Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270110008024/gt3016sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270110008024/gt3016Isup2.hkl |
CCDC reference: 774916
Compound (I) was prepared as described previously (Kline & Serianni, 1992) and crystallized from hot ethanol.
There are two crystallographically independent molecules in the asymmetric unit, differing in their rotation about the furanose–adenine bond. H atoms were located in difference Fourier maps and subsequently refined as riding, with C—H = 0.95–1.00 Å, N—H = 0.88 Å and O—H = 0.84 Å [Please check added text] and with Uiso(H) = 1.2Ueq(C,N,O).
Although the absolute structure parameter [1.2 (11); Flack, 1983] is indicative of the inverted absolute configuration, this is an unreliable measure at the wavelength of radiation used (0.7749 Å), especially for a light-atom structure (a detailed discussion of this problem can be found in Hooft et al., 2008). The correct configuration was therefore determined by the known chirality of the molecule in question. The correct configuration is depicted.
Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007; data reduction: SAINT (Bruker, 2007; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and POV-RAY (Cason, 2003); software used to prepare material for publication: enCIFer (Allen et al., 2004) and publCIF (Westrip, 2010).
C9H11N5O3 | F(000) = 992 |
Mr = 237.23 | Dx = 1.572 Mg m−3 |
Orthorhombic, P212121 | Synchrotron radiation, λ = 0.77490 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 3751 reflections |
a = 4.793 (3) Å | θ = 2.4–30.5° |
b = 11.365 (7) Å | µ = 0.12 mm−1 |
c = 36.79 (2) Å | T = 150 K |
V = 2004 (2) Å3 | Needle, colourless |
Z = 8 | 0.12 × 0.04 × 0.02 mm |
Bruker APEXII CCD area-detector diffractometer | 2910 independent reflections |
Radiation source: synchrotron, beamline 11.3.1, Advanced Light Source | 2556 reflections with I > 2σ(I) |
Channel-cut Si-<111> crystal monochromator | Rint = 0.112 |
Detector resolution: 8.33 pixels mm-1 | θmax = 31.1°, θmin = 1.2° |
ϕ and ω scans | h = −6→6 |
Absorption correction: multi-scan [SADABS (Version 2007/4; Sheldrick, 2008)] | k = −15→15 |
Tmin = 0.986, Tmax = 0.998 | l = −48→48 |
23772 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.047 | H-atom parameters constrained |
wR(F2) = 0.126 | w = 1/[σ2(Fo2) + (0.0556P)2 + 0.337P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max < 0.001 |
2910 reflections | Δρmax = 0.34 e Å−3 |
307 parameters | Δρmin = −0.31 e Å−3 |
0 restraints | Absolute structure: (Flack, 1983), with how many Friedel pairs? |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 1.2 (11) |
C9H11N5O3 | V = 2004 (2) Å3 |
Mr = 237.23 | Z = 8 |
Orthorhombic, P212121 | Synchrotron radiation, λ = 0.77490 Å |
a = 4.793 (3) Å | µ = 0.12 mm−1 |
b = 11.365 (7) Å | T = 150 K |
c = 36.79 (2) Å | 0.12 × 0.04 × 0.02 mm |
Bruker APEXII CCD area-detector diffractometer | 2910 independent reflections |
Absorption correction: multi-scan [SADABS (Version 2007/4; Sheldrick, 2008)] | 2556 reflections with I > 2σ(I) |
Tmin = 0.986, Tmax = 0.998 | Rint = 0.112 |
23772 measured reflections |
R[F2 > 2σ(F2)] = 0.047 | H-atom parameters constrained |
wR(F2) = 0.126 | Δρmax = 0.34 e Å−3 |
S = 1.07 | Δρmin = −0.31 e Å−3 |
2910 reflections | Absolute structure: (Flack, 1983), with how many Friedel pairs? |
307 parameters | Absolute structure parameter: 1.2 (11) |
0 restraints |
Experimental. Data were collected at the Advanced Light Source at Lawrence Berkeley National Laboratory at beamline 11.3.1. The instrumentation is a standard 3-circle diffractometer mounted to account for the plane-polarized X-rays generated by the synchrotron source. Monochromatic radiation was tuned via the use of a channel-cut Si-<111> crystal monochromator and focused at the sample with a toroidal mirror (spot dimensions: 90 × 280 µm). |
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. |
x | y | z | Uiso*/Ueq | ||
N1A | 0.8851 (5) | 0.9013 (2) | 0.33779 (6) | 0.0221 (5) | |
N3A | 0.8258 (5) | 0.8716 (2) | 0.27279 (6) | 0.0202 (5) | |
N6A | 0.6257 (5) | 0.8000 (2) | 0.38155 (6) | 0.0230 (5) | |
H6A | 0.7167 | 0.8377 | 0.3987 | 0.028* | |
H6B | 0.4963 | 0.7484 | 0.3873 | 0.028* | |
N7A | 0.3369 (5) | 0.6785 (2) | 0.31756 (6) | 0.0208 (5) | |
N9A | 0.4502 (5) | 0.7275 (2) | 0.25991 (5) | 0.0188 (5) | |
C2A | 0.9437 (6) | 0.9200 (2) | 0.30235 (7) | 0.0219 (5) | |
H2A | 1.0884 | 0.9751 | 0.2977 | 0.026* | |
C4A | 0.6230 (6) | 0.7938 (2) | 0.28240 (6) | 0.0180 (5) | |
C5A | 0.5474 (6) | 0.7623 (2) | 0.31757 (7) | 0.0198 (5) | |
C6A | 0.6838 (6) | 0.8210 (2) | 0.34680 (7) | 0.0184 (5) | |
C8A | 0.2871 (6) | 0.6601 (2) | 0.28281 (7) | 0.0202 (5) | |
H8A | 0.1518 | 0.6056 | 0.2743 | 0.024* | |
O2'A | 0.1348 (5) | 0.89551 (19) | 0.20231 (5) | 0.0268 (5) | |
H2'C | 0.0649 | 0.8906 | 0.2232 | 0.032* | |
O3'A | 0.3048 (5) | 0.8172 (2) | 0.13806 (5) | 0.0275 (5) | |
H3'C | 0.3621 | 0.8396 | 0.1176 | 0.033* | |
O4'A | 0.6800 (5) | 0.67721 (18) | 0.20637 (5) | 0.0234 (4) | |
C1'A | 0.4303 (6) | 0.7265 (2) | 0.22045 (6) | 0.0181 (5) | |
H1'A | 0.2675 | 0.6773 | 0.2128 | 0.022* | |
C2'A | 0.4083 (6) | 0.8491 (2) | 0.20282 (7) | 0.0200 (5) | |
H2'A | 0.5344 | 0.9049 | 0.2159 | 0.024* | |
C3'A | 0.5261 (6) | 0.8258 (3) | 0.16392 (7) | 0.0226 (6) | |
H3'A | 0.6590 | 0.8895 | 0.1568 | 0.027* | |
C4'A | 0.6814 (7) | 0.7076 (3) | 0.16793 (7) | 0.0270 (6) | |
H4'A | 0.5866 | 0.6457 | 0.1536 | 0.032* | |
H4'B | 0.8755 | 0.7153 | 0.1590 | 0.032* | |
N1B | −0.1972 (5) | 1.1535 (2) | 0.08248 (6) | 0.0203 (5) | |
N3B | −0.0859 (5) | 1.1228 (2) | 0.01876 (6) | 0.0186 (5) | |
N6B | 0.0035 (6) | 1.0481 (2) | 0.12980 (6) | 0.0232 (5) | |
H6C | −0.1046 | 1.0864 | 0.1451 | 0.028* | |
H6D | 0.1215 | 0.9950 | 0.1380 | 0.028* | |
N7B | 0.3554 (5) | 0.9253 (2) | 0.06939 (6) | 0.0203 (5) | |
N9B | 0.2769 (5) | 0.97274 (19) | 0.01061 (5) | 0.0170 (4) | |
C2B | −0.2219 (6) | 1.1742 (2) | 0.04678 (7) | 0.0195 (5) | |
H2B | −0.3531 | 1.2331 | 0.0402 | 0.023* | |
C4B | 0.0994 (6) | 1.0428 (2) | 0.03109 (6) | 0.0166 (5) | |
C5B | 0.1502 (6) | 1.0126 (2) | 0.06722 (6) | 0.0180 (5) | |
C6B | −0.0115 (6) | 1.0705 (2) | 0.09414 (6) | 0.0185 (5) | |
C8B | 0.4222 (6) | 0.9048 (2) | 0.03529 (7) | 0.0202 (5) | |
H8B | 0.5581 | 0.8483 | 0.0283 | 0.024* | |
O2'B | 0.6512 (4) | 1.10071 (16) | −0.04909 (5) | 0.0209 (4) | |
H2'D | 0.7179 | 1.1226 | −0.0291 | 0.025* | |
O3'B | 0.3248 (5) | 0.99703 (18) | −0.10416 (5) | 0.0251 (4) | |
H3'D | 0.4076 | 1.0240 | −0.1225 | 0.030* | |
O4'B | 0.2011 (5) | 0.84730 (17) | −0.03896 (5) | 0.0218 (4) | |
C1'B | 0.2836 (5) | 0.9642 (2) | −0.02894 (6) | 0.0158 (5) | |
H1'B | 0.1487 | 1.0220 | −0.0395 | 0.019* | |
C2'B | 0.5698 (6) | 0.9815 (2) | −0.04667 (6) | 0.0172 (5) | |
H2'B | 0.7145 | 0.9352 | −0.0333 | 0.021* | |
C3'B | 0.5114 (6) | 0.9247 (2) | −0.08394 (7) | 0.0206 (5) | |
H3'B | 0.6863 | 0.9064 | −0.0976 | 0.025* | |
C4'B | 0.3565 (7) | 0.8137 (3) | −0.07176 (7) | 0.0251 (6) | |
H4'C | 0.2274 | 0.7865 | −0.0910 | 0.030* | |
H4'D | 0.4902 | 0.7497 | −0.0663 | 0.030* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1A | 0.0242 (12) | 0.0246 (12) | 0.0175 (10) | −0.0026 (10) | 0.0007 (9) | −0.0020 (9) |
N3A | 0.0233 (11) | 0.0213 (11) | 0.0161 (9) | −0.0014 (10) | 0.0004 (9) | 0.0001 (8) |
N6A | 0.0284 (13) | 0.0264 (12) | 0.0141 (10) | −0.0045 (11) | 0.0000 (9) | −0.0023 (8) |
N7A | 0.0241 (11) | 0.0224 (11) | 0.0161 (10) | −0.0020 (11) | 0.0010 (9) | 0.0014 (8) |
N9A | 0.0217 (11) | 0.0220 (11) | 0.0127 (10) | −0.0020 (10) | −0.0011 (9) | 0.0008 (8) |
C2A | 0.0242 (13) | 0.0214 (13) | 0.0201 (12) | −0.0022 (12) | −0.0004 (11) | −0.0013 (10) |
C4A | 0.0206 (12) | 0.0203 (13) | 0.0132 (10) | 0.0007 (11) | −0.0002 (10) | −0.0010 (9) |
C5A | 0.0214 (12) | 0.0218 (13) | 0.0161 (11) | 0.0009 (12) | 0.0004 (10) | 0.0004 (9) |
C6A | 0.0203 (12) | 0.0191 (12) | 0.0160 (11) | 0.0030 (12) | 0.0007 (10) | −0.0016 (9) |
C8A | 0.0228 (12) | 0.0202 (13) | 0.0178 (11) | −0.0037 (12) | 0.0003 (10) | 0.0009 (9) |
O2'A | 0.0274 (11) | 0.0335 (11) | 0.0194 (9) | 0.0076 (10) | 0.0024 (8) | 0.0024 (8) |
O3'A | 0.0278 (10) | 0.0411 (12) | 0.0138 (8) | 0.0021 (11) | −0.0034 (8) | 0.0047 (8) |
O4'A | 0.0286 (10) | 0.0282 (10) | 0.0132 (8) | 0.0069 (10) | 0.0020 (8) | 0.0003 (7) |
C1'A | 0.0218 (12) | 0.0195 (12) | 0.0130 (11) | −0.0001 (11) | 0.0013 (10) | −0.0006 (9) |
C2'A | 0.0208 (13) | 0.0245 (13) | 0.0147 (11) | 0.0007 (11) | −0.0018 (10) | 0.0014 (10) |
C3'A | 0.0218 (13) | 0.0316 (15) | 0.0144 (11) | −0.0022 (12) | 0.0002 (10) | 0.0022 (10) |
C4'A | 0.0298 (14) | 0.0379 (17) | 0.0132 (11) | 0.0053 (14) | 0.0004 (12) | −0.0010 (11) |
N1B | 0.0247 (11) | 0.0186 (11) | 0.0176 (10) | 0.0018 (10) | 0.0010 (9) | −0.0013 (8) |
N3B | 0.0213 (11) | 0.0198 (11) | 0.0146 (9) | 0.0010 (10) | −0.0007 (9) | −0.0010 (8) |
N6B | 0.0302 (13) | 0.0246 (12) | 0.0147 (10) | 0.0061 (11) | 0.0021 (9) | 0.0006 (9) |
N7B | 0.0218 (11) | 0.0219 (11) | 0.0174 (10) | 0.0024 (10) | 0.0012 (9) | 0.0030 (8) |
N9B | 0.0181 (10) | 0.0188 (11) | 0.0140 (9) | 0.0021 (9) | 0.0014 (8) | 0.0019 (8) |
C2B | 0.0207 (12) | 0.0188 (12) | 0.0190 (11) | 0.0021 (11) | 0.0016 (10) | −0.0016 (10) |
C4B | 0.0194 (12) | 0.0172 (11) | 0.0133 (10) | −0.0025 (10) | 0.0013 (9) | −0.0002 (9) |
C5B | 0.0212 (12) | 0.0187 (12) | 0.0141 (10) | 0.0010 (11) | 0.0002 (10) | 0.0006 (9) |
C6B | 0.0209 (13) | 0.0186 (12) | 0.0159 (11) | −0.0017 (11) | 0.0014 (10) | −0.0013 (9) |
C8B | 0.0224 (12) | 0.0220 (13) | 0.0164 (11) | 0.0028 (12) | 0.0000 (10) | 0.0034 (10) |
O2'B | 0.0262 (10) | 0.0210 (9) | 0.0156 (8) | −0.0043 (9) | −0.0015 (7) | 0.0009 (7) |
O3'B | 0.0278 (10) | 0.0344 (11) | 0.0132 (8) | 0.0000 (10) | −0.0018 (8) | 0.0033 (8) |
O4'B | 0.0272 (10) | 0.0200 (9) | 0.0183 (8) | −0.0052 (9) | 0.0048 (8) | −0.0022 (7) |
C1'B | 0.0168 (11) | 0.0185 (12) | 0.0121 (10) | 0.0009 (10) | 0.0000 (9) | 0.0009 (9) |
C2'B | 0.0181 (11) | 0.0194 (12) | 0.0139 (10) | 0.0013 (10) | 0.0003 (9) | 0.0016 (9) |
C3'B | 0.0226 (13) | 0.0249 (14) | 0.0143 (11) | 0.0008 (12) | 0.0028 (10) | −0.0006 (10) |
C4'B | 0.0366 (16) | 0.0211 (13) | 0.0176 (11) | −0.0024 (13) | 0.0069 (12) | −0.0036 (10) |
N1A—C2A | 1.351 (3) | N1B—C2B | 1.340 (3) |
N1A—C6A | 1.369 (4) | N1B—C6B | 1.366 (4) |
N3A—C2A | 1.343 (3) | N3B—C4B | 1.350 (3) |
N3A—C4A | 1.361 (4) | N3B—C2B | 1.352 (3) |
N6A—C6A | 1.330 (3) | N6B—C6B | 1.338 (3) |
N6A—H6A | 0.8800 | N6B—H6C | 0.8800 |
N6A—H6B | 0.8800 | N6B—H6D | 0.8800 |
N7A—C8A | 1.317 (3) | N7B—C8B | 1.315 (3) |
N7A—C5A | 1.388 (4) | N7B—C5B | 1.400 (4) |
N9A—C8A | 1.381 (3) | N9B—C8B | 1.381 (3) |
N9A—C4A | 1.392 (3) | N9B—C4B | 1.388 (3) |
N9A—C1'A | 1.455 (3) | N9B—C1'B | 1.459 (3) |
C2A—H2A | 0.9500 | C2B—H2B | 0.9500 |
C4A—C5A | 1.390 (3) | C4B—C5B | 1.394 (3) |
C5A—C6A | 1.424 (4) | C5B—C6B | 1.420 (4) |
C8A—H8A | 0.9500 | C8B—H8B | 0.9500 |
O2'A—C2'A | 1.413 (3) | O2'B—C2'B | 1.413 (3) |
O2'A—H2'C | 0.8400 | O2'B—H2'D | 0.8400 |
O3'A—C3'A | 1.428 (3) | O3'B—C3'B | 1.425 (3) |
O3'A—H3'C | 0.8400 | O3'B—H3'D | 0.8400 |
O4'A—C1'A | 1.420 (3) | O4'B—C1'B | 1.435 (3) |
O4'A—C4'A | 1.456 (3) | O4'B—C4'B | 1.469 (3) |
C1'A—C2'A | 1.540 (4) | C1'B—C2'B | 1.531 (4) |
C1'A—H1'A | 1.0000 | C1'B—H1'B | 1.0000 |
C2'A—C3'A | 1.561 (4) | C2'B—C3'B | 1.542 (3) |
C2'A—H2'A | 1.0000 | C2'B—H2'B | 1.0000 |
C3'A—C4'A | 1.542 (4) | C3'B—C4'B | 1.530 (4) |
C3'A—H3'A | 1.0000 | C3'B—H3'B | 1.0000 |
C4'A—H4'A | 0.9900 | C4'B—H4'C | 0.9900 |
C4'A—H4'B | 0.9900 | C4'B—H4'D | 0.9900 |
C2A—N1A—C6A | 119.0 (2) | C2B—N1B—C6B | 119.1 (2) |
C2A—N3A—C4A | 110.9 (2) | C4B—N3B—C2B | 110.6 (2) |
C6A—N6A—H6A | 120.0 | C6B—N6B—H6C | 120.0 |
C6A—N6A—H6B | 120.0 | C6B—N6B—H6D | 120.0 |
H6A—N6A—H6B | 120.0 | H6C—N6B—H6D | 120.0 |
C8A—N7A—C5A | 103.9 (2) | C8B—N7B—C5B | 104.0 (2) |
C8A—N9A—C4A | 105.9 (2) | C8B—N9B—C4B | 105.9 (2) |
C8A—N9A—C1'A | 124.6 (2) | C8B—N9B—C1'B | 127.4 (2) |
C4A—N9A—C1'A | 129.5 (2) | C4B—N9B—C1'B | 126.4 (2) |
N3A—C2A—N1A | 129.0 (3) | N1B—C2B—N3B | 129.0 (3) |
N3A—C2A—H2A | 115.5 | N1B—C2B—H2B | 115.5 |
N1A—C2A—H2A | 115.5 | N3B—C2B—H2B | 115.5 |
N3A—C4A—C5A | 126.5 (2) | N3B—C4B—N9B | 127.4 (2) |
N3A—C4A—N9A | 128.5 (2) | N3B—C4B—C5B | 127.0 (2) |
C5A—C4A—N9A | 105.0 (2) | N9B—C4B—C5B | 105.6 (2) |
N7A—C5A—C4A | 111.5 (2) | C4B—C5B—N7B | 110.6 (2) |
N7A—C5A—C6A | 131.0 (2) | C4B—C5B—C6B | 117.1 (2) |
C4A—C5A—C6A | 117.5 (3) | N7B—C5B—C6B | 132.3 (2) |
N6A—C6A—N1A | 120.0 (2) | N6B—C6B—N1B | 118.3 (2) |
N6A—C6A—C5A | 123.1 (3) | N6B—C6B—C5B | 124.5 (3) |
N1A—C6A—C5A | 116.9 (2) | N1B—C6B—C5B | 117.2 (2) |
N7A—C8A—N9A | 113.7 (2) | N7B—C8B—N9B | 113.9 (2) |
N7A—C8A—H8A | 123.2 | N7B—C8B—H8B | 123.0 |
N9A—C8A—H8A | 123.2 | N9B—C8B—H8B | 123.0 |
C2'A—O2'A—H2'C | 109.5 | C2'B—O2'B—H2'D | 109.5 |
C3'A—O3'A—H3'C | 109.5 | C3'B—O3'B—H3'D | 109.5 |
C1'A—O4'A—C4'A | 105.3 (2) | C1'B—O4'B—C4'B | 108.2 (2) |
O4'A—C1'A—N9A | 108.2 (2) | O4'B—C1'B—N9B | 108.15 (19) |
O4'A—C1'A—C2'A | 105.1 (2) | O4'B—C1'B—C2'B | 104.9 (2) |
N9A—C1'A—C2'A | 114.7 (2) | N9B—C1'B—C2'B | 115.8 (2) |
O4'A—C1'A—H1'A | 109.6 | O4'B—C1'B—H1'B | 109.3 |
N9A—C1'A—H1'A | 109.6 | N9B—C1'B—H1'B | 109.3 |
C2'A—C1'A—H1'A | 109.6 | C2'B—C1'B—H1'B | 109.3 |
O2'A—C2'A—C1'A | 114.0 (2) | O2'B—C2'B—C1'B | 113.4 (2) |
O2'A—C2'A—C3'A | 112.7 (2) | O2'B—C2'B—C3'B | 113.3 (2) |
C1'A—C2'A—C3'A | 102.0 (2) | C1'B—C2'B—C3'B | 99.3 (2) |
O2'A—C2'A—H2'A | 109.3 | O2'B—C2'B—H2'B | 110.1 |
C1'A—C2'A—H2'A | 109.3 | C1'B—C2'B—H2'B | 110.1 |
C3'A—C2'A—H2'A | 109.3 | C3'B—C2'B—H2'B | 110.1 |
O3'A—C3'A—C4'A | 111.3 (2) | O3'B—C3'B—C4'B | 108.9 (2) |
O3'A—C3'A—C2'A | 110.7 (2) | O3'B—C3'B—C2'B | 109.7 (2) |
C4'A—C3'A—C2'A | 103.6 (2) | C4'B—C3'B—C2'B | 99.95 (19) |
O3'A—C3'A—H3'A | 110.4 | O3'B—C3'B—H3'B | 112.5 |
C4'A—C3'A—H3'A | 110.4 | C4'B—C3'B—H3'B | 112.5 |
C2'A—C3'A—H3'A | 110.4 | C2'B—C3'B—H3'B | 112.5 |
O4'A—C4'A—C3'A | 107.3 (2) | O4'B—C4'B—C3'B | 105.8 (2) |
O4'A—C4'A—H4'A | 110.3 | O4'B—C4'B—H4'C | 110.6 |
C3'A—C4'A—H4'A | 110.3 | C3'B—C4'B—H4'C | 110.6 |
O4'A—C4'A—H4'B | 110.3 | O4'B—C4'B—H4'D | 110.6 |
C3'A—C4'A—H4'B | 110.3 | C3'B—C4'B—H4'D | 110.6 |
H4'A—C4'A—H4'B | 108.5 | H4'C—C4'B—H4'D | 108.7 |
C4A—N3A—C2A—N1A | −0.4 (4) | C6B—N1B—C2B—N3B | 0.4 (4) |
C6A—N1A—C2A—N3A | 1.6 (4) | C4B—N3B—C2B—N1B | −1.5 (4) |
C2A—N3A—C4A—C5A | −2.2 (4) | C2B—N3B—C4B—N9B | −179.9 (3) |
C2A—N3A—C4A—N9A | 178.8 (3) | C2B—N3B—C4B—C5B | 0.7 (4) |
C8A—N9A—C4A—N3A | 178.3 (3) | C8B—N9B—C4B—N3B | −179.2 (3) |
C1'A—N9A—C4A—N3A | −2.8 (5) | C1'B—N9B—C4B—N3B | −5.4 (4) |
C8A—N9A—C4A—C5A | −0.9 (3) | C8B—N9B—C4B—C5B | 0.2 (3) |
C1'A—N9A—C4A—C5A | 178.0 (3) | C1'B—N9B—C4B—C5B | 174.0 (2) |
C8A—N7A—C5A—C4A | 0.0 (3) | N3B—C4B—C5B—N7B | 179.4 (3) |
C8A—N7A—C5A—C6A | 177.5 (3) | N9B—C4B—C5B—N7B | 0.0 (3) |
N3A—C4A—C5A—N7A | −178.6 (3) | N3B—C4B—C5B—C6B | 0.9 (4) |
N9A—C4A—C5A—N7A | 0.6 (3) | N9B—C4B—C5B—C6B | −178.6 (2) |
N3A—C4A—C5A—C6A | 3.5 (4) | C8B—N7B—C5B—C4B | −0.2 (3) |
N9A—C4A—C5A—C6A | −177.3 (2) | C8B—N7B—C5B—C6B | 178.1 (3) |
C2A—N1A—C6A—N6A | 179.0 (3) | C2B—N1B—C6B—N6B | −177.7 (3) |
C2A—N1A—C6A—C5A | −0.2 (4) | C2B—N1B—C6B—C5B | 1.4 (4) |
N7A—C5A—C6A—N6A | 1.3 (5) | C4B—C5B—C6B—N6B | 177.1 (3) |
C4A—C5A—C6A—N6A | 178.8 (3) | N7B—C5B—C6B—N6B | −1.0 (5) |
N7A—C5A—C6A—N1A | −179.4 (3) | C4B—C5B—C6B—N1B | −2.0 (4) |
C4A—C5A—C6A—N1A | −2.0 (4) | N7B—C5B—C6B—N1B | 179.9 (3) |
C5A—N7A—C8A—N9A | −0.6 (3) | C5B—N7B—C8B—N9B | 0.3 (3) |
C4A—N9A—C8A—N7A | 1.0 (3) | C4B—N9B—C8B—N7B | −0.3 (3) |
C1'A—N9A—C8A—N7A | −178.0 (2) | C1'B—N9B—C8B—N7B | −174.1 (2) |
C4'A—O4'A—C1'A—N9A | −164.9 (2) | C4'B—O4'B—C1'B—N9B | −146.3 (2) |
C4'A—O4'A—C1'A—C2'A | −41.9 (3) | C4'B—O4'B—C1'B—C2'B | −22.1 (3) |
C8A—N9A—C1'A—O4'A | −112.9 (3) | C8B—N9B—C1'B—O4'B | 58.0 (3) |
C4A—N9A—C1'A—O4'A | 68.4 (3) | C4B—N9B—C1'B—O4'B | −114.5 (3) |
C8A—N9A—C1'A—C2'A | 130.2 (3) | C8B—N9B—C1'B—C2'B | −59.3 (3) |
C4A—N9A—C1'A—C2'A | −48.5 (4) | C4B—N9B—C1'B—C2'B | 128.2 (3) |
O4'A—C1'A—C2'A—O2'A | 158.2 (2) | O4'B—C1'B—C2'B—O2'B | 162.60 (19) |
N9A—C1'A—C2'A—O2'A | −83.2 (3) | N9B—C1'B—C2'B—O2'B | −78.3 (3) |
O4'A—C1'A—C2'A—C3'A | 36.3 (3) | O4'B—C1'B—C2'B—C3'B | 42.0 (2) |
N9A—C1'A—C2'A—C3'A | 155.0 (2) | N9B—C1'B—C2'B—C3'B | 161.2 (2) |
O2'A—C2'A—C3'A—O3'A | −20.3 (3) | O2'B—C2'B—C3'B—O3'B | −50.8 (3) |
C1'A—C2'A—C3'A—O3'A | 102.4 (3) | C1'B—C2'B—C3'B—O3'B | 69.8 (2) |
O2'A—C2'A—C3'A—C4'A | −139.7 (2) | O2'B—C2'B—C3'B—C4'B | −165.1 (2) |
C1'A—C2'A—C3'A—C4'A | −17.0 (3) | C1'B—C2'B—C3'B—C4'B | −44.5 (2) |
C1'A—O4'A—C4'A—C3'A | 30.3 (3) | C1'B—O4'B—C4'B—C3'B | −7.3 (3) |
O3'A—C3'A—C4'A—O4'A | −125.7 (2) | O3'B—C3'B—C4'B—O4'B | −81.9 (3) |
C2'A—C3'A—C4'A—O4'A | −6.7 (3) | C2'B—C3'B—C4'B—O4'B | 33.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N6A—H6A···O2′Bi | 0.88 | 2.14 | 2.988 (3) | 162 |
N6A—H6B···N1Bii | 0.88 | 2.11 | 2.957 (4) | 161 |
O2′A—H2′C···N3Aiii | 0.84 | 2.17 | 2.999 (3) | 171 |
O2′B—H2′D···N3Biv | 0.84 | 2.00 | 2.807 (3) | 162 |
O3′A—H3′C···N7B | 0.84 | 2.02 | 2.820 (3) | 158 |
N6B—H6C···N7Av | 0.88 | 2.05 | 2.934 (3) | 177 |
N6B—H6D···O3′A | 0.88 | 2.20 | 3.011 (4) | 152 |
O3′B—H3′D···N1Avi | 0.84 | 1.96 | 2.798 (3) | 175 |
Symmetry codes: (i) −x+3/2, −y+2, z+1/2; (ii) −x, y−1/2, −z+1/2; (iii) x−1, y, z; (iv) x+1, y, z; (v) −x, y+1/2, −z+1/2; (vi) −x+3/2, −y+2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C9H11N5O3 |
Mr | 237.23 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 150 |
a, b, c (Å) | 4.793 (3), 11.365 (7), 36.79 (2) |
V (Å3) | 2004 (2) |
Z | 8 |
Radiation type | Synchrotron, λ = 0.77490 Å |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.12 × 0.04 × 0.02 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan [SADABS (Version 2007/4; Sheldrick, 2008)] |
Tmin, Tmax | 0.986, 0.998 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23772, 2910, 2556 |
Rint | 0.112 |
(sin θ/λ)max (Å−1) | 0.667 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.126, 1.07 |
No. of reflections | 2910 |
No. of parameters | 307 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.34, −0.31 |
Absolute structure | (Flack, 1983), with how many Friedel pairs? |
Absolute structure parameter | 1.2 (11) |
Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007, SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008) and POV-RAY (Cason, 2003), enCIFer (Allen et al., 2004) and publCIF (Westrip, 2010).
D—H···A | D—H | H···A | D···A | D—H···A |
N6A—H6A···O2'Bi | 0.88 | 2.14 | 2.988 (3) | 162.1 |
N6A—H6B···N1Bii | 0.88 | 2.11 | 2.957 (4) | 161.3 |
O2'A—H2'C···N3Aiii | 0.84 | 2.17 | 2.999 (3) | 171.3 |
O2'B—H2'D···N3Biv | 0.84 | 2.00 | 2.807 (3) | 162.3 |
O3'A—H3'C···N7B | 0.84 | 2.02 | 2.820 (3) | 157.7 |
N6B—H6C···N7Av | 0.88 | 2.05 | 2.934 (3) | 176.7 |
N6B—H6D···O3'A | 0.88 | 2.20 | 3.011 (4) | 152.3 |
O3'B—H3'D···N1Avi | 0.84 | 1.96 | 2.798 (3) | 174.6 |
Symmetry codes: (i) −x+3/2, −y+2, z+1/2; (ii) −x, y−1/2, −z+1/2; (iii) x−1, y, z; (iv) x+1, y, z; (v) −x, y+1/2, −z+1/2; (vi) −x+3/2, −y+2, z−1/2. |
(IA) | (IB) | (II)* | (III) | (IV)* | |
Bond lengths (Å) | |||||
C1'-C2' | 1.540 (4) | 1.531 (4) | 1.530 | 1.548 (3) | 1.544 |
C2'-C3' | 1.561 (4) | 1.542 (3) | 1.528 | 1.528 (3) | 1.547 |
C3'-C4' | 1.542 (4) | 1.530 (4) | 1.522 | 1.512 (3) | 1.546 |
C1'-N1' | 1.475 (2) | ||||
C1'-N9' | 1.455 (3) | 1.459 (3) | 1.467 | 1.465 | |
C1'-O4' | 1.420 (3) | 1.435 (3) | 1.411 | 1.414 (3) | 1.445 |
C4'-O4' | 1.456 (3) | 1.469 (3) | 1.450 | 1.452 (3) | 1.445 |
C2'-O2' | 1.413 (3) | 1.413 (3) | 1.411 | 1.414 (3) | 1.429 |
C3'-O3' | 1.428 (3) | 1.425 (3) | 1.418 | 1.422 (2) | 1.430 |
C2-O2/C4-O4 | 1.234 (3) | ||||
C4-N4 | 1.335 (3) | ||||
C6-N6 | 1.330 (3) | 1.338 (3) | 1.332 | 1.384 | |
Bond angles (°) | |||||
C4'-O4'-C1' | 105.3 (2) | 108.2 (2) | 110.48 | 108.24 (14) | 105.3 |
O4'-C1'-N1 | 110.6 | ||||
O4'-C1'-N9 | 108.2 (2) | 108.15 (19) | 109.31 | 110.3 | |
O4'-C1'-C2' | 105.1 (2) | 104.9 (2) | 107.29 | 107.04 (16) | 104.9 |
C1'-C2'-C3' | 102.0 (2) | 99.3 (2) | 101.36 | 100.67 (15) | 104.0 |
C2'-C3'-C4' | 103.6 (2) | 99.95 (19) | 102.72 | 99.78 (15) | 104.0 |
C3'-C4'-O4' | 107.3 (2) | 105.8 (2) | 104.66 | 104.69 (18) | 104.8 |
C1'-N1-C2 | 121.52 (18) | ||||
C1'-N1-C6 | 117.92 (17) | ||||
C1'-N9-C4 | 129.5 (2) | 126.4 (2) | 124.26 | 126.2 | |
C1'-N9-C8 | 124.6 (2) | 127.4 (2) | 130.01 | 126.3 | |
Torsion angles (°) | |||||
O4'-C1'-N1-C2 | 60.8 (2) (syn, +sc) | ||||
O4'-C1'-N1-C6 | -120.29 (18) | ||||
O4'-C1'-N9-C4 | 68.4 (3) (syn, +sc) | -114.5 (3) (anti, -ac) | -171.38 (anti, ap) | -158.0 (anti, -ac) | |
O4'-C1'-N9-C8 | -112.9 (3) | 58.0 (3) | 9.92 | 22.0 | |
C2'-C1'-N1-C2 | -60.6 (3) | ||||
C2'-C1'-N1-C6 | 118.28 (19) | ||||
C2'-C1'-N9-C4 | -48.5 (4) | 128.2 (3) | 70.11 | 86.5 | |
C2'-C1'-N9-C8 | 130.2 (3) | -59.3 (3) | -108.59 | -93.4 | |
C1'-C2'-C3'-C4' | -17.0 (3) | -44.5 (2) | 35.76 | -40.83 (18) | 0.0 |
C2'-C3'-C4'-O4' | -6.7 (3) | 33.0 (3) | -32.48 | 42.1 | -24.0 |
C3'-C4'-O4'-C1' | 30.3 (3) | -7.3 (3) | 15.92 | -26.19 (19) | 40.5 |
C4'-O4'-C1'-C2' | -41.9 (3) | -22.1 (3) | 7.44 | -0.97 (18) | -40.4 |
O4'-C1'-C2'-C3' | 36.3 (3) | 42.0 (2) | -27.30 | 27.00 (18) | 23.8 |
N1-C2-N3-C4 | -4.6 (3) | ||||
N1-C6-C5-C4 | -2.9 (3) | ||||
N9-C4-N3-C2 | 178.8 (3) | -179.9 (3) | 178.44 | 180.0 | |
N9-C8-N7-C5 | -0.6 (3) | 0.3 (3) | 0.41 | -0.3 | |
furanose | |||||
P (°) | 114.4 | 169.8 | 7.1 | 197.8 | 89.7 |
E1, C1'-exo | 2E, C2'-endo | 3E, C3'-endo | E3, C3'-exo | OE, O1'-endo | |
τm (°) | 42 | 46 | 37 | 44 | 42 |
* Standard uncertainties unavailable. |
Subscribe to Acta Crystallographica Section C: Structural Chemistry
The full text of this article is available to subscribers to the journal.
- Information on subscribing
- Sample issue
- Purchase subscription
- Reduced-price subscriptions
- If you have already subscribed, you may need to register
In a recent report, the crystal structure of the ribonucleoside derivative 1-(β-D-erythrofuranosyl)cytidine (β-erythrocytidine), (III), was determined and its structural parameters compared with those of β-cytidine, β-erythrouridine and β-uridine (Kline et al., 2007). This prior work is extended in the present investigation to the title compound, (I), which lacks the exocyclic C5' hydroxymethyl group found in β-adenosine, (II).
Solution NMR studies of (I) and (II) have revealed significant differences in the furanose conformation. The 3JH1,H2, 3JH2,H3 and 3JH3,H4S spin-couplings in (I) are 6.7, 4.6 and 1.7 Hz, respectively, whereas the corresponding values in (II) are 6.2, 5.3 and 3.3 Hz, respectively (Kline & Serianni, 1992). Pseudorotational analysis of these NMR couplings shows that (I) greatly prefers a south conformation (~95%) (for definitions, see Fig. 1), with P = 180.1° and τm = 40°. For (II), a greater proportion of the north form was found (~23%; P = 19.1° and τm = 38°), and the predominant south form (~77%) had P = 153.3° and τm = 38°.
The crystal structure of (I) (Fig. 2) contains two different molecular conformations in the unit cell, denoted (IA) and (IB). In (IA), the furanose conformation is OT1-E1 (C1'-exo, east), with pseudorotational parameters P = 114.4° and τm = 42° (Table 1). This conformation is best described as an east form in the pseudorotational itinerary (Fig. 1). For (IB), P = 170.1° and τm = 46°, consistent with an 2E-2T3 (C2'-endo, south) conformation (Fig. 1). The latter geometry, which is observed in the common biologically relevant nucleosides/tides, is structurally similar to that observed in the crystal structure of β-erythrocytidine, (III) (P = 197.8° and τm = 44°) (Fig. 1). In comparison, β-adenosine, (II), crystallizes in a 3T2-3E (C3'-endo, north; P = 7.1° and τm = 37°) conformation (Fig. 1). The degree of ring puckering in erythronucleosides (I) and (III), embodied in the τm parameter (44±2°), is significantly greater than that observed in (II) (37°), suggesting that removal of the bulky CH2OH substituent allows greater furanose ring deformation from planarity. This trend also emerged from prior NMR J-coupling analysis (Kline & Serianni, 1992), although the difference is smaller.
The furanose ring conformation influences the conformation about the N-glycoside linkage. The adenine base assumes an anti (-ac) conformation [O4'—C1'—N9—C4 = -114.5 (3)°] in (IB), having the furanose ring in a south (2E) conformation (Table 1). Shifting the furanose conformation towards the east forms, as observed in (IA), causes a radical change in the N-glycoside conformation to the syn (+sc) conformation [O4'—C1'—N9—C4 = 68.4 (3)°]; the quasi-equatorial C1'—N9 bond in the E1 furanose structure readily accommodates this conformation. It should be noted that a similar N-glycoside conformation is observed in (III) (syn, +sc), where the furanose conformation is E3, suggesting that syn conformations can be accommodated in a wider range of furanose conformations in erythronucleosides than in ribo- and 2'-deoxyribonucleosides, in which base interactions with the bulky –CH2OH substituent at C4' limit access to the more sterically demanding syn state. In (II), a north (3E) furanose conformation correlates with an anti (ap) N-glycoside conformation [O4'—C1'—N9—C4 = -171.4°), as expected (Table 1). While the preferred N-glycoside conformation in (I) in solution is currently unknown, these results, and those previously reported (Kline et al., 2007), suggest that an equilibrium mixture of both syn and anti geometries might be expected.
Prior studies (Westhof & Sundaralingam, 1983) have demonstrated the interdependencies between P, τm and endocyclic torsion angles in furanose rings. We tested these correlations using data from (IA), (IB) and (III), given that their constituent furanose ring conformations have P values in the range 114–198° with very similar τm values. The experimentally observed trends in the C4'—O4'—C1', O4'—C1'—C2', C2'—C3'—C4' and C3'—C4'—O4' bond angles are well predicted using the Westhof–Sundaralingam correlations. For example, the C2'—C3'—C4' and C3'—C4'—O4' bond angles are smallest in (III) and largest in (IA) (Table 1), consistent with the predicted trend. Likewise, the small value of the C4'—O4'—C1' bond angle in (IA) relative to those found in (IB) and (III) (Table 1) fulfills predictions based on the observed differences in ring conformation.
A similar treatment of bond lengths in (I)–(III) is complicated by differences in both furanose and N-glycoside conformations. Moderate differences of 0.018–0.024 Å are observed for bonds C1'—C2', C1'—O4' and C4'—O4', and larger differences of ~0.032 Å are found for bonds C2'—C3' and C3'—C4' (Table 1). The last two bonds are significantly extended in (IA), presumably due to its unique furanose conformation and/or to the syn geometry of its N-glycosidic linkage.
The crystal structure, determined to a resolution of 2.0 Å, of a co-crystal of (I) with the enzyme 5'-fluorodeoxyadenosine synthase, (IV), from Streptomyces cattleya (Cobb et al., 2006), shows that the enzyme binds to (I) in a furanose conformation (OE, east; P = 90° and τm = 42°) similar to that observed in (IA), but in an N-glycoside conformation (anti, -ac) similar to that observed in (IB) (Table 1).
The furanose rings of (IA) and (IB) display different intermolecular hydrogen-bonding motifs (see Table 2). In (IA), atom O2'A serves as a donor to atom N3A of an adjacent (IA) unit. Atom O3'A of (IA) serves as a donor to atom N7B of (IB), while atom O3'A serves as an acceptor to amine atom N6B of (IB); in both cases, the (IB) molecule is that found in the same unit cell. Atom O4'A is not involved in hydrogen bonding, and atom O2'A does not serve as an acceptor in (IA). In (IB), atom O2'B serves as a donor to atom N3B of an adjacent (IB) unit, and atom O2'B serves as an acceptor to amine atom N6A of an adjacent (IA) unit. Atom O3'B serves as a donor to atom N1A of the same adjacent (IA) unit. Atom O4'B is not involved in hydrogen bonding, and atom O3'B does not serve as an acceptor in (IB). No intramolecular hydrogen bonds are found in (IA) or (IB).
Intermolecular base–base (non-Watson–Crick) hydrogen bonding is also present in (I). The amine atom N6A (donor) and atom N7A (acceptor) of (IA) are hydrogen-bonded to atom N1B (acceptor) and amine atom N6B (donor), respectively, of an adjacent (IB) molecule (Fig. 3, Table 2). No base–base hydrogen bonding is observed in the crystal structures of (II) and (III).
The crystal packing of (I) consists of units of the base–base hydrogen-bonded pairs of (IA) and (IB) described above. These base–base hydrogen-bonded pairs extend the structure through contacts from the hydroxyl group to nearby adenosine N atoms of other nearby base–base pairs. The adenosine amine N atoms (N6A and N6B) not only form the base–base pair unit, but also form hydrogen bonds to nearby hydroxyl groups (Fig. 4). The overall packing is a three-dimensional hydrogen-bonded network of pairs of (IA) and (IB) molecules. The layers of adenosine moieties adopt a herringbone arrangement within the lattice.