2′-De­oxy-3′,5′-di-O-acetyl­uridine

In the mol­ecule of the title compound, C₁₃H₁₆N₂O₇, the furanose ring adopts an envelope conformation. In the crystal structure, inter­molecular N—H...O hydrogen bonds link the mol­ecules, and these may be effective in the stabilization of the structure.

Key indicators

• Single-crystal X-ray study
• T = 294 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.038
• wR factor = 0.088
• Data-to-parameter ratio = 9.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.98
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C11
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          1
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          1
              C13 H16 N2 O7

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           27.48
           From the CIF: _reflns_number_total               1842
           Count of symmetry unique reflns         1888
           Completeness (_total/calc)             97.56%
           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
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C7     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C8     = .          S

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

   4 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
   1 ALERT type 3 Indicator that the structure quality may be low
   4 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/MSC, 2000); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXL97.

2'-Deoxy-3',5'-di-O-acetyluridine

Crystal data

C13H16N2O7	F(000) = 328
Mr = 312.28	Dx = 1.392 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 3709 reflections
a = 11.284 (2) Å	θ = 2.9–27.5°
b = 5.3270 (11) Å	µ = 0.11 mm^−1
c = 13.184 (3) Å	T = 294 K
β = 109.91 (3)°	Block, colorless
V = 745.2 (3) Å^3	0.45 × 0.20 × 0.20 mm
Z = 2

Data collection

Rigaku R-AXIS RAPID IP diffractometer	1842 independent reflections
Radiation source: fine-focus sealed tube	1274 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.034
Detector resolution: 10.00 pixels mm^-1	θmax = 27.5°, θmin = 2.9°
ω scans	h = −14→14
Absorption correction: empirical (using intensity measurements) (ABSCOR; Higashi, 1995)	k = −4→6
Tmin = 0.950, Tmax = 0.977	l = −17→16
3709 measured reflections

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)] = 0.038	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.088	w = 1/[σ^2(Fo^2) + (0.044P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.05	(Δ/σ)max < 0.001
1842 reflections	Δρmax = 0.18 e Å^−3
204 parameters	Δρmin = −0.16 e Å^−3
1 restraint	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.092 (7)

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
O1	0.45631 (18)	0.8779 (5)	0.20542 (13)	0.0581 (6)
O2	0.40444 (19)	1.2482 (5)	0.49746 (13)	0.0653 (7)
O3	0.16617 (15)	1.2416 (5)	0.00737 (11)	0.0503 (5)
O4	0.04970 (16)	1.7066 (4)	−0.21229 (12)	0.0517 (5)
O5	−0.1068 (2)	1.4297 (5)	−0.28631 (17)	0.0777 (8)
O6	0.31388 (16)	1.1598 (4)	−0.15610 (11)	0.0439 (5)
O7	0.1951 (2)	1.3102 (5)	−0.31799 (13)	0.0662 (7)
N1	0.32533 (18)	1.2197 (5)	0.17617 (13)	0.0397 (5)
N2	0.4293 (2)	1.0736 (5)	0.34962 (16)	0.0457 (6)
HN2	0.473 (3)	0.952 (7)	0.389 (2)	0.063 (10)*
C1	0.3793 (2)	1.2565 (6)	0.39840 (18)	0.0448 (7)
C2	0.3011 (3)	1.4410 (6)	0.3258 (2)	0.0526 (8)
H2	0.2676	1.5755	0.3521	0.063*
C3	0.2778 (3)	1.4141 (6)	0.21997 (18)	0.0468 (7)
H3	0.2268	1.5325	0.1734	0.056*
C4	0.4070 (2)	1.0414 (6)	0.24167 (18)	0.0397 (7)
C5	0.2976 (2)	1.1962 (6)	0.05971 (16)	0.0396 (6)
H5	0.3178	1.0256	0.0430	0.047*
C6	0.3639 (2)	1.3847 (6)	0.01089 (17)	0.0423 (7)
H6A	0.4488	1.3309	0.0190	0.051*
H6B	0.3670	1.5501	0.0425	0.051*
C7	0.2780 (2)	1.3805 (6)	−0.10708 (17)	0.0390 (6)
H7	0.2841	1.5358	−0.1449	0.047*
C8	0.1467 (2)	1.3447 (6)	−0.09960 (16)	0.0390 (7)
H8	0.0983	1.2260	−0.1550	0.047*
C9	0.0723 (3)	1.5904 (6)	−0.1087 (2)	0.0486 (7)
H9A	−0.0075	1.5554	−0.0992	0.058*
H9B	0.1194	1.7048	−0.0521	0.058*
C10	−0.0422 (3)	1.6028 (7)	−0.2971 (2)	0.0551 (8)
C11	−0.0482 (3)	1.7334 (9)	−0.3992 (2)	0.0800 (12)
H11A	0.0146	1.8629	−0.3832	0.120*
H11B	−0.1302	1.8065	−0.4318	0.120*
H11C	−0.0329	1.6144	−0.4480	0.120*
C12	0.2688 (2)	1.1535 (6)	−0.26582 (18)	0.0460 (8)
C13	0.3203 (3)	0.9385 (7)	−0.3084 (2)	0.0557 (8)
H13A	0.3780	0.8468	−0.2495	0.083*
H13B	0.3636	0.9990	−0.3548	0.083*
H13C	0.2526	0.8302	−0.3485	0.083*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0663 (12)	0.0660 (16)	0.0392 (9)	0.0197 (12)	0.0141 (8)	0.0014 (10)
O2	0.0806 (13)	0.0832 (18)	0.0306 (9)	−0.0212 (14)	0.0169 (8)	−0.0114 (11)
O3	0.0392 (9)	0.0765 (16)	0.0329 (8)	−0.0059 (10)	0.0094 (6)	0.0116 (9)
O4	0.0525 (10)	0.0492 (14)	0.0449 (9)	0.0052 (10)	0.0057 (7)	0.0045 (9)
O5	0.0588 (14)	0.073 (2)	0.0783 (15)	−0.0052 (15)	−0.0062 (11)	0.0028 (14)
O6	0.0492 (9)	0.0531 (14)	0.0304 (8)	0.0061 (10)	0.0151 (7)	0.0037 (8)
O7	0.0815 (14)	0.0743 (17)	0.0348 (9)	0.0272 (13)	0.0093 (9)	0.0046 (10)
N1	0.0482 (12)	0.0428 (15)	0.0261 (9)	0.0039 (12)	0.0100 (8)	0.0010 (10)
N2	0.0513 (13)	0.0519 (17)	0.0296 (10)	−0.0003 (13)	0.0084 (9)	0.0048 (11)
C1	0.0468 (14)	0.054 (2)	0.0353 (13)	−0.0172 (14)	0.0157 (10)	−0.0075 (13)
C2	0.0683 (18)	0.049 (2)	0.0459 (14)	−0.0045 (16)	0.0264 (13)	−0.0093 (13)
C3	0.0566 (17)	0.0422 (19)	0.0418 (14)	0.0011 (14)	0.0172 (12)	0.0028 (13)
C4	0.0414 (14)	0.0435 (19)	0.0339 (12)	−0.0030 (13)	0.0123 (11)	0.0004 (12)
C5	0.0434 (13)	0.0438 (18)	0.0276 (10)	0.0013 (14)	0.0071 (9)	0.0013 (12)
C6	0.0382 (14)	0.051 (2)	0.0373 (12)	−0.0046 (14)	0.0125 (10)	−0.0002 (12)
C7	0.0425 (13)	0.0431 (18)	0.0326 (11)	0.0006 (13)	0.0143 (9)	0.0014 (12)
C8	0.0429 (14)	0.0424 (18)	0.0296 (11)	−0.0017 (13)	0.0097 (9)	0.0024 (11)
C9	0.0514 (15)	0.052 (2)	0.0408 (13)	0.0062 (15)	0.0131 (11)	−0.0031 (14)
C10	0.0434 (15)	0.056 (2)	0.0549 (16)	0.0100 (17)	0.0025 (13)	−0.0010 (15)
C11	0.0673 (19)	0.116 (4)	0.0462 (15)	0.016 (3)	0.0060 (13)	0.013 (2)
C12	0.0493 (15)	0.056 (2)	0.0330 (12)	−0.0016 (15)	0.0149 (11)	−0.0002 (13)
C13	0.0672 (19)	0.061 (2)	0.0434 (14)	0.0068 (17)	0.0243 (13)	−0.0038 (14)

Geometric parameters (Å, º)

O1—C4	1.216 (3)	C5—C6	1.520 (4)
O2—C1	1.239 (3)	C5—H5	0.9800
O3—C5	1.427 (3)	C6—C7	1.527 (3)
O3—C8	1.459 (3)	C6—H6A	0.9700
O4—C10	1.358 (3)	C6—H6B	0.9700
O4—C9	1.440 (3)	C7—C8	1.529 (3)
O5—C10	1.213 (4)	C7—H7	0.9800
O6—C12	1.361 (3)	C8—C9	1.537 (4)
O6—C7	1.464 (3)	C8—H8	0.9800
O7—C12	1.213 (4)	C9—H9A	0.9700
N1—C3	1.380 (4)	C9—H9B	0.9700
N1—C4	1.398 (3)	C10—C11	1.496 (4)
N1—C5	1.464 (3)	C11—H11A	0.9600
N2—C4	1.369 (3)	C11—H11B	0.9600
N2—C1	1.388 (4)	C11—H11C	0.9600
N2—HN2	0.87 (4)	C12—C13	1.479 (4)
C1—C2	1.445 (4)	C13—H13A	0.9600
C2—C3	1.336 (3)	C13—H13B	0.9600
C2—H2	0.9300	C13—H13C	0.9600
C3—H3	0.9300
C5—O3—C8	108.70 (17)	C6—C7—C8	103.25 (17)
C10—O4—C9	116.4 (2)	O6—C7—H7	112.0
C12—O6—C7	115.4 (2)	C6—C7—H7	112.0
C3—N1—C4	121.31 (19)	C8—C7—H7	112.0
C3—N1—C5	121.9 (2)	O3—C8—C7	106.21 (18)
C4—N1—C5	116.8 (2)	O3—C8—C9	107.13 (19)
C4—N2—C1	127.6 (3)	C7—C8—C9	113.8 (2)
C4—N2—HN2	113 (2)	O3—C8—H8	109.9
C1—N2—HN2	119 (2)	C7—C8—H8	109.9
O2—C1—N2	118.7 (3)	C9—C8—H8	109.9
O2—C1—C2	126.3 (3)	O4—C9—C8	110.9 (2)
N2—C1—C2	115.1 (2)	O4—C9—H9A	109.5
C3—C2—C1	118.5 (3)	C8—C9—H9A	109.5
C3—C2—H2	120.7	O4—C9—H9B	109.5
C1—C2—H2	120.7	C8—C9—H9B	109.5
C2—C3—N1	123.4 (3)	H9A—C9—H9B	108.1
C2—C3—H3	118.3	O5—C10—O4	122.3 (3)
N1—C3—H3	118.3	O5—C10—C11	127.9 (3)
O1—C4—N2	123.5 (3)	O4—C10—C11	109.8 (3)
O1—C4—N1	122.5 (2)	C10—C11—H11A	109.5
N2—C4—N1	114.0 (2)	C10—C11—H11B	109.5
O3—C5—N1	107.98 (18)	H11A—C11—H11B	109.5
O3—C5—C6	105.3 (2)	C10—C11—H11C	109.5
N1—C5—C6	115.3 (2)	H11A—C11—H11C	109.5
O3—C5—H5	109.4	H11B—C11—H11C	109.5
N1—C5—H5	109.4	O7—C12—O6	121.5 (3)
C6—C5—H5	109.4	O7—C12—C13	126.8 (2)
C5—C6—C7	100.8 (2)	O6—C12—C13	111.7 (2)
C5—C6—H6A	111.6	C12—C13—H13A	109.5
C7—C6—H6A	111.6	C12—C13—H13B	109.5
C5—C6—H6B	111.6	H13A—C13—H13B	109.5
C7—C6—H6B	111.6	C12—C13—H13C	109.5
H6A—C6—H6B	109.4	H13A—C13—H13C	109.5
O6—C7—C6	106.6 (2)	H13B—C13—H13C	109.5
O6—C7—C8	110.4 (2)
C4—N2—C1—O2	175.8 (3)	O3—C5—C6—C7	−39.2 (3)
C4—N2—C1—C2	−4.0 (4)	N1—C5—C6—C7	−158.1 (2)
O2—C1—C2—C3	−176.2 (3)	C12—O6—C7—C6	−165.6 (2)
N2—C1—C2—C3	3.6 (4)	C12—O6—C7—C8	83.0 (2)
C1—C2—C3—N1	−0.5 (4)	C5—C6—C7—O6	−81.0 (2)
C4—N1—C3—C2	−2.8 (4)	C5—C6—C7—C8	35.3 (3)
C5—N1—C3—C2	179.9 (2)	C5—O3—C8—C7	−4.5 (3)
C1—N2—C4—O1	178.8 (3)	C5—O3—C8—C9	−126.4 (2)
C1—N2—C4—N1	1.0 (4)	O6—C7—C8—O3	93.5 (2)
C3—N1—C4—O1	−175.3 (3)	C6—C7—C8—O3	−20.2 (3)
C5—N1—C4—O1	2.1 (4)	O6—C7—C8—C9	−148.9 (2)
C3—N1—C4—N2	2.6 (4)	C6—C7—C8—C9	97.4 (2)
C5—N1—C4—N2	179.9 (2)	C10—O4—C9—C8	76.4 (3)
C8—O3—C5—N1	151.4 (2)	O3—C8—C9—O4	179.5 (2)
C8—O3—C5—C6	27.7 (3)	C7—C8—C9—O4	62.5 (3)
C3—N1—C5—O3	−44.5 (3)	C9—O4—C10—O5	3.7 (4)
C4—N1—C5—O3	138.1 (2)	C9—O4—C10—C11	−176.3 (2)
C3—N1—C5—C6	72.9 (3)	C7—O6—C12—O7	−6.2 (3)
C4—N1—C5—C6	−104.5 (3)	C7—O6—C12—C13	174.1 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—HN2···O2^i	0.87 (4)	1.98 (3)	2.831 (3)	165 (3)

Symmetry code: (i) −x+1, y−1/2, −z+1.