Crystal structure and Hirshfeld surface analysis of the new cyclo­diphosphazane [EtNP(S)NMe2]2

Issaoui, C.; Chebbi, H.; Alouani, K.; Guesmi, A.

doi:10.1107/S2056989017005187

research communications

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ISSN: 2056-9890

Volume 73| Part 5| May 2017| Pages 682-686

https://doi.org/10.1107/S2056989017005187

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Crystal structure and Hirshfeld surface analysis of the new cyclodiphosphazane [EtNP(S)NMe₂]₂

Chokri Issaoui,^a Hammouda Chebbi,^a,^b ^* Khaled Alouani ^c and Abderrahmen Guesmi ^a

^aUniversity of Tunis El Manar, Faculty of Sciences of Tunis, Laboratory of Materials, Crystal Chemistry and Applied Thermodynamics, 2092 El Manar II,Tunis, Tunisia, ^bPreparatory Institute for Engineering Studies of Tunis, Street Jawaher Lel Nehru, 1089 Montfleury, Tunis, Tunisia, and ^cUniversity of Tunis El Manar, Faculty of Sciences of Tunis, Laboratory of Electrochemistry, 2092 El Manar II,Tunis, Tunisia
^*Correspondence e-mail: chebhamouda@yahoo.fr

Edited by S. Parkin, University of Kentucky, USA (Received 28 February 2017; accepted 4 April 2017; online 11 April 2017)

The cyclic compound 2,4-bis(dimethylamino)-1,3-diethylcyclodiphosphazane-2,4-dithione [systematic name: 2,4-bis(dimethylamino)-1,3-diethyl-1,3,2λ⁵,4λ⁵-diazadiphosphetidine-2,4-dithione], C₈H₂₂N₄P₂S₂ or [EtNP(S)NMe₂]₂, is member of a class of molecules that may be used, by virtue of their complexation properties, for the extraction of metals. This compound was characterized in solution by (¹H and ³¹P) NMR, and in the solid state by energy-dispersive X-ray spectroscopy (EDX) and by X-ray crystallography. In the crystal, the molecule sits on an inversion centre such that the P and N atoms form a centrosymmetric cyclic P₂N₂ arrangement. The crystal packing is dominated by van der Waals interactions. The prevalence of these interactions is illustrated by an analysis of the three-dimensional Hirshfeld surface (HS) and by two-dimensional fingerprint plots (FP). The relative contribution of different interactions to the HS indicates that the H⋯H contacts account for 74.3% of the total HS area.

Keywords: crystal structure; cyclodiphosphazane; [EtNP(S)NMe₂]₂; Hirshfeld surface analysis; fingerprint plots.

CCDC reference: 1015789

1. Chemical context

In the study of organophosphorus compounds, one of the aims is to prepare new complexing agents. Indeed, the literature shows many studies of the bidentate organophosphorus ligands HN[P(E)R₂]₂ (E: O, S, Se; Balazs et al. 1999 ; Silvestru et al. 2000 ; Ghesner et al. 2005 ; Cristurean et al. 2008 ) and RN[P(E)R₂]₂ (Benabicha et al. 1986 ; Ladeveze et al. 1986 ; Alouani et al. 2002 , 2007 ; Peulecke et al. 2009 ), etc. All of these ligands may act as chelating agents containing both hard (N) and soft (P) elements. In addition, the flexibility of the (EPNPE) system provides a ready means of altering, and thereby possibly improving, their complexing properties. Several complexes based on these ligands have been reported, such as those described by Bennis & Alouani (2012 ) and by Mejri et al. (2016 ).

We report here the synthesis, characterization by (¹H and ³¹P) NMR and energy-dispersive X-ray (EDX) spectroscopies, and a single-crystal structure of a new cyclodiphosphazane, 1,3-diethyl-2,4-dimethylamine-2,4-dithiocyclodiphosphazane, [EtNP(S)NMe₂]₂ (I). In order to evaluate the nature of the intermolecular interactions in the crystal packing and their associated energies, detailed analyses of Hirshfeld surfaces (HS) and fingerprint plot (FP) calculations were performed (Spackman & McKinnon, 2002 ; Parkin et al., 2007 ; Rohl et al., 2008 ; Spackman & Jayatilaka, 2009 ).

2. Structural commentary

The molecular structure of (I) is shown in Fig. 1, selected crystallographic data are presented in Table 1, and an EDX spectrum confirming the presence of C, N, P and S is shown in Fig. 2.

Table 1
Experimental details

Crystal data
Chemical formula	C₈H₂₂N₄P₂S₂
M_r	300.35
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	7.1975 (10), 11.448 (2), 9.645 (2)
β (°)	96.39 (3)
V (Å³)	789.8 (2)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.52
Crystal size (mm)	0.40 × 0.40 × 0.30

Data collection
Diffractometer	Enraf–Nonius CAD-4
Absorption correction	ψ scan (North et al.,1968 )
T_min, T_max	0.999, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	3150, 1724, 1463
R_int	0.016
(sin θ/λ)_max (Å⁻¹)	0.638

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.127, 1.08
No. of reflections	1724
No. of parameters	76
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.28, −0.27
Computer programs: CAD-4 EXPRESS (Duisenberg, 1992 ; Macíček & Yordanov, 1992 ), XCAD4 (Harms & Wocadlo, 1995 ), SHELXS97 (Sheldrick, 2008 ), SHELXL2014/7 (Sheldrick, 2015 ), Mercury (Macrae et al., 2006 ), WinGX (Farrugia, 2012 ) and publCIF (Westrip, 2010 ).

Figure 1
The molecular structure of (I)

. Atomic displacement parameters for the non-H atoms are drawn at the 30% probability level. Unlabelled atoms are related to labelled ones by the symmetry operation −x + 1, −y + 1, −z.

Figure 2
The EDX spectrum of (I)

, showing the presence of C, N, P, and S.

Each phosphorus atom is bonded to one sulfur and three nitrogen atoms, which are linked to methyl or ethyl groups. Atoms P1 and N1 form a centrosymmetric cyclic P₂N₂ arrangement about an inversion center (½, ½, 0). The P1—N1 distances in the ring [1.6856 (17) and 1.6719 (16) Å] are longer than the P1—N2 distance [1.6325 (19) Å], and the P1—S1 distance is 1.9291 (9) Å. These geometric parameters are in agreement with those observed in related non-cyclic and cyclic neutral ligands (Hill et al., 1994 ; Alouani et al., 2002; Peulecke et al., 2009; Chandrasekaran et al. 2011 ).

With regard to the conformation of (I), its structure differs from that of P₂S₂N₅C₉H₂₇ (S-NIPA) (Benabicha et al. 1986) primarily by the existence of the P₂N₂ ring. The literature also shows several similar ligands, for example trans-[(EtNH)P(S)NEt]₂ (Hill et al. 1994) and cis-P₂S₂N₄C₂₀H₄₂ (Chandrasekaran et al. 2011). The most similar known ligand to (I) is the cyclic molecule trans-[(EtNH)P(S)NEt]₂ (Hill et al. 1994). The two molecules differ in the environments of the nitrogen atoms, which are all bound to ethyl groups in trans-[(EtNH)P(S)NEt]₂, the peripheral carbons of which are all disordered.

3. Supramolecular features

A perspective view of (I) is presented in Fig. 3. Although there are several intra- and intermolecular close contacts of the form C—H⋯A (A = S, N), no classical hydrogen bonds are found and the dominant interactions are van der Waals contacts.

Figure 3
Perspective view of part of the crystal structure of (I)

, viewed approximately down the a axis. H atoms have been omitted for clarity.

4. Hirshfeld surface analysis

Organic small molecule crystal packings are often dominated by a particular type of interaction, e.g. hydrogen bonding or van der Waals contacts. However, the overall crystal packing is determined by a combination of many forces, and hence all of the intermolecular interactions of a structure should be taken into account. Visualization and exploration of intermolecular close contacts of a structure is invaluable, and this can be achieved using the Hirshfeld surface (Spackman & McKinnon, 2002; Spackman & Jayatilaka, 2009). A large range of properties can be visualized on the Hirshfeld surface with the program CrystalExplorer (Wolff et al., 2012 ), including d_e and d_i, which represent the distances from a point on the HS to the nearest atoms outside (external) and inside (internal) the surface, respectively.

Intermolecular distance information on the surface can be condensed into a two-dimensional histogram of d_e and d_i, which is a unique identifier for molecules in a crystal structure, and is known as a fingerprint plot (Parkin et al., 2007; Rohl et al., 2008). Instead of plotting d_e and d_i on the Hirshfeld surface, contact distances are normalized in CrystalExplorer using the van der Waals radius of the appropriate internal (r_i^vdw) and external (r_e^vdw) atom of the surface:

d_norm= (d_i − r_i^vdw)/r_i^vdw + (d_e − r_e^vdw)/r_e^vdw.

For (I), the three-dimensional HS mapped over d_norm is given in Fig. 4. Contacts with distances equal to the sum of the van der Waals radii are shown in white, and contacts with distances shorter than or longer than the related sum values are shown in red (highlighted contacts) or blue, respectively. Two-dimensional FP plots showing the occurrence of all kinds of intermolecular contacts are presented in Fig. 5a.

Figure 4
View of the three-dimensional Hirshfeld surface (HS) of (I)

mapped with d_norm.

Figure 5
The two-dimensional fingerprint plots of (I)

, showing (a) all interactions, and delineated into (b) H⋯H, (c) H⋯S and (d) H⋯N interactions [d_e and d_i represent the distances from a point on the HS to the nearest atoms outside (external) and inside (internal) the surface, respectively].

The H⋯H interactions are shown on the three-dimensional HS as white spots. These contacts appear in the middle of the scattered points in the two-dimensional FP (Fig. 5b), and represent the most significant contribution to the overall three-dimensional HS (74.3%). Significant H⋯S/S⋯H interactions (25.5%) can also be seen, indicated by the pair of wings in the two-dimensional FP with a prominent long spike at d_e + d_i ∼ 1.9Å (Fig. 5c). The H⋯N/N⋯H interactions are shown on the three-dimensional HS marked with a blue spot for long contacts. These comprise only 0.2% of the total Hirshfeld surface, and are represented by two symmetrical narrow pointed spikes with d_e + d_i ∼ 2 Å (Fig. 5d). The presence of these interactions may also be shown by the Hirshfeld surface mapped as a function of curvedness (Fig. 6).

Figure 6
Hirshfeld surface of (I)

mapped over curvedness.

5. Synthesis and crystallization

All reagents and solvents were obtained from commercial sources and used without further purification. The synthesis of (I) was carried out in three steps:

• Step 1: Addition of pyridine dropwise to a solution in anhydrous heptane of 2 mol of (EtNH₂HCl) and 2 mol of PCl₃ at 268 K, gave precipitation in the form of a salt. Then, the reaction mixture was refluxed for 24 h. An oil was obtained after filtration of the pyridinium salt and evaporation of the heptane and the excess PCl₃. This step corresponds to the formation of P₂N₂ cycle, according to the bibliographic data (Chandrasekaran et al. 2011; Hill et al. 1994). All these operations were conducted under a nitrogen atmosphere to avoid hydrolysis of the chlorinated compounds. The yield of this step is 85% with respect to ethylammonium chloride.

• Step 2: At a temperature of 263 K, 1 mol of the synthesized [EtNPCl]₂ was added dropwise to an ether solution containing 2 mol of dimethylamine, 2 mol of triethylamine and 4-dimethylaminopyridine (4-DMAP) as catalyst. After 10 h of agitation, Et₃NHCl was precipitated. Filtration of the salt and evaporation of the ether gave an oil. All these operations were conducted under a nitrogen atmosphere. The yield of this step is 40%.

• Step 3: The sulfurization of [EtNPNMe₂]₂ with 2 mol of sulfur gave the final product, 1,3-diethyl-2,4-dimethyl-2,4-dithio-cyclodiphosphazane (I), in a yield of about 80%.

Crystallization was carried out from ethanol by slow evaporation at room temperature. After one week, yellow single crystals suitable for X-ray diffraction analysis were obtained. A qualitative EDX analysis on some crystals confirmed the presence of C, N, P and S.

Yield: (80%), yellow solid, ¹H NMR (300 MHz, CDCl₃): δ (ppm) 1.17 (t, 1H, ³J_HH = 7.26Hz), 2.91 (d, 1H, ³J_HP = 12.45Hz), 3.03 (m, 2H); ³¹P NMR (300 MHz, CDCl₃): δ (ppm) 60.13 (1P).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1. H atoms attached to CH₃ and CH₂ groups were placed geometrically and refined using a riding model: C—H = 0.96 Å for CH₃ group with U_iso(H) = 1.5U_eq(C) and C—H = 0.97Å for CH₂ group with U_iso(H) = 1.2U_eq(C).

Supporting information

CCDC reference: 1015789

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017005187/pk2598sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017005187/pk2598Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017005187/pk2598Isup3.cml

checkCIF report

Computing details top

Data collection: CAD-4 EXPRESS (Duisenberg, 1992; Macíček & Yordanov, 1992); cell refinement: CAD-4 EXPRESS (Duisenberg, 1992; Macíček & Yordanov, 1992); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014/7 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).

2,4-Bis(dimethylamino)-1,3-diethyl-1,3,2λ⁵,4λ⁵-diazadiphosphetidine-2,4-dithione top

Crystal data top

C₈H₂₂N₄P₂S₂	F(000) = 320
M_r = 300.35	D_x = 1.263 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 7.1975 (10) Å	Cell parameters from 25 reflections
b = 11.448 (2) Å	θ = 10–15°
c = 9.645 (2) Å	µ = 0.52 mm⁻¹
β = 96.39 (3)°	T = 293 K
V = 789.8 (2) Å³	Prism, yellow
Z = 2	0.40 × 0.40 × 0.30 mm

Data collection top

Enraf–Nonius CAD-4 diffractometer	1463 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.016
Graphite monochromator	θ_max = 27.0°, θ_min = 2.8°
ω/2θ scans	h = −9→4
Absorption correction: ψ scan (North et al.,1968)	k = −1→14
T_min = 0.999, T_max = 1.000	l = −12→12
3150 measured reflections	2 standard reflections every 120 reflections
1724 independent reflections	intensity decay: 1%

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.041	H-atom parameters constrained
wR(F²) = 0.127	w = 1/[σ²(F_o²) + (0.0779P)² + 0.1315P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
1724 reflections	Δρ_max = 0.28 e Å⁻³
76 parameters	Δρ_min = −0.27 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
P1	0.50835 (7)	0.50319 (4)	0.13083 (5)	0.0515 (2)
S1	0.33563 (10)	0.44283 (7)	0.25236 (6)	0.0790 (3)
N1	0.4319 (2)	0.58738 (14)	−0.00532 (16)	0.0535 (4)
N2	0.6900 (3)	0.56638 (18)	0.21583 (18)	0.0670 (5)
C1	0.7415 (5)	0.5568 (3)	0.3657 (3)	0.0952 (9)
H1A	0.8411	0.5013	0.3838	0.143*
H1B	0.6352	0.5313	0.4096	0.143*
H1C	0.7821	0.6316	0.4024	0.143*
C2	0.8350 (4)	0.6172 (3)	0.1411 (3)	0.0814 (7)
H2A	0.8611	0.6952	0.1740	0.122*
H2B	0.7932	0.6190	0.0431	0.122*
H2C	0.9465	0.5708	0.1569	0.122*
C3	0.3911 (4)	0.7123 (2)	−0.0151 (3)	0.0779 (7)
H3A	0.4058	0.7454	0.0781	0.093*
H3B	0.4816	0.7496	−0.0679	0.093*
C4	0.2046 (5)	0.7387 (3)	−0.0806 (5)	0.1204 (13)
H4A	0.1842	0.7000	−0.1692	0.181*
H4B	0.1921	0.8216	−0.0940	0.181*
H4C	0.1139	0.7121	−0.0218	0.181*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
P1	0.0546 (3)	0.0576 (3)	0.0405 (3)	0.0050 (2)	−0.0029 (2)	0.00125 (18)
S1	0.0763 (4)	0.1040 (5)	0.0580 (4)	−0.0017 (3)	0.0128 (3)	0.0143 (3)
N1	0.0607 (9)	0.0518 (8)	0.0455 (8)	0.0091 (7)	−0.0047 (6)	0.0007 (6)
N2	0.0686 (11)	0.0823 (12)	0.0463 (8)	−0.0038 (9)	−0.0108 (8)	−0.0049 (8)
C1	0.099 (2)	0.130 (2)	0.0502 (12)	−0.0017 (18)	−0.0202 (13)	−0.0108 (14)
C2	0.0660 (13)	0.0974 (18)	0.0771 (15)	−0.0159 (13)	−0.0078 (11)	−0.0025 (14)
C3	0.0919 (17)	0.0540 (11)	0.0833 (15)	0.0127 (11)	−0.0097 (13)	−0.0028 (11)
C4	0.091 (2)	0.087 (2)	0.178 (4)	0.0302 (17)	−0.007 (2)	0.038 (2)

Geometric parameters (Å, º) top

P1—N2	1.6325 (19)	C1—H1C	0.9600
P1—N1	1.6719 (16)	C2—H2A	0.9600
P1—N1ⁱ	1.6856 (17)	C2—H2B	0.9600
P1—S1	1.9291 (9)	C2—H2C	0.9600
P1—P1ⁱ	2.5143 (10)	C3—C4	1.450 (4)
N1—C3	1.460 (3)	C3—H3A	0.9700
N1—P1ⁱ	1.6857 (17)	C3—H3B	0.9700
N2—C2	1.455 (3)	C4—H4A	0.9600
N2—C1	1.456 (3)	C4—H4B	0.9600
C1—H1A	0.9600	C4—H4C	0.9600
C1—H1B	0.9600

N2—P1—N1	108.31 (10)	H1B—C1—H1C	109.5
N2—P1—N1ⁱ	112.28 (10)	N2—C2—H2A	109.5
N1—P1—N1ⁱ	83.02 (8)	N2—C2—H2B	109.5
N2—P1—S1	112.81 (8)	H2A—C2—H2B	109.5
N1—P1—S1	120.38 (7)	N2—C2—H2C	109.5
N1ⁱ—P1—S1	116.69 (7)	H2A—C2—H2C	109.5
N2—P1—P1ⁱ	117.58 (8)	H2B—C2—H2C	109.5
S1—P1—P1ⁱ	129.60 (4)	C4—C3—N1	113.7 (2)
C3—N1—P1	131.38 (16)	C4—C3—H3A	108.8
C3—N1—P1ⁱ	128.43 (17)	N1—C3—H3A	108.8
P1—N1—P1ⁱ	96.98 (8)	C4—C3—H3B	108.8
C2—N2—C1	113.9 (2)	N1—C3—H3B	108.8
C2—N2—P1	120.47 (15)	H3A—C3—H3B	107.7
C1—N2—P1	124.5 (2)	C3—C4—H4A	109.5
N2—C1—H1A	109.5	C3—C4—H4B	109.5
N2—C1—H1B	109.5	H4A—C4—H4B	109.5
H1A—C1—H1B	109.5	C3—C4—H4C	109.5
N2—C1—H1C	109.5	H4A—C4—H4C	109.5
H1A—C1—H1C	109.5	H4B—C4—H4C	109.5

Symmetry code: (i) −x+1, −y+1, −z.

Acknowledgements

Retired Professor Ahmed Driss, University of Tunis El Manar, Faculty of Sciences of Tunis, is thanked for his assistance in the measurement of the X-ray data.

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