4-Amino-5-fluoro­pyrimidin-2(1H)-one–2-amino-5-fluoro­pyrimidin-4(3H)-one–water (1/1/1)

Hulme, A.T.; Tocher, D.A.

doi:10.1107/S1600536805018179

organic compounds

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ISSN: 2056-9890

Volume 61| Part 7| July 2005| Pages o2112-o2113

https://doi.org/10.1107/S1600536805018179

4-Amino-5-fluoropyrimidin-2(1H)-one–2-amino-5-fluoropyrimidin-4(3H)-one–water (1/1/1)

Ashley T. Hulme ^a ^* and Derek A. Tocher ^a

^aChristopher Ingold Laboratory, Department of Chemistry, 20 Gordon St., London WC1H 0AJ, England
^*Correspondence e-mail: a.hulme@ucl.ac.uk

(Received 1 June 2005; accepted 8 June 2005; online 17 June 2005)

The title co-crystal, C₄H₄FN₃O·C₄H₄FN₃O·H₂O, has one molecule of 4-amino-5-fluoropyrimidin-2(1H)-one, one molecule of its isomer 2-amino-5-fluoropyrimidin-4(3H)-one and a molecule of water in the asymmetric unit. 4-Amino-5-fluoropyrimidin-2(1H)-one is commonly known as 5-fluorocytosine.

Comment

The title co-crystal, (I) (Fig. 1), was grown by evaporation of a 50% aqueous solution of ethanol saturated with 5-fluorocytosine. Two different crystal forms were obtained from this solution. The major crystallisation product exhibited a block morphology and was the known monohydrate of 5-fluorocytosine (Louis et al., 1982 ). A small number of needle-shaped crystals were observed as the minor crystallization product. These crystals proved to be the co-crystal, (I). The isomer of 5-fluorocytosine was assumed to have been present in the commercial sample of 5-fluorocytosine purchased from Fluorochem (98% pure, Old Glossop, UK) that was used to prepare the initial solution.

The simplest hydrogen-bonded subunit observed is a two-molecule unit, containing one molecule of each isomer. Each molecule of 5-fluorocytosine forms three hydrogen bonds to a molecule of the isomer (N4—H2⋯O14, N13—H13⋯N3 and N12—H12⋯O2), forming two adjoining R₂²(8) hydrogen bond rings (Table 1). Two different R₂⁴(8) hydrogen-bond rings join these subunits together to form a ribbon (Fig. 2).

The role of the water molecules in the structure is to join together the ribbons into a hydrogen-bonded sheet. The water hydrogen bonds to two molecules from one ribbon, acting both as donor and acceptor, and as a donor to a third molecule, from a different ribbon (Table 1). The ribbons form stepped sheets, parallel to the 01 $[\overline{1}]$ planes (Fig. 3).

Within the ribbon structure, there is also a close F⋯F contact, between F5 and F15, of 2.9003 (15) Å; however, this is likely to have arisen as a consequence of the adjacent R₂⁴(8) hydrogen-bond ring.

Figure 1
The asymmetric unit of the title co-crystal. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as spheres. Dotted lines indicate hydrogen bonds.

Figure 2
The hydrogen bonded ribbon present in the title structure. Dotted lines indicate hydrogen bonds.

Figure 3
The stepped structure of the sheet, comprising ribbons which are hydrogen bonded (dotted lines) via water molecules.

Experimental

Crystals were grown from a 50% aqueous ethanol solution, by evaporation at room temperature. The crystal form reported was the minor crystallisation product.

Crystal data

C₄H₄FN₃O·C₄H₄FN₃O·H₂O
M_r = 276.22
Triclinic, $[P \overline 1]$
a = 5.4122 (16) Å
b = 8.447 (2) Å
c = 12.083 (4) Å
α = 89.454 (5)°
β = 85.718 (5)°
γ = 77.096 (4)°
V = 536.9 (3) Å³
Z = 2
D_x = 1.708 Mg m⁻³
Mo Kα radiation
Cell parameters from 1511 reflections
θ = 3.0–28.1°
μ = 0.16 mm⁻¹
T = 150 (2) K
Needle, colourless
0.44 × 0.14 × 0.11 mm

Data collection

Bruker SMART APEX diffractometer
ω scans
Absorption correction: multi-scan(SADABS; Sheldrick, 1996 )T_min = 0.934, T_max = 0.984
4532 measured reflections
2405 independent reflections
1884 reflections with I > 2σ(I)
R_int = 0.018
θ_max = 28.3°
h = −6 → 6
k = −11 → 10
l = −15 → 15

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.044
wR(F²) = 0.123
S = 1.05
2405 reflections
212 parameters
All H-atom parameters refined
w = 1/[σ²(F_o²) + (0.0762P)² + 0.0364P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.36 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N12—H11⋯O2ⁱ	0.86 (3)	2.13 (3)	2.870 (2)	143 (2)
N12—H12⋯O2ⁱⁱ	0.91 (2)	1.99 (2)	2.889 (2)	172 (2)
N13—H13⋯N3ⁱⁱ	0.91 (3)	2.01 (3)	2.922 (2)	175 (2)
N1—H1⋯O21ⁱⁱⁱ	0.83 (2)	1.95 (2)	2.775 (2)	173 (2)
N4—H2⋯O14ⁱⁱ	0.88 (2)	2.07 (2)	2.9482 (19)	177 (2)
N4—H3⋯O14	0.91 (3)	2.01 (2)	2.8285 (19)	149 (2)
O21—H21⋯N11	0.84 (3)	1.94 (3)	2.785 (2)	177 (2)
O21—H22⋯O2^iv	0.81 (3)	2.03 (3)	2.826 (2)	170 (2)
Symmetry codes: (i) x, y+1, z+1; (ii) -x+2, -y, -z+1; (iii) x, y-1, z-1; (iv) x-1, y+1, z+1.

All H atoms were located [C—H = 0.95 (2)–0.96 (2), N—H = 0.83 (2)–0.91 (3) and O—H = 0.95 (2)] in a difference map and were refined isotropically.

Data collection: SMART (Bruker, 1998 ); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: CAMERON (Watkin et al., 1996 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536805018179/fl6169sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536805018179/fl6169Isup2.hkl

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXL97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: SHELXL97.

4-Amino-5-fluoropyrimidin-2(1H)-one–2-amino-5-fluoropyrimidin-4(3H)-one–water (1/1/1) top

Crystal data top

C₄H₄FN₃O·C₄H₄FN₃O·H₂O	Z = 2
M_r = 276.22	F(000) = 284
Triclinic, P1	D_x = 1.708 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.4122 (16) Å	Cell parameters from 1511 reflections
b = 8.447 (2) Å	θ = 3.0–28.1°
c = 12.083 (4) Å	µ = 0.16 mm⁻¹
α = 89.454 (5)°	T = 150 K
β = 85.718 (5)°	Lathe, colourless
γ = 77.096 (4)°	0.44 × 0.14 × 0.11 mm
V = 536.9 (3) Å³

Data collection top

Bruker SMART APEX diffractometer	2405 independent reflections
Radiation source: fine-focus sealed tube	1884 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.018
ω rotation with narrow frames scans	θ_max = 28.3°, θ_min = 1.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −6→6
T_min = 0.934, T_max = 0.984	k = −11→10
4532 measured reflections	l = −15→15

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)] = 0.044	Hydrogen site location: difference Fourier map
wR(F²) = 0.123	All H-atom parameters refined
S = 1.05	w = 1/[σ²(F_o²) + (0.0762P)² + 0.0364P] where P = (F_o² + 2F_c²)/3
2405 reflections	(Δ/σ)_max < 0.001
212 parameters	Δρ_max = 0.36 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

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	U_iso*/U_eq
F15	0.24930 (19)	0.40288 (12)	0.53690 (9)	0.0329 (3)
O14	0.7285 (2)	0.21415 (14)	0.57184 (10)	0.0266 (3)
N11	0.4124 (3)	0.59592 (17)	0.77839 (12)	0.0252 (3)
N12	0.7754 (3)	0.5260 (2)	0.87373 (13)	0.0299 (4)
H11	0.710 (4)	0.600 (3)	0.923 (2)	0.045 (6)*
H12	0.917 (4)	0.449 (3)	0.8860 (19)	0.044 (6)*
N13	0.7418 (3)	0.37337 (17)	0.72161 (11)	0.0216 (3)
H13	0.894 (5)	0.306 (3)	0.735 (2)	0.053 (7)*
C12	0.6385 (3)	0.50003 (19)	0.79159 (14)	0.0217 (3)
C14	0.6254 (3)	0.33173 (19)	0.63165 (13)	0.0202 (3)
H14	0.127 (4)	0.631 (3)	0.6791 (18)	0.038 (6)*
C15	0.3812 (3)	0.4364 (2)	0.62024 (14)	0.0230 (4)
C16	0.2874 (3)	0.5612 (2)	0.69146 (15)	0.0246 (4)
F5	0.29725 (18)	0.17388 (12)	0.35499 (8)	0.0297 (3)
O2	0.7937 (2)	−0.28047 (14)	0.06559 (9)	0.0270 (3)
N1	0.4410 (3)	−0.08912 (17)	0.11725 (12)	0.0222 (3)
H1	0.376 (4)	−0.113 (3)	0.0611 (19)	0.036 (6)*
N3	0.7899 (2)	−0.14513 (16)	0.22807 (11)	0.0205 (3)
N4	0.7783 (3)	0.00182 (18)	0.38789 (12)	0.0250 (3)
H2	0.925 (4)	−0.065 (3)	0.3978 (17)	0.035 (6)*
H3	0.703 (4)	0.082 (3)	0.438 (2)	0.044 (6)*
C2	0.6802 (3)	−0.17508 (19)	0.13548 (13)	0.0201 (3)
C4	0.6684 (3)	−0.02817 (19)	0.29956 (13)	0.0195 (3)
C5	0.4193 (3)	0.06105 (19)	0.27865 (13)	0.0214 (4)
C6	0.3091 (3)	0.0281 (2)	0.18955 (14)	0.0229 (4)
H4	0.144 (4)	0.079 (2)	0.1689 (17)	0.033 (5)*
O21	0.1925 (2)	0.82377 (16)	0.94260 (11)	0.0270 (3)
H21	0.261 (4)	0.757 (3)	0.892 (2)	0.043 (6)*
H22	0.089 (5)	0.783 (3)	0.977 (2)	0.051 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F15	0.0266 (5)	0.0369 (6)	0.0339 (6)	−0.0006 (4)	−0.0139 (4)	−0.0056 (5)
O14	0.0257 (6)	0.0249 (6)	0.0269 (7)	0.0010 (5)	−0.0069 (5)	−0.0079 (5)
N11	0.0226 (7)	0.0216 (7)	0.0285 (8)	0.0006 (6)	−0.0002 (6)	−0.0039 (6)
N12	0.0289 (8)	0.0285 (8)	0.0279 (8)	0.0050 (7)	−0.0069 (6)	−0.0128 (7)
N13	0.0181 (7)	0.0224 (7)	0.0222 (7)	0.0010 (6)	−0.0048 (5)	−0.0033 (6)
C12	0.0215 (8)	0.0187 (8)	0.0234 (8)	−0.0020 (6)	0.0009 (6)	−0.0031 (6)
C14	0.0209 (8)	0.0192 (8)	0.0198 (8)	−0.0031 (6)	−0.0019 (6)	−0.0012 (6)
C15	0.0205 (8)	0.0238 (8)	0.0247 (8)	−0.0040 (6)	−0.0055 (6)	0.0007 (7)
C16	0.0188 (8)	0.0225 (8)	0.0300 (9)	0.0007 (6)	−0.0019 (7)	0.0025 (7)
F5	0.0241 (5)	0.0311 (6)	0.0284 (5)	0.0057 (4)	−0.0014 (4)	−0.0101 (4)
O2	0.0236 (6)	0.0320 (7)	0.0237 (6)	−0.0013 (5)	−0.0037 (5)	−0.0104 (5)
N1	0.0191 (7)	0.0273 (7)	0.0196 (7)	−0.0027 (6)	−0.0055 (5)	−0.0009 (6)
N3	0.0180 (6)	0.0220 (7)	0.0199 (7)	−0.0002 (5)	−0.0035 (5)	−0.0028 (5)
N4	0.0216 (7)	0.0265 (7)	0.0230 (7)	0.0046 (6)	−0.0064 (6)	−0.0092 (6)
C2	0.0190 (7)	0.0223 (8)	0.0186 (8)	−0.0038 (6)	−0.0012 (6)	−0.0002 (6)
C4	0.0191 (7)	0.0194 (7)	0.0189 (8)	−0.0021 (6)	−0.0014 (6)	−0.0012 (6)
C5	0.0188 (8)	0.0216 (8)	0.0211 (8)	0.0006 (6)	0.0008 (6)	−0.0025 (6)
C6	0.0168 (7)	0.0262 (8)	0.0241 (8)	−0.0010 (6)	−0.0025 (6)	0.0013 (7)
O21	0.0218 (6)	0.0319 (7)	0.0247 (7)	−0.0004 (5)	−0.0020 (5)	−0.0064 (6)

Geometric parameters (Å, º) top

F15—C15	1.3441 (19)	O2—C2	1.2552 (19)
O14—C14	1.235 (2)	N1—C6	1.364 (2)
N11—C12	1.328 (2)	N1—C2	1.368 (2)
N11—C16	1.359 (2)	N1—H1	0.83 (2)
N12—C12	1.330 (2)	N3—C4	1.340 (2)
N12—H11	0.86 (3)	N3—C2	1.356 (2)
N12—H12	0.91 (2)	N4—C4	1.313 (2)
N13—C12	1.361 (2)	N4—H2	0.88 (2)
N13—C14	1.383 (2)	N4—H3	0.91 (3)
N13—H13	0.91 (3)	C4—C5	1.429 (2)
C14—C15	1.432 (2)	C5—C6	1.330 (2)
C15—C16	1.350 (2)	C6—H4	0.95 (2)
C16—H14	0.96 (2)	O21—H21	0.84 (3)
F5—C5	1.3566 (18)	O21—H22	0.81 (3)

C12—N11—C16	116.74 (14)	C6—N1—H1	120.8 (15)
C12—N12—H11	119.5 (16)	C2—N1—H1	117.5 (15)
C12—N12—H12	117.7 (15)	C4—N3—C2	120.27 (13)
H11—N12—H12	121 (2)	C4—N4—H2	115.2 (14)
C12—N13—C14	124.20 (14)	C4—N4—H3	122.4 (14)
C12—N13—H13	120.2 (16)	H2—N4—H3	122 (2)
C14—N13—H13	115.5 (16)	O2—C2—N3	121.40 (14)
N11—C12—N12	120.83 (15)	O2—C2—N1	118.93 (15)
N11—C12—N13	122.00 (15)	N3—C2—N1	119.67 (14)
N12—C12—N13	117.17 (14)	N4—C4—N3	119.75 (14)
O14—C14—N13	121.03 (14)	N4—C4—C5	121.07 (15)
O14—C14—C15	126.50 (15)	N3—C4—C5	119.18 (15)
N13—C14—C15	112.47 (14)	C6—C5—F5	121.80 (14)
F15—C15—C16	121.88 (14)	C6—C5—C4	120.43 (15)
F15—C15—C14	116.98 (14)	F5—C5—C4	117.71 (14)
C16—C15—C14	121.13 (15)	C5—C6—N1	118.72 (15)
C15—C16—N11	123.46 (15)	C5—C6—H4	126.9 (13)
C15—C16—H14	118.6 (14)	N1—C6—H4	114.3 (13)
N11—C16—H14	117.9 (14)	H21—O21—H22	106 (2)
C6—N1—C2	121.68 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N12—H11···O2ⁱ	0.86 (3)	2.13 (3)	2.870 (2)	143 (2)
N12—H12···O2ⁱⁱ	0.91 (2)	1.99 (2)	2.889 (2)	172 (2)
N13—H13···N3ⁱⁱ	0.91 (3)	2.01 (3)	2.922 (2)	175 (2)
N1—H1···O21ⁱⁱⁱ	0.83 (2)	1.95 (2)	2.775 (2)	173 (2)
N4—H2···O14ⁱⁱ	0.88 (2)	2.07 (2)	2.9482 (19)	177 (2)
N4—H3···O14	0.91 (3)	2.01 (2)	2.8285 (19)	148.9 (19)
O21—H21···N11	0.84 (3)	1.94 (3)	2.785 (2)	177 (2)
O21—H22···O2^iv	0.81 (3)	2.03 (3)	2.826 (2)	170 (2)

Symmetry codes: (i) x, y+1, z+1; (ii) −x+2, −y, −z+1; (iii) x, y−1, z−1; (iv) x−1, y+1, z+1.

Acknowledgements

The authors acknowledge the Research Councils UK Basic Technology Programme for supporting `Control and Prediction of the Organic Solid State' (URL: www.cposs.org.uk).

References

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