organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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1-(3-Chloro­phen­yl)-4,4,6-tri­methyl-3,4-di­hydro­pyrimidine-2(1H)-thione

aSchool of Chemical Sciences and Food Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi Selangor, Malaysia
*Correspondence e-mail: bohari@ukm.my

(Received 19 December 2010; accepted 25 December 2010; online 8 January 2011)

In the title compound, C13H15ClN2S, the dihydro­pyrimidine ring is essentially planar, with a maximum deviation from the least-squares plane of 0.122 (3) Å for the unsubstitued olefinic C atom. The dihedral angle between the dihydro­pyrimidine and benzene rings is 86.62 (13)°. The crystal structure is stabilized by inter­molecular N—H⋯S hydrogen bonds, which form centrosymmetric dimers arranged along the c axis.

Related literature

For related structures, see: Yamin et al. (2005[Yamin, B. M., Kasim, N. A. M. & Hamzah, N. (2005). Acta Cryst. E61, o55-o57.]); Ismail et al. (2007[Ismail, N. L., Othman, E. & Yamin, B. M. (2007). Acta Cryst. E63, o2442-o2443.]); Saeed & Bolte, (2010[Saeed, A. & Bolte, M. (2010). Acta Cryst. E66, o440.]). For the biological activity of dihydro­pyrimidinone/thione derivatives, see: Alam et al. (2005[Alam, O., Imran, M. & Khan, S. A. (2005). Indian J. Heterocycl. Chem. 14, 293-296.]); Kappe (2000[Kappe, C. O. (2000). Acc. Chem. Res. 33, 879-888.]); Sriram et al. (2006[Sriram, D., Yogeeswari, P. & Devakaram, R. V. (2006). Bioorg. Med. Chem. 14, 3113-3118.]); Leite et al. (2006[Leite, A. C. L., Lima, R. S., Moreira, D. R. M., Cardoso, M. V. O., Brito, A. C. G., Santos, L. M. F., Hernandes, M. Z., Kiperstok, A. C., Lima, R. S. & Soares, M. B. P. (2006). Bioorg. Med. Chem. 14, 3749-3757.]). For graph-set theory, see: Etter et al. (1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C13H15ClN2S

  • Mr = 266.78

  • Monoclinic, P 21 /c

  • a = 8.398 (2) Å

  • b = 14.930 (4) Å

  • c = 11.468 (3) Å

  • β = 103.909 (4)°

  • V = 1395.7 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.40 mm−1

  • T = 298 K

  • 0.40 × 0.19 × 0.17 mm

Data collection
  • Bruker SMART APEX CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.855, Tmax = 0.934

  • 8215 measured reflections

  • 2598 independent reflections

  • 2212 reflections with I > 2/s(I)

  • Rint = 0.021

Refinement
  • R[F2 > 2σ(F2)] = 0.048

  • wR(F2) = 0.133

  • S = 1.10

  • 2598 reflections

  • 157 parameters

  • H-atom parameters constrained

  • Δρmax = 0.29 e Å−3

  • Δρmin = −0.14 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1A⋯S1i 0.85 2.58 3.404 (2) 162
Symmetry code: (i) -x+2, -y+2, -z+1.

Data collection: SMART (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEPIII (Burnett & Johnson, 1996[Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.]), ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXL97, PARST (Nardelli, 1995[Nardelli, M. (1995). J. Appl. Cryst. 28, 659.]) and PLATON.

Supporting information


Comment top

The dihydropyrimidinone/thione derivatives are medicinally important due to their therapeutic and pharmacological properties (Kappe, 2000; Alam et al.,2005; Sriram et al., 2006; Leite et al., 2006)).

The title compound (I) is a meta isomer of the previously reported 1-(4-Chlorophenyl)-4,4,6-trimethyl-3,4-dihydropyrimidine-2(1 H) -thione (Saeed & Bolte,2010). The dihydropyrimidine N1/C1/N2/C2/C3/C4 ring is essentially planar with maximum deviation of 0.122 (3) Å for the unsubstituted olefinic carbon C3 atom compare to that in the para isomer where the C4 atom bearing the two methyl substituents deviated by 0.44 (2)%A from the other five almost coplanar atoms (Saeed & Bolte,2010). The dihedral angle between the dihydropyrimidine and benzene ring is 86.62 (13)° (Fig. 1), smaller than that in the para isomer of 89.59 (5) Å. The bond lengths and bond angles agree with closely related structures (Ismail et al., 2007; Yamin et al., 2005).

The molecular packing is also characterized by centrosymmetric dimers connected by the N—H..S intermolecular hydrogen bond forming a R22(8) ring (Etter et al., 1990, Bernstein et al., 1995) and are arranged parallel to the c axis (Table 1, Fig 2).

Related literature top

For related structures, see: Yamin et al. (2005); Ismail et al. (2007); Saeed & Bolte, (2010). For the biological activity of dihydropyrimidinone/thione derivatives, see: Alam et al. (2005); Kappe (2000); Sriram et al. (2006); Leite et al. (2006). For graph-set theory, see: Etter et al. (1990); Bernstein et al. (1995).

Experimental top

The title compound was prepared by the reaction of thiocynic acid (5.4 mmol) and 3-chloroanaline (5.4 mmol) in acetone. The reaction mixture was stirred for 2–3 h. Then the clear was left for slow evaporation at room temperature. Colourless crystals of 1-(3-Chlorophenyl)-4,4,6-trimethyl -3,4-dihydropyrimidine-2 (1H)-thione were obtained after three days with 80% yield. Anal.Calcd for C13 H15 Cl N2 S: C, 58.53; H, 5.67; N, 10.50; S, 12.02%; found:C, 58.49; H,5.72; N, 10.61; S, 12.14,IR(KBr), v (cm-1) 1535 (C=S),1591(C=C),3184 (N—H).

Refinement top

All H atoms attached to C atoms were fixed geometrically and treated as riding with C—H= 0.93 Å(aromatic) or 0.96 Å(methy) with Uiso(H)=1.2Ueq(Caromatic) and 1.5Uaq(Cmethyl). The amino hydrogen atom was located from the difference map and refined freely with Uiso(H)=1.2Ueq(N). In the last cycles of refinement, it was treated as riding on the parent N atom. Both methyl groups attached to C3 display rather elongated ellipsoids however no correct disordered model could be defined and these large ellipsoids may be related to dynamic motion.

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996), ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Molecular view of (I) with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii.
[Figure 2] Fig. 2. The molecular packing of (1) viewed down the a axis. H atoms not involved in hydrogen bondings have been omitted for clarity. H bonds are represented as dashed lines. [Symmetry code: (i) -x+2, -y+2, -z+1]
1-(3-Chlorophenyl)-4,4,6-trimethyl-3,4-dihydropyrimidine-2(1H)-thione top
Crystal data top
C13H15ClN2SF(000) = 560
Mr = 266.78Dx = 1.270 Mg m3
Monoclinic, P21/cMelting point = 427.6–429.6 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 8.398 (2) ÅCell parameters from 2921 reflections
b = 14.930 (4) Åθ = 2.2–25.5°
c = 11.468 (3) ŵ = 0.40 mm1
β = 103.909 (4)°T = 298 K
V = 1395.7 (6) Å3Block, colourless
Z = 40.40 × 0.19 × 0.17 mm
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
2598 independent reflections
Radiation source: fine-focus sealed tube2212 reflections with I > 2/s(I)
Graphite monochromatorRint = 0.021
Detector resolution: 83.66 pixels mm-1θmax = 25.5°, θmin = 2.2°
ω scansh = 1010
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
k = 1318
Tmin = 0.855, Tmax = 0.934l = 1213
8215 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.133H-atom parameters constrained
S = 1.10 w = 1/[σ2(Fo2) + (0.0696P)2 + 0.4092P]
where P = (Fo2 + 2Fc2)/3
2598 reflections(Δ/σ)max < 0.001
157 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = 0.14 e Å3
Crystal data top
C13H15ClN2SV = 1395.7 (6) Å3
Mr = 266.78Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.398 (2) ŵ = 0.40 mm1
b = 14.930 (4) ÅT = 298 K
c = 11.468 (3) Å0.40 × 0.19 × 0.17 mm
β = 103.909 (4)°
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
2598 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
2212 reflections with I > 2/s(I)
Tmin = 0.855, Tmax = 0.934Rint = 0.021
8215 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0480 restraints
wR(F2) = 0.133H-atom parameters constrained
S = 1.10Δρmax = 0.29 e Å3
2598 reflectionsΔρmin = 0.14 e Å3
157 parameters
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
xyzUiso*/Ueq
Cl10.26790 (8)0.97009 (5)0.03961 (6)0.0647 (2)
S10.77220 (7)1.01839 (4)0.36163 (5)0.0496 (2)
N10.8934 (2)0.87127 (13)0.47479 (18)0.0508 (5)
H1A0.97000.90860.50300.061*
N20.6306 (2)0.85790 (12)0.35950 (17)0.0467 (5)
C10.7657 (3)0.90982 (15)0.40192 (19)0.0408 (5)
C20.6333 (3)0.76397 (16)0.3814 (3)0.0598 (7)
C30.7636 (4)0.72845 (18)0.4552 (3)0.0693 (8)
H30.76900.66640.46210.083*
C40.9012 (3)0.78148 (16)0.5276 (2)0.0602 (7)
C50.4926 (4)0.7110 (2)0.3124 (4)0.1029 (13)
H5A0.51330.64840.32830.154*
H5B0.47870.72220.22810.154*
H5C0.39470.72810.33600.154*
C71.0658 (5)0.7413 (2)0.5222 (5)0.1179 (16)
H7A1.07400.73920.44010.177*
H7B1.07450.68180.55470.177*
H7C1.15280.77770.56820.177*
C80.4808 (3)0.90016 (15)0.2952 (2)0.0450 (5)
C90.4507 (3)0.91237 (15)0.1734 (2)0.0448 (5)
H90.52610.89330.13110.054*
C100.3064 (3)0.95355 (15)0.1145 (2)0.0468 (5)
C110.1924 (3)0.98094 (17)0.1755 (3)0.0571 (7)
H110.09591.00880.13510.069*
C120.2238 (3)0.96636 (19)0.2971 (3)0.0644 (7)
H120.14670.98370.33890.077*
C130.3679 (3)0.92637 (18)0.3583 (2)0.0578 (6)
H130.38870.91730.44080.069*
C60.8890 (7)0.7904 (3)0.6570 (3)0.137 (2)
H6A0.97560.82840.70010.206*
H6B0.89890.73230.69400.206*
H6C0.78490.81610.65900.206*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0586 (4)0.0726 (5)0.0561 (4)0.0055 (3)0.0005 (3)0.0109 (3)
S10.0455 (4)0.0420 (3)0.0541 (4)0.0027 (2)0.0022 (3)0.0110 (3)
N10.0452 (11)0.0431 (11)0.0568 (11)0.0034 (8)0.0022 (9)0.0078 (9)
N20.0430 (10)0.0391 (10)0.0546 (11)0.0009 (8)0.0050 (8)0.0046 (8)
C10.0399 (11)0.0419 (12)0.0397 (11)0.0035 (9)0.0077 (9)0.0014 (9)
C20.0618 (16)0.0402 (13)0.0743 (17)0.0030 (11)0.0104 (13)0.0033 (12)
C30.082 (2)0.0373 (13)0.081 (2)0.0015 (13)0.0059 (16)0.0088 (13)
C40.0760 (18)0.0425 (13)0.0546 (14)0.0126 (12)0.0010 (12)0.0076 (11)
C50.082 (2)0.0519 (17)0.158 (4)0.0206 (16)0.004 (2)0.008 (2)
C70.080 (2)0.064 (2)0.185 (5)0.0305 (18)0.015 (2)0.003 (3)
C80.0378 (11)0.0412 (12)0.0534 (13)0.0050 (9)0.0056 (9)0.0017 (10)
C90.0393 (11)0.0438 (12)0.0520 (13)0.0049 (9)0.0123 (10)0.0022 (10)
C100.0412 (12)0.0414 (11)0.0533 (13)0.0084 (10)0.0025 (10)0.0012 (10)
C110.0412 (13)0.0535 (15)0.0714 (17)0.0033 (11)0.0035 (12)0.0057 (12)
C120.0506 (15)0.0716 (19)0.0732 (19)0.0066 (12)0.0195 (14)0.0122 (14)
C130.0538 (15)0.0655 (17)0.0546 (14)0.0006 (12)0.0142 (12)0.0055 (12)
C60.270 (6)0.082 (3)0.058 (2)0.033 (3)0.035 (3)0.0098 (19)
Geometric parameters (Å, º) top
Cl1—C101.736 (3)C7—H7A0.9600
S1—C11.690 (2)C7—H7B0.9600
N1—C11.323 (3)C7—H7C0.9600
N1—C41.466 (3)C8—C91.372 (3)
N1—H1A0.8541C8—C131.380 (3)
N2—C11.364 (3)C9—C101.382 (3)
N2—C21.424 (3)C9—H90.9300
N2—C81.441 (3)C10—C111.376 (4)
C2—C31.323 (4)C11—C121.372 (4)
C2—C51.483 (4)C11—H110.9300
C3—C41.480 (4)C12—C131.381 (4)
C3—H30.9300C12—H120.9300
C4—C61.518 (5)C13—H130.9300
C4—C71.522 (4)C6—H6A0.9600
C5—H5A0.9600C6—H6B0.9600
C5—H5B0.9600C6—H6C0.9600
C5—H5C0.9600
C1—N1—C4127.4 (2)H7A—C7—H7B109.5
C1—N1—H1A112.2C4—C7—H7C109.5
C4—N1—H1A119.1H7A—C7—H7C109.5
C1—N2—C2121.35 (19)H7B—C7—H7C109.5
C1—N2—C8118.85 (18)C9—C8—C13121.0 (2)
C2—N2—C8119.75 (18)C9—C8—N2120.2 (2)
N1—C1—N2117.2 (2)C13—C8—N2118.8 (2)
N1—C1—S1121.01 (17)C8—C9—C10118.8 (2)
N2—C1—S1121.78 (15)C8—C9—H9120.6
C3—C2—N2118.9 (2)C10—C9—H9120.6
C3—C2—C5123.9 (2)C11—C10—C9121.3 (2)
N2—C2—C5117.0 (2)C11—C10—Cl1119.56 (19)
C2—C3—C4124.0 (2)C9—C10—Cl1119.16 (19)
C2—C3—H3118.0C12—C11—C10118.8 (2)
C4—C3—H3118.0C12—C11—H11120.6
N1—C4—C3107.8 (2)C10—C11—H11120.6
N1—C4—C6108.5 (2)C11—C12—C13121.0 (2)
C3—C4—C6111.6 (3)C11—C12—H12119.5
N1—C4—C7107.1 (3)C13—C12—H12119.5
C3—C4—C7111.2 (3)C8—C13—C12119.0 (2)
C6—C4—C7110.5 (3)C8—C13—H13120.5
C2—C5—H5A109.5C12—C13—H13120.5
C2—C5—H5B109.5C4—C6—H6A109.5
H5A—C5—H5B109.5C4—C6—H6B109.5
C2—C5—H5C109.5H6A—C6—H6B109.5
H5A—C5—H5C109.5C4—C6—H6C109.5
H5B—C5—H5C109.5H6A—C6—H6C109.5
C4—C7—H7A109.5H6B—C6—H6C109.5
C4—C7—H7B109.5
C4—N1—C1—N28.0 (4)C2—C3—C4—C6100.9 (4)
C4—N1—C1—S1173.1 (2)C2—C3—C4—C7135.3 (3)
C2—N2—C1—N17.0 (3)C1—N2—C8—C988.4 (3)
C8—N2—C1—N1170.6 (2)C2—N2—C8—C994.0 (3)
C2—N2—C1—S1171.87 (19)C1—N2—C8—C1392.8 (3)
C8—N2—C1—S110.5 (3)C2—N2—C8—C1384.9 (3)
C1—N2—C2—C37.4 (4)C13—C8—C9—C101.5 (3)
C8—N2—C2—C3170.1 (3)N2—C8—C9—C10179.65 (19)
C1—N2—C2—C5168.4 (3)C8—C9—C10—C111.0 (3)
C8—N2—C2—C514.1 (4)C8—C9—C10—Cl1179.51 (17)
N2—C2—C3—C46.8 (4)C9—C10—C11—C120.3 (4)
C5—C2—C3—C4177.7 (3)Cl1—C10—C11—C12179.2 (2)
C1—N1—C4—C319.4 (4)C10—C11—C12—C131.1 (4)
C1—N1—C4—C6101.6 (3)C9—C8—C13—C120.7 (4)
C1—N1—C4—C7139.1 (3)N2—C8—C13—C12179.6 (2)
C2—C3—C4—N118.2 (4)C11—C12—C13—C80.6 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···S1i0.852.583.404 (2)162
Symmetry code: (i) x+2, y+2, z+1.

Experimental details

Crystal data
Chemical formulaC13H15ClN2S
Mr266.78
Crystal system, space groupMonoclinic, P21/c
Temperature (K)298
a, b, c (Å)8.398 (2), 14.930 (4), 11.468 (3)
β (°) 103.909 (4)
V3)1395.7 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.40
Crystal size (mm)0.40 × 0.19 × 0.17
Data collection
DiffractometerBruker SMART APEX CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.855, 0.934
No. of measured, independent and
observed [I > 2/s(I)] reflections
8215, 2598, 2212
Rint0.021
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.133, 1.10
No. of reflections2598
No. of parameters157
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.29, 0.14

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), ORTEPIII (Burnett & Johnson, 1996), ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009), SHELXL97 (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···S1i0.852.583.404 (2)162
Symmetry code: (i) x+2, y+2, z+1.
 

Acknowledgements

The authors thank the Ministry of Higher Education of Malaysia and Universiti Kebagsaan Malaysia for the research grant UKM-ST-06-FRGS0114–2009. A scholarship from the Libyan Goverment to SFH is greatly appreciated.

References

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