4,6-Dihy­droxy-4,6-dimethyl-1,3-diazinane-2-thione

Abstract

In the title compound, C₆H₁₂N₂O₂S, the heterocyclic ring has a sofa conformation. The mol­ecular conformation is stabilized by an intra­molecular O—H⋯O hydrogen-bond inter­action with graph-set motif S(6). In the crystal, mol­ecules are linked by O—H⋯S, N—H⋯S and N—H⋯O hydrogen-bond inter­actions, forming an extended two-dimensional framework parallel to the ac plane.

Related literature

For the preparation of pyrimidines by reactions of 1,3-dicarbonyl compounds (e.g. ethyl acetoacetate, acetyl­acetone) with urea, thio­urea, guanidine, see: Barton & Ollis (1979 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For ring conformations, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

• C₆H₁₂N₂O₂S

• M _r = 176.24

• Triclinic,

• a = 5.2425 (4) Å

• b = 8.7047 (6) Å

• c = 9.4370 (7) Å

• α = 74.812 (1)°

• β = 88.670 (1)°

• γ = 79.708 (1)°

• V = 408.80 (5) ų

• Z = 2

• Mo Kα radiation

• μ = 0.35 mm⁻¹

• T = 296 K

• 0.30 × 0.20 × 0.20 mm

Data collection

• Bruker APEXII CCD diffractometer

• Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ▶) T _min = 0.903, T _max = 0.934

• 4260 measured reflections

• 1760 independent reflections

• 1557 reflections with I > 2σ(I)

• R _int = 0.012

Refinement

• R[F ² > 2σ(F ²)] = 0.029

• wR(F ²) = 0.080

• S = 1.00

• 1760 reflections

• 102 parameters

• H-atom parameters constrained

• Δρ_max = 0.36 e Å⁻³

• Δρ_min = −0.17 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT-Plus (Bruker, 2001 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: OLEX2 (Dolomanov et al., 2009 ▶); software used to prepare material for publication: SHELXTL.

Supplementary Material

Supplementary material file. DOI: 10.1107/S160053681103145X/bt5602Isup3.cml

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1O⋯O2	0.88	1.98	2.727 (2)	143
O2—H2O⋯S1i	0.88	2.37	3.249 (1)	173
N1—H1N⋯S1ii	0.92	2.60	3.414 (1)	149
N2—H2N⋯O1iii	0.92	2.18	3.074 (2)	164

Symmetry codes: (i) ; (ii) ; (iii) .

supplementary crystallographic information

Comment

The biological activity of pyrimidine derivatives attracts great interest to their synthesis. Their derivatives play important part in the functions of the human body. Pyrimidine structural fragment is included into quite a number of natural substances (nucleic acids, vitamin B1), into synthetic medicinals (barbiturates), into chemotherapeutic preparations (fluorouracil). In preparation of pyrimidines are widely used reactions of 1,3-dicarbonyl compounds (e.g. ethyl acetoacetate, acetylacetone) with urea, thiourea, guanidine etc (Barton & Ollis, 1979). In the title compound (I), C₆H₁₂N₂O₂S, the heterocyclo ring has a sofa conformation, (Q_T= 0.459 (13) Å, θ= 127.52 (7)°, φ₂ = 59.54 (4)°, (Cremer & Pople, 1975). The molecular conformation is stabilized by one intramolecular O—H···O hydrogen-bond interaction with set graph motif S(6) (Bernstein, et al. 1995). In the crystal the molecules are linked by O—H···S, N—H···S, N—H···O hydrogen-bond interactions forming an extended two-dimensional framework parallel to ab plane, Table 1, Fig. 2.

Experimental

On the anhydrous ethanol (40 ml) added 18 gram (0.783 mol) small pieces of metallic sodium and wasvigorously stirred until sodium fully reacted with ethanol. Then on theobtained solution was added 10 gram (0.1 mol) of acetylacetone and 7.4 gram (0.1 mol) ofthiourea. Reaction mixture was stirred two hour in room temperature. Then 120 ml distilled water added on reaction mixture and neutralized with 5 ml ofglacial acetic acid. Precipitated unreacted part of thiourea was filtered ofand the obtained filtrate stayed in -10 °C. After two days obtained single crystals of 4,6-dihydroxy-4,6-dimethyltetrahydropyrimidine-2(1h)-thione was collected. Yield 6 gram (42%), m.p. 254–255 °C.

¹H NMR(300 MHz, DMSO-d6) δ 1.32 (s, 6H, 2CH₃), 1.71–2.05 (m, 2H,CH₂), 3.52 (s, 2H, 2OH), 6.16 (s, 1H, NH), 8.67 (s, 1H, NH). ¹³CNMR (75 MHz, DMSO-d6) δ 28.40,43.63, 78.98, 79.07, 175.23, 175.31

Refinement

All H-atoms were placed in calculated positions [C—H = 0.96 to 0.97 Å, U_iso(H) =1.2 to 1.5 U_eq(C), O—H = 0.88 Å, U_iso(H) =1.5 U_eq(O) and N—H = 0.92 Å, U_iso(H)=1.2 U_eq(N)] and were included in the refinement in the riding model approximation.

Figures

Fig. 1.

The structure of (I) showing the atom numbering scheme. The hydrogen bond is showing as dotted line. Displacement ellipsoids are drawn at 30% probability level.

Fig. 2.

Part of the crystal structure showing O—H···S; N—H···S & N—H···O hydrogen-bond interactions parallel to ab plane. The methyl groups and the H atoms on C3 atom have been omitted for clarity.

Crystal data

C6H12N2O2S	Z = 2
Mr = 176.24	F(000) = 188
Triclinic, P1	Dx = 1.432 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.2425 (4) Å	Cell parameters from 2799 reflections
b = 8.7047 (6) Å	θ = 2.2–28.4°
c = 9.4370 (7) Å	µ = 0.35 mm−1
α = 74.812 (1)°	T = 296 K
β = 88.670 (1)°	Needle, colourless
γ = 79.708 (1)°	0.30 × 0.20 × 0.20 mm
V = 408.80 (5) Å3

Data collection

Bruker APEXII CCD diffractometer	1760 independent reflections
Radiation source: fine-focus sealed tube	1557 reflections with I > 2σ(I)
graphite	Rint = 0.012
φ and ω scans	θmax = 27.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −6→6
Tmin = 0.903, Tmax = 0.934	k = −11→11
4260 measured reflections	l = −12→12

Refinement

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)] = 0.029	Hydrogen site location: difference Fourier map
wR(F2) = 0.080	H-atom parameters constrained
S = 1.00	w = 1/[σ2(Fo2) + (0.0543P)2 + 0.0583P] where P = (Fo2 + 2Fc2)/3
1760 reflections	(Δ/σ)max = 0.001
102 parameters	Δρmax = 0.36 e Å−3
0 restraints	Δρmin = −0.17 e Å−3

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 (Ų)

	x	y	z	Uiso*/Ueq
O1	−0.13693 (17)	0.81379 (12)	0.96252 (10)	0.0356 (2)
H1O	−0.2022	0.8234	0.8749	0.053*
O2	−0.14367 (17)	0.74017 (12)	0.69909 (10)	0.0366 (2)
H2O	−0.1954	0.7791	0.6065	0.055*
N1	0.2210 (2)	0.86785 (12)	0.64127 (11)	0.0280 (2)
H1N	0.2746	0.8901	0.5457	0.034*
N2	0.2262 (2)	0.92771 (12)	0.86480 (11)	0.0279 (2)
H2N	0.2349	1.0033	0.9160	0.033*
S1	0.35950 (7)	1.14664 (4)	0.63906 (3)	0.03452 (13)
C1	0.2615 (2)	0.96882 (14)	0.72002 (13)	0.0244 (2)
C2	0.1320 (2)	0.71395 (14)	0.70201 (13)	0.0273 (3)
C3	0.2177 (2)	0.65313 (14)	0.86236 (13)	0.0285 (3)
H3A	0.4050	0.6213	0.8688	0.034*
H3B	0.1433	0.5581	0.9075	0.034*
C4	0.1366 (2)	0.78007 (15)	0.94675 (13)	0.0269 (3)
C5	0.2428 (3)	0.59777 (17)	0.61166 (16)	0.0391 (3)
H5A	0.1869	0.6437	0.5109	0.059*
H5B	0.1827	0.4971	0.6486	0.059*
H5C	0.4287	0.5790	0.6183	0.059*
C6	0.2540 (3)	0.72820 (18)	1.10103 (14)	0.0365 (3)
H6A	0.1999	0.8124	1.1494	0.055*
H6B	0.4397	0.7081	1.0962	0.055*
H6C	0.1966	0.6312	1.1551	0.055*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0260 (4)	0.0510 (6)	0.0316 (5)	−0.0065 (4)	0.0043 (4)	−0.0147 (4)
O2	0.0294 (5)	0.0502 (6)	0.0331 (5)	−0.0117 (4)	−0.0005 (4)	−0.0128 (4)
N1	0.0366 (5)	0.0270 (5)	0.0231 (5)	−0.0107 (4)	0.0039 (4)	−0.0081 (4)
N2	0.0347 (5)	0.0276 (5)	0.0236 (5)	−0.0084 (4)	0.0025 (4)	−0.0091 (4)
S1	0.0502 (2)	0.02887 (19)	0.02849 (18)	−0.01687 (14)	0.00523 (14)	−0.00838 (13)
C1	0.0229 (5)	0.0250 (6)	0.0256 (6)	−0.0036 (4)	0.0006 (4)	−0.0076 (4)
C2	0.0294 (6)	0.0256 (6)	0.0296 (6)	−0.0077 (5)	0.0026 (5)	−0.0104 (5)
C3	0.0303 (6)	0.0249 (6)	0.0293 (6)	−0.0059 (5)	0.0021 (5)	−0.0048 (5)
C4	0.0252 (6)	0.0309 (6)	0.0242 (6)	−0.0048 (4)	0.0018 (4)	−0.0067 (5)
C5	0.0509 (8)	0.0324 (7)	0.0400 (7)	−0.0099 (6)	0.0072 (6)	−0.0188 (6)
C6	0.0388 (7)	0.0420 (7)	0.0256 (6)	−0.0044 (6)	−0.0037 (5)	−0.0050 (5)

Geometric parameters (Å, °)

O1—C4	1.4237 (14)	C2—C5	1.5185 (17)
O1—H1O	0.8800	C3—C4	1.5211 (17)
O2—C2	1.4223 (15)	C3—H3A	0.9700
O2—H2O	0.8800	C3—H3B	0.9700
N1—C1	1.3365 (15)	C4—C6	1.5166 (17)
N1—C2	1.4660 (15)	C5—H5A	0.9600
N1—H1N	0.9200	C5—H5B	0.9600
N2—C1	1.3359 (15)	C5—H5C	0.9600
N2—C4	1.4658 (15)	C6—H6A	0.9600
N2—H2N	0.9199	C6—H6B	0.9600
S1—C1	1.7001 (12)	C6—H6C	0.9600
C2—C3	1.5161 (17)
C4—O1—H1O	104.7	C4—C3—H3B	109.1
C2—O2—H2O	107.2	H3A—C3—H3B	107.9
C1—N1—C2	124.46 (10)	O1—C4—N2	109.54 (10)
C1—N1—H1N	117.0	O1—C4—C6	106.20 (10)
C2—N1—H1N	118.0	N2—C4—C6	109.09 (10)
C1—N2—C4	125.07 (10)	O1—C4—C3	112.36 (10)
C1—N2—H2N	118.2	N2—C4—C3	107.21 (9)
C4—N2—H2N	116.1	C6—C4—C3	112.39 (10)
N2—C1—N1	119.07 (11)	C2—C5—H5A	109.5
N2—C1—S1	119.89 (9)	C2—C5—H5B	109.5
N1—C1—S1	121.04 (9)	H5A—C5—H5B	109.5
O2—C2—N1	109.74 (10)	C2—C5—H5C	109.5
O2—C2—C3	106.53 (10)	H5A—C5—H5C	109.5
N1—C2—C3	107.89 (9)	H5B—C5—H5C	109.5
O2—C2—C5	111.08 (10)	C4—C6—H6A	109.5
N1—C2—C5	108.47 (10)	C4—C6—H6B	109.5
C3—C2—C5	113.05 (11)	H6A—C6—H6B	109.5
C2—C3—C4	112.40 (10)	C4—C6—H6C	109.5
C2—C3—H3A	109.1	H6A—C6—H6C	109.5
C4—C3—H3A	109.1	H6B—C6—H6C	109.5
C2—C3—H3B	109.1
C4—N2—C1—N1	−2.11 (17)	N1—C2—C3—C4	52.12 (13)
C4—N2—C1—S1	178.50 (8)	C5—C2—C3—C4	172.06 (10)
C2—N1—C1—N2	1.77 (18)	C1—N2—C4—O1	−94.88 (13)
C2—N1—C1—S1	−178.85 (9)	C1—N2—C4—C6	149.26 (11)
C1—N1—C2—O2	88.79 (13)	C1—N2—C4—C3	27.30 (15)
C1—N1—C2—C3	−26.90 (16)	C2—C3—C4—O1	68.34 (13)
C1—N1—C2—C5	−149.69 (12)	C2—C3—C4—N2	−52.07 (12)
O2—C2—C3—C4	−65.66 (12)	C2—C3—C4—C6	−171.94 (10)

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1O···O2	0.88	1.98	2.727 (2)	143
O2—H2O···S1i	0.88	2.37	3.249 (1)	173
N1—H1N···S1ii	0.92	2.60	3.414 (1)	149
N2—H2N···O1iii	0.92	2.18	3.074 (2)	164

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