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In the title compound [systematic name: 4-amino-7-(β-D-ribofuranos­yl)-7H-pyrazolo[3,4-d][1,2,3]triazine], C9H12N6O4, the torsion angle of the N-glycosylic bond is high anti [χ = −83.2 (3)°]. The ribofuran­ose moiety adopts the C2′-endo–C1′-exo (2T1) sugar conformation (S-type sugar pucker), with P = 152.4° and τm = 35.0°. The conformation at the C4′—C5′ bond is +sc (gauche,gauche), with the torsion angle γ = 52.0 (3)°. The compound forms a three-dimensional network that is stabilized by several hydrogen bonds (N—H...O, O—H...N and O—H...O).

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S010827010601818X/jz3014sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S010827010601818X/jz3014Isup2.hkl
Contains datablock I

CCDC reference: 616130

Comment top

The aza and deaza derivatives of purine nucleosides attract attention because they are valuable tools in chemistry and biology. Many of them show antifungal, antiviral and anticancer activity (Montgomery & Thomas, 1972; Montgomery et al., 1975; Bennett et al., 1976). They also show unusual base-pairing properties when they are constituents of nucleic acids. 7-Deaza-2,8-diaza-2'-deoxyadenosine forms strong base pairs with 2'-deoxyguanosine and weaker ones with 2'-deoxythymidine in duplex DNA (Seela et al., 2004). We now report the single-crystal X-ray structure of the ribonucleoside 7-deaza-2,8-diazaadenosine, (I).

The title nucleoside was synthesized from 8-aza-7-deazaadenosine, (II), via its 1,N6-etheno derivative (Lin et al., 2005) (purine numbering is used throughout this manuscript). The structure of compound (I) is depicted in Fig. 1. Selected geometric parameters are shown in Table 1.

The N-glycosylic bond torsion angle χ (O4'—C1'—N9—C4) of (I), which describes the orientation of the base relative to the sugar moiety, shows a high anti conformation [χ = −83.2 (3)°] (IUPAC-IUB Joint Commission on Biochemical Nomenclature, 1983). The glycosylic bond conformation of compound (II) is also high anti [χ = −77.6 (3)°; 102.4–180° Significance of this range of angles?; Sprang et al., 1978]. In contrast, 2-azaadenosine, (III), and adenosine, (IV), adopt the anti conformation, with χ = −166.2 and −171.1°, respectively (Singh & Hodgson, 1979; Lai & Marsh, 1972). Thus, the introduction of an additional N atom in the six-membered ring of the purine nucleoside [(VI) (III)] or in the corresponding pyrazolo[3,4-d]pyrimidine analogue [(II) (I)] does not lead to significant changes in the conformation of the glycosylic bond. On the other hand, the shift of the imidazole N atom from position 7 to 8 [(III) (I) or (IV) (II)] changes the conformation towards syn, as is found for the related nucleosides (Sprang et al., 1978; Singh & Hodgson, 1979; Lai & Marsh, 1972). The length of the glycosylic bond (C1'—N9) of (I) is 1.444 (3) Å, which is shorter than those of the nucleosides (II) [1.460 (5) Å], (III) [1.470 (4) Å] or (IV) (1.466 Å) (Sprang et al., 1978; Singh & Hodgson, 1979; Lai & Marsh, 1972).

The sugar moiety of (I) shows a pseudorotation phase angle P of 152.4° and an amplitude τm of 35.0°, which indicates S-conformation (2T1) (Altona & Sundaralingam, 1972; Rao et al., 1981). This is similar to compound (II) (P = 141.9°, τm = −41.9°, 1T2; Sprang et al., 1978). This S-conformation is rather uncommon for ribonucleosides. The conformation of the sugar moiety of compounds (III) and (IV) is N [P = 20.8°, τm = 39.5°, 3T4 for (III), and P = 6.9°, τm = 36.8°, 3T2 for (IV)]. These data are not included in the manuscripts (Singh & Hodgson, 1979; Lai & Marsh, 1972) but are available from the Cambridge Structural Database (CSD, Version?; Allen, 2002). They indicate that the major conformational change results from the alternation of the nitrogen pattern in the five-membered ring (Singh & Hodgson, 1979; Lai & Marsh, 1972). The C3'—C4'—C5'—O5' torsion angle of compound (I) is 52.0 (3)°, which shows that the exocyclic hydroxyl group prefers a gauche,gauche (+sc) conformation. This is similar to compound (III) (γ = 42.28°, +sc; CSD Refcode?), but different from compound (II) (γ = 179.5°, +ap; Sprang et al., 1978) and (IV) (γ = 177.0°, +ap; Lai & Marsh, 1972).

Compound (I) forms a three-dimensional network which is stabilized by several intermolecular hydrogen bonds listed in Table 2 and shown in Figs. 2 and 3. Whereas hydrogen bonds 1, 2 and 5 (numbers relate to entries in Table 2 [Please check added text]) lead to double layers perpendicular to the c axis (Fig. 2), hydrogen bonds 3 and 4 connect the sugar moieties (O3'—H3'1···O2') or the sugar moiety with the base (O2'—H2'1···N2) (Fig. 3). The hydrogen-bond acceptor properties of N2 have been already suggested to be involved in the base pairing of 7-deaza-2,8-diaza-2'-deoxyadenosine with 2'-deoxyguanosine within duplex DNA (Seela et al., 2004).

Experimental top

Compound (I) (Source?) was crystallized from water as colourless crystals (m.p. 481–482 K).

Refinement top

In the absence of suitable anomalous scattering, refinement of the Flack parameter (Flack, 1983) led to inconclusive values. Therefore, Friedel equivalents were merged before the final refinement. The known configuration of the parent molecule was used to define the enantiomer employed in the refined model. All H atoms were found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, H atoms were 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 Uiso(H) = 1.2Ueq(C), 1.5Ueq(O) or 1.2Ueq(N). The OH groups were refined as rigid groups allowed to rotate but not tip.

Computing details top

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

Figures top
[Figure 1] Fig. 1. A perspective view of nucleoside (I), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as spheres of small arbitrary size.
[Figure 2] Fig. 2. The crystal packing of nucleoside (I), viewed down the c axis, showing the layered structure of the crystal. Intermolecular hydrogen bonds 1, 2 and 5 (Table 2) are indicated by dashed lines.
[Figure 3] Fig. 3. The crystal packing of nucleoside (I), viewed down the b axis. Intermolecular hydrogen bonds 3 and 4 (Table 2) are indicated by dashed lines.
4-amino-7-(β-D-ribofuranosyl)-7H-pyrazolo[3,4-d][1,2,3]triazine top
Crystal data top
C9H12N6O4Dx = 1.581 Mg m3
Mr = 268.25Mo Kα radiation, λ = 0.71073 Å
Trigonal, P3221Cell parameters from 40 reflections
Hall symbol: P 32 2"θ = 4.8–12.3°
a = 9.7859 (7) ŵ = 0.13 mm1
c = 20.3813 (14) ÅT = 293 K
V = 1690.3 (2) Å3Transparent block, colourless
Z = 60.3 × 0.2 × 0.2 mm
F(000) = 840
Data collection top
Siemens P4
diffractometer
Rint = 0.045
Radiation source: fine-focus sealed tubeθmax = 30.0°, θmin = 2.4°
Graphite monochromatorh = 113
2θ/ω scansk = 131
4386 measured reflectionsl = 281
1910 independent reflections3 standard reflections every 97 reflections
1587 reflections with I > 2σ(I) intensity decay: none
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.125H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0781P)2 + 0.1318P]
where P = (Fo2 + 2Fc2)/3
1910 reflections(Δ/σ)max < 0.001
175 parametersΔρmax = 0.59 e Å3
0 restraintsΔρmin = 0.30 e Å3
Crystal data top
C9H12N6O4Z = 6
Mr = 268.25Mo Kα radiation
Trigonal, P3221µ = 0.13 mm1
a = 9.7859 (7) ÅT = 293 K
c = 20.3813 (14) Å0.3 × 0.2 × 0.2 mm
V = 1690.3 (2) Å3
Data collection top
Siemens P4
diffractometer
Rint = 0.045
4386 measured reflections3 standard reflections every 97 reflections
1910 independent reflections intensity decay: none
1587 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0440 restraints
wR(F2) = 0.125H-atom parameters constrained
S = 1.01Δρmax = 0.59 e Å3
1910 reflectionsΔρmin = 0.30 e Å3
175 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
xyzUiso*/Ueq
N11.0451 (3)0.9361 (3)0.09555 (11)0.0388 (5)
N21.0616 (3)0.8124 (3)0.10549 (11)0.0397 (5)
N30.9454 (3)0.6640 (3)0.10555 (10)0.0356 (5)
C40.8019 (3)0.6471 (3)0.09600 (11)0.0272 (4)
C50.7669 (3)0.7672 (3)0.08898 (10)0.0283 (5)
C60.9003 (3)0.9211 (3)0.08776 (11)0.0325 (5)
N60.8940 (3)1.0518 (3)0.07817 (13)0.0475 (6)
H6A0.97971.14170.07710.057*
H6B0.80441.04670.07310.057*
C70.6010 (3)0.6887 (3)0.07929 (13)0.0336 (5)
H70.54290.73920.07330.040*
N80.5403 (2)0.5336 (2)0.07985 (11)0.0317 (4)
N90.6642 (2)0.5079 (2)0.09112 (9)0.0284 (4)
C1'0.6525 (3)0.3562 (3)0.08146 (11)0.0272 (4)
H1'0.73860.35430.10520.033*
C2'0.4964 (3)0.2146 (3)0.10230 (11)0.0277 (4)
H2'0.40860.23230.09220.033*
O2'0.5005 (2)0.1873 (2)0.17016 (8)0.0363 (4)
H2'10.42590.18760.18840.054*
C3'0.4894 (3)0.0831 (3)0.05859 (11)0.0297 (5)
H3'0.38010.00380.04830.036*
O3'0.5711 (2)0.0125 (2)0.08815 (9)0.0369 (4)
H3'10.51390.05260.11540.055*
C4'0.5790 (3)0.1704 (3)0.00325 (11)0.0304 (4)
H4'0.65290.13430.01510.036*
C5'0.4767 (4)0.1513 (4)0.06224 (13)0.0431 (6)
H5'A0.54320.22020.09700.052*
H5'B0.42970.04360.07800.052*
O5'0.3560 (3)0.1854 (3)0.04965 (13)0.0544 (6)
H5'10.38420.27570.06150.082*
O4'0.6682 (2)0.3363 (2)0.01341 (8)0.0385 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0299 (10)0.0306 (11)0.0475 (11)0.0089 (9)0.0064 (9)0.0012 (9)
N20.0297 (11)0.0387 (12)0.0484 (12)0.0153 (10)0.0051 (9)0.0008 (10)
N30.0295 (10)0.0350 (11)0.0437 (10)0.0171 (9)0.0050 (8)0.0020 (9)
C40.0277 (11)0.0254 (10)0.0285 (9)0.0133 (9)0.0017 (8)0.0002 (8)
C50.0303 (11)0.0237 (10)0.0311 (10)0.0136 (9)0.0057 (8)0.0033 (8)
C60.0345 (12)0.0265 (11)0.0335 (10)0.0128 (10)0.0052 (9)0.0004 (9)
N60.0432 (14)0.0234 (10)0.0711 (16)0.0130 (10)0.0076 (12)0.0047 (10)
C70.0309 (12)0.0272 (11)0.0466 (12)0.0174 (10)0.0070 (10)0.0046 (10)
N80.0263 (10)0.0269 (10)0.0452 (11)0.0157 (8)0.0034 (8)0.0023 (8)
N90.0271 (10)0.0236 (9)0.0361 (9)0.0140 (8)0.0015 (8)0.0005 (7)
C1'0.0269 (10)0.0235 (10)0.0319 (9)0.0132 (8)0.0030 (8)0.0024 (8)
C2'0.0277 (11)0.0239 (10)0.0347 (10)0.0153 (9)0.0067 (8)0.0049 (8)
O2'0.0444 (10)0.0391 (10)0.0341 (8)0.0275 (8)0.0127 (7)0.0082 (7)
C3'0.0289 (11)0.0220 (10)0.0388 (11)0.0131 (9)0.0035 (9)0.0007 (9)
O3'0.0454 (11)0.0309 (9)0.0451 (9)0.0271 (8)0.0113 (8)0.0101 (8)
C4'0.0308 (11)0.0254 (10)0.0357 (10)0.0146 (9)0.0043 (9)0.0006 (8)
C5'0.0400 (14)0.0459 (16)0.0402 (12)0.0190 (13)0.0020 (11)0.0016 (11)
O5'0.0359 (10)0.0464 (13)0.0774 (15)0.0179 (10)0.0043 (10)0.0102 (11)
O4'0.0459 (11)0.0245 (8)0.0337 (8)0.0090 (8)0.0122 (7)0.0032 (6)
Geometric parameters (Å, º) top
N1—N21.315 (4)C1'—H1'0.9800
N1—C61.359 (4)C2'—O2'1.413 (3)
N2—N31.323 (3)C2'—C3'1.538 (3)
N3—C41.343 (3)C2'—H2'0.9800
C4—N91.359 (3)O2'—H2'10.8200
C4—C51.387 (3)C3'—O3'1.426 (3)
C5—C61.416 (3)C3'—C4'1.529 (3)
C5—C71.420 (3)C3'—H3'0.9800
C6—N61.325 (4)O3'—H3'10.8200
N6—H6A0.8600C4'—O4'1.448 (3)
N6—H6B0.8600C4'—C5'1.515 (4)
C7—N81.325 (3)C4'—H4'0.9800
C7—H70.9300C5'—O5'1.402 (4)
N8—N91.374 (3)C5'—H5'A0.9700
N9—C1'1.444 (3)C5'—H5'B0.9700
C1'—O4'1.419 (3)O5'—H5'10.8200
C1'—C2'1.522 (3)
N2—N1—C6121.3 (2)O2'—C2'—C1'109.6 (2)
N1—N2—N3125.2 (2)O2'—C2'—C3'113.76 (18)
N2—N3—C4114.0 (2)C1'—C2'—C3'101.81 (17)
N3—C4—N9125.9 (2)O2'—C2'—H2'110.5
N3—C4—C5126.7 (2)C1'—C2'—H2'110.5
N9—C4—C5107.5 (2)C3'—C2'—H2'110.5
C4—C5—C6114.6 (2)C2'—O2'—H2'1109.5
C4—C5—C7104.8 (2)O3'—C3'—C4'108.34 (19)
C6—C5—C7140.3 (2)O3'—C3'—C2'111.06 (19)
N6—C6—N1117.5 (3)C4'—C3'—C2'103.74 (18)
N6—C6—C5124.5 (3)O3'—C3'—H3'111.1
N1—C6—C5118.0 (2)C4'—C3'—H3'111.1
C6—N6—H6A120.0C2'—C3'—H3'111.1
C6—N6—H6B120.0C3'—O3'—H3'1109.5
H6A—N6—H6B120.0O4'—C4'—C5'108.4 (2)
N8—C7—C5110.8 (2)O4'—C4'—C3'106.76 (17)
N8—C7—H7124.6C5'—C4'—C3'115.2 (2)
C5—C7—H7124.6O4'—C4'—H4'108.8
C7—N8—N9106.2 (2)C5'—C4'—H4'108.8
C4—N9—N8110.7 (2)C3'—C4'—H4'108.8
C4—N9—C1'124.7 (2)O5'—C5'—C4'114.1 (2)
N8—N9—C1'122.7 (2)O5'—C5'—H5'A108.7
O4'—C1'—N9108.42 (18)C4'—C5'—H5'A108.7
O4'—C1'—C2'105.99 (18)O5'—C5'—H5'B108.7
N9—C1'—C2'115.19 (19)C4'—C5'—H5'B108.7
O4'—C1'—H1'109.0H5'A—C5'—H5'B107.6
N9—C1'—H1'109.0C5'—O5'—H5'1109.5
C2'—C1'—H1'109.0C1'—O4'—C4'109.73 (16)
C6—N1—N2—N33.8 (4)C4—N9—C1'—O4'83.2 (3)
N1—N2—N3—C41.7 (4)N8—N9—C1'—O4'79.6 (3)
N2—N3—C4—N9177.0 (2)C4—N9—C1'—C2'158.2 (2)
N2—N3—C4—C52.6 (4)N8—N9—C1'—C2'38.9 (3)
N3—C4—C5—C64.4 (4)O4'—C1'—C2'—O2'155.32 (18)
N9—C4—C5—C6175.3 (2)N9—C1'—C2'—O2'84.8 (2)
N3—C4—C5—C7179.3 (2)O4'—C1'—C2'—C3'34.6 (2)
N9—C4—C5—C70.4 (3)N9—C1'—C2'—C3'154.44 (19)
N2—N1—C6—N6179.8 (3)O2'—C2'—C3'—O3'31.9 (3)
N2—N1—C6—C51.6 (4)C1'—C2'—C3'—O3'85.9 (2)
C4—C5—C6—N6176.4 (2)O2'—C2'—C3'—C4'148.0 (2)
C7—C5—C6—N64.2 (5)C1'—C2'—C3'—C4'30.3 (2)
C4—C5—C6—N12.1 (3)O3'—C3'—C4'—O4'101.7 (2)
C7—C5—C6—N1174.3 (3)C2'—C3'—C4'—O4'16.4 (2)
C4—C5—C7—N80.5 (3)O3'—C3'—C4'—C5'138.0 (2)
C6—C5—C7—N8172.3 (3)C2'—C3'—C4'—C5'104.0 (2)
C5—C7—N8—N91.1 (3)O4'—C4'—C5'—O5'67.5 (3)
N3—C4—N9—N8178.5 (2)C3'—C4'—C5'—O5'52.0 (3)
C5—C4—N9—N81.1 (3)N9—C1'—O4'—C4'149.78 (19)
N3—C4—N9—C1'13.9 (4)C2'—C1'—O4'—C4'25.6 (2)
C5—C4—N9—C1'165.8 (2)C5'—C4'—O4'—C1'130.1 (2)
C7—N8—N9—C41.4 (3)C3'—C4'—O4'—C1'5.5 (3)
C7—N8—N9—C1'166.4 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···O5i0.862.132.973 (3)166
N6—H6B···O3ii0.862.162.993 (3)164
O2—H21···N2iii0.821.912.727 (3)178
O3—H31···O2iv0.821.992.756 (3)156
O5—H51···N8v0.822.283.071 (3)162
Symmetry codes: (i) y+1, x+1, z; (ii) x, y+1, z; (iii) xy, y+1, z+1/3; (iv) xy, y, z+1/3; (v) y, x, z.

Experimental details

Crystal data
Chemical formulaC9H12N6O4
Mr268.25
Crystal system, space groupTrigonal, P3221
Temperature (K)293
a, c (Å)9.7859 (7), 20.3813 (14)
V3)1690.3 (2)
Z6
Radiation typeMo Kα
µ (mm1)0.13
Crystal size (mm)0.3 × 0.2 × 0.2
Data collection
DiffractometerSiemens P4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
4386, 1910, 1587
Rint0.045
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.125, 1.01
No. of reflections1910
No. of parameters175
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.59, 0.30

Computer programs: XSCANS (Siemens, 1996), XSCANS, SHELXTL (Sheldrick, 1997), SHELXTL and PLATON (Spek, 2003).

Selected geometric parameters (Å, º) top
N1—N21.315 (4)C4—C51.387 (3)
N1—C61.359 (4)C6—N61.325 (4)
N2—N31.323 (3)C7—N81.325 (3)
N3—C41.343 (3)N8—N91.374 (3)
C4—N91.359 (3)N9—C1'1.444 (3)
N2—N1—C6121.3 (2)C4—N9—C1'124.7 (2)
N1—N2—N3125.2 (2)N8—N9—C1'122.7 (2)
N2—N3—C4114.0 (2)O4'—C1'—N9108.42 (18)
N3—C4—N9125.9 (2)N9—C1'—C2'115.19 (19)
C4—N9—N8110.7 (2)C1'—O4'—C4'109.73 (16)
C6—N1—N2—N33.8 (4)N3—C4—N9—C1'13.9 (4)
N1—N2—N3—C41.7 (4)C5—C4—N9—C1'165.8 (2)
N2—N3—C4—N9177.0 (2)C4—N9—C1'—O4'83.2 (3)
N2—N3—C4—C52.6 (4)N8—N9—C1'—O4'79.6 (3)
N9—C4—C5—C6175.3 (2)O3'—C3'—C4'—O4'101.7 (2)
N3—C4—C5—C7179.3 (2)C2'—C3'—C4'—C5'104.0 (2)
N9—C4—C5—C70.4 (3)C3'—C4'—C5'—O5'52.0 (3)
N2—N1—C6—N6179.8 (3)N9—C1'—O4'—C4'149.78 (19)
C4—C5—C6—N6176.4 (2)C2'—C1'—O4'—C4'25.6 (2)
C5—C4—N9—N81.1 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···O5'i0.862.132.973 (3)166.3
N6—H6B···O3'ii0.862.162.993 (3)164.1
O2'—H2'1···N2iii0.821.912.727 (3)178.0
O3'—H3'1···O2'iv0.821.992.756 (3)155.7
O5'—H5'1···N8v0.822.283.071 (3)162.1
Symmetry codes: (i) y+1, x+1, z; (ii) x, y+1, z; (iii) xy, y+1, z+1/3; (iv) xy, y, z+1/3; (v) y, x, z.
 

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