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ISSN: 2056-9890

Ethyl 4-(4-chloro­phen­yl)-6-methyl-2-thioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate

aSolid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India, bSchool of Chemistry, University of KwaZulu-Natal, Durban 4000, South Africa, cDepartment of Chemistry, Indian Institute of Science Education and Research, Bhopal 462 023, India, and dSchool of Pharmacy and Pharmacology, University of Kwazulu-Natal, Durban 4000, South Africa
*Correspondence e-mail: dchopra@iiserbhopal.ac.in

(Received 14 September 2009; accepted 16 September 2009; online 26 September 2009)

In the title compound, C14H15ClN2O2S, the tetra­hydro­pyrimidine ring adopts a twisted boat conformation with the carbonyl group in an s-trans conformation with respect to the C=C double bond of the six-membered tetra­hydro­pyrimidine ring. The mol­ecular conformation is determined by an intra­molecular C—H⋯π inter­action. The crystal structure is further stabilized by inter­molecular N—H⋯O mol­ecular chains and centrosymmetric N—H⋯S dimers.

Related literature

For background to the applications of poly-functionalized dihydro­pyrimidines, see: Corey & Cheng (1995[Corey, E. J. & Cheng, X.-M. (1995). The Logic of Chemical Synthesis. New York: John Wiley & Sons Australia Ltd.]); Hurst & Hull (1961[Hurst, E. W. & Hull, R. (1961). J. Med. Pharm. Chem. 3, 215-229.]); Jauk et al. (2000[Jauk, B., Pernat, T. & Kappe, C. O. (2000). Molecules, 5, 227-239 and references therein.]); Kappe (2000[Kappe, C. O. (2000). Eur. J. Med. Chem. 4835, 1043-1052.]); Mayer et al. (1999[Mayer, T. U., Kapoor, T. M., Haggarty, S. J., King, R. W., Schreiber, S. I. & Mitchison, T. J. (1999). Science, 286, 971-974.]). For ring puckering parameters, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]).

[Scheme 1]

Experimental

Crystal data
  • C14H15ClN2O2S

  • Mr = 310.80

  • Triclinic, [P \overline 1]

  • a = 7.3420 (3) Å

  • b = 9.4895 (4) Å

  • c = 12.0425 (5) Å

  • α = 73.823 (4)°

  • β = 88.512 (3)°

  • γ = 70.264 (4)°

  • V = 756.32 (6) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.39 mm−1

  • T = 292 K

  • 0.24 × 0.22 × 0.18 mm

Data collection
  • Oxford Diffraction Xcalibur diffractometer with Eos (Nova) detector

  • Absorption correction: multi-scan (CrysAlis Pro; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis Pro. Oxford Diffraction Ltd, Yarnton, England.]) Tmin = 0.902, Tmax = 0.933

  • 16944 measured reflections

  • 2960 independent reflections

  • 2232 reflections with I > 2σ(I)

  • Rint = 0.040

Refinement
  • R[F2 > 2σ(F2)] = 0.053

  • wR(F2) = 0.161

  • S = 1.09

  • 2960 reflections

  • 183 parameters

  • H-atom parameters constrained

  • Δρmax = 0.48 e Å−3

  • Δρmin = −0.37 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O1i 0.86 2.25 3.077 (3) 161
N2—H2⋯S1ii 0.86 2.49 3.323 (3) 164
C14—H14⋯Cg1 0.93 2.67 3.146 (4) 113
Symmetry codes: (i) x-1, y, z; (ii) -x+1, -y+1, -z+1. Cg1 is the centroid of the C2=C3 double bond.

Data collection: CrysAlis Pro (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis Pro. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis Pro; data reduction: CrysAlis Pro; program(s) used to solve structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and CAMERON (Watkin et al., 1993[Watkin, D. M., Pearce, L. & Prout, C. K. (1993). CAMERON. Chemical Crystallography Laboratory, University of Oxford, England.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

The logic of chemical reactivity (Corey & Cheng, 1995) has found application in the rational design of a variety of drug molecules. One such class of compounds is the "Bignelli compounds". These are poly-functionalized dihydropyrimidine (DHPM's) exhibiting a broad range of therapeutic and pharmacological properties (Kappe, 2000) namely, antiviral (Hurst et al., 1961), antimimotic (Mayer et al.,1999) and calcium channel modulators (Jauk et al., 2000). In view of immense range of applications of this class of compounds we have undertaken a single-crystal determination of the title compound.

The tetrahydropyrimidine ring adopts a twist boat conformation. The puckering parameters (Cremer & Pople 1975) are Q = 0.277 (3) Å, θ(2) = 108.1 (3)° and ϕ(2) = 349.1 (6)° respectively. The orientation of the chloro-phenyl moiety is such that it bisects the twist boat conformation of the tetrahydropyrimidine ring, the C9—C4—C3—C5 torsion angle being 77.4 (3)°. The molecular conformation is stabilized by an intramolecular C—H···π interaction (2.67 Å, 113°) wherein the aryl hydrogen H14 is oriented towards the π electrons of the C2=C3 double bond (Figure 1). The crystal structure is further stabilized by centrosymmetric N—H···S dimers and N—H···O hydrogen bonds forming molecular chains along the crystallographic a axis (Figure 2).

Related literature top

For background to the applications of poly-functionalized dihydropyrimidines, see: Corey & Cheng (1995); Hurst & Hull (1961); Jauk et al. (2000); Kappe (2000); Mayer et al. (1999). For ring puckering parameters, see: Cremer & Pople (1975). Cg1 is the centroid of the C2=C3 double bond.

Experimental top

A mixture of ethylacetoacetate (0.1 mol), para chlorosubstituted benzaldehyde (0.1 mol) and thiourea was refluxed in 50.0 mL of ethanol for 2.0 hrs in presence of concentrated hydrochloric acid as catalyst. The reaction completion was monitored through thin layer chromatography and and, on completion, the products were poured into ice cold water. The precipitate obtained was filtered, dried and crystallized from methanol to obtain the title compound.

Refinement top

All H atoms were positioned geometrically, C—H = 0.93 Å, 0.96 Å, 0.97 Å, 0.98Å for aromatic, methyl, methylene and methine hydrogen respectively and N—H = 0.86 Å and all refined using a riding model with Uiso(H)= 1.2 Ueq(C, N) for aromatic and amine hydrogen and 1.5 Ueq(C) for methyl, methylene and methine H atoms respectively.

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXL97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and CAMERON (Watkin et al., 1993); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. : The structure of the title compound showing the atom labelling Scheme with displacement ellipsoids for non-H atoms at the 50% probability level. The dotted line shows the C—H···π intramolecular interactions. Cg1 (the orange open circle) denotes the center of gravity of the C2=C3 bond.
[Figure 2] Fig. 2. : The crystal packing showing the molecular chains of N—H···O hydrogen bonds and N—H···S centrosymmetric dimers. Molecules at # and * have the symmetry codes (- x + 1, - y + 1, - z + 1) and (x - 1, y, z) respectively.
Ethyl 4-(4-chlorophenyl)-6-methyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate top
Crystal data top
C14H15ClN2O2SZ = 2
Mr = 310.80F(000) = 324
Triclinic, P1Dx = 1.365 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.7107 Å
a = 7.3420 (3) ÅCell parameters from 340 reflections
b = 9.4895 (4) Åθ = 1.0–28.0°
c = 12.0425 (5) ŵ = 0.39 mm1
α = 73.823 (4)°T = 292 K
β = 88.512 (3)°Block, colorless
γ = 70.264 (4)°0.24 × 0.22 × 0.18 mm
V = 756.32 (6) Å3
Data collection top
Oxford Diffraction Xcalibur with Eos (Nova) detector
diffractometer
2960 independent reflections
Radiation source: Enhance (Mo) X-ray Source2232 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.040
Detector resolution: 16.0839 pixels mm-1θmax = 26.0°, θmin = 3.3°
ω scansh = 99
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
k = 1111
Tmin = 0.902, Tmax = 0.933l = 1414
16944 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)] = 0.053Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.161H-atom parameters constrained
S = 1.09 w = 1/[σ2(Fo2) + (0.094P)2 + 0.1394P]
where P = (Fo2 + 2Fc2)/3
2960 reflections(Δ/σ)max < 0.001
183 parametersΔρmax = 0.48 e Å3
0 restraintsΔρmin = 0.37 e Å3
Crystal data top
C14H15ClN2O2Sγ = 70.264 (4)°
Mr = 310.80V = 756.32 (6) Å3
Triclinic, P1Z = 2
a = 7.3420 (3) ÅMo Kα radiation
b = 9.4895 (4) ŵ = 0.39 mm1
c = 12.0425 (5) ÅT = 292 K
α = 73.823 (4)°0.24 × 0.22 × 0.18 mm
β = 88.512 (3)°
Data collection top
Oxford Diffraction Xcalibur with Eos (Nova) detector
diffractometer
2960 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
2232 reflections with I > 2σ(I)
Tmin = 0.902, Tmax = 0.933Rint = 0.040
16944 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0530 restraints
wR(F2) = 0.161H-atom parameters constrained
S = 1.09Δρmax = 0.48 e Å3
2960 reflectionsΔρmin = 0.37 e Å3
183 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
xyzUiso*/Ueq
S10.19746 (10)0.59669 (9)0.54217 (7)0.0474 (3)
Cl10.98420 (16)0.22640 (13)1.09156 (8)0.0841 (4)
N20.5115 (3)0.6617 (3)0.57987 (18)0.0368 (5)
H20.56870.60380.53680.044*
C30.5079 (4)0.8759 (3)0.6529 (2)0.0337 (6)
N10.2287 (3)0.8143 (3)0.6307 (2)0.0395 (5)
H10.10990.82880.64630.047*
C40.6301 (4)0.7183 (3)0.6403 (2)0.0343 (6)
H40.73600.73200.59220.041*
O20.5259 (3)1.0762 (3)0.7252 (2)0.0562 (6)
O10.7882 (3)0.9466 (2)0.64949 (19)0.0501 (5)
C10.3222 (4)0.6937 (3)0.5869 (2)0.0352 (6)
C90.7198 (3)0.5977 (3)0.7561 (2)0.0330 (6)
C20.3137 (4)0.9158 (3)0.6519 (2)0.0352 (6)
C50.6218 (4)0.9691 (3)0.6732 (2)0.0373 (6)
C140.6506 (4)0.6140 (4)0.8616 (2)0.0467 (7)
H140.54690.70270.86330.056*
C60.6261 (5)1.1724 (4)0.7526 (3)0.0571 (8)
H6A0.75281.10730.79160.069*
H6B0.64341.24520.68210.069*
C80.1693 (4)1.0610 (4)0.6676 (3)0.0520 (8)
H8A0.21701.14610.63950.078*
H8B0.14881.04680.74850.078*
H8C0.04901.08400.62510.078*
C100.8750 (4)0.4642 (4)0.7572 (3)0.0472 (7)
H100.92470.45230.68730.057*
C120.8839 (4)0.3695 (4)0.9625 (3)0.0499 (7)
C110.9569 (4)0.3507 (4)0.8560 (3)0.0489 (7)
H111.05970.26170.85390.059*
C130.7329 (5)0.5008 (4)0.9644 (3)0.0532 (8)
H130.68560.51401.03450.064*
C70.5083 (6)1.2561 (6)0.8271 (5)0.1004 (17)
H7A0.50771.18390.90090.151*
H7B0.37811.30840.79220.151*
H7C0.56081.33170.83790.151*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0396 (4)0.0547 (5)0.0629 (5)0.0215 (3)0.0076 (3)0.0340 (4)
Cl10.0859 (7)0.0806 (7)0.0595 (6)0.0202 (6)0.0165 (5)0.0120 (5)
N20.0311 (12)0.0444 (13)0.0402 (11)0.0104 (10)0.0019 (9)0.0236 (10)
C30.0304 (13)0.0358 (14)0.0366 (13)0.0117 (11)0.0014 (10)0.0124 (11)
N10.0330 (12)0.0468 (13)0.0508 (13)0.0190 (10)0.0131 (10)0.0271 (11)
C40.0300 (13)0.0409 (14)0.0386 (13)0.0156 (11)0.0079 (10)0.0179 (11)
O20.0448 (12)0.0589 (14)0.0878 (16)0.0276 (10)0.0155 (11)0.0453 (13)
O10.0322 (11)0.0551 (13)0.0722 (14)0.0202 (9)0.0073 (9)0.0265 (11)
C10.0369 (14)0.0388 (14)0.0316 (12)0.0127 (11)0.0040 (10)0.0134 (11)
C90.0277 (13)0.0393 (14)0.0378 (13)0.0141 (11)0.0041 (10)0.0171 (11)
C20.0341 (14)0.0353 (14)0.0376 (13)0.0123 (11)0.0015 (10)0.0121 (11)
C50.0404 (16)0.0338 (14)0.0371 (13)0.0120 (12)0.0017 (11)0.0098 (11)
C140.0449 (17)0.0473 (16)0.0463 (16)0.0090 (13)0.0060 (13)0.0195 (14)
C60.056 (2)0.0570 (19)0.079 (2)0.0327 (16)0.0092 (17)0.0356 (18)
C80.0314 (15)0.0469 (17)0.082 (2)0.0096 (13)0.0046 (14)0.0304 (17)
C100.0379 (15)0.0524 (18)0.0508 (17)0.0091 (13)0.0088 (13)0.0224 (15)
C120.0429 (16)0.0570 (18)0.0457 (16)0.0185 (14)0.0079 (13)0.0056 (14)
C110.0324 (15)0.0459 (17)0.0593 (18)0.0023 (13)0.0021 (13)0.0147 (15)
C130.060 (2)0.062 (2)0.0397 (16)0.0214 (16)0.0062 (14)0.0179 (15)
C70.079 (3)0.130 (4)0.152 (4)0.063 (3)0.045 (3)0.103 (4)
Geometric parameters (Å, º) top
S1—C11.688 (3)C2—C81.486 (4)
Cl1—C121.735 (3)C14—C131.382 (4)
N2—C11.324 (3)C14—H140.9300
N2—C41.464 (3)C6—C71.441 (5)
N2—H20.8600C6—H6A0.9700
C3—C21.345 (3)C6—H6B0.9700
C3—C51.474 (4)C8—H8A0.9600
C3—C41.510 (3)C8—H8B0.9600
N1—C11.359 (3)C8—H8C0.9600
N1—C21.390 (3)C10—C111.349 (4)
N1—H10.8600C10—H100.9300
C4—C91.528 (4)C12—C131.365 (5)
C4—H40.9800C12—C111.411 (4)
O2—C51.330 (3)C11—H110.9300
O2—C61.455 (3)C13—H130.9300
O1—C51.208 (3)C7—H7A0.9600
C9—C141.386 (4)C7—H7B0.9600
C9—C101.386 (4)C7—H7C0.9600
C1—N2—C4124.5 (2)C7—C6—O2107.4 (3)
C1—N2—H2117.7C7—C6—H6A110.2
C4—N2—H2117.7O2—C6—H6A110.2
C2—C3—C5126.0 (2)C7—C6—H6B110.2
C2—C3—C4119.9 (2)O2—C6—H6B110.2
C5—C3—C4113.9 (2)H6A—C6—H6B108.5
C1—N1—C2123.8 (2)C2—C8—H8A109.5
C1—N1—H1118.1C2—C8—H8B109.5
C2—N1—H1118.1H8A—C8—H8B109.5
N2—C4—C3109.1 (2)C2—C8—H8C109.5
N2—C4—C9110.3 (2)H8A—C8—H8C109.5
C3—C4—C9113.21 (19)H8B—C8—H8C109.5
N2—C4—H4108.0C11—C10—C9122.5 (3)
C3—C4—H4108.0C11—C10—H10118.7
C9—C4—H4108.0C9—C10—H10118.7
C5—O2—C6118.1 (2)C13—C12—C11120.0 (3)
N2—C1—N1116.0 (2)C13—C12—Cl1119.6 (2)
N2—C1—S1123.59 (19)C11—C12—Cl1120.5 (2)
N1—C1—S1120.36 (19)C10—C11—C12118.9 (3)
C14—C9—C10117.7 (3)C10—C11—H11120.6
C14—C9—C4122.9 (2)C12—C11—H11120.6
C10—C9—C4119.5 (2)C12—C13—C14119.8 (3)
C3—C2—N1118.7 (2)C12—C13—H13120.1
C3—C2—C8128.3 (2)C14—C13—H13120.1
N1—C2—C8112.9 (2)C6—C7—H7A109.5
O1—C5—O2123.2 (2)C6—C7—H7B109.5
O1—C5—C3123.5 (2)H7A—C7—H7B109.5
O2—C5—C3113.2 (2)C6—C7—H7C109.5
C13—C14—C9121.2 (3)H7A—C7—H7C109.5
C13—C14—H14119.4H7B—C7—H7C109.5
C9—C14—H14119.4
C1—N2—C4—C331.3 (3)C1—N1—C2—C8163.8 (3)
C1—N2—C4—C993.6 (3)C6—O2—C5—O11.1 (4)
C2—C3—C4—N224.4 (3)C6—O2—C5—C3178.3 (2)
C5—C3—C4—N2159.3 (2)C2—C3—C5—O1163.6 (3)
C2—C3—C4—C998.8 (3)C4—C3—C5—O120.4 (4)
C5—C3—C4—C977.4 (3)C2—C3—C5—O219.2 (4)
C4—N2—C1—N115.8 (4)C4—C3—C5—O2156.7 (2)
C4—N2—C1—S1165.7 (2)C10—C9—C14—C130.3 (4)
C2—N1—C1—N29.3 (4)C4—C9—C14—C13178.6 (3)
C2—N1—C1—S1169.2 (2)C5—O2—C6—C7169.1 (3)
N2—C4—C9—C14103.7 (3)C14—C9—C10—C111.1 (4)
C3—C4—C9—C1418.9 (3)C4—C9—C10—C11177.8 (3)
N2—C4—C9—C1075.2 (3)C9—C10—C11—C121.0 (5)
C3—C4—C9—C10162.3 (2)C13—C12—C11—C100.0 (5)
C5—C3—C2—N1179.7 (2)Cl1—C12—C11—C10179.8 (2)
C4—C3—C2—N14.6 (4)C11—C12—C13—C140.8 (5)
C5—C3—C2—C81.6 (5)Cl1—C12—C13—C14179.0 (2)
C4—C3—C2—C8177.3 (3)C9—C14—C13—C120.7 (5)
C1—N1—C2—C314.6 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.862.253.077 (3)161
N2—H2···S1ii0.862.493.323 (3)164
C14—H14···Cg10.932.673.146 (4)113
Symmetry codes: (i) x1, y, z; (ii) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC14H15ClN2O2S
Mr310.80
Crystal system, space groupTriclinic, P1
Temperature (K)292
a, b, c (Å)7.3420 (3), 9.4895 (4), 12.0425 (5)
α, β, γ (°)73.823 (4), 88.512 (3), 70.264 (4)
V3)756.32 (6)
Z2
Radiation typeMo Kα
µ (mm1)0.39
Crystal size (mm)0.24 × 0.22 × 0.18
Data collection
DiffractometerOxford Diffraction Xcalibur with Eos (Nova) detector
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
Tmin, Tmax0.902, 0.933
No. of measured, independent and
observed [I > 2σ(I)] reflections
16944, 2960, 2232
Rint0.040
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.053, 0.161, 1.09
No. of reflections2960
No. of parameters183
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.48, 0.37

Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and CAMERON (Watkin et al., 1993), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.86002.25003.077 (3)161.00
N2—H2···S1ii0.86002.49003.323 (3)164.00
C14—H14···Cg10.932.673.146 (4)113.0
Symmetry codes: (i) x1, y, z; (ii) x+1, y+1, z+1.
 

Acknowledgements

We are grateful for funding under DST–FIST (Level II) for the Oxford Diffraction facility at SSCU. SKN thanks CSIR (SRF), India, for financial support.

References

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