(4R,9S)-4-Hydro­xy­methyl-3,8-dioxa-1,6-di­aza­spiro­[4.4]­nonane-2,7-di­thione monohydrate

The title compound, C₆H₈N₂O₃S₂·H₂O, was synthesized from L-erythrulose and the structure of the enantiopure (4R,9S) diastereo­isomer has been determined. The structure is a hydrate and the water mol­ecules establish a hydrogen-bond network that involves the hydroxy­methyl group as well as one N and one S atom.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.051
• wR factor = 0.130
• Data-to-parameter ratio = 8.6

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low .......       0.96

Alert level C
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.70 mm

Alert level G
REFLT03_ALERT_4_G  WARNING: Large fraction of Friedel related reflns may
                     be needed to determine absolute structure
           From the CIF: _diffrn_reflns_theta_max           74.95
           From the CIF: _reflns_number_total               1164
           Count of symmetry unique reflns         1214
           Completeness (_total/calc)             95.88%
           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          yes

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   1 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
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1994); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN (MSC, 1992-1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2001); software used to prepare material for publication: PLATON.

(4R,9S)-4-Hydroxymethyl-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dithione monohydrate

Crystal data

C6H8N2O3S2·H2O	F(000) = 496
Mr = 238.28	Dx = 1.575 Mg m^−3
Orthorhombic, P212121	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2ab	Cell parameters from 24 reflections
a = 7.036 (2) Å	θ = 20.2–23.5°
b = 10.336 (3) Å	µ = 4.80 mm^−1
c = 13.814 (3) Å	T = 293 K
V = 1004.6 (5) Å^3	Prism, colourless
Z = 4	0.7 × 0.2 × 0.2 mm

Data collection

Enraf-Nonius CAD-4 diffractometer	Rint = 0.000
Radiation source: X-ray tube	θmax = 75.0°, θmin = 5.3°
Graphite monochromator	h = 0→8
ω scans	k = 0→12
1164 measured reflections	l = 0→17
1164 independent reflections	2 standard reflections every 120 reflections
1150 reflections with I > 2σ(I)	intensity decay: −3.1%

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)] = 0.051	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.130	w = 1/[σ^2(Fo^2) + (0.0629P)^2 + 0.1989P] where P = (Fo^2 + 2Fc^2)/3
S = 1.08	(Δ/σ)max < 0.001
1164 reflections	Δρmax = 0.51 e Å^−3
136 parameters	Δρmin = −0.37 e Å^−3
3 restraints	Absolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.04 (3)

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
S2	0.30174 (15)	0.28460 (10)	0.60196 (7)	0.0482 (3)
S6	0.77463 (14)	0.51533 (9)	0.19116 (6)	0.0432 (3)
O3	0.1705 (4)	0.4657 (3)	0.48718 (17)	0.0405 (6)
O7	0.4523 (4)	0.3848 (2)	0.18346 (17)	0.0393 (6)
O11	0.0172 (4)	0.7067 (2)	0.4179 (2)	0.0429 (6)
H11	0.0544	0.7687	0.4497	0.064*
O12	0.1867 (4)	0.8983 (3)	0.52506 (19)	0.0424 (6)
N1	0.3471 (5)	0.3241 (3)	0.4119 (2)	0.0352 (6)
H1	0.4047	0.2519	0.4018	0.042*
N5	0.4929 (4)	0.4927 (3)	0.31867 (19)	0.0335 (6)
H5	0.5423	0.5475	0.3582	0.040*
C2	0.2743 (5)	0.3579 (3)	0.4970 (2)	0.0346 (7)
C4	0.1577 (5)	0.5002 (3)	0.3854 (2)	0.0309 (6)
H4	0.0351	0.4714	0.3595	0.037*
C6	0.5667 (5)	0.4633 (3)	0.2330 (2)	0.0314 (6)
C8	0.2761 (5)	0.3711 (3)	0.2354 (2)	0.0373 (7)
H8A	0.2366	0.2812	0.2374	0.045*
H8B	0.1765	0.4219	0.2052	0.045*
C9	0.3189 (5)	0.4215 (3)	0.3379 (2)	0.0292 (6)
C10	0.1744 (6)	0.6446 (3)	0.3742 (3)	0.0393 (7)
H10A	0.2911	0.6743	0.4043	0.047*
H10B	0.1793	0.6667	0.3060	0.047*
H121	0.198 (8)	0.950 (4)	0.479 (3)	0.058 (15)*
H122	0.288 (5)	0.866 (4)	0.544 (3)	0.048 (13)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S2	0.0514 (5)	0.0575 (5)	0.0356 (4)	−0.0010 (5)	−0.0007 (4)	0.0116 (4)
S6	0.0414 (5)	0.0513 (5)	0.0369 (5)	−0.0004 (4)	0.0098 (3)	−0.0032 (3)
O3	0.0491 (13)	0.0416 (11)	0.0306 (11)	0.0089 (12)	0.0069 (11)	0.0005 (9)
O7	0.0493 (14)	0.0410 (11)	0.0277 (10)	0.0000 (11)	0.0007 (11)	−0.0095 (9)
O11	0.0393 (12)	0.0344 (11)	0.0552 (15)	0.0000 (10)	0.0019 (12)	−0.0101 (11)
O12	0.0456 (14)	0.0450 (13)	0.0365 (13)	0.0047 (12)	0.0035 (11)	−0.0063 (11)
N1	0.0420 (14)	0.0299 (12)	0.0337 (12)	0.0040 (12)	0.0016 (12)	0.0008 (11)
N5	0.0357 (13)	0.0362 (12)	0.0286 (12)	−0.0050 (11)	0.0010 (10)	−0.0109 (10)
C2	0.0362 (15)	0.0331 (14)	0.0347 (14)	−0.0055 (14)	0.0012 (13)	0.0006 (12)
C4	0.0339 (14)	0.0299 (14)	0.0287 (14)	−0.0020 (12)	0.0006 (12)	0.0009 (11)
C6	0.0385 (14)	0.0276 (12)	0.0281 (13)	0.0054 (12)	−0.0018 (13)	0.0014 (11)
C8	0.0411 (16)	0.0352 (13)	0.0354 (15)	−0.0046 (14)	−0.0033 (14)	−0.0083 (13)
C9	0.0321 (14)	0.0280 (12)	0.0274 (14)	−0.0022 (12)	0.0006 (12)	−0.0015 (11)
C10	0.0440 (18)	0.0305 (15)	0.0433 (16)	0.0007 (15)	0.0078 (15)	−0.0013 (13)

Geometric parameters (Å, º)

S2—C2	1.648 (3)	N1—H1	0.8600
S6—C6	1.662 (4)	N5—C6	1.328 (4)
O3—C2	1.339 (4)	N5—C9	1.452 (4)
O3—C4	1.454 (4)	N5—H5	0.8600
O7—C6	1.332 (4)	C4—C10	1.505 (4)
O7—C8	1.440 (5)	C4—C9	1.542 (4)
O11—C10	1.414 (4)	C4—H4	0.9800
O11—H11	0.8200	C8—C9	1.538 (4)
O12—H121	0.84 (2)	C8—H8A	0.9700
O12—H122	0.83 (4)	C8—H8B	0.9700
N1—C2	1.329 (4)	C10—H10A	0.9700
N1—C9	1.449 (4)	C10—H10B	0.9700
C2—O3—C4	109.6 (2)	N5—C6—S6	125.5 (3)
C6—O7—C8	108.9 (3)	O7—C6—S6	123.4 (2)
C10—O11—H11	109.5	O7—C8—C9	104.9 (3)
H121—O12—H122	114 (3)	O7—C8—H8A	110.8
C2—N1—C9	112.9 (3)	C9—C8—H8A	110.8
C2—N1—H1	123.6	O7—C8—H8B	110.8
C9—N1—H1	123.6	C9—C8—H8B	110.8
C6—N5—C9	112.1 (3)	H8A—C8—H8B	108.8
C6—N5—H5	123.9	N1—C9—N5	111.5 (3)
C9—N5—H5	123.9	N1—C9—C8	116.1 (2)
N1—C2—O3	109.9 (3)	N5—C9—C8	99.7 (2)
N1—C2—S2	127.8 (3)	N1—C9—C4	99.6 (2)
O3—C2—S2	122.4 (3)	N5—C9—C4	115.5 (2)
O3—C4—C10	109.8 (3)	C8—C9—C4	115.2 (3)
O3—C4—C9	103.7 (2)	O11—C10—C4	110.2 (3)
C10—C4—C9	114.9 (3)	O11—C10—H10A	109.6
O3—C4—H4	109.4	C4—C10—H10A	109.6
C10—C4—H4	109.4	O11—C10—H10B	109.6
C9—C4—H4	109.4	C4—C10—H10B	109.6
N5—C6—O7	111.1 (3)	H10A—C10—H10B	108.1
C9—N1—C2—O3	8.9 (4)	C6—N5—C9—N1	108.9 (3)
C9—N1—C2—S2	−170.7 (3)	C6—N5—C9—C8	−14.3 (3)
C4—O3—C2—N1	5.8 (4)	C6—N5—C9—C4	−138.4 (3)
C4—O3—C2—S2	−174.5 (2)	O7—C8—C9—N1	−102.6 (3)
C2—O3—C4—C10	−140.0 (3)	O7—C8—C9—N5	17.3 (3)
C2—O3—C4—C9	−16.7 (3)	O7—C8—C9—C4	141.5 (3)
C9—N5—C6—O7	5.6 (4)	O3—C4—C9—N1	19.8 (3)
C9—N5—C6—S6	−174.0 (2)	C10—C4—C9—N1	139.6 (3)
C8—O7—C6—N5	7.0 (4)	O3—C4—C9—N5	−99.7 (3)
C8—O7—C6—S6	−173.4 (2)	C10—C4—C9—N5	20.1 (4)
C6—O7—C8—C9	−15.6 (3)	O3—C4—C9—C8	144.8 (3)
C2—N1—C9—N5	104.2 (3)	C10—C4—C9—C8	−95.4 (3)
C2—N1—C9—C8	−142.5 (3)	O3—C4—C10—O11	−65.3 (4)
C2—N1—C9—C4	−18.2 (4)	C9—C4—C10—O11	178.4 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O11—H11···O12	0.82	1.94	2.746 (4)	169
N5—H5···O12^i	0.86	1.99	2.791 (4)	155
O12—H121···S6^ii	0.84 (2)	2.45 (3)	3.234 (3)	156 (5)
O12—H122···O11^i	0.83 (4)	1.86 (2)	2.685 (4)	178 (5)

Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) −x+1, y+1/2, −z+1/2.