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

Suresh, M.; Padusha, M.S.A.; Novina, J.J.; Vasuki, G.; Viswanathan, V.; Velmurugan, D.

doi:10.1107/S2056989014027741

organic compounds

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Volume 71| Part 2| February 2015| Pages o81-o82

doi:10.1107/S2056989014027741

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

M. Suresh,^a M. Syed Ali Padusha,^a J. Josephine Novina,^b G. Vasuki,^c ^* Vijayan Viswanathan ^d and Devadasan Velmurugan ^d

^aPG & Research Department of Chemistry, Jamal Mohamed College (Autonomous), Tiruchirappalli-20, India, ^bDepartment of Physics, Idhaya College for Women, Kumbakonam-1, India, ^cDepartment of Physics, Kunthavai Naachiar Government Arts College (W) (Autonomous), Thanjavur-7, India, and ^dCentre of Advanced study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai-25, India
^*Correspondence e-mail: vasuki.arasi@yahoo.com

Edited by E. R. T. Tiekink, University of Malaya, Malaysia (Received 18 December 2014; accepted 19 December 2014; online 3 January 2015)

In the title compound, C₁₂H₁₄N₂O₂S₂, the dihydropyrimidine ring adopts a sofa conformation, with the C atom bearing the thienyl ring lying above the plane of the five remaining approximately coplanar (r.m.s. deviation = 0.0405 Å) atoms of the ring. The dihedral angle between the five near coplanar atoms of the ring and the thienyl ring is 89.78 (11)°. In the crystal, molecules are linked into a supramolecular chain along [100] via N—H⋯O(carbonyl) hydrogen bonds. Inversion-related chains are linked into double chains via N—H⋯S(thione) hydrogen bonds. The three-dimensional architecture also features methyl–thienyl C—H⋯π interactions.

Keywords: crystal structure; pyrimidine; hydrogen bonding; C—H⋯π interactions; conformation.

CCDC reference: 1040426

1. Related literature

For general background and the biological activity of dihydropyrimidinones, see: Phucho et al. (2009 ); Patil et al. (2011 ).

2. Experimental

2.1. Crystal data

C₁₂H₁₄N₂O₂S₂
M_r = 282.37
Triclinic, $[P \overline 1]$
a = 7.3069 (1) Å
b = 8.3267 (1) Å
c = 11.2461 (1) Å
α = 90.109 (1)°
β = 95.156 (1)°
γ = 101.276 (1)°
V = 668.18 (1) Å³
Z = 2
Mo Kα radiation
μ = 0.39 mm⁻¹
T = 293 K
0.20 × 0.15 × 0.10 mm

2.2. Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ) T_min = 0.925, T_max = 0.962
10188 measured reflections
2762 independent reflections
2325 reflections with I > 2σ(I)
R_int = 0.021

2.3. Refinement

R[F² > 2σ(F²)] = 0.060
wR(F²) = 0.189
S = 1.06
2762 reflections
165 parameters
H-atom parameters constrained
Δρ_max = 0.64 e Å⁻³
Δρ_min = −0.40 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the S1/C1–C4 thiophene ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N1⋯S2ⁱ	0.86	2.63	3.408 (2)	151
N2—H2N2⋯O1ⁱⁱ	0.86	2.15	2.984 (3)	162
C12—H12B⋯Cg1ⁱⁱⁱ	0.96	2.81	3.664 (6)	149
Symmetry codes: (i) -x+2, -y, -z+1; (ii) x+1, y, z; (iii) -x+1, -y+1, -z.

Data collection: APEX2 (Bruker, 2008); cell refinement: APEX2 and SAINT (Bruker, 2008); data reduction: SAINT and XPREP (Bruker, 2008); program(s) used to solve structure: SIR92 (Altomare et al., 1993 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ) and Mercury (Macrae et al., 2008 ); software used to prepare material for publication: PLATON (Spek, 2009 ).

Supporting information

CCDC reference: 1040426

Crystal structure: contains datablocks I, global. DOI: 10.1107/S2056989014027741/tk5352sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989014027741/tk5352Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989014027741/tk5352Isup3.cml

checkCIF report

Structural commentary top

Pyrimidinones or dihydropyrimidinones (DHPMs) are well known for their wide range of bioactivities and their applications in the field of drug research have stimulated the invention of a wide range of synthetic methods for their preparation and chemical transformations (Phucho et al., 2009). Several functionalized dihydropyrimidinones are used as calcium channel modulators, Ca-antagonists, vasodilative and anti-hypertensive agents (Patil et al., 2011). Against this background and in order to obtain detailed information on its molecular conformation, the structure of the title compound has been determined and the results are presented herein.

The asymmetric unit of the title compound is illustrated in Fig. 1. The dihydropyrimidine ring adopts a sofa conformation, with puckering parameters q2 = 0.283 Å, q3 = -0.102 Å, Q = 0.301 Å, Θ = 109.8° and Φ = 232.1°. The dihedral angle between the mean plane of the five essentially planar atoms (N1/C9/N2/C7/C6) of the dihydropyrimidine ring [maximum deviation 0.1944 (18) Å for C5] and the thiophene ring (C1—C4/S1) is 89.78 (11)°.

In the crystal, the molecules are linked via a pair of N—H···S hydrogen bonds forming an inversion dimers with R²₂(8) ring motif and form a chain parallel to the bc plane via N—H···O hydrogen bonds (Fig. 2). Additional stabilization to the structure is afforded by C—H···π contacts (Table 1, Figs 3 and 4).

Synthesis and crystallization top

A mixture of ethyl acetoacetate (0.13 ml, 0.001 mol), thiophene-2-carboxaldehyde (0.1 ml, 0.001 mol) and thiourea (0.228 g, 0.003 mol) in ethanol (5 ml) was heated under reflux in the presence of cerium chloride heptahydrate (25%) for 1 h (monitored by TLC). After the completion of the reaction, the reaction mixture was cooled to room temperature and poured onto crushed ice and stirred for 5–10 min. The solid was separated and filtered under suction, washed with ice-cold water (50 ml), and then recrystallized from hot ethanol to afford pure product [m.pt: 421 K; yield: 98%].

Refinement top

H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with C—H distances fixed in the range 0.93–0.98 Å and N—H = 0.86 Å with U_iso(H) = 1.5U_eq(CH₃) and 1.2U_eq(CH₂,CH, NH).

Related literature top

For general background and the biological activity of dihydropyrimidinones, see: Phucho et al. (2009); Patil et al. (2011).

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: APEX2 and SAINT (Bruker, 2008); data reduction: SAINT and XPREP (Bruker, 2008); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound, with the atom labelling. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Partial crystal packing of the title compound, showing the R²₂(8) ring motif, viewed along the b axis. Hydrogen bonds are shown as dashed lines.
	Fig. 3. Part of the crystal packing of the title compound, showing C—H···π interactions. Viewed along the a axis.
	Fig. 4. Image showing the C—H···π interactions.

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

Crystal data top

C₁₂H₁₄N₂O₂S₂	Z = 2
M_r = 282.37	F(000) = 296
Triclinic, P1	D_x = 1.403 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.3069 (1) Å	Cell parameters from 2762 reflections
b = 8.3267 (1) Å	θ = 1.8–26.5°
c = 11.2461 (1) Å	µ = 0.39 mm⁻¹
α = 90.109 (1)°	T = 293 K
β = 95.156 (1)°	Block, colourless
γ = 101.276 (1)°	0.20 × 0.15 × 0.10 mm
V = 668.18 (1) Å³

Data collection top

Bruker APEXII CCD diffractometer	2762 independent reflections
Radiation source: fine-focus sealed tube	2325 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.021
ω and ϕ scan	θ_max = 26.5°, θ_min = 1.8°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −9→9
T_min = 0.925, T_max = 0.962	k = −10→10
10188 measured reflections	l = −14→14

Refinement top

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)] = 0.060	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.189	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.1181P)² + 0.5067P] where P = (F_o² + 2F_c²)/3
2762 reflections	(Δ/σ)_max < 0.001
165 parameters	Δρ_max = 0.64 e Å⁻³
0 restraints	Δρ_min = −0.40 e Å⁻³

Crystal data top

C₁₂H₁₄N₂O₂S₂	γ = 101.276 (1)°
M_r = 282.37	V = 668.18 (1) Å³
Triclinic, P1	Z = 2
a = 7.3069 (1) Å	Mo Kα radiation
b = 8.3267 (1) Å	µ = 0.39 mm⁻¹
c = 11.2461 (1) Å	T = 293 K
α = 90.109 (1)°	0.20 × 0.15 × 0.10 mm
β = 95.156 (1)°

Data collection top

Bruker APEXII CCD diffractometer	2762 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2008)	2325 reflections with I > 2σ(I)
T_min = 0.925, T_max = 0.962	R_int = 0.021
10188 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.060	0 restraints
wR(F²) = 0.189	H-atom parameters constrained
S = 1.06	Δρ_max = 0.64 e Å⁻³
2762 reflections	Δρ_min = −0.40 e Å⁻³
165 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

	x	y	z	U_iso*/U_eq
C1	0.8629 (5)	0.6238 (4)	0.4026 (3)	0.0584 (9)
H1	0.9131	0.7349	0.4141	0.070*
C2	0.7502 (5)	0.5376 (4)	0.4750 (3)	0.0534 (8)
H2	0.7143	0.5833	0.5425	0.064*
C3	0.6877 (4)	0.3688 (3)	0.4414 (2)	0.0341 (5)
H3	0.6069	0.2922	0.4819	0.041*
C4	0.7703 (3)	0.3372 (3)	0.3350 (2)	0.0338 (5)
C5	0.7577 (3)	0.1734 (3)	0.2747 (2)	0.0336 (6)
H5	0.6314	0.1088	0.2803	0.040*
C9	1.0680 (4)	0.0949 (3)	0.3047 (2)	0.0335 (5)
C7	0.9646 (4)	0.1925 (4)	0.1110 (2)	0.0384 (6)
C8	1.0343 (5)	0.2269 (5)	−0.0103 (3)	0.0581 (9)
H8A	0.9320	0.1960	−0.0709	0.087*
H8B	1.1295	0.1651	−0.0216	0.087*
H8C	1.0856	0.3417	−0.0157	0.087*
C6	0.7909 (4)	0.1904 (4)	0.1437 (2)	0.0371 (6)
C10	0.6280 (4)	0.2135 (4)	0.0657 (2)	0.0439 (7)
C11	0.5131 (5)	0.2937 (7)	−0.1262 (3)	0.0817 (14)
H11A	0.4303	0.1894	−0.1465	0.098*
H11B	0.4413	0.3655	−0.0918	0.098*
C12	0.5900 (7)	0.3646 (9)	−0.2304 (4)	0.115 (2)
H12A	0.6581	0.4738	−0.2117	0.172*
H12B	0.4906	0.3682	−0.2916	0.172*
H12C	0.6732	0.2996	−0.2582	0.172*
N1	0.8939 (3)	0.0838 (3)	0.33419 (19)	0.0359 (5)
H1N1	0.8586	0.0204	0.3916	0.043*
N2	1.1028 (3)	0.1610 (3)	0.1964 (2)	0.0402 (5)
H2N2	1.2174	0.1848	0.1796	0.048*
O1	0.4710 (3)	0.1889 (4)	0.0948 (2)	0.0673 (8)
O2	0.6667 (3)	0.2699 (4)	−0.0409 (2)	0.0718 (9)
S1	0.90646 (12)	0.51126 (11)	0.28681 (8)	0.0557 (3)
S2	1.23669 (10)	0.02700 (10)	0.38956 (6)	0.0442 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0543 (19)	0.0410 (17)	0.077 (2)	0.0109 (14)	−0.0128 (17)	0.0012 (16)
C2	0.0529 (19)	0.059 (2)	0.0520 (17)	0.0243 (15)	−0.0017 (14)	−0.0055 (15)
C3	0.0345 (13)	0.0374 (13)	0.0329 (12)	0.0136 (10)	0.0015 (10)	0.0007 (10)
C4	0.0287 (12)	0.0411 (14)	0.0324 (12)	0.0089 (10)	0.0026 (9)	0.0086 (10)
C5	0.0271 (12)	0.0441 (14)	0.0303 (12)	0.0075 (10)	0.0045 (9)	0.0077 (10)
C9	0.0328 (13)	0.0345 (13)	0.0340 (12)	0.0074 (10)	0.0051 (10)	0.0073 (10)
C7	0.0320 (13)	0.0538 (16)	0.0308 (12)	0.0105 (11)	0.0058 (10)	0.0089 (11)
C8	0.0421 (16)	0.101 (3)	0.0375 (15)	0.0257 (17)	0.0135 (12)	0.0224 (16)
C6	0.0310 (13)	0.0497 (16)	0.0311 (13)	0.0083 (11)	0.0044 (10)	0.0047 (11)
C10	0.0327 (14)	0.0662 (19)	0.0343 (13)	0.0121 (12)	0.0058 (11)	0.0096 (12)
C11	0.0403 (18)	0.156 (5)	0.0490 (19)	0.023 (2)	−0.0035 (15)	0.034 (2)
C12	0.061 (3)	0.214 (7)	0.077 (3)	0.041 (3)	0.010 (2)	0.066 (4)
N1	0.0350 (11)	0.0430 (12)	0.0333 (11)	0.0128 (9)	0.0101 (9)	0.0120 (9)
N2	0.0272 (11)	0.0596 (15)	0.0360 (11)	0.0117 (10)	0.0077 (9)	0.0138 (10)
O1	0.0319 (11)	0.126 (2)	0.0474 (12)	0.0213 (13)	0.0070 (9)	0.0226 (14)
O2	0.0369 (12)	0.138 (3)	0.0425 (12)	0.0217 (14)	0.0055 (9)	0.0377 (14)
S1	0.0519 (5)	0.0531 (5)	0.0613 (5)	0.0053 (4)	0.0108 (4)	0.0143 (4)
S2	0.0372 (4)	0.0567 (5)	0.0429 (4)	0.0181 (3)	0.0060 (3)	0.0170 (3)

Geometric parameters (Å, º) top

C1—C2	1.322 (5)	C7—C8	1.508 (4)
C1—S1	1.691 (4)	C8—H8A	0.9600
C1—H1	0.9300	C8—H8B	0.9600
C2—C3	1.429 (4)	C8—H8C	0.9600
C2—H2	0.9300	C6—C10	1.458 (4)
C3—C4	1.434 (3)	C10—O1	1.200 (3)
C3—H3	0.9300	C10—O2	1.323 (3)
C4—C5	1.505 (4)	C11—C12	1.425 (6)
C4—S1	1.709 (3)	C11—O2	1.454 (4)
C5—N1	1.472 (3)	C11—H11A	0.9700
C5—C6	1.516 (3)	C11—H11B	0.9700
C5—H5	0.9800	C12—H12A	0.9600
C9—N1	1.329 (3)	C12—H12B	0.9600
C9—N2	1.363 (3)	C12—H12C	0.9600
C9—S2	1.677 (3)	N1—H1N1	0.8600
C7—C6	1.350 (4)	N2—H2N2	0.8600
C7—N2	1.393 (3)

C2—C1—S1	113.1 (3)	H8A—C8—H8C	109.5
C2—C1—H1	123.5	H8B—C8—H8C	109.5
S1—C1—H1	123.5	C7—C6—C10	126.4 (2)
C1—C2—C3	114.9 (3)	C7—C6—C5	119.0 (2)
C1—C2—H2	122.6	C10—C6—C5	114.5 (2)
C3—C2—H2	122.6	O1—C10—O2	121.5 (3)
C2—C3—C4	108.7 (3)	O1—C10—C6	124.0 (3)
C2—C3—H3	125.7	O2—C10—C6	114.5 (2)
C4—C3—H3	125.7	C12—C11—O2	108.3 (3)
C3—C4—C5	126.9 (2)	C12—C11—H11A	110.0
C3—C4—S1	111.2 (2)	O2—C11—H11A	110.0
C5—C4—S1	121.73 (19)	C12—C11—H11B	110.0
N1—C5—C4	110.9 (2)	O2—C11—H11B	110.0
N1—C5—C6	109.0 (2)	H11A—C11—H11B	108.4
C4—C5—C6	111.9 (2)	C11—C12—H12A	109.5
N1—C5—H5	108.3	C11—C12—H12B	109.5
C4—C5—H5	108.3	H12A—C12—H12B	109.5
C6—C5—H5	108.3	C11—C12—H12C	109.5
N1—C9—N2	115.7 (2)	H12A—C12—H12C	109.5
N1—C9—S2	123.97 (19)	H12B—C12—H12C	109.5
N2—C9—S2	120.33 (19)	C9—N1—C5	124.1 (2)
C6—C7—N2	119.0 (2)	C9—N1—H1N1	118.0
C6—C7—C8	128.0 (2)	C5—N1—H1N1	118.0
N2—C7—C8	113.1 (2)	C9—N2—C7	124.1 (2)
C7—C8—H8A	109.5	C9—N2—H2N2	117.9
C7—C8—H8B	109.5	C7—N2—H2N2	117.9
H8A—C8—H8B	109.5	C10—O2—C11	118.6 (2)
C7—C8—H8C	109.5	C1—S1—C4	92.16 (16)

S1—C1—C2—C3	−0.2 (4)	C5—C6—C10—O1	−14.5 (5)
C1—C2—C3—C4	1.0 (4)	C7—C6—C10—O2	−12.6 (5)
C2—C3—C4—C5	174.0 (2)	C5—C6—C10—O2	163.4 (3)
C2—C3—C4—S1	−1.3 (3)	N2—C9—N1—C5	−16.3 (4)
C3—C4—C5—N1	−81.0 (3)	S2—C9—N1—C5	166.1 (2)
S1—C4—C5—N1	93.8 (2)	C4—C5—N1—C9	−89.9 (3)
C3—C4—C5—C6	157.1 (2)	C6—C5—N1—C9	33.7 (3)
S1—C4—C5—C6	−28.1 (3)	N1—C9—N2—C7	−10.0 (4)
N2—C7—C6—C10	−177.2 (3)	S2—C9—N2—C7	167.7 (2)
C8—C7—C6—C10	3.3 (5)	C6—C7—N2—C9	14.3 (4)
N2—C7—C6—C5	7.0 (4)	C8—C7—N2—C9	−166.2 (3)
C8—C7—C6—C5	−172.5 (3)	O1—C10—O2—C11	−3.4 (6)
N1—C5—C6—C7	−27.6 (4)	C6—C10—O2—C11	178.7 (4)
C4—C5—C6—C7	95.4 (3)	C12—C11—O2—C10	176.3 (5)
N1—C5—C6—C10	156.1 (2)	C2—C1—S1—C4	−0.5 (3)
C4—C5—C6—C10	−80.9 (3)	C3—C4—S1—C1	1.1 (2)
C7—C6—C10—O1	169.5 (3)	C5—C4—S1—C1	−174.5 (2)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of the S1/C1–C4 thiophene ring.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···S2ⁱ	0.86	2.63	3.408 (2)	151
N2—H2N2···O1ⁱⁱ	0.86	2.15	2.984 (3)	162
C12—H12B···Cg1ⁱⁱⁱ	0.96	2.81	3.664 (6)	149

Symmetry codes: (i) −x+2, −y, −z+1; (ii) x+1, y, z; (iii) −x+1, −y+1, −z.

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of the S1/C1–C4 thiophene ring.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···S2ⁱ	0.86	2.63	3.408 (2)	151
N2—H2N2···O1ⁱⁱ	0.86	2.15	2.984 (3)	162
C12—H12B···Cg1ⁱⁱⁱ	0.96	2.81	3.664 (6)	149

Symmetry codes: (i) −x+2, −y, −z+1; (ii) x+1, y, z; (iii) −x+1, −y+1, −z.

Acknowledgements

The authors thank the TBI X-ray facility, CAS in Crystallography and Biophysics, University of Madras, India, for the data collection.

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Volume 71| Part 2| February 2015| Pages o81-o82

doi:10.1107/S2056989014027741

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

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