Ammonium 4,6-dioxo-2-sulfanylidene-1,3-diazinan-5-ide

Betz, R.; Gerber, T.

doi:10.1107/S1600536811016722

organic compounds

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Volume 67| Part 6| June 2011| Page o1326

doi:10.1107/S1600536811016722

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Ammonium 4,6-dioxo-2-sulfanylidene-1,3-diazinan-5-ide

Richard Betz ^a ^* and Thomas Gerber ^a

^aNelson Mandela Metropolitan University, Summerstrand Campus, Department of Chemistry, University Way, Summerstrand, PO Box 77000, Port Elizabeth 6031, South Africa
^*Correspondence e-mail: richard.betz@webmail.co.za

(Received 11 April 2011; accepted 3 May 2011; online 7 May 2011)

In the title salt, NH₄⁺·C₄H₃N₂O₂S⁻, the asymmetric unit comprises two half-occupied ammonium positions and a 4,6-dioxo-2-sulfanylidene-1,3-diazinan-5-ide anion. The anion shows C₂ as well as C_s symmetry and is present in its diketonic tautomeric form. Intracyclic angles span a range from 116.64 (9)–124.67 (9)°. Intermolecular N—H⋯O hydrogen bonds connect the cations and anions to form a three-dimensional network.

Related literature

For the crystal structures of 2-thiobarbituric acid, its hydrate and several of its tautomeric forms, see: Calas & Martinez (1967 ); Chierotti et al. (2010 ). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ); Bernstein et al. (1995 ).

Experimental

Crystal data

NH₄⁺·C₄H₃N₂O₂S⁻
M_r = 161.19
Monoclinic, P 2/c
a = 11.3308 (4) Å
b = 3.9396 (1) Å
c = 14.6945 (5) Å
β = 98.644 (1)°
V = 648.49 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.44 mm⁻¹
T = 200 K
0.53 × 0.19 × 0.08 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ) T_min = 0.876, T_max = 1.000
6071 measured reflections
1604 independent reflections
1476 reflections with I > 2σ(I)
R_int = 0.017

Refinement

R[F² > 2σ(F²)] = 0.023
wR(F²) = 0.067
S = 1.10
1604 reflections
116 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H71⋯O2ⁱ	0.832 (17)	1.971 (17)	2.8025 (12)	179.0 (16)
N2—H72⋯O1ⁱⁱ	0.874 (16)	1.976 (16)	2.8483 (12)	175.7 (15)
N90—H901⋯S1ⁱⁱⁱ	0.902 (17)	2.426 (16)	3.3252 (8)	174.8 (14)
N90—H902⋯O2	0.866 (17)	1.927 (17)	2.7929 (12)	177.7 (16)
N91—H911⋯O1^iv	0.88 (2)	1.90 (2)	2.7622 (13)	166.0 (18)
N91—H912⋯O1^v	0.87 (2)	2.66 (2)	3.0669 (15)	110.0 (16)
N91—H912⋯S1^vi	0.87 (2)	2.62 (2)	3.3069 (3)	136.0 (19)
Symmetry codes: (i) -x+1, -y+2, -z+1; (ii) -x, -y+1, -z+1; (iii) -x+1, -y+1, -z+1; (iv) x, y+1, z; (v) $[-x, y, -z+{\script{1\over 2}}]$ ; (vi) $[x, -y+2, z-{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2010 ); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997 ) and Mercury (Macrae et al., 2006 ); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811016722/bq2297sup1.cif

Supporting information file. DOI: 10.1107/S1600536811016722/bq2297Isup2.cdx

Structure factors: contains datablock I. DOI: 10.1107/S1600536811016722/bq2297Isup3.hkl

Supporting information file. DOI: 10.1107/S1600536811016722/bq2297Isup4.cml

checkCIF report

Comment top

Multidentate ligands play a major role in the synthesis of coordination polymers and metal-organic framework compounds (MOFs). Especially derivatives of benzoic acid have found widespread use in this aspect and a variety of these coordination polymers have been characterized in solution and in the solid state. Owing to the desire to synthesize functionalized MOFs whose poresizes or even complete architectural set-ups might easily be influenced upon variation of external parameters such as pH value or the presence and concentration of molecules that might reside inside the pores of these MOFs, chelating ligands related to benzoic acid but with the ability to change their bonding behaviour are necessary. In this aspect, 2-thiobarbituric acid seemed of interest since it may adopt several tautomeric forms whose persistence can be influenced by such external parameters. In order to gather structural information to allow for the tailored synthesis of MOFs based on thiobarbituric acid, we determined the crystal structure of its ammonium salt. The crystal structures of 2-thiobarbituric acid, its hydrate as well as several of its tautomeric forms are apparent in the literature (Calas & Martinez (1967); Chierotti et al. (2010)).

The thiobarbituric acid anion is present in its diketonic tautomeric form according to C—O bond lengths. Deprotonation took place on the methylene group. The intracyclic angles span a range from 116.64 (9)–124.67 (9) ° with the biggest angles invariably found on the nitrogen atoms and the smallest angle present on the sulfur-bonded carbon atom. The unit cell comprises two half-occupied ammonium cations (Fig. 1). The small puckering amplitude of the six-membered ring precludes a conformation analysis.

The crystal structure is dominated by hydrogen bonds. All of the ammonium cations' hydrogen atoms act as donors while both ketonic oxygen atoms of the heterocycle as well as the sulfur atom act as acceptors. The intracyclic NH groups participate in hydrogen bonds as well, however, they only have the ketonic oxygen atoms as acceptors. The latter intermolecular interactions connect the thiobarbituric acid anions to chains along [1 1 0] where each dimeric subunit shows inversion symmetry (Fig. 2). In terms of graph-set analysis (Etter et al. (1990); Bernstein et al. (1995)), the descriptor for the hydrogen bonds giving rise to these chains is R²₂(8)R²₂(8) on the unitary level. Taking into account the van-der-Waals radii of the atoms present in the crystal structure, the carbon-bond H atom participates in a C–H···S contact, which is, however, not very pronounced. In total, the molecules in the unit cell are connected to a three-dimensional network where layers of thiobarbituric acid anions are orientated parallel as well as approximately perpendicular towards each other (Fig. 3).

The packing of the compound in the crystal is shown in Figure 4.

Related literature top

For the crystal structures of 2-thiobarbituric acid, its hydrate and several of its tautomeric forms, see: Calas & Martinez (1967); Chierotti et al. (2010). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990); Bernstein et al. (1995). [Author: please check new scheme; original showed anion as C₄H₅N₂O₂S^-]

Experimental top

2-Thiobarbituric acid was obtained commercially (Aldrich). Upon dissolution in hot, aqueous ammonia (c = 1.0 M) and subsequent cooling to room temperature, crystals suitable for the X-ray diffraction study were obtained.

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 50% probability level).
	Fig. 2. Intermolecular contacts among the thiobarbituric acid anions, viewed along [0 - 1 0]. Symmetry operators: (i) -x, -y + 1, -z + 1; (ii) -x + 1, -y + 2, -z + 1.
	Fig. 3. Hydrogen bonding system in the crystal structure of the title compound, viewed along [0 - 1 0]. Colour code for the atoms: green – sulfur, red – oxygen, blue – nitrogen, black – carbon; hydrogen atoms are shown as end of sticks.
	Fig. 4. Molecular packing of the title compound, viewed along [0 1 0].

Ammonium 4,6-dioxo-2-sulfanylidene-1,3-diazinan-5-ide top

Crystal data top

NH₄⁺·C₄H₃N₂O₂S⁻	F(000) = 336
M_r = 161.19	D_x = 1.651 Mg m⁻³
Monoclinic, P2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yc	Cell parameters from 1604 reflections
a = 11.3308 (4) Å	θ = 3.1–28.3°
b = 3.9396 (1) Å	µ = 0.44 mm⁻¹
c = 14.6945 (5) Å	T = 200 K
β = 98.644 (1)°	Rod, colourless
V = 648.49 (4) Å³	0.53 × 0.19 × 0.08 mm
Z = 4

Data collection top

Bruker APEXII CCD diffractometer	1604 independent reflections
Radiation source: fine-focus sealed tube	1476 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.017
ϕ and ω scans	θ_max = 28.3°, θ_min = 1.8°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −14→15
T_min = 0.876, T_max = 1.000	k = −4→5
6071 measured reflections	l = −16→19

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)] = 0.023	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.067	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0357P)² + 0.2247P] where P = (F_o² + 2F_c²)/3
1604 reflections	(Δ/σ)_max = 0.001
116 parameters	Δρ_max = 0.33 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

NH₄⁺·C₄H₃N₂O₂S⁻	V = 648.49 (4) Å³
M_r = 161.19	Z = 4
Monoclinic, P2/c	Mo Kα radiation
a = 11.3308 (4) Å	µ = 0.44 mm⁻¹
b = 3.9396 (1) Å	T = 200 K
c = 14.6945 (5) Å	0.53 × 0.19 × 0.08 mm
β = 98.644 (1)°

Data collection top

Bruker APEXII CCD diffractometer	1604 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2008)	1476 reflections with I > 2σ(I)
T_min = 0.876, T_max = 1.000	R_int = 0.017
6071 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.023	0 restraints
wR(F²) = 0.067	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.33 e Å⁻³
1604 reflections	Δρ_min = −0.20 e Å⁻³
116 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.25562 (2)	1.03184 (7)	0.667084 (17)	0.01875 (10)
O1	0.05012 (7)	0.4191 (2)	0.39646 (5)	0.02247 (19)
O2	0.44635 (7)	0.7956 (3)	0.39645 (6)	0.0262 (2)
N1	0.34683 (8)	0.8796 (3)	0.51685 (6)	0.01740 (19)
H71	0.4077 (15)	0.978 (4)	0.5427 (12)	0.027 (4)*
N2	0.15417 (8)	0.7040 (2)	0.51663 (6)	0.01649 (19)
H72	0.0908 (14)	0.678 (4)	0.5433 (10)	0.024 (4)*
C1	0.25140 (9)	0.8614 (3)	0.56115 (7)	0.0151 (2)
C2	0.14770 (9)	0.5599 (3)	0.42919 (7)	0.0160 (2)
C3	0.24801 (9)	0.5883 (3)	0.38550 (7)	0.0182 (2)
H3	0.2466	0.4960	0.3256	0.022*
C4	0.35073 (9)	0.7513 (3)	0.42884 (7)	0.0177 (2)
N90	0.5000	0.4019 (4)	0.2500	0.0202 (3)
H901	0.5638 (14)	0.272 (4)	0.2710 (11)	0.034 (4)*
H902	0.4821 (15)	0.527 (4)	0.2944 (11)	0.031 (4)*
N91	0.0000	0.9763 (4)	0.2500	0.0234 (3)
H911	0.0284 (17)	1.109 (5)	0.2961 (13)	0.048 (5)*
H912	0.0539 (19)	0.853 (6)	0.2290 (15)	0.064 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.01756 (15)	0.02527 (16)	0.01378 (14)	0.00002 (10)	0.00348 (10)	−0.00417 (9)
O1	0.0173 (4)	0.0325 (4)	0.0175 (4)	−0.0085 (3)	0.0023 (3)	−0.0039 (3)
O2	0.0176 (4)	0.0417 (5)	0.0209 (4)	−0.0090 (4)	0.0085 (3)	−0.0104 (4)
N1	0.0138 (4)	0.0247 (5)	0.0139 (4)	−0.0039 (4)	0.0025 (3)	−0.0034 (4)
N2	0.0136 (4)	0.0234 (5)	0.0130 (4)	−0.0027 (3)	0.0037 (3)	−0.0001 (3)
C1	0.0153 (4)	0.0169 (5)	0.0131 (4)	0.0005 (4)	0.0020 (4)	0.0017 (4)
C2	0.0159 (4)	0.0190 (5)	0.0127 (5)	−0.0013 (4)	0.0007 (4)	0.0012 (4)
C3	0.0184 (5)	0.0237 (5)	0.0128 (5)	−0.0030 (4)	0.0031 (4)	−0.0022 (4)
C4	0.0167 (5)	0.0228 (5)	0.0141 (4)	−0.0014 (4)	0.0043 (4)	−0.0012 (4)
N90	0.0193 (6)	0.0243 (7)	0.0170 (6)	0.000	0.0032 (5)	0.000
N91	0.0251 (7)	0.0260 (7)	0.0204 (7)	0.000	0.0074 (6)	0.000

Geometric parameters (Å, º) top

S1—C1	1.6893 (10)	N2—H72	0.874 (16)
O1—C2	1.2656 (13)	C2—C3	1.3914 (15)
O2—C4	1.2592 (13)	C3—C4	1.3963 (14)
N1—C1	1.3452 (14)	C3—H3	0.9500
N1—C4	1.3955 (13)	N90—H901	0.902 (17)
N1—H71	0.832 (17)	N90—H902	0.866 (17)
N2—C1	1.3453 (13)	N91—H911	0.88 (2)
N2—C2	1.3965 (13)	N91—H912	0.87 (2)

C1—N1—C4	124.67 (9)	O1—C2—N2	116.73 (10)
C1—N1—H71	118.4 (12)	C3—C2—N2	117.27 (9)
C4—N1—H71	116.9 (12)	C2—C3—C4	120.62 (10)
C1—N2—C2	124.11 (9)	C2—C3—H3	119.7
C1—N2—H72	120.3 (10)	C4—C3—H3	119.7
C2—N2—H72	115.5 (10)	O2—C4—N1	116.68 (9)
N1—C1—N2	116.64 (9)	O2—C4—C3	126.64 (10)
N1—C1—S1	120.74 (8)	N1—C4—C3	116.68 (9)
N2—C1—S1	122.62 (8)	H901—N90—H902	109.4 (14)
O1—C2—C3	125.99 (10)	H911—N91—H912	114.2 (19)

C4—N1—C1—N2	0.76 (16)	O1—C2—C3—C4	179.77 (11)
C4—N1—C1—S1	−178.90 (8)	N2—C2—C3—C4	0.82 (16)
C2—N2—C1—N1	0.48 (16)	C1—N1—C4—O2	178.58 (11)
C2—N2—C1—S1	−179.87 (8)	C1—N1—C4—C3	−1.12 (16)
C1—N2—C2—O1	179.70 (10)	C2—C3—C4—O2	−179.40 (12)
C1—N2—C2—C3	−1.25 (16)	C2—C3—C4—N1	0.27 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H71···O2ⁱ	0.832 (17)	1.971 (17)	2.8025 (12)	179.0 (16)
N2—H72···O1ⁱⁱ	0.874 (16)	1.976 (16)	2.8483 (12)	175.7 (15)
N90—H901···S1ⁱⁱⁱ	0.902 (17)	2.426 (16)	3.3252 (8)	174.8 (14)
N90—H902···O2	0.866 (17)	1.927 (17)	2.7929 (12)	177.7 (16)
N91—H911···O1^iv	0.88 (2)	1.90 (2)	2.7622 (13)	166.0 (18)
N91—H912···O1^v	0.87 (2)	2.66 (2)	3.0669 (15)	110.0 (16)
N91—H912···S1^vi	0.87 (2)	2.62 (2)	3.3069 (3)	136.0 (19)

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

Experimental details

Crystal data
Chemical formula	NH₄⁺·C₄H₃N₂O₂S⁻
M_r	161.19
Crystal system, space group	Monoclinic, P2/c
Temperature (K)	200
a, b, c (Å)	11.3308 (4), 3.9396 (1), 14.6945 (5)
β (°)	98.644 (1)
V (Å³)	648.49 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.44
Crystal size (mm)	0.53 × 0.19 × 0.08

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2008)
T_min, T_max	0.876, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	6071, 1604, 1476
R_int	0.017
(sin θ/λ)_max (Å⁻¹)	0.667

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.023, 0.067, 1.10
No. of reflections	1604
No. of parameters	116
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.33, −0.20

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2006), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H71···O2ⁱ	0.832 (17)	1.971 (17)	2.8025 (12)	179.0 (16)
N2—H72···O1ⁱⁱ	0.874 (16)	1.976 (16)	2.8483 (12)	175.7 (15)
N90—H901···S1ⁱⁱⁱ	0.902 (17)	2.426 (16)	3.3252 (8)	174.8 (14)
N90—H902···O2	0.866 (17)	1.927 (17)	2.7929 (12)	177.7 (16)
N91—H911···O1^iv	0.88 (2)	1.90 (2)	2.7622 (13)	166.0 (18)
N91—H912···O1^v	0.87 (2)	2.66 (2)	3.0669 (15)	110.0 (16)
N91—H912···S1^vi	0.87 (2)	2.62 (2)	3.3069 (3)	136.0 (19)

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

Acknowledgements

The authors thank Mrs Clair Noble for helpful discussions.

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