1-(2,4,6-Trioxo-1,3-diazinan-5-yl­idene)thio­semicarbazide

Bittencourt, V.C.D.; Gervini, V.C.; Bresolin, L.; Locatelli, A.; Oliveira, A.B. de

doi:10.1107/S1600536812012007

organic compounds

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ISSN: 2056-9890

Volume 68| Part 4| April 2012| Page o1187

doi:10.1107/S1600536812012007

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1-(2,4,6-Trioxo-1,3-diazinan-5-ylidene)thiosemicarbazide

Viviane C. D. Bittencourt,^a Vanessa Carratu Gervini,^a ^* Leandro Bresolin,^a Aline Locatelli ^b and Adriano Bof de Oliveira ^c

^aEscola de Química e Alimentos, Universidade Federal do Rio Grande, Av. Itália km 08, Campus Carreiros, 96203-900, Rio Grande, RS, Brazil, ^bDepartamento de Química, Universidade Federal de Santa Maria, Av. Roraima, Campus, 97105-900, Santa Maria, RS, Brazil, and ^cDepartamento de Química, Universidade Federal de Sergipe, Av. Marechal Rondon s/n, Campus, 49100-000, São Cristóvão, SE, Brazil
^*Correspondence e-mail: adriano@daad-alumni.de

(Received 15 March 2012; accepted 20 March 2012; online 24 March 2012)

The title molecule, C₅H₅N₅O₃S, is approximately planar, with a maximum deviation from the mean plane through the non-H atoms of 0.182 (3) Å for the amine N atom. In the crystal, molecules are connected via N—H⋯O and N—H⋯S interactions, building a three-dimensional hydrogen-bonded network. Additionally, a weak intramolecular N—H⋯O hydrogen bond is observed.

Related literature

For the synthesis of alloxan-5-thiosemicarbazone, see: Beyer et al. (1956 ). For the antibacterial activity of alloxan-5-thiosemicarbazone against Staphylococcus aureus and Escherichia coli, see: Douros et al. (1973 ).

Experimental

Crystal data

C₅H₅N₅O₃S
M_r = 215.20
Monoclinic, P 2₁ /n
a = 10.6415 (8) Å
b = 7.3370 (6) Å
c = 11.160 (1) Å
β = 107.380 (5)°
V = 831.55 (12) Å³
Z = 4
Mo Kα radiation
μ = 0.38 mm⁻¹
T = 293 K
0.14 × 0.10 × 0.09 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ) T_min = 0.949, T_max = 0.967
15454 measured reflections
1929 independent reflections
955 reflections with I > 2σ(I)
R_int = 0.090

Refinement

R[F² > 2σ(F²)] = 0.056
wR(F²) = 0.148
S = 1.00
1929 reflections
147 parameters
All H-atom parameters refined
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.39 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N5—H4⋯O2ⁱ	0.91 (4)	2.26 (4)	3.036 (4)	143 (3)
N2—H2⋯O3ⁱⁱ	0.86 (4)	1.98 (4)	2.837 (4)	173 (4)
N5—H5⋯O1ⁱⁱⁱ	0.89 (5)	2.08 (5)	2.916 (4)	158 (4)
N4—H3⋯O1	0.88 (4)	2.01 (4)	2.631 (4)	126 (4)
N1—H1⋯O3^iv	0.70 (4)	2.46 (4)	2.923 (4)	125 (4)
N1—H1⋯S1^v	0.70 (4)	3.03 (4)	3.468 (4)	123 (4)
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (ii) -x+1, -y, -z+2; (iii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iv) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (v) -x, -y+1, -z+2.

Data collection: COSMO (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812012007/nc2271sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812012007/nc2271Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812012007/nc2271Isup3.cml

checkCIF report

Comment top

Thiosemicarbazone derivatives have a wide range of biological properties. For example, an alloxan-thiosemicarbazone derivative shows antibacterial activity against several pathologic agents like Staphylococcus aureus and Escherichia coli (Douros et al., 1973). As part of our study of thiosemicarbazone derivatives, we report herein the crystal structure of alloxan-5-thiosemicarbazone. In the title compound (Fig. 1), the molecule is planar and the maximal deviation from the least squares plane through all non-hydrogen atoms is observed for N5 (-0,1822 (30) Å). The mean deviations from the least squares planes for the alloxan fragment C1/C2/C3/C4/N1/N2/O1/O2/O3 and for the thiosemicarbazone fragment C5/N3/N4/N5/S1 amount to 0.0319 (23) Å for O3 and -0.0278 (26) Å for N4, respectively, and the dihedral angle between the two planes is 8,16 (17)°. The bond angles suggest sp² hybridization for the C and N atoms and explain the planarity of the molecule. The crystal packing is stabilized by intermolecular N—H···O and N—H···S as well as intramolecular N—H···O hydrogen bonding building a three-dimensional H-bonded network (Fig. 2 and Table 1).

Related literature top

For the synthesis of alloxan-5-thiosemicarbazone, see: Beyer et al. (1956). For the antibacterial activity of alloxan-5-thiosemicarbazone against Staphylococcus aureus and Escherichia coli, see: Douros et al. (1973).

Experimental top

Starting materials were commercially available and were used without further purification. The synthesis was adapted from a procedure reported previously (Beyer et al., 1956). The hydrochloric acid catalyzed reaction of alloxan monohydrate (6,25 mmol) and thiosemicarbazide (6,25 mmol) in ethanol (60 ml) was refluxed for 7 h. After cooling and filtering, crystals suitable for X-ray diffraction were obtained from a recrystallization in methanol.

Structure description top

For the synthesis of alloxan-5-thiosemicarbazone, see: Beyer et al. (1956). For the antibacterial activity of alloxan-5-thiosemicarbazone against Staphylococcus aureus and Escherichia coli, see: Douros et al. (1973).

Computing details top

Data collection: COSMO (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

	Fig. 1. : The molecular structure of the title compound with labeling and displacement ellipsoids drawn at the 40% probability level.
	Fig. 2. : The crystal structure of the title compound showing the molecules connected through N—H···S hydrogen bonds. Hydrogen bonding is indicated as dashed lines. Symmetry codes: (i) x + 1/2, -y + 1/2, z + 1/2; (ii) -x + 1/2, -y, -z + 2; (iii) x + 1/2, -y + 3/2, z + 1/2; (iv) x - 1/2, -y + 1/2, z - 1/2; (v) -x, -y + 1, -z + 2.

1-(2,4,6-Trioxo-1,3-diazinan-5-ylidene)thiosemicarbazide top

Crystal data top

C₅H₅N₅O₃S	F(000) = 440
M_r = 215.20	D_x = 1.719 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1283 reflections
a = 10.6415 (8) Å	θ = 2.3–19.9°
b = 7.3370 (6) Å	µ = 0.38 mm⁻¹
c = 11.160 (1) Å	T = 293 K
β = 107.380 (5)°	Block, red
V = 831.55 (12) Å³	0.14 × 0.10 × 0.09 mm
Z = 4

Data collection top

Bruker APEXII CCD diffractometer	1929 independent reflections
Radiation source: fine-focus sealed tube	955 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.090
φ and ω scans	θ_max = 27.6°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −13→13
T_min = 0.949, T_max = 0.967	k = −9→9
15454 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)] = 0.056	Hydrogen site location: difference Fourier map
wR(F²) = 0.148	All H-atom parameters refined
S = 1.00	w = 1/[σ²(F_o²) + (0.0543P)² + 0.6101P] where P = (F_o² + 2F_c²)/3
1929 reflections	(Δ/σ)_max < 0.001
147 parameters	Δρ_max = 0.27 e Å⁻³
0 restraints	Δρ_min = −0.39 e Å⁻³

Crystal data top

C₅H₅N₅O₃S	V = 831.55 (12) Å³
M_r = 215.20	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 10.6415 (8) Å	µ = 0.38 mm⁻¹
b = 7.3370 (6) Å	T = 293 K
c = 11.160 (1) Å	0.14 × 0.10 × 0.09 mm
β = 107.380 (5)°

Data collection top

Bruker APEXII CCD diffractometer	1929 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	955 reflections with I > 2σ(I)
T_min = 0.949, T_max = 0.967	R_int = 0.090
15454 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.056	0 restraints
wR(F²) = 0.148	All H-atom parameters refined
S = 1.00	Δρ_max = 0.27 e Å⁻³
1929 reflections	Δρ_min = −0.39 e Å⁻³
147 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
S1	0.17866 (11)	0.94933 (14)	1.13122 (11)	0.0487 (4)
O3	0.4802 (2)	0.2077 (3)	1.0689 (2)	0.0426 (8)
O2	0.1726 (2)	−0.0867 (4)	0.7631 (3)	0.0486 (8)
O1	0.0566 (2)	0.4570 (3)	0.8863 (3)	0.0456 (8)
N5	0.4116 (3)	0.7883 (5)	1.1940 (3)	0.0412 (9)
N3	0.3183 (3)	0.4951 (4)	1.0600 (3)	0.0335 (8)
N4	0.2392 (3)	0.6328 (4)	1.0593 (3)	0.0385 (9)
N2	0.3282 (3)	0.0686 (4)	0.9108 (3)	0.0321 (8)
N1	0.1178 (3)	0.1858 (4)	0.8272 (3)	0.0356 (9)
C5	0.2851 (4)	0.7858 (5)	1.1334 (4)	0.0340 (9)
C4	0.3687 (3)	0.2088 (5)	0.9943 (4)	0.0322 (9)
C3	0.2034 (3)	0.0473 (5)	0.8282 (4)	0.0329 (9)
C1	0.2734 (3)	0.3545 (4)	0.9874 (3)	0.0294 (9)
C2	0.1418 (3)	0.3399 (5)	0.8981 (3)	0.0335 (9)
H4	0.465 (4)	0.694 (5)	1.189 (3)	0.043 (12)*
H2	0.382 (4)	−0.019 (5)	0.912 (3)	0.040 (12)*
H5	0.440 (5)	0.887 (7)	1.240 (5)	0.083 (17)*
H3	0.156 (5)	0.639 (6)	1.015 (4)	0.072 (15)*
H1	0.054 (4)	0.175 (5)	0.785 (4)	0.044 (14)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0504 (7)	0.0356 (6)	0.0614 (8)	0.0045 (5)	0.0185 (5)	−0.0041 (6)
O3	0.0296 (14)	0.0404 (15)	0.0424 (17)	0.0099 (12)	−0.0126 (13)	−0.0101 (13)
O2	0.0382 (15)	0.0385 (17)	0.057 (2)	0.0004 (12)	−0.0034 (14)	−0.0207 (14)
O1	0.0344 (15)	0.0366 (16)	0.0530 (19)	0.0122 (13)	−0.0066 (13)	−0.0042 (14)
N5	0.034 (2)	0.031 (2)	0.052 (2)	−0.0026 (16)	0.0027 (17)	−0.0090 (18)
N3	0.0344 (18)	0.0289 (17)	0.0325 (19)	0.0029 (14)	0.0027 (14)	−0.0003 (14)
N4	0.0332 (19)	0.0305 (18)	0.044 (2)	0.0037 (15)	0.0001 (17)	−0.0064 (16)
N2	0.0257 (17)	0.0281 (17)	0.034 (2)	0.0058 (14)	−0.0034 (14)	−0.0037 (14)
N1	0.0248 (18)	0.0354 (19)	0.037 (2)	0.0010 (15)	−0.0055 (16)	−0.0062 (16)
C5	0.039 (2)	0.0248 (19)	0.037 (2)	−0.0024 (17)	0.0101 (18)	0.0021 (17)
C4	0.0299 (19)	0.030 (2)	0.033 (2)	0.0011 (16)	0.0035 (17)	−0.0035 (17)
C3	0.027 (2)	0.033 (2)	0.036 (2)	0.0024 (17)	0.0047 (17)	0.0017 (19)
C1	0.0280 (19)	0.0268 (19)	0.029 (2)	0.0048 (15)	0.0015 (16)	0.0018 (16)
C2	0.029 (2)	0.032 (2)	0.033 (2)	0.0023 (17)	0.0000 (17)	−0.0010 (17)

Geometric parameters (Å, º) top

S1—C5	1.645 (4)	N4—H3	0.88 (4)
O3—C4	1.229 (4)	N2—C4	1.368 (4)
O2—C3	1.208 (4)	N2—C3	1.380 (4)
O1—C2	1.227 (4)	N2—H2	0.86 (4)
N5—C5	1.314 (4)	N1—C2	1.360 (5)
N5—H4	0.91 (4)	N1—C3	1.362 (5)
N5—H5	0.89 (5)	N1—H1	0.70 (4)
N3—C1	1.311 (4)	C4—C1	1.460 (5)
N3—N4	1.313 (4)	C1—C2	1.460 (5)
N4—C5	1.394 (4)

C5—N5—H4	121 (2)	N5—C5—S1	126.3 (3)
C5—N5—H5	115 (3)	N4—C5—S1	117.5 (3)
H4—N5—H5	123 (4)	O3—C4—N2	120.1 (3)
C1—N3—N4	119.1 (3)	O3—C4—C1	123.7 (3)
N3—N4—C5	120.4 (3)	N2—C4—C1	116.2 (3)
N3—N4—H3	126 (3)	O2—C3—N1	122.8 (3)
C5—N4—H3	114 (3)	O2—C3—N2	121.8 (3)
C4—N2—C3	125.8 (3)	N1—C3—N2	115.4 (3)
C4—N2—H2	119 (2)	N3—C1—C2	125.4 (3)
C3—N2—H2	115 (2)	N3—C1—C4	115.1 (3)
C2—N1—C3	127.3 (3)	C2—C1—C4	119.5 (3)
C2—N1—H1	117 (3)	O1—C2—N1	121.0 (3)
C3—N1—H1	116 (3)	O1—C2—C1	123.3 (3)
N5—C5—N4	116.1 (3)	N1—C2—C1	115.7 (3)

C1—N3—N4—C5	−178.6 (4)	O3—C4—C1—N3	5.6 (6)
N3—N4—C5—N5	5.3 (5)	N2—C4—C1—N3	−174.0 (3)
N3—N4—C5—S1	−177.8 (3)	O3—C4—C1—C2	−178.0 (4)
C3—N2—C4—O3	175.4 (4)	N2—C4—C1—C2	2.5 (5)
C3—N2—C4—C1	−5.1 (6)	C3—N1—C2—O1	178.4 (4)
C2—N1—C3—O2	178.7 (4)	C3—N1—C2—C1	−1.7 (6)
C2—N1—C3—N2	−0.4 (6)	N3—C1—C2—O1	−3.5 (6)
C4—N2—C3—O2	−175.0 (4)	C4—C1—C2—O1	−179.6 (4)
C4—N2—C3—N1	4.1 (6)	N3—C1—C2—N1	176.6 (4)
N4—N3—C1—C2	3.5 (6)	C4—C1—C2—N1	0.6 (5)
N4—N3—C1—C4	179.7 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H4···O2ⁱ	0.91 (4)	2.26 (4)	3.036 (4)	143 (3)
N2—H2···O3ⁱⁱ	0.86 (4)	1.98 (4)	2.837 (4)	173 (4)
N5—H5···O1ⁱⁱⁱ	0.89 (5)	2.08 (5)	2.916 (4)	158 (4)
N4—H3···O1	0.88 (4)	2.01 (4)	2.631 (4)	126 (4)
N1—H1···O3^iv	0.70 (4)	2.46 (4)	2.923 (4)	125 (4)
N1—H1···S1^v	0.70 (4)	3.03 (4)	3.468 (4)	123 (4)

Symmetry codes: (i) x+1/2, −y+1/2, z+1/2; (ii) −x+1, −y, −z+2; (iii) x+1/2, −y+3/2, z+1/2; (iv) x−1/2, −y+1/2, z−1/2; (v) −x, −y+1, −z+2.

Experimental details

Crystal data
Chemical formula	C₅H₅N₅O₃S
M_r	215.20
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	10.6415 (8), 7.3370 (6), 11.160 (1)
β (°)	107.380 (5)
V (Å³)	831.55 (12)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.38
Crystal size (mm)	0.14 × 0.10 × 0.09

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.949, 0.967
No. of measured, independent and observed [I > 2σ(I)] reflections	15454, 1929, 955
R_int	0.090
(sin θ/λ)_max (Å⁻¹)	0.652

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.148, 1.00
No. of reflections	1929
No. of parameters	147
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.39

Computer programs: COSMO (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2006), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H4···O2ⁱ	0.91 (4)	2.26 (4)	3.036 (4)	143 (3)
N2—H2···O3ⁱⁱ	0.86 (4)	1.98 (4)	2.837 (4)	173 (4)
N5—H5···O1ⁱⁱⁱ	0.89 (5)	2.08 (5)	2.916 (4)	158 (4)
N4—H3···O1	0.88 (4)	2.01 (4)	2.631 (4)	126 (4)
N1—H1···O3^iv	0.70 (4)	2.46 (4)	2.923 (4)	125 (4)
N1—H1···S1^v	0.70 (4)	3.03 (4)	3.468 (4)	123 (4)

Symmetry codes: (i) x+1/2, −y+1/2, z+1/2; (ii) −x+1, −y, −z+2; (iii) x+1/2, −y+3/2, z+1/2; (iv) x−1/2, −y+1/2, z−1/2; (v) −x, −y+1, −z+2.

Acknowledgements

We gratefully acknowledge Professor Dr Manfredo Hörner (Federal University of Santa Maria, Brazil) for his help and support with the X-ray measurements. We also acknowledge financial support through the DECIT/SCTIE-MS-CNPq-FAPERGS-Pronem-# 11/2029–1 and PRONEX-CNPq-FAPERGS projects.

References

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Bruker (2005). COSMO, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Douros, J. D. Jr, Brokl, M. & Kerst, A. F. (1973). German Patent DE2232717A1. Google Scholar
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