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ISSN: 2056-9890

1-[4-(4-Fluoro­phen­yl)-6-methyl-2-sulfanyl­­idene-1,2,3,4-tetra­hydro­pyrimidin-5-yl]ethanone

aPG Research Department of Physics, Rajah Serfoji Government College (Autonomous), Thanjavur 613 005, Tamilnadu, India, bDepartment of Chemistry, K.S.R. College of Engineering, K.S.R. Kalvi Nagar, Tiruchengode 637 215, Tamilnadu, India, cDepartment of Chemistry, Government Arts College, C. Mutlur 608 102, Chidambaram, Tamilnadu, India, and dDepartment of Chemistry, Howard University, 525 College Street NW, Washington, DC 20059, USA.
*Correspondence e-mail: thiruvalluvar.a@gmail.com

(Received 24 July 2012; accepted 26 July 2012; online 1 August 2012)

In the title mol­ecule, C13H13FN2OS, the heterocyclic ring adopts a slightly distorted flattened boat conformation, and the plane through the four coplanar atoms makes a dihedral angle of 87.45 (14)° with the benzene ring. The thione, acetyl and methyl groups lie on the opposite side of the heterocyclic mean plane to the fluorophenyl group, which has an axial orientation. N—H⋯O, N—H⋯S, C—H⋯F and C—H⋯O inter­molecular hydrogen bonds and a weak C—H⋯π inter­action involving the benzene ring are found in the crystal structure.

Related literature

For chemical and biological applications of dihydro­pyrimidine derivatives and for the closely related crystal structure of the chloro derivative, see: Anuradha et al. (2009[Anuradha, N., Thiruvalluvar, A., Pandiarajan, K., Chitra, S. & Butcher, R. J. (2009). Acta Cryst. E65, o564-o565.]).

[Scheme 1]

Experimental

Crystal data
  • C13H13FN2OS

  • Mr = 264.32

  • Triclinic, [P \overline 1]

  • a = 7.1775 (11) Å

  • b = 8.1099 (13) Å

  • c = 12.490 (2) Å

  • α = 103.529 (15)°

  • β = 91.933 (14)°

  • γ = 106.971 (14)°

  • V = 672.0 (2) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 2.17 mm−1

  • T = 123 K

  • 0.59 × 0.36 × 0.06 mm

Data collection
  • Oxford Diffraction Xcalibur Ruby Gemini diffractometer

  • Absorption correction: analytical (CrysAlis PRO; Agilent, 2012[Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]) Tmin = 0.515, Tmax = 0.891

  • 3949 measured reflections

  • 2629 independent reflections

  • 2109 reflections with I > 2σ(I)

  • Rint = 0.055

Refinement
  • R[F2 > 2σ(F2)] = 0.080

  • wR(F2) = 0.233

  • S = 1.12

  • 2629 reflections

  • 173 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.82 e Å−3

  • Δρmin = −0.37 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C41–C46 benzene ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O15i 0.82 (5) 2.10 (5) 2.867 (5) 156 (5)
N3—H3⋯S2ii 0.85 (6) 2.50 (6) 3.350 (4) 174 (6)
C16—H16A⋯F4iii 0.98 2.50 3.358 (6) 146
C61—H61A⋯F4iii 0.98 2.47 3.319 (6) 145
C61—H61B⋯O15i 0.98 2.54 3.383 (5) 144
C16—H16CCg2iv 0.98 2.92 3.633 (5) 130
Symmetry codes: (i) x-1, y, z; (ii) -x+1, -y+1, -z+1; (iii) -x+1, -y, -z; (iv) x, y-1, z.

Data collection: CrysAlis PRO (Agilent, 2012[Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: DIRDIF2008 (Beurskens et al., 2008[Beurskens, P. T., Beurskens, G., de Gelder, R., García-Granda, S., Gould, R. O. & Smits, J. M. M. (2008). The DIRDIF2008 Program System. Crystallography Laboratory, University of Nijmegen, The Netherlands.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (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: PLATON.

Supporting information


Comment top

As part of our investigations of dihydropyrimidine derivatives (Anuradha et al., 2009) to compare their chemical and biological activities, we have undertaken the X-ray cryatal structure analysis of the title compound.

In the title molecule, C13H13FN2OS (Fig.1), the heterocyclic ring adopts a slightly distorted flattened boat conformation, and the plane through the four coplanar atoms (C2,N3,C5 and C6) makes a dihedral angle of 87.45 (14)° with the benzene ring. The thione, acetyl and methyl groups have equatorial orientations and the fluorophenyl group has an axial orientation. N1—H1···O15, N3—H3···S2, C16—H16A···F4, and C61—H61B···O15 intermolecular hydrogen bonds and a weak C16—H16C···π interaction involving the benzene (C41—C46) ring are found in the crystal structure (Fig.2, Table 1).

Related literature top

For chemical and biological applications of dihydropyrimidine derivatives and for the closely related crystal structure of the chloro derivative, see: Anuradha et al. (2009).

Experimental top

A solution of acetylacetone (1.0012 g, 0.01 mol), 4-fluorobenzaldehyde (1.25 g, 0.01 mol) and thiourea (1.14 g, 0.015 mol) was heated under reflux in the presence of calcium fluoride (0.07 g, 0.001 mol) for 2 h (monitored by TLC). After completion of the reaction, the reaction mixture was cooled to room temperature and poured into crushed ice. The solid product was filtered under suction and purified by recrystallization from hot methanol to give the product in the pure form. Yield 1.92 g (96%).

Refinement top

The two N-bound H atoms were located in a difference Fourier map and refined freely; N1—H1 = 0.82 (5) Å and N3—H3 = 0.85 (6) Å. The remaining H atoms were positioned geometrically and allowed to ride on their parent atoms, with Csp2—H = 0.95, C(methyl)—H = 0.98, and C(methine)—H = 1.00 Å; Uiso(H) = kUeq(C), where k = 1.5 for methyl and 1.2 for all other H atoms.

Computing details top

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); program(s) used to solve structure: DIRDIF2008 (Beurskens et al., 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level. H atoms are shown as small spheres of arbitrary radius.
[Figure 2] Fig. 2. The packing of the title compound, viewed along the b axis. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted.
1-[4-(4-Fluorophenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidin- 5-yl]ethanone top
Crystal data top
C13H13FN2OSZ = 2
Mr = 264.32F(000) = 276
Triclinic, P1Dx = 1.306 Mg m3
Hall symbol: -P 1Melting point: 509 K
a = 7.1775 (11) ÅCu Kα radiation, λ = 1.54184 Å
b = 8.1099 (13) ÅCell parameters from 1186 reflections
c = 12.490 (2) Åθ = 3.7–75.9°
α = 103.529 (15)°µ = 2.17 mm1
β = 91.933 (14)°T = 123 K
γ = 106.971 (14)°Plate, colourless
V = 672.0 (2) Å30.59 × 0.36 × 0.06 mm
Data collection top
Oxford Diffraction Xcalibur Ruby Gemini
diffractometer
2629 independent reflections
Radiation source: Enhance (Cu) X-ray Source2109 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.055
Detector resolution: 10.5081 pixels mm-1θmax = 76.1°, θmin = 3.7°
ω scansh = 78
Absorption correction: analytical
(CrysAlis PRO; Agilent, 2012)
k = 810
Tmin = 0.515, Tmax = 0.891l = 1511
3949 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)] = 0.080Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.233H atoms treated by a mixture of independent and constrained refinement
S = 1.12 w = 1/[σ2(Fo2) + (0.1003P)2 + 1.2879P]
where P = (Fo2 + 2Fc2)/3
2629 reflections(Δ/σ)max = 0.001
173 parametersΔρmax = 0.82 e Å3
0 restraintsΔρmin = 0.37 e Å3
Crystal data top
C13H13FN2OSγ = 106.971 (14)°
Mr = 264.32V = 672.0 (2) Å3
Triclinic, P1Z = 2
a = 7.1775 (11) ÅCu Kα radiation
b = 8.1099 (13) ŵ = 2.17 mm1
c = 12.490 (2) ÅT = 123 K
α = 103.529 (15)°0.59 × 0.36 × 0.06 mm
β = 91.933 (14)°
Data collection top
Oxford Diffraction Xcalibur Ruby Gemini
diffractometer
2629 independent reflections
Absorption correction: analytical
(CrysAlis PRO; Agilent, 2012)
2109 reflections with I > 2σ(I)
Tmin = 0.515, Tmax = 0.891Rint = 0.055
3949 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0800 restraints
wR(F2) = 0.233H atoms treated by a mixture of independent and constrained refinement
S = 1.12Δρmax = 0.82 e Å3
2629 reflectionsΔρmin = 0.37 e Å3
173 parameters
Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

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 > 2σ(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
S20.18125 (14)0.34721 (13)0.46715 (10)0.0405 (3)
F40.7221 (6)0.3280 (5)0.0587 (3)0.0829 (16)
O150.7912 (4)0.1016 (4)0.3039 (3)0.0520 (12)
N10.2057 (5)0.0276 (4)0.3682 (3)0.0387 (10)
N30.4983 (5)0.2512 (4)0.4147 (3)0.0349 (10)
C20.3046 (5)0.2035 (5)0.4140 (3)0.0351 (11)
C40.6032 (5)0.1414 (5)0.3474 (3)0.0344 (11)
C50.4912 (5)0.0550 (5)0.3312 (3)0.0346 (11)
C60.2961 (6)0.1043 (5)0.3369 (3)0.0352 (11)
C150.6152 (6)0.1729 (5)0.3037 (4)0.0394 (14)
C160.5357 (6)0.3717 (6)0.2740 (4)0.0455 (14)
C410.6337 (6)0.1890 (5)0.2361 (4)0.0380 (11)
C420.4755 (7)0.1672 (6)0.1611 (4)0.0450 (14)
C430.5034 (8)0.2138 (7)0.0611 (4)0.0521 (17)
C440.6923 (9)0.2814 (7)0.0386 (4)0.0581 (17)
C450.8513 (8)0.3036 (7)0.1095 (5)0.0604 (17)
C460.8225 (7)0.2573 (6)0.2092 (4)0.0473 (14)
C610.1533 (5)0.2885 (5)0.3148 (4)0.0403 (13)
H10.087 (7)0.005 (6)0.370 (4)0.036 (12)*
H30.572 (8)0.356 (8)0.446 (4)0.051 (14)*
H40.734780.166380.388220.0414*
H16A0.453430.413430.202850.0679*
H16B0.457000.409810.331580.0679*
H16C0.644430.422380.268190.0679*
H420.345970.119670.178370.0543*
H430.395090.199290.009980.0629*
H450.980070.350050.090890.0727*
H460.932230.272370.259400.0573*
H61A0.155090.354050.238470.0604*
H61B0.021240.280400.325420.0604*
H61C0.190190.351190.366200.0604*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S20.0293 (5)0.0314 (5)0.0635 (7)0.0129 (4)0.0089 (4)0.0121 (4)
F40.093 (3)0.086 (3)0.062 (2)0.003 (2)0.0100 (18)0.0354 (18)
O150.0259 (14)0.0370 (16)0.099 (3)0.0146 (12)0.0106 (15)0.0218 (16)
N10.0226 (16)0.0336 (17)0.061 (2)0.0104 (13)0.0064 (14)0.0118 (15)
N30.0276 (16)0.0267 (16)0.052 (2)0.0093 (13)0.0063 (14)0.0114 (14)
C20.0295 (18)0.0285 (18)0.051 (2)0.0105 (15)0.0064 (16)0.0149 (16)
C40.0245 (17)0.0282 (18)0.053 (2)0.0101 (14)0.0051 (15)0.0127 (16)
C50.0275 (18)0.0242 (17)0.054 (2)0.0083 (14)0.0037 (15)0.0133 (15)
C60.0305 (18)0.0291 (18)0.050 (2)0.0115 (15)0.0048 (15)0.0148 (16)
C150.0275 (19)0.040 (2)0.059 (3)0.0162 (16)0.0079 (17)0.0208 (18)
C160.033 (2)0.038 (2)0.072 (3)0.0183 (17)0.0082 (19)0.017 (2)
C410.037 (2)0.0273 (18)0.054 (2)0.0138 (15)0.0089 (17)0.0129 (16)
C420.039 (2)0.043 (2)0.056 (3)0.0142 (18)0.0075 (19)0.0161 (19)
C430.056 (3)0.049 (3)0.053 (3)0.017 (2)0.000 (2)0.016 (2)
C440.073 (3)0.051 (3)0.047 (3)0.010 (2)0.011 (2)0.017 (2)
C450.055 (3)0.059 (3)0.059 (3)0.001 (2)0.015 (2)0.019 (2)
C460.037 (2)0.046 (2)0.057 (3)0.0072 (18)0.0087 (19)0.016 (2)
C610.0263 (18)0.0289 (19)0.067 (3)0.0078 (15)0.0098 (17)0.0148 (18)
Geometric parameters (Å, º) top
S2—C21.692 (4)C41—C421.390 (7)
F4—C441.360 (6)C42—C431.392 (7)
O15—C151.226 (5)C43—C441.372 (9)
N1—C21.366 (5)C44—C451.363 (8)
N1—C61.395 (5)C45—C461.388 (8)
N3—C21.329 (5)C4—H41.0000
N3—C41.466 (5)C16—H16A0.9800
N1—H10.82 (5)C16—H16B0.9800
N3—H30.85 (6)C16—H16C0.9800
C4—C411.534 (6)C42—H420.9500
C4—C51.522 (6)C43—H430.9500
C5—C61.349 (6)C45—H450.9500
C5—C151.479 (6)C46—H460.9500
C6—C611.501 (6)C61—H61A0.9800
C15—C161.494 (6)C61—H61B0.9800
C41—C461.391 (7)C61—H61C0.9800
C2—N1—C6124.1 (4)C43—C44—C45122.8 (5)
C2—N3—C4124.0 (3)F4—C44—C45118.6 (6)
C2—N1—H1113 (3)C44—C45—C46119.1 (5)
C6—N1—H1123 (3)C41—C46—C45120.3 (5)
C2—N3—H3123 (4)N3—C4—H4108.00
C4—N3—H3113 (4)C5—C4—H4108.00
S2—C2—N3123.5 (3)C41—C4—H4108.00
N1—C2—N3116.3 (3)C15—C16—H16A110.00
S2—C2—N1120.3 (3)C15—C16—H16B109.00
N3—C4—C5109.7 (3)C15—C16—H16C109.00
N3—C4—C41110.6 (3)H16A—C16—H16B109.00
C5—C4—C41111.5 (3)H16A—C16—H16C109.00
C4—C5—C15113.3 (3)H16B—C16—H16C109.00
C6—C5—C15127.3 (4)C41—C42—H42119.00
C4—C5—C6119.3 (3)C43—C42—H42119.00
N1—C6—C5118.9 (4)C42—C43—H43121.00
N1—C6—C61112.2 (4)C44—C43—H43121.00
C5—C6—C61128.9 (4)C44—C45—H45120.00
C5—C15—C16123.3 (4)C46—C45—H45120.00
O15—C15—C5117.4 (4)C41—C46—H46120.00
O15—C15—C16119.3 (4)C45—C46—H46120.00
C4—C41—C46120.0 (4)C6—C61—H61A109.00
C42—C41—C46118.8 (4)C6—C61—H61B109.00
C4—C41—C42121.2 (4)C6—C61—H61C109.00
C41—C42—C43121.2 (5)H61A—C61—H61B109.00
C42—C43—C44117.9 (5)H61A—C61—H61C110.00
F4—C44—C43118.6 (5)H61B—C61—H61C109.00
C6—N1—C2—S2170.5 (3)C4—C5—C6—C61174.5 (4)
C6—N1—C2—N38.8 (6)C15—C5—C6—N1177.7 (4)
C2—N1—C6—C513.1 (6)C15—C5—C6—C611.6 (7)
C2—N1—C6—C61166.4 (4)C4—C5—C15—O154.4 (6)
C4—N3—C2—S2165.1 (3)C4—C5—C15—C16174.3 (4)
C4—N3—C2—N115.6 (5)C6—C5—C15—O15179.3 (4)
C2—N3—C4—C531.5 (5)C6—C5—C15—C161.9 (7)
C2—N3—C4—C4191.8 (4)C4—C41—C42—C43178.7 (4)
N3—C4—C5—C625.6 (5)C46—C41—C42—C430.6 (7)
N3—C4—C5—C15157.8 (3)C4—C41—C46—C45178.9 (4)
C41—C4—C5—C697.2 (4)C42—C41—C46—C450.4 (7)
C41—C4—C5—C1579.4 (4)C41—C42—C43—C440.3 (8)
N3—C4—C41—C4261.6 (5)C42—C43—C44—F4179.9 (5)
N3—C4—C41—C46117.7 (4)C42—C43—C44—C450.2 (8)
C5—C4—C41—C4260.6 (5)F4—C44—C45—C46179.7 (5)
C5—C4—C41—C46120.1 (4)C43—C44—C45—C460.4 (9)
C4—C5—C6—N16.2 (5)C44—C45—C46—C410.1 (8)
Hydrogen-bond geometry (Å, º) top
Cg2 is the centroid of the C41–C46 benzene ring.
D—H···AD—HH···AD···AD—H···A
N1—H1···O15i0.82 (5)2.10 (5)2.867 (5)156 (5)
N3—H3···S2ii0.85 (6)2.50 (6)3.350 (4)174 (6)
C16—H16A···F4iii0.982.503.358 (6)146
C61—H61A···F4iii0.982.473.319 (6)145
C61—H61B···O15i0.982.543.383 (5)144
C16—H16C···Cg2iv0.982.923.633 (5)130
Symmetry codes: (i) x1, y, z; (ii) x+1, y+1, z+1; (iii) x+1, y, z; (iv) x, y1, z.

Experimental details

Crystal data
Chemical formulaC13H13FN2OS
Mr264.32
Crystal system, space groupTriclinic, P1
Temperature (K)123
a, b, c (Å)7.1775 (11), 8.1099 (13), 12.490 (2)
α, β, γ (°)103.529 (15), 91.933 (14), 106.971 (14)
V3)672.0 (2)
Z2
Radiation typeCu Kα
µ (mm1)2.17
Crystal size (mm)0.59 × 0.36 × 0.06
Data collection
DiffractometerOxford Diffraction Xcalibur Ruby Gemini
diffractometer
Absorption correctionAnalytical
(CrysAlis PRO; Agilent, 2012)
Tmin, Tmax0.515, 0.891
No. of measured, independent and
observed [I > 2σ(I)] reflections
3949, 2629, 2109
Rint0.055
(sin θ/λ)max1)0.630
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.080, 0.233, 1.12
No. of reflections2629
No. of parameters173
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.82, 0.37

Computer programs: CrysAlis PRO (Agilent, 2012), DIRDIF2008 (Beurskens et al., 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
Cg2 is the centroid of the C41–C46 benzene ring.
D—H···AD—HH···AD···AD—H···A
N1—H1···O15i0.82 (5)2.10 (5)2.867 (5)156 (5)
N3—H3···S2ii0.85 (6)2.50 (6)3.350 (4)174 (6)
C16—H16A···F4iii0.982.503.358 (6)146
C61—H61A···F4iii0.982.473.319 (6)145
C61—H61B···O15i0.982.543.383 (5)144
C16—H16C···Cg2iv0.982.923.633 (5)130
Symmetry codes: (i) x1, y, z; (ii) x+1, y+1, z+1; (iii) x+1, y, z; (iv) x, y1, z.
 

Acknowledgements

RJB acknowledges the NSF MRI program (grant No. CHE-0619278) for funds to purchase an X-ray diffractometer.

References

First citationAgilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.
First citationAnuradha, N., Thiruvalluvar, A., Pandiarajan, K., Chitra, S. & Butcher, R. J. (2009). Acta Cryst. E65, o564–o565.  Web of Science CSD CrossRef CAS IUCr Journals
First citationBeurskens, P. T., Beurskens, G., de Gelder, R., García-Granda, S., Gould, R. O. & Smits, J. M. M. (2008). The DIRDIF2008 Program System. Crystallography Laboratory, University of Nijmegen, The Netherlands.
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals

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