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In the title compound, C12H13N3O5, the conformation of the gly­cosyl­ic bond is anti [torsion angle = −105.3 (2)°]. The 2′-deoxy­ribo­furan­ose moiety adopts an S-type sugar pucker and the orientation of the exocyclic C—C bond is −sc (trans).

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104008005/jz1612sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270104008005/jz1612Isup2.hkl
Contains datablock I

CCDC reference: 243593

Comment top

Recently, it was shown that the regioisomeric 4-nitroindazole N1– and N2-(2-deoxy-β-D-ribofuranosides) can act as universal nucleosides, thereby stabilizing the DNA duplex structure by stacking interactions (Seela & Jawalekar, 2002). The 4-nitro analogue (I), which was designed for the same purpose?, is expected to show enhanced stacking interaction due to the presence of the nitro group. Although the glycosylation positions of the regioisomeric 4-nitroindazole nucleosides are different, very little influence on the duplex stability was noticed. Seela et al. (2004) have investigated the X-ray structures of the regioisomeric 4-nitroindazole N1-(II) and N2β-D-ribofuranosides. We report here the single-crystal X-ray structure of the title compound, (I).

The structure of (I) is shown in Fig. 1; selected geometric parameters are summarized in Table 1 (systematic numbering is used throughout). The orientation of the nucleobase relative to the sugar moiety is anti, as defined by the χ(O4'—C1'—N9—C4) torsion angle for purine nucleosides (IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983). Normally, the preferred conformation at the N-glycosylic bond in purine nucleosides is in the range −150 χ −140°. The corresponding torsion angle in (I), namely χ(O4'—C1'—N1—C7a), is −105.3 (2)°. This value represents a conformation between anti and high-anti. Stereoelectronic effects and coulombic repulsion between non-bonding electron pairs at atoms O4' and N2 might induce this conformational change (Seela et al., 2000). The conformation of the related 1-β-D-ribofuranosyl-4-nitro-1H-indazole (II) is even more shifted towards high-anti (χ = −93.7°). The glycosylic bond length (N1—C1') of (I) is 1.449 (2) Å, which is almost identical to that of (II) [1.450 (6) Å]. The 2'-deoxyribose ring of (I) shows an S-type pucker [C2'-endo, C3'-exo(2'T3')], while that of (II) is N-type [C2'-exo, C3'-endo (3'T2')]. The phase angle of pseudorotation of (I) (P = 192.6°) is in the south region, with τm = 37.5°; this value is in good agreement with the mean value [τm = 38.6 (3)°; Saenger, 1984]. The γ(O5'—C5'—C4'—C3') torsion angle is −91.5 (2)°, which corresponds to -sc, a conformation often found in nucleosides with (2'T3') sugar pucker.

The base moiety of (I) is essentially planar. The nitro group is slightly out of the plane, with C3A—C4—N4—O42 and C5—C4—N4—O41 torsion angles of −9.5 (3) and −5.6 (3)°, respectively. The mean deviation of the ring atoms (N1/N2/C3/C3a/C4–C7/C7a) from their calculated least-squares plane is 0.0143 Å, with maximum deviations of 0.024 (1) (N1) and 0.019 (2) Å (C5). The ring substituents N4 and C1' show significant deviations, of 0.095 (3) and −0.051 (3) Å, respectively, but lie on the same side of the nucleobase.

In solution, the S-conformer population of (I) is shifted more towards N and shows nearly equal population of N– and S-conformers (N: 46%; S: 54%), a situation that is very similar to that for (II) (N: 53%; S: 47%). The puckering was determined from the vicinal 3J(H,H) coupling constants of the 1H NMR spectra measured in D2O, applying the PSEUROT program (Van Wijk et al., 1993). The increase in the N-conformer population can be attributed to the crystal packing. In solution, the interactions with water molecules have to be considered.

The view along the b axis shows a ribbon structure parallel to the short a axis (Fig. 2); the molecules of (I) are linked by two hydrogen bonds, O3'—H3'A-···O5'i and O3'—H3'A···O5'ii (Table 2). Thus the H atoms on atoms O5' and O3' act as acceptors and the corresponding protons as donors?. The NO2-group does not take part in hydrogen bonding.

In a closely packed structure (Fig. 3), the bases and the sugar moieties are stacked. In addition to the above mentioned classical hydrogen bonding, there is also an interaction between atoms C5(H) and O4', with an H···O distance of 2.47 A, which is still in the range of hydrogen bonding. The electron-withdrawing nitro group might be responsible for the acidity of C5—H.

Experimental top

Pale yellow crystals with a melting point of 413 K were grown from methanol.

Refinement top

In the absence of significant anomalous scattering, Friedel opposites could not be used to determine the absolute structure. Refinement of the Flack (1983) parameter led to inconclusive values (Flack & Bernardinelli, 2000) for this parameter [1.7 (12)]. Therefore, Friedel equivalents were merged before the final refinements. The known configuration of the parent molecule was used to define the enantiomer employed in the refined model. All H atoms were initially found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, H atoms bonded to C were placed in idealized positions (C—H = 0.93–0.98 Å) and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C). The hydroxy H atoms were initially placed in the positions found from the difference map, and were then positioned geometrically and constrained to ride on their parent O atoms, although the chemically equivalent O—H bond lengths were allowed to refine while being constrained to be equal.

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, 1999).

Figures top
[Figure 1] Fig. 1. A perspective view of (I). Displacement ellipsoids for non-H atoms are drawn at the 50% probability level.
[Figure 2] Fig. 2. The ribbon structure of (I), viewed parallel to the b axis.
[Figure 3] Fig. 3. A perspective view demonstrating the stacking between the layers.
(I) top
Crystal data top
C12H13N3O5Dx = 1.492 Mg m3
Mr = 279.25Melting point: 413K K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 39 reflections
a = 6.7444 (12) Åθ = 5.2–15.0°
b = 11.718 (3) ŵ = 0.12 mm1
c = 15.734 (2) ÅT = 293 K
V = 1243.4 (5) Å3Block, yellow
Z = 40.52 × 0.43 × 0.30 mm
F(000) = 584
Data collection top
Bruker P4
diffractometer
Rint = 0.040
Radiation source: fine-focus sealed tubeθmax = 30.0°, θmin = 2.2°
Graphite monochromatorh = 91
2θ/ω scansk = 116
2725 measured reflectionsl = 122
2072 independent reflections3 standard reflections every 97 reflections
1896 reflections with I > 2σ(I) intensity decay: none
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)] = 0.038H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.105 w = 1/[σ2(Fo2) + (0.0526P)2 + 0.1969P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2072 reflectionsΔρmax = 0.20 e Å3
187 parametersΔρmin = 0.19 e Å3
2 restraintsAbsolute structure: see text
Primary atom site location: structure-invariant direct methods
Crystal data top
C12H13N3O5V = 1243.4 (5) Å3
Mr = 279.25Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.7444 (12) ŵ = 0.12 mm1
b = 11.718 (3) ÅT = 293 K
c = 15.734 (2) Å0.52 × 0.43 × 0.30 mm
Data collection top
Bruker P4
diffractometer
Rint = 0.040
2725 measured reflections3 standard reflections every 97 reflections
2072 independent reflections intensity decay: none
1896 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0382 restraints
wR(F2) = 0.105H atoms treated by a mixture of independent and constrained refinement
S = 1.06Δρmax = 0.20 e Å3
2072 reflectionsΔρmin = 0.19 e Å3
187 parametersAbsolute structure: see text
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
N10.9447 (2)0.18593 (14)0.83683 (8)0.0343 (3)
N21.1251 (2)0.21504 (15)0.86881 (10)0.0402 (4)
C31.1294 (3)0.17546 (16)0.94771 (11)0.0367 (4)
H3A1.23620.18370.98460.044*
C3A0.9497 (3)0.11885 (14)0.96871 (9)0.0294 (3)
C40.8641 (3)0.06478 (14)1.03964 (10)0.0343 (3)
N40.9734 (4)0.06203 (16)1.11982 (10)0.0500 (4)
C50.6777 (3)0.01910 (17)1.03628 (12)0.0402 (4)
H5A0.62310.01581.08390.048*
C60.5693 (3)0.02552 (17)0.95994 (12)0.0395 (4)
H6A0.44430.00770.95740.047*
C70.6429 (3)0.07952 (16)0.88898 (10)0.0352 (3)
H7A0.56870.08490.83930.042*
C7A0.8342 (2)0.12618 (14)0.89431 (9)0.0282 (3)
C1'0.8993 (3)0.21000 (16)0.74861 (9)0.0342 (3)
H1'A0.75920.19280.73800.041*
C2'0.9418 (3)0.33327 (15)0.72205 (10)0.0376 (4)
H2'A0.82340.38000.72560.045*
H2'B1.04490.36690.75700.045*
O3'0.8375 (2)0.31046 (17)0.57856 (8)0.0497 (4)
H3'A0.873 (5)0.295 (3)0.5300 (8)0.075*
C3'1.0098 (3)0.31946 (16)0.63066 (10)0.0338 (3)
H3'B1.09530.38270.61270.041*
O4'1.0192 (2)0.13903 (11)0.69586 (8)0.0418 (3)
C4'1.1237 (3)0.20682 (15)0.63477 (9)0.0321 (3)
H4'A1.11660.16930.57920.039*
O5'1.4519 (2)0.2320 (2)0.58513 (10)0.0648 (6)
H5'A1.563 (2)0.257 (3)0.595 (2)0.097*
C5'1.3408 (3)0.21996 (19)0.66008 (11)0.0391 (4)
H5'B1.35760.28660.69590.047*
H5'C1.38480.15330.69150.047*
O410.8909 (3)0.02714 (16)1.18367 (8)0.0611 (5)
O421.1452 (4)0.0936 (3)1.11883 (13)0.1064 (11)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0293 (6)0.0498 (8)0.0239 (5)0.0095 (7)0.0000 (5)0.0028 (6)
N20.0320 (7)0.0547 (9)0.0340 (7)0.0121 (7)0.0018 (6)0.0022 (7)
C30.0334 (8)0.0447 (8)0.0320 (7)0.0065 (8)0.0062 (7)0.0011 (7)
C3A0.0314 (7)0.0306 (6)0.0262 (6)0.0011 (6)0.0027 (6)0.0003 (5)
C40.0433 (9)0.0339 (7)0.0259 (6)0.0006 (8)0.0036 (7)0.0031 (6)
N40.0679 (12)0.0504 (9)0.0317 (7)0.0109 (9)0.0125 (8)0.0102 (7)
C50.0458 (10)0.0416 (8)0.0330 (7)0.0037 (8)0.0053 (8)0.0090 (7)
C60.0328 (8)0.0445 (9)0.0413 (8)0.0065 (8)0.0029 (7)0.0068 (7)
C70.0280 (7)0.0462 (8)0.0313 (7)0.0050 (7)0.0014 (7)0.0035 (7)
C7A0.0269 (7)0.0334 (7)0.0243 (6)0.0008 (6)0.0015 (6)0.0004 (5)
C1'0.0311 (7)0.0490 (9)0.0224 (6)0.0069 (7)0.0021 (6)0.0018 (6)
C2'0.0414 (9)0.0435 (8)0.0280 (7)0.0025 (8)0.0026 (7)0.0001 (7)
O3'0.0264 (6)0.0932 (11)0.0295 (6)0.0005 (8)0.0018 (5)0.0067 (7)
C3'0.0277 (7)0.0478 (8)0.0260 (6)0.0047 (7)0.0006 (6)0.0056 (6)
O4'0.0554 (8)0.0375 (6)0.0326 (5)0.0105 (6)0.0136 (6)0.0022 (5)
C4'0.0294 (7)0.0450 (8)0.0219 (6)0.0066 (7)0.0023 (6)0.0028 (6)
O5'0.0322 (7)0.1303 (17)0.0319 (6)0.0202 (10)0.0018 (6)0.0058 (9)
C5'0.0314 (8)0.0585 (11)0.0275 (7)0.0024 (8)0.0027 (6)0.0014 (7)
O410.0834 (13)0.0708 (10)0.0290 (6)0.0065 (10)0.0006 (7)0.0133 (7)
O420.0930 (16)0.169 (3)0.0577 (11)0.0667 (19)0.0426 (12)0.0467 (14)
Geometric parameters (Å, º) top
N1—N21.360 (2)C1'—O4'1.426 (2)
N1—C7A1.365 (2)C1'—C2'1.531 (3)
N1—C1'1.449 (2)C1'—H1'A0.9800
N2—C31.325 (2)C2'—C3'1.518 (2)
C3—C3A1.420 (3)C2'—H2'A0.9700
C3—H3A0.9300C2'—H2'B0.9700
C3A—C41.407 (2)O3'—C3'1.426 (2)
C3A—C7A1.409 (2)O3'—H3'A0.821 (17)
C4—C51.367 (3)C3'—C4'1.528 (3)
C4—N41.461 (2)C3'—H3'B0.9800
N4—O421.216 (3)O4'—C4'1.432 (2)
N4—O411.219 (2)C4'—C5'1.525 (2)
C5—C61.408 (3)C4'—H4'A0.9800
C5—H5A0.9300O5'—C5'1.404 (2)
C6—C71.376 (2)O5'—H5'A0.819 (19)
C6—H6A0.9300C5'—H5'B0.9700
C7—C7A1.404 (2)C5'—H5'C0.9700
C7—H7A0.9300
N2—N1—C7A111.84 (14)O4'—C1'—H1'A109.1
N2—N1—C1'119.66 (14)N1—C1'—H1'A109.1
C7A—N1—C1'128.23 (15)C2'—C1'—H1'A109.1
C3—N2—N1106.14 (15)C3'—C2'—C1'102.40 (13)
N2—C3—C3A111.28 (15)C3'—C2'—H2'A111.3
N2—C3—H3A124.4C1'—C2'—H2'A111.3
C3A—C3—H3A124.4C3'—C2'—H2'B111.3
C4—C3A—C7A117.38 (15)C1'—C2'—H2'B111.3
C4—C3A—C3138.14 (15)H2'A—C2'—H2'B109.2
C7A—C3A—C3104.46 (13)C3'—O3'—H3'A108 (3)
C5—C4—C3A121.51 (16)O3'—C3'—C2'107.81 (14)
C5—C4—N4119.24 (17)O3'—C3'—C4'111.71 (16)
C3A—C4—N4119.19 (17)C2'—C3'—C4'101.76 (13)
O42—N4—O41123.2 (2)O3'—C3'—H3'B111.7
O42—N4—C4117.56 (19)C2'—C3'—H3'B111.7
O41—N4—C4119.3 (2)C4'—C3'—H3'B111.7
C4—C5—C6119.30 (16)C1'—O4'—C4'110.25 (13)
C4—C5—H5A120.4O4'—C4'—C5'110.69 (14)
C6—C5—H5A120.4O4'—C4'—C3'105.07 (14)
C7—C6—C5121.97 (17)C5'—C4'—C3'113.97 (16)
C7—C6—H6A119.0O4'—C4'—H4'A109.0
C5—C6—H6A119.0C5'—C4'—H4'A109.0
C6—C7—C7A117.53 (16)C3'—C4'—H4'A109.0
C6—C7—H7A121.2C5'—O5'—H5'A112 (3)
C7A—C7—H7A121.2O5'—C5'—C4'107.64 (13)
N1—C7A—C7131.46 (15)O5'—C5'—H5'B110.2
N1—C7A—C3A106.26 (14)C4'—C5'—H5'B110.2
C7—C7A—C3A122.27 (15)O5'—C5'—H5'C110.2
O4'—C1'—N1108.90 (15)C4'—C5'—H5'C110.2
O4'—C1'—C2'106.56 (13)H5'B—C5'—H5'C108.5
N1—C1'—C2'113.92 (14)
C7A—N1—N2—C31.0 (2)C4—C3A—C7A—N1177.29 (15)
C1'—N1—N2—C3175.43 (16)C3—C3A—C7A—N11.23 (18)
N1—N2—C3—C3A0.2 (2)C4—C3A—C7A—C71.6 (2)
N2—C3—C3A—C4177.3 (2)C3—C3A—C7A—C7179.92 (16)
N2—C3—C3A—C7A0.7 (2)N2—N1—C1'—O4'68.2 (2)
C7A—C3A—C4—C51.2 (2)C7A—N1—C1'—O4'105.3 (2)
C3—C3A—C4—C5179.1 (2)N2—N1—C1'—C2'50.6 (2)
C7A—C3A—C4—N4175.93 (16)C7A—N1—C1'—C2'135.96 (19)
C3—C3A—C4—N41.9 (3)O4'—C1'—C2'—C3'25.36 (18)
C5—C4—N4—O42173.3 (3)N1—C1'—C2'—C3'145.47 (15)
C3A—C4—N4—O429.5 (3)C1'—C2'—C3'—O3'81.89 (18)
C5—C4—N4—O415.6 (3)C1'—C2'—C3'—C4'35.74 (17)
C3A—C4—N4—O41171.62 (18)N1—C1'—O4'—C4'127.01 (15)
C3A—C4—C5—C60.5 (3)C2'—C1'—O4'—C4'3.72 (19)
N4—C4—C5—C6177.63 (18)C1'—O4'—C4'—C5'103.93 (18)
C4—C5—C6—C72.0 (3)C1'—O4'—C4'—C3'19.54 (17)
C5—C6—C7—C7A1.6 (3)O3'—C3'—C4'—O4'80.21 (16)
N2—N1—C7A—C7179.86 (18)C2'—C3'—C4'—O4'34.58 (17)
C1'—N1—C7A—C76.0 (3)O3'—C3'—C4'—C5'158.45 (13)
N2—N1—C7A—C3A1.4 (2)C2'—C3'—C4'—C5'86.76 (16)
C1'—N1—C7A—C3A175.26 (16)O4'—C4'—C5'—O5'150.32 (17)
C6—C7—C7A—N1178.36 (18)C3'—C4'—C5'—O5'91.51 (19)
C6—C7—C7A—C3A0.2 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3A···O5i0.82 (2)1.91 (2)2.734 (2)177 (3)
O5—H5A···O3ii0.82 (2)1.97 (1)2.761 (2)162 (4)
Symmetry codes: (i) x1/2, y+1/2, z+1; (ii) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC12H13N3O5
Mr279.25
Crystal system, space groupOrthorhombic, P212121
Temperature (K)293
a, b, c (Å)6.7444 (12), 11.718 (3), 15.734 (2)
V3)1243.4 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.52 × 0.43 × 0.30
Data collection
DiffractometerBruker P4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2725, 2072, 1896
Rint0.040
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.105, 1.06
No. of reflections2072
No. of parameters187
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.20, 0.19
Absolute structureSee text

Computer programs: XSCANS (Siemens, 1996), XSCANS, SHELXTL (Sheldrick, 1997), SHELXTL and PLATON (Spek, 1999).

Selected geometric parameters (Å, º) top
N1—C1'1.449 (2)
N2—N1—C7A111.84 (14)C7A—N1—C1'128.23 (15)
N2—N1—C1'119.66 (14)
C7A—N1—N2—C31.0 (2)C1'—C2'—C3'—O3'81.89 (18)
C1'—N1—N2—C3175.43 (16)C1'—C2'—C3'—C4'35.74 (17)
N1—N2—C3—C3A0.2 (2)N1—C1'—O4'—C4'127.01 (15)
C4—C3A—C7A—C71.6 (2)C1'—O4'—C4'—C5'103.93 (18)
C3—C3A—C7A—C7179.92 (16)C1'—O4'—C4'—C3'19.54 (17)
N2—N1—C1'—O4'68.2 (2)C2'—C3'—C4'—O4'34.58 (17)
C7A—N1—C1'—O4'105.3 (2)O3'—C3'—C4'—C5'158.45 (13)
C7A—N1—C1'—C2'135.96 (19)O4'—C4'—C5'—O5'150.32 (17)
O4'—C1'—C2'—C3'25.36 (18)C3'—C4'—C5'—O5'91.51 (19)
N1—C1'—C2'—C3'145.47 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3'—H3'A···O5'i0.821 (17)1.914 (16)2.734 (2)177 (3)
O5'—H5'A···O3'ii0.819 (19)1.971 (12)2.761 (2)162 (4)
Symmetry codes: (i) x1/2, y+1/2, z+1; (ii) x+1, y, z.
 

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