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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 70| Part 2| February 2014| Page o120
doi:10.1107/S1600536813034995

(2R,3S,4R,5R)-5-(4-Amino-5-iodo-7H-pyrrolo­[2,3-d]pyrimidin-7-yl)-4-fluoro-2-(hy­dr­oxy­meth­yl)tetra­hydro­furan-3-ol

Wei Li,a Ruchun Yanga* and Qiang Xiaoa

aJiangxi Key Laboratory of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang 330013, People's Republic of China
*Correspondence e-mail: ouyangruchun@aliyun.com

(Received 14 November 2013; accepted 31 December 2013; online 8 January 2014)

The title compound, C11H12FIN4O3, is composed of a 7-carbapurine moiety connected via an N atom to 2-de­oxy-2-fluoro-β-D-ribose. The conformation about the N-glycosydic bond is −anti with χ = −129.0 (11)°. The glycosydic N—C bond length is 1.435 (14) Å. The sugar ring adopts an Nconformation with an unsymmetrical twist O-endo-C-exo (oT4). The conformation around the C—C bond is +sc, with a torsion angle of 53.0 (12)°. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, forming chains propagating along the a axis. These chains are linked via O—H⋯I and C—H⋯O hydrogen bonds, forming layers lying parallel to the c axis.

CCDC reference: 979239

Related literature

For the biological activity of fluorinated nucleosides, see: Etzold et al. (1971[Etzold, G., Hintsche, R., Kowollik, G. & Langen, P. (1971). Tetrahedron, 27, 2463-2472.]); Hertel et al. (1988[Hertel, L. W., Kroin, J. S., Misner, J. W. & Tustin, J. M. (1988). J. Org. Chem., 53, 2406-2409.]); Watanabe et al. (1979[Watanabe, K. A., Reichman, U., Hirota, K., Lopez, C. & Fox, J. J. (1979). J. Med. Chem. 22, 21-24.]). For puckering amplitudes, see: Saenger (1983[Saenger, W. (1983). Principles of Nucleic Acid Structure, p. 19. New York: Springer.]). For sugar ring conformations, see: Evans & Boeyens (1989[Evans, D. G. & Boeyens, J. C. A. (1989). Acta Cryst. B45, 581-590.]).

[Scheme 1]

Experimental

Crystal data

  • C11H12FIN4O3

  • Mr = 394.15

  • Triclinic, P 1

  • a = 5.2602 (4) Å

  • b = 7.1570 (6) Å

  • c = 9.0126 (10) Å

  • α = 84.533 (8)°

  • β = 83.400 (8)°

  • γ = 78.679 (7)°

  • V = 329.57 (5) Å3

  • Z = 1

  • Mo Kα radiation

  • μ = 2.46 mm−1

  • T = 293 K

  • 0.40 × 0.20 × 0.10 mm
Data collection

  • Agilent Xcalibur (Eos, Gemini) diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013[Agilent (2013). CrysAlis PRO. Agilent Technologies, Yarnton, England.]) Tmin = 0.440, Tmax = 0.791

  • 1874 measured reflections

  • 1657 independent reflections

  • 1657 reflections with I > 2σ(I)

  • Rint = 0.012
Refinement

  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.101

  • S = 1.12

  • 1657 reflections

  • 184 parameters

  • 543 restraints

  • H-atom parameters constrained

  • Δρmax = 0.81 e Å−3

  • Δρmin = −0.95 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.])

  • Absolute structure parameter: −0.02 (4)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C8—H8⋯O3i 0.98 2.60 3.247 (11) 124
N1—H1A⋯O3ii 0.86 2.55 3.189 (13) 132
O2—H2⋯I1iii 0.82 2.35 2.9933 136
Symmetry codes: (i) x, y+1, z; (ii) x, y+1, z-1; (iii) x+1, y, z+1.

Data collection: CrysAlis PRO (Agilent, 2013[Agilent (2013). CrysAlis PRO. Agilent Technologies, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

CCDC reference: 979239

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536813034995/kp2461sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813034995/kp2461Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813034995/kp2461Isup3.cml

checkCIF report


Comment top

Fluorinated nucleosides, containing fluorine atom(s) or fluorine containing groups in the sugar moiety or in the base moiety of nucleosides, greatly improve the bioactivity and stability of the corresponding compounds. The noteworthy of the fluorinated nucleosides are FMAU, FIAC, FLT, gemcitabine (Etzold, et al., 1971; Watanabe, et al., 1979; Hertel, et al., 1988), which have high antiherpes and in some cases antitumour activities.

In our study, we report a fluorinated nucleoside (Fig. 1). The three-dimensional structure and the packing of the title compound is shown Fig. 2 and hydrogen bonds geometry are summarized in Table 1. The orientation of the base relative to the sugar of purine nucleosides is defined by the torsion angle χ (O1-C7-N4-C5),being in the title compound -anti, withχ= –129.0 (11)°. The phase angle of pseudorotation (P)is 67.6 (11)°, and the maximum amplitude of puckering (τm) is 39.5 (7)° (Saenger, 1983). The sugar ring adopts a D conformation (Evans & Boeyens, 1989), with an unsymmetrical twist O1-endo-C10-exo(oT4). The packing of the title compound is stabilized by hydrogen bonds, leading to a two-dimensional network (Fig. 3 and Table 1). The nucleobases are arranged head-to-head in a staircase-like fashion, in a pattern propagated by the a axis of the unit cell.

Related literature top

For the biological activity of fluorinated nucleosides, see: Etzold et al. (1971); Hertel et al. (1988); Watanabe et al. (1979). For puckering amplitudes, see: Saenger (1983). For sugar ring conformations, see: Evans & Boeyens (1989).

Experimental top

Synthesis of compound 1

2-Deoxy-2-fluoro-3,5-di-O-benzoyl-α-D-arabinofuranosyl bromide (66.4 mg, 1.57 mmol) was added into a well-stirred mixture of 6-chloro-7-iodo-pyrrole[2,3-d]pyrimidine (400 mg, 1.43 mmol), potassium hydroxide (281.1 mg, 5.01 mmol) in anhydrous CH3CN (8 mL) at 273 K. The reaction mixture was allowed to warm to room temperature and kept for 16 h. After the solvent was removed in vacuo, the residue was purified by column chromatography on silicagel to give I as a white solids.

Synthesis of compound 2

1(220.0 mg, 0.354 mmol) was suspended in 30 mL saturated methanolic ammonia and the solution was heated in a sealed bottle at 403 K for 12 h. The solution was evaporated in vacuo. The residue was purified by column chromatography on silica gel to afford 2 as a white solids. Crystals of the title compound (2) were obtained by slow evaporation of methanol.

Refinement top

H atoms bond to N were located in a difference map and refined with distance of N—H = 0.86 Å or O—H = 0.82 Å and Uiso(H) = 1.2Ueq(N). other H atoms attached to C were fixed geometrically and treated as riding with C—H = 0.96 Å (methyl) or 0.93 Å (aromatic) and with Uiso(H) = 1.2Ueq(aromatic) or Uiso(H) = 1.5Ueq(methyl).

Structure description top

Fluorinated nucleosides, containing fluorine atom(s) or fluorine containing groups in the sugar moiety or in the base moiety of nucleosides, greatly improve the bioactivity and stability of the corresponding compounds. The noteworthy of the fluorinated nucleosides are FMAU, FIAC, FLT, gemcitabine (Etzold, et al., 1971; Watanabe, et al., 1979; Hertel, et al., 1988), which have high antiherpes and in some cases antitumour activities.

In our study, we report a fluorinated nucleoside (Fig. 1). The three-dimensional structure and the packing of the title compound is shown Fig. 2 and hydrogen bonds geometry are summarized in Table 1. The orientation of the base relative to the sugar of purine nucleosides is defined by the torsion angle χ (O1-C7-N4-C5),being in the title compound -anti, withχ= –129.0 (11)°. The phase angle of pseudorotation (P)is 67.6 (11)°, and the maximum amplitude of puckering (τm) is 39.5 (7)° (Saenger, 1983). The sugar ring adopts a D conformation (Evans & Boeyens, 1989), with an unsymmetrical twist O1-endo-C10-exo(oT4). The packing of the title compound is stabilized by hydrogen bonds, leading to a two-dimensional network (Fig. 3 and Table 1). The nucleobases are arranged head-to-head in a staircase-like fashion, in a pattern propagated by the a axis of the unit cell.

For the biological activity of fluorinated nucleosides, see: Etzold et al. (1971); Hertel et al. (1988); Watanabe et al. (1979). For puckering amplitudes, see: Saenger (1983). For sugar ring conformations, see: Evans & Boeyens (1989).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2013); cell refinement: CrysAlis PRO (Agilent, 2013); data reduction: CrysAlis PRO (Agilent, 2013); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Displacement ellipsoid plot of C11H12FIN4O3 are drawn at the 30% probability level and H atoms are represented as small spheres of arbitrary radius.
[Figure 2] Fig. 2. Synthesis method of the title compound.
[Figure 3] Fig. 3. The packing of the title compound. Green lines indicate the hydrogen bonds.
(2R,3S,4R,5R)-5-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-fluoro-2-(hydroxymethyl)tetrahydrofuran-3-ol top
Crystal data top
C11H12FIN4O3Z = 1
Mr = 394.15F(000) = 192
Triclinic, P1Dx = 1.986 Mg m−3
Hall symbol: P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.2602 (4) ÅCell parameters from 1312 reflections
b = 7.1570 (6) Åθ = 2.9–28.5°
c = 9.0126 (10) ŵ = 2.46 mm−1
α = 84.533 (8)°T = 293 K
β = 83.400 (8)°Block, colourless
γ = 78.679 (7)°0.40 × 0.20 × 0.10 mm
V = 329.57 (5) Å3
Data collection top
Agilent Xcalibur (Eos, Gemini)
diffractometer		1657 independent reflections
Radiation source: Enhance (Mo) X-ray Source1657 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.012
ω scansθmax = 25.0°, θmin = 2.9°
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2013)		h = −6→6
Tmin = 0.440, Tmax = 0.791k = −8→7
1874 measured reflectionsl = −10→10
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.035 w = 1/[σ2(Fo2) + (0.0711P)2 + 0.4273P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.101(Δ/σ)max < 0.001
S = 1.12Δρmax = 0.81 e Å−3
1657 reflectionsΔρmin = −0.95 e Å−3
184 parametersExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
543 restraintsExtinction coefficient: 0.067 (7)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983)
Secondary atom site location: difference Fourier mapAbsolute structure parameter: −0.02 (4)
Crystal data top
C11H12FIN4O3γ = 78.679 (7)°
Mr = 394.15V = 329.57 (5) Å3
Triclinic, P1Z = 1
a = 5.2602 (4) ÅMo Kα radiation
b = 7.1570 (6) ŵ = 2.46 mm−1
c = 9.0126 (10) ÅT = 293 K
α = 84.533 (8)°0.40 × 0.20 × 0.10 mm
β = 83.400 (8)°
Data collection top
Agilent Xcalibur (Eos, Gemini)
diffractometer		1657 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2013)		1657 reflections with I > 2σ(I)
Tmin = 0.440, Tmax = 0.791Rint = 0.012
1874 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.101Δρmax = 0.81 e Å−3
S = 1.12Δρmin = −0.95 e Å−3
1657 reflectionsAbsolute structure: Flack (1983)
184 parametersAbsolute structure parameter: −0.02 (4)
543 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
I10.19300.64490.34630.0308 (2)
F10.429 (2)0.7543 (16)0.9462 (11)0.057 (3)
N10.461 (2)1.0608 (16)0.2063 (11)0.048 (2)
H1A0.48561.14770.13620.058*
H1B0.36860.97810.19350.058*
N20.711 (2)1.1864 (12)0.3508 (12)0.035 (2)
N30.8208 (15)1.0496 (10)0.5935 (8)0.0301 (14)
N40.667 (2)0.7549 (14)0.6696 (13)0.026 (2)
O10.936 (3)0.4908 (14)0.7689 (12)0.032 (2)
O20.8391 (16)0.4981 (11)1.1671 (8)0.0393 (16)
H20.95730.55791.16650.059*
O30.7857 (18)0.1388 (10)0.8929 (8)0.0499 (19)
H30.68240.23350.86510.075*
C10.430 (2)0.7432 (14)0.4790 (11)0.0288 (17)
C20.5445 (15)0.9116 (11)0.4542 (9)0.0231 (15)
C30.567 (2)1.0544 (15)0.3346 (11)0.0299 (19)
C40.820 (2)1.1806 (15)0.4769 (12)0.034 (2)
H40.90751.27970.48560.040*
C50.6830 (16)0.9159 (11)0.5735 (9)0.0239 (15)
C60.5113 (16)0.6501 (12)0.6100 (9)0.0266 (16)
H60.46930.53500.65250.032*
C70.8350 (17)0.6879 (12)0.7859 (9)0.0278 (16)
H70.97880.75840.77410.033*
C80.7021 (19)0.6988 (13)0.9462 (10)0.0327 (17)
H80.76990.79010.99800.039*
C90.774 (2)0.4980 (17)1.0223 (16)0.025 (2)
H90.62760.43171.02440.030*
C100.9965 (18)0.4065 (12)0.9139 (10)0.0289 (16)
H101.16070.43710.93660.035*
C111.022 (2)0.1922 (15)0.9151 (13)0.045 (2)
H11A1.15440.14450.83690.055*
H11B1.07740.13351.01040.055*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0289 (3)0.0375 (3)0.0286 (3)−0.01214 (17)−0.00417 (17)−0.00181 (17)
F10.056 (5)0.064 (6)0.032 (4)0.024 (4)0.007 (3)0.009 (4)
N10.061 (6)0.051 (5)0.037 (5)−0.022 (5)−0.025 (5)0.025 (4)
N20.044 (4)0.030 (5)0.031 (4)−0.012 (5)−0.008 (3)0.016 (4)
N30.042 (3)0.027 (3)0.024 (3)−0.014 (3)−0.007 (3)0.004 (3)
N40.038 (4)0.023 (4)0.017 (3)−0.011 (3)−0.006 (3)0.010 (3)
O10.048 (4)0.023 (3)0.023 (4)−0.006 (3)0.001 (3)0.006 (3)
O20.057 (4)0.048 (4)0.021 (3)−0.029 (3)−0.017 (3)0.010 (3)
O30.096 (6)0.031 (4)0.031 (4)−0.030 (4)−0.011 (4)−0.002 (3)
C10.030 (3)0.027 (4)0.029 (4)−0.010 (3)−0.004 (3)0.012 (3)
C20.029 (3)0.022 (3)0.017 (3)−0.008 (3)−0.001 (3)0.010 (3)
C30.035 (4)0.029 (4)0.024 (4)−0.008 (3)−0.005 (4)0.012 (3)
C40.042 (5)0.031 (4)0.028 (4)−0.011 (4)−0.005 (4)0.011 (4)
C50.033 (3)0.020 (3)0.018 (3)−0.007 (3)−0.003 (3)0.005 (3)
C60.035 (3)0.027 (3)0.018 (3)−0.012 (3)−0.002 (3)0.007 (3)
C70.040 (3)0.027 (3)0.019 (3)−0.013 (3)−0.008 (3)0.006 (3)
C80.051 (4)0.028 (4)0.019 (3)−0.009 (3)−0.008 (3)0.006 (3)
C90.038 (5)0.023 (4)0.020 (4)−0.016 (4)−0.017 (4)0.007 (3)
C100.039 (4)0.026 (4)0.024 (4)−0.009 (3)−0.013 (3)0.005 (3)
C110.062 (5)0.033 (4)0.037 (5)−0.001 (4)−0.014 (4)0.008 (4)
Geometric parameters (Å, º) top
I1—C12.080 (11)O3—H30.8200
F1—C81.411 (16)C1—C61.369 (13)
N1—C31.332 (14)C1—C21.438 (13)
N1—H1A0.8600C2—C51.372 (12)
N1—H1B0.8600C2—C31.424 (12)
N2—C41.326 (16)C4—H40.9300
N2—C31.350 (18)C6—H60.9300
N3—C41.340 (12)C7—C81.533 (12)
N3—C51.345 (11)C7—H70.9800
N4—C51.384 (12)C8—C91.529 (14)
N4—C61.393 (15)C8—H80.9800
N4—C71.435 (14)C9—C101.519 (17)
O1—C71.423 (14)C9—H90.9800
O1—C101.428 (13)C10—C111.512 (13)
O2—C91.387 (16)C10—H100.9800
O2—H20.8200C11—H11A0.9700
O3—C111.408 (15)C11—H11B0.9700
C3—N1—H1A120.0O1—C7—C8105.9 (7)
C3—N1—H1B120.0N4—C7—C8115.4 (8)
H1A—N1—H1B120.0O1—C7—H7109.4
C4—N2—C3119.3 (9)N4—C7—H7109.4
C4—N3—C5111.9 (8)C8—C7—H7109.4
C5—N4—C6107.7 (9)F1—C8—C9110.9 (9)
C5—N4—C7124.2 (10)F1—C8—C7111.0 (8)
C6—N4—C7126.3 (8)C9—C8—C7105.6 (8)
C7—O1—C10106.5 (9)F1—C8—H8109.8
C9—O2—H2109.5C9—C8—H8109.8
C11—O3—H3109.5C7—C8—H8109.8
C6—C1—C2106.7 (9)O2—C9—C10114.3 (9)
C6—C1—I1124.3 (7)O2—C9—C8113.1 (10)
C2—C1—I1129.0 (6)C10—C9—C8101.9 (9)
C5—C2—C3116.5 (8)O2—C9—H9109.1
C5—C2—C1107.4 (7)C10—C9—H9109.1
C3—C2—C1135.8 (9)C8—C9—H9109.1
N1—C3—N2118.4 (9)O1—C10—C11108.9 (8)
N1—C3—C2123.8 (10)O1—C10—C9105.4 (9)
N2—C3—C2117.7 (9)C11—C10—C9113.3 (9)
N2—C4—N3127.9 (10)O1—C10—H10109.7
N2—C4—H4116.0C11—C10—H10109.7
N3—C4—H4116.0C9—C10—H10109.7
N3—C5—C2126.4 (7)O3—C11—C10112.3 (8)
N3—C5—N4124.6 (9)O3—C11—H11A109.1
C2—C5—N4108.9 (8)C10—C11—H11A109.1
C1—C6—N4109.2 (8)O3—C11—H11B109.1
C1—C6—H6125.4C10—C11—H11B109.1
N4—C6—H6125.4H11A—C11—H11B107.9
O1—C7—N4107.3 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C8—H8···O3i0.982.603.247 (11)124
N1—H1A···O3ii0.862.553.189 (13)132
O2—H2···I1iii0.822.352.9933136
Symmetry codes: (i) x, y+1, z; (ii) x, y+1, z−1; (iii) x+1, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C8—H8···O3i0.982.603.247 (11)123.9
N1—H1A···O3ii0.862.553.189 (13)132
O2—H2···I1iii0.822.352.9933136
Symmetry codes: (i) x, y+1, z; (ii) x, y+1, z−1; (iii) x+1, y, z+1.
 

Acknowledgements

This work was supported by National Natural Science Foundation (NSFC, Nos. 20962009, 21062006) and the Science Fund of the Education Office of Jiangxi (GJJ12583).

References

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COMMUNICATIONS
ISSN: 2056-9890
Volume 70| Part 2| February 2014| Page o120
doi:10.1107/S1600536813034995
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