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The title compound [systematic name: 4-amino-5-cyano-1-(β-D-ribofuranos­yl)-7H-pyrrolo[2,3-d]pyrimidine hemihydrate], C12H13N5O4·0.5H2O, is a regioisomer of toyocamycin with the ribofuranosyl residue attached to the pyrimidine moiety of the heterocycle. This analogue exhibits a syn glycosylic bond conformation with a χ torsion angle of 57.51 (17)°. The ribofuran­ose moiety shows an envelope C2′-endo (2E) sugar conformation (S-type), with P = 161.6 (2)° and τm = 41.3 (1)°. The conformation at the exocyclic C4′—C5′ bond is +sc (gauche, gauche), with a γ torsion angle of 54.4 (2)°. The crystal packing is stabilized by inter­molecular O—H...O, N—H...N and O—H...N hydrogen bonds; water mol­ecules, located on crystallographic twofold axes, participate in inter­actions. An intra­molecular O—H...N hydrogen bond stabilizes the syn conformation of the nucleoside.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270109029813/gg3204sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270109029813/gg3204Isup2.hkl
Contains datablock I

CCDC reference: 749706

Comment top

Toyocamycin is a naturally occurring 7-deazapurine ribonucleoside produced by Streptomyces toyocaensis or other Streptomyces strains (purine numbering is used throughout this discussion) (Nishimura et al., 1956; Ohkuma, 1961). The chemical synthesis of the antibiotic toyocamycin was described by different laboratories (Tolman et al., 1968, 1969; Sharma et al., 1993; Porcari & Townsend, 1999). Moreover, the crystal structure of toyocamycin was reported by Prusiner & Sundaralingam (1978). Recently, the N-3 regioisomer of toyocamycin was synthesized (Leonard et al., 2009). Generally, purine N-3 nucleosides are relatively labile molecules. They are formed as intermediates during convergent nucleoside synthesis under kinetically controlled conditions and are rearranged to the thermodynamically more stable N-9 isomers (Vorbrüggen et al., 1981). In the case of the toyocamycin analogue (Ia), the glycosylic bond is more stable owing to the electronic properties of the 7-deazapurine moiety, a fact which was already reported for other 7-deazapurine nucleosides (Seela & Peng, 2006).

As relatively few X-ray analyses of N-3 nucleosides are known (Kumar et al., 1988, 1989), a single-crystal X-ray analysis of compound (Ia) was performed. The conformation and hydrogen-bonding pattern in the crystalline state is now studied and compared with the closely related structures of toyocamycin, (IIb) (Prusiner & Sundaralingam, 1978), tubercidin, (IIa) (Stroud, 1973; Abola & Sundaralingam, 1973), and 3-isoadenosine, (III) (Kumar et al., 1988). The three-dimensional structure of (Ia) is shown in Fig. 1 and selected geometric parameters are listed in Table 1.

The title compound can form two main tautomers, namely (Ia) and (Ib) as shown in the scheme. Tautomer (Ia) bears an amine group and no H atom at the pyrrole N atom, while tautomer (Ib) carries a pyrrole H atom and an imine group on the pyrimidine moiety. These tautomers differ in bond length. The tautomeric structure (Ia) with two H atoms at N6 is evidenced by X-ray analysis in the solid state and in solution by 1H NMR spectroscopy. For related compounds, it was observed that the rotation around the H2N—C bond of the amine group is restricted, causing two distinct signals in the 1H NMR spectrum due to the different environments adopted by this group (Seela & Bussmann, 1984). This is also found for compound (Ia). The bond lengths between C6 and N6 of the amine substituent are similar in (Ia) and (IIb). On the other hand, in (Ia), the C2—N1 bond is significantly shorter [1.306 (2) Å] than the C4—N3 bond [1.385 (2) Å], while in toyocamycin these bonds are of almost equal length (C2—N1 = 1.3471 Å and C4—N3 = 1.3470 Å; Prusiner & Sundaralingam, 1978). The same effect was observed in the crystal structure of 3-isoadenosine (Kumar et al., 1988). Altogether, this confirms that tautomeric (Ia) exists in the solid state and in dimethyl sulfoxide solution.

For the common purine nucleosides, the preferred conformation at the N-glycosylic bond is usually anti (Saenger, 1984). The orientation of the nucleobase relative to the sugar moiety (syn/anti) of purine nucleosides is defined by the torsion angle χ(O4'—C1'—N9—C4) (purine numbering; IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983). For the N-3 nucleoside (Ia), a different notation has to be used in analogy to the already reported definition for the N-3 nucleoside (III). The torsion angle χ is defined by O4'—C1'—N3—C4 (Kumar et al., 1988).

Contrary to the crystal structure of (III), the glycosylic bond torsion angle of (Ia) is in the syn range, with a χ value of 57.51 (17)°. This conformation differs from that in toyocamycin [N-9 isomer, (IIb)], which adopts an anti conformation at the glycosylic bond (χ = -121.88°; Prusiner & Sundaralingam, 1978). The glycosylic bond conformations of (IIa) and N-3 nucleoside (III) show torsion angle values in the anti range, with χ values of -112.8 (4)° for (IIa) (Abola & Sundaralingam, 1973) and -161.5° for (III) (Kumar et al., 1988). In the tautomeric form (Ib) with an H-atom at the pyrrole N atom, a syn conformation of the glycosylic bond cannot be stabilized by the 5'-OH group acting as H-atom donor. Apparently, this pyrrole N atom is a better H-atom acceptor than that of the imidazole unit in (III). The glycosylic bond length (C1'—N3) of (Ia) is 1.4720 (17) Å. Toyocamycin, C1'-N9 = 1.4490 Å (Prusiner & Sundaralingam, 1978), tubercidin [1.428 (8) Å, Stroud, 1973; 1.438 (4) Å, Abola & Sundaralingam, 1973] and 3-isoadenosine [1.488 (5) Å, Kumar et al., 1988] exhibit longer glycosylic bond lengths.

The most frequently observed sugar ring conformation of purine nucleosides are C2'-endo (`south' or S) and C3'-endo (`north' or N) (Arnott & Hukins, 1972). The sugar moiety of nucleoside (Ia) shows an S conformation with an almost envelope C2'-endo (2E) sugar pucker. The phase angle of pseudorotation (P) and maximum puckering amplitude (τm) (Altona & Sundaralingam, 1972) are 161.6 (2)° and 41.3 (1)°, respectively. In the case of (IIb), the sugar ring conformation is C2'-endo–C3'-exo (2T3,S conformation), with P = 165.7° and τm = 42.5° (Prusiner & Sundaralingam, 1978), and for compound (IIa), C2'-endo–C1'-exo (2T1,S conformation), with P = 149.3° and τm = -43.8° (Abola & Sundaralingam, 1973).

The conformation about the exocyclic C4'—C5' bond, which is defined by the torsion angle γ (O5'—C5'—C4'—C3'), is 54.43 (17)° for (Ia), representing a +sc (gauche, gauche) conformation. This is similar to the parent compound (IIb), which has the torsion angle γ = 57.10° (+sc; gauche, gauche; Prusiner & Sundaralingam, 1978), whereas in compound (IIa), the C4'—C5' bond adopts an ap (gauche, trans) conformation [γ = -178.3 (4)°; Abola & Sundaralingam, 1973].

The 7-deazapurine ring system of (Ia) is nearly planar (for details see the supporting information). The cyano group of (Ia) is slightly inclined by 2.2° with respect to the aromatic ring of the molecule. The amine group is also out of plane; both lie on the same side of the heterocycle [with deviations for C72 of -0.0551 (20) Å, N72 of -0.1360 (24) Å and N6 of -0.1221 (18) Å].

Within the three-dimensional network of (Ia), both the nucleobases and the sugar residues are stacked (Fig. 2). The crystal structure of (Ia) is further stabilized by several intermolecular and one intramolecular hydrogen bonds (O5'—H5'···N9). The intramolecular bond stabilizes the syn conformation of the glycosylic bond. Hydrogen bonds are formed between neighbouring nucleobases with the amine group as H-atom donor (N6—H6A···N72v and N6—H6B···N1iv; see Table 2 for symmetry codes and geometry). The N atom of the cyano group of (Ia) takes part in hydrogen bonding as H-atom acceptor, which is different to the crystal structure of toyocamycin (IIb), in which the cyano group is not involved in any hydrogen bonding (Prusiner & Sundaralingam, 1978). Interbase hydrogen bonding is found in the crystal of (Ia) but not in that of (IIb). Moreover, adjacent sugar residues form hydrogen bonds (O2'—H2'B···O5'iii). The water molecule participates in the hydrogen-bonding pattern as shown in Fig. 3. It acts as a donor (O10—H10···O2'i) as well as an acceptor (O3'—H3'···O10ii) between two nucleoside molecules.

A search for crystallographic nucleoside structures with constrained syn-orientation of the base about the glycosyl bond, caused by an intramolecular hydrogen bond, on the Cambridge Structural Data Base revealed that the large majority of compounds adopts close steric similarities, including the S-conformation of the sugar moiety, the γ+ conformation of the C4'-C5' bond and a syn-conformation with χ = 50–90° (Seela et al., 1998). Although the glycosylation position and the proton acceptor site are different, these properties are also valid for compound (Ia).

Related literature top

For related literature, see: Abola & Sundaralingam (1973); Altona & Sundaralingam (1972); Arnott & Hukins (1972); Flack (1983); Flack & Bernardinelli (2000); Kumar et al. (1988, 1989); Leonard et al. (2009); Nishimura et al. (1956); Ohkuma (1961); Porcari & Townsend (1999); Prusiner & Sundaralingam (1978); Saenger (1984); Seela & Bussmann (1984); Seela & Peng (2006); Seela et al. (1998); Sharma et al. (1993); Stroud (1973); Tolman et al. (1968, 1969); Vorbrüggen et al. (1981).

Experimental top

Compound (Ia) was synthesized as described by Leonard et al. (2009) and crystallized from aqueous methanol (decomposition above 463 K). For the diffraction experiment, a single crystal was mounted on a MiTeGen MicroMounts fibre in a thin smear of oil. [Please check crystal description in CIF: Splitter?]

Refinement top

In the absence of suitable anomalous scattering, Friedel equivalents could not be used to determine the absolute structure. Refinement of the Flack (1983) parameter led to inconclusive values (Flack & Bernardinelli, 2000) [-0.2 (8)]. Therefore, 1339 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, C- and N-bound H atoms were placed in geometrically idealized positions (C—H = 0.93–0.98 Å and N—H = 0.86 Å; AFIX 93) and constrained to ride on their parent atoms with Uiso(H) values of 1.2Ueq(C,N). The OH groups were refined as rigid groups allowed to rotate but not tip [O—H = 0.82 Å and Uiso(H) = 1.5Ueq(O); AFIX 147]. The H atom of the water molecule was also treated as riding but in this case the Uiso(H) parameter was refined.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and Diamond (Brandenburg & Putz, 2004); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. A perspective view of the nucleoside (Ia), 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. The intramolecular hydrogen bond is shown as a dashed line.
[Figure 2] Fig. 2. The crystal packing of (Ia) (projection parallel to the [110] direction), showing the intermolecular hydrogen-bonding network. [Please specify symmetry codes]
[Figure 3] Fig. 3. The crystal packing of (Ia) (projection parallel to the a axis), showing the zigzag arrangement of the molecules and the participitation of the water molecules in hydrogen bonding. [Please specify symmetry codes]
4-amino-5-cyano-1-(β-D-ribofuranosyl)-7H- pyrrolo[2,3-d]pyrimidine hemihydrate top
Crystal data top
C12H13N5O4·0.5H2OF(000) = 1256
Mr = 300.28Dx = 1.495 Mg m3
Orthorhombic, C2221Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2c 2Cell parameters from 9979 reflections
a = 9.5382 (7) Åθ = 2.9–26.4°
b = 9.9155 (6) ŵ = 0.12 mm1
c = 28.2197 (19) ÅT = 296 K
V = 2668.9 (3) Å3Splitter, colourless
Z = 80.30 × 0.10 × 0.10 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer
1790 independent reflections
Radiation source: fine-focus sealed tube1646 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.039
ϕ and ω scansθmax = 27.9°, θmin = 2.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 1112
Tmin = 0.966, Tmax = 0.988k = 1212
41187 measured reflectionsl = 3737
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.031H-atom parameters constrained
wR(F2) = 0.075 w = 1/[σ2(Fo2) + (0.0406P)2 + 1.5275P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max = 0.001
1790 reflectionsΔρmax = 0.27 e Å3
199 parametersΔρmin = 0.21 e Å3
0 restraintsAbsolute structure: established by known chemical absolute configuration
Primary atom site location: structure-invariant direct methods
Crystal data top
C12H13N5O4·0.5H2OV = 2668.9 (3) Å3
Mr = 300.28Z = 8
Orthorhombic, C2221Mo Kα radiation
a = 9.5382 (7) ŵ = 0.12 mm1
b = 9.9155 (6) ÅT = 296 K
c = 28.2197 (19) Å0.30 × 0.10 × 0.10 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer
1790 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
1646 reflections with I > 2σ(I)
Tmin = 0.966, Tmax = 0.988Rint = 0.039
41187 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0310 restraints
wR(F2) = 0.075H-atom parameters constrained
S = 1.08Δρmax = 0.27 e Å3
1790 reflectionsΔρmin = 0.21 e Å3
199 parametersAbsolute structure: established by known chemical absolute configuration
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
N10.01584 (17)0.65934 (16)0.96617 (5)0.0155 (3)
C20.0650 (2)0.5842 (2)0.93975 (6)0.0146 (4)
H2A0.16100.59880.94230.018*
N30.02344 (16)0.48767 (16)0.90916 (5)0.0121 (3)
C40.11907 (19)0.46217 (18)0.90641 (6)0.0125 (4)
C50.21173 (19)0.53915 (19)0.93384 (6)0.0123 (4)
C60.1587 (2)0.64278 (19)0.96291 (6)0.0129 (4)
N60.23575 (17)0.72814 (17)0.98799 (5)0.0164 (4)
H6A0.19580.78911.00490.020*
H6B0.32570.72250.98730.020*
C70.34664 (19)0.48597 (19)0.92184 (6)0.0128 (4)
C720.4797 (2)0.53111 (19)0.93716 (6)0.0140 (4)
N720.58793 (18)0.57019 (19)0.94905 (6)0.0209 (4)
C80.3208 (2)0.38466 (19)0.88905 (6)0.0139 (4)
H8A0.39100.33270.87520.017*
N90.18193 (16)0.36925 (16)0.87919 (5)0.0135 (3)
C1'0.12782 (19)0.42849 (18)0.87687 (6)0.0129 (4)
H1'A0.22170.45710.88680.016*
C2'0.1060 (2)0.46642 (18)0.82469 (6)0.0126 (4)
H2'A0.00670.45600.81660.015*
O2'0.14862 (14)0.59890 (13)0.81417 (5)0.0157 (3)
H2'B0.23410.60100.81100.024*
C3'0.18995 (19)0.35451 (19)0.80091 (6)0.0146 (4)
H3'A0.16240.34040.76780.018*
O3'0.33225 (14)0.39620 (14)0.80541 (5)0.0210 (3)
H3'0.38200.34890.78850.032*
C4'0.1574 (2)0.23186 (19)0.83233 (6)0.0134 (4)
H4'A0.24270.17750.83560.016*
O4'0.11985 (14)0.28641 (13)0.87881 (4)0.0137 (3)
C5'0.0396 (2)0.14183 (19)0.81490 (7)0.0145 (4)
H5'B0.02290.07180.83820.017*
H5'C0.06900.09830.78580.017*
O5'0.08807 (13)0.21210 (13)0.80646 (5)0.0144 (3)
H5'0.10830.25720.82980.022*
O100.50000.24101 (19)0.75000.0164 (4)
H100.54640.19440.76800.036 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0109 (8)0.0193 (8)0.0162 (8)0.0011 (7)0.0012 (6)0.0060 (6)
C20.0098 (9)0.0176 (9)0.0165 (9)0.0013 (8)0.0011 (7)0.0040 (7)
N30.0072 (7)0.0148 (7)0.0144 (7)0.0010 (6)0.0006 (6)0.0015 (6)
C40.0108 (9)0.0128 (9)0.0139 (9)0.0002 (8)0.0007 (7)0.0006 (7)
C50.0106 (8)0.0135 (9)0.0127 (9)0.0002 (7)0.0005 (7)0.0022 (7)
C60.0123 (9)0.0149 (8)0.0114 (8)0.0017 (8)0.0009 (7)0.0005 (7)
N60.0092 (8)0.0196 (9)0.0203 (9)0.0014 (7)0.0013 (6)0.0088 (7)
C70.0095 (8)0.0137 (8)0.0152 (8)0.0013 (7)0.0013 (7)0.0006 (7)
C720.0122 (9)0.0157 (9)0.0140 (8)0.0036 (8)0.0016 (7)0.0010 (7)
N720.0122 (8)0.0279 (10)0.0225 (9)0.0009 (7)0.0001 (7)0.0057 (7)
C80.0112 (9)0.0138 (9)0.0166 (9)0.0025 (7)0.0007 (7)0.0004 (7)
N90.0095 (8)0.0144 (7)0.0167 (8)0.0004 (6)0.0006 (6)0.0031 (6)
C1'0.0085 (9)0.0131 (8)0.0171 (9)0.0010 (7)0.0014 (7)0.0032 (7)
C2'0.0097 (8)0.0134 (9)0.0146 (8)0.0023 (8)0.0000 (7)0.0012 (7)
O2'0.0100 (6)0.0143 (6)0.0227 (7)0.0023 (5)0.0011 (6)0.0008 (5)
C3'0.0110 (9)0.0165 (9)0.0165 (9)0.0033 (7)0.0021 (7)0.0047 (7)
O3'0.0102 (7)0.0212 (7)0.0316 (8)0.0034 (6)0.0068 (6)0.0124 (6)
C4'0.0103 (9)0.0137 (8)0.0163 (9)0.0023 (8)0.0003 (7)0.0038 (7)
O4'0.0145 (7)0.0118 (6)0.0147 (6)0.0012 (5)0.0004 (5)0.0030 (5)
C5'0.0140 (9)0.0117 (8)0.0179 (9)0.0004 (7)0.0030 (7)0.0032 (7)
O5'0.0112 (6)0.0151 (6)0.0170 (6)0.0000 (5)0.0018 (5)0.0037 (5)
O100.0148 (10)0.0156 (9)0.0187 (9)0.0000.0009 (8)0.000
Geometric parameters (Å, º) top
N1—C21.306 (2)C1'—C2'1.534 (2)
N1—C61.375 (3)C1'—H1'A0.9800
C2—N31.349 (2)C2'—O2'1.407 (2)
C2—H2A0.9300C2'—C3'1.524 (3)
N3—C41.385 (2)C2'—H2'A0.9800
N3—C1'1.472 (2)O2'—H2'B0.8200
C4—N91.341 (2)C3'—O3'1.424 (2)
C4—C51.401 (3)C3'—C4'1.537 (3)
C5—C61.409 (3)C3'—H3'A0.9800
C5—C71.431 (3)O3'—H3'0.8200
C6—N61.326 (2)C4'—O4'1.463 (2)
N6—H6A0.8600C4'—C5'1.517 (3)
N6—H6B0.8600C4'—H4'A0.9800
C7—C81.388 (3)C5'—O5'1.423 (2)
C7—C721.414 (3)C5'—H5'B0.9700
C72—N721.153 (3)C5'—H5'C0.9700
C8—N91.362 (3)O5'—H5'0.8200
C8—H8A0.9300O10—H100.8170
C1'—O4'1.412 (2)
C2—N1—C6118.61 (16)N3—C1'—H1'A109.1
N1—C2—N3126.63 (17)C2'—C1'—H1'A109.1
N1—C2—H2A116.7O2'—C2'—C3'115.79 (15)
N3—C2—H2A116.7O2'—C2'—C1'113.10 (15)
C2—N3—C4117.00 (16)C3'—C2'—C1'99.96 (14)
C2—N3—C1'118.71 (15)O2'—C2'—H2'A109.2
C4—N3—C1'123.82 (15)C3'—C2'—H2'A109.2
N9—C4—N3126.61 (17)C1'—C2'—H2'A109.2
N9—C4—C5114.12 (16)C2'—O2'—H2'B109.5
N3—C4—C5119.27 (17)O3'—C3'—C2'104.48 (14)
C4—C5—C6119.51 (17)O3'—C3'—C4'111.76 (16)
C4—C5—C7103.64 (16)C2'—C3'—C4'102.47 (14)
C6—C5—C7136.83 (18)O3'—C3'—H3'A112.5
N6—C6—N1115.94 (17)C2'—C3'—H3'A112.5
N6—C6—C5125.27 (18)C4'—C3'—H3'A112.5
N1—C6—C5118.79 (17)C3'—O3'—H3'109.5
C6—N6—H6A120.0O4'—C4'—C5'109.09 (15)
C6—N6—H6B120.0O4'—C4'—C3'105.91 (14)
H6A—N6—H6B120.0C5'—C4'—C3'115.35 (16)
C8—C7—C72126.33 (17)O4'—C4'—H4'A108.8
C8—C7—C5105.37 (16)C5'—C4'—H4'A108.8
C72—C7—C5128.18 (16)C3'—C4'—H4'A108.8
N72—C72—C7178.6 (2)C1'—O4'—C4'108.71 (14)
N9—C8—C7112.94 (17)O5'—C5'—C4'113.57 (15)
N9—C8—H8A123.5O5'—C5'—H5'B108.9
C7—C8—H8A123.5C4'—C5'—H5'B108.9
C4—N9—C8103.93 (16)O5'—C5'—H5'C108.9
O4'—C1'—N3109.71 (15)C4'—C5'—H5'C108.9
O4'—C1'—C2'105.94 (14)H5'B—C5'—H5'C107.7
N3—C1'—C2'113.88 (15)C5'—O5'—H5'109.5
O4'—C1'—H1'A109.1
C6—N1—C2—N31.1 (3)C5—C4—N9—C80.3 (2)
N1—C2—N3—C42.2 (3)C7—C8—N9—C40.2 (2)
N1—C2—N3—C1'170.30 (18)C2—N3—C1'—O4'130.59 (17)
C2—N3—C4—N9178.61 (17)C4—N3—C1'—O4'57.5 (2)
C1'—N3—C4—N99.3 (3)C2—N3—C1'—C2'110.87 (18)
C2—N3—C4—C52.0 (3)C4—N3—C1'—C2'61.1 (2)
C1'—N3—C4—C5170.10 (16)O4'—C1'—C2'—O2'163.43 (15)
N9—C4—C5—C6178.17 (16)N3—C1'—C2'—O2'75.90 (19)
N3—C4—C5—C61.3 (3)O4'—C1'—C2'—C3'39.72 (17)
N9—C4—C5—C70.2 (2)N3—C1'—C2'—C3'160.38 (15)
N3—C4—C5—C7179.71 (17)O2'—C2'—C3'—O3'43.1 (2)
C2—N1—C6—N6175.38 (16)C1'—C2'—C3'—O3'78.69 (17)
C2—N1—C6—C54.5 (3)O2'—C2'—C3'—C4'159.82 (15)
C4—C5—C6—N6175.27 (17)C1'—C2'—C3'—C4'38.00 (17)
C7—C5—C6—N62.4 (3)O3'—C3'—C4'—O4'86.42 (17)
C4—C5—C6—N14.6 (3)C2'—C3'—C4'—O4'24.92 (19)
C7—C5—C6—N1177.7 (2)O3'—C3'—C4'—C5'152.82 (16)
C4—C5—C7—C80.05 (19)C2'—C3'—C4'—C5'95.84 (18)
C6—C5—C7—C8177.9 (2)N3—C1'—O4'—C4'148.44 (14)
C4—C5—C7—C72176.20 (19)C2'—C1'—O4'—C4'25.10 (19)
C6—C5—C7—C721.7 (3)C5'—C4'—O4'—C1'124.70 (16)
C72—C7—C8—N9176.12 (18)C3'—C4'—O4'—C1'0.0 (2)
C5—C7—C8—N90.1 (2)O4'—C4'—C5'—O5'64.63 (19)
N3—C4—N9—C8179.74 (18)C3'—C4'—C5'—O5'54.4 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O10—H10···O2i0.821.882.6971 (17)174
O5—H5···N90.821.922.728 (2)171
O3—H3···O100.821.902.7153 (17)179
O2—H2B···O5ii0.822.032.7594 (18)148
N6—H6B···N1iii0.862.533.171 (2)132
N6—H6A···N72iv0.862.173.024 (2)175
Symmetry codes: (i) x1/2, y1/2, z; (ii) x1/2, y+1/2, z; (iii) x+1/2, y+3/2, z+2; (iv) x1/2, y+3/2, z+2.

Experimental details

Crystal data
Chemical formulaC12H13N5O4·0.5H2O
Mr300.28
Crystal system, space groupOrthorhombic, C2221
Temperature (K)296
a, b, c (Å)9.5382 (7), 9.9155 (6), 28.2197 (19)
V3)2668.9 (3)
Z8
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.30 × 0.10 × 0.10
Data collection
DiffractometerBruker APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2008)
Tmin, Tmax0.966, 0.988
No. of measured, independent and
observed [I > 2σ(I)] reflections
41187, 1790, 1646
Rint0.039
(sin θ/λ)max1)0.658
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.031, 0.075, 1.08
No. of reflections1790
No. of parameters199
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.27, 0.21
Absolute structureEstablished by known chemical absolute configuration

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXTL (Sheldrick, 2008) and Diamond (Brandenburg & Putz, 2004), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Selected geometric parameters (Å, º) top
N1—C21.306 (2)C7—C721.414 (3)
N3—C41.385 (2)C72—N721.153 (3)
N3—C1'1.472 (2)C8—N91.362 (3)
C4—N91.341 (2)
C2—N1—C6—N6175.38 (16)C2—N3—C1'—O4'130.59 (17)
C4—C5—C6—N6175.27 (17)C4—N3—C1'—O4'57.5 (2)
C6—C5—C7—C721.7 (3)C3'—C4'—C5'—O5'54.4 (2)
C72—C7—C8—N9176.12 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O10—H10···O2'i0.821.882.6971 (17)174.4
O5'—H5'···N90.821.922.728 (2)171.0
O3'—H3'···O100.821.902.7153 (17)178.9
O2'—H2'B···O5'ii0.822.032.7594 (18)148.4
N6—H6B···N1iii0.862.533.171 (2)132.4
N6—H6A···N72iv0.862.173.024 (2)175.4
Symmetry codes: (i) x1/2, y1/2, z; (ii) x1/2, y+1/2, z; (iii) x+1/2, y+3/2, z+2; (iv) x1/2, y+3/2, z+2.
 

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