6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetra­hydro­pyrimidin-5-aminium sulfate monohydrate

Tapmeyer, L.; Prill, D.

doi:10.1107/S2414314619006898

organic compounds

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ISSN: 2414-3146

Volume 4| Part 5| May 2019| x190689

https://doi.org/10.1107/S2414314619006898

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6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetrahydropyrimidin-5-aminium sulfate monohydrate

Lukas Tapmeyer ^a ^* and Dragica Prill ^a

^aInstitute of Inorganic and Analytical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 7, Frankfurt am Main, Hessen, 60438, Germany
^*Correspondence e-mail: tapmeyer@chemie.uni-frankfurt.de

Edited by C. Rizzoli, Universita degli Studi di Parma, Italy (Received 24 April 2019; accepted 13 May 2019; online 17 May 2019)

The title compound, C₄H₉N₅O²⁺·SO₄²⁻·H₂O, is the monohydrate of the commercially available compound `C₄H₇N₅O·H₂SO₄·xH₂O'. It is obtained by reprecipitation of C₄H₇N₅O·H₂SO₄·xH₂O from dilute sodium hydroxide solution with dilute sulfuric acid. The crystal structure of anhydrous 2,4,5-triamino-1,6-dihydropyrimidin-6-one sulfate is known, although called by the authors 5-amminium-6-amino-isocytosinium sulfate [Bieri et al. (1993 ). Private communication (refcode HACDEU). CCDC, Cambridge, England]. In the structure, the sulfate group is deprotonated, whereas one of the amino groups is protonated (R₂C—NH₃⁺) and one is rearranged to a protonated imine group (R₂C=NH₂⁺). This arrangement is very similar to the known crystal structure of the anhydrate. Several tautomeric forms of the investigated molecule are possible, which leads to questionable proton attributions. The measured data allowed the location of all hydrogen atoms from the residual electron density. In the crystal, ions and water molecules are linked into a three-dimensional network by N—H⋯O and O—H⋯O hydrogen bonds.

Keywords: crystal structure; triaminodihydropyrimidinone; hydrogen bonds.

CCDC reference: 1915747

Structure description

2,4,5-Triamino-1,6-dihydropyrimidin-6-one (also called 2,4,5-triamino-6-hydroxypyrimidine sulfate) and/or its tautomer 2,4,5-triamino-6-hydroxypyrimidine are relevant starting materials for either very basic (Traube, 1900 ) or more advanced organic syntheses, including natural materials such as butterfly-wing pigments (Purrmann, 1940 ) and potential novel antiviral lead structures (Abbas et al., 2017 ). The structure of the monohydrate form is herewith elucidated and confirms the protonation of the known structure (CSD refcode: HACDEU; Bieri et al., 1993).

The title compound crystallizes in the triclinic space group P $[\overline{1}]$ . The asymmetric unit is composed of one organic dication ([C₄H₉N₅O]²⁺), one sulfate anion and one water molecule (Fig. 1). The present tautomer is the 2,4,5-triamino-1,6-dihydropyrimidin-6-one. The molecule is almost planar [r.m.s. deviation = 0.026 Å, maximum deviation 0.046 (4) Å for N13], except for the amino group H atoms.

Figure 1
The asymmetric unit of the title compound with displacement ellipsoids drawn at the 50% probability level. Hydrogen bonds are shown as dashed lines.

The title compound shows a layered structure with the most polar compartments oriented in the (100) plane (Fig. 2). Within the layers, the dicationic molecules form hydrogen bonds to the water molecules and to the sulfate dianions. The layers are interlinked by hydrogen bonds between the sulfate dianion and the organic dication (Table 1).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N8—H8A⋯O4ⁱ	0.89	2.46	3.113 (4)	131
N8—H8A⋯O5ⁱ	0.89	1.99	2.827 (4)	157
N8—H8B⋯O3ⁱⁱ	0.89	1.94	2.788 (4)	159
N8—H8C⋯O5ⁱⁱⁱ	0.89	2.13	2.942 (4)	152
N9—H9⋯O4^iv	0.82 (4)	1.93 (4)	2.739 (5)	168 (4)
N10—H10⋯O2	0.88 (4)	1.87 (4)	2.677 (4)	152 (3)
N10—H10⋯O4	0.88 (4)	2.58 (5)	3.329 (4)	143 (4)
N11—H11A⋯O2	0.80 (5)	2.56 (7)	3.106 (6)	126 (5)
N11—H11A⋯OW1^v	0.80 (5)	2.29 (5)	2.956 (4)	142 (5)
N11—H11B⋯O3^iv	0.89 (6)	2.00 (6)	2.845 (6)	158 (5)
N13—H13A⋯OW1ⁱⁱ	0.98 (6)	1.98 (7)	2.924 (5)	161 (5)
N13—H13B⋯O4	0.91 (5)	2.10 (5)	2.961 (4)	156 (5)
OW1—HW12⋯O2	0.96 (6)	2.10 (6)	2.798 (4)	128 (5)
OW1—HW11⋯OW1^vi	0.96 (3)	2.59 (5)	3.390 (5)	141 (3)
Symmetry codes: (i) -x, -y+1, -z+1; (ii) -x+1, -y+1, -z+1; (iii) x, y-1, z+1; (iv) x, y-1, z; (v) -x+1, -y+1, -z; (vi) -x+2, -y+1, -z.

Figure 2
Partial packing diagram of the title compound viewed along the a axis.

Powder data confirmed the phase identity of the single crystals with experimentally obtained bulk material. Furthermore, a commercial sample of C₄H₇N₅O·H₂SO₄·xH₂O could be quantitatively analyzed by Rietveld refinement with TOPAS (Coelho, 2018 ; Rietveld, 2010 ), resulting in a composition of 76.4 (3)% of the known anhydrate phase and 23.6 (3)% of the monohydrate described in this paper (Fig. 3). Since the monohydrate is a yellow solid and the anhydrous form rather colorless, the brown color of the commercial sample could be attributed to minor (and probably amorphous) impurities.

Figure 3
X-ray powder diagrams of (from top to bottom) the known anhydrous title compound (simulated, dark red), the vacuum-dried title compound (red), the commercial sample (black), the title compound (blue) and the pattern simulated from the title compound's single-crystal structure (dark blue).

Synthesis and crystallization

5 g (∼20 mmol) of brown 2,4,5-triamino-6-hydroxypyrimidine sulfate (C₄H₇N₅OH₂·SO₄·xH₂O) as purchased from TCI (purity > 90.0%) were dissolved under stirring at 70°C in 100 ml of water with 2 g of sodium hydroxide (∼50 mmol). The resulting reddish orange solution (with a pH of about 9–10) was filtered into a solution of 2.6 g of H₂SO₄ (96%, 25 mmol) in 900 ml water. The instantaneously formed red-to-brown aggregates were left to settle down for two h and the suspension was then filtered. The yellow filtrate was left at room temperature overnight. The formed pale-yellow crystals of the title compound were filtered off on a nutsch flask. The obtained yield for one purification cycle was about 15%. For efficiency, the filtrate can be boiled down and the brown solid precipitate can be reused in the next batch.

Refinement

Crystal data, data collection, and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₄H₉N₅O²⁺·SO₄²⁻·H₂O
M_r	257.24
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	296
a, b, c (Å)	7.0128 (7), 7.9882 (8), 9.0732 (9)
α, β, γ (°)	74.121 (4), 86.734 (4), 79.290 (4)
V (Å³)	480.36 (8)
Z	2
Radiation type	Cu Kα
μ (mm⁻¹)	3.34
Crystal size (mm)	0.2 × 0.15 × 0.1

Data collection
Diffractometer	Siemens Bruker CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2015 )
T_min, T_max	0.526, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections	20827, 1720, 1599
R_int	0.051

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.080, 0.281, 1.40
No. of reflections	1720
No. of parameters	179
No. of restraints	20
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.63, −1.04
Computer programs: APEX3 (Bruker, 2012 ), SAINT (Bruker, 2015), SHELXT (Sheldrick, 2015a ), SHELXL2018 (Sheldrick, 2015b ), Mercury (Macrae et al., 2008 ), ORTEPIII (Burnett & Johnson, 1996 ) and publCIF (Westrip, 2010 ).

X-ray powder diffraction data were recorded at room temperature in transmission geometry on a Stoe Stadi-P diffractometer equipped with a curved Ge(111) primary monochromator and a linear position-sensitive detector, using Cu K α₁ radiation (λ =1.5406 Å). Samples were rotated in 0.7 mm glass capillaries during measurement.

Structural data

CCDC reference: 1915747

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314619006898/rz4030sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314619006898/rz4030Isup2.hkl

X-ray powder diffraction data (2theta vs counts) for the commercial sample. DOI: https://doi.org/10.1107/S2414314619006898/rz4030sup3.txt

X-ray powder diffraction data (2theta vs counts) for the monohydrate title compound. DOI: https://doi.org/10.1107/S2414314619006898/rz4030sup4.txt

X-ray powder diffraction data (2theta vs counts) for the anhydrate compound. DOI: https://doi.org/10.1107/S2414314619006898/rz4030sup5.txt

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2012); cell refinement: SAINT (Bruker, 2015); data reduction: SAINT (Bruker, 2015); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008) and ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: publCIF (Westrip, 2010).

6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetrahydropyrimidin-5-aminium sulfate monohydrate top

Crystal data top

C₄H₉N₅O²⁺·SO₄²⁻·H₂O	Z = 2
M_r = 257.24	F(000) = 268
Triclinic, P1	D_x = 1.778 Mg m⁻³
a = 7.0128 (7) Å	Cu Kα radiation, λ = 1.54178 Å
b = 7.9882 (8) Å	Cell parameters from 9522 reflections
c = 9.0732 (9) Å	θ = 2.5–69.4°
α = 74.121 (4)°	µ = 3.34 mm⁻¹
β = 86.734 (4)°	T = 296 K
γ = 79.290 (4)°	Block, pale yellow
V = 480.36 (8) Å³	0.2 × 0.15 × 0.1 mm

Data collection top

Siemens Bruker CCD diffractometer	1599 reflections with I > 2σ(I)
Radiation source: microfocus tube	R_int = 0.051
ω and Phi scans	θ_max = 71.1°, θ_min = 5.1°
Absorption correction: multi-scan (SADABS; Bruker, 2015)	h = −8→8
T_min = 0.526, T_max = 0.753	k = −9→9
20827 measured reflections	l = −10→10
1720 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.080	w = 1/[σ²(F_o²) + (0.2P)²] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.281	(Δ/σ)_max = 0.002
S = 1.40	Δρ_max = 0.63 e Å⁻³
1720 reflections	Δρ_min = −1.04 e Å⁻³
179 parameters	Extinction correction: SHELXL2018 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
20 restraints	Extinction coefficient: 0.081 (15)

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. All H atoms could be located by difference Fourier synthesis. Subsequently, H atoms bound to N atoms were refined using a riding model with the amino N–H distances constrained to 0.85 Å and the imino N–H distances constrained to 0.88 Å. For the H atoms of the amino groups, free rotation about their local threefold axis was allowed and their isotropic displacement parameters were set to U_iso(H) = 1.5U_eq(N). The coordinates of the H atoms of the water molecules were refined with the O–H distances restrained to 0.84 (1) Å and the H–H distance restrained to 1.4 (1) Å. Their isotropic displacement parameters were coupled to the equivalent isotropic displacement parameters of the O atoms, with U_iso(H) = 1.2U_eq(O).

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

	x	y	z	U_iso*/U_eq
S1	0.29190 (9)	0.72804 (10)	0.15928 (8)	0.0303 (6)
O2	0.3943 (4)	0.5471 (3)	0.1724 (3)	0.0397 (8)
O3	0.4276 (3)	0.8537 (4)	0.1119 (3)	0.0389 (8)
O4	0.2063 (4)	0.7360 (4)	0.3111 (3)	0.0430 (8)
O5	0.1362 (4)	0.7771 (4)	0.0452 (3)	0.0418 (8)
O6	0.2171 (5)	−0.1764 (4)	0.6728 (3)	0.0520 (9)
N8	0.2102 (4)	0.0973 (4)	0.8136 (3)	0.0338 (8)
H8A	0.098160	0.160461	0.833726	0.051*
H8B	0.307806	0.133069	0.847810	0.051*
H8C	0.211936	−0.016627	0.859976	0.051*
N9	0.2573 (4)	0.0009 (4)	0.4352 (3)	0.0354 (8)
H9	0.237 (4)	−0.085 (5)	0.410 (4)	0.028 (10)*
N10	0.2669 (4)	0.2969 (4)	0.3967 (3)	0.0369 (8)
H10	0.2779 (14)	0.401 (6)	0.335 (6)	0.076 (17)*
N11	0.2988 (6)	0.1773 (6)	0.1914 (4)	0.0481 (10)
H11A	0.325 (7)	0.261 (8)	0.128 (6)	0.055 (15)*
H11B	0.325 (7)	0.092 (7)	0.143 (6)	0.053 (14)*
C12	0.2422 (5)	0.2849 (5)	0.5513 (4)	0.0340 (9)
N13	0.2327 (5)	0.4357 (4)	0.5902 (4)	0.0412 (9)
H13A	0.200 (8)	0.434 (8)	0.697 (7)	0.073 (17)*
H13B	0.225 (7)	0.546 (7)	0.525 (6)	0.054 (13)*
C14	0.2309 (4)	0.1216 (5)	0.6496 (4)	0.0310 (9)
C15	0.2338 (5)	−0.0280 (5)	0.5956 (4)	0.0348 (9)
C16	0.2728 (5)	0.1591 (5)	0.3394 (4)	0.0353 (9)
OW1	0.7873 (5)	0.5365 (4)	0.0944 (3)	0.0496 (9)
HW12	0.687 (8)	0.467 (8)	0.119 (11)	0.16 (4)*
HW11	0.916 (4)	0.473 (7)	0.089 (8)	0.11 (2)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0287 (8)	0.0328 (8)	0.0267 (8)	−0.0044 (5)	0.0017 (4)	−0.0048 (5)
O2	0.0407 (14)	0.0326 (15)	0.0406 (14)	−0.0032 (11)	0.0047 (10)	−0.0041 (11)
O3	0.0345 (13)	0.0414 (15)	0.0413 (15)	−0.0126 (11)	0.0060 (11)	−0.0094 (11)
O4	0.0493 (16)	0.0475 (17)	0.0340 (14)	−0.0118 (12)	0.0090 (12)	−0.0135 (13)
O5	0.0341 (13)	0.0532 (18)	0.0351 (14)	−0.0035 (11)	−0.0040 (10)	−0.0090 (12)
O6	0.075 (2)	0.0427 (18)	0.0351 (15)	−0.0137 (15)	0.0071 (13)	−0.0042 (13)
N8	0.0305 (14)	0.0418 (18)	0.0259 (15)	−0.0051 (12)	−0.0006 (11)	−0.0046 (13)
N9	0.0453 (16)	0.0334 (18)	0.0261 (16)	−0.0069 (13)	0.0025 (12)	−0.0063 (13)
N10	0.0466 (17)	0.0348 (18)	0.0274 (16)	−0.0073 (13)	0.0027 (12)	−0.0056 (13)
N11	0.070 (2)	0.043 (2)	0.0274 (16)	−0.0072 (17)	0.0056 (15)	−0.0061 (17)
C12	0.0307 (15)	0.040 (2)	0.0272 (17)	−0.0040 (14)	0.0026 (13)	−0.0050 (15)
N13	0.061 (2)	0.0304 (18)	0.0309 (16)	−0.0055 (14)	0.0007 (14)	−0.0073 (13)
C14	0.0297 (15)	0.0329 (19)	0.0258 (17)	−0.0026 (13)	−0.0013 (12)	−0.0018 (14)
C15	0.0351 (16)	0.035 (2)	0.0270 (17)	0.0000 (14)	−0.0019 (13)	0.0009 (14)
C16	0.0362 (17)	0.040 (2)	0.0274 (16)	−0.0037 (14)	0.0023 (13)	−0.0074 (15)
OW1	0.0542 (18)	0.0508 (19)	0.0437 (17)	−0.0107 (14)	0.0046 (14)	−0.0125 (14)

Geometric parameters (Å, º) top

S1—O2	1.466 (3)	N10—C12	1.382 (4)
S1—O5	1.471 (2)	N10—H10	0.88 (4)
S1—O3	1.473 (2)	N11—C16	1.316 (5)
S1—O4	1.484 (3)	N11—H11A	0.80 (6)
O6—C15	1.223 (5)	N11—H11B	0.89 (5)
N8—C14	1.449 (4)	C12—N13	1.335 (5)
N8—H8A	0.8900	C12—C14	1.377 (5)
N8—H8B	0.8900	N13—H13A	0.98 (6)
N8—H8C	0.8900	N13—H13B	0.91 (5)
N9—C16	1.343 (5)	C14—C15	1.407 (5)
N9—C15	1.415 (4)	OW1—HW12	0.953 (10)
N9—H9	0.82 (3)	OW1—HW11	0.954 (10)
N10—C16	1.333 (5)

O2—S1—O5	110.53 (16)	C16—N11—H11B	128 (3)
O2—S1—O3	110.29 (15)	H11A—N11—H11B	102 (5)
O5—S1—O3	108.68 (14)	N13—C12—C14	126.4 (3)
O2—S1—O4	108.20 (15)	N13—C12—N10	115.6 (3)
O5—S1—O4	109.32 (14)	C14—C12—N10	118.0 (3)
O3—S1—O4	109.81 (14)	C12—N13—H13A	117 (4)
C14—N8—H8A	109.5	C12—N13—H13B	126 (3)
C14—N8—H8B	109.5	H13A—N13—H13B	115 (4)
H8A—N8—H8B	109.5	C12—C14—C15	121.8 (3)
C14—N8—H8C	109.5	C12—C14—N8	121.3 (3)
H8A—N8—H8C	109.5	C15—C14—N8	116.9 (3)
H8B—N8—H8C	109.5	O6—C15—C14	126.6 (3)
C16—N9—C15	123.3 (3)	O6—C15—N9	118.4 (3)
C16—N9—H9	125 (3)	C14—C15—N9	115.0 (3)
C15—N9—H9	110 (3)	N11—C16—N10	120.3 (4)
C16—N10—C12	122.8 (3)	N11—C16—N9	120.6 (4)
C16—N10—H10	120 (4)	N10—C16—N9	119.0 (3)
C12—N10—H10	117 (4)	HW12—OW1—HW11	116 (5)
C16—N11—H11A	128 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N8—H8A···O4ⁱ	0.89	2.46	3.113 (4)	131
N8—H8A···O5ⁱ	0.89	1.99	2.827 (4)	157
N8—H8B···O3ⁱⁱ	0.89	1.94	2.788 (4)	159
N8—H8C···O5ⁱⁱⁱ	0.89	2.13	2.942 (4)	152
N9—H9···O4^iv	0.82 (4)	1.93 (4)	2.739 (5)	168 (4)
N10—H10···O2	0.88 (4)	1.87 (4)	2.677 (4)	152 (3)
N10—H10···O4	0.88 (4)	2.58 (5)	3.329 (4)	143 (4)
N11—H11A···O2	0.80 (5)	2.56 (7)	3.106 (6)	126 (5)
N11—H11A···OW1^v	0.80 (5)	2.29 (5)	2.956 (4)	142 (5)
N11—H11B···O3^iv	0.89 (6)	2.00 (6)	2.845 (6)	158 (5)
N13—H13A···OW1ⁱⁱ	0.98 (6)	1.98 (7)	2.924 (5)	161 (5)
N13—H13B···O4	0.91 (5)	2.10 (5)	2.961 (4)	156 (5)
OW1—HW12···O2	0.96 (6)	2.10 (6)	2.798 (4)	128 (5)
OW1—HW11···OW1^vi	0.96 (3)	2.59 (5)	3.390 (5)	141 (3)

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

Acknowledgements

The authors wish to express their gratitude to Edith Alig (Goethe-University), who provided us with the X-ray powder measurements, and to Wilhelm Maximilian Hützler, who helped with the interpretation of the single-crystal data.

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