Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S010827010001742X/bm1438sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S010827010001742X/bm1438Isup2.hkl |
CCDC reference: 164644
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.
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).
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.
C4H9N3O7S | F(000) = 504 |
Mr = 243.20 | Dx = 1.843 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54180 Å |
a = 10.579 (2) Å | Cell parameters from 25 reflections |
b = 12.104 (2) Å | θ = 20–30° |
c = 7.003 (2) Å | µ = 3.64 mm−1 |
β = 102.26 (3)° | T = 293 K |
V = 876.3 (3) Å3 | Block, colorless |
Z = 4 | 0.35 × 0.20 × 0.20 mm |
Enraf-Nonius CAD-4 diffractometer | 1474 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.000 |
Graphite monochromator | θmax = 69.7°, θmin = 4.3° |
ω–2θ scans | h = 0→12 |
Absorption correction: empirical (using intensity measurements) via ψ scan (north et al., 1968) ? | k = −14→0 |
Tmin = 0.419, Tmax = 0.482 | l = −8→8 |
1551 measured reflections | 3 standard reflections every 100 reflections |
1551 independent reflections | intensity decay: none |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.052 | H 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 reflections | Δρmax = 0.55 e Å−3 |
138 parameters | Δρmin = −0.50 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0169 (16) |
C4H9N3O7S | V = 876.3 (3) Å3 |
Mr = 243.20 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 10.579 (2) Å | µ = 3.64 mm−1 |
b = 12.104 (2) Å | T = 293 K |
c = 7.003 (2) Å | 0.35 × 0.20 × 0.20 mm |
β = 102.26 (3)° |
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 = 0.482 | 3 standard reflections every 100 reflections |
1551 measured reflections | intensity decay: none |
1551 independent reflections |
R[F2 > 2σ(F2)] = 0.052 | 0 restraints |
wR(F2) = 0.139 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.92 | Δρmax = 0.55 e Å−3 |
1551 reflections | Δρmin = −0.50 e Å−3 |
138 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.68818 (6) | 0.51067 (6) | 0.16774 (10) | 0.0267 (3) | |
N5 | 0.8060 (2) | 0.72052 (19) | 0.3768 (4) | 0.0233 (5) | |
H5A | 0.7247 | 0.7058 | 0.3488 | 0.035* | |
H5B | 0.8328 | 0.7818 | 0.4335 | 0.035* | |
N1 | 0.9451 (2) | 0.4750 (2) | 0.2099 (4) | 0.0275 (6) | |
H1 | 0.9183 | 0.4125 | 0.1582 | 0.033* | |
O4 | 1.0712 (2) | 0.75966 (19) | 0.4719 (4) | 0.0377 (6) | |
O5 | 0.6267 (2) | 0.5992 (2) | 0.0439 (3) | 0.0369 (6) | |
O2 | 1.1559 (2) | 0.4297 (2) | 0.2186 (3) | 0.0352 (6) | |
N3 | 1.1107 (2) | 0.5934 (2) | 0.3456 (4) | 0.0296 (6) | |
H3 | 1.1923 | 0.6067 | 0.3784 | 0.036* | |
O7 | 0.6956 (2) | 0.4070 (2) | 0.0676 (4) | 0.0386 (6) | |
C2 | 1.0751 (3) | 0.4943 (2) | 0.2545 (4) | 0.0271 (6) | |
C4 | 1.0291 (3) | 0.6731 (3) | 0.3891 (4) | 0.0284 (7) | |
O6 | 0.6420 (2) | 0.4978 (2) | 0.3466 (4) | 0.0388 (6) | |
C5 | 0.8915 (3) | 0.6475 (3) | 0.3322 (4) | 0.0281 (7) | |
C6 | 0.8545 (3) | 0.5504 (3) | 0.2435 (4) | 0.0257 (6) | |
O1W | 0.3600 (2) | 0.8106 (2) | −0.1896 (4) | 0.0472 (7) | |
H1WA | 0.3210 | 0.7492 | −0.2044 | 0.071* | |
H1WB | 0.4391 | 0.8000 | −0.1603 | 0.071* | |
H1WC | 0.3439 | 0.8418 | −0.3012 | 0.071* | |
O2W | 0.5817 (3) | 0.8412 (2) | 0.1226 (4) | 0.0518 (7) | |
H2WA | 0.6415 | 0.8766 | 0.0825 | 0.078* | |
H2WB | 0.5745 | 0.8645 | 0.2361 | 0.078* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0198 (4) | 0.0310 (5) | 0.0292 (5) | −0.0008 (3) | 0.0053 (3) | −0.0004 (3) |
N5 | 0.0138 (10) | 0.0218 (11) | 0.0352 (13) | 0.0010 (8) | 0.0074 (9) | −0.0062 (10) |
N1 | 0.0230 (12) | 0.0294 (13) | 0.0296 (13) | −0.0015 (10) | 0.0045 (10) | −0.0026 (10) |
O4 | 0.0338 (12) | 0.0328 (12) | 0.0443 (13) | −0.0052 (9) | 0.0036 (10) | −0.0046 (10) |
O5 | 0.0279 (11) | 0.0412 (13) | 0.0387 (12) | 0.0027 (9) | 0.0004 (9) | 0.0054 (10) |
O2 | 0.0240 (11) | 0.0389 (12) | 0.0428 (13) | 0.0041 (9) | 0.0077 (9) | −0.0033 (10) |
N3 | 0.0210 (12) | 0.0336 (14) | 0.0339 (13) | −0.0028 (10) | 0.0048 (10) | 0.0016 (11) |
O7 | 0.0294 (12) | 0.0372 (13) | 0.0480 (14) | −0.0020 (9) | 0.0054 (10) | −0.0103 (10) |
C2 | 0.0231 (15) | 0.0331 (15) | 0.0256 (14) | 0.0004 (12) | 0.0065 (11) | 0.0037 (11) |
C4 | 0.0277 (15) | 0.0308 (15) | 0.0265 (14) | −0.0009 (12) | 0.0053 (11) | 0.0023 (12) |
O6 | 0.0321 (13) | 0.0513 (14) | 0.0360 (13) | −0.0079 (10) | 0.0140 (10) | −0.0001 (10) |
C5 | 0.0235 (14) | 0.0315 (15) | 0.0297 (15) | 0.0003 (12) | 0.0067 (11) | 0.0017 (12) |
C6 | 0.0212 (13) | 0.0313 (15) | 0.0248 (13) | 0.0005 (11) | 0.0051 (11) | 0.0031 (11) |
O1W | 0.0404 (14) | 0.0533 (16) | 0.0438 (14) | −0.0039 (12) | −0.0004 (11) | 0.0064 (12) |
O2W | 0.0421 (14) | 0.0637 (18) | 0.0491 (15) | 0.0003 (13) | 0.0088 (12) | −0.0002 (13) |
S1—O5 | 1.443 (2) | O2—C2 | 1.223 (4) |
S1—O6 | 1.446 (2) | N3—C4 | 1.372 (4) |
S1—O7 | 1.448 (2) | N3—C2 | 1.373 (4) |
S1—C6 | 1.792 (3) | N3—H3 | 0.8600 |
N5—C5 | 1.347 (4) | C4—C5 | 1.458 (4) |
N5—H5A | 0.8600 | C5—C6 | 1.348 (4) |
N5—H5B | 0.8600 | O1W—H1WA | 0.8454 |
N1—C2 | 1.364 (4) | O1W—H1WB | 0.8282 |
N1—C6 | 1.380 (4) | O1W—H1WC | 0.8523 |
N1—H1 | 0.8600 | O2W—H2WA | 0.8592 |
O4—C4 | 1.234 (4) | O2W—H2WB | 0.8616 |
O5—S1—O6 | 114.13 (15) | O2—C2—N3 | 121.2 (3) |
O5—S1—O7 | 114.58 (15) | N1—C2—N3 | 114.8 (3) |
O6—S1—O7 | 112.89 (15) | O4—C4—N3 | 121.3 (3) |
O5—S1—C6 | 105.48 (14) | O4—C4—C5 | 123.3 (3) |
O6—S1—C6 | 105.27 (14) | N3—C4—C5 | 115.4 (3) |
O7—S1—C6 | 103.04 (14) | N5—C5—C6 | 122.4 (3) |
C5—N5—H5A | 120.0 | N5—C5—C4 | 118.5 (3) |
C5—N5—H5B | 120.0 | C6—C5—C4 | 119.1 (3) |
H5A—N5—H5B | 120.0 | C5—C6—N1 | 120.8 (3) |
C2—N1—C6 | 123.4 (3) | N1—C6—S1 | 116.5 (2) |
C2—N1—H1 | 118.2 | C5—C6—S1 | 122.8 (2) |
C6—N1—H1 | 118.4 | H1WA—O1W—H1WB | 109.6 |
C4—N3—C2 | 126.4 (3) | H1WA—O1W—H1WC | 106.3 |
C4—N3—H3 | 116.9 | H1WB—O1W—H1WC | 106.8 |
C2—N3—H3 | 116.7 | H2WA—O2W—H2WB | 110.7 |
O2—C2—N1 | 123.9 (3) | ||
C6—N1—C2—O2 | −177.1 (3) | C4—C5—C6—N1 | 1.3 (4) |
C6—N1—C2—N3 | 3.2 (4) | N5—C5—C6—S1 | 2.3 (4) |
C4—N3—C2—O2 | 178.4 (3) | C4—C5—C6—S1 | 180.0 (2) |
C4—N3—C2—N1 | −1.9 (4) | C2—N1—C6—C5 | −3.0 (4) |
C2—N3—C4—O4 | 179.9 (3) | C2—N1—C6—S1 | 178.2 (2) |
C2—N3—C4—C5 | 0.4 (4) | O7—S1—C6—C5 | 175.5 (3) |
O4—C4—C5—N5 | −1.8 (5) | O5—S1—C6—N1 | −126.3 (2) |
N3—C4—C5—N5 | 177.7 (3) | O6—S1—C6—N1 | 112.7 (2) |
O4—C4—C5—C6 | −179.6 (3) | C5—C6—S1—O5 | 55.0 (3) |
N3—C4—C5—C6 | 0.0 (4) | C5—C6—S1—O6 | −66.0 (3) |
N5—C5—C6—N1 | −176.3 (3) | N1—C6—S1—O7 | −5.8 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O4i | 0.86 | 2.08 | 2.890 (4) | 158 |
N3—H3···O1Wii | 0.86 | 2.18 | 2.940 (4) | 148 |
N5—H5B···O2iii | 0.86 | 2.10 | 2.671 (3) | 123 |
N5—H5A···O2W | 0.86 | 2.54 | 3.024 (4) | 116 |
O1W—H1WA···O7iv | 0.85 | 2.14 | 2.867 (4) | 144 |
O1W—H1WB···O2W | 0.83 | 2.28 | 2.871 (4) | 129 |
O1W—H1WC···O7v | 0.85 | 1.99 | 2.838 (4) | 177 |
O2W—H2WA···O6vi | 0.86 | 2.25 | 2.909 (4) | 134 |
O2W—H2WA···O2iii | 0.86 | 2.38 | 2.962 (4) | 125 |
O2W—H2WB···O5vii | 0.86 | 2.15 | 2.976 (4) | 159 |
Symmetry codes: (i) −x+2, y−1/2, −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, −z−1/2; (vi) x, −y+3/2, z−1/2; (vii) x, −y+3/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C4H9N3O7S |
Mr | 243.20 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 10.579 (2), 12.104 (2), 7.003 (2) |
β (°) | 102.26 (3) |
V (Å3) | 876.3 (3) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 3.64 |
Crystal size (mm) | 0.35 × 0.20 × 0.20 |
Data collection | |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | Empirical (using intensity measurements) via ψ scan (North et al., 1968) |
Tmin, Tmax | 0.419, 0.482 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1551, 1551, 1474 |
Rint | 0.000 |
(sin θ/λ)max (Å−1) | 0.608 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.052, 0.139, 0.92 |
No. of reflections | 1551 |
No. of parameters | 138 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 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.
S1—O5 | 1.443 (2) | S1—O7 | 1.448 (2) |
S1—O6 | 1.446 (2) | N5—C5 | 1.347 (4) |
O5—S1—O6 | 114.13 (15) | O6—S1—C6 | 105.27 (14) |
O5—S1—O7 | 114.58 (15) | O7—S1—C6 | 103.04 (14) |
O6—S1—O7 | 112.89 (15) | N1—C6—S1 | 116.5 (2) |
O5—S1—C6 | 105.48 (14) | C5—C6—S1 | 122.8 (2) |
C5—C6—S1—O5 | 55.0 (3) | N1—C6—S1—O7 | −5.8 (3) |
C5—C6—S1—O6 | −66.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O4i | 0.86 | 2.08 | 2.890 (4) | 157.7 |
N3—H3···O1Wii | 0.86 | 2.18 | 2.940 (4) | 147.8 |
N5—H5B···O2iii | 0.86 | 2.10 | 2.671 (3) | 123.3 |
N5—H5A···O2W | 0.86 | 2.54 | 3.024 (4) | 116.3 |
O1W—H1WA···O7iv | 0.85 | 2.14 | 2.867 (4) | 143.5 |
O1W—H1WB···O2W | 0.83 | 2.28 | 2.871 (4) | 129.0 |
O1W—H1WC···O7v | 0.85 | 1.99 | 2.838 (4) | 177.0 |
O2W—H2WA···O6vi | 0.86 | 2.25 | 2.909 (4) | 134.0 |
O2W—H2WA···O2iii | 0.86 | 2.38 | 2.962 (4) | 125.2 |
O2W—H2WB···O5vii | 0.86 | 2.15 | 2.976 (4) | 159.3 |
Symmetry codes: (i) −x+2, y−1/2, −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, −z−1/2; (vi) x, −y+3/2, z−1/2; (vii) x, −y+3/2, z+1/2. |
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.