Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104032123/sk1785sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270104032123/sk1785Isup2.hkl |
CCDC reference: 264796
Compound (I) was prepared according to the method described by Seela & Becher (2001). UV (MeOH): λmax 228 (30900), 260 (8100), 262 (8200), 278 (7800) with pKa of 3.3 at 242 nm. Suitable crystals were grown from a solution in methanol. For the diffraction experiment, a single-crystal was fixed at the top of a Lindemann capillary with epoxy resin.
All H atoms were initially found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, H atoms bonded to C atoms were placed in geometrically idealized positions (C—H = 0.97 and 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 difference map positions, then geometrically idealized 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. Treatment of N-bound H atoms?
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 (Sheldrick, 1997) and PLATON (Spek, 1999).
C10H13BrN6O3 | F(000) = 696 |
Mr = 345.17 | Dx = 1.791 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 42 reflections |
a = 7.5939 (10) Å | θ = 5.0–12.5° |
b = 9.2822 (18) Å | µ = 3.23 mm−1 |
c = 18.164 (2) Å | T = 293 K |
V = 1280.3 (3) Å3 | Transparent plate, light brown |
Z = 4 | 0.32 × 0.28 × 0.14 mm |
Bruker P4 diffractometer | 2568 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.042 |
Graphite monochromator | θmax = 30.0°, θmin = 2.2° |
2θ/ω scans | h = −10→10 |
Absorption correction: empirical (using intensity measurements) (SHELXTL; Sheldrick,1997) | k = −13→13 |
Tmin = 0.316, Tmax = 0.519 | l = −25→25 |
4231 measured reflections | 3 standard reflections every 97 reflections |
3682 independent reflections | intensity decay: none |
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)] = 0.056 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.139 | w = 1/[σ2(Fo2) + (0.0688P)2 + 0.0128P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max = 0.001 |
3682 reflections | Δρmax = 0.44 e Å−3 |
199 parameters | Δρmin = −0.89 e Å−3 |
8 restraints | Absolute structure: Flack (1983), 1536 Friedel pairs? |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.020 (16) |
C10H13BrN6O3 | V = 1280.3 (3) Å3 |
Mr = 345.17 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 7.5939 (10) Å | µ = 3.23 mm−1 |
b = 9.2822 (18) Å | T = 293 K |
c = 18.164 (2) Å | 0.32 × 0.28 × 0.14 mm |
Bruker P4 diffractometer | 2568 reflections with I > 2σ(I) |
Absorption correction: empirical (using intensity measurements) (SHELXTL; Sheldrick,1997) | Rint = 0.042 |
Tmin = 0.316, Tmax = 0.519 | 3 standard reflections every 97 reflections |
4231 measured reflections | intensity decay: none |
3682 independent reflections |
R[F2 > 2σ(F2)] = 0.056 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.139 | Δρmax = 0.44 e Å−3 |
S = 1.07 | Δρmin = −0.89 e Å−3 |
3682 reflections | Absolute structure: Flack (1983), 1536 Friedel pairs? |
199 parameters | Absolute structure parameter: 0.020 (16) |
8 restraints |
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 | ||
N1 | 0.1137 (6) | 0.9773 (4) | 0.02381 (18) | 0.0331 (8) | |
N2 | 0.1220 (7) | 1.0731 (4) | 0.0832 (2) | 0.0385 (9) | |
C3 | 0.1229 (8) | 1.2003 (5) | 0.0532 (2) | 0.0344 (10) | |
Br3 | 0.13107 (9) | 1.36522 (5) | 0.11197 (3) | 0.05024 (19) | |
C3A | 0.1134 (7) | 1.1953 (4) | −0.0250 (2) | 0.0319 (9) | |
N4 | 0.1244 (10) | 1.4340 (4) | −0.0763 (3) | 0.0543 (13) | |
H4A | 0.116 (9) | 1.484 (6) | −0.113 (2) | 0.065* | |
H4B | 0.147 (10) | 1.483 (7) | −0.040 (2) | 0.065* | |
C4 | 0.1138 (8) | 1.2912 (5) | −0.0859 (3) | 0.0355 (10) | |
N5 | 0.1009 (5) | 1.2375 (4) | −0.1540 (2) | 0.0337 (9) | |
N6 | 0.0690 (6) | 1.0447 (5) | −0.2317 (2) | 0.0391 (10) | |
H6A | 0.051 (8) | 0.959 (2) | −0.241 (3) | 0.047* | |
H6B | 0.026 (7) | 1.091 (6) | −0.266 (2) | 0.047* | |
C6 | 0.0872 (6) | 1.0917 (5) | −0.1615 (3) | 0.0309 (10) | |
N7 | 0.0927 (5) | 0.9922 (4) | −0.1089 (2) | 0.0294 (8) | |
C7A | 0.1076 (6) | 1.0491 (4) | −0.0409 (2) | 0.0272 (9) | |
C1' | 0.1025 (6) | 0.8241 (4) | 0.0377 (2) | 0.0270 (9) | |
H1' | 0.1193 | 0.7721 | −0.0087 | 0.032* | |
C2' | 0.2376 (6) | 0.7714 (5) | 0.0933 (2) | 0.0319 (10) | |
H2'1 | 0.2823 | 0.6772 | 0.0797 | 0.038* | |
H2'2 | 0.3356 | 0.8381 | 0.0969 | 0.038* | |
C3' | 0.1370 (6) | 0.7642 (4) | 0.1656 (2) | 0.0294 (8) | |
H3'1 | 0.1427 | 0.8570 | 0.1912 | 0.035* | |
O3' | 0.1963 (5) | 0.6507 (4) | 0.21257 (18) | 0.0411 (8) | |
H3' | 0.224 (8) | 0.6834 (18) | 0.2528 (12) | 0.062* | |
C4' | −0.0522 (6) | 0.7333 (5) | 0.1399 (2) | 0.0262 (9) | |
H4' | −0.0709 | 0.6288 | 0.1385 | 0.031* | |
O4' | −0.0644 (4) | 0.7896 (4) | 0.06659 (17) | 0.0387 (8) | |
C5' | −0.1878 (6) | 0.8004 (6) | 0.1888 (3) | 0.0397 (12) | |
H5'1 | −0.1831 | 0.7542 | 0.2367 | 0.048* | |
H5'2 | −0.1589 | 0.9014 | 0.1957 | 0.048* | |
O5' | −0.3636 (5) | 0.7899 (3) | 0.16080 (18) | 0.0354 (7) | |
H5' | −0.380 (3) | 0.7079 (19) | 0.145 (3) | 0.053* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.050 (2) | 0.0267 (17) | 0.0221 (16) | 0.0028 (19) | −0.0005 (18) | −0.0001 (13) |
N2 | 0.057 (3) | 0.0312 (19) | 0.0278 (18) | 0.006 (2) | −0.006 (2) | −0.0016 (15) |
C3 | 0.044 (3) | 0.031 (2) | 0.028 (2) | 0.003 (2) | −0.003 (2) | −0.0009 (16) |
Br3 | 0.0810 (4) | 0.0313 (2) | 0.0384 (2) | 0.0058 (3) | −0.0074 (3) | −0.0074 (2) |
C3A | 0.043 (3) | 0.0255 (19) | 0.027 (2) | 0.003 (2) | −0.001 (2) | 0.0037 (16) |
N4 | 0.090 (4) | 0.027 (2) | 0.045 (3) | −0.006 (3) | −0.007 (3) | 0.0096 (18) |
C4 | 0.040 (3) | 0.029 (2) | 0.038 (2) | −0.002 (2) | −0.004 (2) | 0.0052 (17) |
N5 | 0.039 (2) | 0.0332 (18) | 0.0283 (18) | −0.0039 (18) | −0.0010 (18) | 0.0093 (15) |
N6 | 0.053 (3) | 0.038 (2) | 0.026 (2) | −0.0036 (19) | −0.0040 (18) | 0.0042 (17) |
C6 | 0.030 (2) | 0.034 (2) | 0.029 (2) | −0.0009 (17) | 0.0018 (18) | 0.0022 (17) |
N7 | 0.034 (2) | 0.0275 (16) | 0.0268 (17) | 0.0018 (14) | −0.0004 (17) | 0.0012 (15) |
C7A | 0.032 (2) | 0.0251 (18) | 0.0245 (19) | −0.0004 (19) | −0.0019 (19) | 0.0050 (15) |
C1' | 0.032 (2) | 0.0218 (17) | 0.0272 (19) | 0.0005 (17) | 0.0015 (18) | 0.0024 (14) |
C2' | 0.032 (2) | 0.029 (2) | 0.035 (3) | −0.0006 (19) | 0.0027 (18) | 0.0079 (17) |
C3' | 0.035 (2) | 0.0231 (18) | 0.030 (2) | 0.001 (2) | −0.007 (2) | 0.0017 (15) |
O3' | 0.055 (2) | 0.0349 (18) | 0.0338 (17) | 0.0072 (16) | −0.0137 (15) | 0.0061 (14) |
C4' | 0.036 (2) | 0.0213 (18) | 0.0214 (18) | 0.0006 (17) | −0.0053 (17) | −0.0021 (15) |
O4' | 0.0308 (17) | 0.057 (2) | 0.0280 (16) | −0.0078 (15) | −0.0055 (13) | 0.0124 (16) |
C5' | 0.039 (3) | 0.046 (3) | 0.033 (2) | 0.002 (2) | −0.002 (2) | −0.012 (2) |
O5' | 0.0350 (17) | 0.0335 (16) | 0.0376 (16) | 0.0008 (16) | −0.0001 (16) | −0.0087 (13) |
N1—C7A | 1.353 (5) | C1'—O4' | 1.408 (5) |
N1—N2 | 1.400 (5) | C1'—C2' | 1.520 (6) |
N1—C1' | 1.447 (5) | C1'—H1' | 0.9800 |
N2—C3 | 1.301 (6) | C2'—C3' | 1.520 (6) |
C3—C3A | 1.423 (6) | C2'—H2'1 | 0.9700 |
C3—Br3 | 1.868 (4) | C2'—H2'2 | 0.9700 |
C3A—C7A | 1.388 (6) | C3'—O3' | 1.428 (5) |
C3A—C4 | 1.420 (6) | C3'—C4' | 1.538 (6) |
N4—C4 | 1.340 (6) | C3'—H3'1 | 0.9800 |
N4—H4A | 0.82 (5) | O3'—H3' | 0.82 (3) |
N4—H4B | 0.82 (5) | C4'—O4' | 1.433 (5) |
C4—N5 | 1.337 (6) | C4'—C5' | 1.497 (6) |
N5—C6 | 1.364 (6) | C4'—H4' | 0.9800 |
N6—C6 | 1.355 (6) | C5'—O5' | 1.432 (6) |
N6—H6A | 0.824 (10) | C5'—H5'1 | 0.9700 |
N6—H6B | 0.82 (5) | C5'—H5'2 | 0.9700 |
C6—N7 | 1.331 (6) | O5'—H5' | 0.82 (2) |
N7—C7A | 1.347 (6) | ||
C7A—N1—N2 | 111.0 (3) | O4'—C1'—H1' | 109.0 |
C7A—N1—C1' | 129.4 (4) | N1—C1'—H1' | 109.0 |
N2—N1—C1' | 119.5 (3) | C2'—C1'—H1' | 109.0 |
C3—N2—N1 | 104.7 (4) | C3'—C2'—C1' | 104.4 (4) |
N2—C3—C3A | 112.9 (4) | C3'—C2'—H2'1 | 110.9 |
N2—C3—Br3 | 120.3 (3) | C1'—C2'—H2'1 | 110.9 |
C3A—C3—Br3 | 126.8 (3) | C3'—C2'—H2'2 | 110.9 |
C7A—C3A—C4 | 116.8 (4) | C1'—C2'—H2'2 | 110.9 |
C7A—C3A—C3 | 104.0 (4) | H2'1—C2'—H2'2 | 108.9 |
C4—C3A—C3 | 139.2 (4) | O3'—C3'—C2' | 112.9 (4) |
C4—N4—H4A | 117 (5) | O3'—C3'—C4' | 109.8 (3) |
C4—N4—H4B | 132 (5) | C2'—C3'—C4' | 102.5 (3) |
H4A—N4—H4B | 112 (7) | O3'—C3'—H3'1 | 110.5 |
N5—C4—N4 | 119.6 (4) | C2'—C3'—H3'1 | 110.5 |
N5—C4—C3A | 119.1 (4) | C4'—C3'—H3'1 | 110.5 |
N4—C4—C3A | 121.2 (4) | C3'—O3'—H3' | 110.0 (11) |
C4—N5—C6 | 117.9 (4) | O4'—C4'—C5' | 110.8 (4) |
C6—N6—H6A | 121 (4) | O4'—C4'—C3' | 105.9 (3) |
C6—N6—H6B | 126 (4) | C5'—C4'—C3' | 112.6 (4) |
H6A—N6—H6B | 106 (6) | O4'—C4'—H4' | 109.1 |
N7—C6—N6 | 117.1 (4) | C5'—C4'—H4' | 109.1 |
N7—C6—N5 | 127.9 (4) | C3'—C4'—H4' | 109.1 |
N6—C6—N5 | 115.0 (4) | C1'—O4'—C4' | 111.8 (3) |
C6—N7—C7A | 112.9 (4) | O5'—C5'—C4' | 113.7 (4) |
N7—C7A—N1 | 127.3 (4) | O5'—C5'—H5'1 | 108.8 |
N7—C7A—C3A | 125.2 (4) | C4'—C5'—H5'1 | 108.8 |
N1—C7A—C3A | 107.4 (4) | O5'—C5'—H5'2 | 108.8 |
O4'—C1'—N1 | 109.9 (4) | C4'—C5'—H5'2 | 108.8 |
O4'—C1'—C2' | 106.7 (3) | H5'1—C5'—H5'2 | 107.7 |
N1—C1'—C2' | 113.1 (4) | C5'—O5'—H5' | 109.2 (11) |
C7A—N1—N2—C3 | −0.7 (6) | C1'—N1—C7A—C3A | 176.6 (5) |
C1'—N1—N2—C3 | −177.2 (5) | C4—C3A—C7A—N7 | −3.9 (9) |
N1—N2—C3—C3A | 0.7 (7) | C3—C3A—C7A—N7 | 177.9 (5) |
N1—N2—C3—Br3 | 179.4 (4) | C4—C3A—C7A—N1 | 178.1 (5) |
N2—C3—C3A—C7A | −0.4 (7) | C3—C3A—C7A—N1 | −0.1 (7) |
Br3—C3—C3A—C7A | −179.0 (4) | C7A—N1—C1'—O4' | −105.0 (6) |
N2—C3—C3A—C4 | −178.0 (7) | N2—N1—C1'—O4' | 70.7 (6) |
Br3—C3—C3A—C4 | 3.4 (11) | C7A—N1—C1'—C2' | 135.8 (5) |
C7A—C3A—C4—N5 | 2.9 (8) | N2—N1—C1'—C2' | −48.4 (6) |
C3—C3A—C4—N5 | −179.7 (7) | O4'—C1'—C2'—C3' | −22.9 (4) |
C7A—C3A—C4—N4 | −178.0 (6) | N1—C1'—C2'—C3' | 98.1 (4) |
C3—C3A—C4—N4 | −0.7 (12) | C1'—C2'—C3'—O3' | 147.2 (4) |
N4—C4—N5—C6 | −178.9 (6) | C1'—C2'—C3'—C4' | 29.2 (4) |
C3A—C4—N5—C6 | 0.2 (8) | O3'—C3'—C4'—O4' | −146.1 (3) |
C4—N5—C6—N7 | −3.2 (8) | C2'—C3'—C4'—O4' | −25.9 (4) |
C4—N5—C6—N6 | 178.0 (5) | O3'—C3'—C4'—C5' | 92.6 (5) |
N6—C6—N7—C7A | −178.8 (4) | C2'—C3'—C4'—C5' | −147.2 (4) |
N5—C6—N7—C7A | 2.4 (7) | N1—C1'—O4'—C4' | −116.6 (4) |
C6—N7—C7A—N1 | 178.9 (5) | C2'—C1'—O4'—C4' | 6.4 (5) |
C6—N7—C7A—C3A | 1.3 (7) | C5'—C4'—O4'—C1' | 135.0 (4) |
N2—N1—C7A—N7 | −177.4 (5) | C3'—C4'—O4'—C1' | 12.6 (4) |
C1'—N1—C7A—N7 | −1.4 (9) | O4'—C4'—C5'—O5' | 53.6 (6) |
N2—N1—C7A—C3A | 0.5 (7) | C3'—C4'—C5'—O5' | 172.0 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4A···O5′i | 0.82 (5) | 2.28 (4) | 2.989 (5) | 146 (6) |
N6—H6B···O5′ii | 0.82 (5) | 2.12 (5) | 2.933 (5) | 167 (6) |
O3′—H3′···N5iii | 0.82 (3) | 2.27 (2) | 3.053 (5) | 159 (6) |
O5′—H5′···N7iv | 0.82 (2) | 1.98 (3) | 2.803 (5) | 177 (2) |
Symmetry codes: (i) x+1/2, −y+5/2, −z; (ii) −x−1/2, −y+2, z−1/2; (iii) −x+1/2, −y+2, z+1/2; (iv) x−1/2, −y+3/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C10H13BrN6O3 |
Mr | 345.17 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 293 |
a, b, c (Å) | 7.5939 (10), 9.2822 (18), 18.164 (2) |
V (Å3) | 1280.3 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 3.23 |
Crystal size (mm) | 0.32 × 0.28 × 0.14 |
Data collection | |
Diffractometer | Bruker P4 diffractometer |
Absorption correction | Empirical (using intensity measurements) (SHELXTL; Sheldrick,1997) |
Tmin, Tmax | 0.316, 0.519 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4231, 3682, 2568 |
Rint | 0.042 |
(sin θ/λ)max (Å−1) | 0.703 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.056, 0.139, 1.07 |
No. of reflections | 3682 |
No. of parameters | 199 |
No. of restraints | 8 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.44, −0.89 |
Absolute structure | Flack (1983), 1536 Friedel pairs? |
Absolute structure parameter | 0.020 (16) |
Computer programs: XSCANS (Siemens, 1996), XSCANS, SHELXTL (Sheldrick, 1997) and PLATON (Spek, 1999).
N1—C1' | 1.447 (5) | N6—C6 | 1.355 (6) |
C3—Br3 | 1.868 (4) | C1'—O4' | 1.408 (5) |
N4—C4 | 1.340 (6) | C4'—O4' | 1.433 (5) |
C7A—N1—C1' | 129.4 (4) | N6—C6—N5 | 115.0 (4) |
N2—N1—C1' | 119.5 (3) | O4'—C1'—N1 | 109.9 (4) |
N2—C3—Br3 | 120.3 (3) | N1—C1'—C2' | 113.1 (4) |
C3A—C3—Br3 | 126.8 (3) | O4'—C4'—C5' | 110.8 (4) |
N5—C4—N4 | 119.6 (4) | C1'—O4'—C4' | 111.8 (3) |
C7A—N1—N2—C3 | −0.7 (6) | C1'—C2'—C3'—C4' | 29.2 (4) |
C1'—N1—N2—C3 | −177.2 (5) | C2'—C3'—C4'—O4' | −25.9 (4) |
Br3—C3—C3A—C4 | 3.4 (11) | C2'—C3'—C4'—C5' | −147.2 (4) |
C4—N5—C6—N6 | 178.0 (5) | N1—C1'—O4'—C4' | −116.6 (4) |
C4—C3A—C7A—N7 | −3.9 (9) | C2'—C1'—O4'—C4' | 6.4 (5) |
C7A—N1—C1'—O4' | −105.0 (6) | C5'—C4'—O4'—C1' | 135.0 (4) |
N2—N1—C1'—O4' | 70.7 (6) | C3'—C4'—O4'—C1' | 12.6 (4) |
N1—C1'—C2'—C3' | 98.1 (4) | C3'—C4'—C5'—O5' | 172.0 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4A···O5'i | 0.82 (5) | 2.28 (4) | 2.989 (5) | 146 (6) |
N6—H6B···O5'ii | 0.82 (5) | 2.12 (5) | 2.933 (5) | 167 (6) |
O3'—H3'···N5iii | 0.82 (3) | 2.27 (2) | 3.053 (5) | 159 (6) |
O5'—H5'···N7iv | 0.82 (2) | 1.98 (3) | 2.803 (5) | 177.0 (17) |
Symmetry codes: (i) x+1/2, −y+5/2, −z; (ii) −x−1/2, −y+2, z−1/2; (iii) −x+1/2, −y+2, z+1/2; (iv) x−1/2, −y+3/2, −z. |
3-Bromo-1-(2-deoxy-β-D-erythro-pentofuranosyl)-1H-pyrazolo[3,4-d] pyrimidin-4,6-diamine, (I) (Seela & Becher, 2001), can substitute 2'-deoxyadenosine within dA–dT base pairs, thereby stabilizing DNA duplexes strongly. Moreover, it leads to a harmonization of the `dA'–dT versus the dG–dC base pair stability (He & Seela, 2002a, 2002b). This special property is suggested to result from two structural modifications of the base; firstly, the additional 6-amine group, which can form an extra hydrogen bond within the base pair, and secondly, the 3-bromo substituent, which increases the polarizability of the base, thereby increasing base stacking interactions. (Systematic numbering is used throughout the manuscript.) In the following, we describe the single-crystal X-ray structure of (I) and compare its structural properties with (II) and (III).
The nucleoside (I) exhibits a torsion angle χ(O4'—C1'—N1—C7a) of −105.0 (6)°. This torsion angle is defined in analogy to the torsion angle χ of purines (04'—C1'—N9—C4) (IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983). The torsion angle of compound (I) falls into a range between anti and high-anti, while compound (II) exhibits a high-anti torsion angle (χ = −74.6°; Seela et al., 2000); compound (III) adopts the same anti conformation as compound (I) (χ = −106.3°; Seela et al., 1999), which is the preferred conformation of natural purine 2'-deoxyribonucleosides (Rosemeyer et al., 1997). It has been shown that Coulombic repulsion between the non-bonding electron pairs of atoms O4' and N8 of 8-azatubercidin (Sprang et al., 1978), formycin (Prusiner et al., 1973) and 7-halogenated 8-aza-7-deazapurine 2'- deoxyribonucleosides (Seela et al., 1999; Seela & Zulauf, 1998) forces the N-glycosylic conformation into the high-anti (-sc) range (Klyne & Prelog, 1960).
The nucleobase of compound (I) is nearly planar. The r.m.s. deviation of the ring atoms (N1–C7A) from their calculated least-squares plane is 0.0178 Å; atom N4 has? the maximum deviation (0.038 Å) and lies above the plane, whereas the N atom of the 6-amino group (0.078 Å) lies below this plane. Atoms C1' and Br3 are also coplanar, with deviations of −0.018 and −0.079 Å, respectively. The bond lengths are in the normal range. The C4'—O4' bond is 0.025 Å longer than the O4'—C1' bond, because atom O4' is conjugated with the nucleobase through atom C1'.
The two amine groups of (I) are involved in hydrogen bonding with atom O5' of the sugar moiety, as shown in Table 2.
From numerous X-ray structures it is known that the sugar moieties in natural nucleosides adopt predominantly two distinct conformations, viz. north (N) and south (S). The structures are dynamically interconverted in solutions; however, ribonucleosides prefer the N conformation, while 2'-deoxyribonucleosides are predominantly in the S state. The sugar conformation of nucleosides is also influenced by the base moiety.
The pseudo-rotation phase angle and the amplitude of (I) [P = 5.8 (5)° with τm = 30.0 (3)°] demonstrate N-type sugar puckering, (3'-endo-2'-exo, 3T2). The sugar ring is twisted, as shown by the C3'—C4'—O4'—C1' [ν4= 12.6 (4)°] and C2'—C1'—O4'—C4' [ν0= 6.4 (5)°] torsion angles. Nucleoside (II) has P = 310.9 (4) and τm= 35.0 (3), with a C1'-endo (1E) sugar ring conformation. Such an N conformation is uncommon for 2'-deoxyribonucleosides. In contrast to the above two nucleosides, compound (III) exhibits a C2'-endo–C3'-exo conformation (2T3, S-type sugar), which is the common sugar conformation of 2'-deoxyribonucleosides.
The population in aqueous solution of the two major conformers of nucleoside (I) is 37% N and 63% S, very close to that of (II) (39% N and 61% S; Seela & Zulauf, 1998). This ratio was determined from the vicinal 3J(H,H) coupling constants of the 1H NMR spectra measured in D2O, using the PSEUROT program (van Wijk & Altona, 1993).
Compound (I) forms a three-dimensional network, which is stabilized by hydrogen bonds and by stacking interactions of the heterocyclic base moieties (Fig. 2 and Table 2). The H atoms of the N4H2 and N6H2 groups interact via hydrogen bonds with the O atom of the 5'-hydroxy group of the same neighbouring nucleoside molecule. Intermolecular hydrogen bonds also exist between 03'—H3'···N5 and 05'—H5'···N7 atoms. The halogen substituents form a weak intramolecular hydrogen bond with the other H atom of the N4H2 group (3.481 Å) and an intermolecular interaction with atom C4' of the sugar moiety (3.724 Å). The sugar rings are approximately perpendicular to the nucleobase plane.