The monohydrated molecular adduct cytosine-5-fluorouracil-water (1/1/1) (denoted CytFur) [systematic name: 4-aminopyrimidin-2(1H)-one-5-fluoropyrimidine-2,4(1H,3H)-dione-water (1/1/1)], C4H5N3O·C4H3FN2O2·H2O, was determined some 40 years ago [Voet & Rich (1969). J. Am. Chem. Soc. 91, 3069-3075] and is widely cited as the first example of an intermolecular complex between two pyrimidinic nucleobases. In view of the importance of these base associations, CytFur has been reinvestigated with modern laboratory equipment to higher precision and with the location and free refinement of the H atoms. The new experiment reaffirms the results of the original and clarifies the tautomeric form exhibited by the compounds. The asymmetric unit comprises a hydrogen-bonded adduct of the canonical amino-oxo tautomers in an exact 1:1 ratio and a water molecule of crystallization. This cyclic dimer forms a layered structure approximately parallel to the bc plane by joining through hydrogen bonds other such cyclic dimers. Disordered water molecules run through tunnels formed by surrounding molecular adducts along the a axis.
Supporting information
CCDC reference: 655512
Cytosine and 5-fluorouracil were purchased from Sigma Aldrich (99% purity) and
used as obtained. Crystals of CytFur were grown from an aqueous solution (0.1 mmol of each compound in ca 8 ml) by slow evaporation of the solvent.
All H atoms of the molecular adduct were found in a difference Fourier map and
refined isotropically [C—H = 0.976 (15)–1.006 (17) Å and N—H =
0.882 (16)–0.961 (16) Å]. The uncoordinated water molecule is disordered over
two sites, O4 and O41, and their occupancies refined to close to 0.5.
Eventually, atoms O4 and O41 were refined by imposing that their occupancy
factors must add up to precisely one. The attached H atoms could not be
reliably located in difference maps and were not included in the final
refinement, although they are included in the chemical formula.
Data collection: XCS (Colapietro et al., 1992); cell refinement: XCS; data reduction: XCS; program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
4-amino-2-hydroxypyrimidine–2,4-dihydroxy-5-fluoropyrimidine–water (1/1/1)
top
Crystal data top
C4H5N3O·C4H3FN2O2·H2O | Z = 2 |
Mr = 259.21 | F(000) = 268 |
Triclinic, P1 | Dx = 1.588 Mg m−3 Dm = 1.591 Mg m−3 Dm measured by flotation in n-hexane/bromoform solution |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71069 Å |
a = 4.2629 (1) Å | Cell parameters from 90 reflections |
b = 9.5372 (5) Å | θ = 20–24° |
c = 13.9639 (9) Å | µ = 0.14 mm−1 |
α = 102.562 (5)° | T = 298 K |
β = 91.055 (7)° | Tablet, colourless |
γ = 101.331 (7)° | 0.20 × 0.20 × 0.15 mm |
V = 542.22 (5) Å3 | |
Data collection top
Huber CS four-circle diffractometer | Rint = 0.020 |
Radiation source: X-Ray tube | θmax = 34.0°, θmin = 2.2° |
Graphite monochromator | h = 0→6 |
ω scan | k = −14→14 |
4833 measured reflections | l = −21→21 |
4399 independent reflections | 3 standard reflections every 97 reflections |
2901 reflections with I > 2σ(I) | intensity decay: 1% |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.149 | All H-atom parameters refined |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0999P)2] where P = (Fo2 + 2Fc2)/3 |
4399 reflections | (Δ/σ)max = 0.001 |
205 parameters | Δρmax = 0.37 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
Crystal data top
C4H5N3O·C4H3FN2O2·H2O | γ = 101.331 (7)° |
Mr = 259.21 | V = 542.22 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 4.2629 (1) Å | Mo Kα radiation |
b = 9.5372 (5) Å | µ = 0.14 mm−1 |
c = 13.9639 (9) Å | T = 298 K |
α = 102.562 (5)° | 0.20 × 0.20 × 0.15 mm |
β = 91.055 (7)° | |
Data collection top
Huber CS four-circle diffractometer | Rint = 0.020 |
4833 measured reflections | 3 standard reflections every 97 reflections |
4399 independent reflections | intensity decay: 1% |
2901 reflections with I > 2σ(I) | |
Refinement top
R[F2 > 2σ(F2)] = 0.047 | 0 restraints |
wR(F2) = 0.149 | All H-atom parameters refined |
S = 1.03 | Δρmax = 0.37 e Å−3 |
4399 reflections | Δρmin = −0.22 e Å−3 |
205 parameters | |
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 | x | y | z | Uiso*/Ueq | Occ. (<1) |
F1 | 0.41678 (16) | 1.02448 (8) | 0.28654 (5) | 0.0600 (2) | |
O1 | −0.57905 (18) | 0.67971 (8) | 0.05587 (5) | 0.0499 (2) | |
O2 | 0.27161 (18) | 1.06695 (8) | 0.10323 (5) | 0.0505 (2) | |
N1 | −0.26955 (19) | 0.73651 (9) | 0.19892 (5) | 0.04058 (18) | |
N3 | −0.15354 (18) | 0.87343 (8) | 0.08128 (5) | 0.03846 (17) | |
C2 | −0.3480 (2) | 0.75749 (10) | 0.10881 (6) | 0.03721 (18) | |
C4 | 0.1070 (2) | 0.96753 (10) | 0.13497 (6) | 0.03750 (18) | |
C5 | 0.1650 (2) | 0.93732 (10) | 0.22963 (6) | 0.0401 (2) | |
C6 | −0.0180 (2) | 0.82560 (11) | 0.25868 (6) | 0.04083 (19) | |
H1 | −0.415 (4) | 0.6596 (15) | 0.2192 (11) | 0.059 (4)* | |
H3 | −0.208 (3) | 0.8830 (15) | 0.0190 (12) | 0.061 (4)* | |
H6 | 0.026 (3) | 0.8043 (14) | 0.3239 (10) | 0.054 (3)* | |
O3 | 0.5990 (2) | 0.60984 (8) | 0.41160 (5) | 0.0528 (2) | |
N4 | 0.30856 (19) | 0.51940 (8) | 0.26553 (5) | 0.03902 (17) | |
N5 | 0.2073 (2) | 0.40599 (9) | 0.39846 (6) | 0.04209 (19) | |
N6 | 0.0146 (2) | 0.42522 (11) | 0.11931 (6) | 0.0506 (2) | |
C7 | 0.0715 (2) | 0.41747 (9) | 0.21206 (6) | 0.03730 (18) | |
C8 | 0.3793 (2) | 0.51599 (9) | 0.35967 (6) | 0.03848 (19) | |
C9 | −0.0347 (2) | 0.30240 (11) | 0.34506 (7) | 0.0443 (2) | |
C10 | −0.1138 (2) | 0.30418 (10) | 0.25139 (7) | 0.0426 (2) | |
H5 | 0.264 (4) | 0.4096 (15) | 0.4601 (11) | 0.054 (3)* | |
H9 | −0.139 (3) | 0.2295 (16) | 0.3800 (11) | 0.061 (4)* | |
H10 | −0.307 (4) | 0.2353 (18) | 0.2133 (12) | 0.069 (4)* | |
H16 | −0.157 (4) | 0.3607 (17) | 0.0828 (11) | 0.072 (4)* | |
H161 | 0.131 (4) | 0.5012 (17) | 0.0992 (11) | 0.069 (4)* | |
O4 | −0.1404 (18) | −0.0821 (4) | 0.4956 (2) | 0.124 (2) | 0.495 (9) |
O41 | 0.458 (2) | 0.1020 (5) | 0.5188 (3) | 0.149 (3) | 0.505 (9) |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
F1 | 0.0555 (4) | 0.0673 (4) | 0.0458 (3) | −0.0233 (3) | −0.0212 (3) | 0.0226 (3) |
O1 | 0.0511 (4) | 0.0532 (4) | 0.0377 (3) | −0.0123 (3) | −0.0134 (3) | 0.0157 (3) |
O2 | 0.0510 (4) | 0.0539 (4) | 0.0418 (3) | −0.0137 (3) | −0.0086 (3) | 0.0237 (3) |
N1 | 0.0406 (4) | 0.0442 (4) | 0.0346 (3) | −0.0051 (3) | −0.0062 (3) | 0.0172 (3) |
N3 | 0.0385 (4) | 0.0432 (4) | 0.0316 (3) | −0.0042 (3) | −0.0064 (3) | 0.0160 (3) |
C2 | 0.0381 (4) | 0.0394 (4) | 0.0318 (4) | −0.0013 (3) | −0.0042 (3) | 0.0118 (3) |
C4 | 0.0369 (4) | 0.0415 (4) | 0.0326 (4) | −0.0012 (3) | −0.0027 (3) | 0.0137 (3) |
C5 | 0.0370 (4) | 0.0461 (4) | 0.0332 (4) | −0.0056 (3) | −0.0083 (3) | 0.0141 (3) |
C6 | 0.0411 (4) | 0.0468 (4) | 0.0326 (4) | −0.0028 (3) | −0.0066 (3) | 0.0162 (3) |
O3 | 0.0609 (4) | 0.0488 (4) | 0.0386 (3) | −0.0182 (3) | −0.0188 (3) | 0.0168 (3) |
N4 | 0.0427 (4) | 0.0405 (4) | 0.0293 (3) | −0.0073 (3) | −0.0083 (3) | 0.0132 (3) |
N5 | 0.0466 (4) | 0.0442 (4) | 0.0314 (3) | −0.0080 (3) | −0.0067 (3) | 0.0164 (3) |
N6 | 0.0578 (5) | 0.0537 (5) | 0.0320 (4) | −0.0109 (4) | −0.0147 (3) | 0.0135 (3) |
C7 | 0.0392 (4) | 0.0383 (4) | 0.0309 (4) | −0.0010 (3) | −0.0058 (3) | 0.0090 (3) |
C8 | 0.0424 (4) | 0.0382 (4) | 0.0311 (4) | −0.0047 (3) | −0.0073 (3) | 0.0123 (3) |
C9 | 0.0448 (5) | 0.0426 (4) | 0.0409 (4) | −0.0080 (4) | −0.0040 (3) | 0.0154 (4) |
C10 | 0.0419 (4) | 0.0410 (4) | 0.0378 (4) | −0.0085 (3) | −0.0078 (3) | 0.0097 (3) |
O4 | 0.173 (6) | 0.0875 (18) | 0.0831 (19) | −0.014 (2) | 0.001 (2) | −0.0014 (14) |
O41 | 0.240 (9) | 0.114 (3) | 0.097 (2) | 0.064 (4) | −0.004 (3) | 0.0099 (19) |
Geometric parameters (Å, º) top
F1—C5 | 1.3436 (9) | N4—C7 | 1.3394 (10) |
O1—C2 | 1.2306 (10) | N4—C8 | 1.3521 (10) |
O2—C4 | 1.2331 (10) | N5—C9 | 1.3590 (11) |
N1—C2 | 1.3621 (11) | N5—C8 | 1.3753 (11) |
N1—C6 | 1.3670 (11) | N5—H5 | 0.882 (16) |
N1—H1 | 0.961 (16) | N6—C7 | 1.3338 (11) |
N3—C4 | 1.3734 (11) | N6—H16 | 0.921 (16) |
N3—C2 | 1.3763 (11) | N6—H161 | 0.896 (17) |
N3—H3 | 0.925 (16) | C7—C10 | 1.4255 (12) |
C4—C5 | 1.4398 (12) | C9—C10 | 1.3493 (13) |
C5—C6 | 1.3347 (12) | C9—H9 | 0.976 (15) |
C6—H6 | 0.997 (13) | C10—H10 | 1.006 (17) |
O3—C8 | 1.2517 (10) | | |
| | | |
C2—N1—C6 | 122.44 (7) | C9—N5—C8 | 121.65 (7) |
C2—N1—H1 | 114.6 (9) | C9—N5—H5 | 123.6 (10) |
C6—N1—H1 | 122.8 (9) | C8—N5—H5 | 114.8 (10) |
C4—N3—C2 | 126.66 (7) | C7—N6—H16 | 118.7 (9) |
C4—N3—H3 | 119.9 (9) | C7—N6—H161 | 117.1 (9) |
C2—N3—H3 | 113.4 (9) | H16—N6—H161 | 123.7 (13) |
O1—C2—N1 | 122.59 (8) | N6—C7—N4 | 117.31 (8) |
O1—C2—N3 | 122.00 (7) | N6—C7—C10 | 120.64 (8) |
N1—C2—N3 | 115.40 (7) | N4—C7—C10 | 122.05 (7) |
O2—C4—N3 | 122.05 (7) | O3—C8—N4 | 121.40 (7) |
O2—C4—C5 | 124.57 (8) | O3—C8—N5 | 119.61 (7) |
N3—C4—C5 | 113.38 (7) | N4—C8—N5 | 118.98 (7) |
C6—C5—F1 | 121.40 (7) | C10—C9—N5 | 120.72 (8) |
C6—C5—C4 | 121.60 (8) | C10—C9—H9 | 124.8 (8) |
F1—C5—C4 | 116.98 (7) | N5—C9—H9 | 114.5 (8) |
C5—C6—N1 | 120.50 (8) | C9—C10—C7 | 116.70 (8) |
C5—C6—H6 | 121.1 (8) | C9—C10—H10 | 121.7 (9) |
N1—C6—H6 | 118.4 (8) | C7—C10—H10 | 121.3 (9) |
C7—N4—C8 | 119.89 (7) | | |
| | | |
C6—N1—C2—O1 | −178.16 (9) | C2—N1—C6—C5 | −0.80 (16) |
C6—N1—C2—N3 | 0.93 (14) | C8—N4—C7—N6 | −179.28 (9) |
C4—N3—C2—O1 | 179.29 (9) | C8—N4—C7—C10 | 0.48 (15) |
C4—N3—C2—N1 | 0.19 (14) | C7—N4—C8—O3 | −179.86 (9) |
C2—N3—C4—O2 | 178.48 (10) | C7—N4—C8—N5 | 0.73 (14) |
C2—N3—C4—C5 | −1.30 (14) | C9—N5—C8—O3 | 179.51 (10) |
O2—C4—C5—C6 | −178.36 (11) | C9—N5—C8—N4 | −1.07 (15) |
N3—C4—C5—C6 | 1.40 (14) | C8—N5—C9—C10 | 0.14 (17) |
O2—C4—C5—F1 | 0.03 (16) | N5—C9—C10—C7 | 1.03 (16) |
N3—C4—C5—F1 | 179.80 (8) | N6—C7—C10—C9 | 178.38 (10) |
F1—C5—C6—N1 | −178.78 (9) | N4—C7—C10—C9 | −1.37 (16) |
C4—C5—C6—N1 | −0.46 (16) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N4i | 0.961 (16) | 1.837 (16) | 2.7970 (11) | 176.6 (13) |
N3—H3···O2ii | 0.925 (16) | 1.897 (16) | 2.8137 (10) | 170.5 (13) |
N5—H5···O3iii | 0.882 (16) | 1.932 (16) | 2.8076 (10) | 171.9 (13) |
N6—H16···O1iv | 0.921 (16) | 2.141 (16) | 2.9103 (11) | 140.4 (12) |
N6—H161···O1v | 0.896 (17) | 2.108 (17) | 3.0027 (12) | 177.6 (14) |
C10—H10···O2vi | 1.006 (17) | 2.421 (17) | 3.4202 (11) | 172.4 (13) |
Symmetry codes: (i) x−1, y, z; (ii) −x, −y+2, −z; (iii) −x+1, −y+1, −z+1; (iv) −x−1, −y+1, −z; (v) x+1, y, z; (vi) x−1, y−1, z. |
Experimental details
Crystal data |
Chemical formula | C4H5N3O·C4H3FN2O2·H2O |
Mr | 259.21 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 298 |
a, b, c (Å) | 4.2629 (1), 9.5372 (5), 13.9639 (9) |
α, β, γ (°) | 102.562 (5), 91.055 (7), 101.331 (7) |
V (Å3) | 542.22 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.20 × 0.20 × 0.15 |
|
Data collection |
Diffractometer | Huber CS four-circle diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4833, 4399, 2901 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.787 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.149, 1.03 |
No. of reflections | 4399 |
No. of parameters | 205 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.37, −0.22 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N4i | 0.961 (16) | 1.837 (16) | 2.7970 (11) | 176.6 (13) |
N3—H3···O2ii | 0.925 (16) | 1.897 (16) | 2.8137 (10) | 170.5 (13) |
N5—H5···O3iii | 0.882 (16) | 1.932 (16) | 2.8076 (10) | 171.9 (13) |
N6—H16···O1iv | 0.921 (16) | 2.141 (16) | 2.9103 (11) | 140.4 (12) |
N6—H161···O1v | 0.896 (17) | 2.108 (17) | 3.0027 (12) | 177.6 (14) |
C10—H10···O2vi | 1.006 (17) | 2.421 (17) | 3.4202 (11) | 172.4 (13) |
Symmetry codes: (i) x−1, y, z; (ii) −x, −y+2, −z; (iii) −x+1, −y+1, −z+1; (iv) −x−1, −y+1, −z; (v) x+1, y, z; (vi) x−1, y−1, z. |
Selected geometric parameters (Å) for CytFura,
5-Furacb and Cytosmc top | CytFura | 5Furacb | | CytFura | Cytosmc |
F1—C5 | 1.3436 (9) | 1.348 (1) | O3-C8 | 1.2517 (10) | 1.251 (2) |
O1—C2 | 1.2306 (10) | 1.223 (1) | N4-C7 | 1.3394 (10) | 1.341 (2) |
O2—C4 | 1.2331 (10) | 1.235 (1) | N4-C8 | 1.3521 (10) | 1.350 (2) |
N1—C2 | 1.3621 (11) | 1.362 (1) | N5-C8 | 1.3753 (11) | 1.371 (2) |
N1—C6 | 1.3670 (11) | 1.367 (1) | N5-C9 | 1.3590 (11) | 1.353 (2) |
N3—C2 | 1.3763 (11) | 1.378 (1) | N6-C7 | 1.3338 (11) | 1.326 (2) |
N3—C4 | 1.3734 (11) | 1.374 (1) | C7-C10 | 1.4255 (12) | 1.425 (2) |
C4—C5 | 1.4398 (12) | 1.435 (1) | C9-C10 | 1.3493 (13) | 1.333 (2) |
C5—C6 | 1.3347 (12) | 1.332 (1) | – | – | – |
Notes: (a) this work;
(b) Hulme et al. (2005);
(c) McClure & Craven (1973). |
In the past two decades, much attention has been paid to non-Watson–Crick base associations (mismatch) to further the understanding of their influence on the structure of duplex DNA and RNA (Hunter & Brown, 1999, and references therein). Among the eight nonstandard base pairings in RNA, the three pyrimidine–pyrimidine mismatches (C·C, U·U and C·U) have proved difficult to characterize, but there are a few examples of C·U and U·U base-pair incorporation in duplex RNA (Holbrook et al., 1991). In particular, in the C·U mispair there is single N—H···O hydrogen bond involving the cytosine N6 and uracil O2 atoms and a bridging water molecule linking the two N3 groups. In noncanonical base pairing these conventional hydrogen bonds can be flanked by weaker interbase C—H···O hydrogen bonds (Desiraju & Steiner, 1999), and they occur in a number of interactions involving modified bases and in triplexes. For example, in the crystal structure of the RNA hexamer UUCGCG, a mismatch U—U pair linked by an N—H···O and a C—H···O hydrogen bond was observed, the so-called `Calcutta pair' (Wahl et al., 1996). The theory of mispair association relies on the formation of rare tautomer forms of the bases (Strazewski & Tamm, 1990). However, there is no direct experimental evidence for these base pairs, owing to crystallographic resolution problems (Hunter & Brown, 1999).
The structure of the title compound, (I), CytFur, has been known for a long time as the first example of an intermolecular complex between two pyrimidinic nucleobases, viz. cytosine and the chemotherapeutic agent 5-fluorouracil, and the latter is well known to incorporate into DNA in vivo (Pinedo & Peters, 1988). CytFur was determined as a monohydrate some 40 years ago (Voet & Rich, 1969), with remarkable accuracy for that time. 1730 unique reflections were collected at ambient temperature by photographic techniques using Cu Kα radiation and their intensities were estimated visually. Patterson methods were employed to solve the crystal structure, but only non-H atoms were positioned and refined. The final refinement, carried out on a fairly small data set (1189 observed reflections of non-zero weight), led to R = 0.162 with a data-to-parameter ratio of 6.9, and standard deviations of 0.01 Å in bond lengths and 1° in bond angles, but with a number of problems. Specifically, in the refinement, the matrices of the anisotropic displacement parameters for 5-fluorouracil atoms C4 and C5 and cytosine atom N4 were not positive definite quantities. This situation, together with the large shifts in the displacement parameters for these atoms and the high value of the residual after the final refinement, was attributed by the authors to the disorder of the water molecule [the sum of the unconstrained refined occupancy factors for the two disorder components was only close to unity, 0.76 (11) and 0.26 (8), respectively].
As a part of our continuing study of crystal adducts of DNA/RNA pyrimidine bases coupled with amino-derivatives of aromatic N-heterocycles via multiple hydrogen bonds (Portalone et al., 1999, 2002; Brunetti et al., 2000, 2002; Portalone & Colapietro, 2004a,b, 2006, 2007a,b,c), we report here a reinvestigation of (I), with a full description of the molecular and supramolecular structures. Our results reaffirm Voet's work, providing also the locations of the H atoms, a lower R value, a data-to-parameter ratio of 14.2 and a significant increase in the precision of the geometric parameters.
The asymmetric unit of (I) consists of 1:1 hydrogen-bonded coplanar canonical aminooxo tautomers of the two nucleobases and a water molecule (Fig. 1). The water molecule is distributed over two sites with 50:50 occupancy factors. A comparison of the geometric parameters of the molecular components of CytFur with those reported for cytosine monohydrate (Cytosm; McClure & Craven, 1973) and for 5-fluorouracil (5Furac; Hulme et al., 2005) shows that the corresponding bond lengths and angles are equal within experimental error (Table 1), but with minor exceptions that can be attributed to different hydrogen-bonding configurations. For instance, in the crystal structure of CytFur, the hydrogen-bonding scheme involves all H-atom donor/acceptor sites of the pyrimidinic bases, at variance with that observed in 5-fluorouracil, where atom O1 remains partially unsaturated. As a consequence, the C2—O1 bond length in CytFur is slightly longer than the corresponding bond in 5Furac by 0.008 (1) Å.
As previously mentioned, CytFur crystallizes as a monohydrated 1:1 molecular adduct. The supramolecular structure of (I) is dominated by two main motifs based on four structurally significant hydrogen bonds, one each of types O—H···O, N—H···O, N—H···N and C—H···O (Table 2). Firstly, an R22(8) ring (Etter et al., 1990; Bernstein et al., 1995; Motherwell et al., 1999) forms from N—H···O and N—H···N double intermolecular hydrogen bonds between coplanar base pairs. Propagation and inversion of the base pair through R22(8) N—H···O double intermolecular hydrogen bonds generate infinite chains of centrosymmetric rings running approximately parallel to the [011] direction (Fig. 2). In other words, this hydrogen-bonding scheme corresponds to an alternating double repetition of cytosine and 5-fluorouracil residues. These infinite chains are then cross-linked by symmetry-related N—H···O intermolecular hydrogen bonds between two sets of cytosine and 5-fluorouracil molecules in a tetrameric arrangement, and form the second major motif, also shown in Fig. 2, namely an R24(8) ring. The hydrogen bonds so far discussed build a two-dimensional array, which is modestly reinforced by the C10—H10···O2vi [symmetry code: (vi) x - 1, y - 1, z] intermolecular interaction between adjacent cytosine and 5-fluorouracil molecules. Disordered water molecules run through tunnels formed by surrounding centrosymmetric molecular adducts along the a axis. As their H atoms could not be located, it was impossible to assess the involvement of water molecules in hydrogen bonding. Nevertheless, the distance between cytosine atom O3 and the positions of the partial Owater atom O4 [2.902 (3) Å], as well as the good agreement between the C8—O3 bond lengths of Cytfur and Cytosm (in Cytosm, atom O3 forms three hydrogen bonds, and two of them involve two water molecules) could suggest participation of water molecules in a weak hydrogen bond.