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

Kadir, A.; Abd Malek, N.A.; Mohd Zaki, H.; Hasbullah, S.A.; Yamin, B.M.

doi:10.1107/S2414314616011895

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 7| July 2016| x161189

https://doi.org/10.1107/S2414314616011895

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

Aisyah Kadir,^a Normyzatul Akmal Abd Malek,^b Hamizah Mohd Zaki,^b ^* Siti Aishah Hasbullah ^a and Bohari M. Yamin ^a

^aSchool of Chemical Sciences and Food Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor D.E., Malaysia, and ^bSchool of Chemistry, Faculty of Applied Science, Universiti Teknologi MARA, 40450 Shah Alam, Selangor D.E., Malaysia
^*Correspondence e-mail: hamiz410@salam.uitm.edu.my

Edited by A. J. Lough, University of Toronto, Canada (Received 25 May 2016; accepted 21 July 2016; online 26 July 2016)

In the title molecule, C₁₃H₁₅FN₂S, the dihydropyrimidine ring is in a flattened boat conformation with deviations of 0.135 (2) and 0.371 (2) Å for the fluorophenyl-substituted N atom and the dimethyl-substituted C atom, respectively, from the four other essentially co-planar atoms. In the crystal, pairs of molecules related by twofold rotation axes are linked by N—H⋯S hydrogen bonds, forming dimers.

Keywords: crystal structure; 1-(4-fluorophenyl)-4,4,6-trimethyltetrahydropyrimidine-2(1H)-thione; tetrahydropyrimidine; twisted; envelope.

CCDC reference: 1495083

Structure description

The title compound is related to 4,4,6-trimethyl-1-phenyl-3,4- dihydropyrimidne-2-(1H)-thione (Yamin et al., 2005 ; Ismail et al., 2007 ), and isomeric to (S)-1-(3-fluorophenyl)-4,4,6-trimethyltetrahydropyrimidine-2(1H)-thione (Yamin et al., 2011 ) in which the dihydropyrimidine rings are in flattened sofa conformations. The dihydropyrimidine ring (N1/N2/C7–C10) in the title compound (Fig. 1) is in a flattened boat conformation with deviations of 0.135 (2) and 0.371 (2) Å for atoms N1 and C10, respectively, from the mean plane through atoms C7/C8/C9/N2. The benzene (C1–C6) and four planar atoms (C7/C8/C9/N2) of the dihydropyrimidine ring form a dihedral angle of 85.78 (13)°. The bond length and angles are in normal ranges and comparable to those in the above mentioned analogs. In the crystal, pairs of molecules related by twofold rotation axes are linked by N—H⋯S hydrogen bonds, forming dimers (Table 1 and Fig. 2).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H14A⋯S1ⁱ	0.86 (2)	2.57 (2)	3.422 (2)	172 (2)
Symmetry code: (i) $[-x, y, -z+{\script{1\over 2}}]$ .

Figure 1
The molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level.

Figure 2
The crystal packing of the title compound viewed along the b axis. The dashed lines indicate hydrogen bonds.

Synthesis and crystallization

A procedure similar to that used for the preparation of 1-(3-fluorophenyl)-4,4,6-trimethyl-3,4-dihydropyrimidine-2(1H)-thione (Yamin et al., 2011) was followed. Equimolar quantities of thiocyanic acid and 4-fluoro-aniline (5.4 mmol) in acetone were stirred for 2–3 h. Colourless crystals of 78% yield were obtained after three days by evaporation at room temperature. Melting point 456.8–458.9 K. Analysis calculated for C₁₃H₁₅F₁N₂S₁: C, 58.53; H, 5.67; N,10.50; S, 12.02%; found: C, 62.32; H, 5.99; F, 7.59; N, 11.19; S, 12.78, IR(KBr), v (cm⁻¹) 1535 (C=S), 1591 (C=C), 3184 (N—H). ¹H NMR (CDCl₃, 400 MHz): δ 1.34 (6H, s, 2CH₃), 1.49 (3H, s, CH₃), 4.83 (1H, s, CH), 11.50 (1H, s, NH), 7.06–7.50 (C₆H₅ ring); ¹³C{¹H}: δ 20.9 (CH₃), 31.6 (2CH₃), 52.4, 112.3, 132.4 (3C_quaternary), 128–130.1 (C₆H₅ ring) and 177.4 (C=S).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₅FN₂S
M_r	250.33
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	303
a, b, c (Å)	21.231 (3), 10.8714 (14), 14.589 (4)
β (°)	128.524 (3)
V (Å³)	2634.3 (8)
Z	8
Radiation type	Mo Kα
μ (mm⁻¹)	0.24
Crystal size (mm)	0.47 × 0.46 × 0.19

Data collection
Diffractometer	Bruker SMART APEX CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2000 )
T_min, T_max	0.897, 0.956
No. of measured, independent and observed [I > 2σ(I)] reflections	35963, 2452, 2017
R_int	0.043
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.102, 1.10
No. of reflections	2452
No. of parameters	158
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.27
Computer programs: SMART and SAINT (Bruker, 2000), SHELXTL (Sheldrick, 2008 ) and PLATON (Spek, 2009 ).

Structural data

CCDC reference: 1495083

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314616011895/lh4008sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616011895/lh4008Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616011895/lh4008Isup3.cml

checkCIF report

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

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

Crystal data top

C₁₃H₁₅FN₂S	F(000) = 1056
M_r = 250.33	D_x = 1.262 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 9935 reflections
a = 21.231 (3) Å	θ = 3.3–28.1°
b = 10.8714 (14) Å	µ = 0.24 mm⁻¹
c = 14.589 (4) Å	T = 303 K
β = 128.524 (3)°	Block, colourless
V = 2634.3 (8) Å³	0.47 × 0.46 × 0.19 mm
Z = 8

Data collection top

Bruker SMART APEX CCD diffractometer	2452 independent reflections
Radiation source: fine-focus sealed tube	2017 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.043
Detector resolution: 83.66 pixels mm^-1	θ_max = 25.5°, θ_min = 3.3°
ω scans	h = −25→25
Absorption correction: multi-scan (SADABS; Bruker, 2000)	k = −13→13
T_min = 0.897, T_max = 0.956	l = −17→17
35963 measured reflections

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.102	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0435P)² + 2.1835P] where P = (F_o² + 2F_c²)/3
2452 reflections	(Δ/σ)_max = 0.001
158 parameters	Δρ_max = 0.21 e Å⁻³
1 restraint	Δρ_min = −0.27 e Å⁻³

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 > 2sigma(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
S1	0.07442 (3)	0.80412 (5)	0.43577 (4)	0.04451 (17)
N1	−0.02089 (8)	0.72028 (14)	0.48345 (12)	0.0373 (3)
N2	−0.07352 (8)	0.71633 (15)	0.29028 (12)	0.0420 (4)
F1	0.19803 (9)	0.90181 (15)	0.93207 (11)	0.0869 (5)
C1	0.16002 (12)	0.7460 (2)	0.79555 (16)	0.0543 (5)
H1A	0.2064	0.7022	0.8522	0.065*
C2	0.14420 (13)	0.8571 (2)	0.82123 (16)	0.0531 (5)
C3	0.07749 (13)	0.92469 (19)	0.74188 (18)	0.0528 (5)
H3A	0.0686	0.9998	0.7627	0.063*
C4	0.02300 (11)	0.87899 (18)	0.62920 (16)	0.0447 (4)
H4A	−0.0231	0.9235	0.5730	0.054*
C5	0.03739 (10)	0.76731 (16)	0.60068 (14)	0.0364 (4)
C6	0.10517 (12)	0.70054 (18)	0.68297 (16)	0.0467 (5)
H6A	0.1142	0.6250	0.6631	0.056*
C7	−0.01163 (10)	0.74492 (16)	0.40060 (14)	0.0338 (4)
C8	−0.08797 (11)	0.65017 (17)	0.45490 (16)	0.0431 (4)
C9	−0.15077 (11)	0.63413 (18)	0.34358 (16)	0.0455 (4)
H9A	−0.1926	0.5838	0.3253	0.055*
C10	−0.15696 (10)	0.69430 (17)	0.24567 (15)	0.0414 (4)
C11	−0.19692 (13)	0.6099 (2)	0.13948 (17)	0.0592 (6)
H11A	−0.1681	0.5335	0.1627	0.089*
H11B	−0.1963	0.6486	0.0809	0.089*
H11C	−0.2516	0.5945	0.1080	0.089*
C12	−0.20189 (12)	0.8167 (2)	0.2106 (2)	0.0599 (6)
H12A	−0.1762	0.8688	0.2782	0.090*
H12B	−0.2566	0.8020	0.1791	0.090*
H12C	−0.2011	0.8560	0.1524	0.090*
C13	−0.07976 (15)	0.5930 (2)	0.55542 (19)	0.0670 (7)
H13A	−0.1280	0.5485	0.5262	0.100*
H13B	−0.0713	0.6563	0.6079	0.100*
H13C	−0.0347	0.5376	0.5964	0.100*
H14A	−0.0688 (12)	0.7351 (19)	0.2377 (14)	0.052 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0318 (2)	0.0689 (3)	0.0334 (3)	−0.0048 (2)	0.0206 (2)	−0.0011 (2)
N1	0.0375 (8)	0.0477 (9)	0.0288 (7)	−0.0032 (6)	0.0216 (6)	−0.0019 (6)
N2	0.0330 (8)	0.0655 (10)	0.0288 (7)	−0.0041 (7)	0.0199 (7)	−0.0017 (7)
F1	0.0906 (10)	0.0940 (11)	0.0403 (7)	−0.0210 (8)	0.0233 (7)	−0.0230 (7)
C1	0.0508 (12)	0.0621 (13)	0.0353 (10)	0.0047 (10)	0.0197 (9)	0.0064 (9)
C2	0.0574 (12)	0.0620 (13)	0.0343 (10)	−0.0166 (10)	0.0257 (10)	−0.0112 (9)
C3	0.0612 (13)	0.0486 (11)	0.0534 (12)	−0.0070 (10)	0.0381 (11)	−0.0144 (9)
C4	0.0450 (10)	0.0464 (11)	0.0439 (10)	0.0026 (8)	0.0283 (9)	−0.0017 (8)
C5	0.0392 (9)	0.0445 (10)	0.0302 (8)	−0.0030 (7)	0.0238 (8)	−0.0014 (7)
C6	0.0520 (11)	0.0482 (11)	0.0388 (10)	0.0062 (9)	0.0277 (9)	0.0000 (8)
C7	0.0328 (8)	0.0401 (9)	0.0294 (8)	0.0041 (7)	0.0197 (7)	0.0017 (7)
C8	0.0468 (10)	0.0472 (10)	0.0458 (10)	−0.0068 (8)	0.0340 (9)	−0.0027 (8)
C9	0.0415 (10)	0.0505 (11)	0.0486 (11)	−0.0093 (8)	0.0301 (9)	−0.0042 (9)
C10	0.0304 (9)	0.0504 (11)	0.0377 (9)	−0.0061 (8)	0.0184 (8)	−0.0033 (8)
C11	0.0513 (12)	0.0700 (14)	0.0408 (11)	−0.0159 (10)	0.0211 (10)	−0.0114 (10)
C12	0.0440 (11)	0.0606 (13)	0.0680 (14)	0.0035 (10)	0.0314 (11)	0.0068 (11)
C13	0.0764 (16)	0.0826 (17)	0.0574 (13)	−0.0205 (13)	0.0493 (13)	0.0003 (12)

Geometric parameters (Å, º) top

S1—C7	1.6875 (17)	C6—H6A	0.9300
N1—C7	1.366 (2)	C8—C9	1.322 (3)
N1—C8	1.430 (2)	C8—C13	1.499 (3)
N1—C5	1.443 (2)	C9—C10	1.501 (3)
N2—C7	1.334 (2)	C9—H9A	0.9300
N2—C10	1.477 (2)	C10—C11	1.524 (3)
N2—H14A	0.858 (9)	C10—C12	1.528 (3)
F1—C2	1.362 (2)	C11—H11A	0.9600
C1—C2	1.367 (3)	C11—H11B	0.9600
C1—C6	1.384 (3)	C11—H11C	0.9600
C1—H1A	0.9300	C12—H12A	0.9600
C2—C3	1.358 (3)	C12—H12B	0.9600
C3—C4	1.385 (3)	C12—H12C	0.9600
C3—H3A	0.9300	C13—H13A	0.9600
C4—C5	1.378 (3)	C13—H13B	0.9600
C4—H4A	0.9300	C13—H13C	0.9600
C5—C6	1.374 (2)

C7—N1—C8	120.85 (14)	N1—C8—C13	116.62 (16)
C7—N1—C5	119.30 (14)	C8—C9—C10	122.35 (16)
C8—N1—C5	119.84 (14)	C8—C9—H9A	118.8
C7—N2—C10	125.38 (14)	C10—C9—H9A	118.8
C7—N2—H14A	116.6 (14)	N2—C10—C9	106.33 (14)
C10—N2—H14A	114.8 (14)	N2—C10—C11	107.52 (16)
C2—C1—C6	118.16 (19)	C9—C10—C11	111.60 (16)
C2—C1—H1A	120.9	N2—C10—C12	109.50 (15)
C6—C1—H1A	120.9	C9—C10—C12	111.38 (17)
C3—C2—F1	118.5 (2)	C11—C10—C12	110.33 (16)
C3—C2—C1	123.24 (18)	C10—C11—H11A	109.5
F1—C2—C1	118.21 (19)	C10—C11—H11B	109.5
C2—C3—C4	118.33 (19)	H11A—C11—H11B	109.5
C2—C3—H3A	120.8	C10—C11—H11C	109.5
C4—C3—H3A	120.8	H11A—C11—H11C	109.5
C5—C4—C3	119.74 (18)	H11B—C11—H11C	109.5
C5—C4—H4A	120.1	C10—C12—H12A	109.5
C3—C4—H4A	120.1	C10—C12—H12B	109.5
C6—C5—C4	120.68 (16)	H12A—C12—H12B	109.5
C6—C5—N1	120.46 (16)	C10—C12—H12C	109.5
C4—C5—N1	118.85 (16)	H12A—C12—H12C	109.5
C5—C6—C1	119.84 (18)	H12B—C12—H12C	109.5
C5—C6—H6A	120.1	C8—C13—H13A	109.5
C1—C6—H6A	120.1	C8—C13—H13B	109.5
N2—C7—N1	116.45 (15)	H13A—C13—H13B	109.5
N2—C7—S1	121.47 (13)	C8—C13—H13C	109.5
N1—C7—S1	122.06 (12)	H13A—C13—H13C	109.5
C9—C8—N1	119.19 (16)	H13B—C13—H13C	109.5
C9—C8—C13	124.10 (18)

C6—C1—C2—C3	0.0 (3)	C8—N1—C7—N2	9.5 (2)
C6—C1—C2—F1	179.83 (19)	C5—N1—C7—N2	−169.62 (15)
F1—C2—C3—C4	179.86 (18)	C8—N1—C7—S1	−168.57 (14)
C1—C2—C3—C4	−0.3 (3)	C5—N1—C7—S1	12.3 (2)
C2—C3—C4—C5	0.2 (3)	C7—N1—C8—C9	−16.1 (3)
C3—C4—C5—C6	0.2 (3)	C5—N1—C8—C9	163.03 (17)
C3—C4—C5—N1	178.83 (16)	C7—N1—C8—C13	160.48 (18)
C7—N1—C5—C6	−88.4 (2)	C5—N1—C8—C13	−20.4 (3)
C8—N1—C5—C6	92.4 (2)	N1—C8—C9—C10	−4.4 (3)
C7—N1—C5—C4	93.0 (2)	C13—C8—C9—C10	179.3 (2)
C8—N1—C5—C4	−86.2 (2)	C7—N2—C10—C9	−34.3 (2)
C4—C5—C6—C1	−0.5 (3)	C7—N2—C10—C11	−153.97 (18)
N1—C5—C6—C1	−179.11 (17)	C7—N2—C10—C12	86.1 (2)
C2—C1—C6—C5	0.4 (3)	C8—C9—C10—N2	26.1 (3)
C10—N2—C7—N1	18.2 (3)	C8—C9—C10—C11	143.1 (2)
C10—N2—C7—S1	−163.71 (14)	C8—C9—C10—C12	−93.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H14A···S1ⁱ	0.86 (2)	2.57 (2)	3.422 (2)	172 (2)

Symmetry code: (i) −x, y, −z+1/2.

Acknowledgements

The authors thank the Ministry of Higher Education of Malaysia and Universiti Kebangsaan Malaysia for the research grant FRGS 1/2015/ST01/UKM/02/2 and Universiti Teknologi MARA FRGS/2/2014/SKK03/UITM/02/1 for the publication.

References

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