In the structure of the title compound, C
11H
13N
5O
4, the glycosidic torsion angle, χ, is −107.1 (2)° [nucleic acid nomenclature used throughout the manuscript; IUPAC–IUB Joint Commision on Biochemical Nomenclature (1983).
Eur. J. Biochem. 131, 9–15], indicating the
anti conformation. The furanosyl ring adopts an N-type sugar pucker with the following pseudorotational parameters:
PN = 50.5 (2)° and ν
max = 34.9 (1)°. The conformation around the C5′—C6′ bond is
ap (
gauche,
trans;
gt; −
g), with a torsion angle γ of 176.28 (19)°. The 1′,2′-oxetane ring is not planar but folded along C3′
C1′, with an angle of 9.6 (1)°.
Supporting information
CCDC reference: 628520
The synthesis of compound (I) has been described (Roivainen et al., 2002). Samples for X-ray analyses were crystallized from a mixture of methanol and 2-propanol. Single crystals suitable for X-ray diffraction were selected directly from the sample as prepared.
In the absence of suitable anomalous scattering atoms, refinement of the Flack (1983) parameter (Flack, 1983) led to an inconclusive result. All H atoms were initially found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, the H atoms bonded to C atoms were placed in geometrically idealized positions (C—H = 0.93–0.98 Å) and constrained to ride on their parent atoms. In order to describe the hydrogen-bonding scheme as well as possible, the positions of the H atoms of the OH und NH2 groups were first allowed to refine restrained to common O—H and N—H bond lengths (DFIX). After refinement, the positions of these H atoms were also constrained (AFIX 3) to ride on their parent atoms.
Data collection: XSCANS (Siemens, 1996); cell refinement: XSCANS (Siemens, 1996); 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.
9-(1,3-Anhydro-
β-
D-psicofuranosyl)adenine
top
Crystal data top
C11H13N5O4 | F(000) = 292 |
Mr = 279.26 | Dx = 1.518 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 32 reflections |
a = 5.4154 (5) Å | θ = 4.3–12.5° |
b = 9.8941 (8) Å | µ = 0.12 mm−1 |
c = 11.4431 (12) Å | T = 293 K |
β = 94.970 (14)° | Plate, colourless |
V = 610.82 (10) Å3 | 0.35 × 0.22 × 0.08 mm |
Z = 2 | |
Data collection top
Bruker P4 diffractometer | 1686 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.023 |
Graphite monochromator | θmax = 30.0°, θmin = 1.8° |
ω scans | h = 0→7 |
2053 measured reflections | k = −13→0 |
1878 independent reflections | l = −16→16 |
Refinement top
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.041 | w = 1/[σ2(Fo2) + (0.0627P)2 + 0.0578P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.109 | (Δ/σ)max < 0.001 |
S = 1.04 | Δρmax = 0.24 e Å−3 |
1878 reflections | Δρmin = −0.23 e Å−3 |
186 parameters | Extinction correction: SHELXTL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
5 restraints | Extinction coefficient: 0.037 (8) |
Primary atom site location: structure-invariant direct methods | Absolute structure: based on known absolute configuration of the chemical entity |
Secondary atom site location: difference Fourier map | Absolute structure parameter: −0.7 (13) |
Crystal data top
C11H13N5O4 | V = 610.82 (10) Å3 |
Mr = 279.26 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 5.4154 (5) Å | µ = 0.12 mm−1 |
b = 9.8941 (8) Å | T = 293 K |
c = 11.4431 (12) Å | 0.35 × 0.22 × 0.08 mm |
β = 94.970 (14)° | |
Data collection top
Bruker P4 diffractometer | 1686 reflections with I > 2σ(I) |
2053 measured reflections | Rint = 0.023 |
1878 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.041 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.109 | Δρmax = 0.24 e Å−3 |
S = 1.04 | Δρmin = −0.23 e Å−3 |
1878 reflections | Absolute structure: based on known absolute configuration of the chemical entity |
186 parameters | Absolute structure parameter: −0.7 (13) |
5 restraints | |
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 | x | y | z | Uiso*/Ueq | |
N1 | 1.0645 (4) | −0.0648 (2) | 0.70622 (17) | 0.0413 (5) | |
C2 | 1.0944 (5) | −0.1224 (3) | 0.6016 (2) | 0.0421 (6) | |
H21 | 1.2235 | −0.1844 | 0.6015 | 0.047 (2)* | |
N3 | 0.9656 (4) | −0.1035 (2) | 0.49783 (19) | 0.0380 (5) | |
C4 | 0.7818 (4) | −0.0143 (2) | 0.50832 (17) | 0.0287 (4) | |
C5 | 0.7304 (4) | 0.0553 (2) | 0.60914 (17) | 0.0310 (4) | |
C6 | 0.8844 (4) | 0.0297 (2) | 0.71232 (18) | 0.0338 (5) | |
N6 | 0.8554 (4) | 0.0924 (2) | 0.81362 (17) | 0.0451 (5) | |
H61 | 0.7459 | 0.1562 | 0.8137 | 0.047 (2)* | |
H62 | 0.9613 | 0.0757 | 0.8731 | 0.047 (2)* | |
N7 | 0.5259 (4) | 0.1393 (2) | 0.58820 (16) | 0.0398 (5) | |
C8 | 0.4570 (4) | 0.1198 (3) | 0.47760 (18) | 0.0370 (5) | |
H81 | 0.3227 | 0.1642 | 0.4385 | 0.047 (2)* | |
N9 | 0.6010 (3) | 0.02752 (19) | 0.42329 (14) | 0.0289 (4) | |
C1' | 0.6795 (4) | −0.1284 (2) | 0.25069 (18) | 0.0320 (4) | |
H1'1 | 0.8107 | −0.1123 | 0.1998 | 0.047 (2)* | |
H1'2 | 0.7307 | −0.1942 | 0.3108 | 0.047 (2)* | |
O4' | 0.1036 (3) | 0.00909 (19) | 0.05149 (12) | 0.0359 (4) | |
H4'O | 0.2009 | −0.0501 | 0.0152 | 0.047 (2)* | |
C2' | 0.5720 (3) | 0.0016 (2) | 0.29920 (16) | 0.0269 (4) | |
C3' | 0.3213 (4) | −0.0476 (3) | 0.24248 (17) | 0.0305 (4) | |
H3' | 0.201 (6) | −0.081 (3) | 0.297 (3) | 0.047 (2)* | |
O3' | 0.4400 (3) | −0.15917 (17) | 0.18710 (13) | 0.0354 (4) | |
C5' | 0.4817 (4) | 0.1302 (2) | 0.13100 (17) | 0.0312 (4) | |
H5' | 0.5636 | 0.0810 | 0.0709 | 0.047 (2)* | |
C4' | 0.2366 (4) | 0.0606 (2) | 0.15315 (17) | 0.0310 (4) | |
H4' | 0.1315 | 0.1255 | 0.1904 | 0.047 (2)* | |
O5' | 0.6307 (3) | 0.12337 (17) | 0.24239 (12) | 0.0329 (3) | |
O6' | 0.6916 (5) | 0.3373 (2) | 0.08697 (17) | 0.0678 (7) | |
H6'O | 0.7672 | 0.3653 | 0.1571 | 0.047 (2)* | |
C6' | 0.4583 (6) | 0.2775 (3) | 0.0989 (2) | 0.0508 (7) | |
H6'1 | 0.3555 | 0.2865 | 0.0255 | 0.047 (2)* | |
H6'2 | 0.3771 | 0.3250 | 0.1590 | 0.047 (2)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0474 (11) | 0.0458 (12) | 0.0282 (9) | 0.0127 (10) | −0.0103 (7) | 0.0002 (9) |
C2 | 0.0437 (12) | 0.0482 (14) | 0.0324 (10) | 0.0160 (11) | −0.0086 (9) | −0.0036 (10) |
N3 | 0.0368 (10) | 0.0447 (11) | 0.0311 (8) | 0.0070 (9) | −0.0043 (7) | −0.0037 (8) |
C4 | 0.0300 (9) | 0.0324 (10) | 0.0227 (8) | −0.0009 (8) | −0.0037 (7) | 0.0010 (7) |
C5 | 0.0358 (10) | 0.0345 (10) | 0.0212 (8) | 0.0046 (9) | −0.0052 (7) | 0.0001 (7) |
C6 | 0.0419 (11) | 0.0342 (11) | 0.0236 (8) | 0.0020 (9) | −0.0073 (8) | 0.0032 (8) |
N6 | 0.0622 (13) | 0.0448 (12) | 0.0253 (8) | 0.0159 (10) | −0.0141 (8) | −0.0034 (8) |
N7 | 0.0449 (10) | 0.0455 (11) | 0.0273 (8) | 0.0133 (9) | −0.0059 (7) | −0.0027 (8) |
C8 | 0.0373 (11) | 0.0451 (13) | 0.0271 (9) | 0.0105 (10) | −0.0055 (7) | −0.0016 (9) |
N9 | 0.0308 (8) | 0.0343 (9) | 0.0203 (7) | 0.0023 (7) | −0.0045 (6) | −0.0007 (6) |
C1' | 0.0318 (10) | 0.0347 (11) | 0.0285 (9) | −0.0015 (9) | −0.0028 (7) | −0.0012 (8) |
O4' | 0.0340 (7) | 0.0461 (9) | 0.0255 (6) | 0.0034 (7) | −0.0096 (5) | −0.0043 (7) |
C2' | 0.0272 (8) | 0.0330 (10) | 0.0196 (7) | −0.0040 (8) | −0.0027 (6) | 0.0024 (7) |
C3' | 0.0269 (9) | 0.0408 (11) | 0.0234 (8) | −0.0083 (8) | −0.0006 (7) | 0.0009 (8) |
O3' | 0.0407 (8) | 0.0323 (8) | 0.0312 (7) | −0.0048 (6) | −0.0089 (6) | −0.0019 (6) |
C5' | 0.0356 (10) | 0.0348 (11) | 0.0220 (8) | −0.0046 (9) | −0.0040 (7) | 0.0005 (8) |
C4' | 0.0281 (9) | 0.0402 (11) | 0.0236 (8) | 0.0014 (9) | −0.0042 (7) | −0.0021 (8) |
O5' | 0.0359 (7) | 0.0338 (8) | 0.0271 (7) | −0.0106 (6) | −0.0077 (5) | 0.0054 (6) |
O6' | 0.1016 (17) | 0.0658 (14) | 0.0316 (8) | −0.0446 (14) | −0.0198 (9) | 0.0164 (9) |
C6' | 0.0721 (18) | 0.0414 (14) | 0.0354 (12) | −0.0086 (13) | −0.0157 (12) | 0.0089 (10) |
Geometric parameters (Å, º) top
N1—C2 | 1.349 (3) | C1'—H1'1 | 0.9700 |
N1—C6 | 1.357 (3) | C1'—H1'2 | 0.9700 |
C2—N3 | 1.337 (3) | O4'—C4' | 1.409 (2) |
C2—H21 | 0.9300 | O4'—H4'O | 0.9115 |
N3—C4 | 1.343 (3) | C2'—O5' | 1.418 (2) |
C4—N9 | 1.383 (2) | C2'—C3' | 1.533 (3) |
C4—C5 | 1.392 (3) | C3'—O3' | 1.451 (3) |
C5—N7 | 1.389 (3) | C3'—C4' | 1.523 (3) |
C5—C6 | 1.408 (3) | C3'—H3' | 1.00 (3) |
C6—N6 | 1.336 (3) | C5'—O5' | 1.450 (2) |
N6—H61 | 0.8666 | C5'—C6' | 1.506 (4) |
N6—H62 | 0.8665 | C5'—C4' | 1.536 (3) |
N7—C8 | 1.302 (3) | C5'—H5' | 0.9800 |
C8—N9 | 1.383 (3) | C4'—H4' | 0.9800 |
C8—H81 | 0.9300 | O6'—C6' | 1.412 (4) |
N9—C2' | 1.438 (2) | O6'—H6'O | 0.9117 |
C1'—O3' | 1.463 (3) | C6'—H6'1 | 0.9700 |
C1'—C2' | 1.535 (3) | C6'—H6'2 | 0.9700 |
| | | |
C2—N1—C6 | 118.60 (19) | O5'—C2'—C3' | 107.53 (16) |
N3—C2—N1 | 129.5 (2) | N9—C2'—C3' | 119.45 (16) |
N3—C2—H21 | 115.3 | O5'—C2'—C1' | 116.03 (16) |
N1—C2—H21 | 115.3 | N9—C2'—C1' | 119.60 (17) |
C2—N3—C4 | 110.3 (2) | C3'—C2'—C1' | 86.02 (16) |
N3—C4—N9 | 128.23 (19) | O3'—C3'—C4' | 111.13 (16) |
N3—C4—C5 | 127.01 (18) | O3'—C3'—C2' | 90.96 (15) |
N9—C4—C5 | 104.76 (18) | C4'—C3'—C2' | 105.38 (18) |
N7—C5—C4 | 111.52 (17) | O3'—C3'—H3' | 111 (2) |
N7—C5—C6 | 131.1 (2) | C4'—C3'—H3' | 118.5 (19) |
C4—C5—C6 | 117.3 (2) | C2'—C3'—H3' | 116.2 (18) |
N6—C6—N1 | 120.23 (19) | C3'—O3'—C1' | 91.80 (15) |
N6—C6—C5 | 122.6 (2) | O5'—C5'—C6' | 106.79 (18) |
N1—C6—C5 | 117.2 (2) | O5'—C5'—C4' | 104.89 (16) |
C6—N6—H61 | 118.1 | C6'—C5'—C4' | 114.8 (2) |
C6—N6—H62 | 118.2 | O5'—C5'—H5' | 110.1 |
H61—N6—H62 | 123.0 | C6'—C5'—H5' | 110.1 |
C8—N7—C5 | 103.66 (19) | C4'—C5'—H5' | 110.1 |
N7—C8—N9 | 114.16 (18) | O4'—C4'—C3' | 113.7 (2) |
N7—C8—H81 | 122.9 | O4'—C4'—C5' | 114.41 (17) |
N9—C8—H81 | 122.9 | C3'—C4'—C5' | 102.24 (15) |
C4—N9—C8 | 105.90 (16) | O4'—C4'—H4' | 108.7 |
C4—N9—C2' | 130.66 (18) | C3'—C4'—H4' | 108.7 |
C8—N9—C2' | 122.95 (17) | C5'—C4'—H4' | 108.7 |
O3'—C1'—C2' | 90.40 (15) | C2'—O5'—C5' | 108.25 (15) |
O3'—C1'—H1'1 | 113.6 | C6'—O6'—H6'O | 112.3 |
C2'—C1'—H1'1 | 113.6 | O6'—C6'—C5' | 111.8 (3) |
O3'—C1'—H1'2 | 113.6 | O6'—C6'—H6'1 | 109.3 |
C2'—C1'—H1'2 | 113.6 | C5'—C6'—H6'1 | 109.3 |
H1'1—C1'—H1'2 | 110.8 | O6'—C6'—H6'2 | 109.3 |
C4'—O4'—H4'O | 109.5 | C5'—C6'—H6'2 | 109.3 |
O5'—C2'—N9 | 106.95 (17) | H6'1—C6'—H6'2 | 107.9 |
| | | |
C6—N1—C2—N3 | −1.9 (5) | C8—N9—C2'—C1' | −161.9 (2) |
N1—C2—N3—C4 | −1.1 (4) | O3'—C1'—C2'—O5' | −100.92 (17) |
C2—N3—C4—N9 | −176.7 (2) | O3'—C1'—C2'—N9 | 128.49 (18) |
C2—N3—C4—C5 | 2.4 (3) | O3'—C1'—C2'—C3' | 6.66 (15) |
N3—C4—C5—N7 | −179.9 (2) | O5'—C2'—C3'—O3' | 109.34 (17) |
N9—C4—C5—N7 | −0.6 (3) | N9—C2'—C3'—O3' | −128.69 (19) |
N3—C4—C5—C6 | −0.7 (4) | C1'—C2'—C3'—O3' | −6.72 (15) |
N9—C4—C5—C6 | 178.6 (2) | O5'—C2'—C3'—C4' | −2.9 (2) |
C2—N1—C6—N6 | −177.6 (3) | N9—C2'—C3'—C4' | 119.1 (2) |
C2—N1—C6—C5 | 3.7 (4) | C1'—C2'—C3'—C4' | −118.96 (17) |
N7—C5—C6—N6 | −2.2 (4) | C4'—C3'—O3'—C1' | 113.95 (17) |
C4—C5—C6—N6 | 178.7 (2) | C2'—C3'—O3'—C1' | 7.04 (16) |
N7—C5—C6—N1 | 176.5 (3) | C2'—C1'—O3'—C3' | −7.03 (16) |
C4—C5—C6—N1 | −2.5 (3) | O3'—C3'—C4'—O4' | 48.4 (2) |
C4—C5—N7—C8 | 0.1 (3) | C2'—C3'—C4'—O4' | 145.60 (17) |
C6—C5—N7—C8 | −178.9 (3) | O3'—C3'—C4'—C5' | −75.4 (2) |
C5—N7—C8—N9 | 0.5 (3) | C2'—C3'—C4'—C5' | 21.7 (2) |
N3—C4—N9—C8 | −179.9 (2) | O5'—C5'—C4'—O4' | −156.69 (19) |
C5—C4—N9—C8 | 0.9 (2) | C6'—C5'—C4'—O4' | 86.5 (2) |
N3—C4—N9—C2' | −7.9 (4) | O5'—C5'—C4'—C3' | −33.3 (2) |
C5—C4—N9—C2' | 172.8 (2) | C6'—C5'—C4'—C3' | −150.12 (19) |
N7—C8—N9—C4 | −0.9 (3) | N9—C2'—O5'—C5' | −148.35 (16) |
N7—C8—N9—C2' | −173.6 (2) | C3'—C2'—O5'—C5' | −18.9 (2) |
C4—N9—C2'—O5' | −107.1 (2) | C1'—C2'—O5'—C5' | 75.3 (2) |
C8—N9—C2'—O5' | 63.7 (2) | C6'—C5'—O5'—C2' | 155.3 (2) |
C4—N9—C2'—C3' | 130.6 (2) | C4'—C5'—O5'—C2' | 33.1 (2) |
C8—N9—C2'—C3' | −58.6 (3) | O5'—C5'—C6'—O6' | 60.5 (3) |
C4—N9—C2'—C1' | 27.4 (3) | C4'—C5'—C6'—O6' | 176.28 (19) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H61···O3′i | 0.87 | 2.09 | 2.932 (3) | 166 |
N6—H62···O4′ii | 0.87 | 2.22 | 3.043 (2) | 159 |
O4′—H4′O···O6′iii | 0.91 | 1.75 | 2.633 (3) | 162 |
O6′—H6′O···N1iv | 0.91 | 1.87 | 2.782 (3) | 175 |
Symmetry codes: (i) −x+1, y+1/2, −z+1; (ii) x+1, y, z+1; (iii) −x+1, y−1/2, −z; (iv) −x+2, y+1/2, −z+1. |
Experimental details
Crystal data |
Chemical formula | C11H13N5O4 |
Mr | 279.26 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 293 |
a, b, c (Å) | 5.4154 (5), 9.8941 (8), 11.4431 (12) |
β (°) | 94.970 (14) |
V (Å3) | 610.82 (10) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.35 × 0.22 × 0.08 |
|
Data collection |
Diffractometer | Bruker P4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2053, 1878, 1686 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.703 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.109, 1.04 |
No. of reflections | 1878 |
No. of parameters | 186 |
No. of restraints | 5 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.24, −0.23 |
Absolute structure | Based on known absolute configuration of the chemical entity |
Absolute structure parameter | −0.7 (13) |
Selected geometric parameters (Å, º) topN9—C2' | 1.438 (2) | C2'—O5' | 1.418 (2) |
C1'—O3' | 1.463 (3) | C2'—C3' | 1.533 (3) |
C1'—C2' | 1.535 (3) | C3'—O3' | 1.451 (3) |
O4'—C4' | 1.409 (2) | C5'—O5' | 1.450 (2) |
| | | |
C8—N9—C2' | 122.95 (17) | O3'—C3'—C4' | 111.13 (16) |
O5'—C2'—N9 | 106.95 (17) | O3'—C3'—C2' | 90.96 (15) |
N9—C2'—C3' | 119.45 (16) | C3'—O3'—C1' | 91.80 (15) |
O5'—C2'—C1' | 116.03 (16) | O5'—C5'—C4' | 104.89 (16) |
N9—C2'—C1' | 119.60 (17) | C3'—C4'—C5' | 102.24 (15) |
C3'—C2'—C1' | 86.02 (16) | C2'—O5'—C5' | 108.25 (15) |
| | | |
C2—N3—C4—N9 | −176.7 (2) | C3'—C2'—O5'—C5' | −18.9 (2) |
N7—C5—C6—N6 | −2.2 (4) | C1'—C2'—O5'—C5' | 75.3 (2) |
N3—C4—N9—C8 | −179.9 (2) | C6'—C5'—O5'—C2' | 155.3 (2) |
C4—N9—C2'—O5' | −107.1 (2) | C4'—C5'—O5'—C2' | 33.1 (2) |
N9—C2'—O5'—C5' | −148.35 (16) | C4'—C5'—C6'—O6' | 176.28 (19) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H61···O3'i | 0.87 | 2.09 | 2.932 (3) | 165.7 |
N6—H62···O4'ii | 0.87 | 2.22 | 3.043 (2) | 158.8 |
O4'—H4'O···O6'iii | 0.91 | 1.75 | 2.633 (3) | 162.2 |
O6'—H6'O···N1iv | 0.91 | 1.87 | 2.782 (3) | 174.9 |
Symmetry codes: (i) −x+1, y+1/2, −z+1; (ii) x+1, y, z+1; (iii) −x+1, y−1/2, −z; (iv) −x+2, y+1/2, −z+1. |
In recent years conformationally rigid 1,3-anhydro-β-D-psicofuranosyl nucleosides have attracted much attention as constituents of oligonucleotides, the exciting biochemical and biophysical properties of which have been investigated in detail by Chattopadhyaya and co-workers (Bogucka et al., 2005, and references therein); however, structural data have not heretofore been published. Recently, we described the synthesis of the anhydro nucleoside (I) (Roivainen et al., 2002), and deduced its structure from UV and NMR spectroscopic data to be consistent with that of (I) in the scheme below. Its single-crystal X-ray structure (Fig. 1), which we determined in order to confirm this assignment, is reported here.
Selected geometric parameters for the anhydro nucleoside (I) are given in Table 1. As might be expected, the structures of the adenine bases of (I) and adenosine (II) (Lai & Marsh, 1972), which represents the conformationally unrigid counterpart to (I), are very similar. The orientation of the almost planar adenine base of (I) relative to the sugar ring is anti, with glycosyl torsion angle χ (C4—N9—C2'—O5') (IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983) of −107.1 (2)° and differs substantially from that of −170.1° found for adenosine. The furanosyl ring of nucleoside (I) in the solid state adopts the N-type sugar pucker with following pseudorotational parameters: PN = 50.5 (2)° (C5'-exo) and νmax = 34.9 (1)°. The N-conformation was also found in the crystal structure of adenosine, although through somewhat different pseudorotational parameters, viz. PN = 7.2° (C2'-exo/C3'-endo; 3T2) and νmax = 36.0° (Lai & Marsh, 1972). It is noteworthy that the insertion of the 1',2'-oxetane ring into the molecule of adenosine did not lead to an essential change of bond distances within the furanose ring (the deviations are ±0.007 Å for all bonds, but the C5'—C4' bond was shorter by 0.014 Å than the relevant C3'—C4' bond of adenosine). Thus, the C5'—O5' bond [1.450 (2) Å] is longer than O5'—C2' [1.418 (2) Å], in accordance with an analogous correlation in most purine nucleosides (Seela et al., 1999). The 1',2'-oxetane ring itself is not planar but folded along C3'—C1' with an angle of 9.6 (1)°.
The glycosidic bond length of the nucleoside (I) C2'—N9 of 1.438 (2) Å is shorter than that of adenosine by 0.028 Å (Lai & Marsh, 1972). The conformations around the exocyclic C5'—C6' bond in the solid state of the nucleoside (I) and the corresponding C4'—C5' bond of adenosine are similar, viz. ap (gauche,trans; gt;-g), with torsion angles γ of 176.28 (19) and 177.0°, respectively.
In the extended structure all molecules are linked together via a three-dimensional network of hydrogen bonds. The main intermolecular feature, an eight-membered ring (Fig. 2), consists of the hydroxy groups O6' and O4' of two different molecules and the amino group N6 and atom N1 of a third molecule. Whereas the hydroxy groups function both as donors and as acceptors of hydrogen bonds, atom N1 serves only as an acceptor and the NH2– group as a donor. Three of the four intermolecular hydrogen bonds are found within this ring system. The fourth connects a fourth, exocyclic molecule with the NH2-groups inside the eight-membered supramolecular ring. The geometric details of all four hydrogen bonds are given in Table 2. As can be seen from the donor–acceptor distances, which are in the range 2.633 (3) to 3.043 (2) Å, only the hydrogen bond between the hydroxyl groups is relatively strong, whereas the other three are weaker.