3-(Dimethoxy­thio­phospho­rylamido)-2-(2′,3′,4′-tri-O-acetyl-β-D-xylopyranos-1′-ylimino)-1,3-thia­zolidin-4-one

In the title compound, C₁₆H₂₄N₃O₁₀PS₂, the thia­zolidine ring is approximately planar and the tetra­hydro­pyran ring adopts a chair conformation. The crystal packing is stabilized by inter­molecular N—H...O, C—H...S and C—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 113 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.040
• wR factor = 0.084
• Data-to-parameter ratio = 17.8

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT413_ALERT_2_B Short Inter XH3 .. XHn     H7B    ..  H16A    ..       2.07 Ang.

Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.03 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.86 Ratio

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           27.85
           From the CIF: _reflns_number_total               5317
           Count of symmetry unique reflns         2946
           Completeness (_total/calc)            180.48%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      2371
           Fraction of Friedel pairs measured     0.805
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C6     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C8     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C9     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C10    = .          R

   0 ALERT level A = In general: serious problem
   1 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
   2 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
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

Computing details

Data collection: CrystalClear (Rigaku/MSC, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; 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: CrystalStructure (Rigaku/MSC, 2005).

3-(Dimethoxythiophosphorylamido)-2-(2',3',4'-tri-O-acetyl-β-D– xylopyranos-1'-ylimino)-1,3-thiazolidin-4-one

Crystal data

C16H24N3O10PS2	F(000) = 536
Mr = 513.47	Dx = 1.490 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71070 Å
Hall symbol: P 2yb	Cell parameters from 3246 reflections
a = 7.517 (4) Å	θ = 1.8–27.8°
b = 6.819 (3) Å	µ = 0.36 mm^−1
c = 22.574 (11) Å	T = 113 K
β = 98.626 (7)°	Prism, colourless
V = 1144.0 (10) Å^3	0.12 × 0.12 × 0.12 mm
Z = 2

Data collection

Rigaku Saturn diffractometer	5317 independent reflections
Radiation source: Rotating anode	4572 reflections with I > 2σ(I)
Confocal monochromator	Rint = 0.040
Detector resolution: 7.31 pixels mm^-1	θmax = 27.9°, θmin = 1.8°
ω scans	h = −9→9
Absorption correction: multi-scan (Jacobson, 1998)	k = −8→8
Tmin = 0.958, Tmax = 0.958	l = −29→29
12248 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)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.084	w = 1/[σ^2(Fo^2) + (0.041P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.02	(Δ/σ)max = 0.001
5317 reflections	Δρmax = 0.23 e Å^−3
299 parameters	Δρmin = −0.28 e Å^−3
2 restraints	Absolute structure: Flack (1983), 2369 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.01 (6)

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
P1	1.27299 (8)	1.00950 (9)	0.41121 (3)	0.02107 (14)
S1	0.76207 (8)	1.37077 (9)	0.30835 (3)	0.02099 (13)
S2	1.34386 (9)	1.19672 (10)	0.35610 (3)	0.02885 (16)
O1	1.3000 (3)	0.7882 (3)	0.39418 (8)	0.0276 (4)
O2	1.3728 (2)	1.0092 (3)	0.47781 (7)	0.0254 (4)
O3	1.0379 (2)	1.4066 (3)	0.46618 (8)	0.0301 (4)
O4	0.6442 (2)	0.7630 (2)	0.26237 (7)	0.0209 (4)
O5	0.5524 (3)	0.2977 (3)	0.13984 (9)	0.0326 (4)
O6	0.5693 (2)	0.6059 (3)	0.10502 (8)	0.0272 (4)
O7	0.8927 (3)	1.0823 (3)	0.06911 (9)	0.0457 (6)
O8	0.9080 (2)	0.7906 (3)	0.11631 (8)	0.0267 (4)
O9	1.2034 (2)	1.0073 (3)	0.19712 (9)	0.0342 (4)
O10	0.9277 (2)	1.1226 (2)	0.20528 (7)	0.0197 (4)
N1	1.0612 (3)	1.0299 (3)	0.42213 (9)	0.0230 (4)
H1	1.038 (4)	0.984 (4)	0.4573 (7)	0.035 (8)*
N2	0.9539 (3)	1.1789 (3)	0.39393 (8)	0.0193 (4)
N3	0.8374 (3)	0.9761 (3)	0.31576 (8)	0.0183 (4)
C1	1.2593 (4)	0.7227 (4)	0.33309 (12)	0.0312 (6)
H1A	1.1295	0.7331	0.3197	0.047*
H1B	1.2970	0.5858	0.3304	0.047*
H1C	1.3237	0.8046	0.3076	0.047*
C2	1.5678 (3)	0.9869 (5)	0.48845 (13)	0.0323 (6)
H2A	1.6015	0.8676	0.4686	0.048*
H2B	1.6093	0.9772	0.5316	0.048*
H2C	1.6238	1.1009	0.4723	0.048*
C3	0.9513 (3)	1.3632 (4)	0.41845 (10)	0.0228 (5)
C4	0.8219 (3)	1.4938 (4)	0.37981 (10)	0.0245 (5)
H4A	0.8786	1.6221	0.3741	0.029*
H4B	0.7132	1.5165	0.3988	0.029*
C5	0.8509 (3)	1.1458 (3)	0.33800 (10)	0.0179 (5)
C6	0.7331 (3)	0.9452 (3)	0.25780 (10)	0.0178 (5)
H6	0.6448	1.0539	0.2471	0.021*
C7	0.5415 (3)	0.7061 (4)	0.20668 (11)	0.0235 (5)
H7A	0.4580	0.8130	0.1913	0.028*
H7B	0.4694	0.5880	0.2124	0.028*
C8	0.6690 (3)	0.6627 (4)	0.16199 (10)	0.0205 (5)
H8	0.7551	0.5566	0.1777	0.025*
C9	0.7709 (3)	0.8482 (4)	0.15154 (10)	0.0208 (5)
H9	0.6885	0.9486	0.1299	0.025*
C10	0.8616 (3)	0.9265 (3)	0.21165 (10)	0.0179 (5)
H10	0.9641	0.8388	0.2278	0.021*
C11	0.5240 (3)	0.4131 (4)	0.09965 (12)	0.0266 (6)
C12	0.4350 (5)	0.3669 (5)	0.03717 (13)	0.0481 (8)
H12A	0.5273	0.3414	0.0117	0.072*
H12B	0.3610	0.4785	0.0211	0.072*
H12C	0.3588	0.2507	0.0379	0.072*
C13	0.9619 (4)	0.9255 (5)	0.07871 (11)	0.0341 (7)
C14	1.1199 (5)	0.8508 (6)	0.05268 (14)	0.0539 (9)
H14A	1.0832	0.7380	0.0268	0.081*
H14B	1.2146	0.8107	0.0851	0.081*
H14C	1.1657	0.9546	0.0290	0.081*
C15	1.1032 (3)	1.1417 (4)	0.19986 (11)	0.0245 (6)
C16	1.1503 (4)	1.3544 (5)	0.19700 (14)	0.0395 (7)
H16A	1.2796	1.3679	0.1961	0.059*
H16B	1.1188	1.4220	0.2323	0.059*
H16C	1.0831	1.4126	0.1607	0.059*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
P1	0.0240 (3)	0.0189 (3)	0.0200 (3)	−0.0001 (3)	0.0023 (2)	0.0019 (3)
S1	0.0254 (3)	0.0166 (3)	0.0209 (3)	0.0011 (3)	0.0033 (2)	−0.0006 (2)
S2	0.0311 (4)	0.0244 (3)	0.0328 (4)	−0.0012 (3)	0.0105 (3)	0.0052 (3)
O1	0.0369 (10)	0.0226 (10)	0.0224 (9)	0.0028 (8)	0.0018 (8)	0.0008 (7)
O2	0.0223 (9)	0.0265 (10)	0.0250 (9)	0.0007 (8)	−0.0050 (7)	−0.0011 (8)
O3	0.0305 (9)	0.0384 (12)	0.0218 (9)	−0.0037 (9)	0.0053 (7)	−0.0106 (8)
O4	0.0239 (9)	0.0187 (9)	0.0204 (8)	−0.0052 (7)	0.0042 (7)	−0.0005 (6)
O5	0.0337 (10)	0.0231 (10)	0.0419 (12)	−0.0035 (8)	0.0080 (9)	−0.0034 (9)
O6	0.0335 (10)	0.0193 (9)	0.0256 (9)	−0.0044 (8)	−0.0060 (8)	−0.0040 (7)
O7	0.0637 (15)	0.0455 (14)	0.0290 (11)	−0.0110 (12)	0.0108 (10)	0.0103 (10)
O8	0.0314 (10)	0.0282 (10)	0.0221 (9)	−0.0036 (8)	0.0096 (7)	−0.0055 (7)
O9	0.0229 (9)	0.0353 (11)	0.0467 (11)	0.0011 (9)	0.0127 (8)	−0.0067 (10)
O10	0.0207 (8)	0.0183 (9)	0.0206 (8)	−0.0032 (7)	0.0046 (7)	−0.0006 (6)
N1	0.0255 (10)	0.0275 (12)	0.0155 (10)	0.0026 (10)	0.0018 (8)	0.0053 (9)
N2	0.0241 (10)	0.0183 (10)	0.0153 (9)	0.0024 (9)	0.0019 (8)	0.0002 (8)
N3	0.0190 (9)	0.0198 (11)	0.0163 (9)	0.0000 (8)	0.0036 (7)	0.0015 (8)
C1	0.0407 (16)	0.0228 (15)	0.0299 (14)	0.0038 (12)	0.0041 (12)	−0.0033 (11)
C2	0.0239 (13)	0.0340 (16)	0.0365 (15)	0.0020 (12)	−0.0038 (11)	0.0000 (13)
C3	0.0220 (11)	0.0293 (13)	0.0192 (12)	−0.0033 (12)	0.0103 (9)	−0.0041 (11)
C4	0.0260 (12)	0.0226 (13)	0.0265 (13)	0.0005 (11)	0.0088 (10)	−0.0053 (11)
C5	0.0182 (11)	0.0203 (13)	0.0163 (11)	−0.0001 (9)	0.0060 (9)	0.0028 (9)
C6	0.0182 (11)	0.0144 (11)	0.0201 (11)	−0.0008 (9)	0.0009 (9)	0.0014 (9)
C7	0.0180 (12)	0.0249 (14)	0.0264 (12)	−0.0040 (11)	−0.0012 (10)	−0.0030 (11)
C8	0.0229 (12)	0.0202 (13)	0.0172 (11)	−0.0017 (10)	−0.0014 (9)	−0.0030 (10)
C9	0.0246 (12)	0.0191 (13)	0.0184 (11)	−0.0007 (10)	0.0024 (9)	−0.0033 (10)
C10	0.0194 (11)	0.0164 (12)	0.0180 (11)	−0.0005 (9)	0.0029 (9)	−0.0004 (9)
C11	0.0231 (13)	0.0245 (14)	0.0321 (14)	−0.0048 (11)	0.0039 (11)	−0.0078 (11)
C12	0.062 (2)	0.0381 (18)	0.0401 (17)	−0.0163 (18)	−0.0055 (15)	−0.0134 (15)
C13	0.0440 (17)	0.0421 (19)	0.0172 (13)	−0.0156 (15)	0.0071 (12)	−0.0074 (12)
C14	0.057 (2)	0.069 (3)	0.0421 (18)	−0.018 (2)	0.0285 (15)	−0.0164 (18)
C15	0.0220 (13)	0.0296 (15)	0.0223 (13)	−0.0063 (11)	0.0045 (10)	−0.0050 (11)
C16	0.0351 (15)	0.0300 (16)	0.0571 (19)	−0.0155 (14)	0.0196 (14)	−0.0078 (15)

Geometric parameters (Å, º)

P1—O2	1.5764 (18)	C2—H2A	0.98
P1—O1	1.578 (2)	C2—H2B	0.98
P1—N1	1.653 (2)	C2—H2C	0.98
P1—S2	1.9132 (11)	C3—C4	1.499 (4)
S1—C5	1.765 (2)	C4—H4A	0.99
S1—C4	1.814 (3)	C4—H4B	0.99
O1—C1	1.438 (3)	C6—C10	1.529 (3)
O2—C2	1.457 (3)	C6—H6	1.00
O3—C3	1.209 (3)	C7—C8	1.521 (3)
O4—C6	1.422 (3)	C7—H7A	0.99
O4—C7	1.427 (3)	C7—H7B	0.99
O5—C11	1.196 (3)	C8—C9	1.515 (4)
O6—C11	1.359 (3)	C8—H8	1.00
O6—C8	1.441 (3)	C9—C10	1.521 (3)
O7—C13	1.194 (4)	C9—H9	1.00
O8—C13	1.354 (3)	C10—H10	1.00
O8—C9	1.448 (3)	C11—C12	1.501 (4)
O9—C15	1.193 (3)	C12—H12A	0.98
O10—C15	1.350 (3)	C12—H12B	0.98
O10—C10	1.441 (3)	C12—H12C	0.98
N1—N2	1.391 (3)	C13—C14	1.492 (4)
N1—H1	0.897 (10)	C14—H14A	0.98
N2—C3	1.374 (3)	C14—H14B	0.98
N2—C5	1.397 (3)	C14—H14C	0.98
N3—C5	1.259 (3)	C15—C16	1.497 (4)
N3—C6	1.436 (3)	C16—H16A	0.98
C1—H1A	0.98	C16—H16B	0.98
C1—H1B	0.98	C16—H16C	0.98
C1—H1C	0.98
O2—P1—O1	99.82 (10)	O4—C7—H7A	109.9
O2—P1—N1	100.92 (10)	C8—C7—H7A	109.9
O1—P1—N1	106.21 (11)	O4—C7—H7B	109.9
O2—P1—S2	118.81 (8)	C8—C7—H7B	109.9
O1—P1—S2	114.91 (8)	H7A—C7—H7B	108.3
N1—P1—S2	114.15 (8)	O6—C8—C9	107.03 (19)
C5—S1—C4	92.04 (12)	O6—C8—C7	110.42 (19)
C1—O1—P1	120.92 (16)	C9—C8—C7	108.9 (2)
C2—O2—P1	118.74 (16)	O6—C8—H8	110.1
C6—O4—C7	111.81 (18)	C9—C8—H8	110.1
C11—O6—C8	115.5 (2)	C7—C8—H8	110.1
C13—O8—C9	117.7 (2)	O8—C9—C8	106.11 (19)
C15—O10—C10	117.05 (19)	O8—C9—C10	108.93 (19)
N2—N1—P1	119.93 (16)	C8—C9—C10	108.88 (19)
N2—N1—H1	118.9 (19)	O8—C9—H9	110.9
P1—N1—H1	115.2 (18)	C8—C9—H9	110.9
C3—N2—N1	121.71 (19)	C10—C9—H9	110.9
C3—N2—C5	118.20 (19)	O10—C10—C9	110.61 (19)
N1—N2—C5	120.04 (19)	O10—C10—C6	104.66 (17)
C5—N3—C6	119.9 (2)	C9—C10—C6	113.11 (19)
O1—C1—H1A	109.5	O10—C10—H10	109.4
O1—C1—H1B	109.5	C9—C10—H10	109.4
H1A—C1—H1B	109.5	C6—C10—H10	109.4
O1—C1—H1C	109.5	O5—C11—O6	123.7 (2)
H1A—C1—H1C	109.5	O5—C11—C12	125.4 (3)
H1B—C1—H1C	109.5	O6—C11—C12	110.9 (3)
O2—C2—H2A	109.5	C11—C12—H12A	109.5
O2—C2—H2B	109.5	C11—C12—H12B	109.5
H2A—C2—H2B	109.5	H12A—C12—H12B	109.5
O2—C2—H2C	109.5	C11—C12—H12C	109.5
H2A—C2—H2C	109.5	H12A—C12—H12C	109.5
H2B—C2—H2C	109.5	H12B—C12—H12C	109.5
O3—C3—N2	123.0 (2)	O7—C13—O8	124.0 (3)
O3—C3—C4	126.1 (2)	O7—C13—C14	125.8 (3)
N2—C3—C4	110.9 (2)	O8—C13—C14	110.2 (3)
C3—C4—S1	107.18 (18)	C13—C14—H14A	109.5
C3—C4—H4A	110.3	C13—C14—H14B	109.5
S1—C4—H4A	110.3	H14A—C14—H14B	109.5
C3—C4—H4B	110.3	C13—C14—H14C	109.5
S1—C4—H4B	110.3	H14A—C14—H14C	109.5
H4A—C4—H4B	108.5	H14B—C14—H14C	109.5
N3—C5—N2	120.6 (2)	O9—C15—O10	124.3 (2)
N3—C5—S1	130.12 (18)	O9—C15—C16	126.0 (2)
N2—C5—S1	109.21 (16)	O10—C15—C16	109.8 (2)
O4—C6—N3	105.08 (18)	C15—C16—H16A	109.5
O4—C6—C10	109.19 (18)	C15—C16—H16B	109.5
N3—C6—C10	108.59 (18)	H16A—C16—H16B	109.5
O4—C6—H6	111.3	C15—C16—H16C	109.5
N3—C6—H6	111.3	H16A—C16—H16C	109.5
C10—C6—H6	111.3	H16B—C16—H16C	109.5
O4—C7—C8	109.01 (19)
O2—P1—O1—C1	−168.66 (19)	C5—N3—C6—C10	101.8 (2)
N1—P1—O1—C1	86.8 (2)	C6—O4—C7—C8	66.6 (2)
S2—P1—O1—C1	−40.4 (2)	C11—O6—C8—C9	156.8 (2)
O1—P1—O2—C2	69.4 (2)	C11—O6—C8—C7	−84.8 (3)
N1—P1—O2—C2	178.1 (2)	O4—C7—C8—O6	−179.66 (19)
S2—P1—O2—C2	−56.3 (2)	O4—C7—C8—C9	−62.4 (3)
O2—P1—N1—N2	126.30 (18)	C13—O8—C9—C8	150.6 (2)
O1—P1—N1—N2	−130.00 (18)	C13—O8—C9—C10	−92.3 (2)
S2—P1—N1—N2	−2.3 (2)	O6—C8—C9—O8	−69.2 (2)
P1—N1—N2—C3	−85.9 (2)	C7—C8—C9—O8	171.43 (18)
P1—N1—N2—C5	91.3 (2)	O6—C8—C9—C10	173.72 (18)
N1—N2—C3—O3	−1.7 (3)	C7—C8—C9—C10	54.3 (2)
C5—N2—C3—O3	−178.9 (2)	C15—O10—C10—C9	−97.3 (2)
N1—N2—C3—C4	−178.78 (19)	C15—O10—C10—C6	140.52 (19)
C5—N2—C3—C4	4.0 (3)	O8—C9—C10—O10	76.8 (2)
O3—C3—C4—S1	169.9 (2)	C8—C9—C10—O10	−167.87 (18)
N2—C3—C4—S1	−13.1 (2)	O8—C9—C10—C6	−166.14 (19)
C5—S1—C4—C3	14.67 (18)	C8—C9—C10—C6	−50.8 (3)
C6—N3—C5—N2	−179.05 (19)	O4—C6—C10—O10	173.39 (17)
C6—N3—C5—S1	−1.4 (3)	N3—C6—C10—O10	−72.6 (2)
C3—N2—C5—N3	−174.4 (2)	O4—C6—C10—C9	52.9 (3)
N1—N2—C5—N3	8.3 (3)	N3—C6—C10—C9	166.97 (19)
C3—N2—C5—S1	7.5 (2)	C8—O6—C11—O5	4.8 (4)
N1—N2—C5—S1	−169.77 (16)	C8—O6—C11—C12	−175.1 (2)
C4—S1—C5—N3	169.3 (2)	C9—O8—C13—O7	−6.7 (4)
C4—S1—C5—N2	−12.85 (17)	C9—O8—C13—C14	172.2 (2)
C7—O4—C6—N3	−176.84 (18)	C10—O10—C15—O9	3.8 (3)
C7—O4—C6—C10	−60.5 (2)	C10—O10—C15—C16	−177.0 (2)
C5—N3—C6—O4	−141.5 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O3^i	0.90 (1)	1.97 (1)	2.861 (3)	173 (3)
C1—H1B···S2^ii	0.98	2.73	3.666 (3)	161
C7—H7A···O9^iii	0.99	2.35	3.250 (3)	151
C14—H14A···O7^iv	0.98	2.44	3.293 (4)	145

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