organic compounds
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
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 et al. (2009).
of the chloro derivative, see: AnuradhaExperimental
Crystal data
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Refinement
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Data collection: CrysAlis PRO (Agilent, 2012); cell CrysAlis PRO; data reduction: CrysAlis PRO; 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.
Supporting information
10.1107/S1600536812033727/wn2486sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812033727/wn2486Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812033727/wn2486Isup3.cdx
Supporting information file. DOI: 10.1107/S1600536812033727/wn2486Isup4.cml
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%).
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.
Data collection: CrysAlis PRO (Agilent, 2012); cell
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).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. | |
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. |
C13H13FN2OS | Z = 2 |
Mr = 264.32 | F(000) = 276 |
Triclinic, P1 | Dx = 1.306 Mg m−3 |
Hall symbol: -P 1 | Melting point: 509 K |
a = 7.1775 (11) Å | Cu Kα radiation, λ = 1.54184 Å |
b = 8.1099 (13) Å | Cell parameters from 1186 reflections |
c = 12.490 (2) Å | θ = 3.7–75.9° |
α = 103.529 (15)° | µ = 2.17 mm−1 |
β = 91.933 (14)° | T = 123 K |
γ = 106.971 (14)° | Plate, colourless |
V = 672.0 (2) Å3 | 0.59 × 0.36 × 0.06 mm |
Oxford Diffraction Xcalibur Ruby Gemini diffractometer | 2629 independent reflections |
Radiation source: Enhance (Cu) X-ray Source | 2109 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.055 |
Detector resolution: 10.5081 pixels mm-1 | θmax = 76.1°, θmin = 3.7° |
ω scans | h = −7→8 |
Absorption correction: analytical (CrysAlis PRO; Agilent, 2012) | k = −8→10 |
Tmin = 0.515, Tmax = 0.891 | l = −15→11 |
3949 measured reflections |
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)] = 0.080 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.233 | H 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 parameters | Δρmax = 0.82 e Å−3 |
0 restraints | Δρmin = −0.37 e Å−3 |
C13H13FN2OS | γ = 106.971 (14)° |
Mr = 264.32 | V = 672.0 (2) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.1775 (11) Å | Cu Kα radiation |
b = 8.1099 (13) Å | µ = 2.17 mm−1 |
c = 12.490 (2) Å | T = 123 K |
α = 103.529 (15)° | 0.59 × 0.36 × 0.06 mm |
β = 91.933 (14)° |
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 = 0.891 | Rint = 0.055 |
3949 measured reflections |
R[F2 > 2σ(F2)] = 0.080 | 0 restraints |
wR(F2) = 0.233 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | Δρmax = 0.82 e Å−3 |
2629 reflections | Δρmin = −0.37 e Å−3 |
173 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
S2 | 0.18125 (14) | 0.34721 (13) | 0.46715 (10) | 0.0405 (3) | |
F4 | 0.7221 (6) | 0.3280 (5) | −0.0587 (3) | 0.0829 (16) | |
O15 | 0.7912 (4) | −0.1016 (4) | 0.3039 (3) | 0.0520 (12) | |
N1 | 0.2057 (5) | 0.0276 (4) | 0.3682 (3) | 0.0387 (10) | |
N3 | 0.4983 (5) | 0.2512 (4) | 0.4147 (3) | 0.0349 (10) | |
C2 | 0.3046 (5) | 0.2035 (5) | 0.4140 (3) | 0.0351 (11) | |
C4 | 0.6032 (5) | 0.1414 (5) | 0.3474 (3) | 0.0344 (11) | |
C5 | 0.4912 (5) | −0.0550 (5) | 0.3312 (3) | 0.0346 (11) | |
C6 | 0.2961 (6) | −0.1043 (5) | 0.3369 (3) | 0.0352 (11) | |
C15 | 0.6152 (6) | −0.1729 (5) | 0.3037 (4) | 0.0394 (14) | |
C16 | 0.5357 (6) | −0.3717 (6) | 0.2740 (4) | 0.0455 (14) | |
C41 | 0.6337 (6) | 0.1890 (5) | 0.2361 (4) | 0.0380 (11) | |
C42 | 0.4755 (7) | 0.1672 (6) | 0.1611 (4) | 0.0450 (14) | |
C43 | 0.5034 (8) | 0.2138 (7) | 0.0611 (4) | 0.0521 (17) | |
C44 | 0.6923 (9) | 0.2814 (7) | 0.0386 (4) | 0.0581 (17) | |
C45 | 0.8513 (8) | 0.3036 (7) | 0.1095 (5) | 0.0604 (17) | |
C46 | 0.8225 (7) | 0.2573 (6) | 0.2092 (4) | 0.0473 (14) | |
C61 | 0.1533 (5) | −0.2885 (5) | 0.3148 (4) | 0.0403 (13) | |
H1 | 0.087 (7) | 0.005 (6) | 0.370 (4) | 0.036 (12)* | |
H3 | 0.572 (8) | 0.356 (8) | 0.446 (4) | 0.051 (14)* | |
H4 | 0.73478 | 0.16638 | 0.38822 | 0.0414* | |
H16A | 0.45343 | −0.41343 | 0.20285 | 0.0679* | |
H16B | 0.45700 | −0.40981 | 0.33158 | 0.0679* | |
H16C | 0.64443 | −0.42238 | 0.26819 | 0.0679* | |
H42 | 0.34597 | 0.11967 | 0.17837 | 0.0543* | |
H43 | 0.39509 | 0.19929 | 0.00998 | 0.0629* | |
H45 | 0.98007 | 0.35005 | 0.09089 | 0.0727* | |
H46 | 0.93223 | 0.27237 | 0.25940 | 0.0573* | |
H61A | 0.15509 | −0.35405 | 0.23847 | 0.0604* | |
H61B | 0.02124 | −0.28040 | 0.32542 | 0.0604* | |
H61C | 0.19019 | −0.35119 | 0.36620 | 0.0604* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S2 | 0.0293 (5) | 0.0314 (5) | 0.0635 (7) | 0.0129 (4) | 0.0089 (4) | 0.0121 (4) |
F4 | 0.093 (3) | 0.086 (3) | 0.062 (2) | 0.003 (2) | 0.0100 (18) | 0.0354 (18) |
O15 | 0.0259 (14) | 0.0370 (16) | 0.099 (3) | 0.0146 (12) | 0.0106 (15) | 0.0218 (16) |
N1 | 0.0226 (16) | 0.0336 (17) | 0.061 (2) | 0.0104 (13) | 0.0064 (14) | 0.0118 (15) |
N3 | 0.0276 (16) | 0.0267 (16) | 0.052 (2) | 0.0093 (13) | 0.0063 (14) | 0.0114 (14) |
C2 | 0.0295 (18) | 0.0285 (18) | 0.051 (2) | 0.0105 (15) | 0.0064 (16) | 0.0149 (16) |
C4 | 0.0245 (17) | 0.0282 (18) | 0.053 (2) | 0.0101 (14) | 0.0051 (15) | 0.0127 (16) |
C5 | 0.0275 (18) | 0.0242 (17) | 0.054 (2) | 0.0083 (14) | 0.0037 (15) | 0.0133 (15) |
C6 | 0.0305 (18) | 0.0291 (18) | 0.050 (2) | 0.0115 (15) | 0.0048 (15) | 0.0148 (16) |
C15 | 0.0275 (19) | 0.040 (2) | 0.059 (3) | 0.0162 (16) | 0.0079 (17) | 0.0208 (18) |
C16 | 0.033 (2) | 0.038 (2) | 0.072 (3) | 0.0183 (17) | 0.0082 (19) | 0.017 (2) |
C41 | 0.037 (2) | 0.0273 (18) | 0.054 (2) | 0.0138 (15) | 0.0089 (17) | 0.0129 (16) |
C42 | 0.039 (2) | 0.043 (2) | 0.056 (3) | 0.0142 (18) | 0.0075 (19) | 0.0161 (19) |
C43 | 0.056 (3) | 0.049 (3) | 0.053 (3) | 0.017 (2) | 0.000 (2) | 0.016 (2) |
C44 | 0.073 (3) | 0.051 (3) | 0.047 (3) | 0.010 (2) | 0.011 (2) | 0.017 (2) |
C45 | 0.055 (3) | 0.059 (3) | 0.059 (3) | 0.001 (2) | 0.015 (2) | 0.019 (2) |
C46 | 0.037 (2) | 0.046 (2) | 0.057 (3) | 0.0072 (18) | 0.0087 (19) | 0.016 (2) |
C61 | 0.0263 (18) | 0.0289 (19) | 0.067 (3) | 0.0078 (15) | 0.0098 (17) | 0.0148 (18) |
S2—C2 | 1.692 (4) | C41—C42 | 1.390 (7) |
F4—C44 | 1.360 (6) | C42—C43 | 1.392 (7) |
O15—C15 | 1.226 (5) | C43—C44 | 1.372 (9) |
N1—C2 | 1.366 (5) | C44—C45 | 1.363 (8) |
N1—C6 | 1.395 (5) | C45—C46 | 1.388 (8) |
N3—C2 | 1.329 (5) | C4—H4 | 1.0000 |
N3—C4 | 1.466 (5) | C16—H16A | 0.9800 |
N1—H1 | 0.82 (5) | C16—H16B | 0.9800 |
N3—H3 | 0.85 (6) | C16—H16C | 0.9800 |
C4—C41 | 1.534 (6) | C42—H42 | 0.9500 |
C4—C5 | 1.522 (6) | C43—H43 | 0.9500 |
C5—C6 | 1.349 (6) | C45—H45 | 0.9500 |
C5—C15 | 1.479 (6) | C46—H46 | 0.9500 |
C6—C61 | 1.501 (6) | C61—H61A | 0.9800 |
C15—C16 | 1.494 (6) | C61—H61B | 0.9800 |
C41—C46 | 1.391 (7) | C61—H61C | 0.9800 |
C2—N1—C6 | 124.1 (4) | C43—C44—C45 | 122.8 (5) |
C2—N3—C4 | 124.0 (3) | F4—C44—C45 | 118.6 (6) |
C2—N1—H1 | 113 (3) | C44—C45—C46 | 119.1 (5) |
C6—N1—H1 | 123 (3) | C41—C46—C45 | 120.3 (5) |
C2—N3—H3 | 123 (4) | N3—C4—H4 | 108.00 |
C4—N3—H3 | 113 (4) | C5—C4—H4 | 108.00 |
S2—C2—N3 | 123.5 (3) | C41—C4—H4 | 108.00 |
N1—C2—N3 | 116.3 (3) | C15—C16—H16A | 110.00 |
S2—C2—N1 | 120.3 (3) | C15—C16—H16B | 109.00 |
N3—C4—C5 | 109.7 (3) | C15—C16—H16C | 109.00 |
N3—C4—C41 | 110.6 (3) | H16A—C16—H16B | 109.00 |
C5—C4—C41 | 111.5 (3) | H16A—C16—H16C | 109.00 |
C4—C5—C15 | 113.3 (3) | H16B—C16—H16C | 109.00 |
C6—C5—C15 | 127.3 (4) | C41—C42—H42 | 119.00 |
C4—C5—C6 | 119.3 (3) | C43—C42—H42 | 119.00 |
N1—C6—C5 | 118.9 (4) | C42—C43—H43 | 121.00 |
N1—C6—C61 | 112.2 (4) | C44—C43—H43 | 121.00 |
C5—C6—C61 | 128.9 (4) | C44—C45—H45 | 120.00 |
C5—C15—C16 | 123.3 (4) | C46—C45—H45 | 120.00 |
O15—C15—C5 | 117.4 (4) | C41—C46—H46 | 120.00 |
O15—C15—C16 | 119.3 (4) | C45—C46—H46 | 120.00 |
C4—C41—C46 | 120.0 (4) | C6—C61—H61A | 109.00 |
C42—C41—C46 | 118.8 (4) | C6—C61—H61B | 109.00 |
C4—C41—C42 | 121.2 (4) | C6—C61—H61C | 109.00 |
C41—C42—C43 | 121.2 (5) | H61A—C61—H61B | 109.00 |
C42—C43—C44 | 117.9 (5) | H61A—C61—H61C | 110.00 |
F4—C44—C43 | 118.6 (5) | H61B—C61—H61C | 109.00 |
C6—N1—C2—S2 | −170.5 (3) | C4—C5—C6—C61 | 174.5 (4) |
C6—N1—C2—N3 | 8.8 (6) | C15—C5—C6—N1 | 177.7 (4) |
C2—N1—C6—C5 | −13.1 (6) | C15—C5—C6—C61 | −1.6 (7) |
C2—N1—C6—C61 | 166.4 (4) | C4—C5—C15—O15 | 4.4 (6) |
C4—N3—C2—S2 | −165.1 (3) | C4—C5—C15—C16 | −174.3 (4) |
C4—N3—C2—N1 | 15.6 (5) | C6—C5—C15—O15 | −179.3 (4) |
C2—N3—C4—C5 | −31.5 (5) | C6—C5—C15—C16 | 1.9 (7) |
C2—N3—C4—C41 | 91.8 (4) | C4—C41—C42—C43 | 178.7 (4) |
N3—C4—C5—C6 | 25.6 (5) | C46—C41—C42—C43 | −0.6 (7) |
N3—C4—C5—C15 | −157.8 (3) | C4—C41—C46—C45 | −178.9 (4) |
C41—C4—C5—C6 | −97.2 (4) | C42—C41—C46—C45 | 0.4 (7) |
C41—C4—C5—C15 | 79.4 (4) | C41—C42—C43—C44 | 0.3 (8) |
N3—C4—C41—C42 | −61.6 (5) | C42—C43—C44—F4 | −179.9 (5) |
N3—C4—C41—C46 | 117.7 (4) | C42—C43—C44—C45 | 0.2 (8) |
C5—C4—C41—C42 | 60.6 (5) | F4—C44—C45—C46 | 179.7 (5) |
C5—C4—C41—C46 | −120.1 (4) | C43—C44—C45—C46 | −0.4 (9) |
C4—C5—C6—N1 | −6.2 (5) | C44—C45—C46—C41 | 0.1 (8) |
Cg2 is the centroid of the C41–C46 benzene ring. |
D—H···A | D—H | H···A | D···A | 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—H16C···Cg2iv | 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. |
Experimental details
Crystal data | |
Chemical formula | C13H13FN2OS |
Mr | 264.32 |
Crystal system, space group | Triclinic, 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) |
V (Å3) | 672.0 (2) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 2.17 |
Crystal size (mm) | 0.59 × 0.36 × 0.06 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur Ruby Gemini diffractometer |
Absorption correction | Analytical (CrysAlis PRO; Agilent, 2012) |
Tmin, Tmax | 0.515, 0.891 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3949, 2629, 2109 |
Rint | 0.055 |
(sin θ/λ)max (Å−1) | 0.630 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.080, 0.233, 1.12 |
No. of reflections | 2629 |
No. of parameters | 173 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 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).
Cg2 is the centroid of the C41–C46 benzene ring. |
D—H···A | D—H | H···A | D···A | 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—H16C···Cg2iv | 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. |
Acknowledgements
RJB acknowledges the NSF MRI program (grant No. CHE-0619278) for funds to purchase an X-ray diffractometer.
References
Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England. Google Scholar
Anuradha, N., Thiruvalluvar, A., Pandiarajan, K., Chitra, S. & Butcher, R. J. (2009). Acta Cryst. E65, o564–o565. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
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. Google Scholar
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Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).