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Acta Crystallogr Sect E Struct Rep Online. 2008 February 1; 64(Pt 2): o352.
Published online 2008 January 4. doi:  10.1107/S160053680706730X
PMCID: PMC2960298

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

Abstract

In the title mol­ecule, C18H21ClN2O3S, the pyrimidine ring exhibits a half-chair conformation. The ethyl group is disordered between two positions in a ratio 0.74:0.26. In the crystal structure, the mol­ecules are linked into chains along the a axis by N—H(...)O hydrogen bonds.

Related literature

For the crystal structure of a related compound, see Jiang et al. (2007 [triangle]).

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Object name is e-64-0o352-scheme1.jpg

Experimental

Crystal data

  • C18H21ClN2O3S
  • M r = 380.88
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o352-efi1.jpg
  • a = 7.5227 (12) Å
  • b = 9.7163 (15) Å
  • c = 14.122 (2) Å
  • α = 72.617 (6)°
  • β = 87.300 (6)°
  • γ = 71.296 (6)°
  • V = 931.7 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.34 mm−1
  • T = 273 (2) K
  • 0.14 × 0.12 × 0.10 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.954, T max = 0.967
  • 10470 measured reflections
  • 3233 independent reflections
  • 2743 reflections with I > 2σ(I)
  • R int = 0.021

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.166
  • S = 1.00
  • 3233 reflections
  • 242 parameters
  • 63 restraints
  • H-atom parameters constrained
  • Δρmax = 0.92 e Å−3
  • Δρmin = −0.71 e Å−3

Data collection: SMART (Siemens, 1996 [triangle]); cell refinement: SAINT (Siemens, 1996 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a [triangle]); molecular graphics: SHELXTL (Sheldrick, 1997b [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680706730X/cv2372sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680706730X/cv2372Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors acknowledge the support of the National Natural Science Foundation of Liaocheng University (No. X051040).

supplementary crystallographic information

Comment

Herewith we present the crystal strusture of the title compound, (I), which was synthesized through the reaction of 2-chlorobenzaldehyde and ethyl acetoacetate with urea derivative under solvent-free conditions.

In (I) (Fig. 1), bond lengths and angles are normal and comparable with those observed in reported compound (Jiang et al., 2007). The pyrimidine ring exhibits a half-chair conformation with the maximal deviation of 0.168 Å for C6 from mean plane.

In the crystal, the molecules related by translation along axis a are linked into chains by N—H···O hydrogen bonds (Table 1).

Experimental

2-Chlorobenzaldehyde (2 mmol), ethyl acetoacetate (2 mmol), urea derivatives (2.4 mmol) and H3BO3(0.4 mmol), in glacial acetic acid (10 ml) was heated at 373 K, while stirring for 1 h, then cooled to room temperature, and poured into ice water (50 ml), and recrystallized from EtOH, affording the title compound as a colourless crystalline solid. Elemental analysis: calculated for C18H21ClN2O3S: C 56.76, H 5.56, N 7.35%; found: C 56.68, H 5.45, N 7.44%.

Refinement

All H atoms were placed in geometrically idealized positions (N—H 0.86, C—H 0.93–0.97 Å) and treated as riding on their parent atoms, with Uiso(H) = 1.2 Ueq(C, N). Atoms C16 and C17 were treated as disordered between two positions with refined occupancies of 0.740 (1) and 0.26 (1), respectively.

Figures

Fig. 1.
The molecular structure of (I) showing the atomic numbering and 30% probability displacement ellipsoids. Only major parts of disordered atoms is shown. H atoms omitted for clarity.

Crystal data

C18H21ClN2O3SZ = 2
Mr = 380.88F000 = 400
Triclinic, P1Dx = 1.358 Mg m3
a = 7.5227 (12) ÅMo Kα radiation λ = 0.71073 Å
b = 9.7163 (15) ÅCell parameters from 5002 reflections
c = 14.122 (2) Åθ = 2.3–27.4º
α = 72.617 (6)ºµ = 0.34 mm1
β = 87.300 (6)ºT = 273 (2) K
γ = 71.296 (6)ºBlock, colourless
V = 931.7 (3) Å30.14 × 0.12 × 0.10 mm

Data collection

Bruker SMART CCD area-detector diffractometer3233 independent reflections
Radiation source: fine-focus sealed tube2743 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.021
T = 273(2) Kθmax = 25.0º
[var phi] and ω scansθmin = 1.5º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)h = −8→8
Tmin = 0.954, Tmax = 0.967k = −11→10
10470 measured reflectionsl = −16→16

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.055H-atom parameters constrained
wR(F2) = 0.166  w = 1/[σ2(Fo2) + (0.0856P)2 + 1.0486P] where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max = 0.002
3233 reflectionsΔρmax = 0.92 e Å3
242 parametersΔρmin = −0.71 e Å3
63 restraintsExtinction correction: SHELXL97 (Sheldrick, 1997a), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.019 (5)

Special details

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)

xyzUiso*/UeqOcc. (<1)
S10.25980 (13)0.52300 (10)0.37239 (6)0.0576 (3)
C10.7929 (7)0.7860 (5)0.2049 (3)0.0787 (12)
H1A0.86450.79900.14670.094*
H1B0.84730.81050.25530.094*
H1C0.66570.85230.18850.094*
O20.8603 (4)0.1939 (5)0.0855 (2)0.0915 (11)
O30.5995 (5)0.2294 (6)0.0050 (3)0.1280 (14)
N10.3010 (3)0.4024 (3)0.22578 (18)0.0459 (6)
H10.18190.41880.22940.055*
N20.5778 (3)0.3881 (3)0.29602 (17)0.0409 (6)
O10.8827 (3)0.5317 (3)0.2018 (2)0.0647 (7)
C20.7951 (4)0.6252 (4)0.2424 (2)0.0507 (7)
C30.6906 (5)0.5828 (4)0.3335 (2)0.0505 (7)
H3A0.56210.65110.32180.061*
H3B0.74680.59940.38780.061*
C40.6868 (5)0.4201 (3)0.3659 (2)0.0465 (7)
H4A0.81480.35110.37310.056*
H4B0.63340.39990.43050.056*
C50.3905 (4)0.4316 (3)0.2963 (2)0.0419 (6)
C60.6877 (4)0.2778 (3)0.2446 (2)0.0378 (6)
H60.80020.30500.22110.045*
C70.5756 (4)0.2894 (3)0.1548 (2)0.0431 (7)
C80.3869 (4)0.3488 (3)0.1493 (2)0.0437 (7)
C90.7520 (4)0.1183 (3)0.3179 (2)0.0388 (6)
C100.9389 (4)0.0353 (3)0.3472 (2)0.0445 (7)
C110.9927 (5)−0.1094 (4)0.4150 (3)0.0569 (8)
H111.1193−0.16250.43240.068*
C120.8590 (6)−0.1737 (4)0.4562 (3)0.0592 (9)
H120.8942−0.27050.50200.071*
C130.6714 (5)−0.0942 (4)0.4295 (3)0.0574 (8)
H130.5800−0.13730.45750.069*
C140.6196 (4)0.0488 (4)0.3613 (2)0.0483 (7)
H140.49280.10060.34380.058*
C150.6932 (5)0.2335 (5)0.0802 (3)0.0619 (9)
C160.7016 (11)0.2217 (13)−0.0899 (6)0.1280 (14)0.740 (10)
H16A0.62530.2918−0.14890.154*0.740 (10)
H16B0.82110.2397−0.08920.154*0.740 (10)
C170.7244 (13)0.0688 (10)−0.0813 (8)0.119 (3)0.740 (10)
H17A0.81240.0031−0.02680.178*0.740 (10)
H17B0.77080.0476−0.14170.178*0.740 (10)
H17C0.60550.0515−0.06960.178*0.740 (10)
C16'0.719 (3)0.101 (2)−0.0367 (13)0.124 (4)0.260 (10)
H16C0.84340.0499−0.00340.148*0.260 (10)
H16D0.65740.0267−0.03490.148*0.260 (10)
C17'0.725 (3)0.195 (3)−0.1337 (12)0.119 (5)0.260 (10)
H17D0.60470.2722−0.15320.179*0.260 (10)
H17E0.75260.1341−0.17860.179*0.260 (10)
H17F0.82000.2412−0.13540.179*0.260 (10)
C180.2497 (5)0.3678 (5)0.0689 (3)0.0608 (9)
H18A0.31700.34010.01440.073*
H18B0.17030.47210.04640.073*
H18C0.17400.30330.09460.073*
Cl11.11696 (11)0.11095 (11)0.30061 (7)0.0646 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0587 (5)0.0578 (5)0.0593 (5)−0.0108 (4)0.0111 (4)−0.0317 (4)
C10.097 (3)0.060 (2)0.081 (3)−0.031 (2)0.015 (2)−0.019 (2)
O20.0477 (15)0.158 (3)0.0847 (19)−0.0197 (17)0.0138 (13)−0.074 (2)
O30.0798 (19)0.245 (4)0.096 (2)−0.039 (2)0.0175 (16)−0.120 (3)
N10.0346 (12)0.0521 (15)0.0538 (14)−0.0099 (11)0.0009 (10)−0.0243 (12)
N20.0438 (13)0.0361 (12)0.0431 (12)−0.0083 (10)−0.0040 (10)−0.0165 (10)
O10.0564 (14)0.0666 (16)0.0822 (17)−0.0224 (12)0.0144 (12)−0.0371 (14)
C20.0461 (17)0.0491 (18)0.0602 (18)−0.0144 (14)−0.0057 (14)−0.0209 (15)
C30.0572 (19)0.0451 (17)0.0556 (18)−0.0152 (14)−0.0027 (14)−0.0247 (14)
C40.0529 (17)0.0434 (16)0.0436 (15)−0.0117 (13)−0.0077 (13)−0.0163 (13)
C50.0437 (16)0.0353 (14)0.0448 (15)−0.0093 (12)0.0011 (12)−0.0130 (12)
C60.0353 (14)0.0370 (14)0.0429 (14)−0.0095 (11)0.0003 (11)−0.0164 (12)
C70.0427 (16)0.0487 (17)0.0416 (15)−0.0152 (13)0.0013 (12)−0.0180 (13)
C80.0432 (16)0.0476 (17)0.0433 (15)−0.0154 (13)0.0017 (12)−0.0169 (13)
C90.0405 (15)0.0351 (14)0.0444 (14)−0.0097 (11)0.0008 (11)−0.0197 (12)
C100.0410 (15)0.0432 (16)0.0527 (17)−0.0110 (12)−0.0025 (12)−0.0210 (13)
C110.0548 (19)0.0435 (18)0.065 (2)−0.0028 (15)−0.0165 (16)−0.0176 (15)
C120.077 (2)0.0376 (17)0.0578 (19)−0.0124 (16)−0.0051 (17)−0.0123 (14)
C130.069 (2)0.0486 (19)0.0612 (19)−0.0262 (17)0.0147 (16)−0.0200 (16)
C140.0410 (16)0.0449 (17)0.0612 (18)−0.0123 (13)0.0065 (13)−0.0216 (14)
C150.049 (2)0.093 (3)0.0526 (19)−0.0214 (18)0.0071 (15)−0.0365 (19)
C160.0798 (19)0.245 (4)0.096 (2)−0.039 (2)0.0175 (16)−0.120 (3)
C170.115 (5)0.119 (6)0.129 (7)−0.028 (5)0.036 (5)−0.063 (5)
C16'0.095 (6)0.222 (8)0.081 (6)−0.025 (6)0.020 (6)−0.116 (6)
C17'0.104 (9)0.196 (10)0.076 (8)−0.034 (9)0.028 (7)−0.088 (8)
C180.0491 (19)0.079 (2)0.0567 (19)−0.0157 (17)−0.0071 (15)−0.0273 (18)
Cl10.0387 (5)0.0689 (6)0.0853 (6)−0.0185 (4)−0.0042 (4)−0.0190 (5)

Geometric parameters (Å, °)

S1—C51.680 (3)C8—C181.500 (4)
C1—C21.487 (5)C9—C101.388 (4)
C1—H1A0.9600C9—C141.396 (4)
C1—H1B0.9600C10—C111.387 (5)
C1—H1C0.9600C10—Cl11.740 (3)
O2—C151.189 (4)C11—C121.368 (5)
O3—C151.318 (5)C11—H110.9300
O3—C161.523 (7)C12—C131.381 (5)
O3—C16'1.545 (10)C12—H120.9300
N1—C51.371 (4)C13—C141.378 (5)
N1—C81.382 (4)C13—H130.9300
N1—H10.8600C14—H140.9300
N2—C51.335 (4)C16—C171.408 (11)
N2—C41.472 (4)C16—H16A0.9700
N2—C61.483 (3)C16—H16B0.9700
O1—C21.215 (4)C17—H17A0.9600
C2—C31.497 (5)C17—H17B0.9600
C3—C41.519 (4)C17—H17C0.9600
C3—H3A0.9700C16'—C17'1.407 (13)
C3—H3B0.9700C16'—H16C0.9700
C4—H4A0.9700C16'—H16D0.9700
C4—H4B0.9700C17'—H17D0.9600
C6—C71.512 (4)C17'—H17E0.9600
C6—C91.521 (4)C17'—H17F0.9600
C6—H60.9800C18—H18A0.9600
C7—C81.346 (4)C18—H18B0.9600
C7—C151.461 (4)C18—H18C0.9600
C2—C1—H1A109.5C10—C9—C14116.3 (3)
C2—C1—H1B109.5C10—C9—C6123.7 (3)
H1A—C1—H1B109.5C14—C9—C6120.0 (2)
C2—C1—H1C109.5C11—C10—C9122.3 (3)
H1A—C1—H1C109.5C11—C10—Cl1117.0 (2)
H1B—C1—H1C109.5C9—C10—Cl1120.8 (2)
C15—O3—C16117.8 (4)C12—C11—C10119.8 (3)
C15—O3—C16'109.7 (9)C12—C11—H11120.1
C16—O3—C16'44.4 (9)C10—C11—H11120.1
C5—N1—C8125.2 (2)C11—C12—C13119.6 (3)
C5—N1—H1117.4C11—C12—H12120.2
C8—N1—H1117.4C13—C12—H12120.2
C5—N2—C4120.3 (2)C14—C13—C12120.1 (3)
C5—N2—C6122.7 (2)C14—C13—H13120.0
C4—N2—C6115.6 (2)C12—C13—H13120.0
O1—C2—C1121.0 (3)C13—C14—C9121.9 (3)
O1—C2—C3121.7 (3)C13—C14—H14119.0
C1—C2—C3117.2 (3)C9—C14—H14119.0
C2—C3—C4115.6 (3)O2—C15—O3121.8 (3)
C2—C3—H3A108.4O2—C15—C7123.6 (3)
C4—C3—H3A108.4O3—C15—C7114.6 (3)
C2—C3—H3B108.4C17—C16—O397.9 (7)
C4—C3—H3B108.4C17—C16—H16A112.2
H3A—C3—H3B107.4O3—C16—H16A112.2
N2—C4—C3113.4 (2)C17—C16—H16B112.2
N2—C4—H4A108.9O3—C16—H16B112.2
C3—C4—H4A108.9H16A—C16—H16B109.8
N2—C4—H4B108.9C17'—C16'—O396.5 (10)
C3—C4—H4B108.9C17'—C16'—H16C112.5
H4A—C4—H4B107.7O3—C16'—H16C112.5
N2—C5—N1116.0 (2)C17'—C16'—H16D112.5
N2—C5—S1125.3 (2)O3—C16'—H16D112.5
N1—C5—S1118.7 (2)H16C—C16'—H16D110.0
N2—C6—C7110.4 (2)C16'—C17'—H17D109.5
N2—C6—C9109.7 (2)C16'—C17'—H17E109.5
C7—C6—C9113.2 (2)H17D—C17'—H17E109.5
N2—C6—H6107.8C16'—C17'—H17F109.5
C7—C6—H6107.8H17D—C17'—H17F109.5
C9—C6—H6107.8H17E—C17'—H17F109.5
C8—C7—C15126.8 (3)C8—C18—H18A109.5
C8—C7—C6120.1 (3)C8—C18—H18B109.5
C15—C7—C6113.1 (2)H18A—C18—H18B109.5
C7—C8—N1118.3 (3)C8—C18—H18C109.5
C7—C8—C18128.8 (3)H18A—C18—H18C109.5
N1—C8—C18112.9 (3)H18B—C18—H18C109.5
O1—C2—C3—C4−5.4 (4)C7—C6—C9—C10122.2 (3)
C1—C2—C3—C4176.6 (3)N2—C6—C9—C1464.6 (3)
C5—N2—C4—C3−79.4 (3)C7—C6—C9—C14−59.2 (3)
C6—N2—C4—C3114.0 (3)C14—C9—C10—C110.7 (4)
C2—C3—C4—N2−67.4 (4)C6—C9—C10—C11179.3 (3)
C4—N2—C5—N1177.4 (2)C14—C9—C10—Cl1−178.5 (2)
C6—N2—C5—N1−17.0 (4)C6—C9—C10—Cl10.1 (4)
C4—N2—C5—S1−0.3 (4)C9—C10—C11—C12−0.8 (5)
C6—N2—C5—S1165.4 (2)Cl1—C10—C11—C12178.4 (3)
C8—N1—C5—N2−7.7 (4)C10—C11—C12—C130.3 (5)
C8—N1—C5—S1170.1 (2)C11—C12—C13—C140.3 (5)
C5—N2—C6—C730.6 (4)C12—C13—C14—C9−0.4 (5)
C4—N2—C6—C7−163.1 (2)C10—C9—C14—C13−0.1 (4)
C5—N2—C6—C9−94.8 (3)C6—C9—C14—C13−178.7 (3)
C4—N2—C6—C971.4 (3)C16—O3—C15—O2−19.1 (9)
N2—C6—C7—C8−22.2 (4)C16'—O3—C15—O228.9 (11)
C9—C6—C7—C8101.3 (3)C16—O3—C15—C7161.1 (6)
N2—C6—C7—C15156.9 (3)C16'—O3—C15—C7−150.9 (10)
C9—C6—C7—C15−79.7 (3)C8—C7—C15—O2173.4 (4)
C15—C7—C8—N1−176.9 (3)C6—C7—C15—O2−5.5 (6)
C6—C7—C8—N12.0 (4)C8—C7—C15—O3−6.8 (6)
C15—C7—C8—C182.5 (6)C6—C7—C15—O3174.3 (4)
C6—C7—C8—C18−178.6 (3)C15—O3—C16—C17107.2 (7)
C5—N1—C8—C715.2 (4)C16'—O3—C16—C1716.9 (14)
C5—N1—C8—C18−164.4 (3)C15—O3—C16'—C17'−120.7 (15)
N2—C6—C9—C10−114.0 (3)C16—O3—C16'—C17'−10.6 (11)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.862.162.984 (3)160

Symmetry codes: (i) x−1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2372).

References

  • Jiang, H., Yu, C.-X., Tu, S.-J., Wang, X.-S. & Yao, C.-S. (2007). Acta Cryst. E63, o298–o299.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (1997a). SHELXS97 and SHELXL97 University of Göttingen, Germany.
  • Sheldrick, G. M. (1997b). SHELXTL. Version 5.1. Bruker AXS Inc., Madison, Wisconsin, USA.
  • Siemens (1996). SMART and SAINT Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography