2′-Deoxy-5-fluorotubercidin

In the title compound, 4-amino-7-(2-deoxy-β-D-erythro-pentofuranosyl)-5-fluoro-7H-pyrrolo[2,3-d]pyrimidine, C₁₁H₁₃FN₄O₃, the conformation of the glycosyl bond lies between anti and high anti [χ = −101.1 (3)°]. The furanose moiety adopts the S-type sugar pucker (²T₃), with P = 164.7 (3)° and τ = 40.1 (2)°. The extended structure is a three-dimensional hydrogen-bond network involving a C—H...F, two N—H...O and two O—H...O hydrogen bonds.

S1. Comment

Fluorine-substituted analogues of nucleic acid components have become established as antiviral, antitumour and antifungal agents. Nucleosides with fluorine in the sugar part, usually at the 2'- and 3'-positions, have attracted considerable attention in the last few decades. There are some promising compounds, such as D-FMAU (Fanucchi, et al. 1983) and 3'-fluoro-3'-deoxythymidine (Etzold et al., 1971). One of the most successful cases is 5-fluorouracil, with the F atom in the base moiety. Accordingly, it was conceivable to introduce an F atom at the 7-position of the 7-deazapurine system, which is considered to be a matching position for the 5-position in pyrimidines (Gourlain et al., 2001). (Purine numbering is used throughout this discussion.) Recently, Wang et al. (2004) reported that the 7-fluoro analogue of tubercidin exhibits reduced cytotoxicity compared with the parent nucleoside. In continuation of our efforts to correlate nucleoside structure with biological activity, we have synthesized 7-fluoro-2'-deoxytubercidin, (I), and incorporated it into oligonucleotides. Here, we report on the single-crystal X-ray structure of compound (I).

Canonical purine 2'-deoxyribonucleosides tend to adopt the anti conformation. The orientation of the base relative to the sugar moiety (syn/anti) of purine nucleosides is defined by the torsion angle χ (O4'—C1'—N9—C4; IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983). In the crystal structure of compound (I), the torsion angle of the glycosylic bond is between the anti and high anti range, with χ = −101.1 (3)° (Fig. 1 and Table 1). This conformation is close to that of the parent compound, (II), which has no substituent at the 7-position, with χ = −104.4 (3)° (Zabel et al., 1987). The iodo derivative, (III), has a much larger torsion angle χ = −147.1 (8)° (Seela et al., 1996), showing an anti conformation. The glycosyl bond length (N9–C1') in (I) is 1.444 (4) Å, which is almost identical to those in (II) [1.449 (2) Å] and (III) [1.453 (5) Å].

The most frequently observed ring conformations of nucleosides are C2'-endo and C3'-endo (Arnott & Hukins, 1972). The pseudorotation phase angle P and the puckering amplitude angle τ (Rao et al., 1981) show that the sugar ring of (I) adopts an S conformation, with an unsymmetrical twist of C2'-endo–C3'-exo (²T₃), and a P value of 164.7 (3)° and τ value of 40.1 (2)°. This is consistent with the conformation in solution, where nucleoside (I) shows a predominantly S (70%) population (Seela, Chittepu et al., 2005). In the case of (II), the sugar ring conformation is ₃T², with P = 186.6 (2)°. Compound (III) has a ₃E sugar conformation (P = 197°). The conformation about the C4'—C5' bond of (I) is -ap (gauche, trans), with γ = −179.7 (2)°, whereas in (II), the C4'—C5' bond shows an ap (gauche, trans) conformation, with γ = 179.6 (2)°.

In the three-dimensional network of (I), both nucleobases and sugar residues are stacked. The bases are arranged head-to-head and separated by 6.878 (4) Å (N3···N3; Fig. 2). This distance is longer than observed for related nucleosides (Seela, Shaikh & Eickmeier, 2005), which results from steric hindrance by the sugar moiety. The structure is stabilized by several hydrogen bonds (Table 2 and Fig. 2). All four H atoms bonded to heteroatoms take part in the formation of the three-dimensional network (O3'—H3'···O4', O5'—H5'···N3, N6—H6A···O3' and N6—H6B···O5'). Additionally, the 2'α H atom forms a hydrogen bond with the F atom of an adjacent molecule (C2'—H2'···F). The contact distance is 2.33 Å (Table 2), which is significantly shorter than the sum of the van der Waals radii (2.67 Å; Reference?). This is unusual, not only for nucleoside crystal structures but also for other organic fluorinated compounds. Statistical analysis of crystal structures taken from the Cambridge Structural Database (Version 5.09, April 1995 release; Allen, 2002) and the Brookhaven Protein Data Bank (ceased operation 30t h June 1999; October 1994 release; Bernstein et al., 1977) show that covalently bonded fluorine hardly ever acts as a hydrogen-bond acceptor (Dunitz & Taylor, 1997). Recently, Haufe et al. (2002) reported C—F···H—C contacts in the X-ray crystal structures of monofluorinated cyclopropanes, with corresponding distances in the range 2.17–2.41 Å.

S2. Experimental

Nucleoside (I) was synthesized as described by Seela, Chittepu et al. (2005). The nucleoside was dissolved in a small volume of methanol at 323 K and then half of this volume of dichloromethane was added. Crystals of (I) (m.p. 438 K) were grown by storing the solution overnight at room temperature.

S3. Refinement

In the absence of suitable anomalous scattering, Friedel equivalents could not be used to determine the absolute structure. Therefore, Friedel equivalents were merged before the final refinement. The known configuration of the parent molecule was used to define the enantiomer of the final model. All H atoms were initially found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, the H atoms were then placed in geometrically idealized positions (C—H = 0.93–0.98 Å, O—H = 0.82 Å and N—H = 0.86 Å) and constrained to ride on their parent atoms, with U_iso(H) = 1.2U_eq(C), 1.2U_eq(N) or 1.5U_eq(O).

Computing details

Data collection: XSCANS (Siemens, 1996); cell refinement: XSCANS; data reduction: SHELXTL (Sheldrick, 1997a); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997b); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997b); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003).

Figures

	Fig. 1. A perspective view of the nucleoside moiety of (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary size.
	Fig. 2. The crystal packing of (I), showing the intermolecular hydrogen-bonding network, [100] projection.

7-Fluoro-2'-deoxytubercidin

Crystal data

C11H13FN4O3	F(000) = 560
Mr = 268.25	Dx = 1.478 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 37 reflections
a = 6.8780 (18) Å	θ = 5.1–12.4°
b = 10.144 (2) Å	µ = 0.12 mm^−1
c = 17.283 (2) Å	T = 293 K
V = 1205.8 (4) Å^3	Transparent prism, colourless
Z = 4	0.6 × 0.4 × 0.3 mm

Data collection

Bruker P4 diffractometer	Rint = 0.030
Radiation source: fine-focus sealed tube	θmax = 29.0°, θmin = 2.3°
Graphite monochromator	h = −9→1
2θ/ω scans	k = −1→13
2482 measured reflections	l = −1→23
1858 independent reflections	3 standard reflections every 97 reflections
1355 reflections with I > 2σ(I)	intensity decay: none

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.045	H-atom parameters constrained
wR(F^2) = 0.120	w = 1/[σ^2(Fo^2) + (0.0526P)^2 + 0.1524P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max < 0.001
1858 reflections	Δρmax = 0.20 e Å^−3
175 parameters	Δρmin = −0.20 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997b), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.010 (3)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
N1	1.4476 (4)	−0.1233 (3)	−0.00344 (15)	0.0470 (6)
C2	1.4767 (5)	−0.0679 (3)	0.06557 (18)	0.0463 (7)
H2	1.5895	−0.0943	0.0908	0.056*
N3	1.3684 (4)	0.0200 (2)	0.10403 (13)	0.0398 (6)
C4	1.2060 (4)	0.0533 (3)	0.06441 (16)	0.0331 (6)
C5	1.1577 (4)	0.0042 (3)	−0.00883 (16)	0.0366 (6)
C6	1.2861 (4)	−0.0870 (3)	−0.04253 (15)	0.0365 (6)
N6	1.2574 (4)	−0.1397 (2)	−0.11275 (14)	0.0450 (6)
H6A	1.3403	−0.1946	−0.1314	0.054*
H6B	1.1560	−0.1186	−0.1391	0.054*
C7	0.9787 (5)	0.0651 (4)	−0.02741 (18)	0.0500 (8)
F7	0.8811 (4)	0.0448 (3)	−0.09415 (13)	0.0834 (9)
C8	0.9232 (5)	0.1457 (3)	0.03042 (18)	0.0515 (8)
H8	0.8102	0.1960	0.0319	0.062*
N9	1.0659 (4)	0.1400 (2)	0.08772 (13)	0.0393 (6)
C1'	1.0505 (4)	0.1982 (2)	0.16372 (16)	0.0347 (6)
H1'	1.1753	0.1892	0.1906	0.042*
C2'	0.9864 (5)	0.3413 (2)	0.16663 (17)	0.0403 (7)
H2'1	0.8875	0.3599	0.1281	0.048*
H2'2	1.0953	0.4008	0.1593	0.048*
C3'	0.9051 (4)	0.3507 (2)	0.24818 (15)	0.0334 (6)
H3'1	0.8130	0.4240	0.2531	0.040*
O3'	1.0563 (3)	0.35974 (18)	0.30408 (13)	0.0458 (5)
H3'	1.1014	0.4346	0.3039	0.069*
C4'	0.8047 (4)	0.2183 (2)	0.25837 (16)	0.0329 (6)
H4'	0.8214	0.1880	0.3118	0.040*
C5'	0.5904 (4)	0.2213 (3)	0.23862 (19)	0.0436 (7)
H5'1	0.5254	0.2854	0.2712	0.052*
H5'2	0.5743	0.2484	0.1852	0.052*
O5'	0.5041 (4)	0.0965 (2)	0.24932 (13)	0.0506 (6)
H5'	0.4605	0.0700	0.2080	0.076*
O4'	0.9033 (3)	0.12907 (17)	0.20644 (12)	0.0450 (6)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0453 (14)	0.0490 (14)	0.0467 (14)	0.0131 (13)	0.0009 (12)	−0.0068 (12)
C2	0.0404 (16)	0.0532 (17)	0.0453 (16)	0.0119 (15)	−0.0048 (14)	−0.0059 (14)
N3	0.0384 (12)	0.0450 (14)	0.0360 (12)	0.0106 (12)	−0.0027 (11)	−0.0036 (11)
C4	0.0325 (13)	0.0356 (13)	0.0311 (13)	0.0027 (12)	0.0031 (11)	0.0030 (11)
C5	0.0356 (13)	0.0403 (13)	0.0339 (14)	0.0039 (13)	0.0016 (12)	−0.0014 (13)
C6	0.0401 (16)	0.0348 (13)	0.0345 (14)	−0.0014 (13)	0.0050 (12)	0.0001 (11)
N6	0.0471 (14)	0.0466 (13)	0.0415 (13)	0.0008 (13)	0.0008 (12)	−0.0114 (12)
C7	0.0441 (16)	0.068 (2)	0.0377 (14)	0.0132 (17)	−0.0108 (14)	−0.0061 (15)
F7	0.0640 (13)	0.130 (2)	0.0559 (12)	0.0355 (16)	−0.0287 (11)	−0.0296 (13)
C8	0.0455 (17)	0.064 (2)	0.0452 (16)	0.0238 (18)	−0.0072 (15)	−0.0053 (16)
N9	0.0378 (12)	0.0434 (12)	0.0367 (11)	0.0105 (12)	0.0015 (11)	−0.0047 (11)
C1'	0.0340 (14)	0.0333 (12)	0.0367 (13)	0.0025 (12)	0.0075 (13)	0.0004 (11)
C2'	0.0456 (16)	0.0277 (12)	0.0475 (15)	0.0006 (13)	0.0101 (14)	0.0042 (12)
C3'	0.0349 (13)	0.0256 (11)	0.0397 (13)	0.0036 (12)	0.0005 (13)	−0.0005 (11)
O3'	0.0516 (13)	0.0290 (8)	0.0568 (12)	−0.0069 (10)	−0.0153 (11)	−0.0007 (9)
C4'	0.0373 (13)	0.0303 (12)	0.0313 (13)	−0.0015 (11)	0.0045 (12)	−0.0006 (11)
C5'	0.0344 (14)	0.0438 (15)	0.0526 (17)	−0.0014 (13)	−0.0006 (15)	−0.0044 (14)
O5'	0.0509 (12)	0.0588 (12)	0.0421 (10)	−0.0234 (11)	−0.0013 (11)	0.0001 (10)
O4'	0.0559 (14)	0.0244 (8)	0.0547 (11)	0.0022 (10)	0.0218 (11)	−0.0030 (9)

Geometric parameters (Å, º)

N1—C2	1.334 (4)	C1'—O4'	1.436 (3)
N1—C6	1.351 (4)	C1'—C2'	1.518 (3)
C2—N3	1.338 (4)	C1'—H1'	0.9800
C2—H2	0.9300	C2'—C3'	1.519 (4)
N3—C4	1.353 (4)	C2'—H2'1	0.9700
C4—N9	1.365 (3)	C2'—H2'2	0.9700
C4—C5	1.400 (4)	C3'—O3'	1.422 (3)
C5—C6	1.405 (4)	C3'—C4'	1.521 (3)
C5—C7	1.415 (4)	C3'—H3'1	0.9800
C6—N6	1.341 (3)	O3'—H3'	0.8200
N6—H6A	0.8600	C4'—O4'	1.444 (3)
N6—H6B	0.8600	C4'—C5'	1.513 (4)
C7—C8	1.346 (4)	C4'—H4'	0.9800
C7—F7	1.351 (4)	C5'—O5'	1.410 (4)
C8—N9	1.396 (4)	C5'—H5'1	0.9700
C8—H8	0.9300	C5'—H5'2	0.9700
N9—C1'	1.444 (4)	O5'—H5'	0.8200
C2—N1—C6	117.1 (3)	N9—C1'—H1'	109.2
N1—C2—N3	129.9 (3)	C2'—C1'—H1'	109.2
N1—C2—H2	115.0	C1'—C2'—C3'	101.4 (2)
N3—C2—H2	115.0	C1'—C2'—H2'1	111.5
C2—N3—C4	112.0 (2)	C3'—C2'—H2'1	111.5
N3—C4—N9	126.5 (2)	C1'—C2'—H2'2	111.5
N3—C4—C5	124.3 (3)	C3'—C2'—H2'2	111.5
N9—C4—C5	109.2 (2)	H2'1—C2'—H2'2	109.3
C4—C5—C6	117.4 (3)	O3'—C3'—C2'	111.4 (2)
C4—C5—C7	104.8 (2)	O3'—C3'—C4'	108.1 (2)
C6—C5—C7	137.8 (3)	C2'—C3'—C4'	102.7 (2)
N6—C6—N1	117.7 (3)	O3'—C3'—H3'1	111.4
N6—C6—C5	123.0 (3)	C2'—C3'—H3'1	111.4
N1—C6—C5	119.3 (3)	C4'—C3'—H3'1	111.4
C6—N6—H6A	120.0	C3'—O3'—H3'	109.5
C6—N6—H6B	120.0	O4'—C4'—C5'	109.2 (2)
H6A—N6—H6B	120.0	O4'—C4'—C3'	105.6 (2)
C8—C7—F7	125.9 (3)	C5'—C4'—C3'	113.5 (2)
C8—C7—C5	110.1 (3)	O4'—C4'—H4'	109.5
F7—C7—C5	124.0 (3)	C5'—C4'—H4'	109.5
C7—C8—N9	107.6 (3)	C3'—C4'—H4'	109.5
C7—C8—H8	126.2	O5'—C5'—C4'	111.3 (2)
N9—C8—H8	126.2	O5'—C5'—H5'1	109.4
C4—N9—C8	108.3 (2)	C4'—C5'—H5'1	109.4
C4—N9—C1'	125.7 (2)	O5'—C5'—H5'2	109.4
C8—N9—C1'	125.2 (2)	C4'—C5'—H5'2	109.4
O4'—C1'—N9	108.6 (2)	H5'1—C5'—H5'2	108.0
O4'—C1'—C2'	104.2 (2)	C5'—O5'—H5'	109.5
N9—C1'—C2'	116.3 (2)	C1'—O4'—C4'	110.14 (18)
O4'—C1'—H1'	109.2
C6—N1—C2—N3	0.5 (5)	N3—C4—N9—C1'	−9.4 (4)
N1—C2—N3—C4	0.5 (5)	C5—C4—N9—C1'	171.6 (3)
C2—N3—C4—N9	179.9 (3)	C7—C8—N9—C4	−1.2 (4)
C2—N3—C4—C5	−1.2 (4)	C7—C8—N9—C1'	−171.5 (3)
N3—C4—C5—C6	0.9 (4)	C4—N9—C1'—O4'	−101.1 (3)
N9—C4—C5—C6	179.9 (2)	C8—N9—C1'—O4'	67.6 (4)
N3—C4—C5—C7	−179.9 (3)	C4—N9—C1'—C2'	141.8 (3)
N9—C4—C5—C7	−0.9 (3)	C8—N9—C1'—C2'	−49.5 (4)
C2—N1—C6—N6	178.5 (3)	O4'—C1'—C2'—C3'	37.5 (3)
C2—N1—C6—C5	−0.9 (4)	N9—C1'—C2'—C3'	157.0 (2)
C4—C5—C6—N6	−179.1 (3)	C1'—C2'—C3'—O3'	77.3 (3)
C7—C5—C6—N6	2.1 (6)	C1'—C2'—C3'—C4'	−38.1 (3)
C4—C5—C6—N1	0.3 (4)	O3'—C3'—C4'—O4'	−92.2 (3)
C7—C5—C6—N1	−178.6 (3)	C2'—C3'—C4'—O4'	25.6 (3)
C4—C5—C7—C8	0.2 (4)	O3'—C3'—C4'—C5'	148.1 (2)
C6—C5—C7—C8	179.1 (4)	C2'—C3'—C4'—C5'	−94.0 (3)
C4—C5—C7—F7	179.7 (3)	O4'—C4'—C5'—O5'	62.7 (3)
C6—C5—C7—F7	−1.4 (6)	C3'—C4'—C5'—O5'	−179.8 (2)
F7—C7—C8—N9	−178.9 (3)	N9—C1'—O4'—C4'	−147.0 (2)
C5—C7—C8—N9	0.6 (4)	C2'—C1'—O4'—C4'	−22.5 (3)
N3—C4—N9—C8	−179.7 (3)	C5'—C4'—O4'—C1'	120.3 (2)
C5—C4—N9—C8	1.3 (3)	C3'—C4'—O4'—C1'	−2.1 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N6—H6A···O3′^i	0.86	2.13	2.948 (3)	158
N6—H6B···O5′^ii	0.86	2.23	3.018 (3)	152
O3′—H3′···O4′^iii	0.82	1.98	2.752 (3)	156
O5′—H5′···N3^iv	0.82	1.97	2.789 (3)	175
C2′—H2′2···F7^v	0.97	2.33	3.205 (4)	150

Symmetry codes: (i) −x+5/2, −y, z−1/2; (ii) −x+3/2, −y, z−1/2; (iii) −x+2, y+1/2, −z+1/2; (iv) x−1, y, z; (v) x+1/2, −y+1/2, −z.