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

Yamin, B.M.; Lawi, R.L.; Salem, H.F.

doi:10.1107/S1600536811023671

organic compounds

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ISSN: 2056-9890

Volume 67| Part 7| July 2011| Page o1810

doi:10.1107/S1600536811023671

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

Bohari M. Yamin,^a ^* Ruhana L. Lawi ^a and Halima F. Salem ^a

^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 ); 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

Crystal data

C₁₃H₁₅FN₂S
M_r = 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 ) T_min = 0.892, T_max = 0.954
7116 measured reflections
2497 independent reflections
1764 reflections with I > 2σ(I)
R_int = 0.034

Refinement

R[F² > 2σ(F²)] = 0.059
wR(F²) = 0.153
S = 1.06
2497 reflections
157 parameters
H-atom parameters constrained
Δρ_max = 0.37 e Å⁻³
Δρ_min = −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	D⋯A	D—H⋯A
N1—H1A⋯S1ⁱ	0.86	2.57	3.400 (3)	162
C9—H9A⋯Cg1ⁱⁱ	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); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; 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, PARST (Nardelli, 1995 ) and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811023671/ld2016sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811023671/ld2016Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811023671/ld2016Isup3.cml

checkCIF report

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 (C_g1: 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.

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

	Fig. 1. Molecular structure of (1), with the atomic-labelling scheme. Displacement ellipsoid are drawn at the 50% probablity level.
	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

C₁₃H₁₅FN₂S	F(000) = 528
M_r = 250.33	D_x = 1.238 Mg m⁻³
Monoclinic, P2₁/c	Melting point = 458.9–456.8 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 8.814 (3) Å	Cell parameters from 2497 reflections
b = 14.997 (5) Å	θ = 2.3–25.5°
c = 10.215 (3) Å	µ = 0.23 mm⁻¹
β = 95.711 (6)°	T = 298 K
V = 1343.6 (7) Å³	Block, colourless
Z = 4	0.50 × 0.29 × 0.20 mm

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	2497 independent reflections
Radiation source: fine-focus sealed tube	1764 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.034
ω scans	θ_max = 25.5°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −10→10
T_min = 0.892, T_max = 0.954	k = −16→18
7116 measured reflections	l = −12→11

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.153	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.0666P)² + 0.4935P] where P = (F_o² + 2F_c²)/3
2497 reflections	(Δ/σ)_max = 0.001
157 parameters	Δρ_max = 0.37 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₁₃H₁₅FN₂S	V = 1343.6 (7) Å³
M_r = 250.33	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 8.814 (3) Å	µ = 0.23 mm⁻¹
b = 14.997 (5) Å	T = 298 K
c = 10.215 (3) Å	0.50 × 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)
T_min = 0.892, T_max = 0.954	R_int = 0.034
7116 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.059	0 restraints
wR(F²) = 0.153	H-atom parameters constrained
S = 1.06	Δρ_max = 0.37 e Å⁻³
2497 reflections	Δρ_min = −0.17 e Å⁻³
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

	x	y	z	U_iso*/U_eq
F1	0.9699 (2)	0.40143 (14)	0.6648 (2)	0.0938 (7)
S1	0.65807 (8)	0.11011 (5)	0.47356 (8)	0.0623 (3)
N1	0.3831 (3)	0.11471 (16)	0.5539 (2)	0.0620 (7)
H1A	0.3939	0.0577	0.5561	0.074*
N2	0.4991 (2)	0.25140 (15)	0.5427 (2)	0.0519 (6)
C1	0.5038 (3)	0.1608 (2)	0.5251 (3)	0.0506 (7)
C2	0.3725 (3)	0.2932 (2)	0.5938 (3)	0.0601 (8)
C3	0.2523 (4)	0.2442 (2)	0.6138 (4)	0.0780 (10)
H3A	0.1727	0.2723	0.6507	0.094*
C4	0.2343 (3)	0.1480 (2)	0.5824 (3)	0.0644 (8)
C5	0.3852 (4)	0.3902 (2)	0.6208 (4)	0.0895 (12)
H5A	0.2904	0.4120	0.6471	0.134*
H5B	0.4085	0.4209	0.5428	0.134*
H5C	0.4650	0.4006	0.6902	0.134*
C6	0.1856 (5)	0.0964 (3)	0.6999 (5)	0.1206 (18)
H6A	0.2611	0.1035	0.7736	0.181*
H6B	0.1757	0.0343	0.6777	0.181*
H6C	0.0895	0.1188	0.7222	0.181*
C7	0.1209 (5)	0.1335 (3)	0.4636 (5)	0.1154 (16)
H7A	0.1512	0.1673	0.3908	0.173*
H7B	0.0217	0.1525	0.4832	0.173*
H7C	0.1177	0.0713	0.4412	0.173*
C8	0.6272 (3)	0.30394 (18)	0.5099 (3)	0.0493 (7)
C9	0.6358 (4)	0.3306 (2)	0.3822 (3)	0.0653 (8)
H9A	0.5581	0.3160	0.3174	0.078*
C10	0.7597 (5)	0.3789 (2)	0.3506 (4)	0.0802 (11)
H10A	0.7663	0.3960	0.2638	0.096*
C11	0.8726 (4)	0.4018 (2)	0.4449 (4)	0.0747 (10)
H11A	0.9569	0.4341	0.4238	0.090*
C12	0.8593 (3)	0.3763 (2)	0.5706 (3)	0.0606 (8)
C13	0.7392 (3)	0.32727 (19)	0.6068 (3)	0.0538 (7)
H13A	0.7338	0.3104	0.6938	0.065*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.0710 (13)	0.0981 (17)	0.1111 (16)	−0.0189 (11)	0.0028 (12)	−0.0109 (12)
S1	0.0536 (4)	0.0493 (5)	0.0878 (6)	−0.0031 (3)	0.0263 (4)	−0.0071 (4)
N1	0.0512 (14)	0.0491 (15)	0.0893 (18)	−0.0086 (11)	0.0249 (13)	−0.0059 (13)
N2	0.0487 (12)	0.0461 (14)	0.0630 (14)	−0.0021 (11)	0.0151 (11)	−0.0044 (11)
C1	0.0491 (15)	0.0509 (18)	0.0527 (16)	−0.0045 (13)	0.0093 (13)	−0.0007 (13)
C2	0.0531 (17)	0.0572 (19)	0.0717 (19)	0.0065 (14)	0.0151 (15)	−0.0071 (16)
C3	0.0562 (18)	0.072 (2)	0.110 (3)	0.0044 (17)	0.0322 (19)	−0.011 (2)
C4	0.0487 (16)	0.066 (2)	0.082 (2)	−0.0057 (15)	0.0223 (16)	−0.0062 (17)
C5	0.073 (2)	0.063 (2)	0.137 (3)	0.0071 (17)	0.032 (2)	−0.021 (2)
C6	0.125 (4)	0.109 (4)	0.142 (4)	0.007 (3)	0.086 (3)	0.021 (3)
C7	0.071 (3)	0.134 (4)	0.137 (4)	−0.004 (2)	−0.010 (3)	−0.038 (3)
C8	0.0523 (16)	0.0392 (16)	0.0582 (17)	−0.0004 (12)	0.0142 (14)	−0.0044 (13)
C9	0.079 (2)	0.060 (2)	0.0577 (18)	−0.0084 (17)	0.0093 (16)	−0.0043 (15)
C10	0.116 (3)	0.059 (2)	0.071 (2)	−0.019 (2)	0.034 (2)	0.0013 (17)
C11	0.090 (2)	0.053 (2)	0.088 (3)	−0.0223 (17)	0.042 (2)	−0.0133 (18)
C12	0.0552 (17)	0.0483 (18)	0.079 (2)	−0.0063 (14)	0.0102 (16)	−0.0146 (15)
C13	0.0556 (16)	0.0470 (17)	0.0605 (17)	−0.0005 (13)	0.0138 (14)	0.0029 (14)

Geometric parameters (Å, º) top

F1—C12	1.353 (3)	C6—H6A	0.9600
S1—C1	1.687 (3)	C6—H6B	0.9600
N1—C1	1.326 (3)	C6—H6C	0.9600
N1—C4	1.460 (4)	C7—H7A	0.9600
N1—H1A	0.8600	C7—H7B	0.9600
N2—C1	1.372 (4)	C7—H7C	0.9600
N2—C2	1.423 (3)	C8—C13	1.372 (4)
N2—C8	1.443 (3)	C8—C9	1.374 (4)
C2—C3	1.321 (4)	C9—C10	1.376 (5)
C2—C5	1.483 (4)	C9—H9A	0.9300
C3—C4	1.483 (5)	C10—C11	1.359 (5)
C3—H3A	0.9300	C10—H10A	0.9300
C4—C7	1.509 (5)	C11—C12	1.356 (5)
C4—C6	1.526 (5)	C11—H11A	0.9300
C5—H5A	0.9600	C12—C13	1.369 (4)
C5—H5B	0.9600	C13—H13A	0.9300
C5—H5C	0.9600

C1—N1—C4	128.5 (3)	H6A—C6—H6B	109.5
C1—N1—H1A	115.7	C4—C6—H6C	109.5
C4—N1—H1A	115.7	H6A—C6—H6C	109.5
C1—N2—C2	121.3 (2)	H6B—C6—H6C	109.5
C1—N2—C8	118.4 (2)	C4—C7—H7A	109.5
C2—N2—C8	120.3 (2)	C4—C7—H7B	109.5
N1—C1—N2	116.8 (2)	H7A—C7—H7B	109.5
N1—C1—S1	121.6 (2)	C4—C7—H7C	109.5
N2—C1—S1	121.5 (2)	H7A—C7—H7C	109.5
C3—C2—N2	118.8 (3)	H7B—C7—H7C	109.5
C3—C2—C5	124.3 (3)	C13—C8—C9	120.5 (3)
N2—C2—C5	116.9 (3)	C13—C8—N2	119.7 (2)
C2—C3—C4	125.3 (3)	C9—C8—N2	119.8 (3)
C2—C3—H3A	117.4	C8—C9—C10	119.8 (3)
C4—C3—H3A	117.4	C8—C9—H9A	120.1
N1—C4—C3	107.3 (2)	C10—C9—H9A	120.1
N1—C4—C7	109.1 (3)	C11—C10—C9	120.6 (3)
C3—C4—C7	111.3 (3)	C11—C10—H10A	119.7
N1—C4—C6	108.1 (3)	C9—C10—H10A	119.7
C3—C4—C6	110.9 (3)	C12—C11—C10	118.3 (3)
C7—C4—C6	110.1 (3)	C12—C11—H11A	120.9
C2—C5—H5A	109.5	C10—C11—H11A	120.9
C2—C5—H5B	109.5	F1—C12—C11	118.0 (3)
H5A—C5—H5B	109.5	F1—C12—C13	118.7 (3)
C2—C5—H5C	109.5	C11—C12—C13	123.3 (3)
H5A—C5—H5C	109.5	C12—C13—C8	117.5 (3)
H5B—C5—H5C	109.5	C12—C13—H13A	121.2
C4—C6—H6A	109.5	C8—C13—H13A	121.2
C4—C6—H6B	109.5

C4—N1—C1—N2	10.7 (4)	C2—C3—C4—C7	−107.0 (4)
C4—N1—C1—S1	−171.0 (2)	C2—C3—C4—C6	130.1 (4)
C2—N2—C1—N1	2.1 (4)	C1—N2—C8—C13	−96.2 (3)
C8—N2—C1—N1	−178.8 (2)	C2—N2—C8—C13	82.9 (3)
C2—N2—C1—S1	−176.1 (2)	C1—N2—C8—C9	84.1 (3)
C8—N2—C1—S1	2.9 (3)	C2—N2—C8—C9	−96.8 (3)
C1—N2—C2—C3	−5.8 (4)	C13—C8—C9—C10	1.8 (5)
C8—N2—C2—C3	175.2 (3)	N2—C8—C9—C10	−178.5 (3)
C1—N2—C2—C5	174.3 (3)	C8—C9—C10—C11	−1.1 (5)
C8—N2—C2—C5	−4.7 (4)	C9—C10—C11—C12	−0.4 (5)
N2—C2—C3—C4	−2.6 (5)	C10—C11—C12—F1	−178.1 (3)
C5—C2—C3—C4	177.3 (4)	C10—C11—C12—C13	1.2 (5)
C1—N1—C4—C3	−16.9 (4)	F1—C12—C13—C8	178.9 (2)
C1—N1—C4—C7	103.7 (4)	C11—C12—C13—C8	−0.5 (5)
C1—N1—C4—C6	−136.5 (3)	C9—C8—C13—C12	−1.0 (4)
C2—C3—C4—N1	12.2 (5)	N2—C8—C13—C12	179.3 (2)

Hydrogen-bond geometry (Å, º) top

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

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···S1ⁱ	0.86	2.57	3.400 (3)	162
C9—H9A···Cg1ⁱⁱ	0.93	2.89	3.788 (4)	163

Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, −y−1/2, z−3/2.

Experimental details

Crystal data
Chemical formula	C₁₃H₁₅FN₂S
M_r	250.33
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	8.814 (3), 14.997 (5), 10.215 (3)
β (°)	95.711 (6)
V (Å³)	1343.6 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.23
Crystal size (mm)	0.50 × 0.29 × 0.20

Data collection
Diffractometer	Bruker SMART APEX CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2000)
T_min, T_max	0.892, 0.954
No. of measured, independent and observed [I > 2σ(I)] reflections	7116, 2497, 1764
R_int	0.034
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.059, 0.153, 1.06
No. of reflections	2497
No. of parameters	157
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
N1—H1A···S1ⁱ	0.86	2.57	3.400 (3)	162
C9—H9A···Cg1ⁱⁱ	0.93	2.89	3.788 (4)	163

Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, −y−1/2, z−3/2.

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.

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Volume 67| Part 7| July 2011| Page o1810

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