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

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ISSN: 2056-9890

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

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

(Received 11 June 2011; accepted 17 June 2011; online 25 June 2011)

In the title compound, C13H15FN2S, the dihydro­pyrimidine ring is essentially planar, with a maximum deviation of 0.086 (3) Å from the mean plane of the rest of the ring for the dimethyl­ated C atom. The benzene ring is almost perpendicular to the dihydro­pyrimidine ring, with a dihedral angle of 83.97 (14)°. The crystal packing is characterized by centrosymmetric dimers resulting from pairs of inter­molecular N—H⋯S hydrogen bonds. There are also C—H⋯π inter­actions.

Related literature

For the biological properties of related compounds, see: Rovnyak et al. (1995[Rovnyak, G. C., Kimball, S. D., Beyer, B., Cucinotta, G., DiMarco, J. D., Gougoutas, J., Hedberg, A., Malley, M., McCarthy, J. P., Zhang, R. & Moreland, S. (1995). J. Med. Chem. 38, 119-129.]); Kappe (2000[Kappe, C. O. (2000). Acc. Chem. Res. 33, 879-888.]); Alam et al. (2005[Alam, O., Imran, M. & Khan, S. A. (2005). Indian J. Heterocycl. Chem. 14, 293-296.]); 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 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 et al. (2010[Saeed, A., Khera, R. A. & Parvez, M. (2010). Acta Cryst. E66, o635.]); Yamin & Salem (2011[Yamin, B. M. & Salem, H. F. (2011). Acta Cryst. E67, o282.]). For standard bond lengths, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]).

[Scheme 1]

Experimental

Crystal data
  • C13H15FN2S

  • Mr = 250.33

  • Monoclinic, P 21 /c

  • a = 8.814 (3) Å

  • b = 14.997 (5) Å

  • c = 10.215 (3) Å

  • β = 95.711 (6)°

  • V = 1343.6 (7) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.23 mm−1

  • T = 298 K

  • 0.50 × 0.29 × 0.20 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 = 0.892, Tmax = 0.954

  • 7116 measured reflections

  • 2497 independent reflections

  • 1764 reflections with I > 2σ(I)

  • Rint = 0.034

Refinement
  • R[F2 > 2σ(F2)] = 0.059

  • wR(F2) = 0.153

  • S = 1.06

  • 2497 reflections

  • 157 parameters

  • H-atom parameters constrained

  • Δρmax = 0.37 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the N1/N2/C1–C4 pyrimidine ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1A⋯S1i 0.86 2.57 3.400 (3) 162
C9—H9ACg1ii 0.93 2.89 3.788 (4) 163
Symmetry codes: (i) -x+1, -y, -z+1; (ii) [x, -y-{\script{1\over 2}}, z-{\script{3\over 2}}].

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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL, PARST (Nardelli, 1995[Nardelli, M. (1995). J. Appl. Cryst. 28, 659.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Pyrimidine-2(1H)-ones/thiones are calcium channel blocker compounds (Rovnyak et al., 1995). They also have other biological activities such as antibacterial, antifungal and antiviral (Kappe, 2000; Alam et al., 2005; Sriram et al., 2006; Leite et al., 2006). The 4,4,6-trimethyl-1-aryl-3,4-dihydropyrimidine-2-(1H)-thiones open a new series of 3,4-dihydro pyrimidine-2-(1H)-thione derivatives following publication of 4,4,6- trimethyl-1-phenyl-3,4-dihydropyrimidine-2-(1H)-thione (Yamin et al., 2005; Ismail et al., 2007). The title compound is isomorphous to 4,4,6-trimethyl-1-(3-chlorophenyl)-3,4-dihydropyrimidine-2-(1H)-thione (Yamin & Salem, 2011) and 4,4,6-trimethyl-1-(3-methylphenyl)-3,4-dihydropyrimidine-2-(1H)-thione (Saeed et al., 2010). The dihydropyrimidine (N1,N2,C1—C4) ring is planar with maximum deviation of 0.086 (3)Å for C4 atom from the least square plane. The benzene ring is perpendicular to the dihydropyrimidine with dihedral angle of 83.97 (14)°, slightly smaller than that in the meta- chloro analog (86.62 (13)°). The bond lenghts and angles are in normal ranges (Allen et al., 1987) and are comparable to those in the above mentioned analogs. In the crystal, the molecules are linked by N1—H1A···S1 intermolecular hydrogen bonds (see symmetry code in Table 2) to form centrosymmetric dimers parallel to the ab face (Fig 2). There is also a C9—H9A···π interaction involving the pyrimidine (Cg1: N1/N2/(C1—C4)) ring (Table 2).

Related literature top

For the biological properties of related compounds, see: Rovnyak et al. (1995); Kappe (2000); Alam et al. (2005); Sriram et al. (2006); Leite et al. (2006). For related structures, see: Yamin et al. (2005); Ismail et al. (2007); Saeed et al. (2010); Yamin & Salem (2011). For standard bond lengths, see: Allen et al. (1987).

Experimental top

A procedure similar to that used for the preparation of 4,4,6-Trimethyl-1-(3-chlorophenyl)-3,4-dihydropyrimidine-2-(1H)-thione (Yamin & Salem,2011) was followed. Equimolar quantities of thiocyanic acid and 3-fluoroaniline (5.4 mmol) in acetone were stirred for 2–3 h. Colourless crystals of 78% yield were obtained after 3 days by evaporation at room temperature. Melting point 456.8–458.9 K.

Refinement top

H atoms on the C and N atoms were positioned geometrically with C—H= 0.93 (aromatic and olefinic), 0.96 Å (methyl) and N—H = 0.86 Å respectively, and constrained to ride and rotate (for Me groups) on their parent atoms with Uiso=xeq(parent atom) where x=1.2 for N, aromatic C and olefinic C and x=1.5 for methyl C. There is a highest peak and deepest hole of 0.45 from H10 and 0.76Å from F1 atom the respectively.

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: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Molecular structure of (1), with the atomic-labelling scheme. Displacement ellipsoid are drawn at the 50% probablity level.
[Figure 2] Fig. 2. The packing of (1) viewed down the c axis. Hydrogen bonds are shown by dashed lines.
1-(3-Fluorophenyl)-4,4,6-trimethyl-3,4-dihydropyrimidine-2(1H)-thione top
Crystal data top
C13H15FN2SF(000) = 528
Mr = 250.33Dx = 1.238 Mg m3
Monoclinic, P21/cMelting point = 458.9–456.8 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 8.814 (3) ÅCell parameters from 2497 reflections
b = 14.997 (5) Åθ = 2.3–25.5°
c = 10.215 (3) ŵ = 0.23 mm1
β = 95.711 (6)°T = 298 K
V = 1343.6 (7) Å3Block, colourless
Z = 40.50 × 0.29 × 0.20 mm
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
2497 independent reflections
Radiation source: fine-focus sealed tube1764 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.034
ω scansθmax = 25.5°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 1010
Tmin = 0.892, Tmax = 0.954k = 1618
7116 measured reflectionsl = 1211
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)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.153H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0666P)2 + 0.4935P]
where P = (Fo2 + 2Fc2)/3
2497 reflections(Δ/σ)max = 0.001
157 parametersΔρmax = 0.37 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
C13H15FN2SV = 1343.6 (7) Å3
Mr = 250.33Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.814 (3) ŵ = 0.23 mm1
b = 14.997 (5) ÅT = 298 K
c = 10.215 (3) Å0.50 × 0.29 × 0.20 mm
β = 95.711 (6)°
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
2497 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
1764 reflections with I > 2σ(I)
Tmin = 0.892, Tmax = 0.954Rint = 0.034
7116 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0590 restraints
wR(F2) = 0.153H-atom parameters constrained
S = 1.06Δρmax = 0.37 e Å3
2497 reflectionsΔρmin = 0.17 e Å3
157 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
xyzUiso*/Ueq
F10.9699 (2)0.40143 (14)0.6648 (2)0.0938 (7)
S10.65807 (8)0.11011 (5)0.47356 (8)0.0623 (3)
N10.3831 (3)0.11471 (16)0.5539 (2)0.0620 (7)
H1A0.39390.05770.55610.074*
N20.4991 (2)0.25140 (15)0.5427 (2)0.0519 (6)
C10.5038 (3)0.1608 (2)0.5251 (3)0.0506 (7)
C20.3725 (3)0.2932 (2)0.5938 (3)0.0601 (8)
C30.2523 (4)0.2442 (2)0.6138 (4)0.0780 (10)
H3A0.17270.27230.65070.094*
C40.2343 (3)0.1480 (2)0.5824 (3)0.0644 (8)
C50.3852 (4)0.3902 (2)0.6208 (4)0.0895 (12)
H5A0.29040.41200.64710.134*
H5B0.40850.42090.54280.134*
H5C0.46500.40060.69020.134*
C60.1856 (5)0.0964 (3)0.6999 (5)0.1206 (18)
H6A0.26110.10350.77360.181*
H6B0.17570.03430.67770.181*
H6C0.08950.11880.72220.181*
C70.1209 (5)0.1335 (3)0.4636 (5)0.1154 (16)
H7A0.15120.16730.39080.173*
H7B0.02170.15250.48320.173*
H7C0.11770.07130.44120.173*
C80.6272 (3)0.30394 (18)0.5099 (3)0.0493 (7)
C90.6358 (4)0.3306 (2)0.3822 (3)0.0653 (8)
H9A0.55810.31600.31740.078*
C100.7597 (5)0.3789 (2)0.3506 (4)0.0802 (11)
H10A0.76630.39600.26380.096*
C110.8726 (4)0.4018 (2)0.4449 (4)0.0747 (10)
H11A0.95690.43410.42380.090*
C120.8593 (3)0.3763 (2)0.5706 (3)0.0606 (8)
C130.7392 (3)0.32727 (19)0.6068 (3)0.0538 (7)
H13A0.73380.31040.69380.065*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0710 (13)0.0981 (17)0.1111 (16)0.0189 (11)0.0028 (12)0.0109 (12)
S10.0536 (4)0.0493 (5)0.0878 (6)0.0031 (3)0.0263 (4)0.0071 (4)
N10.0512 (14)0.0491 (15)0.0893 (18)0.0086 (11)0.0249 (13)0.0059 (13)
N20.0487 (12)0.0461 (14)0.0630 (14)0.0021 (11)0.0151 (11)0.0044 (11)
C10.0491 (15)0.0509 (18)0.0527 (16)0.0045 (13)0.0093 (13)0.0007 (13)
C20.0531 (17)0.0572 (19)0.0717 (19)0.0065 (14)0.0151 (15)0.0071 (16)
C30.0562 (18)0.072 (2)0.110 (3)0.0044 (17)0.0322 (19)0.011 (2)
C40.0487 (16)0.066 (2)0.082 (2)0.0057 (15)0.0223 (16)0.0062 (17)
C50.073 (2)0.063 (2)0.137 (3)0.0071 (17)0.032 (2)0.021 (2)
C60.125 (4)0.109 (4)0.142 (4)0.007 (3)0.086 (3)0.021 (3)
C70.071 (3)0.134 (4)0.137 (4)0.004 (2)0.010 (3)0.038 (3)
C80.0523 (16)0.0392 (16)0.0582 (17)0.0004 (12)0.0142 (14)0.0044 (13)
C90.079 (2)0.060 (2)0.0577 (18)0.0084 (17)0.0093 (16)0.0043 (15)
C100.116 (3)0.059 (2)0.071 (2)0.019 (2)0.034 (2)0.0013 (17)
C110.090 (2)0.053 (2)0.088 (3)0.0223 (17)0.042 (2)0.0133 (18)
C120.0552 (17)0.0483 (18)0.079 (2)0.0063 (14)0.0102 (16)0.0146 (15)
C130.0556 (16)0.0470 (17)0.0605 (17)0.0005 (13)0.0138 (14)0.0029 (14)
Geometric parameters (Å, º) top
F1—C121.353 (3)C6—H6A0.9600
S1—C11.687 (3)C6—H6B0.9600
N1—C11.326 (3)C6—H6C0.9600
N1—C41.460 (4)C7—H7A0.9600
N1—H1A0.8600C7—H7B0.9600
N2—C11.372 (4)C7—H7C0.9600
N2—C21.423 (3)C8—C131.372 (4)
N2—C81.443 (3)C8—C91.374 (4)
C2—C31.321 (4)C9—C101.376 (5)
C2—C51.483 (4)C9—H9A0.9300
C3—C41.483 (5)C10—C111.359 (5)
C3—H3A0.9300C10—H10A0.9300
C4—C71.509 (5)C11—C121.356 (5)
C4—C61.526 (5)C11—H11A0.9300
C5—H5A0.9600C12—C131.369 (4)
C5—H5B0.9600C13—H13A0.9300
C5—H5C0.9600
C1—N1—C4128.5 (3)H6A—C6—H6B109.5
C1—N1—H1A115.7C4—C6—H6C109.5
C4—N1—H1A115.7H6A—C6—H6C109.5
C1—N2—C2121.3 (2)H6B—C6—H6C109.5
C1—N2—C8118.4 (2)C4—C7—H7A109.5
C2—N2—C8120.3 (2)C4—C7—H7B109.5
N1—C1—N2116.8 (2)H7A—C7—H7B109.5
N1—C1—S1121.6 (2)C4—C7—H7C109.5
N2—C1—S1121.5 (2)H7A—C7—H7C109.5
C3—C2—N2118.8 (3)H7B—C7—H7C109.5
C3—C2—C5124.3 (3)C13—C8—C9120.5 (3)
N2—C2—C5116.9 (3)C13—C8—N2119.7 (2)
C2—C3—C4125.3 (3)C9—C8—N2119.8 (3)
C2—C3—H3A117.4C8—C9—C10119.8 (3)
C4—C3—H3A117.4C8—C9—H9A120.1
N1—C4—C3107.3 (2)C10—C9—H9A120.1
N1—C4—C7109.1 (3)C11—C10—C9120.6 (3)
C3—C4—C7111.3 (3)C11—C10—H10A119.7
N1—C4—C6108.1 (3)C9—C10—H10A119.7
C3—C4—C6110.9 (3)C12—C11—C10118.3 (3)
C7—C4—C6110.1 (3)C12—C11—H11A120.9
C2—C5—H5A109.5C10—C11—H11A120.9
C2—C5—H5B109.5F1—C12—C11118.0 (3)
H5A—C5—H5B109.5F1—C12—C13118.7 (3)
C2—C5—H5C109.5C11—C12—C13123.3 (3)
H5A—C5—H5C109.5C12—C13—C8117.5 (3)
H5B—C5—H5C109.5C12—C13—H13A121.2
C4—C6—H6A109.5C8—C13—H13A121.2
C4—C6—H6B109.5
C4—N1—C1—N210.7 (4)C2—C3—C4—C7107.0 (4)
C4—N1—C1—S1171.0 (2)C2—C3—C4—C6130.1 (4)
C2—N2—C1—N12.1 (4)C1—N2—C8—C1396.2 (3)
C8—N2—C1—N1178.8 (2)C2—N2—C8—C1382.9 (3)
C2—N2—C1—S1176.1 (2)C1—N2—C8—C984.1 (3)
C8—N2—C1—S12.9 (3)C2—N2—C8—C996.8 (3)
C1—N2—C2—C35.8 (4)C13—C8—C9—C101.8 (5)
C8—N2—C2—C3175.2 (3)N2—C8—C9—C10178.5 (3)
C1—N2—C2—C5174.3 (3)C8—C9—C10—C111.1 (5)
C8—N2—C2—C54.7 (4)C9—C10—C11—C120.4 (5)
N2—C2—C3—C42.6 (5)C10—C11—C12—F1178.1 (3)
C5—C2—C3—C4177.3 (4)C10—C11—C12—C131.2 (5)
C1—N1—C4—C316.9 (4)F1—C12—C13—C8178.9 (2)
C1—N1—C4—C7103.7 (4)C11—C12—C13—C80.5 (5)
C1—N1—C4—C6136.5 (3)C9—C8—C13—C121.0 (4)
C2—C3—C4—N112.2 (5)N2—C8—C13—C12179.3 (2)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the N1/N2/C1–C4 pyrimidine ring.
D—H···AD—HH···AD···AD—H···A
N1—H1A···S1i0.862.573.400 (3)162
C9—H9A···Cg1ii0.932.893.788 (4)163
Symmetry codes: (i) x+1, y, z+1; (ii) x, y1/2, z3/2.

Experimental details

Crystal data
Chemical formulaC13H15FN2S
Mr250.33
Crystal system, space groupMonoclinic, P21/c
Temperature (K)298
a, b, c (Å)8.814 (3), 14.997 (5), 10.215 (3)
β (°) 95.711 (6)
V3)1343.6 (7)
Z4
Radiation typeMo Kα
µ (mm1)0.23
Crystal size (mm)0.50 × 0.29 × 0.20
Data collection
DiffractometerBruker SMART APEX CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.892, 0.954
No. of measured, independent and
observed [I > 2σ(I)] reflections
7116, 2497, 1764
Rint0.034
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.059, 0.153, 1.06
No. of reflections2497
No. of parameters157
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.37, 0.17

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the N1/N2/C1–C4 pyrimidine ring.
D—H···AD—HH···AD···AD—H···A
N1—H1A···S1i0.862.573.400 (3)162
C9—H9A···Cg1ii0.932.893.788 (4)163
Symmetry codes: (i) x+1, y, z+1; (ii) x, y1/2, z3/2.
 

Acknowledgements

The authors thank both The Ministry of Higher Education of Malaysia for the Research Grant UKM-ST-06-FRGS-0114–2009 and Universiti Kebangsaan Malaysian for the research facilities. The National Science Fellowship (NSF) from The Ministry of Science and Technology (MOSTI) given to RLL is greatly appreciated.

References

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