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In 2-(2-deoxy-β-D-erythro-pentofuranosyl)-1,2,4-triazine-3,5(2H,4H)-dione (6-aza-2′-deoxy­uridine), C8H11N3O5, (I), the conformation of the glycosylic bond is between anti and high-anti [χ = −94.0 (3)°], whereas the derivative 2-(2-deoxy-β-D-erythro-pentofuranosyl)-N4-(2-methoxy­benzoyl)-1,2,4-triazine-3,5(2H,4H)-dione (N3-anisoyl-6-aza-2′-deoxy­uridine), C16H17N3O7, (II), displays a high-anti conformation [χ = −86.4 (3)°]. The furanosyl moiety in (I) adopts the S-type sugar pucker (2T3), with P = 188.1 (2)° and τm = 40.3 (2)°, while the sugar pucker in (II) is N (3T4), with P = 36.1 (3)° and τm = 33.5 (2)°. The crystal structures of (I) and (II) are stabilized by inter­molecular N—H...O and O—H...O inter­actions.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270107002016/gg3052sup1.cif
Contains datablocks I, II, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270107002016/gg3052Isup2.hkl
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270107002016/gg3052IIsup3.hkl
Contains datablock II

CCDC references: 641807; 641808

Comment top

6-Azapyrimidine nucleosides show significant antiviral activity (Mitchell et al., 1986), while the N3-substituted derivatives possess hypnotic and sedative properties to exhibit central depressant effects in mice (Koshigami et al., 1991). 6-Azauridine 5'-monophosphate is a strong inhibitor of the enzyme orotidine 5'-monophosphate decarboxylase (Miller et al., 2000) which, when linked to agarose, leads to an affinity resin used for the purification of this enzyme (Rosemeyer & Seela, 1979). The first synthesis of an anomeric mixture of 6-aza-2'-deoxyuridine was reported in 1963 (Pliml et al., 1963), employing Hg derivatives of 6-azauracil and 2-deoxy-3,5-di-O-(4-methylbenzoyl)-α-D-erythro-pentofuranosyl chloride. Introducing an N atom at the 6-position of the pyrimidine moiety has a profound effect on the physical and biological properties of the nucleobase, which plays a significant role in the catalytic activity of ribozymes (Oyelere & Strobel, 2001) and promotes M-DNA formation under neutral conditions (Seela, Peng et al., 2005). The pKa value of (I) is 6.8 and that of 2'-deoxyuridine is 9.5. Compared with these pKa values, the 6-azapyrimidine nucleoside is acidic and therefore it is already deprotonated under neutral conditions. We have shown that this influences the duplex stability when (I) is a constituent of a nucleic acid. Oligonucleotides containing 6-aza-2'-deoxyuridine show a pH dependence on base-pair formation. The lower pKa value of (I) causes problems during phosphoramidite synthesis. To circumvent this problem, various protecting groups were introduced at the N3-position. The o-anisoyl residue was found to be efficient at allowing multiple incorporations into the oligonucleotide chain using phosphoramidite chemistry, with coupling yields identical to those of standard phosphoramidites. These properties prompted single-crystal analyses of (I) and its N3-protected derivative, (II).

6-Aza-2'-deoxyuridine, (I), has an O4'—C1'—N1—C2 torsion angle χ = -94.0 (3)° (IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983) (Fig. 1, Table 1), which falls into the range of anti/high-anti conformations and which is almost identical to that of the corresponding ribonucleoside, (III), with χ = -93.3° (Schwalbe et al., 1971; Schwalbe & Saenger, 1973). The protected nucleoside, (II), exhibits a high-anti conformation, with a torsion angle χ = -86.4 (3)° (Fig. 2 and Table 3), and these values are similar to those of other ortho-azanucleosides with an N atom next to the glycosylation position, with χ values close to -90°. This results from the coulombic repulsion between the non-bonding electron pairs of atom O4' and atom at position N-6 in pyrimidine nucleosides or N-8 in 8-azapurine nucleosides (8-aza-7-deaza-7-iodo-2'-deoxyadenosine with χ = -106.3°; Seela et al., 1999). The glycosylic torsion angles of related nucleosides, such as 6-aza-2'-deoxythymidine (χ = -86.6°; Banerjee & Saenger, 1978) and 6-aza-2'-deoxy-5-methyl-isocytidine (χ = -103.4°; Seela et al., 2003), also lie in the anti/high-anti range.

The sugar moiety of (I) shows a pseudorotational phase angle P = 188.1 (2)° with an amplitude τm = 40.3 (2)°, indicating an S-type sugar pucker (C2'-endo–C3'-exo, 2T3; Rao et al., 1981), whereas its anisoyl-protected derivative, (II), adopts an N sugar conformation (C4'-exo, 3T4), with P = 36.1 (3)° and τm = 33.5 (2)°. This is similar to that of ribonucleoside (III) (C3'-endo, 3E; Schwalbe & Saenger, 1973), which has P = 27.6° and τm = 37.6°. The N conformation is uncommon for 2'-deoxyribonucleosides. The conformation around the C4'—C5' bond defined by the torsion angle χ (O5'—C5'—C4'—C3') is similar for these two nucleosides [-175.3 (2)° for (I) and -176.2 (2)° for (II)], representing an ap (trans) orientation.

The base moiety of (I) is nearly planar, with an r.m.s deviation of the ring atoms (N1/C2/N3/C4/C5/N6) from the least-squares plane of 0.0173 (2) Å and a maximum deviation of 0.025 (7) Å for atom C2. The maximum deviation of the pyrimidine ring (N1/N2/C3/C4/N5/C6) of (II) is 0.023 (2) Å [0.034 (5) Å for atom N5 and 0.020 (3) Å for atom N1]. The presence of the N3-anisoyl protecting group does not show much influence on the bond lengths of the nucleobase.

Compound (I) is stabilized by three intermolecular hydrogen bonds (N3—H3···O5', O3'—H3'···O2 and O5'—H5'···O4) and two intramolecular hydrogen bonds (C1'—H1'···O2 and C2'—H2'···N6), leading to the formation of layered sheets (Fig. 3 and Table 2) where the nucleobases stack. Compound (II) forms a three-dimensional network which is stabilized by both intermolecular hydrogen bonds (O3'—H3'···O5' and O5'—H5'···O2) and intramolecular hydrogen bonds formed between the sugar and the nucleobase (C1'—H1'···O2 and C2'—H2'···N6). In the close-packed network of (II), the protecting group shows a perpendicular orientation with respect to the nucleobase in the ac plane. The aromatic H atoms (on atoms C15 and C17) form weak intermolecular hydrogen bonds with atoms O2 (3.310 Å) and O4 (3.211 Å) of the adjacent nucleobase, and there is also an intramolecular C12—H12···O1 hydrogen bond (Fig. 4 and Table 4).

Related literature top

For related literature, see: Banerjee & Saenger (1978); Flack (1983); IUPAC–IUB (1983); Koshigami et al. (1991); Miller et al. (2000); Mitchell et al. (1986); Oyelere & Strobel (2001); Pliml et al. (1963); Rao et al. (1981); Rosemeyer & Seela (1979); Schwalbe & Saenger (1973); Schwalbe et al. (1971); Seela et al. (1999); Seela, Chittepu, He, He & Xu (2005); Seela, He & Eickmeier (2003); Seela, Peng, Li, Chittepu, Shaikh, He, He & Mikhailopulo (2005).

Experimental top

Compound (I) was prepared according to the method described by Freskos (l989). The anomeric configuration assignment has been reported previously (Seela et al., 2003). Suitable crystals were grown from CH2Cl2–CH3OH (9:1 v/v). Compound (II) was prepared from (I) by protection of the lactam group with o-anisoyl chloride using transient protection (Seela, Chittepu et al., 2005). Crystallization from methanol furnished colourless crystals (m.p. 414 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 refinements. 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, with C—H = 0.93–0.98 Å and N—H = 0.86 Å, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C,N).

Computing details top

For both compounds, 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 (I), with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. A perspective view of (II), with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 3] Fig. 3. A stereoview of the packing in (I), viewed in the bc plane, with hydrogen bonds shown as dashed lines. H atoms not involved in hydrogen bonding have been omitted for clarity. [The diagram submitted is not a stereoview. Please correct either the plot or the caption]
[Figure 4] Fig. 4. The principal interactions in (II), shown as dashed lines. H atoms not involved in hydrogen bonding have been omitted for clarity. [Symmetry codes: (i) -x, y - 1/2, 3/2 - z; (#) x, 1 + y, z; ($) -x, y + 1/2, 3/2 - z.] [No symmetry codes are shown. Please correct either the plot or the caption]
(I) 2-(2-deoxy-β-D-erythro-pentofuranosyl)-1,2,4-triazin-3,5(2H,4H)-dione top
Crystal data top
C8H11N3O5Dx = 1.527 Mg m3
Mr = 229.20Melting point: 414 K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 40 reflections
a = 7.8817 (17) Åθ = 4.9–12.5°
b = 8.6832 (11) ŵ = 0.13 mm1
c = 14.5715 (15) ÅT = 293 K
V = 997.2 (3) Å3Block, colourless
Z = 40.4 × 0.3 × 0.2 mm
F(000) = 480
Data collection top
Bruker P4
diffractometer
Rint = 0.020
Radiation source: fine-focus sealed tubeθmax = 30.0°, θmin = 2.7°
Graphite monochromatorh = 110
ω/2θ scansk = 112
2127 measured reflectionsl = 120
1580 independent reflections3 standard reflections every 97 reflections
1313 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)] = 0.045H-atom parameters constrained
wR(F2) = 0.121 w = 1/[σ2(Fo2) + (0.055P)2 + 0.2159P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
1580 reflectionsΔρmax = 0.37 e Å3
148 parametersΔρmin = 0.23 e Å3
0 restraintsExtinction correction: SHELXTL (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.026 (4)
Crystal data top
C8H11N3O5V = 997.2 (3) Å3
Mr = 229.20Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 7.8817 (17) ŵ = 0.13 mm1
b = 8.6832 (11) ÅT = 293 K
c = 14.5715 (15) Å0.4 × 0.3 × 0.2 mm
Data collection top
Bruker P4
diffractometer
Rint = 0.020
2127 measured reflections3 standard reflections every 97 reflections
1580 independent reflections intensity decay: none
1313 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0450 restraints
wR(F2) = 0.121H-atom parameters constrained
S = 1.07Δρmax = 0.37 e Å3
1580 reflectionsΔρmin = 0.23 e Å3
148 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
N10.9203 (3)0.3721 (2)0.97874 (13)0.0382 (5)
C20.9105 (4)0.2146 (3)0.98997 (16)0.0394 (6)
O20.8824 (4)0.1266 (2)0.92734 (13)0.0626 (7)
N30.9340 (3)0.1642 (2)1.07827 (13)0.0388 (5)
H30.92230.06721.08850.047*
C40.9744 (4)0.2558 (3)1.15120 (17)0.0394 (6)
O40.9992 (3)0.2042 (3)1.22786 (12)0.0582 (6)
C50.9896 (4)0.4186 (3)1.12720 (17)0.0443 (6)
H51.01870.48761.17340.053*
N60.9652 (3)0.4720 (3)1.04659 (15)0.0432 (5)
C1'0.9134 (4)0.4360 (3)0.88600 (16)0.0405 (6)
H1'0.85380.36360.84570.049*
C2'0.8285 (4)0.5929 (4)0.8795 (2)0.0530 (8)
H2'10.84420.65230.93530.064*
H2'20.70820.58360.86670.064*
C3'0.9239 (4)0.6641 (4)0.7989 (2)0.0506 (7)
H3'10.91590.77670.79830.061*
O3'0.8573 (3)0.5964 (4)0.71685 (16)0.0712 (8)
H3'0.91810.61910.67330.107*
C4'1.1034 (4)0.6083 (3)0.81644 (16)0.0385 (6)
H4'1.16340.60100.75770.046*
O4'1.0825 (3)0.4558 (2)0.85361 (12)0.0410 (4)
C5'1.2065 (4)0.7061 (3)0.88127 (19)0.0442 (6)
H5'11.20670.81190.85980.053*
H5'21.15470.70420.94170.053*
O5'1.3768 (3)0.6518 (2)0.88754 (14)0.0458 (5)
H5'1.43200.68530.84420.069*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0489 (13)0.0361 (10)0.0297 (9)0.0050 (10)0.0015 (9)0.0029 (8)
C20.0457 (14)0.0377 (12)0.0347 (11)0.0096 (12)0.0015 (11)0.0029 (10)
O20.103 (2)0.0462 (11)0.0388 (9)0.0221 (13)0.0059 (12)0.0028 (9)
N30.0501 (13)0.0328 (9)0.0334 (9)0.0050 (10)0.0005 (10)0.0034 (8)
C40.0444 (14)0.0399 (12)0.0339 (10)0.0004 (11)0.0011 (11)0.0015 (10)
O40.0857 (16)0.0513 (11)0.0377 (10)0.0010 (12)0.0159 (11)0.0068 (9)
C50.0578 (16)0.0376 (12)0.0375 (12)0.0004 (13)0.0012 (12)0.0060 (11)
N60.0568 (14)0.0333 (10)0.0393 (10)0.0012 (10)0.0015 (10)0.0014 (9)
C1'0.0428 (13)0.0438 (13)0.0349 (11)0.0063 (12)0.0015 (11)0.0086 (11)
C2'0.0398 (14)0.0614 (19)0.0578 (16)0.0084 (14)0.0005 (14)0.0199 (16)
C3'0.0475 (15)0.0523 (15)0.0520 (14)0.0057 (14)0.0086 (13)0.0186 (13)
O3'0.0641 (15)0.0954 (19)0.0541 (11)0.0226 (15)0.0222 (11)0.0224 (13)
C4'0.0440 (14)0.0385 (12)0.0330 (10)0.0050 (12)0.0018 (11)0.0062 (9)
O4'0.0451 (10)0.0369 (9)0.0409 (8)0.0010 (9)0.0075 (8)0.0035 (8)
C5'0.0466 (14)0.0364 (12)0.0496 (13)0.0007 (12)0.0048 (13)0.0035 (12)
O5'0.0443 (11)0.0400 (10)0.0531 (11)0.0014 (9)0.0058 (9)0.0061 (9)
Geometric parameters (Å, º) top
N1—N61.362 (3)C2'—C3'1.526 (4)
N1—C21.380 (3)C2'—H2'10.9700
N1—C1'1.462 (3)C2'—H2'20.9700
C2—O21.210 (3)C3'—O3'1.431 (4)
C2—N31.372 (3)C3'—C4'1.517 (4)
N3—C41.365 (3)C3'—H3'10.9800
N3—H30.8600O3'—H3'0.8200
C4—O41.219 (3)C4'—O4'1.440 (3)
C4—C51.462 (4)C4'—C5'1.508 (4)
C5—N61.277 (3)C4'—H4'0.9800
C5—H50.9300C5'—O5'1.426 (3)
C1'—O4'1.425 (4)C5'—H5'10.9700
C1'—C2'1.521 (4)C5'—H5'20.9700
C1'—H1'0.9800O5'—H5'0.8200
N6—N1—C2124.0 (2)C1'—C2'—H2'2111.5
N6—N1—C1'116.0 (2)C3'—C2'—H2'2111.5
C2—N1—C1'118.9 (2)H2'1—C2'—H2'2109.4
O2—C2—N3122.0 (2)O3'—C3'—C4'110.6 (3)
O2—C2—N1123.1 (2)O3'—C3'—C2'107.2 (2)
N3—C2—N1114.8 (2)C4'—C3'—C2'101.6 (2)
C4—N3—C2125.1 (2)O3'—C3'—H3'1112.3
C4—N3—H3117.4C4'—C3'—H3'1112.3
C2—N3—H3117.4C2'—C3'—H3'1112.3
O4—C4—N3122.5 (2)C3'—O3'—H3'109.5
O4—C4—C5124.2 (2)O4'—C4'—C5'110.1 (2)
N3—C4—C5113.4 (2)O4'—C4'—C3'104.5 (2)
N6—C5—C4124.0 (2)C5'—C4'—C3'115.4 (2)
N6—C5—H5118.0O4'—C4'—H4'108.9
C4—C5—H5118.0C5'—C4'—H4'108.9
C5—N6—N1118.4 (2)C3'—C4'—H4'108.9
O4'—C1'—N1108.5 (2)C1'—O4'—C4'110.0 (2)
O4'—C1'—C2'106.4 (2)O5'—C5'—C4'111.2 (2)
N1—C1'—C2'114.5 (2)O5'—C5'—H5'1109.4
O4'—C1'—H1'109.1C4'—C5'—H5'1109.4
N1—C1'—H1'109.1O5'—C5'—H5'2109.4
C2'—C1'—H1'109.1C4'—C5'—H5'2109.4
C1'—C2'—C3'101.2 (2)H5'1—C5'—H5'2108.0
C1'—C2'—H2'1111.5C5'—O5'—H5'109.5
C3'—C2'—H2'1111.5
N6—N1—C2—O2174.4 (3)C2—N1—C1'—C2'147.3 (3)
C1'—N1—C2—O26.2 (5)O4'—C1'—C2'—C3'29.4 (3)
N6—N1—C2—N36.0 (4)N1—C1'—C2'—C3'149.2 (2)
C1'—N1—C2—N3174.2 (2)C1'—C2'—C3'—O3'76.9 (3)
O2—C2—N3—C4176.5 (3)C1'—C2'—C3'—C4'39.1 (3)
N1—C2—N3—C43.9 (4)O3'—C3'—C4'—O4'77.7 (2)
C2—N3—C4—O4177.6 (3)C2'—C3'—C4'—O4'35.9 (3)
C2—N3—C4—C50.7 (4)O3'—C3'—C4'—C5'161.3 (2)
O4—C4—C5—N6179.2 (3)C2'—C3'—C4'—C5'85.1 (3)
N3—C4—C5—N61.0 (5)N1—C1'—O4'—C4'130.9 (2)
C4—C5—N6—N10.9 (5)C2'—C1'—O4'—C4'7.3 (3)
C2—N1—N6—C54.6 (4)C5'—C4'—O4'—C1'106.3 (3)
C1'—N1—N6—C5173.1 (3)C3'—C4'—O4'—C1'18.2 (3)
N6—N1—C1'—O4'75.1 (3)O4'—C4'—C5'—O5'66.8 (3)
C2—N1—C1'—O4'94.0 (3)C3'—C4'—C5'—O5'175.2 (2)
N6—N1—C1'—C2'43.6 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O5—H5···O4i0.822.022.816 (3)163
O3—H3···O2ii0.822.152.948 (4)164
N3—H3···O5iii0.861.972.825 (3)176
C1—H1···O20.982.392.764 (3)102
C2—H21···N60.972.452.862 (4)105
Symmetry codes: (i) x+5/2, y+1, z1/2; (ii) x+2, y+1/2, z+3/2; (iii) x1/2, y+1/2, z+2.
(II) 2-(2-deoxy-β-D-erythro-pentofuranosyl)-N4-(2-methoxybenzoyl)-1,2,4- triazin-3,5(2H,4H)-dione top
Crystal data top
C16H17N3O7Dx = 1.433 Mg m3
Mr = 363.33Melting point: 414 K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 52 reflections
a = 7.452 (3) Åθ = 3.3–12.5°
b = 9.117 (1) ŵ = 0.11 mm1
c = 24.780 (3) ÅT = 293 K
V = 1683.6 (7) Å3Block, colourless
Z = 40.4 × 0.2 × 0.1 mm
F(000) = 760
Data collection top
Bruker P4
diffractometer
Rint = 0.036
Radiation source: fine-focus sealed tubeθmax = 25.0°, θmin = 2.4°
Graphite monochromatorh = 81
ω/2θ scansk = 1010
7561 measured reflectionsl = 2929
1732 independent reflections3 standard reflections every 97 reflections
1367 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)] = 0.035H-atom parameters constrained
wR(F2) = 0.094 w = 1/[σ2(Fo2) + (0.0574P)2 + 0.0428P]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
1732 reflectionsΔρmax = 0.11 e Å3
239 parametersΔρmin = 0.14 e Å3
0 restraintsExtinction correction: SHELXTL (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0083 (16)
Crystal data top
C16H17N3O7V = 1683.6 (7) Å3
Mr = 363.33Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 7.452 (3) ŵ = 0.11 mm1
b = 9.117 (1) ÅT = 293 K
c = 24.780 (3) Å0.4 × 0.2 × 0.1 mm
Data collection top
Bruker P4
diffractometer
Rint = 0.036
7561 measured reflections3 standard reflections every 97 reflections
1732 independent reflections intensity decay: none
1367 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.094H-atom parameters constrained
S = 1.02Δρmax = 0.11 e Å3
1732 reflectionsΔρmin = 0.14 e Å3
239 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
C110.0039 (5)0.5317 (3)0.92659 (11)0.0734 (9)
C120.0421 (7)0.6787 (4)0.93813 (13)0.0946 (11)
H120.04090.73800.95570.113*
C130.2012 (8)0.7351 (5)0.92455 (15)0.1151 (14)
H130.22850.83200.93290.138*
C140.3248 (7)0.6483 (4)0.89809 (16)0.1081 (13)
H140.43590.68690.88860.130*
C150.2845 (5)0.5045 (4)0.88569 (12)0.0813 (9)
H150.36860.44730.86760.098*
C160.1235 (4)0.4451 (4)0.89952 (10)0.0679 (8)
O170.0785 (3)0.3040 (2)0.88841 (9)0.0851 (7)
C170.2083 (4)0.2079 (4)0.86577 (11)0.0785 (9)
H17A0.24400.24370.83100.118*
H17B0.31110.20330.88900.118*
H17C0.15740.11170.86200.118*
C10.1808 (5)0.4849 (4)0.94492 (12)0.0847 (10)
O10.2925 (4)0.5603 (3)0.96575 (13)0.1370 (12)
N10.3002 (3)0.1396 (2)0.87928 (8)0.0611 (6)
C20.2813 (4)0.2866 (3)0.88746 (10)0.0583 (7)
O20.3132 (3)0.37828 (18)0.85317 (7)0.0664 (5)
N30.2251 (3)0.3277 (3)0.93813 (8)0.0683 (6)
C40.1672 (5)0.2311 (5)0.97691 (12)0.0869 (10)
O40.0985 (4)0.2730 (4)1.01860 (8)0.1170 (10)
C50.1913 (6)0.0789 (4)0.96162 (12)0.0914 (11)
H50.16250.00770.98710.110*
N60.2494 (4)0.0348 (3)0.91567 (9)0.0833 (8)
C1'0.3325 (4)0.0879 (3)0.82376 (11)0.0615 (7)
H1'0.40120.16200.80390.074*
C2'0.4282 (5)0.0580 (3)0.82047 (13)0.0773 (8)
H2'10.47680.08550.85540.093*
H2'20.52530.05410.79440.093*
C3'0.2843 (4)0.1661 (3)0.80256 (10)0.0636 (7)
H3'10.22500.20920.83410.076*
O3'0.3602 (3)0.2777 (2)0.77021 (9)0.0825 (6)
H3'0.28780.34470.76660.124*
C4'0.1546 (4)0.0682 (3)0.77219 (10)0.0599 (7)
H4'0.19770.05570.73510.072*
C5'0.0356 (5)0.1193 (3)0.77074 (13)0.0789 (9)
H5'10.03990.21810.75630.095*
H5'20.08280.12200.80720.095*
O5'0.1443 (4)0.0264 (3)0.73873 (11)0.1120 (9)
H5'0.18890.07400.71410.168*
O4'0.1620 (3)0.07015 (19)0.79935 (7)0.0663 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C110.077 (2)0.085 (2)0.0581 (15)0.0076 (18)0.0038 (15)0.0131 (15)
C120.127 (3)0.072 (2)0.085 (2)0.005 (2)0.009 (2)0.0090 (18)
C130.152 (4)0.084 (2)0.109 (3)0.022 (3)0.014 (3)0.014 (2)
C140.105 (3)0.108 (3)0.111 (3)0.017 (3)0.009 (3)0.035 (2)
C150.074 (2)0.096 (2)0.0739 (18)0.004 (2)0.0064 (17)0.0161 (17)
C160.0627 (18)0.086 (2)0.0551 (13)0.0055 (17)0.0016 (14)0.0028 (14)
O170.0565 (12)0.0937 (16)0.1050 (15)0.0065 (12)0.0114 (11)0.0389 (13)
C170.0633 (18)0.100 (2)0.0724 (16)0.0202 (18)0.0066 (15)0.0250 (16)
C10.079 (2)0.097 (2)0.0783 (19)0.010 (2)0.0106 (18)0.0355 (18)
O10.101 (2)0.135 (2)0.175 (3)0.0096 (19)0.042 (2)0.089 (2)
N10.0650 (14)0.0607 (12)0.0575 (11)0.0097 (12)0.0090 (12)0.0053 (10)
C20.0507 (15)0.0673 (16)0.0570 (14)0.0090 (14)0.0154 (13)0.0008 (13)
O20.0724 (13)0.0615 (10)0.0652 (10)0.0085 (10)0.0097 (10)0.0003 (9)
N30.0655 (15)0.0836 (15)0.0558 (12)0.0092 (14)0.0114 (12)0.0118 (11)
C40.080 (2)0.127 (3)0.0532 (16)0.023 (2)0.0106 (16)0.0052 (18)
O40.121 (2)0.176 (3)0.0541 (11)0.020 (2)0.0023 (13)0.0137 (15)
C50.113 (3)0.105 (2)0.0557 (16)0.038 (2)0.0133 (19)0.0148 (16)
N60.103 (2)0.0788 (16)0.0678 (14)0.0242 (17)0.0182 (15)0.0168 (12)
C1'0.0551 (16)0.0640 (15)0.0653 (14)0.0019 (14)0.0095 (13)0.0006 (12)
C2'0.0646 (18)0.0685 (17)0.0989 (19)0.0087 (16)0.0138 (17)0.0065 (16)
C3'0.0716 (18)0.0576 (14)0.0617 (13)0.0059 (15)0.0064 (14)0.0002 (12)
O3'0.0869 (15)0.0629 (11)0.0978 (13)0.0111 (11)0.0139 (13)0.0090 (11)
C4'0.0711 (19)0.0585 (15)0.0502 (12)0.0016 (15)0.0022 (13)0.0092 (12)
C5'0.076 (2)0.0707 (18)0.091 (2)0.0000 (18)0.0107 (18)0.0268 (16)
O5'0.105 (2)0.0998 (16)0.132 (2)0.0273 (16)0.0571 (17)0.0463 (15)
O4'0.0671 (12)0.0569 (10)0.0749 (11)0.0061 (10)0.0185 (10)0.0096 (9)
Geometric parameters (Å, º) top
C11—C161.405 (4)N3—C41.373 (4)
C11—C121.412 (5)C4—O41.215 (4)
C11—C11.459 (5)C4—C51.450 (5)
C12—C131.335 (6)C5—N61.282 (4)
C12—H120.9300C5—H50.9300
C13—C141.380 (6)C1'—O4'1.416 (3)
C13—H130.9300C1'—C2'1.511 (4)
C14—C151.380 (5)C1'—H1'0.9800
C14—H140.9300C2'—C3'1.523 (4)
C15—C161.360 (5)C2'—H2'10.9700
C15—H150.9300C2'—H2'20.9700
C16—O171.357 (4)C3'—O3'1.414 (3)
O17—C171.421 (3)C3'—C4'1.516 (4)
C17—H17A0.9600C3'—H3'10.9800
C17—H17B0.9600O3'—H3'0.8200
C17—H17C0.9600C4'—O4'1.431 (3)
C1—O11.197 (4)C4'—C5'1.492 (5)
C1—N31.480 (4)C4'—H4'0.9800
N1—C21.363 (3)C5'—O5'1.415 (4)
N1—N61.367 (3)C5'—H5'10.9700
N1—C1'1.474 (3)C5'—H5'20.9700
C2—O21.215 (3)O5'—H5'0.8200
C2—N31.376 (3)
C16—C11—C12117.8 (3)N3—C4—C5113.1 (3)
C16—C11—C1126.5 (3)N6—C5—C4125.0 (3)
C12—C11—C1115.7 (3)N6—C5—H5117.5
C13—C12—C11122.0 (4)C4—C5—H5117.5
C13—C12—H12119.0C5—N6—N1117.4 (3)
C11—C12—H12119.0O4'—C1'—N1106.8 (2)
C12—C13—C14119.5 (4)O4'—C1'—C2'107.5 (2)
C12—C13—H13120.3N1—C1'—C2'114.1 (2)
C14—C13—H13120.3O4'—C1'—H1'109.5
C15—C14—C13120.4 (4)N1—C1'—H1'109.5
C15—C14—H14119.8C2'—C1'—H1'109.5
C13—C14—H14119.8C1'—C2'—C3'104.7 (2)
C16—C15—C14120.9 (4)C1'—C2'—H2'1110.8
C16—C15—H15119.5C3'—C2'—H2'1110.8
C14—C15—H15119.5C1'—C2'—H2'2110.8
O17—C16—C15123.0 (3)C3'—C2'—H2'2110.8
O17—C16—C11117.5 (3)H2'1—C2'—H2'2108.9
C15—C16—C11119.5 (3)O3'—C3'—C4'113.4 (2)
C16—O17—C17119.8 (2)O3'—C3'—C2'110.5 (2)
O17—C17—H17A109.5C4'—C3'—C2'102.3 (2)
O17—C17—H17B109.5O3'—C3'—H3'1110.1
H17A—C17—H17B109.5C4'—C3'—H3'1110.1
O17—C17—H17C109.5C2'—C3'—H3'1110.1
H17A—C17—H17C109.5C3'—O3'—H3'109.5
H17B—C17—H17C109.5O4'—C4'—C5'108.9 (2)
O1—C1—C11126.5 (3)O4'—C4'—C3'105.1 (2)
O1—C1—N3116.8 (3)C5'—C4'—C3'115.7 (2)
C11—C1—N3116.7 (3)O4'—C4'—H4'109.0
C2—N1—N6124.1 (2)C5'—C4'—H4'109.0
C2—N1—C1'118.0 (2)C3'—C4'—H4'109.0
N6—N1—C1'115.9 (2)O5'—C5'—C4'111.7 (3)
O2—C2—N1123.5 (2)O5'—C5'—H5'1109.3
O2—C2—N3120.7 (3)C4'—C5'—H5'1109.3
N1—C2—N3115.8 (2)O5'—C5'—H5'2109.3
C4—N3—C2124.0 (3)C4'—C5'—H5'2109.3
C4—N3—C1118.1 (3)H5'1—C5'—H5'2107.9
C2—N3—C1115.8 (3)C5'—O5'—H5'109.5
O4—C4—N3121.7 (3)C1'—O4'—C4'109.6 (2)
O4—C4—C5125.2 (3)
C16—C11—C12—C130.6 (5)C11—C1—N3—C281.0 (4)
C1—C11—C12—C13178.7 (3)C2—N3—C4—O4170.9 (3)
C11—C12—C13—C140.5 (6)C1—N3—C4—O47.8 (5)
C12—C13—C14—C150.0 (6)C2—N3—C4—C57.1 (4)
C13—C14—C15—C160.5 (6)C1—N3—C4—C5170.1 (3)
C14—C15—C16—O17179.6 (3)O4—C4—C5—N6173.6 (4)
C14—C15—C16—C110.3 (5)N3—C4—C5—N64.3 (5)
C12—C11—C16—O17179.8 (3)C4—C5—N6—N13.2 (6)
C1—C11—C16—O170.9 (5)C2—N1—N6—C54.8 (5)
C12—C11—C16—C150.2 (4)C1'—N1—N6—C5168.5 (3)
C1—C11—C16—C15179.0 (3)C2—N1—C1'—O4'86.4 (3)
C15—C16—O17—C175.9 (4)N6—N1—C1'—O4'78.4 (3)
C11—C16—O17—C17174.0 (2)C2—N1—C1'—C2'155.0 (3)
C16—C11—C1—O1176.3 (3)N6—N1—C1'—C2'40.2 (4)
C12—C11—C1—O14.4 (5)O4'—C1'—C2'—C3'11.0 (3)
C16—C11—C1—N35.1 (5)N1—C1'—C2'—C3'107.2 (3)
C12—C11—C1—N3174.2 (3)C1'—C2'—C3'—O3'147.5 (2)
N6—N1—C2—O2173.8 (3)C1'—C2'—C3'—C4'26.5 (3)
C1'—N1—C2—O210.3 (4)O3'—C3'—C4'—O4'152.0 (2)
N6—N1—C2—N37.2 (4)C2'—C3'—C4'—O4'33.0 (3)
C1'—N1—C2—N3170.7 (2)O3'—C3'—C4'—C5'87.9 (3)
O2—C2—N3—C4172.3 (3)C2'—C3'—C4'—C5'153.2 (2)
N1—C2—N3—C48.6 (4)O4'—C4'—C5'—O5'65.7 (3)
O2—C2—N3—C18.9 (4)C3'—C4'—C5'—O5'176.2 (2)
N1—C2—N3—C1172.0 (3)N1—C1'—O4'—C4'133.2 (2)
O1—C1—N3—C495.3 (4)C2'—C1'—O4'—C4'10.4 (3)
C11—C1—N3—C483.4 (4)C5'—C4'—O4'—C1'152.3 (2)
O1—C1—N3—C2100.2 (4)C3'—C4'—O4'—C1'27.7 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O5i0.821.982.789 (3)171
O5—H5···O2i0.821.962.743 (3)161
C1—H1···O20.982.412.750 (3)100
C2—H21···N60.972.512.839 (5)100
C12—H12···O10.932.492.802 (6)100
Symmetry code: (i) x, y1/2, z+3/2.

Experimental details

(I)(II)
Crystal data
Chemical formulaC8H11N3O5C16H17N3O7
Mr229.20363.33
Crystal system, space groupOrthorhombic, P212121Orthorhombic, P212121
Temperature (K)293293
a, b, c (Å)7.8817 (17), 8.6832 (11), 14.5715 (15)7.452 (3), 9.117 (1), 24.780 (3)
V3)997.2 (3)1683.6 (7)
Z44
Radiation typeMo KαMo Kα
µ (mm1)0.130.11
Crystal size (mm)0.4 × 0.3 × 0.20.4 × 0.2 × 0.1
Data collection
DiffractometerBruker P4
diffractometer
Bruker P4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2127, 1580, 1313 7561, 1732, 1367
Rint0.0200.036
(sin θ/λ)max1)0.7030.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.121, 1.07 0.035, 0.094, 1.02
No. of reflections15801732
No. of parameters148239
H-atom treatmentH-atom parameters constrainedH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.37, 0.230.11, 0.14

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

Selected geometric parameters (Å, º) for (I) top
N1—N61.362 (3)C4—O41.219 (3)
N1—C21.380 (3)C4—C51.462 (4)
N1—C1'1.462 (3)C5—N61.277 (3)
C2—N31.372 (3)C1'—O4'1.425 (4)
N3—C41.365 (3)C4'—O4'1.440 (3)
C2—N1—C1'118.9 (2)O4'—C1'—C2'106.4 (2)
O4—C4—N3122.5 (2)C1'—C2'—C3'101.2 (2)
N6—N1—C2—O2174.4 (3)C1'—C2'—C3'—C4'39.1 (3)
N1—C2—N3—C43.9 (4)C2'—C3'—C4'—O4'35.9 (3)
N3—C4—C5—N61.0 (5)O3'—C3'—C4'—C5'161.3 (2)
C4—C5—N6—N10.9 (5)N1—C1'—O4'—C4'130.9 (2)
C2—N1—N6—C54.6 (4)C2'—C1'—O4'—C4'7.3 (3)
C2—N1—C1'—O4'94.0 (3)C3'—C4'—O4'—C1'18.2 (3)
O4'—C1'—C2'—C3'29.4 (3)O4'—C4'—C5'—O5'66.8 (3)
N1—C1'—C2'—C3'149.2 (2)C3'—C4'—C5'—O5'175.2 (2)
Hydrogen-bond geometry (Å, º) for (I) top
D—H···AD—HH···AD···AD—H···A
O5'—H5'···O4i0.822.022.816 (3)163
O3'—H3'···O2ii0.822.152.948 (4)164
N3—H3···O5'iii0.861.972.825 (3)176
C1'—H1'···O20.982.392.764 (3)102
C2'—H2'1···N60.972.452.862 (4)105
Symmetry codes: (i) x+5/2, y+1, z1/2; (ii) x+2, y+1/2, z+3/2; (iii) x1/2, y+1/2, z+2.
Selected geometric parameters (Å, º) for (II) top
C11—C11.459 (5)C2—N31.376 (3)
C16—O171.357 (4)N3—C41.373 (4)
C1—O11.197 (4)C4—O41.215 (4)
C1—N31.480 (4)C4—C51.450 (5)
N1—C21.363 (3)C5—N61.282 (4)
N1—N61.367 (3)C1'—O4'1.416 (3)
N1—C1'1.474 (3)C4'—O4'1.431 (3)
C16—C11—C12117.8 (3)C11—C1—N3116.7 (3)
C16—C11—C1126.5 (3)O4—C4—N3121.7 (3)
C12—C11—C1115.7 (3)O4'—C1'—C2'107.5 (2)
C16—O17—C17119.8 (2)N1—C1'—C2'114.1 (2)
O1—C1—N3116.8 (3)C1'—C2'—C3'104.7 (2)
C11—C12—C13—C140.5 (6)O4'—C1'—C2'—C3'11.0 (3)
C11—C16—O17—C17174.0 (2)N1—C1'—C2'—C3'107.2 (3)
C16—C11—C1—O1176.3 (3)C1'—C2'—C3'—C4'26.5 (3)
C16—C11—C1—N35.1 (5)C2'—C3'—C4'—O4'33.0 (3)
N6—N1—C2—O2173.8 (3)O3'—C3'—C4'—C5'87.9 (3)
N1—C2—N3—C48.6 (4)O4'—C4'—C5'—O5'65.7 (3)
N3—C4—C5—N64.3 (5)C3'—C4'—C5'—O5'176.2 (2)
C4—C5—N6—N13.2 (6)N1—C1'—O4'—C4'133.2 (2)
C2—N1—N6—C54.8 (5)C2'—C1'—O4'—C4'10.4 (3)
C2—N1—C1'—O4'86.4 (3)C3'—C4'—O4'—C1'27.7 (3)
Hydrogen-bond geometry (Å, º) for (II) top
D—H···AD—HH···AD···AD—H···A
O3'—H3'···O5'i0.821.982.789 (3)171
O5'—H5'···O2i0.821.962.743 (3)161
C1'—H1'···O20.982.412.750 (3)100
C2'—H2'1···N60.972.512.839 (5)100
C12—H12···O10.932.492.802 (6)100
Symmetry code: (i) x, y1/2, z+3/2.
 

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