(4R,5R)-4,5-Bis{2-[3-(2,6-diisopropyl­phen­yl)-2-thioxoimidazolidin-3-yl]eth­yl}-2,2-dimethyl-1,3-dioxolane

In the chiral title compound, C₃₉H₅₈N₄O₂S₂, the complete mol­ecule is generated by crystallographic twofold symmetry, with one C atom lying on the rotation axis. The packing is established by van der Waals forces.

Key indicators

• Single-crystal X-ray study
• T = 120 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.058
• wR factor = 0.110
• Data-to-parameter ratio = 21.0

checkCIF/PLATON results

No syntax errors found



Alert level B
RINTA01_ALERT_3_B  The value of Rint is greater than 0.15
            Rint given   0.170
PLAT020_ALERT_3_B The value of Rint is greater than 0.10 .........       0.17

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           27.49
           From the CIF: _reflns_number_total               4596
           Count of symmetry unique reflns         2638
           Completeness (_total/calc)            174.22%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1958
           Fraction of Friedel pairs measured     0.742
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          R

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

   1 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
   0 ALERT type 5 Informative message, check

---

S1. Comment

As part of our ongoing investigations of chiral, C₂-symmetric catalysts (Marshall & Harrison, 2007), the title compound, (I), C₃₉H₅₈N₄O₂S₂, an intermediate in such materials, has been synthesized and structurally characterized.

The complete molecule of (I) is generated by crystallographic 2-fold symmetry, with C2 lying on the rotation axis (Fig. 1). Thus, of course, both C3 and C3ⁱ (i = 1=x, 1 - y, z) must show the same chiralities, where are the expected R configurations. The dihedral angle between the C9–C14 and C9ⁱ–C14ⁱ rings is 67.10 (7)°

The C—N and (nominal) C═S bonds in the 5-membered rings display typical geometrical parameters, which can be correlated with the contribution of resonance structures involving the lone pair electrons of the adjacent N atoms (Williamson et al., 2006). Otherwise, the geometries of the two molecules may be regarded as normal (Allen et al., 1995).

The crystal packing for (I) is established only by van der Waals forces.

Related literature

For background, see: Marshall & Harrison (2007); Williamson et al. (2006). For reference structural data, see: Allen et al. (1995).

S2. Experimental

A mixture of (4R,5R)-4,5-bis[1-(2,6-diisopropylphenyl)-imidazolidinium-3-ethyl]-2,2- dimethyl-1,3-dioxolane dibromide (0.75 g, 0.963 mmol), sulfur (0.09 g, 2.89 mmol), methanol (10 cm3), pyridine (1.5 cm3) and 1,8-diazabicyclo[5.4.0]undec-7-ene (0.65 g, 4.29 mmol) was heated at 338 K for 18 h. Once cooled to room temperature the mixture was opened to water (40 ml) and extracted with chloroform (3 × 20 ml). The combined extracts were dried over magnesium sulfate, filtered and concentrated under reduced pressure to leave a brown residue. The crude product was purified by column chromatography (SiO₂, ethyl acetate:petroleum ether v/v 1:1, loaded as a dichloromethane solution) to give the title compound (0.48 g, 73%) as a colourless solid. Colourless rods and needles of (I) were recrystallized from diethyl ether/acetone (v/v 1:1). M.p 351 K.

S3. Refinement

The H atoms were placed in calculated positions (C—H = 0.95–1.00 Å) and refined as riding with U_iso(H) = 1.2U_eq(C) or 1.5U_eq(methyl C). The methyl groups were allowed to rotate, but not to tip, to best fit the electron density.

Computing details

Data collection: COLLECT (Nonius, 1998); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: SCALEPACK (Otwinowski & Minor, 1997), DENZO (Otwinowski & Minor, 1997) and SORTAV (Blessing, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures

Fig. 1. View of the molecular structure of (I) showing 50% displacement ellipsoids. All the H atoms except H3 (represented as arbitrary spheres) are omitted for clarity. Symmetry code: (i) 1 - x, 1 - y, z.

(4R,5R)-4,5-Bis{2-[3-(2,6-diisopropylphenyl)-2- thioxoimidazolidin-3-yl]ethyl}-2,2-dimethyl-1,3-dioxolane

Crystal data

C39H58N4O2S2	F(000) = 736
Mr = 679.02	Dx = 1.119 Mg m^−3
Orthorhombic, P21212	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2 2ab	Cell parameters from 9370 reflections
a = 13.5581 (7) Å	θ = 2.9–27.5°
b = 19.3022 (9) Å	µ = 0.17 mm^−1
c = 7.7028 (3) Å	T = 120 K
V = 2015.83 (16) Å^3	Rod, colourless
Z = 2	0.40 × 0.04 × 0.04 mm

Data collection

Enraf–Nonius KappaCCD diffractometer	4595 independent reflections
Radiation source: fine-focus sealed tube	2574 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.171
ω scans	θmax = 27.5°, θmin = 2.1°
Absorption correction: multi-scan (SORTAV; Blessing, 1995)	h = −17→17
Tmin = 0.936, Tmax = 0.995	k = −25→22
16730 measured reflections	l = −9→9

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.058	w = 1/[σ^2(Fo^2) + (0.0178P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.110	(Δ/σ)max = 0.001
S = 0.93	Δρmax = 0.25 e Å^−3
4595 reflections	Δρmin = −0.25 e Å^−3
219 parameters	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0070 (11)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), with 1958 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: −0.04 (9)

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	0.5915 (2)	0.50945 (16)	1.2187 (4)	0.0320 (8)
H1A	0.5822	0.5486	1.2982	0.048*
H1B	0.6480	0.5187	1.1426	0.048*
H1C	0.6040	0.4672	1.2859	0.048*
C2	0.5000	0.5000	1.1103 (5)	0.0296 (11)
C3	0.4899 (2)	0.46133 (13)	0.8247 (3)	0.0253 (7)
H3	0.4184	0.4523	0.8028	0.030*
C4	0.5526 (2)	0.41930 (13)	0.7009 (4)	0.0268 (7)
H4A	0.6231	0.4258	0.7301	0.032*
H4B	0.5422	0.4362	0.5810	0.032*
C5	0.5272 (2)	0.34231 (14)	0.7100 (4)	0.0258 (7)
H5A	0.5168	0.3292	0.8329	0.031*
H5B	0.4646	0.3343	0.6472	0.031*
C6	0.6906 (2)	0.28145 (17)	0.7370 (4)	0.0350 (9)
H6A	0.6734	0.2558	0.8441	0.042*
H6B	0.7275	0.3239	0.7684	0.042*
C7	0.7496 (2)	0.23626 (18)	0.6123 (3)	0.0343 (8)
H7A	0.8207	0.2481	0.6149	0.041*
H7B	0.7413	0.1864	0.6389	0.041*
C8	0.6161 (2)	0.28675 (14)	0.4647 (4)	0.0239 (7)
C9	0.7430 (2)	0.22828 (16)	0.2855 (4)	0.0280 (7)
C10	0.80994 (19)	0.27006 (15)	0.1907 (4)	0.0274 (7)
C11	0.8526 (2)	0.24189 (17)	0.0437 (4)	0.0292 (8)
H11	0.8986	0.2686	−0.0208	0.035*
C12	0.8296 (2)	0.17542 (16)	−0.0116 (4)	0.0315 (8)
H12	0.8604	0.1567	−0.1121	0.038*
C13	0.7618 (2)	0.13650 (16)	0.0801 (4)	0.0279 (8)
H13	0.7451	0.0915	0.0397	0.033*
C14	0.7174 (2)	0.16141 (16)	0.2295 (4)	0.0279 (8)
C15	0.6440 (2)	0.11698 (17)	0.3277 (4)	0.0348 (8)
H15	0.6224	0.1438	0.4320	0.042*
C16	0.6897 (3)	0.04963 (19)	0.3921 (5)	0.0575 (11)
H16A	0.7466	0.0601	0.4662	0.086*
H16B	0.7113	0.0219	0.2926	0.086*
H16C	0.6407	0.0236	0.4590	0.086*
C17	0.5526 (2)	0.10291 (17)	0.2180 (5)	0.0484 (10)
H17A	0.5040	0.0776	0.2874	0.073*
H17B	0.5710	0.0752	0.1165	0.073*
H17C	0.5242	0.1470	0.1795	0.073*
C18	0.8353 (2)	0.34351 (17)	0.2495 (4)	0.0352 (9)
H18	0.7933	0.3548	0.3523	0.042*
C19	0.8121 (3)	0.39612 (17)	0.1065 (4)	0.0440 (10)
H19A	0.8264	0.4430	0.1487	0.066*
H19B	0.7423	0.3928	0.0749	0.066*
H19C	0.8529	0.3863	0.0044	0.066*
C20	0.9436 (2)	0.34825 (18)	0.3058 (5)	0.0543 (10)
H20A	0.9570	0.3947	0.3516	0.081*
H20B	0.9864	0.3394	0.2056	0.081*
H20C	0.9567	0.3137	0.3961	0.081*
N1	0.60327 (17)	0.29785 (12)	0.6361 (3)	0.0254 (6)
N2	0.70470 (16)	0.25442 (13)	0.4446 (3)	0.0289 (6)
O1	0.51541 (16)	0.44164 (10)	0.9980 (2)	0.0380 (6)
S1	0.53936 (5)	0.30782 (4)	0.30485 (10)	0.0304 (2)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0428 (18)	0.0205 (18)	0.0326 (17)	−0.0024 (15)	0.0070 (17)	0.0058 (15)
C2	0.052 (3)	0.017 (3)	0.020 (2)	0.004 (2)	0.000	0.000
C3	0.0364 (16)	0.0186 (16)	0.0209 (15)	−0.0012 (14)	−0.0003 (14)	0.0030 (13)
C4	0.0330 (17)	0.0227 (17)	0.0247 (15)	−0.0001 (14)	0.0065 (16)	−0.0004 (15)
C5	0.0296 (16)	0.0216 (16)	0.0263 (15)	0.0010 (14)	0.0069 (16)	−0.0037 (14)
C6	0.0418 (19)	0.037 (2)	0.0257 (17)	0.0109 (16)	0.0008 (15)	−0.0028 (14)
C7	0.0357 (18)	0.044 (2)	0.0236 (15)	0.0088 (17)	−0.0064 (14)	−0.0027 (16)
C8	0.0283 (16)	0.0173 (18)	0.0260 (16)	0.0008 (14)	0.0041 (14)	−0.0005 (14)
C9	0.0278 (16)	0.033 (2)	0.0236 (15)	0.0123 (14)	−0.0023 (15)	−0.0033 (16)
C10	0.0271 (16)	0.0285 (19)	0.0265 (16)	0.0064 (14)	−0.0034 (16)	−0.0002 (16)
C11	0.0265 (16)	0.037 (2)	0.0243 (16)	0.0096 (16)	−0.0035 (14)	0.0014 (16)
C12	0.0340 (18)	0.038 (2)	0.0227 (17)	0.0127 (17)	−0.0051 (15)	−0.0009 (15)
C13	0.0335 (17)	0.025 (2)	0.0252 (16)	0.0037 (15)	−0.0045 (15)	−0.0022 (15)
C14	0.0255 (16)	0.032 (2)	0.0260 (18)	0.0083 (15)	−0.0011 (14)	0.0028 (15)
C15	0.0367 (18)	0.034 (2)	0.0335 (19)	0.0036 (16)	0.0034 (17)	−0.0002 (17)
C16	0.059 (2)	0.049 (3)	0.064 (3)	0.010 (2)	0.014 (2)	0.023 (2)
C17	0.042 (2)	0.048 (2)	0.056 (2)	−0.0065 (18)	0.0016 (19)	−0.006 (2)
C18	0.0380 (19)	0.035 (2)	0.033 (2)	0.0054 (16)	−0.0051 (15)	−0.0059 (16)
C19	0.055 (2)	0.029 (2)	0.047 (2)	0.0102 (18)	−0.0042 (18)	−0.0010 (18)
C20	0.055 (2)	0.041 (2)	0.067 (2)	0.0038 (19)	−0.022 (2)	−0.011 (2)
N1	0.0295 (13)	0.0227 (16)	0.0239 (13)	0.0041 (13)	−0.0001 (11)	−0.0032 (11)
N2	0.0305 (14)	0.0379 (18)	0.0185 (13)	0.0119 (13)	−0.0024 (12)	−0.0016 (12)
O1	0.0749 (16)	0.0188 (12)	0.0203 (10)	0.0094 (12)	−0.0002 (11)	−0.0002 (9)
S1	0.0317 (4)	0.0306 (5)	0.0288 (4)	0.0073 (4)	−0.0040 (4)	−0.0021 (4)

Geometric parameters (Å, º)

C1—C2	1.507 (3)	C9—N2	1.424 (4)
C1—H1A	0.9800	C10—C11	1.383 (4)
C1—H1B	0.9800	C10—C18	1.527 (4)
C1—H1C	0.9800	C11—C12	1.387 (4)
C2—O1	1.435 (3)	C11—H11	0.9500
C2—O1^i	1.435 (3)	C12—C13	1.382 (4)
C2—C1^i	1.507 (3)	C12—H12	0.9500
C3—O1	1.430 (3)	C13—C14	1.384 (4)
C3—C4	1.513 (4)	C13—H13	0.9500
C3—C3^i	1.518 (5)	C14—C15	1.515 (4)
C3—H3	1.0000	C15—C16	1.523 (4)
C4—C5	1.527 (4)	C15—C17	1.524 (4)
C4—H4A	0.9900	C15—H15	1.0000
C4—H4B	0.9900	C16—H16A	0.9800
C5—N1	1.457 (3)	C16—H16B	0.9800
C5—H5A	0.9900	C16—H16C	0.9800
C5—H5B	0.9900	C17—H17A	0.9800
C6—N1	1.451 (3)	C17—H17B	0.9800
C6—C7	1.524 (4)	C17—H17C	0.9800
C6—H6A	0.9900	C18—C19	1.531 (4)
C6—H6B	0.9900	C18—C20	1.534 (4)
C7—N2	1.470 (3)	C18—H18	1.0000
C7—H7A	0.9900	C19—H19A	0.9800
C7—H7B	0.9900	C19—H19B	0.9800
C8—N1	1.349 (3)	C19—H19C	0.9800
C8—N2	1.362 (3)	C20—H20A	0.9800
C8—S1	1.663 (3)	C20—H20B	0.9800
C9—C14	1.405 (4)	C20—H20C	0.9800
C9—C10	1.416 (4)
C2—C1—H1A	109.5	C12—C11—H11	119.3
C2—C1—H1B	109.5	C13—C12—C11	119.7 (3)
H1A—C1—H1B	109.5	C13—C12—H12	120.2
C2—C1—H1C	109.5	C11—C12—H12	120.2
H1A—C1—H1C	109.5	C12—C13—C14	121.7 (3)
H1B—C1—H1C	109.5	C12—C13—H13	119.1
O1—C2—O1^i	105.9 (3)	C14—C13—H13	119.1
O1—C2—C1^i	111.03 (14)	C13—C14—C9	117.8 (3)
O1^i—C2—C1^i	108.00 (15)	C13—C14—C15	120.2 (3)
O1—C2—C1	108.00 (15)	C9—C14—C15	122.0 (3)
O1^i—C2—C1	111.03 (14)	C14—C15—C16	112.3 (3)
C1^i—C2—C1	112.7 (3)	C14—C15—C17	110.9 (3)
O1—C3—C4	108.1 (2)	C16—C15—C17	111.0 (3)
O1—C3—C3^i	102.59 (16)	C14—C15—H15	107.4
C4—C3—C3^i	115.2 (2)	C16—C15—H15	107.4
O1—C3—H3	110.2	C17—C15—H15	107.4
C4—C3—H3	110.2	C15—C16—H16A	109.5
C3^i—C3—H3	110.2	C15—C16—H16B	109.5
C3—C4—C5	111.5 (2)	H16A—C16—H16B	109.5
C3—C4—H4A	109.3	C15—C16—H16C	109.5
C5—C4—H4A	109.3	H16A—C16—H16C	109.5
C3—C4—H4B	109.3	H16B—C16—H16C	109.5
C5—C4—H4B	109.3	C15—C17—H17A	109.5
H4A—C4—H4B	108.0	C15—C17—H17B	109.5
N1—C5—C4	113.3 (2)	H17A—C17—H17B	109.5
N1—C5—H5A	108.9	C15—C17—H17C	109.5
C4—C5—H5A	108.9	H17A—C17—H17C	109.5
N1—C5—H5B	108.9	H17B—C17—H17C	109.5
C4—C5—H5B	108.9	C10—C18—C19	110.9 (2)
H5A—C5—H5B	107.7	C10—C18—C20	110.8 (3)
N1—C6—C7	102.5 (2)	C19—C18—C20	111.1 (3)
N1—C6—H6A	111.3	C10—C18—H18	108.0
C7—C6—H6A	111.3	C19—C18—H18	108.0
N1—C6—H6B	111.3	C20—C18—H18	108.0
C7—C6—H6B	111.3	C18—C19—H19A	109.5
H6A—C6—H6B	109.2	C18—C19—H19B	109.5
N2—C7—C6	101.5 (2)	H19A—C19—H19B	109.5
N2—C7—H7A	111.5	C18—C19—H19C	109.5
C6—C7—H7A	111.5	H19A—C19—H19C	109.5
N2—C7—H7B	111.5	H19B—C19—H19C	109.5
C6—C7—H7B	111.5	C18—C20—H20A	109.5
H7A—C7—H7B	109.3	C18—C20—H20B	109.5
N1—C8—N2	107.3 (2)	H20A—C20—H20B	109.5
N1—C8—S1	127.2 (2)	C18—C20—H20C	109.5
N2—C8—S1	125.4 (2)	H20A—C20—H20C	109.5
C14—C9—C10	121.6 (3)	H20B—C20—H20C	109.5
C14—C9—N2	120.0 (3)	C8—N1—C6	112.6 (2)
C10—C9—N2	118.4 (3)	C8—N1—C5	124.5 (2)
C11—C10—C9	117.8 (3)	C6—N1—C5	119.8 (2)
C11—C10—C18	120.9 (3)	C8—N2—C9	125.6 (2)
C9—C10—C18	121.3 (3)	C8—N2—C7	112.0 (2)
C10—C11—C12	121.4 (3)	C9—N2—C7	121.4 (2)
C10—C11—H11	119.3	C3—O1—C2	108.6 (2)
O1—C3—C4—C5	66.0 (3)	C9—C10—C18—C20	113.4 (3)
C3^i—C3—C4—C5	180.0 (2)	N2—C8—N1—C6	8.0 (3)
C3—C4—C5—N1	−162.3 (2)	S1—C8—N1—C6	−172.1 (2)
N1—C6—C7—N2	19.2 (3)	N2—C8—N1—C5	168.0 (2)
C14—C9—C10—C11	−2.4 (4)	S1—C8—N1—C5	−12.2 (4)
N2—C9—C10—C11	175.0 (2)	C7—C6—N1—C8	−17.8 (3)
C14—C9—C10—C18	178.2 (3)	C7—C6—N1—C5	−178.9 (2)
N2—C9—C10—C18	−4.4 (4)	C4—C5—N1—C8	−79.0 (3)
C9—C10—C11—C12	1.1 (4)	C4—C5—N1—C6	79.6 (3)
C18—C10—C11—C12	−179.6 (3)	N1—C8—N2—C9	174.5 (3)
C10—C11—C12—C13	0.9 (4)	S1—C8—N2—C9	−5.3 (5)
C11—C12—C13—C14	−1.7 (4)	N1—C8—N2—C7	6.1 (3)
C12—C13—C14—C9	0.4 (4)	S1—C8—N2—C7	−173.7 (2)
C12—C13—C14—C15	−179.4 (3)	C14—C9—N2—C8	−85.7 (4)
C10—C9—C14—C13	1.7 (4)	C10—C9—N2—C8	96.9 (3)
N2—C9—C14—C13	−175.7 (3)	C14—C9—N2—C7	81.7 (4)
C10—C9—C14—C15	−178.5 (3)	C10—C9—N2—C7	−95.8 (3)
N2—C9—C14—C15	4.1 (4)	C6—C7—N2—C8	−16.5 (3)
C13—C14—C15—C16	60.6 (4)	C6—C7—N2—C9	174.6 (3)
C9—C14—C15—C16	−119.2 (3)	C4—C3—O1—C2	150.36 (19)
C13—C14—C15—C17	−64.3 (4)	C3^i—C3—O1—C2	28.2 (3)
C9—C14—C15—C17	115.9 (3)	O1^i—C2—O1—C3	−11.50 (14)
C11—C10—C18—C19	57.9 (4)	C1^i—C2—O1—C3	105.5 (3)
C9—C10—C18—C19	−122.7 (3)	C1—C2—O1—C3	−130.5 (2)
C11—C10—C18—C20	−65.9 (4)

Symmetry code: (i) −x+1, −y+1, z.