2,2′-Anhydro-2′-C-methyl-1-(β-D-arabinofuranos­yl)uracil (2,2′-anhydro-2′-C-methyluridine)

The structure of anhydro-2′-C-methyl­uridine, C₁₀H₁₂N₂O₅, is firmly established by X-ray crystallography, with the sugar adopting a furan­ose ring. The absolute stereochemistry is inferred from the use of 2-C-methyl-D-arabinose as the starting material. The mol­ecules are linked by two conventional O—H...O hydrogen bonds, and one C—H...π hydrogen bond.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.031
• wR factor = 0.065
• Data-to-parameter ratio = 8.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       0.98
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT153_ALERT_1_C The su's on the Cell Axes are Equal (x 100000) .         30 Ang.

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           27.43
           From the CIF: _reflns_number_total               1242
           Count of symmetry unique reflns         1267
           Completeness (_total/calc)             98.03%
           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 C1     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C12    = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C13    = .          R

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 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
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check


checkCIF publication errors

Alert level A
PUBL024_ALERT_1_A The number of authors is greater than 5.
              Please specify the role of each of the co-authors
              for your paper.

Author Response: Fleet, George W. J. - Preparative Group Leader Jones, Nigel A. - Post Doc preparative chemist and crystallographer Jenkinson, Sarah F. - Post Doc preparative chemist and crystallographer Moussa, Adel - Industrial collaborator (Idenix) on project Stewart, Alistair - Industrial collaborator (Idenix) on project Heinz, Thomas - Industrial collaborator (Novartis) on project Watkin, David J. - Crystallographic Advisor

   1 ALERT level A = Data missing that is essential or data in wrong format
   0 ALERT level G = General alerts. Data that may be required is missing

---

Computing details

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.

2,2'-Anhydro-2'-C-methyl-1-(β-D-arabinofuranosyl)uracil

Crystal data

C10H12N2O5	Dx = 1.551 Mg m^−3
Mr = 240.22	Melting point = 513–516 K
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
a = 8.6134 (3) Å	Cell parameters from 994 reflections
b = 7.4803 (3) Å	θ = 5–27°
c = 8.8106 (3) Å	µ = 0.13 mm^−1
β = 115.0716 (18)°	T = 150 K
V = 514.19 (3) Å^3	Plate, colourless
Z = 2	0.50 × 0.30 × 0.20 mm
F(000) = 252

Data collection

Nonius KappaCCD area-detector diffractometer	1242 reflections with I > −3σ(I)
Graphite monochromator	Rint = 0.022
ω scans	θmax = 27.4°, θmin = 5.1°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −11→11
Tmin = 0.919, Tmax = 1.0	k = −9→8
3462 measured reflections	l = −11→11
1242 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.031	H-atom parameters constrained
wR(F^2) = 0.065	w = 1/[σ^2(F^2) + (0.02P)^2 + 0.15P], where P = [max(Fo^2,0) + 2Fc^2]/3
S = 0.98	(Δ/σ)max = 0.000166
1242 reflections	Δρmax = 0.23 e Å^−3
154 parameters	Δρmin = −0.21 e Å^−3
1 restraint

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.2686 (2)	0.0562 (3)	0.7703 (2)	0.0158
C2	0.1665 (2)	0.1706 (3)	0.6128 (2)	0.0159
N3	0.29994 (18)	0.2904 (2)	0.61261 (18)	0.0163
C4	0.4480 (2)	0.2742 (3)	0.7522 (2)	0.0151
O5	0.43446 (15)	0.1497 (2)	0.85555 (16)	0.0168
N6	0.58915 (19)	0.3610 (2)	0.78899 (19)	0.0179
C7	0.5870 (2)	0.4885 (3)	0.6726 (2)	0.0194
C8	0.4292 (2)	0.5148 (3)	0.5225 (2)	0.0210
C9	0.2903 (2)	0.4148 (3)	0.4941 (2)	0.0189
O10	0.71883 (17)	0.5753 (2)	0.69889 (18)	0.0280
O11	0.03602 (15)	0.2615 (2)	0.63784 (15)	0.0188
C12	0.0706 (2)	0.2547 (3)	0.8150 (2)	0.0166
C13	0.1696 (2)	0.0806 (3)	0.8791 (2)	0.0160
O14	0.04747 (17)	−0.0572 (2)	0.84954 (18)	0.0214
C15	0.1620 (2)	0.4203 (3)	0.9110 (3)	0.0203
O16	0.06795 (19)	0.5788 (2)	0.8420 (2)	0.0258
C17	0.3066 (2)	−0.1330 (3)	0.7364 (3)	0.0206
H21	0.1167	0.1019	0.5078	0.0186*
H81	0.4260	0.6034	0.4459	0.0270*
H91	0.1839	0.4273	0.3985	0.0205*
H121	−0.0451	0.2478	0.8178	0.0198*
H131	0.2502	0.0870	0.9987	0.0190*
H151	0.1800	0.4039	1.0302	0.0228*
H152	0.2750	0.4303	0.9033	0.0237*
H171	0.3705	−0.1896	0.8427	0.0314*
H172	0.2019	−0.1942	0.6764	0.0307*
H173	0.3720	−0.1277	0.6706	0.0302*
H10	−0.0367	0.5603	0.8191	0.0403*
H16	0.0970	−0.1580	0.8758	0.0334*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0139 (8)	0.0162 (9)	0.0160 (8)	−0.0031 (8)	0.0052 (7)	−0.0006 (7)
C2	0.0155 (8)	0.0160 (9)	0.0161 (8)	−0.0002 (8)	0.0066 (7)	−0.0001 (7)
N3	0.0156 (7)	0.0180 (8)	0.0145 (7)	−0.0004 (7)	0.0057 (6)	0.0017 (7)
C4	0.0177 (8)	0.0145 (9)	0.0141 (8)	0.0013 (8)	0.0078 (7)	−0.0010 (8)
O5	0.0146 (6)	0.0176 (7)	0.0161 (6)	−0.0025 (6)	0.0045 (5)	0.0033 (5)
N6	0.0171 (7)	0.0174 (8)	0.0195 (8)	−0.0012 (7)	0.0082 (6)	−0.0011 (7)
C7	0.0211 (9)	0.0175 (9)	0.0229 (9)	−0.0017 (8)	0.0127 (8)	−0.0015 (8)
C8	0.0258 (9)	0.0196 (10)	0.0211 (9)	0.0019 (8)	0.0133 (8)	0.0058 (8)
C9	0.0208 (9)	0.0201 (9)	0.0163 (8)	0.0030 (9)	0.0082 (7)	0.0032 (8)
O10	0.0233 (7)	0.0287 (8)	0.0326 (8)	−0.0068 (7)	0.0123 (6)	0.0040 (7)
O11	0.0167 (6)	0.0223 (7)	0.0171 (6)	0.0037 (6)	0.0068 (5)	0.0031 (6)
C12	0.0178 (8)	0.0159 (8)	0.0177 (8)	0.0004 (8)	0.0091 (7)	0.0021 (8)
C13	0.0171 (8)	0.0143 (9)	0.0168 (8)	−0.0011 (8)	0.0074 (7)	0.0002 (8)
O14	0.0213 (7)	0.0130 (7)	0.0318 (8)	−0.0009 (6)	0.0131 (6)	0.0028 (6)
C15	0.0208 (9)	0.0157 (9)	0.0250 (10)	0.0011 (8)	0.0103 (8)	−0.0006 (8)
O16	0.0232 (7)	0.0127 (7)	0.0431 (9)	0.0000 (6)	0.0157 (7)	0.0020 (7)
C17	0.0226 (9)	0.0160 (9)	0.0246 (9)	0.0007 (8)	0.0114 (8)	−0.0013 (8)

Geometric parameters (Å, º)

C1—C2	1.548 (3)	C9—H91	0.951
C1—O5	1.478 (2)	O11—C12	1.460 (2)
C1—C13	1.540 (2)	C12—C13	1.528 (3)
C1—C17	1.511 (3)	C12—C15	1.518 (3)
C2—N3	1.458 (2)	C12—H121	1.009
C2—O11	1.408 (2)	C13—O14	1.416 (2)
C2—H21	0.984	C13—H131	0.987
N3—C4	1.351 (2)	O14—H16	0.849
N3—C9	1.374 (2)	C15—O16	1.419 (2)
C4—O5	1.342 (2)	C15—H151	1.003
C4—N6	1.293 (2)	C15—H152	1.006
N6—C7	1.395 (2)	O16—H10	0.848
C7—C8	1.453 (3)	C17—H171	0.960
C7—O10	1.242 (2)	C17—H172	0.948
C8—C9	1.342 (3)	C17—H173	0.966
C8—H81	0.937
C2—C1—O5	104.69 (14)	C8—C9—H91	124.0
C2—C1—C13	103.79 (14)	C2—O11—C12	109.58 (13)
O5—C1—C13	107.35 (14)	O11—C12—C13	104.74 (15)
C2—C1—C17	115.42 (15)	O11—C12—C15	112.93 (16)
O5—C1—C17	107.46 (14)	C13—C12—C15	114.41 (14)
C13—C1—C17	117.21 (16)	O11—C12—H121	105.7
C1—C2—N3	101.08 (13)	C13—C12—H121	110.5
C1—C2—O11	108.34 (14)	C15—C12—H121	108.2
N3—C2—O11	112.68 (16)	C1—C13—C12	103.87 (15)
C1—C2—H21	114.2	C1—C13—O14	111.29 (15)
N3—C2—H21	110.5	C12—C13—O14	107.32 (14)
O11—C2—H21	109.9	C1—C13—H131	110.2
C2—N3—C4	112.60 (15)	C12—C13—H131	112.5
C2—N3—C9	128.54 (15)	O14—C13—H131	111.3
C4—N3—C9	118.83 (15)	C13—O14—H16	110.4
N3—C4—O5	111.11 (15)	C12—C15—O16	112.08 (15)
N3—C4—N6	127.44 (16)	C12—C15—H151	107.3
O5—C4—N6	121.44 (15)	O16—C15—H151	111.0
C1—O5—C4	109.07 (13)	C12—C15—H152	108.1
C4—N6—C7	116.17 (15)	O16—C15—H152	107.6
N6—C7—C8	118.54 (16)	H151—C15—H152	110.8
N6—C7—O10	119.61 (17)	C15—O16—H10	108.8
C8—C7—O10	121.84 (18)	C1—C17—H171	107.7
C7—C8—C9	120.68 (18)	C1—C17—H172	109.1
C7—C8—H81	118.8	H171—C17—H172	110.4
C9—C8—H81	120.5	C1—C17—H173	108.1
N3—C9—C8	118.29 (17)	H171—C17—H173	111.3
N3—C9—H91	117.7	H172—C17—H173	110.2

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O16—H10···O10^i	0.85	1.92	2.724 (2)	158
O14—H16···O16^ii	0.85	1.99	2.732 (2)	145

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