Crystal structure of methyl 4-(2-fluorophenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate

In the title compound, C13H13FN2O2S, the pyrimidine ring adopts a twist-boat conformation with the MeCN and methine-C atoms displaced by 0.0938 (6) and 0.2739 (3) Å, respectively, from the mean plane through the other four atoms of the ring. The 2-fluorobenzene ring is positioned axially and forms a dihedral angle of 89.13 (4)° with the mean plane through the pyrimidine ring. The crystal structure features N—H⋯O, N—H⋯S and C—H⋯O hydrogen bonds that link molecules into supramolecular chains along the b axis. These chains are linked into a layer parallel to (10-1) by C—H⋯π interactions; layers stack with no specific interactions between them.

Data collection: SMART (Bruker, 1998); cell refinement: SAINT-Plus (Bruker,1998); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and CAMERON (Watkin et al., 1996); software used to prepare material for publication: WinGX (Farrugia, 2012 In recent years, dihydropyrimidines (DHPMs) and their derivatives have attracted considerable attention in synthetic organic chemistry because of their wide range of biological activities , such as antibacterial, antiviral, antitumor and anti-inflammatory activities (Mayer et al., 1999). The Biginelli reaction (Biginelli et al., 1893), a one-pot condensation of aldehyde, acetoacetate and urea under strongly acidic conditions, is one of the most useful multicomponent reactions (MCRs), gaining increasing importance in organic and medicinal chemistry because of its capacity to generate multifunctionalized products including 3,4-dihydropyrimidin-2-ones, their thione analogs, and other related heterocyclic compounds. They are also noteworthy as calcium channel modulators (Kappe, 1998;Jauk et al., 2000). respectively. The carbonyl group of the exocyclic ester at C5 adopts a trans orientation with respect to C5=C6 double bond. The 2-fluorobenzene ring shows an anti periplanar conformation with respect to C4-H4 bond of the pyrimidine ring. The molecular structure is stabilized by intermolecular C1-H1B···O1 and N1-H1···O1 interactions generating bifurcated bonds from two donor atoms C1 and N1, to the same acceptor O1 to form an R 2 2 (6) ring motif, which are in turn linked to form a molecular chain along crystallographic b axis. The packing is further stabilized by intermolecular N -H···S hydrogen bonds (N2-H2···S1) resulting in a centrosymmetric head to head dimer with graph set R 2 2 (8) notation (Table 1; Fig. 2). In addition, the crystal structure is stabilized by C10-H10···Cg (Cg is the centroid of aryl ring C8-C13) interaction (Table 1).

S2. Experimental
The title compound was synthesized by the reaction of 2-fluorobenzaldehyde (1.24 g, 10 mmol), methylacetoacetate (1.38 g, 12 mmol) and thiourea (1.14 g, 15 mmol) in 15 ml ethanol. The solution was refluxed for 6 h in the presence of concentrated hydrochloric acid as a catalyst. The reaction was monitored with TLC and the reaction medium was quenched in ice cold water. The precipitate obtained was filtered and dried. The compound was recrystallized from ethanol solvent by slow evaporation method, yielding colorless blocks suitable for X-ray diffraction studies (yield 72%; m.p. 476 K).

S3. Refinement
The H atoms were placed at calculated positions in the riding-model approximation with N-H = 0.86 Å and C-H = 0.93-0.96 Å, and with U iso (H) = 1.5U eq (C) for methyl H atoms and U iso (H) = 1.2U eq (N, C) for the other hydrogen atoms.

Figure 1
The molecular structure of the title compound with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are presented as small spheres of arbitrary radius.

sup-3
Acta Cryst. (2015). E71, o838-o839  Special details Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.