1-(1,1-Dioxo-3′-de­oxy-2,3,5,6-tetra­hydro-1,4-oxathiine-β-D-ribofuranos­yl)uracil: a bicyclic nucleoside analogue

In the title compound, C₁₁H₁₄N₂O₇S, the furan­ose ring adopts a 3′-endo,4′-exo conformation ₄T³. The orientation of the pyrimidine ring with respect to the sugar group is anti. The crystal packing is stabilized by inter­molecular N—H...O and O—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.039
• wR factor = 0.078
• Data-to-parameter ratio = 15.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?

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           27.47
           From the CIF: _reflns_number_total               2969
           Count of symmetry unique reflns         1626
           Completeness (_total/calc)            182.60%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1343
           Fraction of Friedel pairs measured     0.826
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C7     = .          R

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   5 ALERT level G = General alerts; check

   5 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
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: RAPID-AUTO (Rigaku Corporation, 1998); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97.

1-(3'-Deoxy-2,3,5,6-tetrahydro-1,4-oxathiine-1,1-dioxido-β-D– ribofuranosyl)uracil

Crystal data

C11H14N2O7S	F(000) = 332
Mr = 318.30	Dx = 1.613 Mg m^−3
Monoclinic, P21	Melting point: 580 K
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 5.2752 (11) Å	Cell parameters from 5431 reflections
b = 7.1294 (14) Å	θ = 6.2–54.9°
c = 17.425 (4) Å	µ = 0.29 mm^−1
β = 90.45 (3)°	T = 295 K
V = 655.3 (2) Å^3	Block, colourless
Z = 2	0.15 × 0.11 × 0.09 mm

Data collection

Rigaku R-AXIS RAPID diffractometer	2969 independent reflections
Radiation source: fine-focus sealed tube	2408 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.036
ω scans	θmax = 27.5°, θmin = 3.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −6→6
Tmin = 0.960, Tmax = 0.974	k = −9→9
6545 measured reflections	l = −21→22

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.078	w = 1/[σ^2(Fo^2) + (0.0308P)^2 + 0.0765P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max < 0.001
2969 reflections	Δρmax = 0.20 e Å^−3
195 parameters	Δρmin = −0.23 e Å^−3
1 restraint	Absolute structure: Flack (1983), 1343 Friedel pairs???
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.04 (8)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.2009 (6)	0.5894 (4)	0.05288 (14)	0.0343 (6)
H1	0.2447	0.6042	−0.0007	0.041*
H2	0.0189	0.5720	0.0560	0.041*
C2	0.2777 (6)	0.7640 (4)	0.09721 (13)	0.0409 (7)
H4	0.4600	0.7802	0.0947	0.049*
H3	0.1981	0.8732	0.0742	0.049*
C3	0.3517 (5)	0.6194 (4)	0.21774 (12)	0.0282 (5)
H5	0.5312	0.6548	0.2196	0.034*
C4	0.3125 (4)	0.4169 (3)	0.19153 (11)	0.0233 (5)
H6	0.4377	0.3378	0.2179	0.028*
C5	0.0520 (4)	0.3709 (4)	0.22314 (11)	0.0246 (5)
H7	−0.0788	0.4211	0.1886	0.029*
C6	0.0029 (5)	0.1664 (4)	0.23709 (15)	0.0352 (6)
H8	0.0489	0.0943	0.1921	0.042*
H9	0.1052	0.1229	0.2801	0.042*
C7	0.2326 (5)	0.6134 (4)	0.29728 (12)	0.0285 (5)
H10	0.1539	0.7347	0.3087	0.034*
C8	0.5782 (5)	0.7155 (4)	0.37963 (13)	0.0310 (6)
C9	0.8061 (5)	0.5005 (4)	0.46493 (15)	0.0352 (6)
C10	0.6463 (5)	0.3534 (4)	0.43785 (13)	0.0353 (6)
H12	0.6692	0.2316	0.4557	0.042*
C11	0.4628 (4)	0.3915 (4)	0.38660 (12)	0.0329 (5)
H11	0.3570	0.2948	0.3702	0.039*
H14	0.839 (4)	0.761 (4)	0.4475 (12)	0.034 (6)*
N1	0.4258 (4)	0.5677 (3)	0.35762 (10)	0.0283 (5)
N2	0.7584 (4)	0.6739 (3)	0.43355 (12)	0.0323 (5)
O1	0.2346 (4)	0.2248 (3)	0.06374 (11)	0.0425 (5)
O2	0.6239 (3)	0.4117 (3)	0.07853 (8)	0.0414 (5)
O3	0.2027 (4)	0.7485 (2)	0.17542 (9)	0.0365 (4)
O4	0.0464 (3)	0.4725 (3)	0.29558 (9)	0.0327 (4)
O5	−0.2565 (4)	0.1403 (3)	0.25314 (13)	0.0543 (6)
H13	−0.2711	0.0714	0.2905	0.082*
O6	0.5524 (4)	0.8721 (3)	0.35275 (10)	0.0449 (5)
O7	0.9801 (4)	0.4848 (3)	0.51245 (12)	0.0533 (6)
S1	0.35615 (11)	0.39248 (9)	0.09076 (3)	0.02675 (14)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0353 (15)	0.0402 (16)	0.0273 (12)	0.0031 (12)	−0.0040 (10)	0.0067 (12)
C2	0.0654 (19)	0.0280 (15)	0.0294 (13)	0.0016 (14)	0.0015 (12)	0.0081 (11)
C3	0.0322 (14)	0.0283 (14)	0.0241 (11)	−0.0015 (11)	−0.0017 (9)	0.0014 (9)
C4	0.0220 (11)	0.0257 (14)	0.0222 (9)	0.0026 (10)	−0.0006 (7)	0.0022 (10)
C5	0.0252 (11)	0.0232 (13)	0.0253 (10)	0.0024 (11)	−0.0011 (8)	0.0006 (10)
C6	0.0322 (15)	0.0282 (15)	0.0453 (15)	−0.0005 (11)	0.0007 (11)	0.0055 (11)
C7	0.0339 (14)	0.0256 (14)	0.0259 (11)	−0.0006 (11)	0.0014 (9)	0.0024 (10)
C8	0.0377 (14)	0.0305 (15)	0.0249 (11)	−0.0026 (12)	0.0011 (10)	0.0015 (10)
C9	0.0373 (16)	0.0312 (15)	0.0369 (14)	0.0039 (12)	−0.0011 (11)	−0.0001 (12)
C10	0.0441 (16)	0.0269 (17)	0.0348 (12)	0.0010 (12)	0.0001 (10)	0.0056 (10)
C11	0.0414 (13)	0.0273 (13)	0.0299 (11)	−0.0054 (15)	0.0008 (9)	0.0013 (13)
N1	0.0365 (12)	0.0249 (11)	0.0236 (9)	−0.0051 (9)	−0.0017 (8)	0.0025 (9)
N2	0.0378 (14)	0.0299 (13)	0.0291 (11)	−0.0054 (11)	−0.0056 (9)	−0.0024 (9)
O1	0.0545 (13)	0.0352 (12)	0.0378 (10)	−0.0066 (10)	−0.0024 (9)	−0.0075 (9)
O2	0.0260 (9)	0.0644 (14)	0.0339 (8)	0.0032 (10)	0.0044 (6)	0.0014 (10)
O3	0.0589 (12)	0.0225 (10)	0.0280 (8)	0.0080 (9)	−0.0003 (8)	0.0038 (7)
O4	0.0335 (10)	0.0366 (11)	0.0282 (8)	−0.0071 (8)	0.0073 (7)	−0.0034 (7)
O5	0.0338 (12)	0.0483 (14)	0.0810 (15)	−0.0035 (10)	0.0056 (10)	0.0313 (11)
O6	0.0586 (12)	0.0307 (11)	0.0451 (10)	−0.0085 (11)	−0.0123 (8)	0.0076 (9)
O7	0.0580 (14)	0.0376 (12)	0.0639 (13)	0.0046 (11)	−0.0296 (11)	0.0028 (10)
S1	0.0267 (3)	0.0302 (3)	0.0233 (2)	0.0005 (3)	−0.00005 (18)	−0.0027 (3)

Geometric parameters (Å, º)

C1—C2	1.518 (4)	C6—H9	0.9700
C1—S1	1.752 (3)	C7—O4	1.405 (3)
C1—H1	0.9700	C7—N1	1.495 (3)
C1—H2	0.9700	C7—H10	0.9800
C2—O3	1.426 (3)	C8—O6	1.218 (3)
C2—H4	0.9700	C8—N2	1.364 (3)
C2—H3	0.9700	C8—N1	1.378 (3)
C3—O3	1.414 (3)	C9—O7	1.236 (3)
C3—C7	1.527 (3)	C9—N2	1.374 (3)
C3—C4	1.528 (3)	C9—C10	1.424 (4)
C3—H5	0.9800	C10—C11	1.340 (3)
C4—C5	1.520 (3)	C10—H12	0.9300
C4—S1	1.781 (2)	C11—N1	1.367 (3)
C4—H6	0.9800	C11—H11	0.9300
C5—O4	1.456 (3)	N2—H14	0.79 (3)
C5—C6	1.501 (4)	O1—S1	1.435 (2)
C5—H7	0.9800	O2—S1	1.4366 (17)
C6—O5	1.411 (3)	O5—H13	0.8200
C6—H8	0.9700
C2—C1—S1	110.08 (19)	H8—C6—H9	108.3
C2—C1—H1	109.6	O4—C7—N1	109.36 (19)
S1—C1—H1	109.6	O4—C7—C3	107.05 (19)
C2—C1—H2	109.6	N1—C7—C3	111.2 (2)
S1—C1—H2	109.6	O4—C7—H10	109.7
H1—C1—H2	108.2	N1—C7—H10	109.7
O3—C2—C1	110.4 (2)	C3—C7—H10	109.7
O3—C2—H4	109.6	O6—C8—N2	122.6 (2)
C1—C2—H4	109.6	O6—C8—N1	122.1 (2)
O3—C2—H3	109.6	N2—C8—N1	115.3 (2)
C1—C2—H3	109.6	O7—C9—N2	118.7 (3)
H4—C2—H3	108.1	O7—C9—C10	126.2 (3)
O3—C3—C7	105.10 (19)	N2—C9—C10	115.1 (2)
O3—C3—C4	112.70 (19)	C11—C10—C9	119.7 (3)
C7—C3—C4	100.92 (19)	C11—C10—H12	120.2
O3—C3—H5	112.4	C9—C10—H12	120.2
C7—C3—H5	112.4	C10—C11—N1	122.2 (3)
C4—C3—H5	112.4	C10—C11—H11	118.9
C5—C4—C3	102.48 (18)	N1—C11—H11	118.9
C5—C4—S1	117.42 (15)	C11—N1—C8	121.3 (2)
C3—C4—S1	111.64 (15)	C11—N1—C7	123.7 (2)
C5—C4—H6	108.3	C8—N1—C7	114.9 (2)
C3—C4—H6	108.3	C8—N2—C9	126.5 (2)
S1—C4—H6	108.3	C8—N2—H14	114.2 (17)
O4—C5—C6	109.77 (19)	C9—N2—H14	119.3 (17)
O4—C5—C4	103.39 (18)	C3—O3—C2	113.06 (19)
C6—C5—C4	115.2 (2)	C7—O4—C5	110.79 (17)
O4—C5—H7	109.4	C6—O5—H13	109.5
C6—C5—H7	109.4	O1—S1—O2	117.93 (13)
C4—C5—H7	109.4	O1—S1—C1	109.75 (12)
O5—C6—C5	109.2 (2)	O2—S1—C1	108.95 (14)
O5—C6—H8	109.8	O1—S1—C4	110.12 (11)
C5—C6—H8	109.8	O2—S1—C4	105.78 (10)
O5—C6—H9	109.8	C1—S1—C4	103.26 (12)
C5—C6—H9	109.8
S1—C1—C2—O3	−62.3 (3)	O4—C7—N1—C11	20.5 (3)
O3—C3—C4—C5	−73.6 (2)	C3—C7—N1—C11	−97.5 (3)
C7—C3—C4—C5	38.0 (2)	O4—C7—N1—C8	−163.20 (19)
O3—C3—C4—S1	52.9 (2)	C3—C7—N1—C8	78.8 (3)
C7—C3—C4—S1	164.53 (15)	O6—C8—N2—C9	−177.6 (2)
C3—C4—C5—O4	−35.3 (2)	N1—C8—N2—C9	2.5 (3)
S1—C4—C5—O4	−157.95 (16)	O7—C9—N2—C8	178.7 (3)
C3—C4—C5—C6	−155.0 (2)	C10—C9—N2—C8	−0.8 (4)
S1—C4—C5—C6	82.3 (2)	C7—C3—O3—C2	−176.4 (2)
O4—C5—C6—O5	74.1 (3)	C4—C3—O3—C2	−67.4 (3)
C4—C5—C6—O5	−169.76 (18)	C1—C2—O3—C3	72.5 (3)
O3—C3—C7—O4	89.5 (2)	N1—C7—O4—C5	−114.5 (2)
C4—C3—C7—O4	−27.8 (2)	C3—C7—O4—C5	6.1 (3)
O3—C3—C7—N1	−151.1 (2)	C6—C5—O4—C7	141.9 (2)
C4—C3—C7—N1	91.6 (2)	C4—C5—O4—C7	18.5 (3)
O7—C9—C10—C11	179.3 (3)	C2—C1—S1—O1	164.3 (2)
N2—C9—C10—C11	−1.3 (4)	C2—C1—S1—O2	−65.2 (2)
C9—C10—C11—N1	1.5 (4)	C2—C1—S1—C4	46.9 (2)
C10—C11—N1—C8	0.4 (3)	C5—C4—S1—O1	−41.7 (2)
C10—C11—N1—C7	176.5 (2)	C3—C4—S1—O1	−159.61 (17)
O6—C8—N1—C11	177.9 (2)	C5—C4—S1—O2	−170.2 (2)
N2—C8—N1—C11	−2.3 (3)	C3—C4—S1—O2	71.9 (2)
O6—C8—N1—C7	1.4 (3)	C5—C4—S1—C1	75.4 (2)
N2—C8—N1—C7	−178.7 (2)	C3—C4—S1—C1	−42.5 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H14···O7^i	0.79 (3)	1.98 (3)	2.772 (3)	176 (2)
O5—H13···O6^ii	0.82	2.02	2.777 (3)	153

Symmetry codes: (i) −x+2, y+1/2, −z+1; (ii) x−1, y−1, z.