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The title compound, C16H18N2O3S, is of inter­est with respect to anti­bacterial and anti­cancer activity and shows some trypanocidal activity. The crystal packing displays O—H...N and C—H...S hydrogen bonds, forming a chain parallel to the [100] direction. The crystal structure also shows a short inter­molecular C=O...π-ring inter­action connecting centrosymmetrically related mol­ecules.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807019952/cf2102sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807019952/cf2102Isup2.hkl
Contains datablock I

CCDC reference: 601659

Key indicators

  • Single-crystal X-ray study
  • T = 297 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.061
  • wR factor = 0.156
  • Data-to-parameter ratio = 14.0

checkCIF/PLATON results

No syntax errors found



Alert level B PLAT430_ALERT_2_B Short Inter D...A Contact O15 .. N1 .. 2.86 Ang.
Alert level C PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.97 PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.06 PLAT764_ALERT_4_C Overcomplete CIF Bond List Detected (Rep/Expd) . 1.13 Ratio
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 3 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 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

Comment top

In continuation of our structural studies of bioactive thioxopyrimidine (Sabino et al., 2007), we present the analysis of the 4-thioxopyrimidine derivative I, which exhibited some level of trypanocidal activity. This derivative differs from 1-[1-(2-hydroxyethyl)-6-methyl-2-phenyl-4-thioxo-1,4-dihydro-5-pyrimidinyl]-1-ethanone by a substituent on the ring atom C5, where (I) has a carboxylate group instead of an acetyl group.

The molecular structure of (I) is depicted in Fig. 1. The conformation of I is defined by steric effects. The angle between the pyrimidine mean plane (r.m.s. 0.017 Å) and the mean plane through the phenyl ring is 87.71 (8)°. The torsion angle C20—C19—N1—C6 is -89.1 (2)° and C4—C5—C14—O15 is 91.1 (3)°. Bond lengths are within the expected ranges with the exception of the C2–C7 and C5–C14 bonds which present the same elongation of 0.03 Å from the formal single bond distance.

The crystal packing (Fig. 2) is mediated by a hydrogen bond of type O21–H21···N3ii and a non-classical hydrogen bond of type C13–H13B···Sii [Symmetry code: (ii) 1 - x, -y, 1 - z], which connect neighboring molecules in a linear chain along [100]. Intermolecular contacts of type C14 O15i···π-ring [Symmetry code: (i)1 - x, -y, 1 - z] mediate the packing via the sp2 ring atoms C6, N1 and C2, building a dimer about an inversion center. The distance N1···O15i is 2.858 (2) Å, 0.21 Å shorter than the sum of van der Waals radii of the atoms involved.

Related literature top

For the synthesis, see: Cunha et al. (2007). The corresponding compound with an acetyl group on C5 is described by Sabino et al. (2007). Despite the different chemical nature of these substituent groups, both compounds pack in a similar manner.

Experimental top

Compound (I) [m.p. >573 K] was prepared according to a known procedure (Cunha et al., 2007). Single crystals of I were obtained by slow evaporation of a solution in CHCl3 at room temperature.

Refinement top

All H atoms were positioned in idealized coordinates with distances 0.93–0.97 and 0.82 Å for the C atoms and O atoms, respectively. H atoms were refined isotropicaly and allowed to ride on their parent atoms with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(methyl C,O).

Structure description top

In continuation of our structural studies of bioactive thioxopyrimidine (Sabino et al., 2007), we present the analysis of the 4-thioxopyrimidine derivative I, which exhibited some level of trypanocidal activity. This derivative differs from 1-[1-(2-hydroxyethyl)-6-methyl-2-phenyl-4-thioxo-1,4-dihydro-5-pyrimidinyl]-1-ethanone by a substituent on the ring atom C5, where (I) has a carboxylate group instead of an acetyl group.

The molecular structure of (I) is depicted in Fig. 1. The conformation of I is defined by steric effects. The angle between the pyrimidine mean plane (r.m.s. 0.017 Å) and the mean plane through the phenyl ring is 87.71 (8)°. The torsion angle C20—C19—N1—C6 is -89.1 (2)° and C4—C5—C14—O15 is 91.1 (3)°. Bond lengths are within the expected ranges with the exception of the C2–C7 and C5–C14 bonds which present the same elongation of 0.03 Å from the formal single bond distance.

The crystal packing (Fig. 2) is mediated by a hydrogen bond of type O21–H21···N3ii and a non-classical hydrogen bond of type C13–H13B···Sii [Symmetry code: (ii) 1 - x, -y, 1 - z], which connect neighboring molecules in a linear chain along [100]. Intermolecular contacts of type C14 O15i···π-ring [Symmetry code: (i)1 - x, -y, 1 - z] mediate the packing via the sp2 ring atoms C6, N1 and C2, building a dimer about an inversion center. The distance N1···O15i is 2.858 (2) Å, 0.21 Å shorter than the sum of van der Waals radii of the atoms involved.

For the synthesis, see: Cunha et al. (2007). The corresponding compound with an acetyl group on C5 is described by Sabino et al. (2007). Despite the different chemical nature of these substituent groups, both compounds pack in a similar manner.

Computing details top

Data collection: CAD-4-PC (Enraf–Nonius, 1993); cell refinement: CAD-4-PC; data reduction: XCAD4 (Harms & Wocadlo, 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) and PLATON (Spek, 2003); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. View of (I) with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitray radius.
[Figure 2] Fig. 2. Packing diagram of (I). Intra- and intermolecular contacts are shown as dashed lines. Only the H atoms involved in H-bonds are shown.
ethyl 1-(2-hydroxyethyl)-6-methyl-2-phenyl-4-thioxo-1,4-dihydropyrimidine- 5-carboxylate top
Crystal data top
C16H18N2O3SZ = 2
Mr = 318.39F(000) = 336
Triclinic, P1Dx = 1.291 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.5418 Å
a = 8.2262 (15) ÅCell parameters from 25 reflections
b = 11.0683 (18) Åθ = 16.4–50.6°
c = 11.112 (2) ŵ = 1.88 mm1
α = 60.317 (15)°T = 297 K
β = 74.555 (16)°Prism, yellow
γ = 69.765 (16)°0.35 × 0.3 × 0.2 mm
V = 819.1 (3) Å3
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.025
non–profiled ω/2θ scansθmax = 67.1°, θmin = 4.6°
Absorption correction: ψ scan
(North et al., 1968)
h = 99
Tmin = 0.597, Tmax = 0.686k = 1113
2997 measured reflectionsl = 013
2837 independent reflections2 standard reflections every 120 min
2630 reflections with I > 2σ(I) intensity decay: 1%
Refinement top
Refinement on F2H-atom parameters constrained
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.0886P)2 + 0.1677P]
where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.061(Δ/σ)max < 0.001
wR(F2) = 0.156Δρmax = 0.33 e Å3
S = 1.18Δρmin = 0.38 e Å3
2837 reflectionsExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
203 parametersExtinction coefficient: 0.181 (8)
0 restraints
Crystal data top
C16H18N2O3Sγ = 69.765 (16)°
Mr = 318.39V = 819.1 (3) Å3
Triclinic, P1Z = 2
a = 8.2262 (15) ÅCu Kα radiation
b = 11.0683 (18) ŵ = 1.88 mm1
c = 11.112 (2) ÅT = 297 K
α = 60.317 (15)°0.35 × 0.3 × 0.2 mm
β = 74.555 (16)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
2630 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968)
Rint = 0.025
Tmin = 0.597, Tmax = 0.6862 standard reflections every 120 min
2997 measured reflections intensity decay: 1%
2837 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0610 restraints
wR(F2) = 0.156H-atom parameters constrained
S = 1.18Δρmax = 0.33 e Å3
2837 reflectionsΔρmin = 0.38 e Å3
203 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S0.87159 (7)0.12970 (7)0.20413 (8)0.0745 (3)
N10.30304 (19)0.27798 (15)0.30438 (15)0.0430 (4)
C20.4169 (2)0.35827 (18)0.27024 (18)0.0430 (4)
N30.5847 (2)0.31579 (16)0.24112 (17)0.0495 (4)
C40.6574 (3)0.1819 (2)0.2448 (2)0.0488 (5)
C50.5435 (2)0.09323 (18)0.28549 (18)0.0456 (5)
C60.3693 (2)0.13928 (18)0.31766 (18)0.0449 (4)
C70.3467 (2)0.50303 (18)0.2683 (2)0.0468 (5)
C80.3321 (3)0.5140 (2)0.3891 (2)0.0645 (6)
H80.36740.43230.47030.077*
C90.2646 (4)0.6472 (3)0.3889 (3)0.0757 (7)
H90.25320.65510.47050.091*
C100.2147 (4)0.7674 (3)0.2692 (3)0.0799 (8)
H100.16830.85660.26980.096*
C110.2326 (4)0.7569 (2)0.1498 (3)0.0876 (9)
H110.19940.83920.06850.105*
C120.2999 (4)0.6243 (2)0.1476 (2)0.0686 (6)
H120.31320.61770.06520.082*
C130.2481 (3)0.0445 (2)0.3715 (3)0.0632 (6)
H13A0.30960.04390.36560.095*
H13B0.15240.09240.31650.095*
H13C0.20450.02430.46690.095*
C140.6211 (3)0.0571 (2)0.2998 (2)0.0520 (5)
O150.6649 (3)0.15931 (16)0.40618 (18)0.0888 (7)
O160.63106 (19)0.06239 (13)0.18248 (14)0.0546 (4)
C170.7073 (3)0.2034 (2)0.1833 (2)0.0651 (6)
H17A0.63870.27020.25070.078*
H17B0.82540.24180.2080.078*
C180.7075 (4)0.1824 (3)0.0412 (3)0.0876 (9)
H18A0.75890.27260.0370.131*
H18B0.77380.11470.02460.131*
H18C0.58970.14620.01880.131*
C190.1130 (2)0.3349 (2)0.3320 (2)0.0515 (5)
H19A0.09280.40450.36670.062*
H19B0.06280.25680.40350.062*
C200.0236 (3)0.4058 (2)0.2020 (3)0.0636 (6)
H20A0.06890.4870.13120.076*
H20B0.04520.33770.16510.076*
O210.1572 (2)0.45270 (19)0.2374 (3)0.0871 (6)
H210.210.41360.21980.131*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S0.0453 (4)0.0706 (4)0.1179 (6)0.0022 (3)0.0192 (3)0.0558 (4)
N10.0458 (8)0.0357 (8)0.0484 (8)0.0048 (6)0.0136 (6)0.0191 (6)
C20.0487 (10)0.0354 (9)0.0458 (9)0.0077 (7)0.0110 (7)0.0181 (8)
N30.0491 (9)0.0390 (8)0.0632 (10)0.0073 (6)0.0104 (7)0.0255 (7)
C40.0513 (10)0.0429 (10)0.0552 (10)0.0033 (8)0.0176 (8)0.0242 (8)
C50.0572 (11)0.0347 (9)0.0467 (10)0.0034 (7)0.0190 (7)0.0185 (8)
C60.0565 (10)0.0351 (9)0.0466 (9)0.0073 (7)0.0192 (7)0.0172 (8)
C70.0478 (10)0.0353 (9)0.0580 (11)0.0076 (7)0.0078 (8)0.0226 (8)
C80.0837 (15)0.0487 (11)0.0625 (13)0.0103 (10)0.0110 (10)0.0287 (10)
C90.0861 (17)0.0671 (15)0.0901 (17)0.0139 (12)0.0023 (13)0.0545 (14)
C100.0803 (16)0.0480 (13)0.124 (2)0.0007 (11)0.0272 (15)0.0513 (15)
C110.120 (2)0.0358 (11)0.105 (2)0.0075 (12)0.0478 (17)0.0210 (12)
C120.0980 (18)0.0420 (11)0.0653 (13)0.0137 (11)0.0219 (12)0.0202 (10)
C130.0647 (13)0.0467 (11)0.0855 (15)0.0147 (9)0.0221 (11)0.0281 (11)
C140.0648 (12)0.0380 (10)0.0541 (11)0.0025 (8)0.0212 (8)0.0211 (9)
O150.1527 (19)0.0406 (8)0.0626 (10)0.0108 (9)0.0489 (10)0.0206 (8)
O160.0703 (9)0.0381 (7)0.0556 (8)0.0038 (6)0.0226 (6)0.0250 (6)
C170.0788 (15)0.0417 (11)0.0746 (14)0.0060 (9)0.0219 (11)0.0334 (10)
C180.119 (2)0.0667 (15)0.0732 (15)0.0008 (15)0.0080 (14)0.0458 (13)
C190.0454 (10)0.0467 (10)0.0645 (12)0.0078 (8)0.0085 (8)0.0278 (9)
C200.0557 (12)0.0510 (11)0.0833 (15)0.0028 (9)0.0277 (10)0.0268 (11)
O210.0531 (9)0.0676 (10)0.1593 (18)0.0065 (7)0.0400 (10)0.0650 (12)
Geometric parameters (Å, º) top
S—C41.665 (2)O16—C171.463 (2)
N1—C21.365 (2)C17—C181.478 (3)
N1—C61.384 (2)C19—C201.512 (3)
N1—C191.480 (2)C20—O211.412 (3)
N1—O15i2.858 (2)O21—H210.82
C2—O15i3.182 (3)C8—H80.93
C6—O15i3.117 (2)C9—H90.93
C2—N31.302 (2)C10—H100.93
C2—C71.494 (2)C11—H110.93
N3—C41.377 (2)C12—H120.93
C4—C51.420 (3)C13—H13A0.96
C5—C61.358 (3)C13—H13B0.96
C5—C141.503 (2)C13—H13C0.96
C6—C131.496 (3)C17—H17A0.97
C7—C121.372 (3)C17—H17B0.97
C7—C81.377 (3)C18—H18A0.96
C8—C91.384 (3)C18—H18B0.96
C9—C101.367 (4)C18—H18C0.96
C10—C111.354 (4)C19—H19A0.97
C11—C121.388 (3)C19—H19B0.97
C14—O151.195 (3)C20—H20A0.97
C14—O161.313 (2)C20—H20B0.97
C2—N1—C6118.59 (15)C6—C13—H13B109.5
C2—N1—C19121.19 (14)H13A—C13—H13B109.5
C6—N1—C19120.19 (15)C6—C13—H13C109.5
N3—C2—N1124.07 (15)H13A—C13—H13C109.5
N3—C2—C7117.36 (15)H13B—C13—H13C109.5
N1—C2—C7118.55 (15)O15—C14—O16124.43 (17)
C2—N3—C4119.96 (16)O15—C14—C5123.69 (18)
N3—C4—C5117.43 (17)O16—C14—C5111.86 (15)
N3—C4—S119.70 (15)C14—O16—C17116.71 (15)
C5—C4—S122.87 (15)O16—C17—C18106.96 (17)
C6—C5—C4121.37 (16)O16—C17—H17A110.3
C6—C5—C14120.09 (17)C18—C17—H17A110.3
C4—C5—C14118.46 (17)O16—C17—H17B110.3
C5—C6—N1118.38 (16)C18—C17—H17B110.3
C5—C6—C13122.62 (17)H17A—C17—H17B108.6
N1—C6—C13118.97 (17)C17—C18—H18A109.5
C12—C7—C8120.04 (18)C17—C18—H18B109.5
C12—C7—C2120.84 (17)H18A—C18—H18B109.5
C8—C7—C2119.11 (17)C17—C18—H18C109.5
C7—C8—C9119.5 (2)H18A—C18—H18C109.5
C7—C8—H8120.2H18B—C18—H18C109.5
C9—C8—H8120.2N1—C19—C20111.69 (17)
C10—C9—C8120.2 (2)N1—C19—H19A109.3
C10—C9—H9119.9C20—C19—H19A109.3
C8—C9—H9119.9N1—C19—H19B109.3
C11—C10—C9120.2 (2)C20—C19—H19B109.3
C11—C10—H10119.9H19A—C19—H19B107.9
C9—C10—H10119.9O21—C20—C19108.4 (2)
C10—C11—C12120.6 (2)O21—C20—H20A110
C10—C11—H11119.7C19—C20—H20A110
C12—C11—H11119.7O21—C20—H20B110
C7—C12—C11119.4 (2)C19—C20—H20B110
C7—C12—H12120.3H20A—C20—H20B108.4
C11—C12—H12120.3C20—O21—H21109.5
C6—C13—H13A109.5
C6—N1—C2—N34.2 (3)N1—C2—C7—C1292.5 (2)
C19—N1—C2—N3178.05 (16)N3—C2—C7—C890.3 (2)
C6—N1—C2—C7174.66 (15)N1—C2—C7—C888.7 (2)
C19—N1—C2—C73.1 (2)C12—C7—C8—C92.2 (3)
N1—C2—N3—C40.5 (3)C2—C7—C8—C9179.0 (2)
C7—C2—N3—C4178.33 (15)C7—C8—C9—C100.8 (4)
C2—N3—C4—C52.0 (3)C8—C9—C10—C110.7 (4)
C2—N3—C4—S178.69 (14)C9—C10—C11—C120.7 (5)
N3—C4—C5—C60.9 (3)C8—C7—C12—C112.1 (4)
S—C4—C5—C6179.84 (13)C2—C7—C12—C11179.0 (2)
N3—C4—C5—C14175.92 (15)C10—C11—C12—C70.7 (4)
S—C4—C5—C143.4 (2)C6—C5—C14—O1585.8 (3)
C4—C5—C6—N12.7 (3)C4—C5—C14—O1591.1 (3)
C14—C5—C6—N1179.42 (15)C6—C5—C14—O1692.9 (2)
C4—C5—C6—C13175.09 (17)C4—C5—C14—O1690.3 (2)
C14—C5—C6—C131.7 (3)O15—C14—O16—C172.3 (3)
C2—N1—C6—C55.1 (2)C5—C14—O16—C17179.06 (17)
C19—N1—C6—C5177.14 (15)C14—O16—C17—C18179.1 (2)
C2—N1—C6—C13172.76 (16)C2—N1—C19—C2093.1 (2)
C19—N1—C6—C135.0 (2)C6—N1—C19—C2089.1 (2)
N3—C2—C7—C1288.6 (2)N1—C19—C20—O21177.98 (15)
Symmetry code: (i) x+1, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O21—H21···N3ii0.822.212.986 (2)159
C13—H13B···Sii0.962.733.640 (2)160
Symmetry code: (ii) x1, y, z.

Experimental details

Crystal data
Chemical formulaC16H18N2O3S
Mr318.39
Crystal system, space groupTriclinic, P1
Temperature (K)297
a, b, c (Å)8.2262 (15), 11.0683 (18), 11.112 (2)
α, β, γ (°)60.317 (15), 74.555 (16), 69.765 (16)
V3)819.1 (3)
Z2
Radiation typeCu Kα
µ (mm1)1.88
Crystal size (mm)0.35 × 0.3 × 0.2
Data collection
DiffractometerEnraf–Nonius CAD-4
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.597, 0.686
No. of measured, independent and
observed [I > 2σ(I)] reflections
2997, 2837, 2630
Rint0.025
(sin θ/λ)max1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.061, 0.156, 1.18
No. of reflections2837
No. of parameters203
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.33, 0.38

Computer programs: CAD-4-PC (Enraf–Nonius, 1993), CAD-4-PC, XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2003), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O21—H21···N3i0.822.212.986 (2)158.5
C13—H13B···Si0.962.733.640 (2)159.5
Symmetry code: (i) x1, y, z.
 

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