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

Aliyeva, K.N.; Maharramov, A.M.; Allahverdiyev, M.A.; Gurbanov, A.V.; Brito, I.

doi:10.1107/S160053681103145X

organic compounds

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Volume 67| Part 9| September 2011| Page o2293

doi:10.1107/S160053681103145X

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

Khatira N. Aliyeva,^a Abel M. Maharramov,^a Mirze A. Allahverdiyev,^a Atash V. Gurbanov ^a and Iván Brito ^b ^*

^aDepartment of Organic Chemistry, Baku State University, Baku, Azerbaijan, and ^bDepartamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
^*Correspondence e-mail: ivanbritob@yahoo.com

(Received 2 August 2011; accepted 3 August 2011; online 11 August 2011)

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, $[P \overline 1]$
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) Å³
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[F² > 2σ(F²)] = 0.029
wR(F²) = 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

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) -x, -y+2, -z+1; (ii) -x+1, -y+2, -z+1; (iii) -x, -y+2, -z+2.

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.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053681103145X/bt5602sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S160053681103145X/bt5602Isup2.hkl

Supporting information file. DOI: 10.1107/S160053681103145X/bt5602Isup3.cml

checkCIF report

Comment top

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.

Related literature top

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 top

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

Computing details top

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

Figures top

	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.

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

Crystal data top

C₆H₁₂N₂O₂S	Z = 2
M_r = 176.24	F(000) = 188
Triclinic, P1	D_x = 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 top

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

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)] = 0.029	Hydrogen site location: difference Fourier map
wR(F²) = 0.080	H-atom parameters constrained
S = 1.00	w = 1/[σ²(F_o²) + (0.0543P)² + 0.0583P] where P = (F_o² + 2F_c²)/3
1760 reflections	(Δ/σ)_max = 0.001
102 parameters	Δρ_max = 0.36 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₆H₁₂N₂O₂S	γ = 79.708 (1)°
M_r = 176.24	V = 408.80 (5) Å³
Triclinic, P1	Z = 2
a = 5.2425 (4) Å	Mo Kα radiation
b = 8.7047 (6) Å	µ = 0.35 mm⁻¹
c = 9.4370 (7) Å	T = 296 K
α = 74.812 (1)°	0.30 × 0.20 × 0.20 mm
β = 88.670 (1)°

Data collection top

Bruker APEXII CCD diffractometer	1760 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	1557 reflections with I > 2σ(I)
T_min = 0.903, T_max = 0.934	R_int = 0.012
4260 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.029	0 restraints
wR(F²) = 0.080	H-atom parameters constrained
S = 1.00	Δρ_max = 0.36 e Å⁻³
1760 reflections	Δρ_min = −0.17 e Å⁻³
102 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
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 (Å²) top

	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, º) top

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, º) top

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.

Experimental details

Crystal data
Chemical formula	C₆H₁₂N₂O₂S
M_r	176.24
Crystal system, space group	Triclinic, P1
Temperature (K)	296
a, b, c (Å)	5.2425 (4), 8.7047 (6), 9.4370 (7)
α, β, γ (°)	74.812 (1), 88.670 (1), 79.708 (1)
V (Å³)	408.80 (5)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.35
Crystal size (mm)	0.30 × 0.20 × 0.20

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2003)
T_min, T_max	0.903, 0.934
No. of measured, independent and observed [I > 2σ(I)] reflections	4260, 1760, 1557
R_int	0.012
(sin θ/λ)_max (Å⁻¹)	0.639

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.080, 1.00
No. of reflections	1760
No. of parameters	102
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.36, −0.17

Computer programs: APEX2 (Bruker, 2005), SAINT-Plus (Bruker, 2001), SHELXTL (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).

Hydrogen-bond geometry (Å, º) top

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.

Acknowledgements

The authors are grateful to Baku State University for supporting this study. IB thanks the Spanish Research Council (CSIC) for the provision of a free-of-charge licence to the Cambridge Structural Database.

References

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