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

Xie, F.; Huang, H.; Liu, G.; Liu, C.-J.

doi:10.1107/S1600536807025639

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

F. Xie, H. Huang, G. Liu and C.-J. Liu

In the crystal structure of the title compound, C₁₆H₁₇N₅O₂S, molecules are linked by two N—H

S hydrogen bonds, with N—S distances of 3.3469 (13) and 3.3703 (13) Å and N—H

S angles of 158 and 162°.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807025639/bx2087sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807025639/bx2087Isup2.hkl Contains datablock I

CCDC reference: 653168

checkCIF report

Key indicators

Single-crystal X-ray study
T = 153 K
Mean (C-C) = 0.003 Å
R factor = 0.043
wR factor = 0.124
Data-to-parameter ratio = 17.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.65 mm
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.31
PLAT154_ALERT_1_C The su's on the Cell Angles are Equal  (x 10000)        200 Deg.
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.07 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.05 Ratio
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C13

Alert level G
PLAT793_ALERT_1_G Check the Absolute Configuration of C9     = ...          R

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   6 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

3,4-Dihydropyrimidin-2(1H)-ones and their derivatives have attracted considerable interest because of their therapeutic and pharmaceutical properties, such as antiviral, antibacterial, anti-inflammatory and antitumour activities (Kappe, 1993). Their particular structure has been found in natural marine alkaloid Batzelladine A and B which are the first low molecular weight natural products reported in the literature to inhibit the binding of HIV gp-120 to CD4 cells, so disclosing a new field towards the development of AIDS therapy (Patil et al., 1995). Additionally, functionalized dihydropyrimidinones have been used as antihypertensive agents, potent calcium channel blockers, adrenergic and neuropeptide Y (NPY) antagonist (Atwal et al., 1990). The X-ray crystal structure analysis of the title compound, was undertaken in order to study its stereochemistry and crystal packing. 4-(3,4-Methylenedioxylphenyl)-6-methyl-5-ethoxycaronyl-3,4-dihydropyrimidin- 2(H)-one has been reported (Tu et al., 2004). 4-(4-Chlorophenyl)-6-methyl-5-methoxycaronyl-3,4-dihydropyrimidin-2(H)-one has been reported (Hua et al., 2004). N-acylated 3,4-dihydropyrimidin-2-ones have been reported (Singh & Singh et al., 2006).

Related literature top

For related literature, see: Atwal et al. (1990); Hua et al. (2004); Kappe (1993); Patil et al. (1995); Singh & Singh (2006); Tu et al. (2004).

Experimental top

A mixture of 2-phenyl-1,2,3-triazolyl-4-formaldehyde (1 mmol), ethyl acetoacetate (1 mmol), thiourea (1.5 mmol) in absolute EtOH was refluxing in the presence of Sm(ClO₄)₃ (as catalyst) for 9 h between 343–353 K. The product was isolated by filtration, and dried at room temperature. Yield 76.1% (0.261 g), m.p. 476–478 K. Block-like single-crystal of compound (I) was grown from solution of ethanol by slow evaporation.

Structure description top

For related literature, see: Atwal et al. (1990); Hua et al. (2004); Kappe (1993); Patil et al. (1995); Singh & Singh (2006); Tu et al. (2004).

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2004); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top

Fig. 1. A view of the molecule structure of (I), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.

Ethyl 6-methyl-4-(2-phenyltriazol-4-yl)-2-thioxo-1,2,3,6- tetrahydropyrimidine-5-carboxylate top

Crystal data top

C₁₆H₁₇N₅O₂S	Z = 2
M_r = 343.41	F(000) = 360
Triclinic, P1	D_x = 1.379 Mg m⁻³
Hall symbol: -P 1	Melting point = 476–478 K
a = 8.3998 (5) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.4733 (5) Å	Cell parameters from 7493 reflections
c = 11.4989 (8) Å	θ = 3.1–27.5°
α = 76.516 (2)°	µ = 0.22 mm⁻¹
β = 87.552 (2)°	T = 153 K
γ = 68.564 (2)°	Block, colourless
V = 827.33 (9) Å³	0.65 × 0.56 × 0.48 mm

Data collection top

Rigaku R-AXIS SPIDER diffractometer	3754 independent reflections
Radiation source: fine-focus sealed tube	3399 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
ω scans	θ_max = 27.5°, θ_min = 3.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −10→10
T_min = 0.873, T_max = 0.904	k = −12→12
8180 measured reflections	l = −14→14

Refinement top

Refinement on F²	H-atom parameters constrained
Least-squares matrix: full	w = 1/[σ²(F_o²) + (0.0705P)² + 0.458P] where P = (F_o² + 2F_c²)/3
R[F² > 2σ(F²)] = 0.043	(Δ/σ)_max = 0.001
wR(F²) = 0.125	Δρ_max = 0.90 e Å⁻³
S = 1.03	Δρ_min = −0.39 e Å⁻³
3754 reflections	Extinction correction: SHELXL97 (Sheldrick, 1997)
218 parameters	Extinction coefficient: 0.038 (5)
0 restraints

Crystal data top

C₁₆H₁₇N₅O₂S	γ = 68.564 (2)°
M_r = 343.41	V = 827.33 (9) Å³
Triclinic, P1	Z = 2
a = 8.3998 (5) Å	Mo Kα radiation
b = 9.4733 (5) Å	µ = 0.22 mm⁻¹
c = 11.4989 (8) Å	T = 153 K
α = 76.516 (2)°	0.65 × 0.56 × 0.48 mm
β = 87.552 (2)°

Data collection top

Rigaku R-AXIS SPIDER diffractometer	3754 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	3399 reflections with I > 2σ(I)
T_min = 0.873, T_max = 0.904	R_int = 0.026
8180 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	0 restraints
wR(F²) = 0.125	H-atom parameters constrained
S = 1.03	Δρ_max = 0.90 e Å⁻³
3754 reflections	Δρ_min = −0.39 e Å⁻³
218 parameters

Special details top

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

	x	y	z	U_iso*/U_eq
S1	0.21949 (5)	0.56030 (4)	0.49008 (4)	0.02980 (15)
O1	0.43152 (15)	−0.21361 (13)	0.71966 (12)	0.0306 (3)
O2	0.68489 (15)	−0.18789 (14)	0.68174 (12)	0.0325 (3)
N1	0.63345 (18)	0.12860 (16)	0.94892 (12)	0.0261 (3)
N2	0.75123 (16)	0.17112 (15)	0.88427 (11)	0.0209 (3)
N3	0.74361 (16)	0.17441 (14)	0.76805 (11)	0.0201 (3)
N4	0.47347 (16)	0.28931 (15)	0.56353 (11)	0.0224 (3)
H4A	0.5403	0.3382	0.5287	0.027*
N5	0.20505 (16)	0.27995 (14)	0.57783 (12)	0.0212 (3)
H5A	0.0935	0.3296	0.5752	0.025*
C1	0.9596 (2)	0.2957 (2)	0.85709 (17)	0.0318 (4)
H1B	0.9323	0.3267	0.7734	0.038*
C2	1.0837 (3)	0.3331 (3)	0.9050 (2)	0.0440 (5)
H2A	1.1433	0.3892	0.8538	0.053*
C3	1.1212 (3)	0.2888 (2)	1.0276 (2)	0.0459 (5)
H3B	1.2067	0.3142	1.0599	0.055*
C4	1.0351 (3)	0.2086 (2)	1.10218 (18)	0.0403 (5)
H4B	1.0600	0.1804	1.1861	0.048*
C5	0.9116 (2)	0.1681 (2)	1.05613 (16)	0.0307 (4)
H5B	0.8528	0.1114	1.1076	0.037*
C6	0.87629 (19)	0.21229 (17)	0.93394 (14)	0.0237 (3)
C7	0.5428 (2)	0.10392 (19)	0.86819 (14)	0.0245 (3)
H7A	0.4476	0.0721	0.8844	0.029*
C8	0.61077 (18)	0.13249 (16)	0.75636 (13)	0.0185 (3)
C9	0.55561 (18)	0.12922 (16)	0.63452 (12)	0.0184 (3)
H9A	0.6604	0.0765	0.5935	0.022*
C10	0.30548 (19)	0.36575 (17)	0.54804 (13)	0.0205 (3)
C11	0.43724 (18)	0.03984 (17)	0.64066 (12)	0.0191 (3)
C12	0.26849 (18)	0.11694 (16)	0.61245 (12)	0.0190 (3)
C13	0.1318 (2)	0.05172 (18)	0.60777 (15)	0.0253 (3)
H13A	0.1816	−0.0624	0.6324	0.030*
H13B	0.0823	0.0834	0.5259	0.030*
H13C	0.0420	0.0914	0.6620	0.030*
C14	0.5302 (2)	−0.13067 (17)	0.68061 (13)	0.0225 (3)
C15	0.5229 (3)	−0.3808 (2)	0.7656 (2)	0.0406 (5)
H15A	0.5880	−0.4273	0.7014	0.049*
H15B	0.6047	−0.3990	0.8319	0.049*
C16	0.3980 (3)	−0.4527 (2)	0.8085 (3)	0.0562 (6)
H16A	0.4576	−0.5650	0.8401	0.067*
H16B	0.3185	−0.4353	0.7421	0.067*
H16C	0.3342	−0.4060	0.8720	0.067*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0185 (2)	0.0194 (2)	0.0458 (3)	−0.00878 (15)	−0.00867 (16)	0.00795 (16)
O1	0.0261 (6)	0.0169 (5)	0.0438 (7)	−0.0072 (5)	0.0011 (5)	0.0017 (5)
O2	0.0218 (6)	0.0241 (6)	0.0447 (7)	−0.0040 (5)	−0.0055 (5)	−0.0007 (5)
N1	0.0287 (7)	0.0302 (7)	0.0207 (6)	−0.0148 (6)	0.0005 (5)	−0.0017 (5)
N2	0.0207 (6)	0.0215 (6)	0.0193 (6)	−0.0080 (5)	−0.0032 (5)	−0.0015 (5)
N3	0.0184 (6)	0.0211 (6)	0.0192 (6)	−0.0074 (5)	−0.0029 (4)	−0.0010 (5)
N4	0.0165 (6)	0.0224 (6)	0.0246 (6)	−0.0098 (5)	−0.0050 (5)	0.0070 (5)
N5	0.0135 (5)	0.0181 (6)	0.0294 (6)	−0.0064 (5)	−0.0024 (5)	0.0008 (5)
C1	0.0285 (8)	0.0318 (9)	0.0380 (9)	−0.0139 (7)	−0.0031 (7)	−0.0081 (7)
C2	0.0336 (10)	0.0426 (11)	0.0649 (14)	−0.0210 (9)	−0.0034 (9)	−0.0172 (10)
C3	0.0313 (10)	0.0417 (11)	0.0691 (14)	−0.0083 (8)	−0.0187 (9)	−0.0254 (10)
C4	0.0383 (10)	0.0333 (9)	0.0441 (11)	−0.0007 (8)	−0.0210 (8)	−0.0153 (8)
C5	0.0306 (8)	0.0251 (8)	0.0310 (8)	−0.0026 (7)	−0.0107 (7)	−0.0065 (6)
C6	0.0200 (7)	0.0203 (7)	0.0291 (8)	−0.0035 (6)	−0.0062 (6)	−0.0075 (6)
C7	0.0238 (7)	0.0282 (7)	0.0220 (7)	−0.0134 (6)	−0.0005 (6)	−0.0001 (6)
C8	0.0157 (6)	0.0161 (6)	0.0203 (7)	−0.0047 (5)	−0.0036 (5)	0.0009 (5)
C9	0.0143 (6)	0.0189 (6)	0.0190 (6)	−0.0057 (5)	−0.0033 (5)	0.0010 (5)
C10	0.0181 (7)	0.0214 (7)	0.0200 (6)	−0.0088 (6)	−0.0036 (5)	0.0019 (5)
C11	0.0185 (7)	0.0194 (7)	0.0189 (6)	−0.0080 (6)	−0.0022 (5)	−0.0014 (5)
C12	0.0191 (7)	0.0185 (7)	0.0193 (6)	−0.0085 (5)	−0.0013 (5)	−0.0013 (5)
C13	0.0199 (7)	0.0224 (7)	0.0346 (8)	−0.0112 (6)	−0.0037 (6)	−0.0023 (6)
C14	0.0229 (7)	0.0206 (7)	0.0215 (7)	−0.0063 (6)	−0.0040 (5)	−0.0022 (5)
C15	0.0365 (10)	0.0179 (8)	0.0556 (12)	−0.0037 (7)	0.0026 (8)	0.0033 (7)
C16	0.0514 (13)	0.0256 (10)	0.0841 (18)	−0.0128 (9)	0.0099 (12)	−0.0018 (10)

Geometric parameters (Å, º) top

S1—C10	1.6906 (15)	C4—C5	1.392 (2)
O1—C14	1.336 (2)	C4—H4B	0.9500
O1—C15	1.4603 (19)	C5—C6	1.381 (2)
O2—C14	1.2106 (19)	C5—H5B	0.9500
N1—N2	1.3351 (18)	C7—C8	1.393 (2)
N1—C7	1.337 (2)	C7—H7A	0.9500
N2—N3	1.3332 (17)	C8—C9	1.5049 (19)
N2—C6	1.4270 (19)	C9—C11	1.5140 (19)
N3—C8	1.3351 (18)	C9—H9A	1.0000
N4—C10	1.3272 (19)	C11—C12	1.349 (2)
N4—C9	1.4658 (17)	C11—C14	1.481 (2)
N4—H4A	0.8800	C12—C13	1.4975 (19)
N5—C10	1.3551 (19)	C13—H13A	0.9800
N5—C12	1.3989 (18)	C13—H13B	0.9800
N5—H5A	0.8800	C13—H13C	0.9800
C1—C6	1.386 (2)	C15—C16	1.458 (3)
C1—C2	1.388 (2)	C15—H15A	0.9900
C1—H1B	0.9500	C15—H15B	0.9900
C2—C3	1.388 (3)	C16—H16A	0.9800
C2—H2A	0.9500	C16—H16B	0.9800
C3—C4	1.371 (3)	C16—H16C	0.9800
C3—H3B	0.9500

C14—O1—C15	115.45 (13)	N4—C9—C8	109.47 (12)
N2—N1—C7	103.47 (12)	N4—C9—C11	110.43 (11)
N3—N2—N1	115.25 (12)	C8—C9—C11	112.63 (12)
N3—N2—C6	121.51 (13)	N4—C9—H9A	108.1
N1—N2—C6	123.24 (13)	C8—C9—H9A	108.1
N2—N3—C8	103.71 (12)	C11—C9—H9A	108.1
C10—N4—C9	124.65 (12)	N4—C10—N5	116.91 (13)
C10—N4—H4A	117.7	N4—C10—S1	121.95 (11)
C9—N4—H4A	117.7	N5—C10—S1	121.11 (11)
C10—N5—C12	123.79 (12)	C12—C11—C14	127.96 (13)
C10—N5—H5A	118.1	C12—C11—C9	120.18 (13)
C12—N5—H5A	118.1	C14—C11—C9	111.86 (12)
C6—C1—C2	118.56 (18)	C11—C12—N5	119.08 (13)
C6—C1—H1B	120.7	C11—C12—C13	128.73 (13)
C2—C1—H1B	120.7	N5—C12—C13	112.15 (12)
C3—C2—C1	120.2 (2)	C12—C13—H13A	109.5
C3—C2—H2A	119.9	C12—C13—H13B	109.5
C1—C2—H2A	119.9	H13A—C13—H13B	109.5
C4—C3—C2	120.23 (17)	C12—C13—H13C	109.5
C4—C3—H3B	119.9	H13A—C13—H13C	109.5
C2—C3—H3B	119.9	H13B—C13—H13C	109.5
C3—C4—C5	120.62 (18)	O2—C14—O1	123.33 (14)
C3—C4—H4B	119.7	O2—C14—C11	121.53 (14)
C5—C4—H4B	119.7	O1—C14—C11	115.08 (13)
C6—C5—C4	118.49 (18)	C16—C15—O1	108.53 (16)
C6—C5—H5B	120.8	C16—C15—H15A	110.0
C4—C5—H5B	120.8	O1—C15—H15A	110.0
C5—C6—C1	121.85 (15)	C16—C15—H15B	110.0
C5—C6—N2	119.63 (15)	O1—C15—H15B	110.0
C1—C6—N2	118.51 (14)	H15A—C15—H15B	108.4
N1—C7—C8	108.86 (13)	C15—C16—H16A	109.5
N1—C7—H7A	125.6	C15—C16—H16B	109.5
C8—C7—H7A	125.6	H16A—C16—H16B	109.5
N3—C8—C7	108.71 (13)	C15—C16—H16C	109.5
N3—C8—C9	119.77 (13)	H16A—C16—H16C	109.5
C7—C8—C9	131.48 (13)	H16B—C16—H16C	109.5

C7—N1—N2—N3	−0.48 (17)	C7—C8—C9—N4	105.08 (17)
C7—N1—N2—C6	178.83 (13)	N3—C8—C9—C11	164.70 (13)
N1—N2—N3—C8	0.57 (16)	C7—C8—C9—C11	−18.2 (2)
C6—N2—N3—C8	−178.75 (12)	C9—N4—C10—N5	−14.8 (2)
C6—C1—C2—C3	−0.7 (3)	C9—N4—C10—S1	166.99 (11)
C1—C2—C3—C4	−0.4 (3)	C12—N5—C10—N4	−6.2 (2)
C2—C3—C4—C5	1.2 (3)	C12—N5—C10—S1	172.03 (11)
C3—C4—C5—C6	−0.8 (3)	N4—C9—C11—C12	−16.86 (19)
C4—C5—C6—C1	−0.3 (3)	C8—C9—C11—C12	105.88 (15)
C4—C5—C6—N2	179.47 (14)	N4—C9—C11—C14	163.74 (12)
C2—C1—C6—C5	1.1 (3)	C8—C9—C11—C14	−73.53 (15)
C2—C1—C6—N2	−178.70 (15)	C14—C11—C12—N5	179.19 (13)
N3—N2—C6—C5	−162.42 (14)	C9—C11—C12—N5	−0.1 (2)
N1—N2—C6—C5	18.3 (2)	C14—C11—C12—C13	−3.4 (3)
N3—N2—C6—C1	17.4 (2)	C9—C11—C12—C13	177.27 (14)
N1—N2—C6—C1	−161.88 (15)	C10—N5—C12—C11	13.4 (2)
N2—N1—C7—C8	0.18 (17)	C10—N5—C12—C13	−164.41 (14)
N2—N3—C8—C7	−0.41 (16)	C15—O1—C14—O2	0.4 (2)
N2—N3—C8—C9	177.30 (12)	C15—O1—C14—C11	−176.65 (14)
N1—C7—C8—N3	0.15 (18)	C12—C11—C14—O2	165.89 (16)
N1—C7—C8—C9	−177.20 (15)	C9—C11—C14—O2	−14.8 (2)
C10—N4—C9—C8	−99.22 (16)	C12—C11—C14—O1	−17.0 (2)
C10—N4—C9—C11	25.3 (2)	C9—C11—C14—O1	162.37 (13)
N3—C8—C9—N4	−72.04 (16)	C14—O1—C15—C16	177.85 (18)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···S1ⁱ	0.88	2.52	3.3469 (13)	158
N5—H5A···S1ⁱⁱ	0.88	2.52	3.3703 (13)	162

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₆H₁₇N₅O₂S
M_r	343.41
Crystal system, space group	Triclinic, P1
Temperature (K)	153
a, b, c (Å)	8.3998 (5), 9.4733 (5), 11.4989 (8)
α, β, γ (°)	76.516 (2), 87.552 (2), 68.564 (2)
V (Å³)	827.33 (9)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.22
Crystal size (mm)	0.65 × 0.56 × 0.48

Data collection
Diffractometer	Rigaku R-AXIS SPIDER
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.873, 0.904
No. of measured, independent and observed [I > 2σ(I)] reflections	8180, 3754, 3399
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.125, 1.03
No. of reflections	3754
No. of parameters	218
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.90, −0.39

Computer programs: RAPID-AUTO (Rigaku, 2004), RAPID-AUTO, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997), WinGX (Farrugia, 1999).

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