Redetermination of the structure of 2-amino-8-thia-1,5-di­aza­spiro­[4.5]dec-1-en-5-ium chloride monohydrate

Kayukova, L.A.; Yergaliyeva, E.M.; Vologzhanina, A.V.

doi:10.1107/S2056989022000111

research communications

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ISSN: 2056-9890

Volume 78| Part 2| February 2022| Pages 164-168

https://doi.org/10.1107/S2056989022000111

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Redetermination of the structure of 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride monohydrate

Lyudmila A. Kayukova,^a Elmira M. Yergaliyeva ^a and Anna V. Vologzhanina ^b ^*

^aJSC A. B. Bekturov Institute of Chemical Sciences, 106 Shokan Ualikhanov str., 050010, Almaty, Kazakhstan, and ^bX-Ray Structural Centre, A.N. Nesmeyanov Institute of Organoelement Compounds, RAS, 28 Vavilova str., 119991 Moscow, Russian Federation
^*Correspondence e-mail: vologzhanina@mail.ru

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 11 November 2021; accepted 5 January 2022; online 11 January 2022)

The reaction of β-(thiomorpholin-1-yl)propioamidoxime with tosyl chloride in CHCl₃ in the presence of DIPEA when heated at 343 K for 8 h afforded the title hydrated salt, C₇H₁₄N₃S⁺·Cl⁻·H₂O, in 84% yield. This course of the tosylation reaction differs from the result of tosylation obtained for this substrate at room temperature, when only 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-ene-5-ammonium tosylate was isolated in 56% yield. The structure of the reaction product was established by physicochemical methods, spectroscopy, and X-ray diffraction. The single-crystal data demonstrated that the previously reported crystal structure of this compound [Kayukova et al. (2021). Chem. J. Kaz, 74, 21–31] had been refined in a wrong space group. In the extended structure, the chloride anions, water molecules and amine groups of the cations form two-periodic hydrogen-bonded networks with the fes topology.

Keywords: crystal structure; hydrogen bonding; redetermination; spiro[4.5]dec-1-en-5-ium; tosylation.

CCDC references: 2106799; 2106798

1. Chemical context

Sulfochlorination of amidoximes is known to afford stable products of acylation at the oxygen atom of the amidoxime group; at the same time, the sulfochlorination reaction of derivatives of primary amidoximes can, depending on the structure of the starting amidoxime and reaction conditions, lead to rearranged products with the formation of ureas and substituted cyanamides (Tiemann, 1891 ; Bakunov et al., 2000 ; Doulou et al., 2014 ) .

Previously, in our studies of the acylation of β-aminopropioamidoximes with acid chlorides of substituted benzoic acids, only O-acyl-β-aminopropioamidoximes were identified as acylation reaction products. Their structures have been determined by the complex use of spectroscopic methods, as well as X-ray structural analysis (Kayukova, 2003 ; Beketov et al., 2004 ; Kayukova et al., 2010a ). The dehydration of the products of the O-acylation of β-aminopropioamidoximes allows for 3,5-disubstituted 1,2,4-oxadiazoles to be obtained, which under conditions of acid hydrolysis and in the presence of moisture are capable of undergoing a Boulton–Katritsky rearrangement to 2-amino-1,5-diazaspiro[4.5]dec-1-en-5-ium salts (Kayukova et al., 2010b , 2018 , 2021a ).

Recently, we found that the arylsulfochlorination reaction of β-aminopropioamidoximes at room temperature afforded 2-amino-8-(hetera)-1,5-diazaspiro[4.5]dec-1-en-5-ium arylsulfonates as the main products (Kayukova et al., 2020 , 2021b ). Herein we report on the result of β-(thiomorpholin-1-yl)propioamidoxime tosylation at the boiling point of the solvent. By means of such a high-temperature process, the formation of the most stable reaction product is expected. Under such conditions of thermodynamic control of the tosylation reaction of β-(thiomorpholin-1-yl)propioamidoxime (1) upon prolonged heating for 8 h at the boiling point of the solvent [CHCl₃, 8 h, 343 K (bath temperature)], in the presence of DIPEA, the title hydrated salt, 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride monohydrate (3) was obtained in good yield (84%). In our opinion, the source of hydrate formation was air moisture, since the formation of single crystals took place over a long time under conditions of natural evaporation of the solvent for crystallization with air access. This result of the amidoxime (1) tosylation differs from the result of the same reaction performed at room temperature, when the main kinetic product of the reaction was 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium tosylate (2) (Fig. 1, yield 56%; Kayukova et al., 2021b).

Figure 1
Results of the β-(thiomorpholin-1-yl)propioamidoxime (1) tosylation reaction at r.t. and at the boiling point of the solvent.

Spiropyrazolinium chloride monohydrate 3 is a white opaque precipitate, poorly soluble in chloroform. When the reaction was complete, it was filtered off from the reaction mixture and recrystallized from propanol-2 solution over three weeks in the form of transparent prisms with a melting point of 575 K. We previously isolated a compound with the same chemical composition and melting point during the acid hydrolysis of 5-aryl-3-(β-thiomorpholinoethyl)-1,2,4-oxadiazoles (Kayukova et al., 2010b). Not only the composition, but also the orthorhombic unit-cell parameters were similar for 3 and the previously reported structure; however, the space groups were different: P2₁2₁2₁ at room temperature (Kayukova et al., 2010b) and Pbca at 120.0 (2) K for 3, thus a single crystal of the reaction product was also determined at 295.0 (2) K and the resulting crystal structures were compared with the previously reported one.

2. Structural commentary

The molecular structure of 3 is shown in Fig. 2. The C3—N1 and N1—N2 bonds are elongated as compared with typical single bonds at 1.521 (1) and 1.463 (1) Å, respectively, which can be related to the anomeric effect of the lone pair of atom N2. The six- and five-membered rings of the C₇H₁₄N₃S⁺ cation adopt chair and envelope conformations, respectively. It may be noted that in respect to a chair conformation of the six-membered ring, atom N2 can be situated in the equatorial and axial positions of the N1 atom; however, in this and previously reported salts, only the axial disposition of the N2 atom is observed. This is in accord with our B3LYP/6-31++G(d,p) calculations of standard Gibbs free energies of reactions leading to the formation of various products. We established that the axial stereoisomer is more stable than the equatorial one (ΔG = −144.29 and −124.23 kJ mol⁻¹, respectively; Yergaliyeva et al., 2021 ).

Figure 2
Asymmetric unit of 3 at low temperature with displacement ellipsoids at the 50% probability level.

The envelope conformation of the C1/C2/C3/N1/N2 five-membered ring in 3 is expressed as the deviation of C3 from the mean plane formed by atoms N1/N2/C1/C2 (r.m.s. deviation = 0.005 Å): it is equal to 0.401 (1) Å, and the two molecular conformers (corresponding to different directions of this carbon atom shifted in respect to the N—N=C—C mean plane) are equally present in this centrosymmetric crystal. However, the previously reported crystal structure (Kayukova et al., 2010b) [refcode APOBOX in the Cambridge Crystallographic Database (CSD; Groom et al., 2016 )] contains two independent spiro-cations in the asymmetric unit with two different conformations of the five-membered ring (Fig. 3). A question arises as to whether these structures are polymorphs of the same salt, or if the previously reported structure was incorrectly solved and refined. Our study of the same single crystal of 3 at room temperature confirmed that no phase transition occurs between 120 and 295 K. Unfortunately, crystallographic data for APOBOX stored in the CSD could not be re-refined. Thus, we compared the crystal packing and the system of hydrogen bonds for the two models refined in different space groups.

Figure 3
The two independent 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium cations observed in APOBOX depicted as overlaid molecules.

3. Supramolecular features

First, the system of hydrogen bonds was compared for the two solids at 120.0 (2) and 295.0 (2) K (Tables 1 and 2) and they are essentially the same, apart from a slight lengthening of the H⋯X contacts at the higher temperature. In both cases, the amine acts as a donor of hydrogen bonds with a water molecule, an anion and the water molecules act as acceptors of N—H⋯O bonds and as donors in two O—H⋯Cl interactions, and the chloride anion is an acceptor of three hydrogen bonds. As a result, infinite layers parallel to the (001) plane are observed (Fig. 4). A topological analysis of the system of hydrogen bonds, where the spiro-cations act as linkers and water molecules and anions are three-connected nodes, indicates that both layers are isoreticular and have the fes topology (the three-letter code is given in terms of the RSCR notation; O'Keeffe et al., 2008 ).

Table 1
Hydrogen-bond geometry (Å, °) for the low-temperature structure

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯Cl1ⁱ	0.88	2.38	3.2560 (9)	175
N3—H3B⋯O1	0.88	1.95	2.7970 (11)	161
O1—H1A⋯Cl1	0.85	2.26	3.1042 (9)	175
O1—H1B⋯Cl1ⁱⁱ	0.85	2.27	3.1152 (9)	176
C5—H5B⋯N2ⁱⁱⁱ	0.99	2.58	3.3778 (12)	138
C6—H6A⋯N2^iv	0.99	2.55	3.3346 (12)	136
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (ii) ; (iii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iv) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z]$ .

Table 2
Hydrogen-bond geometry (Å, °) for the room-temperature structure

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯Cl1ⁱ	0.86	2.42	3.2786 (18)	174
N3—H3B⋯O1ⁱⁱ	0.86	1.99	2.821 (2)	162
O1—H1C⋯Cl1	0.85	2.28	3.1244 (17)	173
O1—H1D⋯Cl1ⁱⁱⁱ	0.85	2.29	3.1343 (17)	175
C6—H6B⋯N2^iv	0.97	2.61	3.391 (2)	138
Symmetry codes: (i) x, y+1, z; (ii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (iii) ; (iv) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ .

Figure 4
Top: fragment of the hydrogen-bonded layers in 3. Hydrogen bonds are depicted as dotted lines. C-bound H atoms are omitted. Bottom: underlying net of hydrogen bonds in 3 with a fes topology.

Additional analysis of the crystal packing by means of the PLATON package (Spek, 2020 ) suggests that the Pbca space group is correct for both solids, and by means of the `Crystal Packing Similarity' tool implemented within Mercury (Macrae et al., 2020 ) as described by Childs et al. (2009 ) or by Vologzhanina (2019 ) denotes that the packings of 30-molecule clusters for the two solids are also very close to each other (the average r.m.s. deviation of 0.15 Å can be explained by the different experimental temperatures). Thus, we propose that 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride monohydrate crystallizes in the Pbca space group both at low and room temperatures in contrast with the data given previously in space group P2₁2₁2₁(Kayukova et al., 2010b).

4. Synthesis and crystallization

IR spectra were obtained on a Thermo Scientific Nicolet 5700 FTIR instrument in KBr pellets. ¹H and ¹³C NMR spectra were recorded on a Bruker Avance III 500 MHz NMR spectrometer (500 and 126 MHz, respectively). Melting points were determined on a TPL apparatus (Khimlabpribor, Russia). The progress of the reaction was monitored using Sorbfil TLC plates (Sorbpolymer, Russia) coated with CTX-1A silica gel, grain size 5–17 µm, UV-254 indicator. The spots were developed in I₂ vapours and in the UV light of a chromatoscope (λ = 254 nm) TSX 254/365 (PETROLASER). The eluent for the analysis was a mixture of EtOH:benzene = 1:1 + a few drops of a 25% aqueous solution of NH₃. Microanalysis according to the Pregl method was carried out on an elemental analyser with the absorption of CO₂ and O₂ isolated during combustion with a two-degree repetition of combustion.

The tosylation of β-(thiomorpholin-1-yl)propioamidoxime (1) was performed in dried CHCl₃ with tosyl chloride in the presence of DIPEA, purchased from Sigma–Aldrich and used without purification. Solvents for synthesis, recrystallization and TLC analysis (EtOH, 2-PrOH, benzene, CHCl₃) were purified according to the standard procedures described for each solvent.

Synthesis of 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride hydrate (3):

To a solution of 1.00 g (0.0053 mol) of β-(thiomorpholin-1-yl)propioamidoxime (1) in 40 ml of CHCl₃, 0.92 ml (0.0053 mol) of DIPEA were added. The reaction mixture was cooled to 272 K, and a solution of 1.01 g (0.00530 mol) of tosyl chloride in 4 ml of CHCl₃ was added dropwise under stirring. The reaction mixture was stirred for 1 h at room temperature and was then heated and stirred at the reflux temperature of CHCl₃ for 8 h until the completion of the reaction, the progress of the reaction being monitored by TLC. The formed white precipitate of the chloride hydrate 3 was filtered off and recrystallized from 2-PrOH solution. The yield of 3 was 1.01 g (84%), m.p. 575 K, R_f 0.08. Found, %: C 37.67, H 7.49. C₇H₁₆ClN₃OS. Calculated, %: C 37.24, H 7.14. IR, cm⁻¹: 1659 (ν C=N); 1612 [d C—N; d (H)2—O]; 670 (ν S—C); 3135, 3230, 3380, 3384 (ν H—O, ν H—N). ¹H NMR, δ, ppm (J, Hz): 2.88 [m, 2H, S(CH_eq)₂], 3.14 [m, 2H, S(CH_ax)₂], 3.14 [m, 2H, N(+)CH₂CH₂]^§, 3.37 (br. s, 2H, H₂O), 3.62 [m, 2H, N(+)C(H_eq)₂], 3.74 [m, 2H, N(+)C(Hax)₂], 3.88 [t, 2H, J = 7.0, N(+)CH₂CH₂], 7.48 (br s, 2H, NH₂). The signals for the methylene protons of the N(+)CH₂CH₂ group in 3 coincide with the signals of the S(CH_ax)₂ group at δ 3.14 ppm.

5. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. The positions of hydrogen atoms were calculated and included in the refinement in isotropic approximation using a riding model with U_iso(H) = 1.5U_eq(O) and 1.2U_eq(X) for the other atoms.

Table 3
Experimental details

	120 K	295 K
Crystal data
Chemical formula	C₇H₁₄N₃S⁺·Cl⁻·H₂O	C₇H₁₄N₃S⁺·Cl⁻·H₂O
M_r	225.74	225.74
Crystal system, space group	Orthorhombic, Pbca	Orthorhombic, Pbca
a, b, c (Å)	11.0360 (18), 10.1005 (16), 19.291 (3)	11.0924 (4), 10.1898 (4), 19.6434 (8)
V (Å³)	2150.4 (6)	2220.28 (15)
Z	8	8
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	0.52	0.50
Crystal size (mm)	0.41 × 0.36 × 0.32	0.41 × 0.36 × 0.32

Data collection
Diffractometer	Bruker APEXII CCD	Bruker D8 Quest PHOTON area detector
Absorption correction	Multi-scan (SADABS; Bruker, 2016 )	Multi-scan (SADABS; Bruker, 2016)
T_min, T_max	0.633, 0.747	0.518, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	29600, 5145, 3893	29622, 2969, 2269
R_int	0.032	0.106
(sin θ/λ)_max (Å⁻¹)	0.830	0.684

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.030, 0.087, 1.06	0.048, 0.124, 1.05
No. of reflections	5145	2969
No. of parameters	121	118
H-atom treatment	H-atom parameters constrained	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.34	0.29, −0.34
Computer programs: APEX2 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC references: 2106799; 2106798

Crystal structure: contains datablocks 3_LT, 3_RT. DOI: https://doi.org/10.1107/S2056989022000111/hb8000sup1.cif

Structure factors: contains datablock 3_LT. DOI: https://doi.org/10.1107/S2056989022000111/hb80003_LTsup2.hkl

Structure factors: contains datablock 3_RT. DOI: https://doi.org/10.1107/S2056989022000111/hb80003_RTsup3.hkl

checkCIF report

Computing details top

For both structures, data collection: APEX2 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

2-Amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride monohydrate (3_LT) top

Crystal data top

C₇H₁₄N₃S⁺·Cl⁻·H₂O	D_x = 1.395 Mg m⁻³
M_r = 225.74	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 8488 reflections
a = 11.0360 (18) Å	θ = 2.8–35.6°
b = 10.1005 (16) Å	µ = 0.52 mm⁻¹
c = 19.291 (3) Å	T = 120 K
V = 2150.4 (6) Å³	Prism, colourless
Z = 8	0.41 × 0.36 × 0.32 mm
F(000) = 960

Data collection top

Bruker APEXII CCD diffractometer	3893 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.032
Absorption correction: multi-scan (SADABS; Bruker, 2016)	θ_max = 36.2°, θ_min = 2.1°
T_min = 0.633, T_max = 0.747	h = −18→18
29600 measured reflections	k = −16→16
5145 independent reflections	l = −26→32

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.030	H-atom parameters constrained
wR(F²) = 0.087	w = 1/[σ²(F_o²) + (0.050P)²] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max = 0.002
5145 reflections	Δρ_max = 0.44 e Å⁻³
121 parameters	Δρ_min = −0.34 e Å⁻³

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.

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

	x	y	z	U_iso*/U_eq
Cl1	−0.00746 (2)	0.63396 (2)	0.39143 (2)	0.02000 (6)
S1	0.70833 (2)	0.12361 (2)	0.74087 (2)	0.02033 (6)
N1	0.55731 (6)	0.31961 (6)	0.64122 (3)	0.01183 (11)
N2	0.53333 (6)	0.45906 (6)	0.62609 (4)	0.01348 (12)
N3	0.38623 (7)	0.57594 (7)	0.56713 (4)	0.02087 (15)
H3A	0.4200	0.6520	0.5782	0.025*
H3B	0.3199	0.5747	0.5418	0.025*
C1	0.43545 (7)	0.46295 (7)	0.58861 (4)	0.01473 (14)
C2	0.38062 (8)	0.33120 (8)	0.57138 (5)	0.02009 (16)
H2A	0.3594	0.3249	0.5216	0.024*
H2B	0.3077	0.3134	0.5997	0.024*
C3	0.48341 (7)	0.23868 (8)	0.58991 (4)	0.01713 (15)
H3C	0.5320	0.2156	0.5485	0.021*
H3D	0.4527	0.1564	0.6115	0.021*
C4	0.51885 (7)	0.29562 (8)	0.71514 (4)	0.01528 (14)
H4A	0.4304	0.3102	0.7189	0.018*
H4B	0.5595	0.3611	0.7454	0.018*
C5	0.54806 (8)	0.15791 (8)	0.74105 (4)	0.01851 (16)
H5A	0.5063	0.0922	0.7114	0.022*
H5B	0.5166	0.1479	0.7888	0.022*
C6	0.73185 (8)	0.16153 (8)	0.65050 (4)	0.01875 (16)
H6A	0.8190	0.1519	0.6393	0.022*
H6B	0.6862	0.0975	0.6217	0.022*
C7	0.69134 (7)	0.30023 (8)	0.63285 (4)	0.01590 (14)
H7A	0.7345	0.3637	0.6632	0.019*
H7B	0.7141	0.3200	0.5843	0.019*
O1	0.16762 (6)	0.51532 (7)	0.50099 (3)	0.02415 (14)
H1A	0.1157	0.5460	0.4727	0.036*
H1B	0.1256	0.4764	0.5318	0.036*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.02624 (11)	0.01477 (9)	0.01898 (10)	0.00288 (7)	0.00057 (7)	0.00344 (7)
S1	0.02337 (11)	0.01616 (10)	0.02145 (11)	0.00301 (7)	−0.00515 (8)	0.00290 (7)
N1	0.0134 (3)	0.0084 (2)	0.0137 (3)	−0.0004 (2)	−0.0002 (2)	−0.0008 (2)
N2	0.0158 (3)	0.0082 (3)	0.0165 (3)	0.0001 (2)	−0.0017 (2)	0.0006 (2)
N3	0.0217 (3)	0.0126 (3)	0.0283 (4)	0.0003 (3)	−0.0115 (3)	0.0011 (3)
C1	0.0149 (3)	0.0123 (3)	0.0171 (3)	−0.0004 (3)	−0.0010 (3)	−0.0010 (3)
C2	0.0198 (4)	0.0125 (3)	0.0279 (4)	−0.0015 (3)	−0.0091 (3)	−0.0019 (3)
C3	0.0215 (4)	0.0110 (3)	0.0189 (4)	−0.0006 (3)	−0.0058 (3)	−0.0036 (3)
C4	0.0183 (3)	0.0138 (3)	0.0137 (3)	0.0017 (3)	0.0035 (3)	0.0007 (3)
C5	0.0221 (4)	0.0153 (3)	0.0181 (4)	−0.0005 (3)	0.0025 (3)	0.0038 (3)
C6	0.0178 (4)	0.0169 (3)	0.0216 (4)	0.0057 (3)	0.0005 (3)	−0.0005 (3)
C7	0.0121 (3)	0.0163 (3)	0.0192 (4)	0.0010 (3)	0.0026 (3)	0.0024 (3)
O1	0.0161 (3)	0.0358 (4)	0.0205 (3)	−0.0016 (3)	−0.0015 (2)	0.0046 (3)

Geometric parameters (Å, º) top

S1—C5	1.8024 (9)	C3—H3C	0.9900
S1—C6	1.8038 (9)	C3—H3D	0.9900
N1—N2	1.4626 (9)	C4—H4A	0.9900
N1—C3	1.5210 (10)	C4—H4B	0.9900
N1—C4	1.5074 (10)	C4—C5	1.5128 (11)
N1—C7	1.5007 (10)	C5—H5A	0.9900
N2—C1	1.3003 (10)	C5—H5B	0.9900
N3—H3A	0.8800	C6—H6A	0.9900
N3—H3B	0.8800	C6—H6B	0.9900
N3—C1	1.3301 (10)	C6—C7	1.5093 (11)
C1—C2	1.4992 (11)	C7—H7A	0.9900
C2—H2A	0.9900	C7—H7B	0.9900
C2—H2B	0.9900	O1—H1A	0.8501
C2—C3	1.5125 (11)	O1—H1B	0.8499

C5—S1—C6	95.87 (4)	N1—C4—H4A	108.8
N2—N1—C3	106.89 (6)	N1—C4—H4B	108.8
N2—N1—C4	107.01 (5)	N1—C4—C5	113.60 (6)
N2—N1—C7	106.41 (6)	H4A—C4—H4B	107.7
C4—N1—C3	112.23 (6)	C5—C4—H4A	108.8
C7—N1—C3	112.85 (6)	C5—C4—H4B	108.8
C7—N1—C4	111.00 (6)	S1—C5—H5A	109.1
C1—N2—N1	106.89 (6)	S1—C5—H5B	109.1
H3A—N3—H3B	120.0	C4—C5—S1	112.66 (6)
C1—N3—H3A	120.0	C4—C5—H5A	109.1
C1—N3—H3B	120.0	C4—C5—H5B	109.1
N2—C1—N3	122.58 (7)	H5A—C5—H5B	107.8
N2—C1—C2	115.57 (7)	S1—C6—H6A	109.2
N3—C1—C2	121.84 (7)	S1—C6—H6B	109.2
C1—C2—H2A	111.5	H6A—C6—H6B	107.9
C1—C2—H2B	111.5	C7—C6—S1	111.87 (6)
C1—C2—C3	101.15 (6)	C7—C6—H6A	109.2
H2A—C2—H2B	109.4	C7—C6—H6B	109.2
C3—C2—H2A	111.5	N1—C7—C6	112.88 (6)
C3—C2—H2B	111.5	N1—C7—H7A	109.0
N1—C3—H3C	111.2	N1—C7—H7B	109.0
N1—C3—H3D	111.2	C6—C7—H7A	109.0
C2—C3—N1	102.94 (6)	C6—C7—H7B	109.0
C2—C3—H3C	111.2	H7A—C7—H7B	107.8
C2—C3—H3D	111.2	H1A—O1—H1B	104.5
H3C—C3—H3D	109.1

S1—C6—C7—N1	−64.89 (8)	C3—N1—C4—C5	68.11 (8)
N1—N2—C1—N3	178.26 (7)	C3—N1—C7—C6	−66.08 (9)
N1—N2—C1—C2	−1.35 (10)	C4—N1—N2—C1	−103.39 (7)
N1—C4—C5—S1	61.65 (8)	C4—N1—C3—C2	91.71 (8)
N2—N1—C3—C2	−25.32 (8)	C4—N1—C7—C6	60.89 (8)
N2—N1—C4—C5	−174.93 (6)	C5—S1—C6—C7	56.71 (7)
N2—N1—C7—C6	176.99 (6)	C6—S1—C5—C4	−55.24 (7)
N2—C1—C2—C3	−14.59 (10)	C7—N1—N2—C1	137.87 (7)
N3—C1—C2—C3	165.80 (8)	C7—N1—C3—C2	−141.97 (7)
C1—C2—C3—N1	22.86 (8)	C7—N1—C4—C5	−59.21 (8)
C3—N1—N2—C1	17.04 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···Cl1ⁱ	0.88	2.38	3.2560 (9)	175
N3—H3B···O1	0.88	1.95	2.7970 (11)	161
O1—H1A···Cl1	0.85	2.26	3.1042 (9)	175
O1—H1B···Cl1ⁱⁱ	0.85	2.27	3.1152 (9)	176
C5—H5B···N2ⁱⁱⁱ	0.99	2.58	3.3778 (12)	138
C6—H6A···N2^iv	0.99	2.55	3.3346 (12)	136

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

2-Amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride monohydrate (3_RT) top

Crystal data top

C₇H₁₄N₃S⁺·Cl⁻·H₂O	D_x = 1.351 Mg m⁻³
M_r = 225.74	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 8223 reflections
a = 11.0924 (4) Å	θ = 2.8–28.8°
b = 10.1898 (4) Å	µ = 0.50 mm⁻¹
c = 19.6434 (8) Å	T = 295 K
V = 2220.28 (15) Å³	Prism, colourless
Z = 8	0.41 × 0.36 × 0.32 mm
F(000) = 960

Data collection top

Bruker D8 Quest PHOTON area detector diffractometer	2269 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.106
phi and ω scans	θ_max = 29.1°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2016)	h = −15→14
T_min = 0.518, T_max = 0.746	k = −11→13
29622 measured reflections	l = −26→26
2969 independent reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.048	H-atom parameters constrained
wR(F²) = 0.124	w = 1/[σ²(F_o²) + (0.0532P)² + 0.7125P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
2969 reflections	Δρ_max = 0.29 e Å⁻³
118 parameters	Δρ_min = −0.34 e Å⁻³
0 restraints

Special details top

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

	x	y	z	U_iso*/U_eq
Cl1	0.50712 (5)	−0.13596 (5)	0.60611 (3)	0.04965 (17)
S1	0.28950 (5)	0.12409 (5)	0.73957 (3)	0.04811 (17)
N1	0.44413 (12)	0.31778 (13)	0.64306 (7)	0.0269 (3)
N2	0.46759 (13)	0.45621 (14)	0.62725 (8)	0.0308 (3)
N3	0.61220 (16)	0.57229 (17)	0.56826 (10)	0.0481 (5)
H3A	0.5789	0.6458	0.5787	0.058*
H3B	0.6764	0.5712	0.5437	0.058*
C1	0.52107 (19)	0.23660 (19)	0.59441 (11)	0.0433 (5)
H1A	0.5539	0.1599	0.6170	0.052*
H1B	0.4746	0.2086	0.5552	0.052*
C2	0.61951 (18)	0.32998 (19)	0.57400 (12)	0.0463 (5)
H2A	0.6923	0.3153	0.6003	0.056*
H2B	0.6382	0.3225	0.5259	0.056*
C3	0.56420 (16)	0.45980 (17)	0.59016 (9)	0.0325 (4)
C4	0.47724 (18)	0.29721 (19)	0.71662 (9)	0.0364 (4)
H4A	0.4345	0.3610	0.7442	0.044*
H4B	0.5629	0.3132	0.7222	0.044*
C5	0.4484 (2)	0.1611 (2)	0.74256 (11)	0.0438 (5)
H5A	0.4764	0.1533	0.7892	0.053*
H5B	0.4918	0.0972	0.7154	0.053*
C6	0.27154 (18)	0.1587 (2)	0.65017 (11)	0.0442 (5)
H6A	0.3183	0.0961	0.6240	0.053*
H6B	0.1875	0.1479	0.6378	0.053*
C7	0.31144 (16)	0.2961 (2)	0.63200 (10)	0.0384 (4)
H7A	0.2924	0.3128	0.5846	0.046*
H7B	0.2666	0.3585	0.6594	0.046*
O1	0.33147 (14)	−0.01611 (18)	0.49843 (8)	0.0577 (5)
H1C	0.3755	−0.0450	0.5305	0.087*
H1D	0.3711	0.0261	0.4686	0.087*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0635 (4)	0.0357 (3)	0.0498 (3)	0.0080 (2)	0.0013 (2)	0.0113 (2)
S1	0.0550 (3)	0.0369 (3)	0.0524 (3)	−0.0082 (2)	0.0144 (2)	0.0064 (2)
N1	0.0311 (7)	0.0193 (6)	0.0302 (7)	0.0009 (5)	0.0013 (5)	−0.0024 (5)
N2	0.0360 (8)	0.0194 (7)	0.0370 (8)	0.0012 (6)	0.0059 (6)	0.0009 (6)
N3	0.0517 (10)	0.0287 (8)	0.0640 (12)	−0.0021 (7)	0.0241 (8)	0.0024 (8)
C1	0.0537 (12)	0.0260 (9)	0.0500 (11)	0.0012 (8)	0.0201 (9)	−0.0096 (8)
C2	0.0443 (11)	0.0301 (10)	0.0644 (13)	0.0043 (8)	0.0196 (9)	−0.0042 (9)
C3	0.0358 (9)	0.0261 (8)	0.0355 (9)	0.0015 (7)	0.0037 (7)	−0.0016 (7)
C4	0.0446 (10)	0.0318 (9)	0.0326 (9)	−0.0055 (7)	−0.0092 (7)	0.0009 (7)
C5	0.0549 (12)	0.0363 (10)	0.0401 (10)	−0.0013 (9)	−0.0076 (9)	0.0111 (8)
C6	0.0400 (11)	0.0384 (11)	0.0540 (12)	−0.0131 (8)	−0.0035 (9)	−0.0026 (9)
C7	0.0319 (9)	0.0390 (10)	0.0444 (10)	−0.0051 (8)	−0.0081 (7)	0.0061 (8)
O1	0.0387 (8)	0.0872 (13)	0.0473 (8)	−0.0039 (8)	−0.0054 (6)	0.0084 (8)

Geometric parameters (Å, º) top

S1—C5	1.804 (2)	C2—H2B	0.9700
S1—C6	1.802 (2)	C2—C3	1.492 (2)
N1—N2	1.4676 (19)	C4—H4A	0.9700
N1—C1	1.525 (2)	C4—H4B	0.9700
N1—C4	1.506 (2)	C4—C5	1.512 (3)
N1—C7	1.504 (2)	C5—H5A	0.9700
N2—C3	1.296 (2)	C5—H5B	0.9700
N3—H3A	0.8600	C6—H6A	0.9700
N3—H3B	0.8600	C6—H6B	0.9700
N3—C3	1.335 (2)	C6—C7	1.511 (3)
C1—H1A	0.9700	C7—H7A	0.9700
C1—H1B	0.9700	C7—H7B	0.9700
C1—C2	1.503 (3)	O1—H1C	0.8500
C2—H2A	0.9700	O1—H1D	0.8499

C6—S1—C5	95.67 (9)	N1—C4—H4A	108.9
N2—N1—C1	106.83 (13)	N1—C4—H4B	108.9
N2—N1—C4	107.07 (13)	N1—C4—C5	113.56 (15)
N2—N1—C7	106.50 (13)	H4A—C4—H4B	107.7
C4—N1—C1	112.92 (15)	C5—C4—H4A	108.9
C7—N1—C1	112.18 (14)	C5—C4—H4B	108.9
C7—N1—C4	110.91 (14)	S1—C5—H5A	109.0
C3—N2—N1	107.02 (13)	S1—C5—H5B	109.0
H3A—N3—H3B	120.0	C4—C5—S1	112.80 (14)
C3—N3—H3A	120.0	C4—C5—H5A	109.0
C3—N3—H3B	120.0	C4—C5—H5B	109.0
N1—C1—H1A	111.1	H5A—C5—H5B	107.8
N1—C1—H1B	111.1	S1—C6—H6A	109.1
H1A—C1—H1B	109.1	S1—C6—H6B	109.1
C2—C1—N1	103.32 (15)	H6A—C6—H6B	107.9
C2—C1—H1A	111.1	C7—C6—S1	112.28 (14)
C2—C1—H1B	111.1	C7—C6—H6A	109.1
C1—C2—H2A	111.4	C7—C6—H6B	109.1
C1—C2—H2B	111.4	N1—C7—C6	112.86 (15)
H2A—C2—H2B	109.3	N1—C7—H7A	109.0
C3—C2—C1	101.88 (15)	N1—C7—H7B	109.0
C3—C2—H2A	111.4	C6—C7—H7A	109.0
C3—C2—H2B	111.4	C6—C7—H7B	109.0
N2—C3—N3	122.34 (16)	H7A—C7—H7B	107.8
N2—C3—C2	115.74 (16)	H1C—O1—H1D	112.9
N3—C3—C2	121.91 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···Cl1ⁱ	0.86	2.42	3.2786 (18)	174
N3—H3B···O1ⁱⁱ	0.86	1.99	2.821 (2)	162
O1—H1C···Cl1	0.85	2.28	3.1244 (17)	173
O1—H1D···Cl1ⁱⁱⁱ	0.85	2.29	3.1343 (17)	175
C6—H6B···N2^iv	0.97	2.61	3.391 (2)	138

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

Acknowledgements

The XRD study was carried out using the equipment of Center for Molecular Composition Studies of INEOS RAS.

Funding information

This research was funded by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (grant No. BR10965255).

References

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Volume 78| Part 2| February 2022| Pages 164-168

https://doi.org/10.1107/S2056989022000111

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Redetermination of the structure of 2-amino-8-thia-1,5-di­aza­spiro­[4.5]dec-1-en-5-ium chloride monohydrate

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Synthesis and crystallization

5. Refinement

Supporting information

Acknowledgements

Funding information

References

research communications

Redetermination of the structure of 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride monohydrate

3. Supramolecular features