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In the title compound, oxonium 5-amino-2,6-dioxo-1,2,3,6-tetra­hydro­pyrimidine-4-sulfonate hydrate, H3O+·­C4H4­N3­O5S-·­H2O, the sulfonate group is in the anionic form and charge balance is provided by an o­xonium cation, H3O+. Screw-related mol­ecules overlap significantly and are hydrogen bonded to form a zigzag chain of the uracil skeleton along the direction of the c screw axis. The partially stacked bases and their glide-related equivalents run parallel to the a axis to form hydro­phobic zones separated by hydro­philic zones built up by a network of hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S010827010001742X/bm1438sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S010827010001742X/bm1438Isup2.hkl
Contains datablock I

CCDC reference: 164644

Comment top

The structural analysis of the title compound is a continuation of our earlier work involving systematic conformational studies on nucleic acid constituents in the form of their derivatives and metal complexes to understand structure-function relationships. The purpose of the present study is to understand the effect of substituents on the ring structure of the uracil base. The bond lengths and angles of the uracil derivative (Fig. 1) are in close agreement with those of a neutral uracil base (Taylor et al., 1982). As expected, the uracil base is planar with maximum deviation of 0.014 (3) Å for C2. The orientation of the sulfonyl group with respect to the uracil base is given by torsion angles about the bond C6—S1 (Table 1). The torsion angles C5—C6—S1—O5 [55.0 (3)°] and C5—C6—S1—O6 [-66.0 (3)°] indicate that the bonds S1—O5 and S1—O6 are staggered with respect to the base while the torsion angle N1—C6—S1—O7 [-5.8 (3)°] indicates an eclipsed position for the S1—O7 bond and brings the atom O7 closer to the N—H group [N1···O7 = 2.743 (3) Å] of the ring. This disposition is probably due to a weak electrostatic interaction between the N—H group and O7 atom,which is further evidenced by the asymmetry of the exocyclic bond angles N1—C6—S1 and C5—C6—S1 of 116.5 (2) and 122.8 (2)°, respectively. The three S—O bond lengths S1—O5 [1.443 (2) Å], S1—O6 [1.446 (2) Å] and S1—O7[1.448 (2) Å] are equal within three standard deviations indicating that sulphonate group SO3 is in an anionic form. The three O—S—O angles O5—S1—O6 [114.13 (5)°], O5—S1—O7 [114.58 (15)°] and O6—S1—O7 [112.89 (15)°] and the three C—S—O angles O5—S1—C6 [105.48 (14)] O6—S1—C6 [105.27 (14)] and O7—S1—C6 [103.04 (14)°] have average values 113.9 (7) and 104.6 (11)°, respectively; these deviations from the normal tetrahedral angles in sulphonate groups have been established by many accurate structure analyses; e.g. 112.9 and 106.7° in the structure of taurine 2-aminoethyl sulfonic acid (Okaya, 1966) and 112.1 (2) and 106.6 (2)° in hexaaquacobalt(II) bis(2-aminotolune-4-sulfonate) (Gunderman et al., 1997). A search of the Cambridge Structural Database (Allen et al.,1991) has shown that the deformation of the sulfonate groups from ideal tetrahedral geometry is common. The N5—C5 bond length [1.347 (4) Å] is close to the normal C—N bond distances found in other neutral nucleic acid bases (Taylor et al., 1982). The molecular packing and hydrogen-bonding scheme is shown in Fig.2. The uracil bases are tilted at an angle of 24.9° to the screw-axis and the centroid of the ring-structure of the base is 0.38 Å away from this axis. Significant overlap is overlapped between the screw-related bases is present: the shortest intermolecular contacts between O4 of one molecule and C2 and O7 of the screw-related molecule at (-x + 2, 1/2 + y, 1/2 - z) are 3.455 (4) and 3.104 (3) Å, respectively, indicating that the screw-related bases are partially stacked. These partially stacked bases are further linked by a hydrogen bond between N1 and O4 forming a chain of uracil bases along the direction of the screw-axis (Table 2, Fig. 2). The partially stacked bases, together with their glide-related equivalents run parallel to the a axis and form hydrophobic zones separated by hydrophilic zones where the sulfonyl anions and H3O+ cations, a second water molecule, amino nitrogen N5 and the ring nitrogen N3 form a network of hydrogen bonds. O1W is part of an H3O+ cation which has three close neighbours; O7 (related by an inversion centre), O7 (screw-related) and O2W with O···O distances of 2.868 (4), 2.838 (4) and 2.871 (4) Å, respectively, and these are arranged in a fashion similar to that found in tris(1-phenacyl-2-pyridone)hydroxonium tetrafluoroborate (Zhukov et al., 1997) and hydronium 2-carboxybenzenesulfonate (Ng, 1997). O2W forms a bifurcated hydrogen bond to O2 and O6 through H2WA and also links to O5 through H2WB. These interactions generate an infinite three-dimensional network of cations, anions and water molecules.

Related literature top

For related literature, see: Allen et al. (1991); Gunderman et al. (1997); IUPAC-IUB (1983); Ng (1997); Okaya (1966); Taylor & Kennard (1982); Zhukov et al. (1997).

Experimental top

The title compound was synthesized by the reaction of hot aqueous solution of sulfuric acid and 5-aminouracil. The mixture was kept on a hot water bath for about six hours and crystals were obtained after few days at room temperature.

Refinement top

H atoms attached to N were fixed geometrically and refined isotropically using a riding model with Uiso(H) = 1.2Ueq(N) for ring nitrogen and U(H) = 1.5Ueq(N) for the amino group, respectively. H atoms of water molecules were located from a difference Fourier synthesis and refined isotropically with U(H) = 1.5 Ueq(O) for water molecules using restraints for O—H bond distances and H—O—H angles. The numbering scheme shown in Fig 1. is consistent with the rules of the IUPAC-IUB Commission on Biochemical Nomenclature (IUPAC-IUB,1983).

Computing details top

Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS86 (Sheldrick, 1985); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII(Johnson,1976); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. An ORTEPII (Johnson, 1976) plot of the molecule showing atom labelling. Ellipsoids are drawn at 30% probability.
[Figure 2] Fig. 2. A view approximately along the c direction showing the extensive three-dimensional hydrogen-bonded network linking H3O+ cations, C4H4N3O5S- anions and water molecules. Hydrogen bonds are indicated by dashed lines.
(I) top
Crystal data top
C4H9N3O7SF(000) = 504
Mr = 243.20Dx = 1.843 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54180 Å
a = 10.579 (2) ÅCell parameters from 25 reflections
b = 12.104 (2) Åθ = 20–30°
c = 7.003 (2) ŵ = 3.64 mm1
β = 102.26 (3)°T = 293 K
V = 876.3 (3) Å3Block, colorless
Z = 40.35 × 0.20 × 0.20 mm
Data collection top
Enraf-Nonius CAD-4
diffractometer
1474 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.000
Graphite monochromatorθmax = 69.7°, θmin = 4.3°
ω–2θ scansh = 012
Absorption correction: empirical (using intensity measurements) via ψ scan (north et al., 1968)
?
k = 140
Tmin = 0.419, Tmax = 0.482l = 88
1551 measured reflections3 standard reflections every 100 reflections
1551 independent reflections intensity decay: none
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.052H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.139 w = 1/[σ2(Fo2) + (0.0935P)2 + 1.9742P]
where P = (Fo2 + 2Fc2)/3
S = 0.92(Δ/σ)max < 0.001
1551 reflectionsΔρmax = 0.55 e Å3
138 parametersΔρmin = 0.50 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0169 (16)
Crystal data top
C4H9N3O7SV = 876.3 (3) Å3
Mr = 243.20Z = 4
Monoclinic, P21/cCu Kα radiation
a = 10.579 (2) ŵ = 3.64 mm1
b = 12.104 (2) ÅT = 293 K
c = 7.003 (2) Å0.35 × 0.20 × 0.20 mm
β = 102.26 (3)°
Data collection top
Enraf-Nonius CAD-4
diffractometer
1474 reflections with I > 2σ(I)
Absorption correction: empirical (using intensity measurements) via ψ scan (north et al., 1968)
?
Rint = 0.000
Tmin = 0.419, Tmax = 0.4823 standard reflections every 100 reflections
1551 measured reflections intensity decay: none
1551 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.139H atoms treated by a mixture of independent and constrained refinement
S = 0.92Δρmax = 0.55 e Å3
1551 reflectionsΔρmin = 0.50 e Å3
138 parameters
Special details top

Experimental. Data collection CAD-4 Software (Enraf–Nonius, 1989). Cell refinement: CAD-4 Software. Programs used to solve structure: SHELXS86 (Sheldrick,1985). Programs used to refine structure: SHELXL97 (Sheldrick, 1997). Moleculer graphics: ORTEP II (Johnson,1976). Software used to prepare material for publication: SHELXL97 and PARST(Nardelli,1983).

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
S10.68818 (6)0.51067 (6)0.16774 (10)0.0267 (3)
N50.8060 (2)0.72052 (19)0.3768 (4)0.0233 (5)
H5A0.72470.70580.34880.035*
H5B0.83280.78180.43350.035*
N10.9451 (2)0.4750 (2)0.2099 (4)0.0275 (6)
H10.91830.41250.15820.033*
O41.0712 (2)0.75966 (19)0.4719 (4)0.0377 (6)
O50.6267 (2)0.5992 (2)0.0439 (3)0.0369 (6)
O21.1559 (2)0.4297 (2)0.2186 (3)0.0352 (6)
N31.1107 (2)0.5934 (2)0.3456 (4)0.0296 (6)
H31.19230.60670.37840.036*
O70.6956 (2)0.4070 (2)0.0676 (4)0.0386 (6)
C21.0751 (3)0.4943 (2)0.2545 (4)0.0271 (6)
C41.0291 (3)0.6731 (3)0.3891 (4)0.0284 (7)
O60.6420 (2)0.4978 (2)0.3466 (4)0.0388 (6)
C50.8915 (3)0.6475 (3)0.3322 (4)0.0281 (7)
C60.8545 (3)0.5504 (3)0.2435 (4)0.0257 (6)
O1W0.3600 (2)0.8106 (2)0.1896 (4)0.0472 (7)
H1WA0.32100.74920.20440.071*
H1WB0.43910.80000.16030.071*
H1WC0.34390.84180.30120.071*
O2W0.5817 (3)0.8412 (2)0.1226 (4)0.0518 (7)
H2WA0.64150.87660.08250.078*
H2WB0.57450.86450.23610.078*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0198 (4)0.0310 (5)0.0292 (5)0.0008 (3)0.0053 (3)0.0004 (3)
N50.0138 (10)0.0218 (11)0.0352 (13)0.0010 (8)0.0074 (9)0.0062 (10)
N10.0230 (12)0.0294 (13)0.0296 (13)0.0015 (10)0.0045 (10)0.0026 (10)
O40.0338 (12)0.0328 (12)0.0443 (13)0.0052 (9)0.0036 (10)0.0046 (10)
O50.0279 (11)0.0412 (13)0.0387 (12)0.0027 (9)0.0004 (9)0.0054 (10)
O20.0240 (11)0.0389 (12)0.0428 (13)0.0041 (9)0.0077 (9)0.0033 (10)
N30.0210 (12)0.0336 (14)0.0339 (13)0.0028 (10)0.0048 (10)0.0016 (11)
O70.0294 (12)0.0372 (13)0.0480 (14)0.0020 (9)0.0054 (10)0.0103 (10)
C20.0231 (15)0.0331 (15)0.0256 (14)0.0004 (12)0.0065 (11)0.0037 (11)
C40.0277 (15)0.0308 (15)0.0265 (14)0.0009 (12)0.0053 (11)0.0023 (12)
O60.0321 (13)0.0513 (14)0.0360 (13)0.0079 (10)0.0140 (10)0.0001 (10)
C50.0235 (14)0.0315 (15)0.0297 (15)0.0003 (12)0.0067 (11)0.0017 (12)
C60.0212 (13)0.0313 (15)0.0248 (13)0.0005 (11)0.0051 (11)0.0031 (11)
O1W0.0404 (14)0.0533 (16)0.0438 (14)0.0039 (12)0.0004 (11)0.0064 (12)
O2W0.0421 (14)0.0637 (18)0.0491 (15)0.0003 (13)0.0088 (12)0.0002 (13)
Geometric parameters (Å, º) top
S1—O51.443 (2)O2—C21.223 (4)
S1—O61.446 (2)N3—C41.372 (4)
S1—O71.448 (2)N3—C21.373 (4)
S1—C61.792 (3)N3—H30.8600
N5—C51.347 (4)C4—C51.458 (4)
N5—H5A0.8600C5—C61.348 (4)
N5—H5B0.8600O1W—H1WA0.8454
N1—C21.364 (4)O1W—H1WB0.8282
N1—C61.380 (4)O1W—H1WC0.8523
N1—H10.8600O2W—H2WA0.8592
O4—C41.234 (4)O2W—H2WB0.8616
O5—S1—O6114.13 (15)O2—C2—N3121.2 (3)
O5—S1—O7114.58 (15)N1—C2—N3114.8 (3)
O6—S1—O7112.89 (15)O4—C4—N3121.3 (3)
O5—S1—C6105.48 (14)O4—C4—C5123.3 (3)
O6—S1—C6105.27 (14)N3—C4—C5115.4 (3)
O7—S1—C6103.04 (14)N5—C5—C6122.4 (3)
C5—N5—H5A120.0N5—C5—C4118.5 (3)
C5—N5—H5B120.0C6—C5—C4119.1 (3)
H5A—N5—H5B120.0C5—C6—N1120.8 (3)
C2—N1—C6123.4 (3)N1—C6—S1116.5 (2)
C2—N1—H1118.2C5—C6—S1122.8 (2)
C6—N1—H1118.4H1WA—O1W—H1WB109.6
C4—N3—C2126.4 (3)H1WA—O1W—H1WC106.3
C4—N3—H3116.9H1WB—O1W—H1WC106.8
C2—N3—H3116.7H2WA—O2W—H2WB110.7
O2—C2—N1123.9 (3)
C6—N1—C2—O2177.1 (3)C4—C5—C6—N11.3 (4)
C6—N1—C2—N33.2 (4)N5—C5—C6—S12.3 (4)
C4—N3—C2—O2178.4 (3)C4—C5—C6—S1180.0 (2)
C4—N3—C2—N11.9 (4)C2—N1—C6—C53.0 (4)
C2—N3—C4—O4179.9 (3)C2—N1—C6—S1178.2 (2)
C2—N3—C4—C50.4 (4)O7—S1—C6—C5175.5 (3)
O4—C4—C5—N51.8 (5)O5—S1—C6—N1126.3 (2)
N3—C4—C5—N5177.7 (3)O6—S1—C6—N1112.7 (2)
O4—C4—C5—C6179.6 (3)C5—C6—S1—O555.0 (3)
N3—C4—C5—C60.0 (4)C5—C6—S1—O666.0 (3)
N5—C5—C6—N1176.3 (3)N1—C6—S1—O75.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O4i0.862.082.890 (4)158
N3—H3···O1Wii0.862.182.940 (4)148
N5—H5B···O2iii0.862.102.671 (3)123
N5—H5A···O2W0.862.543.024 (4)116
O1W—H1WA···O7iv0.852.142.867 (4)144
O1W—H1WB···O2W0.832.282.871 (4)129
O1W—H1WC···O7v0.851.992.838 (4)177
O2W—H2WA···O6vi0.862.252.909 (4)134
O2W—H2WA···O2iii0.862.382.962 (4)125
O2W—H2WB···O5vii0.862.152.976 (4)159
Symmetry codes: (i) x+2, y1/2, z+1/2; (ii) x+1, y+3/2, z+1/2; (iii) x+2, y+1/2, z+1/2; (iv) x+1, y+1, z; (v) x+1, y+1/2, z1/2; (vi) x, y+3/2, z1/2; (vii) x, y+3/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC4H9N3O7S
Mr243.20
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)10.579 (2), 12.104 (2), 7.003 (2)
β (°) 102.26 (3)
V3)876.3 (3)
Z4
Radiation typeCu Kα
µ (mm1)3.64
Crystal size (mm)0.35 × 0.20 × 0.20
Data collection
DiffractometerEnraf-Nonius CAD-4
diffractometer
Absorption correctionEmpirical (using intensity measurements) via ψ scan (North et al., 1968)
Tmin, Tmax0.419, 0.482
No. of measured, independent and
observed [I > 2σ(I)] reflections
1551, 1551, 1474
Rint0.000
(sin θ/λ)max1)0.608
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.139, 0.92
No. of reflections1551
No. of parameters138
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.55, 0.50

Computer programs: CAD-4 Software (Enraf-Nonius, 1989), CAD-4 Software, SHELXS86 (Sheldrick, 1985), SHELXL97 (Sheldrick, 1997), ORTEPII(Johnson,1976), SHELXL97.

Selected geometric parameters (Å, º) top
S1—O51.443 (2)S1—O71.448 (2)
S1—O61.446 (2)N5—C51.347 (4)
O5—S1—O6114.13 (15)O6—S1—C6105.27 (14)
O5—S1—O7114.58 (15)O7—S1—C6103.04 (14)
O6—S1—O7112.89 (15)N1—C6—S1116.5 (2)
O5—S1—C6105.48 (14)C5—C6—S1122.8 (2)
C5—C6—S1—O555.0 (3)N1—C6—S1—O75.8 (3)
C5—C6—S1—O666.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O4i0.862.082.890 (4)157.7
N3—H3···O1Wii0.862.182.940 (4)147.8
N5—H5B···O2iii0.862.102.671 (3)123.3
N5—H5A···O2W0.862.543.024 (4)116.3
O1W—H1WA···O7iv0.852.142.867 (4)143.5
O1W—H1WB···O2W0.832.282.871 (4)129.0
O1W—H1WC···O7v0.851.992.838 (4)177.0
O2W—H2WA···O6vi0.862.252.909 (4)134.0
O2W—H2WA···O2iii0.862.382.962 (4)125.2
O2W—H2WB···O5vii0.862.152.976 (4)159.3
Symmetry codes: (i) x+2, y1/2, z+1/2; (ii) x+1, y+3/2, z+1/2; (iii) x+2, y+1/2, z+1/2; (iv) x+1, y+1, z; (v) x+1, y+1/2, z1/2; (vi) x, y+3/2, z1/2; (vii) x, y+3/2, z+1/2.
 

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