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ISSN: 2056-9890

4-Meth­­oxy-4-methyl-6-phenyl-1,3-diazinane-2-thione

aMangalore University, Department of Studies in Chemistry, Mangalagangotri 574 199, India, bUniversity of Mysore, Department of Studies in Chemistry, Manasagangotri, Mysore 570 006, India, and cNelson Mandela Metropolitan University, Summerstrand Campus, Department of Chemistry, University Way, Summerstrand, PO Box 77000, Port Elizabeth, 6031, South Africa
*Correspondence e-mail: richard.betz@webmail.co.za

(Received 13 October 2012; accepted 29 October 2012; online 3 November 2012)

In the title pyrimidine derivative, C12H16N2OS, the tetra­hydro­pyrimidine ring adopts an envelope conformation with the C atom of the methyl­ene –CH2– group as the flap. In the crystal, N—H⋯O and N—H⋯S hydrogen bonds connect mol­ecules into undulating sheets perpendicular to the a axis.

Related literature

For the pharmacological importance of pyrimidines, see: Selvam et al. (2012[Selvam, T. P., James, C. R., Dniandev, P. V. & Valzita, S. K. (2012). Res. Pharm. 2, 1-9.]); Gupta et al. (2010[Gupta, J. K., Chaudhary, A., Dudhe, R., Varuna, K., Sharma, P. K. & Verma, P. K. (2010). Int. J. Pharm. Sci. Res. 1, 34-49.]); Lagoja (2005[Lagoja, I. M. (2005). Chem. Biodivers. 2, 1-50.]). For the crystal structures of related compounds, see: Kant et al. (2012[Kant, R., Gupta, V. K., Kapoor, K., Samshuddin, S. & Narayana, B. (2012). Acta Cryst. E68, o2398.]); Fun et al. (2012[Fun, H.-K., Chia, T. S., Samshuddin, S., Narayana, B. & Sarojini, B. K. (2012). Acta Cryst. E68, o807-o808.]); Betz et al. (2012[Betz, R., Gerber, T., Hosten, E., Samshuddin, S., Narayana, B. & Sarojini, B. K. (2012). Acta Cryst. E68, o476-o477.]). For puckering analysis of six-membered rings, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]); Boeyens (1978[Boeyens, J. C. A. (1978). J. Cryst. Mol. Struct. 8, 317-320.]). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C12H16N2OS

  • Mr = 236.33

  • Monoclinic, P 21 /c

  • a = 10.1894 (3) Å

  • b = 14.6889 (4) Å

  • c = 9.2026 (2) Å

  • β = 111.719 (1)°

  • V = 1279.58 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.24 mm−1

  • T = 200 K

  • 0.47 × 0.41 × 0.33 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2008[Bruker (2008). SADABS. Bruker Inc., Madison, Wisconsin, USA.]) Tmin = 0.898, Tmax = 0.926

  • 12126 measured reflections

  • 3173 independent reflections

  • 2876 reflections with I > 2σ(I)

  • Rint = 0.011

Refinement
  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 0.089

  • S = 1.07

  • 3173 reflections

  • 155 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯S1i 0.862 (15) 2.503 (16) 3.3527 (9) 168.8 (12)
N2—H2⋯O1ii 0.841 (15) 2.076 (16) 2.8863 (12) 161.7 (13)
Symmetry codes: (i) -x+2, -y, -z; (ii) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2010[Bruker (2010). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2010[Bruker (2010). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (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 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Pyrimidine and its derivatives exhibit remarkable pharmacological activities including anticonvulsant, antiinflammatory, antibacterial, antifungal, antiviral and anticancer properties (Selvam et al., 2012; Gupta et al., 2010). They constitute important building blocks of natural biologically active compounds like nucleic acids, several vitamins, coenzymes, purines and some marine microorganisms (Lagoja, 2005). Pyrimidine and its derivatives form a component in a number of marketed drugs including flucytosine (antimycotic), floxuridine (antimetabolite), ambrisentan (endothelin receptor antagonist), fluorouracil (antimetabolite), pyrimethamine (antimalarial), piribedil (antiparkinsonian), minoxidil (antihypertensive), carmofur (antineoplastic), bosentan (endothelin receptor antagonist) and many more. The crystal structures of some pyrimidine derivatives such as 2-[3,5-bis(4-methoxyphenyl)-4,5- dihydro-1H-pyrazol-1-yl]-4,6-bis(4-methoxyphenyl)pyrimidine (Kant et al., 2012) and 2-[3,5-bis(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl]- 4,6-bis(4-fluorophenyl)pyrimidine (Fun et al., 2012) have been reported. In view of the pharmacological importance of pyrimidine derivatives and in continuation of our work on synthesis of pyrimidine derivatives (Betz et al., 2012), we have determined the crystal structure of the title compound, 4-methoxy-4-methyl-6-phenyl-1,3-diazinane-2-thione.

According to a puckering analysis (Cremer & Pople, 1975; Boeyens, 1978), the tetrahydropyrimidine ring adopts an 5E conformation with atom C4 as the flap (C(4)E). The aromatic substituent is found in a nearly perpendicular conformation with respect to the tetrahydropyrimidine ring with the least-squares planes defined by the intracyclic atoms of the phenyl group on the one hand and the five essentially planar atoms [C1/C2/C3/N1/N2] of the 1,3-diazacyclohexane ring on the other hand intersecting at an angle of 74.95 (7) ° (Fig. 1).

In the crystal, N–H···O and N–H···S hydrogen bonds connect molecules into undulating sheets perpendicular to the crystallographic a axis. In terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptor for these contacts is C11(6)R22(8) on the unary level. Metrical parameters as well as information about the symmetry of these contacts are summarized in Table 1. The shortest intercentroid distance between two aromatic systems is 4.9991 (9) Å (Fig. 2).

Related literature top

For the pharmacological importance of pyrimidines, see: Selvam et al. (2012); Gupta et al. (2010); Lagoja (2005). For the crystal structures of related compounds, see: Kant et al. (2012); Fun et al. (2012); Betz et al. (2012). For puckering analysis of six-membered rings, see: Cremer & Pople (1975); Boeyens (1978). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990); Bernstein et al. (1995).

Experimental top

To a mixture of benzylidene acetone (1.46 g, 0.01 mol) and thiourea (1.1 g, 0.015 mol) in methanol (20 ml), sodium methoxide solution (1 ml) was added and the batch was refluxed for 8 h. The precipitate formed was collected by filtration and dried, yield: 82%. The single crystal was grown from a DMF solution of the title compound by slow evaporation at room temperature.

Refinement top

Carbon-bound H atoms were placed in calculated positions (C—H 0.95 Å for aromatic carbon atoms, C—H 0.98Å for methyl groups, C—H 0.99 Å for the methylene group and C—H 1.00 Å for the methine group) and were included in the refinement in the riding model approximation, with U(H) set to 1.2Ueq(C). The H atoms of the methyl groups were allowed to rotate with a fixed angle around the C—C bond to best fit the experimental electron density (HFIX 137 in the SHELX program suite (Sheldrick, 2008), with U(H) set to 1.5Ueq(C). Both nitrogen-bound H atoms were located on a difference Fourier map and refined freely.

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with anisotropic displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. The hydrogen bond motif (dashed lines), viewed along [0 1 0]. Symmetry operators: (i) x, -y + 1/2, z + 1/2; (ii) x, -y + 1/2, z - 1/2; (iii) -x + 2, -y, -z.
4-Methoxy-4-methyl-6-phenyl-1,3-diazinane-2-thione top
Crystal data top
C12H16N2OSF(000) = 504
Mr = 236.33Dx = 1.227 Mg m3
Monoclinic, P21/cMelting point: 538 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 10.1894 (3) ÅCell parameters from 8597 reflections
b = 14.6889 (4) Åθ = 2.8–28.3°
c = 9.2026 (2) ŵ = 0.24 mm1
β = 111.719 (1)°T = 200 K
V = 1279.58 (6) Å3Block, yellow
Z = 40.47 × 0.41 × 0.33 mm
Data collection top
Bruker APEXII CCD
diffractometer
3173 independent reflections
Radiation source: fine-focus sealed tube2876 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.011
ϕ and ω scansθmax = 28.3°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 1313
Tmin = 0.898, Tmax = 0.926k = 1918
12126 measured reflectionsl = 1112
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)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.089H atoms treated by a mixture of independent and constrained refinement
S = 1.07 w = 1/[σ2(Fo2) + (0.045P)2 + 0.354P]
where P = (Fo2 + 2Fc2)/3
3173 reflections(Δ/σ)max < 0.001
155 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C12H16N2OSV = 1279.58 (6) Å3
Mr = 236.33Z = 4
Monoclinic, P21/cMo Kα radiation
a = 10.1894 (3) ŵ = 0.24 mm1
b = 14.6889 (4) ÅT = 200 K
c = 9.2026 (2) Å0.47 × 0.41 × 0.33 mm
β = 111.719 (1)°
Data collection top
Bruker APEXII CCD
diffractometer
3173 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
2876 reflections with I > 2σ(I)
Tmin = 0.898, Tmax = 0.926Rint = 0.011
12126 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.089H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.33 e Å3
3173 reflectionsΔρmin = 0.23 e Å3
155 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.93913 (3)0.10930 (2)0.17540 (4)0.03661 (10)
O10.83361 (8)0.14192 (5)0.27715 (9)0.03043 (18)
N10.84364 (9)0.06949 (6)0.04949 (10)0.02460 (18)
H10.9003 (15)0.0236 (10)0.0685 (16)0.035 (3)*
N20.75092 (9)0.19789 (6)0.09623 (11)0.02608 (18)
H20.7641 (14)0.2391 (10)0.1528 (17)0.034 (3)*
C10.66034 (10)0.21995 (7)0.00883 (11)0.02360 (19)
H1A0.71380.26070.08060.028*
C20.83890 (10)0.12684 (7)0.06586 (11)0.0237 (2)
C30.76328 (10)0.08187 (7)0.14971 (11)0.02301 (19)
C40.62693 (10)0.13127 (7)0.05627 (12)0.0250 (2)
H4A0.57350.14450.12440.030*
H4B0.56760.09210.03080.030*
C50.73786 (12)0.01063 (8)0.20866 (14)0.0331 (2)
H5A0.68470.04930.11950.050*
H5B0.68370.00290.27640.050*
H5C0.82880.03940.26810.050*
C70.97628 (15)0.12213 (10)0.37158 (17)0.0499 (4)
H7A1.03530.12820.30880.075*
H7B0.98290.05970.41140.075*
H7C1.00900.16480.45960.075*
C110.52944 (11)0.26970 (8)0.11439 (12)0.0284 (2)
C120.43381 (12)0.22891 (10)0.24745 (15)0.0396 (3)
H120.45030.16880.27470.048*
C130.31340 (14)0.27604 (13)0.34123 (19)0.0581 (4)
H130.24840.24790.43250.070*
C140.28830 (16)0.36287 (14)0.3024 (2)0.0655 (5)
H140.20530.39430.36560.079*
C150.3827 (2)0.40383 (13)0.1729 (2)0.0688 (5)
H150.36570.46410.14670.083*
C160.50400 (17)0.35781 (10)0.07860 (18)0.0479 (3)
H160.56960.38710.01080.057*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.04262 (18)0.03902 (18)0.03912 (17)0.01582 (12)0.02784 (14)0.01265 (11)
O10.0299 (4)0.0309 (4)0.0259 (4)0.0042 (3)0.0050 (3)0.0048 (3)
N10.0276 (4)0.0221 (4)0.0272 (4)0.0053 (3)0.0137 (3)0.0038 (3)
N20.0264 (4)0.0259 (4)0.0299 (4)0.0049 (3)0.0150 (3)0.0078 (3)
C10.0232 (4)0.0244 (4)0.0234 (4)0.0032 (4)0.0089 (4)0.0013 (3)
C20.0229 (4)0.0246 (5)0.0238 (5)0.0003 (3)0.0090 (4)0.0004 (3)
C30.0244 (4)0.0228 (4)0.0230 (4)0.0003 (3)0.0102 (4)0.0008 (3)
C40.0220 (4)0.0279 (5)0.0260 (5)0.0012 (4)0.0099 (4)0.0028 (4)
C50.0355 (5)0.0280 (5)0.0402 (6)0.0011 (4)0.0192 (5)0.0092 (4)
C70.0379 (7)0.0491 (8)0.0437 (7)0.0081 (6)0.0070 (6)0.0078 (6)
C110.0260 (5)0.0318 (5)0.0301 (5)0.0062 (4)0.0134 (4)0.0082 (4)
C120.0298 (5)0.0447 (7)0.0385 (6)0.0028 (5)0.0059 (5)0.0109 (5)
C130.0289 (6)0.0783 (11)0.0543 (8)0.0064 (7)0.0005 (6)0.0294 (8)
C140.0392 (7)0.0798 (12)0.0785 (12)0.0273 (8)0.0227 (8)0.0470 (10)
C150.0746 (12)0.0558 (10)0.0820 (12)0.0406 (9)0.0359 (10)0.0253 (9)
C160.0579 (8)0.0387 (7)0.0479 (7)0.0200 (6)0.0205 (7)0.0063 (6)
Geometric parameters (Å, º) top
S1—C21.6994 (10)C5—H5B0.9800
O1—C71.4206 (14)C5—H5C0.9800
O1—C31.4301 (12)C7—H7A0.9800
N1—C21.3420 (13)C7—H7B0.9800
N1—C31.4536 (12)C7—H7C0.9800
N1—H10.862 (15)C11—C161.3835 (17)
N2—C21.3362 (13)C11—C121.3873 (17)
N2—C11.4674 (12)C12—C131.3949 (18)
N2—H20.841 (15)C12—H120.9500
C1—C111.5159 (13)C13—C141.374 (3)
C1—C41.5241 (14)C13—H130.9500
C1—H1A1.0000C14—C151.364 (3)
C3—C51.5203 (14)C14—H140.9500
C3—C41.5206 (13)C15—C161.394 (2)
C4—H4A0.9900C15—H150.9500
C4—H4B0.9900C16—H160.9500
C5—H5A0.9800
C7—O1—C3117.66 (9)C3—C5—H5B109.5
C2—N1—C3124.02 (8)H5A—C5—H5B109.5
C2—N1—H1118.5 (9)C3—C5—H5C109.5
C3—N1—H1117.4 (9)H5A—C5—H5C109.5
C2—N2—C1124.55 (8)H5B—C5—H5C109.5
C2—N2—H2116.4 (10)O1—C7—H7A109.5
C1—N2—H2117.2 (10)O1—C7—H7B109.5
N2—C1—C11109.75 (8)H7A—C7—H7B109.5
N2—C1—C4107.70 (8)O1—C7—H7C109.5
C11—C1—C4113.10 (8)H7A—C7—H7C109.5
N2—C1—H1A108.7H7B—C7—H7C109.5
C11—C1—H1A108.7C16—C11—C12118.81 (11)
C4—C1—H1A108.7C16—C11—C1119.76 (11)
N2—C2—N1118.74 (9)C12—C11—C1121.43 (10)
N2—C2—S1119.89 (8)C11—C12—C13120.09 (14)
N1—C2—S1121.36 (8)C11—C12—H12120.0
O1—C3—N1111.63 (8)C13—C12—H12120.0
O1—C3—C5111.01 (8)C14—C13—C12120.37 (16)
N1—C3—C5108.97 (8)C14—C13—H13119.8
O1—C3—C4104.19 (8)C12—C13—H13119.8
N1—C3—C4108.19 (8)C15—C14—C13119.86 (13)
C5—C3—C4112.80 (8)C15—C14—H14120.1
C3—C4—C1109.87 (8)C13—C14—H14120.1
C3—C4—H4A109.7C14—C15—C16120.42 (16)
C1—C4—H4A109.7C14—C15—H15119.8
C3—C4—H4B109.7C16—C15—H15119.8
C1—C4—H4B109.7C11—C16—C15120.43 (15)
H4A—C4—H4B108.2C11—C16—H16119.8
C3—C5—H5A109.5C15—C16—H16119.8
C2—N2—C1—C11151.62 (10)N2—C1—C4—C353.96 (10)
C2—N2—C1—C428.10 (13)C11—C1—C4—C3175.41 (8)
C1—N2—C2—N11.84 (15)N2—C1—C11—C16117.76 (12)
C1—N2—C2—S1179.57 (8)C4—C1—C11—C16121.95 (12)
C3—N1—C2—N22.99 (15)N2—C1—C11—C1262.03 (13)
C3—N1—C2—S1178.44 (7)C4—C1—C11—C1258.26 (13)
C7—O1—C3—N152.81 (13)C16—C11—C12—C130.99 (18)
C7—O1—C3—C568.98 (13)C1—C11—C12—C13179.21 (11)
C7—O1—C3—C4169.33 (11)C11—C12—C13—C140.3 (2)
C2—N1—C3—O183.72 (11)C12—C13—C14—C151.1 (2)
C2—N1—C3—C5153.33 (10)C13—C14—C15—C160.7 (3)
C2—N1—C3—C430.35 (13)C12—C11—C16—C151.4 (2)
O1—C3—C4—C163.61 (10)C1—C11—C16—C15178.77 (14)
N1—C3—C4—C155.28 (10)C14—C15—C16—C110.6 (3)
C5—C3—C4—C1175.90 (8)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···S1i0.862 (15)2.503 (16)3.3527 (9)168.8 (12)
N2—H2···O1ii0.841 (15)2.076 (16)2.8863 (12)161.7 (13)
Symmetry codes: (i) x+2, y, z; (ii) x, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC12H16N2OS
Mr236.33
Crystal system, space groupMonoclinic, P21/c
Temperature (K)200
a, b, c (Å)10.1894 (3), 14.6889 (4), 9.2026 (2)
β (°) 111.719 (1)
V3)1279.58 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.24
Crystal size (mm)0.47 × 0.41 × 0.33
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2008)
Tmin, Tmax0.898, 0.926
No. of measured, independent and
observed [I > 2σ(I)] reflections
12126, 3173, 2876
Rint0.011
(sin θ/λ)max1)0.667
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.089, 1.07
No. of reflections3173
No. of parameters155
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.33, 0.23

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SAINT (Bruker, 2010, SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···S1i0.862 (15)2.503 (16)3.3527 (9)168.8 (12)
N2—H2···O1ii0.841 (15)2.076 (16)2.8863 (12)161.7 (13)
Symmetry codes: (i) x+2, y, z; (ii) x, y+1/2, z1/2.
 

Acknowledgements

BN thanks the UGC for financial assistance through a BSR one-time grant for the purchase of chemicals. HSY thanks Mysore University for the research facilities.

References

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