, U., Terzis, A. & Tsangaris, J. M. (1992). J. Chem. Soc. Dalton Trans. pp. 2729-2733.]); Weber & Craven (1990[Weber, H.-P. & Craven, B. M. (1990). Acta Cryst. B46, 532-538.]); Sivanesan et al. (2000[Sivanesan, D., Babu, K., Gadre, S. R., Subramanian, V. & Ramasami, T. (2000). J. Phys. Chem. A, 104, 10887-10894.]). For hydrogen bonds, see: Blessing (1986[Blessing, R. H. (1986). Acta Cryst. B42, 613-621.]); Masse & Levy (1991[Masse, R. & Levy, J. P. (1991). J. Solid State Chem. 93, 88-95.]). For related structures, see: Bendheif et al. (2003[Bendheif, L., Benali-Cherif, N., Benguedouar, L., Bouchouit, K. & Merazig, H. (2003). Acta Cryst. E59, o141-o142.]); Bouchouit et al. (2005[Bouchouit, K., Benali-Cherif, N., Dahaoui, S., Bendeif, E.-E. & Lecomte, C. (2005). Acta Cryst. E61, o2755-o2757.]); Benali-Cherif, Abouimrane et al. (2002[Benali-Cherif, N., Abouimrane, A., Sbai, K., Merazig, H., Cherouana, A. & Bendjeddou, L. (2002). Acta Cryst. E58, o160-o161.]); Benali-Cherif et al. (2007[Benali-Cherif, N., Allouche, F., Direm, A., Boukli-H-Benmenni, L. & Soudani, K. (2007). Acta Cryst. E63, o2643-o2645.]); Benali-Cherif, Benguedouar et al. (2002[Benali-Cherif, N., Benguedouar, L., Cherouana, A., Bendjeddou, L. & Merazig, H. (2002). Acta Cryst. E58, o822-o824.]); Bendjeddou et al. (2003[Bendjeddou, L., Cherouana, A., Dahaoui, S., Benali-Cherif, N. & Lecomte, C. (2003). Acta Cryst. E59, o649-o651.]); Cherouana, Benali-Cherif & Bendjeddou (2003[Cherouana, A., Benali-Cherif, N. & Bendjeddou, L. (2003). Acta Cryst. E59, o180-o182.]); Cherouana, Bouchouit et al. (2003[Cherouana, A., Bouchouit, K., Bendjeddou, L. & Benali-Cherif, N. (2003). Acta Cryst. E59, o983-o985.]); Messai et al. (2009[Messai, A., Direm, A., Benali-Cherif, N., Luneau, D. & Jeanneau, E. (2009). Acta Cryst. E65, o460.]).

[Scheme 1]

Experimental

Crystal data
  • C4H6N3O+·H2PO3

  • Mr = 193.10

  • Triclinic, P 1

  • 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[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 580 with Friedel pairs

  • Flack parameter: 0.06 (10)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O2i 0.86 1.86 2.713 (3) 170
O1—H1A⋯O3ii 0.82 1.75 2.542 (3) 163
N3—H3⋯O3iii 0.86 1.94 2.797 (3) 175
N8—H7⋯O2iii 0.86 1.89 2.750 (3) 178
N8—H8⋯O1ii 0.86 2.29 3.034 (3) 145
N8—H8⋯O3ii 0.86 2.44 3.153 (3) 141
Symmetry codes: (i) x, y+1, z+1; (ii) x+1, y, z; (iii) x+1, y, z+1.

Data collection: COLLECT (Nonius, 1997–2000[Nonius (1997-2000). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997[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.]); data reduction: DENZO (Otwinowski & Minor, 1997[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.]) and SCALEPACK; program(s) used to solve structure: SIR2004 (Burla et al., 2005[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.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

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.

Related literature top

For related literature, see: Benali-Cherif, Abouimrane et al. (2002); Benali-Cherif et al. (2007); Benali-Cherif, Benguedouar et al. (2002); Bendheif et al. (2003); Bendjeddou et al. (2003); Blessing (1986); Bouchouit et al. (2005); Cherouana, Benali-Cherif & Bendjeddou (2003); Cherouana, Bouchouit et al. (2003); Jeffrey & Saenger (1991); Kabanos et al. (1992); Masse & Levy (1991); Messai et al. (2009); Sivanesan et al. (2000); Weber & Craven (1990). [From the Section Editors: It would be much more useful to readers if the "Related literature" section had some kind of simple sub-division, so that, instead of just "For related literature, see···" it said, for example, "For general background, see···. For related structures, see···." etc. Please revise this section as indicated.]

Experimental top

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 top

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).

Computing details top

Data collection: COLLECT (Nonius, 2000); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO (Otwinowski & Minor, 1997) and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. ORTEP view of asymmetric unit.
[Figure 2] Fig. 2. PLUTON view down a axis, showing alternate layers of cations and anions stabilized by N—H···O hydrogen bonds.
Cytosinium dihydrogen phosphite top
Crystal data top
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 top
Nonius KappaCCD
diffractometer
1430 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.000
Horizonally mounted graphite crystal monochromatorθmax = 28.0°, θmin = 3.2°
Detector resolution: 9 pixels mm-1h = 65
CCD rotation images, thick slices scansk = 88
1500 measured reflectionsl = 88
1500 independent reflections
Refinement top
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) = 0.084 w = 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 methodsAbsolute structure parameter: 0.06 (10)
Crystal data top
C4H6N3O+·H2PO3γ = 98.627 (5)°
Mr = 193.10V = 192.21 (2) Å3
Triclinic, P1Z = 1
a = 4.5625 (3) ÅMo Kα radiation
b = 6.4739 (4) ŵ = 0.34 mm1
c = 6.5933 (6) ÅT = 293 K
α = 92.934 (4)°0.1 × 0.1 × 0.1 mm
β = 91.236 (4)°
Data collection top
Nonius KappaCCD
diffractometer
1430 reflections with I > 2σ(I)
1500 measured reflectionsRint = 0.000
1500 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.084Δρmax = 0.25 e Å3
S = 1.13Δρmin = 0.33 e Å3
1500 reflectionsAbsolute structure: Flack (1983), with how many Friedel pairs?
112 parametersAbsolute structure parameter: 0.06 (10)
4 restraints
Special details top

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) top
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*
P10.06174 (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)
O30.2857 (4)0.1487 (3)0.1256 (3)0.0214 (4)
H90.172 (6)0.1857 (19)0.137 (5)0.026*
Atomic displacement parameters (Å2) top
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, º) top
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—O7176.3 (2)C2—N3—C4—C50.3 (4)
C6—N1—C2—N34.5 (3)N8—C4—C5—C6178.0 (3)
C4—N3—C2—O7177.1 (2)N3—C4—C5—C62.4 (4)
C4—N3—C2—N13.7 (3)C4—C5—C6—N11.7 (4)
C2—N3—C4—N8179.2 (2)C2—N1—C6—C52.0 (4)
Hydrogen-bond geometry (Å, º) top
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.

Experimental details

Crystal data
Chemical formulaC4H6N3O+·H2PO3
Mr193.10
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)4.5625 (3), 6.4739 (4), 6.5933 (6)
α, β, γ (°)92.934 (4), 91.236 (4), 98.627 (5)
V3)192.21 (2)
Z1
Radiation typeMo Kα
µ (mm1)0.34
Crystal size (mm)0.1 × 0.1 × 0.1
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
1500, 1500, 1430
Rint0.000
(sin θ/λ)max1)0.660
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.084, 1.13
No. of reflections1500
No. of parameters112
No. of restraints4
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.25, 0.33
Absolute structureFlack (1983), with how many Friedel pairs?
Absolute structure parameter0.06 (10)

Computer programs: COLLECT (Nonius, 2000), SCALEPACK (Otwinowski & Minor, 1997), DENZO (Otwinowski & Minor, 1997) and SCALEPACK (Otwinowski & Minor, 1997), SIR2004 (Burla et al., 2005), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.86001.86002.713 (3)170.00
O1—H1A···O3ii0.82001.75002.542 (3)163.00
N3—H3···O3iii0.86001.94002.797 (3)175.00
N8—H7···O2iii0.86001.89002.750 (3)178.00
N8—H8···O1ii0.86002.29003.034 (3)145.00
N8—H8···O3ii0.86002.44003.153 (3)141.00
Symmetry codes: (i) x, y+1, z+1; (ii) x+1, y, z; (iii) x+1, y, z+1.
 

Acknowledgements

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.

References

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Volume 65| Part 5| May 2009| Pages o1147-o1148
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