rac-1-Acetyl-5-benzyl-2-thioxoimidazolidin-4-one

Uzcátegui, M.C.; Delgado, G.E.; Mora, A.J.; González, T.; Briceño, A.

doi:10.1107/S1600536808041883

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 1| January 2009| Page o104

doi:10.1107/S1600536808041883

Open

access

rac-1-Acetyl-5-benzyl-2-thioxoimidazolidin-4-one

Mary C. Uzcátegui,^a Gerzon E. Delgado,^a ^* Asiloé J. Mora,^a Teresa González ^b and Alexander Briceño ^b

^aLaboratorio de Cristalografía, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela, and ^bCentro de Química, Instituto Venezolano de Investigaciones, Científicas (IVIC), Apartado 21827, Caracas 1020-A, Venezuela
^*Correspondence e-mail: gerzon@ula.ve

(Received 1 December 2008; accepted 9 December 2008; online 13 December 2008)

In the title compound, C₁₂H₁₂N₂O₂S, the molecules have a wing-like conformation, with a distance of 3.797 (2) Å between the centroids of the five- and six-membered rings. In the crystal structure, molecules are linked by N—H⋯O hydrogen bonds, forming infinite one-dimensional zigzag chains, running along [001], with a C(4) graph-set motif.

Related literature

For related compounds, see: Seijas et al. (2006 , 2007 ); Delgado et al. (2007 ); Sulbaran et al. (2007 ). For racemization of amino acids, see: Yamada et al. (1983 ); Yoshioka (2007 ). For reference structural data, see: Allen et al. (2002 ). For hydrogen-bond motifs in graph-set notation, see Etter (1990 ).

Experimental

Crystal data

C₁₂H₁₂N₂O₂S
M_r = 248.30
Monoclinic, P 2₁ /c
a = 11.696 (5) Å
b = 13.479 (6) Å
c = 7.767 (4) Å
β = 94.41 (1)°
V = 1220.8 (9) Å³
Z = 4
Mo Kα radiation
μ = 0.26 mm⁻¹
T = 298 (2) K
0.4 × 0.3 × 0.2 mm

Data collection

Rigaku AFC-7S Mercury diffractometer
Absorption correction: multi-scan (Jacobson, 1998 ) T_min = 0.900, T_max = 0.950
12945 measured reflections
2349 independent reflections
2065 reflections with I > 2σ(I)
R_int = 0.026

Refinement

R[F² > 2σ(F²)] = 0.045
wR(F²) = 0.124
S = 1.05
2349 reflections
156 parameters
H-atom parameters constrained
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.27 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3⋯O4ⁱ	0.86	1.98	2.834 (2)	175
Symmetry code: (i) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku, 2002 ); cell refinement: CrystalClear; data reduction: CrystalStructure (Rigaku/MSC, 2004 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 1999 ); software used to prepare material for publication: PLATON (Spek, 2003 ) and publCIF (Westrip, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808041883/cv2495sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808041883/cv2495Isup2.hkl

checkCIF report

Comment top

In continuation of our study of N-carbamoyl, hydantoin and thiohydantoin derivatives of α-amino acids (Seijas et al., 2006, 2007; Delgado et al., 2007; Sulbaran et al., 2007), we report here the structure of the title compound (I) - the N-acetylthiohydantoin derivative of the α-amino acid L-phenylalanine.

Compound (I) (Fig. 1) crystallizes in a centrosymmetric space group, which implies that L-phenylalanine suffered an amino acid racemization produced by the use of acetic acid in the synthesis (Yamada et al. 1983; Yoshioka, 2007). All bond distances and angles are normal (Allen, 2002). The thiohydantoin ring is essentially planar with a maximum deviations of 0.023 (1) Å in C4 and -0.025 (2) Å in C5. The molecular structure and crystal packing of (I) are stabilized by intermolecular N3—H3···O4 (x, 1/2 - y, 1/2 + z) hydrogen bonds (Table 1), forming infinite one-dimentional zigzag chains that run along [001] direction, which can be described in graph-set notation as C(4) (Etter, 1990) (Figure 2).

Related literature top

For related compounds, see: Seijas et al. (2006, 2007); Delgado et al. (2007); Sulbaran et al. (2007). For amino acids racemization, see: Yamada et al. (1983); Yoshioka (2007). For reference structural data, see: Allen et al. (2002); For hydrogen-bond motifs in graph-set notation, see Etter (1990).

Experimental top

L-phenylalanine (3.4 mmol) and NH₄SCN (3.4 mmol) was dissolved in a 9 ml acetic anhydride - 1 ml acetic acid mixture and transferred in a round-bottom flask. The mixture was warmed, with agitation, to 363 K over a period of 30 min. The resulting solution was cooled in a ice/water mixture and stored in a freezer overnight. The resulting white solid was filtered off and washed with cool water (m.p. 441–443 K). Crystal of (I) suitable for X-ray diffraction analysis were obtained by slow evaporation of a 1:1 ethanol-methanol solution.

Computing details top

Data collection: CrystalClear (Rigaku, 2002); cell refinement: CrystalClear (Rigaku, 2002); data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 1999); software used to prepare material for publication: PLATON (Spek, 2003) and publCIF (Westrip, 2009).

Figures top

	Fig. 1. The molecular structure of (I), showing the atomic numbering scheme. Displacement elipsoids are drawn at the 25% probability level and H atoms are shown as spheres of arbitrary radii.
	Fig. 2. A portion of the crystal packing viewed along the a-axis. Hydrogen bonds are marked with dashed lines. H atoms not involved in hydrogen bonding have been omitted for clarity.

rac-1-Acetyl-5-benzyl-2-thioxoimidazolidin-4-one top

Crystal data top

C₁₂H₁₂N₂O₂S	F(000) = 520
M_r = 248.30	D_x = 1.351 Mg m⁻³
Monoclinic, P2₁/c	Melting point = 441–443 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71070 Å
a = 11.696 (5) Å	Cell parameters from 4020 reflections
b = 13.479 (6) Å	θ = 2.4–27.8°
c = 7.767 (4) Å	µ = 0.26 mm⁻¹
β = 94.41 (1)°	T = 298 K
V = 1220.8 (9) Å³	Block, colourless
Z = 4	0.4 × 0.3 × 0.2 mm

Data collection top

Rigaku AFC-7S Mercury diffractometer	2349 independent reflections
Radiation source: Normal-focus sealed tube	2065 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
Detector resolution: 14.6306 pixels mm^-1	θ_max = 28.0°, θ_min = 2.3°
ω scans	h = −13→13
Absorption correction: multi-scan (Jacobson, 1998)	k = −15→15
T_min = 0.900, T_max = 0.950	l = −9→6
12945 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.045	H-atom parameters constrained
wR(F²) = 0.124	w = 1/[σ²(F_o²) + (0.0616P)² + 0.4929P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
2349 reflections	Δρ_max = 0.24 e Å⁻³
156 parameters	Δρ_min = −0.27 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.013 (2)

Crystal data top

C₁₂H₁₂N₂O₂S	V = 1220.8 (9) Å³
M_r = 248.30	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 11.696 (5) Å	µ = 0.26 mm⁻¹
b = 13.479 (6) Å	T = 298 K
c = 7.767 (4) Å	0.4 × 0.3 × 0.2 mm
β = 94.41 (1)°

Data collection top

Rigaku AFC-7S Mercury diffractometer	2349 independent reflections
Absorption correction: multi-scan (Jacobson, 1998)	2065 reflections with I > 2σ(I)
T_min = 0.900, T_max = 0.950	R_int = 0.026
12945 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.045	0 restraints
wR(F²) = 0.124	H-atom parameters constrained
S = 1.05	Δρ_max = 0.24 e Å⁻³
2349 reflections	Δρ_min = −0.27 e Å⁻³
156 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
S2	0.84958 (5)	0.53330 (4)	0.61947 (7)	0.0501 (2)
O2	0.88296 (18)	0.61004 (12)	0.0516 (2)	0.0689 (5)
O4	0.87718 (14)	0.24785 (10)	0.23095 (18)	0.0512 (4)
N1	0.85248 (14)	0.50588 (12)	0.26762 (19)	0.0366 (4)
N3	0.86134 (14)	0.37142 (11)	0.42952 (19)	0.0383 (4)
H3	0.8622	0.3343	0.5196	0.046*
C2	0.85359 (16)	0.47307 (13)	0.4365 (2)	0.0356 (4)
C4	0.86755 (17)	0.33477 (14)	0.2669 (2)	0.0378 (4)
C5	0.85594 (17)	0.42208 (14)	0.1459 (2)	0.0385 (4)
H5	0.9237	0.4272	0.0796	0.046*
C6	0.86200 (19)	0.60326 (15)	0.2013 (3)	0.0476 (5)
C7	0.8434 (2)	0.69011 (16)	0.3128 (3)	0.0626 (7)
H7A	0.8421	0.7495	0.2445	0.094*
H7B	0.9046	0.6941	0.4024	0.094*
H7C	0.7716	0.6829	0.3637	0.094*
C8	0.74690 (19)	0.41292 (17)	0.0231 (3)	0.0487 (5)
H8A	0.7375	0.4732	−0.0446	0.058*
H8B	0.7565	0.3585	−0.0561	0.058*
C9	0.63988 (19)	0.39550 (17)	0.1147 (3)	0.0496 (5)
C10	0.5823 (2)	0.4733 (2)	0.1867 (3)	0.0634 (7)
H10	0.6101	0.5376	0.1786	0.076*
C11	0.4837 (3)	0.4563 (3)	0.2707 (4)	0.0837 (10)
H11	0.4463	0.5092	0.3190	0.100*
C12	0.4967 (3)	0.2862 (3)	0.2141 (7)	0.1180 (15)
H12	0.4681	0.2223	0.2237	0.142*
C13	0.4415 (3)	0.3629 (4)	0.2826 (5)	0.1022 (12)
H13	0.3749	0.3518	0.3378	0.123*
C14	0.5954 (3)	0.3015 (2)	0.1296 (5)	0.0825 (9)
H14	0.6319	0.2478	0.0826	0.099*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S2	0.0680 (4)	0.0440 (4)	0.0399 (3)	−0.0022 (2)	0.0150 (2)	−0.0088 (2)
O2	0.1084 (15)	0.0490 (10)	0.0522 (10)	0.0001 (9)	0.0243 (9)	0.0161 (7)
O4	0.0777 (11)	0.0330 (8)	0.0435 (8)	0.0035 (7)	0.0093 (7)	−0.0038 (6)
N1	0.0462 (10)	0.0304 (8)	0.0341 (8)	0.0014 (7)	0.0091 (6)	0.0021 (6)
N3	0.0531 (10)	0.0312 (8)	0.0312 (8)	−0.0013 (7)	0.0075 (6)	0.0022 (6)
C2	0.0369 (10)	0.0348 (10)	0.0358 (10)	−0.0015 (7)	0.0081 (7)	0.0009 (7)
C4	0.0439 (11)	0.0342 (10)	0.0356 (10)	0.0009 (8)	0.0067 (7)	−0.0014 (7)
C5	0.0491 (12)	0.0344 (10)	0.0335 (10)	0.0021 (8)	0.0118 (8)	0.0006 (7)
C6	0.0571 (14)	0.0352 (11)	0.0516 (13)	0.0004 (9)	0.0110 (10)	0.0083 (9)
C7	0.0881 (19)	0.0330 (12)	0.0679 (16)	0.0020 (11)	0.0140 (13)	0.0055 (10)
C8	0.0588 (14)	0.0552 (13)	0.0319 (10)	0.0042 (10)	0.0029 (9)	−0.0021 (9)
C9	0.0471 (13)	0.0623 (14)	0.0385 (11)	0.0045 (10)	−0.0029 (8)	−0.0030 (9)
C10	0.0547 (15)	0.0767 (19)	0.0582 (15)	0.0128 (12)	−0.0001 (11)	−0.0111 (12)
C11	0.0587 (18)	0.126 (3)	0.0657 (18)	0.0246 (18)	0.0017 (13)	−0.0179 (18)
C12	0.070 (2)	0.102 (3)	0.186 (4)	−0.022 (2)	0.034 (3)	0.016 (3)
C13	0.060 (2)	0.144 (4)	0.106 (3)	0.000 (2)	0.0263 (18)	0.009 (2)
C14	0.0598 (17)	0.0713 (19)	0.118 (3)	−0.0079 (14)	0.0165 (16)	−0.0138 (17)

Geometric parameters (Å, º) top

S2—C2	1.6402 (19)	C7—H7C	0.9600
O2—C6	1.210 (3)	C8—C9	1.505 (3)
O4—C4	1.212 (2)	C8—H8A	0.9700
N1—C2	1.384 (2)	C8—H8B	0.9700
N1—C6	1.418 (2)	C9—C14	1.378 (4)
N1—C5	1.476 (2)	C9—C10	1.387 (3)
N3—C4	1.363 (2)	C10—C11	1.387 (4)
N3—C2	1.374 (2)	C10—H10	0.9300
N3—H3	0.8600	C11—C13	1.358 (5)
C4—C5	1.506 (3)	C11—H11	0.9300
C5—C8	1.537 (3)	C12—C13	1.349 (5)
C5—H5	0.9800	C12—C14	1.386 (5)
C6—C7	1.482 (3)	C12—H12	0.9300
C7—H7A	0.9600	C13—H13	0.9300
C7—H7B	0.9600	C14—H14	0.9300

C2—N1—C6	130.19 (17)	H7B—C7—H7C	109.5
C2—N1—C5	111.36 (15)	C9—C8—C5	113.59 (16)
C6—N1—C5	117.97 (16)	C9—C8—H8A	108.8
C4—N3—C2	113.97 (15)	C5—C8—H8A	108.8
C4—N3—H3	123.0	C9—C8—H8B	108.8
C2—N3—H3	123.0	C5—C8—H8B	108.8
N3—C2—N1	106.08 (15)	H8A—C8—H8B	107.7
N3—C2—S2	122.29 (14)	C14—C9—C10	117.5 (2)
N1—C2—S2	131.63 (15)	C14—C9—C8	121.1 (2)
O4—C4—N3	125.20 (18)	C10—C9—C8	121.3 (2)
O4—C4—C5	128.11 (17)	C9—C10—C11	120.9 (3)
N3—C4—C5	106.65 (16)	C9—C10—H10	119.6
N1—C5—C4	101.76 (14)	C11—C10—H10	119.6
N1—C5—C8	113.36 (16)	C13—C11—C10	120.3 (3)
C4—C5—C8	110.80 (17)	C13—C11—H11	119.9
N1—C5—H5	110.2	C10—C11—H11	119.9
C4—C5—H5	110.2	C13—C12—C14	120.9 (4)
C8—C5—H5	110.2	C13—C12—H12	119.5
O2—C6—N1	116.53 (19)	C14—C12—H12	119.5
O2—C6—C7	123.47 (19)	C12—C13—C11	119.8 (3)
N1—C6—C7	119.98 (18)	C12—C13—H13	120.1
C6—C7—H7A	109.5	C11—C13—H13	120.1
C6—C7—H7B	109.5	C12—C14—C9	120.7 (3)
H7A—C7—H7B	109.5	C12—C14—H14	119.7
C6—C7—H7C	109.5	C9—C14—H14	119.7
H7A—C7—H7C	109.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O4ⁱ	0.86	1.98	2.834 (2)	175

Symmetry code: (i) x, −y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₂N₂O₂S
M_r	248.30
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	11.696 (5), 13.479 (6), 7.767 (4)
β (°)	94.41 (1)
V (Å³)	1220.8 (9)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.26
Crystal size (mm)	0.4 × 0.3 × 0.2

Data collection
Diffractometer	Rigaku AFC-7S Mercury diffractometer
Absorption correction	Multi-scan (Jacobson, 1998)
T_min, T_max	0.900, 0.950
No. of measured, independent and observed [I > 2σ(I)] reflections	12945, 2349, 2065
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.659

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.045, 0.124, 1.05
No. of reflections	2349
No. of parameters	156
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.24, −0.27

Computer programs: CrystalClear (Rigaku, 2002), CrystalStructure (Rigaku/MSC, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 1999), PLATON (Spek, 2003) and publCIF (Westrip, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O4ⁱ	0.86	1.98	2.834 (2)	175.4

Symmetry code: (i) x, −y+1/2, z+1/2.

Acknowledgements

This work was supported by Consejo de Desarrollo Científico, Humanístico y Tecnológico de la Universidad de Los Andes, CDCHT-ULA (grants C-1616–08-A and C-1617–08-F) and Fondo Nacional de Ciencia, Tecnología e Innovación, FONACIT (grant LAB-97000821).

References

Allen, F. H. (2002). Acta Cryst. B58, 380–388. Web of Science CrossRef CAS IUCr Journals Google Scholar
Brandenburg, K. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Delgado, G. E., Mora, A. J., Uzcátegui, J., Bahsas, A. & Briceño, A. (2007). Acta Cryst. C63, o448–o450. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Etter, M. C. (1990). Acc. Chem. Res. 23, 120–126. CrossRef CAS Web of Science Google Scholar
Jacobson, R. (1998). Private communication to Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (2002). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku/MSC (2004). CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA. Google Scholar
Seijas, L. E., Delgado, G. E., Mora, A. J., Bahsas, A. & Briceño, A. (2007). Acta Cryst. C63, o303–o305. Web of Science CSD CrossRef IUCr Journals Google Scholar
Seijas, L. E., Delgado, G. E., Mora, A. J., Bahsas, A. & Uzcátegui, J. (2006). Av. Quím. 1, 3–7. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sulbaran, M. E., Delgado, G. E., Mora, A. J., Bahsas, A., Novoa de Armas, H. & Blaton, N. (2007). Acta Cryst. C63, o543–o545. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Westrip, S. P. (2009). publCIF. In preparation. Google Scholar
Yamada, S., Hongo, C., Yoshioka, R. & Chibata, I. (1983). J. Org. Chem. 48, 843–846. CrossRef CAS Web of Science Google Scholar
Yoshioka, R. (2007). Top. Curr. Chem. 269, 83–132. CrossRef CAS PubMed Google Scholar