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

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

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[Barton, D. & Ollis, W. D. (1979). Editors. Comprehensive Organic Chemistry. Oxford: Pergamon Press. Translated under the title Obshchayaorganicheskaya khimiya, 1961, Vol. 6. Khimiya: Moscow.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]). For ring conformations, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]).

[Scheme 1]

Experimental

Crystal data
  • C6H12N2O2S

  • Mr = 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[Sheldrick, G. M. (2003). SADABS University of Göttingen, Germany.]) Tmin = 0.903, Tmax = 0.934

  • 4260 measured reflections

  • 1760 independent reflections

  • 1557 reflections with I > 2σ(I)

  • Rint = 0.012

Refinement
  • R[F2 > 2σ(F2)] = 0.029

  • wR(F2) = 0.080

  • S = 1.00

  • 1760 reflections

  • 102 parameters

  • H-atom parameters constrained

  • Δρmax = 0.36 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Bruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 2001[Bruker (2001). SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]); software used to prepare material for publication: SHELXTL.

Supporting information


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, (QT= 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

Refinement top

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

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
[Figure 1] 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.
[Figure 2] 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
C6H12N2O2SZ = 2
Mr = 176.24F(000) = 188
Triclinic, P1Dx = 1.432 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.2425 (4) ÅCell parameters from 2799 reflections
b = 8.7047 (6) Åθ = 2.2–28.4°
c = 9.4370 (7) ŵ = 0.35 mm1
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 tube1557 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.012
ϕ and ω scansθmax = 27.0°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 66
Tmin = 0.903, Tmax = 0.934k = 1111
4260 measured reflectionsl = 1212
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)] = 0.029Hydrogen site location: difference Fourier map
wR(F2) = 0.080H-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 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
C6H12N2O2Sγ = 79.708 (1)°
Mr = 176.24V = 408.80 (5) Å3
Triclinic, P1Z = 2
a = 5.2425 (4) ÅMo Kα radiation
b = 8.7047 (6) ŵ = 0.35 mm1
c = 9.4370 (7) ÅT = 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)
Tmin = 0.903, Tmax = 0.934Rint = 0.012
4260 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0290 restraints
wR(F2) = 0.080H-atom parameters constrained
S = 1.00Δρmax = 0.36 e Å3
1760 reflectionsΔρmin = 0.17 e Å3
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
xyzUiso*/Ueq
O10.13693 (17)0.81379 (12)0.96252 (10)0.0356 (2)
H1O0.20220.82340.87490.053*
O20.14367 (17)0.74017 (12)0.69909 (10)0.0366 (2)
H2O0.19540.77910.60650.055*
N10.2210 (2)0.86785 (12)0.64127 (11)0.0280 (2)
H1N0.27460.89010.54570.034*
N20.2262 (2)0.92771 (12)0.86480 (11)0.0279 (2)
H2N0.23491.00330.91600.033*
S10.35950 (7)1.14664 (4)0.63906 (3)0.03452 (13)
C10.2615 (2)0.96882 (14)0.72002 (13)0.0244 (2)
C20.1320 (2)0.71395 (14)0.70201 (13)0.0273 (3)
C30.2177 (2)0.65313 (14)0.86236 (13)0.0285 (3)
H3A0.40500.62130.86880.034*
H3B0.14330.55810.90750.034*
C40.1366 (2)0.78007 (15)0.94675 (13)0.0269 (3)
C50.2428 (3)0.59777 (17)0.61166 (16)0.0391 (3)
H5A0.18690.64370.51090.059*
H5B0.18270.49710.64860.059*
H5C0.42870.57900.61830.059*
C60.2540 (3)0.72820 (18)1.10103 (14)0.0365 (3)
H6A0.19990.81241.14940.055*
H6B0.43970.70811.09620.055*
H6C0.19660.63121.15510.055*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0260 (4)0.0510 (6)0.0316 (5)0.0065 (4)0.0043 (4)0.0147 (4)
O20.0294 (5)0.0502 (6)0.0331 (5)0.0117 (4)0.0005 (4)0.0128 (4)
N10.0366 (5)0.0270 (5)0.0231 (5)0.0107 (4)0.0039 (4)0.0081 (4)
N20.0347 (5)0.0276 (5)0.0236 (5)0.0084 (4)0.0025 (4)0.0091 (4)
S10.0502 (2)0.02887 (19)0.02849 (18)0.01687 (14)0.00523 (14)0.00838 (13)
C10.0229 (5)0.0250 (6)0.0256 (6)0.0036 (4)0.0006 (4)0.0076 (4)
C20.0294 (6)0.0256 (6)0.0296 (6)0.0077 (5)0.0026 (5)0.0104 (5)
C30.0303 (6)0.0249 (6)0.0293 (6)0.0059 (5)0.0021 (5)0.0048 (5)
C40.0252 (6)0.0309 (6)0.0242 (6)0.0048 (4)0.0018 (4)0.0067 (5)
C50.0509 (8)0.0324 (7)0.0400 (7)0.0099 (6)0.0072 (6)0.0188 (6)
C60.0388 (7)0.0420 (7)0.0256 (6)0.0044 (6)0.0037 (5)0.0050 (5)
Geometric parameters (Å, º) top
O1—C41.4237 (14)C2—C51.5185 (17)
O1—H1O0.8800C3—C41.5211 (17)
O2—C21.4223 (15)C3—H3A0.9700
O2—H2O0.8800C3—H3B0.9700
N1—C11.3365 (15)C4—C61.5166 (17)
N1—C21.4660 (15)C5—H5A0.9600
N1—H1N0.9200C5—H5B0.9600
N2—C11.3359 (15)C5—H5C0.9600
N2—C41.4658 (15)C6—H6A0.9600
N2—H2N0.9199C6—H6B0.9600
S1—C11.7001 (12)C6—H6C0.9600
C2—C31.5161 (17)
C4—O1—H1O104.7C4—C3—H3B109.1
C2—O2—H2O107.2H3A—C3—H3B107.9
C1—N1—C2124.46 (10)O1—C4—N2109.54 (10)
C1—N1—H1N117.0O1—C4—C6106.20 (10)
C2—N1—H1N118.0N2—C4—C6109.09 (10)
C1—N2—C4125.07 (10)O1—C4—C3112.36 (10)
C1—N2—H2N118.2N2—C4—C3107.21 (9)
C4—N2—H2N116.1C6—C4—C3112.39 (10)
N2—C1—N1119.07 (11)C2—C5—H5A109.5
N2—C1—S1119.89 (9)C2—C5—H5B109.5
N1—C1—S1121.04 (9)H5A—C5—H5B109.5
O2—C2—N1109.74 (10)C2—C5—H5C109.5
O2—C2—C3106.53 (10)H5A—C5—H5C109.5
N1—C2—C3107.89 (9)H5B—C5—H5C109.5
O2—C2—C5111.08 (10)C4—C6—H6A109.5
N1—C2—C5108.47 (10)C4—C6—H6B109.5
C3—C2—C5113.05 (11)H6A—C6—H6B109.5
C2—C3—C4112.40 (10)C4—C6—H6C109.5
C2—C3—H3A109.1H6A—C6—H6C109.5
C4—C3—H3A109.1H6B—C6—H6C109.5
C2—C3—H3B109.1
C4—N2—C1—N12.11 (17)N1—C2—C3—C452.12 (13)
C4—N2—C1—S1178.50 (8)C5—C2—C3—C4172.06 (10)
C2—N1—C1—N21.77 (18)C1—N2—C4—O194.88 (13)
C2—N1—C1—S1178.85 (9)C1—N2—C4—C6149.26 (11)
C1—N1—C2—O288.79 (13)C1—N2—C4—C327.30 (15)
C1—N1—C2—C326.90 (16)C2—C3—C4—O168.34 (13)
C1—N1—C2—C5149.69 (12)C2—C3—C4—N252.07 (12)
O2—C2—C3—C465.66 (12)C2—C3—C4—C6171.94 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1O···O20.881.982.727 (2)143
O2—H2O···S1i0.882.373.249 (1)173
N1—H1N···S1ii0.922.603.414 (1)149
N2—H2N···O1iii0.922.183.074 (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 formulaC6H12N2O2S
Mr176.24
Crystal system, space groupTriclinic, 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)
V3)408.80 (5)
Z2
Radiation typeMo Kα
µ (mm1)0.35
Crystal size (mm)0.30 × 0.20 × 0.20
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.903, 0.934
No. of measured, independent and
observed [I > 2σ(I)] reflections
4260, 1760, 1557
Rint0.012
(sin θ/λ)max1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.029, 0.080, 1.00
No. of reflections1760
No. of parameters102
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
O1—H1O···O20.881.982.727 (2)143
O2—H2O···S1i0.882.373.249 (1)173
N1—H1N···S1ii0.922.603.414 (1)149
N2—H2N···O1iii0.922.183.074 (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

First citationBarton, D. & Ollis, W. D. (1979). Editors. Comprehensive Organic Chemistry. Oxford: Pergamon Press. Translated under the title Obshchayaorganicheskaya khimiya, 1961, Vol. 6. Khimiya: Moscow.  Google Scholar
First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationBruker (2001). SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.  CrossRef CAS Web of Science Google Scholar
First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2003). SADABS University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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