organic compounds
4-(Pyrimidin-2-yl)-1-thia-4-azaspiro[4.5]decan-3-one
aDepartamento de Química Orgânica, Universidade Federal de Pelotas (UFPel), Campus Universitário, s/n°, Caixa Postal 354, 96010-900 Pelotas, RS, Brazil, bFundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos–Farmanguinhos, R. Sizenando Nabuco 100, Manguinhos, 21041-250, Rio de Janeiro, RJ, Brazil, cDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia, dCentro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Casa Amarela, Campus de Manguinhos, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil, and eCHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY, Scotland
*Correspondence e-mail: edward.tiekink@gmail.com
The title compound, C12H15N3OS, features an for the 1,3-thiazolidin-4-one ring with the S atom as the flap atom. The pyrimidine ring is almost orthogonal to the 1,3-thiazolidin-4-one ring as indicated by the N—C—C—N torsion angle of −111.96 (18)°. Supramolecular dimers are formed in the through the agency of C—H⋯O contacts occurring between centrosymmetrically related molecules. These are linked into supramolecular tapes along [100] via C—H⋯S contacts.
Related literature
For the biological activity of thiazolidinones, see: Cunico et al. (2008a); Solomon et al. (2007); Kavitha et al. (2006); Sharma et al. (2006); Ravichandran et al. (2009); Rao et al. (2004). For background to the synthesis, see: Cunico et al. (2008b); Rawal et al. (2008). For related studies on the synthesis and biological evaluation of thiazolidinones, see: Cunico et al. (2006, 2007).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Hooft, 1998); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2009).
Supporting information
10.1107/S1600536809049460/hg2601sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809049460/hg2601Isup2.hkl
A mixture of 2-aminopyrimidine (1 mmol), cyclohexanone (2 mmol) and mercaptoacetic acid (3 mmol) in toluene (35 ml) was heated at 403 K with a Dean-Stark trap for 16 h. The reaction was cooled, washed with NaHCO3 (3 x 20 ml), and dried with MgSO4. The crude product was washed with a hot solvent mixture of hexane/ethyl acetate (9:1) and recrystallized from EtOH. Yield 80%. m. pt. 475–476 K. 1H NMR (200 MHz, CDCl3): δ 8.76 (s, 2H, aryl), 7.22 (s, 1H, aryl), 3.66 (s, 2H, H5), 2.21–1.57 (m, 10H, CH2) p.p.m. 13C NMR (100 MHz, CDCl3): δ 172.4 (CO), 158.5, 158.4, 119.3 (aryl), 75.7 (C2), 39.5 (CH2), 38.0 (CH2), 31.9 (C5), 24.4 (CH2), 23.6 (CH2) p.p.m.
The C-bound H atoms were geometrically placed with C—H = 0.95–0.99 Å, and refined as riding with Uiso(H) = 1.2Ueq(C).
Data collection: COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2009).C12H15N3OS | F(000) = 528 |
Mr = 249.33 | Dx = 1.393 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 7514 reflections |
a = 6.2466 (2) Å | θ = 2.9–27.5° |
b = 8.6748 (2) Å | µ = 0.26 mm−1 |
c = 22.0439 (6) Å | T = 120 K |
β = 95.698 (1)° | Block, colourless |
V = 1188.61 (6) Å3 | 0.26 × 0.22 × 0.14 mm |
Z = 4 |
Nonius KappaCCD area-detector diffractometer | 2661 independent reflections |
Radiation source: Enraf Nonius FR591 rotating anode | 2227 reflections with I > 2σ(I) |
10 cm confocal mirrors monochromator | Rint = 0.054 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.0° |
ϕ and ω scans | h = −8→7 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −10→11 |
Tmin = 0.658, Tmax = 0.746 | l = −28→28 |
14004 measured reflections |
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)] = 0.038 | H-atom parameters constrained |
wR(F2) = 0.113 | w = 1/[σ2(Fo2) + (0.0508P)2 + 0.5459P] where P = (Fo2 + 2Fc2)/3 |
S = 1.14 | (Δ/σ)max < 0.001 |
2661 reflections | Δρmax = 0.36 e Å−3 |
155 parameters | Δρmin = −0.40 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: 0.012 (2) |
C12H15N3OS | V = 1188.61 (6) Å3 |
Mr = 249.33 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 6.2466 (2) Å | µ = 0.26 mm−1 |
b = 8.6748 (2) Å | T = 120 K |
c = 22.0439 (6) Å | 0.26 × 0.22 × 0.14 mm |
β = 95.698 (1)° |
Nonius KappaCCD area-detector diffractometer | 2661 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2227 reflections with I > 2σ(I) |
Tmin = 0.658, Tmax = 0.746 | Rint = 0.054 |
14004 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.113 | H-atom parameters constrained |
S = 1.14 | Δρmax = 0.36 e Å−3 |
2661 reflections | Δρmin = −0.40 e Å−3 |
155 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.30913 (6) | 0.59301 (5) | 0.14394 (2) | 0.02184 (17) | |
O1 | 0.19102 (19) | 0.33684 (15) | 0.00174 (6) | 0.0215 (3) | |
N1 | −0.2660 (2) | 0.24603 (17) | 0.08348 (7) | 0.0189 (3) | |
N2 | 0.0587 (2) | 0.09881 (17) | 0.08941 (8) | 0.0206 (3) | |
N3 | 0.0732 (2) | 0.36704 (16) | 0.09593 (6) | 0.0147 (3) | |
C2 | 0.0699 (2) | 0.47007 (19) | 0.14937 (7) | 0.0143 (3) | |
C4 | 0.1922 (2) | 0.40748 (19) | 0.04984 (8) | 0.0161 (4) | |
C5 | 0.3225 (3) | 0.5513 (2) | 0.06440 (8) | 0.0207 (4) | |
H5A | 0.2630 | 0.6384 | 0.0390 | 0.025* | |
H5B | 0.4737 | 0.5349 | 0.0561 | 0.025* | |
C6 | 0.0987 (3) | 0.3792 (2) | 0.20899 (8) | 0.0194 (4) | |
H6A | 0.2353 | 0.3207 | 0.2110 | 0.023* | |
H6B | −0.0204 | 0.3041 | 0.2098 | 0.023* | |
C7 | 0.1015 (3) | 0.4855 (2) | 0.26444 (8) | 0.0239 (4) | |
H7A | 0.1098 | 0.4224 | 0.3020 | 0.029* | |
H7B | 0.2311 | 0.5517 | 0.2665 | 0.029* | |
C8 | −0.0989 (3) | 0.5870 (2) | 0.26138 (8) | 0.0230 (4) | |
H8A | −0.2266 | 0.5217 | 0.2655 | 0.028* | |
H8B | −0.0852 | 0.6607 | 0.2959 | 0.028* | |
C9 | −0.1310 (3) | 0.6762 (2) | 0.20155 (8) | 0.0186 (4) | |
H9A | −0.0129 | 0.7518 | 0.1999 | 0.022* | |
H9B | −0.2683 | 0.7338 | 0.1996 | 0.022* | |
C10 | −0.1346 (2) | 0.5672 (2) | 0.14669 (8) | 0.0159 (4) | |
H10A | −0.2612 | 0.4983 | 0.1461 | 0.019* | |
H10B | −0.1486 | 0.6284 | 0.1086 | 0.019* | |
C11 | −0.0534 (2) | 0.22881 (19) | 0.08959 (8) | 0.0144 (3) | |
C12 | −0.3796 (3) | 0.1143 (2) | 0.07570 (9) | 0.0214 (4) | |
H12 | −0.5323 | 0.1194 | 0.0722 | 0.026* | |
C13 | −0.2817 (3) | −0.0280 (2) | 0.07264 (8) | 0.0215 (4) | |
H13 | −0.3630 | −0.1200 | 0.0658 | 0.026* | |
C14 | −0.0591 (3) | −0.0296 (2) | 0.08007 (9) | 0.0246 (4) | |
H14 | 0.0131 | −0.1256 | 0.0785 | 0.030* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0154 (2) | 0.0251 (3) | 0.0259 (3) | −0.00679 (16) | 0.00633 (17) | −0.00990 (19) |
O1 | 0.0249 (6) | 0.0233 (7) | 0.0168 (6) | −0.0011 (5) | 0.0045 (5) | −0.0020 (5) |
N1 | 0.0163 (7) | 0.0159 (8) | 0.0243 (8) | −0.0001 (5) | 0.0017 (6) | −0.0026 (6) |
N2 | 0.0177 (7) | 0.0163 (8) | 0.0279 (9) | −0.0001 (5) | 0.0023 (6) | −0.0012 (6) |
N3 | 0.0144 (6) | 0.0138 (7) | 0.0161 (7) | −0.0015 (5) | 0.0033 (5) | −0.0025 (6) |
C2 | 0.0123 (7) | 0.0152 (8) | 0.0154 (8) | −0.0015 (6) | 0.0015 (6) | −0.0035 (7) |
C4 | 0.0137 (7) | 0.0186 (9) | 0.0161 (9) | 0.0030 (6) | 0.0016 (6) | 0.0023 (7) |
C5 | 0.0195 (8) | 0.0224 (9) | 0.0204 (9) | −0.0039 (7) | 0.0037 (7) | 0.0002 (8) |
C6 | 0.0230 (8) | 0.0171 (9) | 0.0173 (9) | 0.0021 (7) | −0.0019 (7) | 0.0006 (7) |
C7 | 0.0331 (10) | 0.0221 (10) | 0.0156 (9) | 0.0008 (8) | −0.0021 (7) | 0.0002 (8) |
C8 | 0.0297 (9) | 0.0236 (10) | 0.0168 (9) | −0.0026 (7) | 0.0071 (7) | −0.0045 (8) |
C9 | 0.0156 (7) | 0.0195 (9) | 0.0208 (9) | 0.0015 (6) | 0.0028 (6) | −0.0026 (7) |
C10 | 0.0133 (7) | 0.0171 (9) | 0.0173 (9) | 0.0016 (6) | 0.0017 (6) | −0.0012 (7) |
C11 | 0.0158 (7) | 0.0144 (8) | 0.0130 (8) | −0.0010 (6) | 0.0015 (6) | −0.0017 (6) |
C12 | 0.0166 (8) | 0.0230 (10) | 0.0243 (10) | −0.0034 (7) | 0.0008 (7) | −0.0023 (8) |
C13 | 0.0243 (9) | 0.0166 (9) | 0.0235 (10) | −0.0050 (7) | 0.0017 (7) | −0.0041 (7) |
C14 | 0.0243 (9) | 0.0164 (9) | 0.0334 (11) | 0.0015 (7) | 0.0036 (8) | −0.0018 (8) |
S1—C5 | 1.8004 (19) | C6—H6B | 0.9900 |
S1—C2 | 1.8494 (16) | C7—C8 | 1.527 (3) |
O1—C4 | 1.224 (2) | C7—H7A | 0.9900 |
N1—C11 | 1.330 (2) | C7—H7B | 0.9900 |
N1—C12 | 1.347 (2) | C8—C9 | 1.525 (3) |
N2—C11 | 1.328 (2) | C8—H8A | 0.9900 |
N2—C14 | 1.339 (2) | C8—H8B | 0.9900 |
N3—C4 | 1.363 (2) | C9—C10 | 1.533 (2) |
N3—C11 | 1.436 (2) | C9—H9A | 0.9900 |
N3—C2 | 1.480 (2) | C9—H9B | 0.9900 |
C2—C10 | 1.527 (2) | C10—H10A | 0.9900 |
C2—C6 | 1.528 (2) | C10—H10B | 0.9900 |
C4—C5 | 1.507 (2) | C12—C13 | 1.382 (3) |
C5—H5A | 0.9900 | C12—H12 | 0.9500 |
C5—H5B | 0.9900 | C13—C14 | 1.384 (2) |
C6—C7 | 1.530 (3) | C13—H13 | 0.9500 |
C6—H6A | 0.9900 | C14—H14 | 0.9500 |
C5—S1—C2 | 93.63 (8) | H7A—C7—H7B | 108.0 |
C11—N1—C12 | 115.20 (15) | C9—C8—C7 | 111.57 (14) |
C11—N2—C14 | 115.15 (15) | C9—C8—H8A | 109.3 |
C4—N3—C11 | 118.58 (14) | C7—C8—H8A | 109.3 |
C4—N3—C2 | 119.29 (14) | C9—C8—H8B | 109.3 |
C11—N3—C2 | 122.06 (13) | C7—C8—H8B | 109.3 |
N3—C2—C10 | 112.34 (13) | H8A—C8—H8B | 108.0 |
N3—C2—C6 | 111.29 (14) | C8—C9—C10 | 111.08 (15) |
C10—C2—C6 | 110.16 (13) | C8—C9—H9A | 109.4 |
N3—C2—S1 | 102.80 (10) | C10—C9—H9A | 109.4 |
C10—C2—S1 | 110.96 (12) | C8—C9—H9B | 109.4 |
C6—C2—S1 | 109.06 (11) | C10—C9—H9B | 109.4 |
O1—C4—N3 | 124.04 (15) | H9A—C9—H9B | 108.0 |
O1—C4—C5 | 123.77 (15) | C2—C10—C9 | 111.29 (13) |
N3—C4—C5 | 112.18 (15) | C2—C10—H10A | 109.4 |
C4—C5—S1 | 107.29 (12) | C9—C10—H10A | 109.4 |
C4—C5—H5A | 110.3 | C2—C10—H10B | 109.4 |
S1—C5—H5A | 110.3 | C9—C10—H10B | 109.4 |
C4—C5—H5B | 110.3 | H10A—C10—H10B | 108.0 |
S1—C5—H5B | 110.3 | N2—C11—N1 | 128.08 (15) |
H5A—C5—H5B | 108.5 | N2—C11—N3 | 115.10 (13) |
C2—C6—C7 | 111.52 (15) | N1—C11—N3 | 116.80 (14) |
C2—C6—H6A | 109.3 | N1—C12—C13 | 122.23 (16) |
C7—C6—H6A | 109.3 | N1—C12—H12 | 118.9 |
C2—C6—H6B | 109.3 | C13—C12—H12 | 118.9 |
C7—C6—H6B | 109.3 | C12—C13—C14 | 116.59 (16) |
H6A—C6—H6B | 108.0 | C12—C13—H13 | 121.7 |
C8—C7—C6 | 111.59 (15) | C14—C13—H13 | 121.7 |
C8—C7—H7A | 109.3 | N2—C14—C13 | 122.69 (17) |
C6—C7—H7A | 109.3 | N2—C14—H14 | 118.7 |
C8—C7—H7B | 109.3 | C13—C14—H14 | 118.7 |
C6—C7—H7B | 109.3 | ||
C4—N3—C2—C10 | 101.41 (16) | C2—C6—C7—C8 | 54.95 (19) |
C11—N3—C2—C10 | −75.57 (19) | C6—C7—C8—C9 | −53.8 (2) |
C4—N3—C2—C6 | −134.54 (15) | C7—C8—C9—C10 | 54.38 (19) |
C11—N3—C2—C6 | 48.48 (19) | N3—C2—C10—C9 | −178.32 (14) |
C4—N3—C2—S1 | −17.93 (17) | C6—C2—C10—C9 | 57.00 (18) |
C11—N3—C2—S1 | 165.09 (12) | S1—C2—C10—C9 | −63.87 (16) |
C5—S1—C2—N3 | 19.77 (12) | C8—C9—C10—C2 | −56.35 (18) |
C5—S1—C2—C10 | −100.52 (12) | C14—N2—C11—N1 | 2.2 (3) |
C5—S1—C2—C6 | 137.96 (12) | C14—N2—C11—N3 | −176.42 (16) |
C11—N3—C4—O1 | 3.4 (2) | C12—N1—C11—N2 | −0.6 (3) |
C2—N3—C4—O1 | −173.65 (15) | C12—N1—C11—N3 | 177.99 (15) |
C11—N3—C4—C5 | −177.71 (14) | C4—N3—C11—N2 | 66.8 (2) |
C2—N3—C4—C5 | 5.2 (2) | C2—N3—C11—N2 | −116.21 (17) |
O1—C4—C5—S1 | −170.17 (14) | C4—N3—C11—N1 | −111.96 (18) |
N3—C4—C5—S1 | 10.98 (18) | C2—N3—C11—N1 | 65.0 (2) |
C2—S1—C5—C4 | −18.17 (13) | C11—N1—C12—C13 | −1.7 (3) |
N3—C2—C6—C7 | 178.46 (13) | N1—C12—C13—C14 | 2.1 (3) |
C10—C2—C6—C7 | −56.27 (18) | C11—N2—C14—C13 | −1.6 (3) |
S1—C2—C6—C7 | 65.74 (15) | C12—C13—C14—N2 | −0.4 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C10—H10a···S1i | 0.99 | 2.80 | 3.4765 (13) | 126 |
C10—H10b···O1ii | 0.99 | 2.44 | 3.361 (2) | 155 |
Symmetry codes: (i) x−1, y, z; (ii) −x, −y+1, −z. |
Experimental details
Crystal data | |
Chemical formula | C12H15N3OS |
Mr | 249.33 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 120 |
a, b, c (Å) | 6.2466 (2), 8.6748 (2), 22.0439 (6) |
β (°) | 95.698 (1) |
V (Å3) | 1188.61 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.26 |
Crystal size (mm) | 0.26 × 0.22 × 0.14 |
Data collection | |
Diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.658, 0.746 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 14004, 2661, 2227 |
Rint | 0.054 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.113, 1.14 |
No. of reflections | 2661 |
No. of parameters | 155 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.36, −0.40 |
Computer programs: , DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2006), publCIF (Westrip, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
C10—H10a···S1i | 0.99 | 2.80 | 3.4765 (13) | 126 |
C10—H10b···O1ii | 0.99 | 2.44 | 3.361 (2) | 155 |
Symmetry codes: (i) x−1, y, z; (ii) −x, −y+1, −z. |
Footnotes
‡Additional correspondence author, e-mail: j.wardell@abdn.ac.uk.
Acknowledgements
The use of the EPSRC X-ray crystallographic service at the University of Southampton, England and the valuable assistance of the staff there is gratefully acknowledged. JLW acknowledges support from FAPEMIG (Brazil).
References
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Thiazolidinones constitute an important group of heterocyclic compounds (Cunico et al., 2008a), having valuable biological uses, for example, as anti-malarial (Solomon et al., 2007), anti-microbial (Kavitha et al., 2006), anti-inflammatory (Sharma et al., 2006), and anti-viral agents, especially as anti-HIV agents (Ravichandran et al., 2009; Rao et al., 2004). The main synthetic routes to 1,3-thiazolidin-4-ones involve three components (an aldehyde, an amine and mercaptoacetic acid), either in a one- or two-step process (Cunico et al., 2008a; Rawal et al., 2006). In continuation of our research on thiazolidinones, (Cunico et al., 2006; Cunico et al., 2007: Cunico et al., 2008b), we report the structure of the title compound, 1-thia-4-azaspiro[4.5]decan-3-one, (I).
The molecule structure of (I) shows the five-membered 1,3-thiazolidin-4-one ring to adopt an envelope conformation with the S1 atom as the flap atom. The cyclohexyl ring adopts a regular chair conformation. The pyrimidine is twisted out of the plane of the 1,3-thiazolidin-4-one ring as seen in the value of the C4–N3–C11–N1 torsion angle of -111.96 (18) °. When viewed along the plane through the N1, C2, C4 and C5 atoms, the molecule, with the exception of the S1 atom, has approximate mirror symmetry.
In the crystal structure, centrosymmetric pairs associate via C—H···O contacts to form dimers, Table 1. The dimeric aggregates are linked into a supramolecular tape aligned along [1 0 0] via C—H···S contacts, Table 1 and Fig.2. The pivotal role of the C10-methylene group is noted in the stabilization of the crystal structure as each of the C10-bound H atoms forms a significant intermolecular contact.