Crystal structure of the 1:2 adduct of bis­(piperidinium) sulfate and 1,3-di­methyl­thio­urea

Döring, C.; Lueck, J.F.D.; Jones, P.G.

doi:10.1107/S2056989017004820

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Volume 73| Part 5| May 2017| Pages 651-653

https://doi.org/10.1107/S2056989017004820

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Crystal structure of the 1:2 adduct of bis(piperidinium) sulfate and 1,3-dimethylthiourea

Cindy Döring,^a Julian F. D. Lueck ^a and Peter G. Jones ^a ^*

^aInstitut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Postfach 3329, D-38023 Braunschweig, Germany
^*Correspondence e-mail: p.jones@tu-bs.de

Edited by P. C. Healy, Griffith University, Australia (Received 18 March 2017; accepted 28 March 2017; online 4 April 2017)

In the title compound, 2C₅H₁₂N⁺·SO₄²⁻·2C₃H₈N₂S, the C=S groups of the two independent 1,3-dimethylurea molecules and the sulfur atom of the anion lie on twofold axes. The packing is centred on bis(piperidinium) sulfate ribbons parallel to the c axis; the cations are hydrogen bonded to the sulfate by N—H⋯O and C—H⋯O interactions. The 1,3-dimethylurea molecules are also hydrogen bonded to sulfate O atoms, and project outwards from the ribbon parallel to the b axis.

Keywords: crystal structure; hydrogen bonds; piperidine; sulfate; dimethylthiourea.

CCDC reference: 1540583

1. Chemical context

We are interested in the structures of adducts of urea and thiourea, and simple derivatives of these compounds, with neutral molecules. We have published two reports on adducts of dioxane and morpholine with various methylthioureas (Jones et al., 2013 ; Taouss & Jones, 2016 ). In the course of our current investigations, we attempted to obtain adducts of methylthioureas with piperidine, although monoamines are not good adduct partners for ureas and thioureas. Indeed, no simple adducts were obtained. In one case, however, we overlayered a solution of 1,3-dimethylthiourea (1,3-DMT) in piperidine with diethyl ether and obtained colourless crystals, the structure of which is reported here.

2. Structural commentary

The crystals proved to be a 1:2 adduct of bis(piperidinium) sulfate and 1,3-DMT (Fig. 1), with the sulfate anion presumably generated by partial hydrolysis and/or decomposition of the 1,3-DMT under the influence of peroxides in the ether. The C=S bonds of both 1,3-DMT molecules lie along twofold axes. The sulfate sulfur atom also lies on a twofold axis. The piperidine lies on a general position. Molecular dimensions may be regarded as normal. Both 1,3-DMT molecules are essentially planar (r.m.s. deviation of non-H atoms: 0.004 and 0.010 Å). Both NH functions of each 1,3-DMT are trans to the C=S double bond across the respective C—N bond (associated with the hydrogen-bonding pattern, see below), so that the methyl groups are cis, with C_methyl—N—C=S torsion angles are close to zero [C11—N1—C1—S1 = 0.9 (2)° and S2—C2—N2—C21 = −2.05 (17)°]. Free 1,3-DMT crystallizes with four independent molecules, each of which has one NH group cis and one trans to C=S, but the structure is severely disordered (Jones et al., 2013).

Figure 1
The structure of the title compound in the crystal. Only the asymmetric unit is labelled. Displacement ellipsoids represent 50% probability levels. The dashed lines represent hydrogen bonds.

3. Supramolecular features

The packing is based on bis(piperidinium) sulfate ribbons parallel to the c axis in the region x, y ≃ 1/2 (Fig. 2) and also at x, y ≃ 0, etc.; the cations are hydrogen bonded to the sulfate by N—H⋯O interactions, as expected, but also by a short interaction C15—H15A⋯O2 (Table 1). Each pair of successive sulfate ions in the ribbon is bridged by two piperidinium cations. The 1,3-DMT molecules are also hydrogen bonded to sulfate oxygens (Figs. 1 and 3); each 1,3-DMT bridges two oxygens of the same anion and projects outwards from the ribbons parallel to the b axis. In the presence of the sulfate oxygen atoms as strong hydrogen-bond acceptors, the 1,3-DMT sulfur atoms do not accept any classical hydrogen bonds.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H03⋯O1	0.86 (3)	2.06 (3)	2.9062 (18)	173 (2)
N2—H04⋯O2	0.89 (2)	2.00 (2)	2.8874 (17)	172 (2)
N11—H01⋯O1ⁱ	0.83 (2)	1.98 (2)	2.7953 (18)	167.4 (19)
N11—H02⋯O2	0.91 (2)	1.85 (2)	2.7589 (17)	176 (2)
C12—H12A⋯S1ⁱⁱ	0.99	2.94	3.8213 (17)	150
C15—H15A⋯O2ⁱⁱⁱ	0.99	2.49	3.435 (2)	158
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) $[x-{\script{1\over 2}}, y+{\script{1\over 2}}, z]$ ; (iii) $[x, -y+1, z+{\script{1\over 2}}]$ .

Figure 2
Packing diagram of the title compound: the bis(piperidinium) sulfate substructure viewed parallel to the b axis. Dashed lines represent hydrogen bonds. Hydrogen atoms not involved in hydrogen bonds are omitted for clarity.

Figure 3
Packing diagram of the title compound: attachment of the thiourea molecules to the bis(piperidinium) sulfate chain, viewed perpendicular to the bc plane. Dashed lines represent hydrogen bonds. Methylene hydrogen atoms are omitted for clarity.

4. Database survey

A search of the Cambridge Database (Version 1.19; Groom et al., 2016 ) found three adducts of 1,3-DMT, excluding metal complexes. The 1:2 adduct between 18-crown-6 and 1,3-DMT (Weber, 1983 ) also displays a trans geometry for both NH functions, but the 1:2 adduct between 1,4-dioxane and 1,3-DMT (Jones et al., 2013) and a 1,3-DMT adduct of a 1,3-DMT-gold(I) complex (Eikens et al., 1994 ) both have one NH function cis and one trans. Only one other piperidinium sulfate derivative was found, namely tris(piperidinium) hydrogensulfate sulfate (Lukianova et al., 2015 ).

5. Synthesis and crystallization

208 mg (2 mmol) 1,3-DMT were dissolved in 2 mL piperidine. The solution was overlayered with diethyl ether. Colourless needles formed overnight.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The asymmetric unit was chosen such that the occupied twofold axis is $[1\over2]$ , y, $[1\over4]$ . The NH hydrogen atoms were refined freely. The H atoms of the methyl groups were identified in a difference synthesis, idealized and refined as rigid groups allowed to rotate but not tip (C—H 0.98 Å, H—C—H 109.5°). Methylene H atoms were included using a riding model starting from calculated positions (C—H 0.99 Å).

Table 2
Experimental details

Crystal data
Chemical formula	2C₅H₁₂N⁺·SO₄²⁻·2C₃H₈N₂S
M_r	476.72
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	100
a, b, c (Å)	12.5899 (5), 17.5691 (6), 11.8980 (5)
β (°)	101.326 (4)
V (Å³)	2580.52 (17)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	2.89
Crystal size (mm)	0.25 × 0.05 × 0.02

Data collection
Diffractometer	Oxford Diffraction Xcalibur, Atlas, Nova
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2014 )
T_min, T_max	0.514, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	21112, 2701, 2295
R_int	0.073
(sin θ/λ)_max (Å⁻¹)	0.630

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.034, 0.084, 1.03
No. of reflections	2701
No. of parameters	152
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.38
Computer programs: CrysAlis PRO (Agilent, 2014), SHELXS97, SHELXL97 and XP (Sheldrick, 2008 ).

Supporting information

CCDC reference: 1540583

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989017004820/hg5484sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017004820/hg5484Isup2.hkl

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Bis(piperidin-1-ium) sulfate–1,3-dimethylthiourea (1/2) top

Crystal data top

2C₅H₁₂N⁺·SO₄²⁻·2C₃H₈N₂S	F(000) = 1032
M_r = 476.72	D_x = 1.227 Mg m⁻³
Monoclinic, C2/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -C 2yc	Cell parameters from 6031 reflections
a = 12.5899 (5) Å	θ = 4.4–76.2°
b = 17.5691 (6) Å	µ = 2.89 mm⁻¹
c = 11.8980 (5) Å	T = 100 K
β = 101.326 (4)°	Lath, colourless
V = 2580.52 (17) Å³	0.25 × 0.05 × 0.02 mm
Z = 4

Data collection top

Oxford Diffraction Xcalibur, Atlas, Nova diffractometer	2701 independent reflections
Radiation source: sealed X-ray tube	2295 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.073
Detector resolution: 10.3543 pixels mm^-1	θ_max = 76.2°, θ_min = 4.4°
ω scan	h = −15→15
Absorption correction: multi-scan (CrysAlisPro; Agilent, 2014)	k = −22→22
T_min = 0.514, T_max = 1.000	l = −14→14
21112 measured reflections

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)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.084	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.0415P)² + 0.6886P] where P = (F_o² + 2F_c²)/3
2701 reflections	(Δ/σ)_max = 0.001
152 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.38 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.

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 > 2sigma(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	0.5000	0.15866 (3)	0.2500	0.03441 (16)
N1	0.50629 (13)	0.29584 (8)	0.34615 (12)	0.0309 (3)
H03	0.509 (2)	0.3444 (14)	0.342 (2)	0.043 (6)*
C1	0.5000	0.25465 (12)	0.2500	0.0257 (4)
C11	0.5151 (2)	0.26298 (12)	0.45902 (17)	0.0474 (5)
H11A	0.4555	0.2271	0.4586	0.071*
H11B	0.5116	0.3035	0.5148	0.071*
H11C	0.5844	0.2361	0.4802	0.071*
S2	0.5000	0.85910 (3)	0.2500	0.02659 (14)
C2	0.5000	0.76309 (12)	0.2500	0.0225 (4)
N11	0.32010 (11)	0.51380 (7)	0.44604 (12)	0.0221 (3)
H01	0.3664 (18)	0.5141 (11)	0.5057 (19)	0.024 (5)*
H02	0.3518 (18)	0.5281 (12)	0.387 (2)	0.033 (5)*
C12	0.23562 (13)	0.57046 (9)	0.46151 (15)	0.0298 (3)
H12A	0.1816	0.5756	0.3892	0.036*
H12B	0.2697	0.6208	0.4809	0.036*
C13	0.18007 (15)	0.54456 (11)	0.55658 (17)	0.0361 (4)
H13A	0.1217	0.5809	0.5640	0.043*
H13B	0.2330	0.5441	0.6301	0.043*
C14	0.13203 (15)	0.46502 (11)	0.53210 (16)	0.0347 (4)
H14A	0.0996	0.4481	0.5972	0.042*
H14B	0.0739	0.4666	0.4627	0.042*
C15	0.21891 (14)	0.40868 (10)	0.51400 (14)	0.0305 (4)
H15A	0.2731	0.4031	0.5860	0.037*
H15B	0.1855	0.3583	0.4936	0.037*
C16	0.27441 (13)	0.43579 (9)	0.41936 (15)	0.0274 (3)
H16A	0.3334	0.4001	0.4114	0.033*
H16B	0.2217	0.4367	0.3457	0.033*
S3	0.5000	0.50921 (3)	0.2500	0.01895 (12)
O1	0.52691 (9)	0.46061 (6)	0.35314 (9)	0.0235 (2)
O2	0.40655 (9)	0.55785 (6)	0.26031 (9)	0.0233 (2)
N2	0.40879 (11)	0.72181 (8)	0.24440 (12)	0.0267 (3)
H04	0.4138 (19)	0.6711 (13)	0.246 (2)	0.036 (6)*
C21	0.30262 (14)	0.75398 (10)	0.24149 (17)	0.0331 (4)
H21A	0.2771	0.7787	0.1673	0.050*
H21B	0.3067	0.7916	0.3030	0.050*
H21C	0.2521	0.7134	0.2522	0.050*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0329 (3)	0.0197 (3)	0.0475 (4)	0.000	0.0000 (3)	0.000
N1	0.0440 (8)	0.0225 (7)	0.0268 (7)	−0.0030 (6)	0.0080 (6)	0.0015 (5)
C1	0.0233 (10)	0.0230 (10)	0.0304 (12)	0.000	0.0047 (9)	0.000
C11	0.0703 (15)	0.0421 (11)	0.0295 (10)	−0.0070 (10)	0.0092 (10)	0.0057 (8)
S2	0.0272 (3)	0.0187 (2)	0.0334 (3)	0.000	0.0047 (2)	0.000
C2	0.0274 (11)	0.0228 (10)	0.0170 (9)	0.000	0.0038 (8)	0.000
N11	0.0200 (6)	0.0247 (6)	0.0219 (6)	−0.0015 (5)	0.0046 (6)	−0.0001 (5)
C12	0.0247 (8)	0.0268 (8)	0.0375 (9)	0.0050 (6)	0.0047 (7)	0.0004 (6)
C13	0.0282 (8)	0.0425 (10)	0.0408 (10)	−0.0003 (7)	0.0145 (8)	−0.0107 (8)
C14	0.0262 (8)	0.0466 (10)	0.0347 (9)	−0.0073 (7)	0.0141 (7)	−0.0030 (7)
C15	0.0303 (8)	0.0301 (8)	0.0304 (8)	−0.0075 (6)	0.0041 (7)	0.0025 (6)
C16	0.0250 (8)	0.0258 (8)	0.0323 (9)	−0.0036 (6)	0.0077 (6)	−0.0051 (6)
S3	0.0194 (2)	0.0182 (2)	0.0195 (2)	0.000	0.00437 (18)	0.000
O1	0.0262 (5)	0.0221 (5)	0.0217 (5)	−0.0004 (4)	0.0033 (4)	0.0014 (4)
O2	0.0224 (5)	0.0219 (5)	0.0270 (6)	0.0033 (4)	0.0085 (4)	0.0017 (4)
N2	0.0289 (7)	0.0200 (6)	0.0310 (7)	−0.0007 (5)	0.0056 (6)	0.0008 (5)
C21	0.0284 (8)	0.0282 (8)	0.0428 (10)	−0.0022 (6)	0.0071 (7)	0.0009 (7)

Geometric parameters (Å, º) top

S1—C1	1.687 (2)	C13—H13A	0.9900
N1—C1	1.3428 (19)	C13—H13B	0.9900
N1—C11	1.446 (2)	C14—C15	1.522 (3)
N1—H03	0.86 (3)	C14—H14A	0.9900
C1—N1ⁱ	1.3427 (19)	C14—H14B	0.9900
C11—H11A	0.9800	C15—C16	1.514 (2)
C11—H11B	0.9800	C15—H15A	0.9900
C11—H11C	0.9800	C15—H15B	0.9900
S2—C2	1.687 (2)	C16—H16A	0.9900
C2—N2	1.3487 (18)	C16—H16B	0.9900
C2—N2ⁱ	1.3488 (18)	S3—O2	1.4786 (10)
N11—C12	1.494 (2)	S3—O2ⁱ	1.4786 (10)
N11—C16	1.4961 (19)	S3—O1ⁱ	1.4787 (11)
N11—H01	0.83 (2)	S3—O1	1.4787 (11)
N11—H02	0.91 (2)	N2—C21	1.445 (2)
C12—C13	1.512 (3)	N2—H04	0.89 (2)
C12—H12A	0.9900	C21—H21A	0.9800
C12—H12B	0.9900	C21—H21B	0.9800
C13—C14	1.528 (3)	C21—H21C	0.9800

C1—N1—C11	123.85 (16)	C15—C14—C13	110.69 (14)
C1—N1—H03	119.0 (16)	C15—C14—H14A	109.5
C11—N1—H03	117.0 (16)	C13—C14—H14A	109.5
N1ⁱ—C1—N1	114.8 (2)	C15—C14—H14B	109.5
N1ⁱ—C1—S1	122.61 (10)	C13—C14—H14B	109.5
N1—C1—S1	122.61 (10)	H14A—C14—H14B	108.1
N1—C11—H11A	109.5	C16—C15—C14	110.50 (14)
N1—C11—H11B	109.5	C16—C15—H15A	109.5
H11A—C11—H11B	109.5	C14—C15—H15A	109.5
N1—C11—H11C	109.5	C16—C15—H15B	109.5
H11A—C11—H11C	109.5	C14—C15—H15B	109.5
H11B—C11—H11C	109.5	H15A—C15—H15B	108.1
N2—C2—N2ⁱ	114.94 (19)	N11—C16—C15	110.17 (13)
N2—C2—S2	122.53 (9)	N11—C16—H16A	109.6
N2ⁱ—C2—S2	122.53 (9)	C15—C16—H16A	109.6
C12—N11—C16	112.53 (13)	N11—C16—H16B	109.6
C12—N11—H01	106.8 (14)	C15—C16—H16B	109.6
C16—N11—H01	111.5 (13)	H16A—C16—H16B	108.1
C12—N11—H02	110.0 (14)	O2—S3—O2ⁱ	109.39 (9)
C16—N11—H02	107.4 (14)	O2—S3—O1ⁱ	110.26 (6)
H01—N11—H02	108.6 (19)	O2ⁱ—S3—O1ⁱ	108.74 (6)
N11—C12—C13	109.67 (14)	O2—S3—O1	108.74 (6)
N11—C12—H12A	109.7	O2ⁱ—S3—O1	110.26 (6)
C13—C12—H12A	109.7	O1ⁱ—S3—O1	109.46 (9)
N11—C12—H12B	109.7	C2—N2—C21	124.43 (14)
C13—C12—H12B	109.7	C2—N2—H04	118.6 (15)
H12A—C12—H12B	108.2	C21—N2—H04	116.9 (15)
C12—C13—C14	110.89 (15)	N2—C21—H21A	109.5
C12—C13—H13A	109.5	N2—C21—H21B	109.5
C14—C13—H13A	109.5	H21A—C21—H21B	109.5
C12—C13—H13B	109.5	N2—C21—H21C	109.5
C14—C13—H13B	109.5	H21A—C21—H21C	109.5
H13A—C13—H13B	108.0	H21B—C21—H21C	109.5

C11—N1—C1—N1ⁱ	−179.1 (2)	C13—C14—C15—C16	−55.77 (19)
C11—N1—C1—S1	0.9 (2)	C12—N11—C16—C15	−58.13 (18)
C16—N11—C12—C13	57.99 (18)	C14—C15—C16—N11	56.16 (18)
N11—C12—C13—C14	−56.3 (2)	N2ⁱ—C2—N2—C21	177.95 (17)
C12—C13—C14—C15	56.1 (2)	S2—C2—N2—C21	−2.05 (17)

Symmetry code: (i) −x+1, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H03···O1	0.86 (3)	2.06 (3)	2.9062 (18)	173 (2)
N2—H04···O2	0.89 (2)	2.00 (2)	2.8874 (17)	172 (2)
N11—H01···O1ⁱⁱ	0.83 (2)	1.98 (2)	2.7953 (18)	167.4 (19)
N11—H02···O2	0.91 (2)	1.85 (2)	2.7589 (17)	176 (2)
C12—H12A···S1ⁱⁱⁱ	0.99	2.94	3.8213 (17)	150
C15—H15A···O2^iv	0.99	2.49	3.435 (2)	158

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

References

Agilent (2014). CrysAlis PRO. Agilent Technologies Ltd, Yarnton, England. Google Scholar
Eikens, W., Jones, P. G., Lautner, J. & Thöne, C. (1994). Z. Naturforsch. Teil B, 49, 21–26. CAS Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals Google Scholar
Jones, P. G., Taouss, C., Teschmit, N. & Thomas, L. (2013). Acta Cryst. B69, 405–413. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Lukianova, T. J., Kinzhybalo, V. & Pietraszko, A. (2015). Acta Cryst. E71, 1444–1446. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Taouss, C. & Jones, P. G. (2016). Z. Naturforsch. Teil B, 71, 905–907. CAS Google Scholar
Weber, G. (1983). Acta Cryst. C39, 896–899. CSD CrossRef CAS Web of Science IUCr Journals Google Scholar

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