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

Abstract

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,

• a = 10.6415 (8) Å

• b = 7.3370 (6) Å

• c = 11.160 (1) Å

• β = 107.380 (5)°

• V = 831.55 (12) ų

• 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[F ² > 2σ(F ²)] = 0.056

• wR(F ²) = 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

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 ▶).

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536812012007/nc2271Isup3.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
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⋯O3iv	0.70 (4)	2.46 (4)	2.923 (4)	125 (4)
N1—H1⋯S1v	0.70 (4)	3.03 (4)	3.468 (4)	123 (4)

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

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

All hydrogen atoms were localized in a difference density Fourier map. Their positions and isotropic displacement parameters were refined.

Figures

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.

Crystal data

C5H5N5O3S	F(000) = 440
Mr = 215.20	Dx = 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

Bruker APEXII CCD diffractometer	1929 independent reflections
Radiation source: fine-focus sealed tube	955 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.090
φ and ω scans	θmax = 27.6°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −13→13
Tmin = 0.949, Tmax = 0.967	k = −9→9
15454 measured reflections	l = −14→14

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)] = 0.056	Hydrogen site location: difference Fourier map
wR(F2) = 0.148	All H-atom parameters refined
S = 1.00	w = 1/[σ2(Fo2) + (0.0543P)2 + 0.6101P] where P = (Fo2 + 2Fc2)/3
1929 reflections	(Δ/σ)max < 0.001
147 parameters	Δρmax = 0.27 e Å−3
0 restraints	Δρmin = −0.39 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
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 (Ų)

	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)

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)

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···O3iv	0.70 (4)	2.46 (4)	2.923 (4)	125 (4)
N1—H1···S1v	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.