The title nucleoside, C
13H
16N
2O
5, was prepared and characterized by X-ray crystallographic techniques. The crystal structure determination reveals that the furanose ring adopts a C2′-
endo conformation, while the orientation of the benzimidazole moiety with respect to the sugar moiety is mid-
anti. The crystal structure is stabilized by intermolecular O—H
O and N—H
O hydrogen bonds.
Supporting information
CCDC reference: 270277
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.003 Å
- R factor = 0.031
- wR factor = 0.080
- Data-to-parameter ratio = 9.6
checkCIF/PLATON results
No syntax errors found
Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
correct. If it is not, please give the correct count in the
_publ_section_exptl_refinement section of the submitted CIF.
From the CIF: _diffrn_reflns_theta_max 28.10
From the CIF: _reflns_number_total 1775
Count of symmetry unique reflns 1784
Completeness (_total/calc) 99.50%
TEST3: Check Friedels for noncentro structure
Estimate of Friedel pairs measured 0
Fraction of Friedel pairs measured 0.000
Are heavy atom types Z>Si present no
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
0 ALERT level C = Check and explain
1 ALERT level G = General alerts; check
0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
0 ALERT type 2 Indicator that the structure model may be wrong or deficient
0 ALERT type 3 Indicator that the structure quality may be low
1 ALERT type 4 Improvement, methodology, query or suggestion
Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1999); software used to prepare material for publication: SHELXTL.
7-Methyl-1-(
β-
D-
erythro-pentofuranosyl)-1
H-benzimidazol-2(3
H)-one
top
Crystal data top
C13H16N2O5 | F(000) = 592 |
Mr = 280.28 | Dx = 1.480 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 2668 reflections |
a = 6.741 (4) Å | θ = 2.4–26.8° |
b = 9.119 (5) Å | µ = 0.12 mm−1 |
c = 20.465 (11) Å | T = 293 K |
V = 1258.0 (11) Å3 | Plate, colourless |
Z = 4 | 0.38 × 0.22 × 0.10 mm |
Data collection top
Bruker APEX CCD area-detector diffractometer | 1775 independent reflections |
Radiation source: fine-focus sealed tube | 1496 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.025 |
φ and ω scans | θmax = 28.1°, θmin = 2.0° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −8→8 |
Tmin = 0.940, Tmax = 0.989 | k = −10→12 |
8479 measured reflections | l = −24→27 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.031 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.080 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0515P)2] where P = (Fo2 + 2Fc2)/3 |
1775 reflections | (Δ/σ)max = 0.001 |
185 parameters | Δρmax = 0.16 e Å−3 |
1 restraint | Δρmin = −0.23 e Å−3 |
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 | |
O1 | 0.8797 (2) | 0.32719 (14) | 0.06649 (6) | 0.0392 (3) | |
O2 | 0.67897 (19) | 0.46504 (11) | 0.18654 (6) | 0.0315 (3) | |
O3 | 0.37270 (18) | 0.15609 (13) | 0.14385 (6) | 0.0317 (3) | |
H3 | 0.2794 | 0.1898 | 0.1647 | 0.048* | |
O4 | 0.4279 (2) | 0.25002 (13) | 0.27149 (6) | 0.0352 (3) | |
H4 | 0.3872 | 0.1696 | 0.2834 | 0.053* | |
O5 | 1.0122 (2) | 0.25416 (16) | 0.18538 (6) | 0.0431 (3) | |
H5 | 0.9612 | 0.2856 | 0.1518 | 0.065* | |
N1 | 0.7005 (3) | 0.42131 (17) | −0.02001 (7) | 0.0351 (4) | |
H1A | 0.7823 | 0.4033 | −0.0513 | 0.042* | |
N2 | 0.5689 (2) | 0.43856 (15) | 0.07808 (6) | 0.0297 (3) | |
C1 | 0.7326 (3) | 0.38848 (18) | 0.04336 (9) | 0.0314 (4) | |
C2 | 0.5168 (3) | 0.48833 (18) | −0.02782 (8) | 0.0311 (4) | |
C3 | 0.4237 (3) | 0.53647 (19) | −0.08395 (9) | 0.0405 (5) | |
H3A | 0.4807 | 0.5239 | −0.1250 | 0.049* | |
C4 | 0.2427 (4) | 0.6039 (2) | −0.07627 (9) | 0.0432 (5) | |
H4A | 0.1730 | 0.6354 | −0.1129 | 0.052* | |
C5 | 0.1631 (3) | 0.62554 (19) | −0.01487 (10) | 0.0403 (5) | |
H5A | 0.0426 | 0.6747 | −0.0115 | 0.048* | |
C6 | 0.2546 (3) | 0.57719 (18) | 0.04250 (9) | 0.0318 (4) | |
C7 | 0.1634 (4) | 0.6124 (2) | 0.10749 (9) | 0.0448 (5) | |
H7A | 0.1234 | 0.5232 | 0.1286 | 0.067* | |
H7B | 0.0496 | 0.6741 | 0.1012 | 0.067* | |
H7C | 0.2587 | 0.6624 | 0.1343 | 0.067* | |
C8 | 0.4334 (3) | 0.50389 (17) | 0.03394 (8) | 0.0275 (4) | |
C9 | 0.5341 (3) | 0.39709 (17) | 0.14516 (7) | 0.0268 (4) | |
H9 | 0.4024 | 0.4321 | 0.1580 | 0.032* | |
C10 | 0.5472 (3) | 0.23236 (17) | 0.16008 (7) | 0.0252 (4) | |
H10 | 0.6578 | 0.1905 | 0.1352 | 0.030* | |
C11 | 0.6009 (3) | 0.23129 (17) | 0.23258 (8) | 0.0264 (3) | |
H11 | 0.6729 | 0.1419 | 0.2446 | 0.032* | |
C12 | 0.7299 (3) | 0.36694 (19) | 0.24067 (8) | 0.0293 (4) | |
H12 | 0.6956 | 0.4151 | 0.2820 | 0.035* | |
C13 | 0.9514 (3) | 0.3409 (2) | 0.23898 (9) | 0.0370 (4) | |
H13A | 1.0188 | 0.4347 | 0.2370 | 0.044* | |
H13B | 0.9912 | 0.2927 | 0.2792 | 0.044* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0334 (7) | 0.0513 (8) | 0.0329 (7) | 0.0105 (7) | 0.0044 (6) | 0.0011 (6) |
O2 | 0.0397 (7) | 0.0279 (6) | 0.0268 (6) | −0.0024 (5) | −0.0025 (6) | 0.0000 (5) |
O3 | 0.0276 (7) | 0.0393 (6) | 0.0282 (6) | −0.0019 (6) | −0.0008 (5) | −0.0062 (5) |
O4 | 0.0357 (8) | 0.0398 (7) | 0.0300 (6) | −0.0013 (6) | 0.0093 (5) | 0.0006 (5) |
O5 | 0.0306 (7) | 0.0651 (9) | 0.0335 (7) | 0.0098 (7) | −0.0030 (6) | −0.0039 (6) |
N1 | 0.0391 (10) | 0.0436 (8) | 0.0227 (7) | 0.0023 (8) | 0.0052 (6) | 0.0005 (6) |
N2 | 0.0307 (8) | 0.0349 (7) | 0.0235 (7) | 0.0069 (6) | 0.0026 (6) | 0.0031 (5) |
C1 | 0.0343 (10) | 0.0336 (9) | 0.0262 (8) | 0.0020 (8) | 0.0067 (8) | 0.0004 (7) |
C2 | 0.0386 (11) | 0.0271 (8) | 0.0275 (8) | −0.0036 (8) | 0.0015 (8) | 0.0001 (6) |
C3 | 0.0615 (14) | 0.0354 (9) | 0.0246 (9) | −0.0051 (10) | −0.0029 (9) | 0.0049 (7) |
C4 | 0.0586 (14) | 0.0384 (10) | 0.0326 (10) | −0.0030 (10) | −0.0141 (10) | 0.0099 (8) |
C5 | 0.0409 (12) | 0.0343 (9) | 0.0458 (11) | 0.0023 (9) | −0.0107 (9) | 0.0068 (8) |
C6 | 0.0353 (10) | 0.0270 (8) | 0.0329 (9) | 0.0001 (8) | −0.0016 (8) | 0.0028 (7) |
C7 | 0.0450 (13) | 0.0502 (11) | 0.0393 (10) | 0.0186 (10) | 0.0024 (9) | 0.0026 (9) |
C8 | 0.0346 (10) | 0.0240 (7) | 0.0239 (8) | −0.0002 (7) | −0.0039 (7) | 0.0015 (6) |
C9 | 0.0282 (9) | 0.0324 (8) | 0.0196 (7) | 0.0041 (7) | 0.0002 (7) | 0.0005 (6) |
C10 | 0.0231 (8) | 0.0296 (8) | 0.0229 (8) | 0.0007 (7) | 0.0000 (6) | −0.0029 (6) |
C11 | 0.0269 (9) | 0.0286 (8) | 0.0237 (8) | 0.0028 (7) | −0.0001 (7) | 0.0013 (6) |
C12 | 0.0315 (10) | 0.0360 (9) | 0.0203 (8) | −0.0013 (8) | −0.0014 (7) | −0.0009 (6) |
C13 | 0.0314 (10) | 0.0500 (11) | 0.0296 (9) | −0.0036 (9) | −0.0036 (8) | 0.0004 (8) |
Geometric parameters (Å, º) top
O1—C1 | 1.232 (2) | C4—C5 | 1.380 (3) |
O2—C9 | 1.433 (2) | C4—H4A | 0.93 |
O2—C12 | 1.465 (2) | C5—C6 | 1.398 (3) |
O3—C10 | 1.406 (2) | C5—H5A | 0.93 |
O3—H3 | 0.82 | C6—C8 | 1.389 (3) |
O4—C11 | 1.422 (2) | C6—C7 | 1.500 (3) |
O4—H4 | 0.82 | C7—H7A | 0.96 |
O5—C13 | 1.413 (2) | C7—H7B | 0.96 |
O5—H5 | 0.82 | C7—H7C | 0.96 |
N1—C1 | 1.349 (2) | C9—C10 | 1.535 (2) |
N1—C2 | 1.390 (3) | C9—H9 | 0.98 |
N1—H1A | 0.86 | C10—C11 | 1.527 (2) |
N2—C1 | 1.390 (2) | C10—H10 | 0.98 |
N2—C8 | 1.416 (2) | C11—C12 | 1.521 (2) |
N2—C9 | 1.443 (2) | C11—H11 | 0.98 |
C2—C3 | 1.380 (3) | C12—C13 | 1.512 (3) |
C2—C8 | 1.390 (2) | C12—H12 | 0.98 |
C3—C4 | 1.376 (3) | C13—H13A | 0.97 |
C3—H3A | 0.93 | C13—H13B | 0.97 |
| | | |
C9—O2—C12 | 110.03 (12) | C6—C8—C2 | 120.96 (16) |
C10—O3—H3 | 109.5 | C6—C8—N2 | 132.98 (15) |
C11—O4—H4 | 109.5 | C2—C8—N2 | 106.01 (16) |
C13—O5—H5 | 109.5 | O2—C9—N2 | 109.77 (14) |
C1—N1—C2 | 110.56 (15) | O2—C9—C10 | 105.46 (13) |
C1—N1—H1A | 124.7 | N2—C9—C10 | 115.87 (13) |
C2—N1—H1A | 124.7 | O2—C9—H9 | 108.5 |
C1—N2—C8 | 108.94 (14) | N2—C9—H9 | 108.5 |
C1—N2—C9 | 121.94 (14) | C10—C9—H9 | 108.5 |
C8—N2—C9 | 127.75 (15) | O3—C10—C11 | 115.12 (14) |
O1—C1—N1 | 126.81 (17) | O3—C10—C9 | 112.90 (15) |
O1—C1—N2 | 126.27 (16) | C11—C10—C9 | 102.30 (13) |
N1—C1—N2 | 106.92 (16) | O3—C10—H10 | 108.7 |
C3—C2—N1 | 129.80 (17) | C11—C10—H10 | 108.7 |
C3—C2—C8 | 122.69 (19) | C9—C10—H10 | 108.7 |
N1—C2—C8 | 107.50 (14) | O4—C11—C12 | 108.07 (13) |
C4—C3—C2 | 116.76 (18) | O4—C11—C10 | 110.41 (14) |
C4—C3—H3A | 121.6 | C12—C11—C10 | 103.65 (13) |
C2—C3—H3A | 121.6 | O4—C11—H11 | 111.5 |
C3—C4—C5 | 120.84 (18) | C12—C11—H11 | 111.5 |
C3—C4—H4A | 119.6 | C10—C11—H11 | 111.5 |
C5—C4—H4A | 119.6 | O2—C12—C13 | 108.08 (16) |
C4—C5—C6 | 123.2 (2) | O2—C12—C11 | 106.28 (13) |
C4—C5—H5A | 118.4 | C13—C12—C11 | 115.73 (16) |
C6—C5—H5A | 118.4 | O2—C12—H12 | 108.9 |
C8—C6—C5 | 115.39 (18) | C13—C12—H12 | 108.9 |
C8—C6—C7 | 124.77 (17) | C11—C12—H12 | 108.9 |
C5—C6—C7 | 119.77 (18) | O5—C13—C12 | 113.09 (16) |
C6—C7—H7A | 109.5 | O5—C13—H13A | 109.0 |
C6—C7—H7B | 109.5 | C12—C13—H13A | 109.0 |
H7A—C7—H7B | 109.5 | O5—C13—H13B | 109.0 |
C6—C7—H7C | 109.5 | C12—C13—H13B | 109.0 |
H7A—C7—H7C | 109.5 | H13A—C13—H13B | 107.8 |
H7B—C7—H7C | 109.5 | | |
| | | |
C2—N1—C1—O1 | 179.10 (17) | C1—N2—C8—C2 | 1.55 (19) |
C2—N1—C1—N2 | −1.60 (19) | C9—N2—C8—C2 | −165.15 (15) |
C8—N2—C1—O1 | 179.31 (16) | C12—O2—C9—N2 | −145.15 (13) |
C9—N2—C1—O1 | −13.1 (3) | C12—O2—C9—C10 | −19.67 (18) |
C8—N2—C1—N1 | 0.00 (19) | C1—N2—C9—O2 | 69.80 (19) |
C9—N2—C1—N1 | 167.63 (15) | C8—N2—C9—O2 | −125.05 (17) |
C1—N1—C2—C3 | −178.43 (19) | C1—N2—C9—C10 | −49.5 (2) |
C1—N1—C2—C8 | 2.6 (2) | C8—N2—C9—C10 | 115.67 (19) |
N1—C2—C3—C4 | −177.87 (17) | O2—C9—C10—O3 | 157.36 (13) |
C8—C2—C3—C4 | 1.0 (3) | N2—C9—C10—O3 | −81.04 (19) |
C2—C3—C4—C5 | 1.9 (3) | O2—C9—C10—C11 | 33.03 (17) |
C3—C4—C5—C6 | −2.3 (3) | N2—C9—C10—C11 | 154.64 (15) |
C4—C5—C6—C8 | −0.4 (3) | O3—C10—C11—O4 | −40.83 (18) |
C4—C5—C6—C7 | 176.7 (2) | C9—C10—C11—O4 | 82.01 (15) |
C5—C6—C8—C2 | 3.2 (2) | O3—C10—C11—C12 | −156.36 (13) |
C7—C6—C8—C2 | −173.65 (18) | C9—C10—C11—C12 | −33.52 (17) |
C5—C6—C8—N2 | −179.61 (18) | C9—O2—C12—C13 | 122.87 (15) |
C7—C6—C8—N2 | 3.5 (3) | C9—O2—C12—C11 | −1.96 (18) |
C3—C2—C8—C6 | −3.7 (3) | O4—C11—C12—O2 | −94.45 (16) |
N1—C2—C8—C6 | 175.37 (15) | C10—C11—C12—O2 | 22.73 (17) |
C3—C2—C8—N2 | 178.47 (16) | O4—C11—C12—C13 | 145.58 (15) |
N1—C2—C8—N2 | −2.47 (19) | C10—C11—C12—C13 | −97.24 (17) |
C1—N2—C8—C6 | −175.91 (17) | O2—C12—C13—O5 | −70.0 (2) |
C9—N2—C8—C6 | 17.4 (3) | C11—C12—C13—O5 | 49.0 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O3i | 0.86 | 2.06 | 2.876 (3) | 157 |
O3—H3···O5ii | 0.82 | 1.94 | 2.725 (2) | 160 |
O4—H4···O2iii | 0.82 | 2.01 | 2.830 (2) | 173 |
O5—H5···O1 | 0.82 | 1.87 | 2.676 (2) | 168 |
C10—H10···O1 | 0.98 | 2.40 | 3.072 (3) | 125 |
Symmetry codes: (i) x+1/2, −y+1/2, −z; (ii) x−1, y, z; (iii) −x+1, y−1/2, −z+1/2. |