research papers 1. Introduction
Acta Crystallographica Section C
Structural Chemistry ISSN 2053-2296
Two new thiophosphoramide structures: N,N0 ,N0 0 -tricyclohexylphosphorothioic triamide and O,O0 -diethyl (2-phenylhydrazin-1-yl)thiophosphonate
Up to now, for the P(S)[N]3 and P(S)[O]2[N] skeletons, 78 and 187 structures, respectively, have been deposited in the Cambridge Structural Database (CSD, Version 5.35, August 2014 update; Allen, 2002) (metal complexes were not considered and duplicated structures were excluded; however, different X-ray measurements for the same compound were considered separately).
Mehrdad Pourayoubi,a* Mozhgan Abrishami,b Va´clav Eigner,c,d Marek Necˇas,e Michal Dusˇekd and Mahmoud Delavarb a
Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran, Department of Chemistry, Payame Noor University, 19395-4697 Tehran, Iran, c Department of Solid State Chemistry, Institute of Chemical Technology, Technicka´ 5, 166 28 Prague, Czech Republic, dInstitute of Physics AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic, and eCEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic Correspondence e-mail: [email protected] b
Received 11 September 2014 Accepted 14 October 2014
The compound N,N0 ,N00 -tricyclohexylphosphorothioic triamide, C18H36N3PS or P(S)[NHC6H11]3, (I), crystallizes in the space group Pnma with the molecule lying across a mirror plane; one N atom lies on the mirror plane, whereas the bondangle sum at the other N atom has a deviation of some 8 from the ideal value of 360 for a planar configuration. The orientation of the atoms attached to this nonplanar N atom corresponds to an anti orientation of the corresponding lone electron pair (LEP) with respect to the P S group. The P S ˚ is within the expected range for bond length of 1.9785 (6) A compounds with a P(S)[N]3 skeleton; however, it is in the region of the longest bond lengths found for analogous structures. This may be due to the involvement of the P S group in N—H S P hydrogen bonds. In O,O0 -diethyl (2-phenylhydrazin-1-yl)thiophosphonate, C10H17N2O2PS or P(S)[OC2H5]2[NHNHC6H5], (II), the bond-angle sum at the N atom attached to the phenyl ring is 345.1 , whereas, for the N atom bonded to the P atom, a practically planar environment is observed, with a bond-angle sum of 359.1 . A Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B58, 380–388] analysis shows a shift of the maximum population of P S bond lengths in compounds with a P(S)[O]2[N] skeleton to the shorter bond lengths relative to compounds with a P(S)[N]3 skeleton. The influence of this difference on the collective tendencies of N S distances in N—H S hydrogen bonds for structures with P(S)[N]3 and P(S)[O]2[N] segments were studied through a CSD analysis. Keywords: crystal structure; thiophosphoramide; database analysis; P(S)[O]2[N] skeleton; phosphorothioic triamide; P(S)[N]3 skeleton; N—H S hydrogen bond; NMR experiment. Acta Cryst. (2014). C70, 1147–1152
Among the results of the P(S)[N]3 search, there are a few reports on the structure determinations of phosphorothioic triamides with a P(S)[N(C)(C)]3 skeleton, for example, [(CH3)2N]3P(S) (CSD refcode NAHWUO; Rudd et al., 1996). However, there is no report of a diffraction study of an [RNH]3P(S) phosphorothioic triamide. In fact, only one example of a compound with a P(S)[NH]3 skeleton {and not a P(S)[NH(C)]3 skeleton} was found in the CSD for the structure of [Me3SiNH]2P(S)–NH–P(S)[NHSiMe3]–NH–P(S)[NHSiMe3]2 (CSD refcode ICEDEZ; Pinkas & Verkade, 1998). For the P(S)[O]2[N] search, the variety of compounds deposited is larger compared with the P(S)[N]3 skeleton and structures with [O]2P(S)[N–C(S)] (Babashkina et al., 2011), [O]2P(S)[N–S(O)2] (Oltean et al., 2013) and [O]2P(S)[N–N] (Rybarczyk-Pirek et al., 2006) segments, and some others, were deposited. In a continuation of our previous reports on the structure determinations of phosphoramide (Pourayoubi, Necˇas & Negari, 2012; Tarahhomi et al., 2013) and thiophosphoramide compounds (Raissi Shabari et al., 2012; Sabbaghi et al., 2012) and a CSD analysis of different aspects of phosphoramide structures (Pourayoubi et al., 2013; Pourayoubi, Jasinski et al., 2012), we report here a study of thiophosphoramide structures. Thus, two thiophosphoramides, with P(S)[N]3 and P(S)[O]2[N] skeletons, have been studied, viz. P(S)[NHC6H11]3,
doi:10.1107/S2053229614022608
# 2014 International Union of Crystallography
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research papers Table 1 Experimental details.
Crystal data Chemical formula Mr Crystal system, space group Temperature (K) ˚) a, b, c (A , , ( ) ˚ 3) V (A Z Radiation type (mm1) Crystal size (mm) Data collection Diffractometer Absorption correction Tmin, Tmax No. of measured, independent and observed [I > 3(I)] reflections Rint ˚ 1) (sin / )max (A Refinement R[F 2 > 3(F 2)], wR(F 2), S No. of reflections No. of parameters H-atom treatment ˚ 3) max, min (e A
(I)
(II)
C18H36N3PS 357.5 Orthorhombic, Pnma 120 9.0897 (7), 18.6342 (15), 12.2598 (8) 90, 90, 90 2076.6 (3) 4 Mo K 0.24 0.30 0.30 0.25
C10H17N2O2PS 260.3 Monoclinic, P21/c 120 9.938 (1), 16.3798 (10), 8.4156 (6) 90, 104.553 (11), 90 1325.96 (19) 4 Mo K 0.35 0.72 0.50 0.24
Rigaku Saturn724+ (2x2 bin mode) diffractometer Multi-scan (CrystalClear-SM Expert; Rigaku, 2011) 0.852, 1.000 18907, 3731, 2645
Agilent Xcalibur Atlas Gemini ultra diffractometer Analytical (CrysAlis PRO; Agilent, 2012) 0.834, 0.925 9959, 3038, 2628
0.033 0.767
0.018 0.669
0.046, 0.130, 1.80 3731 117 H atoms treated by a mixture of independent and constrained refinement 0.55, 0.43
0.034, 0.106, 1.78 3038 170 H atoms treated by a mixture of independent and constrained refinement 0.28, 0.22
Computer programs: CrystalClear-SM Expert (Rigaku, 2011), CrysAlis PRO (Agilent, 2012), SUPERFLIP (Palatinus & Chapuis, 2007), JANA2006 (Petrˇı´cˇek et al., 2014), DIAMOND (Brandenburg & Putz, 2005), Mercury (Macrae et al., 2008) and enCIFer (Allen et al., 2004).
(I), and P(S)[OC2H5]2[NHNHC6H5], (II). Some differences and similarities of the structures with these skeletons are discussed considering structures (I) and (II) and analogous structures deposited in the CSD.
2. Experimental 2.1. Synthesis and crystallization
A previous article mentioned the general procedure for the synthesis of P(S)[NHR]3 phosphorothioic triamide and reported the 31P NMR data for some derivatives, such as P(S)[NHC6H11]3 (Hursthouse et al., 1986). Moreover, Mel’nikov & Zen’kevich (1955) reported a general method for the synthesis of some amides and hydrazides of dialkoxythiophosphoric acids, such as P(S)[OC2H5]2[NHNHC6H5], together with its melting point and the elemental analysis for the P atom. In a more recent article (Riesel & Helbing, 1992), the phosphorous chemical shift of P(S)[OC2H5]2[NHNHC6H5] was found. The procedures reported here for the synthesis of (I) and (II) are similar to the literature methods but with a few modifications, for example, using an ice-bath temperature in this work instead of the reflux conditions used by Hursthouse et al. (1986). The syntheses for the preparation of (I) and (II) began with the reagents being combined at ice-bath temperature and the mixture then allowed to come to room temperature for the rest of the procedure. For the synthesis of (I), a solution of C6H11NH2 (60 mmol) in dry CH3CN (20 ml) was added to a
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solution of Cl3P(S) (10 mmol) in the same solvent (10 ml) at 273 K. After stirring for 4 h, the solid that formed was filtered off and the filtered solution was evaporated in vacuo to obtain the crude product as a solid which was washed with distilled water. Single crystals suitable for X-ray crystallography were obtained from a solution of (I) in CH3C(O)CH3/CH3CN (1:1 v/v) by slow evaporation at room temperature. IR (cm1): 3348, 3248, 2932, 2851, 1450, 1420, 1092, 883, 652. 31P NMR (162.0 MHz, DMSO-d6): 57.25 (m); 1H NMR (400.1 MHz, DMSO-d6): 1.05 (m, 6H), 1.15 (m, 9H), 1.51 (br m, 3H), 1.64 (br m, 6H), 1.85 (br m, 6H), 2.95 (br m, 3H), 3.63 (pseudo-t, J = 9.2/9.6 Hz, 3H, NH); 13C NMR (100.6 MHz, DMSO-d6): 25.75 (d, JP,C = 4.7 Hz), 35.72 (d, JP,C = 4.9 Hz), 40.44 (s), 50.48 (s) {the 31P chemical shift of P(S)[NHC6H11]3 in CDCl3 was reported at 59.1 p.p.m.; Hursthouse et al., 1986}. Compound (II) was synthesized from the reaction of C6H5NHNH2 (20 mmol) and P(S)[OC2H5]2Cl (10 mmol) in dry CH3CN [with a stirring time of 3 h and using the purification procedure mentioned for (I)]. Single crystals were obtained from a solution of the product in CH3C(O)CH3/ CH3CN (1:1 v/v) after slow evaporation at room temperature. IR (cm1): 3305, 2978, 2932, 2901, 1601, 1497, 1022, 957, 806, 644. 31P NMR (202.4 MHz, DMSO-d6): 71.08 (doublet of quintets, J = 42.7 Hz, J = 8.7/9.4/9.2/8.3 Hz); 1H NMR (500.1 MHz, DMSO-d6): 1.13 (t, J = 7.0 Hz, 6H), 3.55 (NH, evidence of a peak is observed near the signal 3.47 p.p.m. of water in d6-DMSO in the noted chemical shift), 3.94 (m, 4H), 6.63 (t, J = 7.2/6.6 Hz, 1H), 6.77 (d, J = 8.4 Hz, 2H), 7.08 (t, J = 7.4/7.5 Hz, 2H), 7.33 (d, J = 43.0 Hz, 1H); 13C NMR Acta Cryst. (2014). C70, 1147–1152
research papers Table 2 ˚ , ) for (I). Selected geometric parameters (A S1—P1 P1—N1 P1—N1i
1.9785 (6) 1.6475 (11) 1.6475 (11)
P1—N2 N1—C1 N2—C7
1.6284 (15) 1.4637 (15) 1.470 (2)
S1—P1—N1 S1—P1—N1i S1—P1—N2 N1—P1—N1i
116.50 (4) 116.50 (4) 108.46 (5) 98.51 (6)
N1—P1—N2 N1i—P1—N2 P1—N1—C1 P1—N2—C7
108.09 (5) 108.09 (5) 123.08 (9) 123.54 (11)
Symmetry code: (i) x; y þ 12; z.
(125.8 MHz, DMSO-d6): 16.61 (d, JP,C = 7.9 Hz), 63.38 (d, JP,C = 5.0 Hz), 113.19 (s), 119.19 (s), 129.36 (s), 150.57 (d, JP,C = 3.9 Hz) {in the paper published by Riesel & Helbing (1992), ethanol was used as solvent for the 31P NMR experiment of P(S)[OC2H5]2[NHNHC6H5] (75.1 p.p.m.)}.
Figure 2
2.2. Refinement
The anti orientation of the N1 lone electron pair (LEP) relative to the P S group in compound (I). For the C6H11NH groups, only the NH(C) segments are shown for clarity.
Crystal data, data collection and structure refinement details are summarized in Table 1. For both (I) and (II), all H atoms were discernible in difference Fourier maps and could be refined to reasonable geometry. According to common practice, H atoms bonded to C atoms were kept in ideal ˚ , while the positions of H atoms positions, with C—H = 0.96 A bonded to N atoms were refined freely; in both cases, Uiso(H) values were set at 1.2Ueq(C,N). All non-H atoms were refined using harmonic refinement. The disordered ethoxy group in (II) was refined freely with the sum of the occupancies restrained to 1.
3. Results and discussion
P1 S1 group lying on the mirror plane (Fig. 1). Selected bond lengths and angles for (I) are given in Table 2. The P atom is bonded in a distorted tetrahedral P(S)[N]3 environment with the three N—P—N angles more contracted than the three N—P—S angles; the smallest and largest angles are N1—P1—N1i = 98.51 (6) and N1—P1—S1/N1i—P1—S1 = 116.50 (4) [symmetry code: (i) x, y + 12, z]. The maximum and minimum angles are related to the S1/N1/N1i part of the tetrahedron formed by the S atom and the three N atoms around the P atom. Related to each cyclohexyl group, the rest of the NHP(S)[NHC6H11]2 segment occupies the equatorial position.
Compound (I) is the first X-ray diffraction study of an [RNH]3P(S) phosphorothioic triamide. The compound was synthesized from the reaction of P(S)Cl3 with cyclohexylamine (1:6 molar ratio) in dry CH3CN. This molecule has crystallographically imposed mirror symmetry, with atoms N2, C7 and C10 (and related H atoms) of one C6H11NH group and the
Figure 3 Figure 1 Displacement ellipsoid plot (50% probability level) and the atomnumbering scheme for (I). [Symmetry code: (i) x, y + 12, z.] Acta Cryst. (2014). C70, 1147–1152
Histogram of the P S bond lengths in compounds with a P(S)[N]3 segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column. Pourayoubi et al.
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research papers Table 3 ˚ , ) for (I). Hydrogen-bond geometry (A D—H A ii
N1—H1N1 S1 N2—H1N2 S1iii
D—H
H A
D A
D—H A
0.819 (17) 0.81 (2)
2.67 (2) 2.87 (3)
3.4720 (12) 3.6201 (18)
161.6 (16) 151.3 (19)
Symmetry codes: (ii) x 12; y þ 12; z þ 12; (iii) x þ 12; y þ 12; z þ 12.
Table 4 ˚ , ) for (II). Selected geometric parameters (A P1—S1 P1—N1 P1—O1 P1—O2
1.9302 (6) 1.6335 (14) 1.5734 (12) 1.543 (2)
N1—N2 N2—C1 O2—C9 O20 —C90
1.3970 (17) 1.399 (2) 1.449 (4) 1.461 (6)
S1—P1—N1 S1—P1—O1 S1—P1—O2 N1—P1—O1 N1—P1—O2
111.04 (5) 115.45 (4) 114.96 (10) 107.99 (7) 99.55 (10)
O1—P1—O2 P1—N1—N2 N1—N2—C1 P1—O1—C7 P1—O2—C9
106.49 (12) 119.69 (9) 118.31 (13) 120.67 (9) 117.59 (19)
The sp2 character of the N atom should be reflected in the P—N—C angles and the sum of the surrounding angles at the N atom; the angles at N1 and N2 do not show significant differences [at N1 = 123.08 (9) and at N2 = 123.54 (11) ]. Although the sums of the surrounding angles at these N atoms (P—N—C + C—N—H + H—N—P) show a distortion from planarity for N1 (a minor shift towards sp3-hybridization is observed), as the sum at N1 shows a deviation of about 8 from the value of 360 for a planar configuration, whereas the bond-angle sum at atom N2 is 360 . This difference in the contribution of the p-orbital in hybridization is reflected in the ˚ and P1—N2 = P—N bond lengths [P1—N1 = 1.6475 (11) A ˚ ]. Interestingly, the orientation of the atoms 1.6284 (15) A attached to N1 (and N1i) suggests an anti orientation of the lone electron pair (LEP) on this N atom with respect to the P S group (Fig. 2). This observation is similar to what was found for RC(O)NHP(O)[NR1R2]2 phosphoric triamide
Figure 5 Part of the crystal packing of (I), showing the linear arrangement built from (N—H )2(N—H )S P groups. The hydrogen bonds are shown as dotted lines and C-bound H atoms have been omitted for clarity. [Symmetry codes: (i) x, y + 12, z; (ii) x 12, y + 12, z + 12; (iii) x + 12, y + 12, z + 12.]
structures, where the orientation of atoms attached to the more pyramidal N atom suggests an anti orientation with respect to the P O group (Pourayoubi, Jasinski et al., 2012).
Figure 6 Figure 4 ˚ ) against P—Nave values in Scatterplot of P S bond lengths (A compounds with a P(S)[N]3 segment deposited in the CSD (Allen, 2002).
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Histogram of the N S distances of N—H S P hydrogen bonds in compounds with a P(S)[N]3 segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column. Acta Cryst. (2014). C70, 1147–1152
research papers Table 5 ˚ , ) for (II). Hydrogen-bond geometry (A D—H A i
N1—H1N1 O1 N2—H1N2 S1ii
D—H
H A
D A
D—H A
0.839 (18) 0.790 (18)
2.338 (17) 2.708 (18)
3.1301 (16) 3.4420 (15)
157.6 (18) 155.5 (16)
Symmetry codes: (i) x; y þ 32; z 12; (ii) x; y þ 32; z þ 12.
Figure 7 Displacement ellipsoid plot (50% probability level) and atom-numbering scheme for (II).
˚ ] is within the expected The P S bond length [1.9785 (6) A range for compounds with a P(S)[N]3 skeleton; however, it is located on the right extremity of the histogram obtained from a CSD analysis of P S bond lengths (the region of the longest bond lengths; Fig. 3) for such compounds. Fig. 4 shows the scatterplot of P S bond lengths against the related P—Nave value, i.e. (P—N1 + P—N2 + P—N3)/3, in compounds with a P(S)[N]3 skeleton. The P—Nave value may be considered as an indication of P—N bond strength and also of the amount of electron delocalization from the N atoms towards the P atom. Figure 9 Part of the crystal packing of (II), showing the linear arrangement built from N—H S P and N—H O hydrogen bonds. The hydrogen bonds are shown as dotted lines and C-bound H atoms have been omitted for clarity.
Figure 8 Histogram of the P S bond lengths in compounds with a P(S)[O]2[N] segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column. Acta Cryst. (2014). C70, 1147–1152
As can be seen, there is a trend for elongation of the P S bond length with smaller P—Nave values; however, there is considerable scatter in this correlation due to the other factors affecting these two values. ˚ ) is in the For compound (I), the P—Nave value (1.641 A region of the smallest P—Nave values of analogous compounds deposited in the CSD (Fig. 4). Thus, the electronic effect can be considered for interpretation of the relatively long P S bond length in (I). Moreover, the effect of hydrogen bonding is important, as in the crystal structure of (I) there is (N— H )2(N—H )S P hydrogen bonding (Fig. 5 and Table 3) connecting the molecules into extended chains parallel to the a axis. The N S distances in the mentioned hydrogen˚ , which are bonded group are 3.4720 (12) and 3.6201 (18) A within the expected range of N—H S P hydrogen bonds, shown as a histogram for related N S distances in compounds with a P(S)[N]3 skeleton deposited in the CSD {including compounds with P(S)[NH][N]2 and P(S)[NH]2[N] segments and one example for each of the P(S)[N–NH]3 (CSD Pourayoubi et al.
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research papers the LEP orientation on this pyramidal N atom is on the opposite side of the P S bond vector. The P1—O1—C7 bond angle of 120.67 (9) is similar to the P—O—C angles in compounds with a P(S)—O—R segment. The O2/O20 atoms of the ethoxy group in (II) indicate disorder over two sites. In the crystal structure, molecules are linked via ˚ ] and N—H O N—H S P [N S = 3.4420 (15) A ˚ [N O = 3.1301 (16) A] hydrogen bonds into a one-dimensional chain parallel to the c axis (Fig. 9 and Table 5). The N S distance in (II) is shorter than in (I) and this may be because of the anti co-operativity (Steiner, 2002) of the three hydrogen bonds received by one acceptor in (I); the collective tendency of N—H S distances in structures with a P(S)[O]2[N] segment (Fig. 10) shows more population in the longer distances for N S interactions relative to the collective tendency for structures with a P(S)[N]3 skeleton (due to the differences in the electron densities on S atoms in the mentioned skeletons being reflected in differences in the corresponding P S bond lengths). Figure 10 Histogram of the N S distances of N—H S P hydrogen bonds in compounds with a P(S)[O]2[N] segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column.
Michal Dusˇek acknowledges Czech Science Foundation (grant No. GACR 14–03276S).
References refcode JAQMOE; Chandrasekhar & Azhakar, 2005) and P(S)[NH]3 segments (CSD refcode ICEDEZ; Pinkas & Verkade, 1998) (Fig. 6); the 30 entries of N S distances in compounds with a P(S)[N]3 skeleton were found in the CSD}. Compound (II) was synthesized from the reaction of P(S)[OC2H5]2Cl with phenylhydrazine (1:2 molar ratio) in dry CH3CN. Selected bond lengths and angles for (II) are given in Table 4. The P atom is bonded in a distorted tetrahedral P(S)[O]2[N] ˚] environment (Fig. 7) and the P S bond length [1.9302 (6) A is shorter than the P S bond length of (I). A CSD analysis of P S bond lengths for compounds with a P(S)[N]3 skeleton shows the maximum population to be in the ˚ , which is populated by 70 bond lengths out range 1.92–1.94 A of 143 (about 49% of bonds found in the CSD); a similar analysis for compounds with a P(S)[O]2[N] skeleton shows the maximum population shift to shorter bond lengths and to be in ˚ (about 57%, 147 bonds from the total the range 1.90–1.92 A bonds of 260) (Fig. 8). This is an expected result because of the higher electronegativity of the two O atoms in the P(S)[O]2[N] segment with respect to the atoms of the P(S)[N]3 segment. It should be noted that the exact prediction of bond length (or the exact prediction of increasing/lowering of bond lengths with changing the groups) is impossible as electronegativity is only one of the factors affecting bond lengths and the effects of different factors and the overall tendency may not be predicted exactly. Of the two N atoms in the C6H5NHNH segment, atom N2 is significantly shifted towards sp3-hybridization relative to atom N1, which is almost perfectly planar (the bond-angle sums are 345.1 and 359.1 , respectively). Atom N2 is separated by the other N atom from the P S group and the vector introducing
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Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England. Allen, F. H. (2002). Acta Cryst. B58, 380–388. Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst. 37, 335–338. Babashkina, M. G., Safin, D. A., Bolte, M., Srebro, M., Mitoraj, M., Uthe, A., Klein, A. & Ko¨ckerling, M. (2011). Dalton Trans. 40, 3142–3153. Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany. Chandrasekhar, V. & Azhakar, R. (2005). CrystEngComm, 7, 346–349. Hursthouse, M. B., Ibrahim, E. H., Parkes, H. G., Shaw (ne´e Go¨zen), L. S., Shaw, R. A. & Watkins, D. A. (1986). Phosphorus Sulfur, 28, 261–266. Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470. Mel’nikov, N. N. & Zen’kevich, A. G. (1955). Zh. Obshch. Khim. 25, 828– 831. Oltean, D., Po¨llnitz, A. & Silvestru, A. (2013). Polyhedron, 53, 67–75. Palatinus, L. & Chapuis, G. (2007). J. Appl. Cryst. 40, 786–790. Petrˇı´cˇek, V., Dusˇek, M. & Palatinus, L. (2014). Z. Kristallogr. 229, 345–352. Pinkas, J. & Verkade, J. G. (1998). Heteroatom Chem. 9, 115–121. Pourayoubi, M., Jasinski, J. P., Shoghpour Bayraq, S., Eshghi, H., Keeley, A. C., Bruno, G. & Amiri Rudbari, H. (2012). Acta Cryst. C68, o399–o404. Pourayoubi, M., Necˇas, M. & Negari, M. (2012). Acta Cryst. C68, o51– o56. Pourayoubi, M., Toghraee, M., Divjakovic, V., van der Lee, A., Mancilla Percino, T., Leyva Ramı´rez, M. A. & Saneei, A. (2013). Acta Cryst. B69, 184–194. Raissi Shabari, A., Sabbaghi, F., Pourayoubi, M., Necˇas, M. & Babiak, M. (2012). Acta Cryst. E68, o3074. Riesel, L. & Helbing, R. (1992). Z. Anorg. Allg. Chem. 617, 148–154. Rigaku (2011). CrystalClear-SM Expert. Rigaku Americas Corporation, The Woodlands, Texas, USA. Rudd, M. D., Lindeman, S. V. & Husebye, S. (1996). Acta Chem. Scand. 50, 759–774. Rybarczyk-Pirek, A. J., Dubis, A. T., Grabowski, S. J. & Nawrot-Modranka, J. (2006). Chem. Phys. 320, 247–258. Sabbaghi, F., Pourayoubi, M. & Necˇas, M. (2012). Acta Cryst. E68, o2891. Steiner, T. (2002). Angew. Chem. Int. Ed. 41, 48–76. Tarahhomi, A., Pourayoubi, M., Golen, J. A., Zargaran, P., Elahi, B., Rheingold, A. L., Leyva Ramı´rez, M. A. & Mancilla Percino, T. (2013). Acta Cryst. B69, 260–270. Acta Cryst. (2014). C70, 1147–1152
Acta Crystallographica Section C
Structural Chemistry ISSN 2053-2296
Two new thiophosphoramide structures: N,N0 ,N0 0 -tricyclohexylphosphorothioic triamide and O,O0 -diethyl (2-phenylhydrazin-1-yl)thiophosphonate
Up to now, for the P(S)[N]3 and P(S)[O]2[N] skeletons, 78 and 187 structures, respectively, have been deposited in the Cambridge Structural Database (CSD, Version 5.35, August 2014 update; Allen, 2002) (metal complexes were not considered and duplicated structures were excluded; however, different X-ray measurements for the same compound were considered separately).
Mehrdad Pourayoubi,a* Mozhgan Abrishami,b Va´clav Eigner,c,d Marek Necˇas,e Michal Dusˇekd and Mahmoud Delavarb a
Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran, Department of Chemistry, Payame Noor University, 19395-4697 Tehran, Iran, c Department of Solid State Chemistry, Institute of Chemical Technology, Technicka´ 5, 166 28 Prague, Czech Republic, dInstitute of Physics AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic, and eCEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic Correspondence e-mail: [email protected] b
Received 11 September 2014 Accepted 14 October 2014
The compound N,N0 ,N00 -tricyclohexylphosphorothioic triamide, C18H36N3PS or P(S)[NHC6H11]3, (I), crystallizes in the space group Pnma with the molecule lying across a mirror plane; one N atom lies on the mirror plane, whereas the bondangle sum at the other N atom has a deviation of some 8 from the ideal value of 360 for a planar configuration. The orientation of the atoms attached to this nonplanar N atom corresponds to an anti orientation of the corresponding lone electron pair (LEP) with respect to the P S group. The P S ˚ is within the expected range for bond length of 1.9785 (6) A compounds with a P(S)[N]3 skeleton; however, it is in the region of the longest bond lengths found for analogous structures. This may be due to the involvement of the P S group in N—H S P hydrogen bonds. In O,O0 -diethyl (2-phenylhydrazin-1-yl)thiophosphonate, C10H17N2O2PS or P(S)[OC2H5]2[NHNHC6H5], (II), the bond-angle sum at the N atom attached to the phenyl ring is 345.1 , whereas, for the N atom bonded to the P atom, a practically planar environment is observed, with a bond-angle sum of 359.1 . A Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B58, 380–388] analysis shows a shift of the maximum population of P S bond lengths in compounds with a P(S)[O]2[N] skeleton to the shorter bond lengths relative to compounds with a P(S)[N]3 skeleton. The influence of this difference on the collective tendencies of N S distances in N—H S hydrogen bonds for structures with P(S)[N]3 and P(S)[O]2[N] segments were studied through a CSD analysis. Keywords: crystal structure; thiophosphoramide; database analysis; P(S)[O]2[N] skeleton; phosphorothioic triamide; P(S)[N]3 skeleton; N—H S hydrogen bond; NMR experiment. Acta Cryst. (2014). C70, 1147–1152
Among the results of the P(S)[N]3 search, there are a few reports on the structure determinations of phosphorothioic triamides with a P(S)[N(C)(C)]3 skeleton, for example, [(CH3)2N]3P(S) (CSD refcode NAHWUO; Rudd et al., 1996). However, there is no report of a diffraction study of an [RNH]3P(S) phosphorothioic triamide. In fact, only one example of a compound with a P(S)[NH]3 skeleton {and not a P(S)[NH(C)]3 skeleton} was found in the CSD for the structure of [Me3SiNH]2P(S)–NH–P(S)[NHSiMe3]–NH–P(S)[NHSiMe3]2 (CSD refcode ICEDEZ; Pinkas & Verkade, 1998). For the P(S)[O]2[N] search, the variety of compounds deposited is larger compared with the P(S)[N]3 skeleton and structures with [O]2P(S)[N–C(S)] (Babashkina et al., 2011), [O]2P(S)[N–S(O)2] (Oltean et al., 2013) and [O]2P(S)[N–N] (Rybarczyk-Pirek et al., 2006) segments, and some others, were deposited. In a continuation of our previous reports on the structure determinations of phosphoramide (Pourayoubi, Necˇas & Negari, 2012; Tarahhomi et al., 2013) and thiophosphoramide compounds (Raissi Shabari et al., 2012; Sabbaghi et al., 2012) and a CSD analysis of different aspects of phosphoramide structures (Pourayoubi et al., 2013; Pourayoubi, Jasinski et al., 2012), we report here a study of thiophosphoramide structures. Thus, two thiophosphoramides, with P(S)[N]3 and P(S)[O]2[N] skeletons, have been studied, viz. P(S)[NHC6H11]3,
doi:10.1107/S2053229614022608
# 2014 International Union of Crystallography
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research papers Table 1 Experimental details.
Crystal data Chemical formula Mr Crystal system, space group Temperature (K) ˚) a, b, c (A , , ( ) ˚ 3) V (A Z Radiation type (mm1) Crystal size (mm) Data collection Diffractometer Absorption correction Tmin, Tmax No. of measured, independent and observed [I > 3(I)] reflections Rint ˚ 1) (sin / )max (A Refinement R[F 2 > 3(F 2)], wR(F 2), S No. of reflections No. of parameters H-atom treatment ˚ 3) max, min (e A
(I)
(II)
C18H36N3PS 357.5 Orthorhombic, Pnma 120 9.0897 (7), 18.6342 (15), 12.2598 (8) 90, 90, 90 2076.6 (3) 4 Mo K 0.24 0.30 0.30 0.25
C10H17N2O2PS 260.3 Monoclinic, P21/c 120 9.938 (1), 16.3798 (10), 8.4156 (6) 90, 104.553 (11), 90 1325.96 (19) 4 Mo K 0.35 0.72 0.50 0.24
Rigaku Saturn724+ (2x2 bin mode) diffractometer Multi-scan (CrystalClear-SM Expert; Rigaku, 2011) 0.852, 1.000 18907, 3731, 2645
Agilent Xcalibur Atlas Gemini ultra diffractometer Analytical (CrysAlis PRO; Agilent, 2012) 0.834, 0.925 9959, 3038, 2628
0.033 0.767
0.018 0.669
0.046, 0.130, 1.80 3731 117 H atoms treated by a mixture of independent and constrained refinement 0.55, 0.43
0.034, 0.106, 1.78 3038 170 H atoms treated by a mixture of independent and constrained refinement 0.28, 0.22
Computer programs: CrystalClear-SM Expert (Rigaku, 2011), CrysAlis PRO (Agilent, 2012), SUPERFLIP (Palatinus & Chapuis, 2007), JANA2006 (Petrˇı´cˇek et al., 2014), DIAMOND (Brandenburg & Putz, 2005), Mercury (Macrae et al., 2008) and enCIFer (Allen et al., 2004).
(I), and P(S)[OC2H5]2[NHNHC6H5], (II). Some differences and similarities of the structures with these skeletons are discussed considering structures (I) and (II) and analogous structures deposited in the CSD.
2. Experimental 2.1. Synthesis and crystallization
A previous article mentioned the general procedure for the synthesis of P(S)[NHR]3 phosphorothioic triamide and reported the 31P NMR data for some derivatives, such as P(S)[NHC6H11]3 (Hursthouse et al., 1986). Moreover, Mel’nikov & Zen’kevich (1955) reported a general method for the synthesis of some amides and hydrazides of dialkoxythiophosphoric acids, such as P(S)[OC2H5]2[NHNHC6H5], together with its melting point and the elemental analysis for the P atom. In a more recent article (Riesel & Helbing, 1992), the phosphorous chemical shift of P(S)[OC2H5]2[NHNHC6H5] was found. The procedures reported here for the synthesis of (I) and (II) are similar to the literature methods but with a few modifications, for example, using an ice-bath temperature in this work instead of the reflux conditions used by Hursthouse et al. (1986). The syntheses for the preparation of (I) and (II) began with the reagents being combined at ice-bath temperature and the mixture then allowed to come to room temperature for the rest of the procedure. For the synthesis of (I), a solution of C6H11NH2 (60 mmol) in dry CH3CN (20 ml) was added to a
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solution of Cl3P(S) (10 mmol) in the same solvent (10 ml) at 273 K. After stirring for 4 h, the solid that formed was filtered off and the filtered solution was evaporated in vacuo to obtain the crude product as a solid which was washed with distilled water. Single crystals suitable for X-ray crystallography were obtained from a solution of (I) in CH3C(O)CH3/CH3CN (1:1 v/v) by slow evaporation at room temperature. IR (cm1): 3348, 3248, 2932, 2851, 1450, 1420, 1092, 883, 652. 31P NMR (162.0 MHz, DMSO-d6): 57.25 (m); 1H NMR (400.1 MHz, DMSO-d6): 1.05 (m, 6H), 1.15 (m, 9H), 1.51 (br m, 3H), 1.64 (br m, 6H), 1.85 (br m, 6H), 2.95 (br m, 3H), 3.63 (pseudo-t, J = 9.2/9.6 Hz, 3H, NH); 13C NMR (100.6 MHz, DMSO-d6): 25.75 (d, JP,C = 4.7 Hz), 35.72 (d, JP,C = 4.9 Hz), 40.44 (s), 50.48 (s) {the 31P chemical shift of P(S)[NHC6H11]3 in CDCl3 was reported at 59.1 p.p.m.; Hursthouse et al., 1986}. Compound (II) was synthesized from the reaction of C6H5NHNH2 (20 mmol) and P(S)[OC2H5]2Cl (10 mmol) in dry CH3CN [with a stirring time of 3 h and using the purification procedure mentioned for (I)]. Single crystals were obtained from a solution of the product in CH3C(O)CH3/ CH3CN (1:1 v/v) after slow evaporation at room temperature. IR (cm1): 3305, 2978, 2932, 2901, 1601, 1497, 1022, 957, 806, 644. 31P NMR (202.4 MHz, DMSO-d6): 71.08 (doublet of quintets, J = 42.7 Hz, J = 8.7/9.4/9.2/8.3 Hz); 1H NMR (500.1 MHz, DMSO-d6): 1.13 (t, J = 7.0 Hz, 6H), 3.55 (NH, evidence of a peak is observed near the signal 3.47 p.p.m. of water in d6-DMSO in the noted chemical shift), 3.94 (m, 4H), 6.63 (t, J = 7.2/6.6 Hz, 1H), 6.77 (d, J = 8.4 Hz, 2H), 7.08 (t, J = 7.4/7.5 Hz, 2H), 7.33 (d, J = 43.0 Hz, 1H); 13C NMR Acta Cryst. (2014). C70, 1147–1152
research papers Table 2 ˚ , ) for (I). Selected geometric parameters (A S1—P1 P1—N1 P1—N1i
1.9785 (6) 1.6475 (11) 1.6475 (11)
P1—N2 N1—C1 N2—C7
1.6284 (15) 1.4637 (15) 1.470 (2)
S1—P1—N1 S1—P1—N1i S1—P1—N2 N1—P1—N1i
116.50 (4) 116.50 (4) 108.46 (5) 98.51 (6)
N1—P1—N2 N1i—P1—N2 P1—N1—C1 P1—N2—C7
108.09 (5) 108.09 (5) 123.08 (9) 123.54 (11)
Symmetry code: (i) x; y þ 12; z.
(125.8 MHz, DMSO-d6): 16.61 (d, JP,C = 7.9 Hz), 63.38 (d, JP,C = 5.0 Hz), 113.19 (s), 119.19 (s), 129.36 (s), 150.57 (d, JP,C = 3.9 Hz) {in the paper published by Riesel & Helbing (1992), ethanol was used as solvent for the 31P NMR experiment of P(S)[OC2H5]2[NHNHC6H5] (75.1 p.p.m.)}.
Figure 2
2.2. Refinement
The anti orientation of the N1 lone electron pair (LEP) relative to the P S group in compound (I). For the C6H11NH groups, only the NH(C) segments are shown for clarity.
Crystal data, data collection and structure refinement details are summarized in Table 1. For both (I) and (II), all H atoms were discernible in difference Fourier maps and could be refined to reasonable geometry. According to common practice, H atoms bonded to C atoms were kept in ideal ˚ , while the positions of H atoms positions, with C—H = 0.96 A bonded to N atoms were refined freely; in both cases, Uiso(H) values were set at 1.2Ueq(C,N). All non-H atoms were refined using harmonic refinement. The disordered ethoxy group in (II) was refined freely with the sum of the occupancies restrained to 1.
3. Results and discussion
P1 S1 group lying on the mirror plane (Fig. 1). Selected bond lengths and angles for (I) are given in Table 2. The P atom is bonded in a distorted tetrahedral P(S)[N]3 environment with the three N—P—N angles more contracted than the three N—P—S angles; the smallest and largest angles are N1—P1—N1i = 98.51 (6) and N1—P1—S1/N1i—P1—S1 = 116.50 (4) [symmetry code: (i) x, y + 12, z]. The maximum and minimum angles are related to the S1/N1/N1i part of the tetrahedron formed by the S atom and the three N atoms around the P atom. Related to each cyclohexyl group, the rest of the NHP(S)[NHC6H11]2 segment occupies the equatorial position.
Compound (I) is the first X-ray diffraction study of an [RNH]3P(S) phosphorothioic triamide. The compound was synthesized from the reaction of P(S)Cl3 with cyclohexylamine (1:6 molar ratio) in dry CH3CN. This molecule has crystallographically imposed mirror symmetry, with atoms N2, C7 and C10 (and related H atoms) of one C6H11NH group and the
Figure 3 Figure 1 Displacement ellipsoid plot (50% probability level) and the atomnumbering scheme for (I). [Symmetry code: (i) x, y + 12, z.] Acta Cryst. (2014). C70, 1147–1152
Histogram of the P S bond lengths in compounds with a P(S)[N]3 segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column. Pourayoubi et al.
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research papers Table 3 ˚ , ) for (I). Hydrogen-bond geometry (A D—H A ii
N1—H1N1 S1 N2—H1N2 S1iii
D—H
H A
D A
D—H A
0.819 (17) 0.81 (2)
2.67 (2) 2.87 (3)
3.4720 (12) 3.6201 (18)
161.6 (16) 151.3 (19)
Symmetry codes: (ii) x 12; y þ 12; z þ 12; (iii) x þ 12; y þ 12; z þ 12.
Table 4 ˚ , ) for (II). Selected geometric parameters (A P1—S1 P1—N1 P1—O1 P1—O2
1.9302 (6) 1.6335 (14) 1.5734 (12) 1.543 (2)
N1—N2 N2—C1 O2—C9 O20 —C90
1.3970 (17) 1.399 (2) 1.449 (4) 1.461 (6)
S1—P1—N1 S1—P1—O1 S1—P1—O2 N1—P1—O1 N1—P1—O2
111.04 (5) 115.45 (4) 114.96 (10) 107.99 (7) 99.55 (10)
O1—P1—O2 P1—N1—N2 N1—N2—C1 P1—O1—C7 P1—O2—C9
106.49 (12) 119.69 (9) 118.31 (13) 120.67 (9) 117.59 (19)
The sp2 character of the N atom should be reflected in the P—N—C angles and the sum of the surrounding angles at the N atom; the angles at N1 and N2 do not show significant differences [at N1 = 123.08 (9) and at N2 = 123.54 (11) ]. Although the sums of the surrounding angles at these N atoms (P—N—C + C—N—H + H—N—P) show a distortion from planarity for N1 (a minor shift towards sp3-hybridization is observed), as the sum at N1 shows a deviation of about 8 from the value of 360 for a planar configuration, whereas the bond-angle sum at atom N2 is 360 . This difference in the contribution of the p-orbital in hybridization is reflected in the ˚ and P1—N2 = P—N bond lengths [P1—N1 = 1.6475 (11) A ˚ ]. Interestingly, the orientation of the atoms 1.6284 (15) A attached to N1 (and N1i) suggests an anti orientation of the lone electron pair (LEP) on this N atom with respect to the P S group (Fig. 2). This observation is similar to what was found for RC(O)NHP(O)[NR1R2]2 phosphoric triamide
Figure 5 Part of the crystal packing of (I), showing the linear arrangement built from (N—H )2(N—H )S P groups. The hydrogen bonds are shown as dotted lines and C-bound H atoms have been omitted for clarity. [Symmetry codes: (i) x, y + 12, z; (ii) x 12, y + 12, z + 12; (iii) x + 12, y + 12, z + 12.]
structures, where the orientation of atoms attached to the more pyramidal N atom suggests an anti orientation with respect to the P O group (Pourayoubi, Jasinski et al., 2012).
Figure 6 Figure 4 ˚ ) against P—Nave values in Scatterplot of P S bond lengths (A compounds with a P(S)[N]3 segment deposited in the CSD (Allen, 2002).
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Histogram of the N S distances of N—H S P hydrogen bonds in compounds with a P(S)[N]3 segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column. Acta Cryst. (2014). C70, 1147–1152
research papers Table 5 ˚ , ) for (II). Hydrogen-bond geometry (A D—H A i
N1—H1N1 O1 N2—H1N2 S1ii
D—H
H A
D A
D—H A
0.839 (18) 0.790 (18)
2.338 (17) 2.708 (18)
3.1301 (16) 3.4420 (15)
157.6 (18) 155.5 (16)
Symmetry codes: (i) x; y þ 32; z 12; (ii) x; y þ 32; z þ 12.
Figure 7 Displacement ellipsoid plot (50% probability level) and atom-numbering scheme for (II).
˚ ] is within the expected The P S bond length [1.9785 (6) A range for compounds with a P(S)[N]3 skeleton; however, it is located on the right extremity of the histogram obtained from a CSD analysis of P S bond lengths (the region of the longest bond lengths; Fig. 3) for such compounds. Fig. 4 shows the scatterplot of P S bond lengths against the related P—Nave value, i.e. (P—N1 + P—N2 + P—N3)/3, in compounds with a P(S)[N]3 skeleton. The P—Nave value may be considered as an indication of P—N bond strength and also of the amount of electron delocalization from the N atoms towards the P atom. Figure 9 Part of the crystal packing of (II), showing the linear arrangement built from N—H S P and N—H O hydrogen bonds. The hydrogen bonds are shown as dotted lines and C-bound H atoms have been omitted for clarity.
Figure 8 Histogram of the P S bond lengths in compounds with a P(S)[O]2[N] segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column. Acta Cryst. (2014). C70, 1147–1152
As can be seen, there is a trend for elongation of the P S bond length with smaller P—Nave values; however, there is considerable scatter in this correlation due to the other factors affecting these two values. ˚ ) is in the For compound (I), the P—Nave value (1.641 A region of the smallest P—Nave values of analogous compounds deposited in the CSD (Fig. 4). Thus, the electronic effect can be considered for interpretation of the relatively long P S bond length in (I). Moreover, the effect of hydrogen bonding is important, as in the crystal structure of (I) there is (N— H )2(N—H )S P hydrogen bonding (Fig. 5 and Table 3) connecting the molecules into extended chains parallel to the a axis. The N S distances in the mentioned hydrogen˚ , which are bonded group are 3.4720 (12) and 3.6201 (18) A within the expected range of N—H S P hydrogen bonds, shown as a histogram for related N S distances in compounds with a P(S)[N]3 skeleton deposited in the CSD {including compounds with P(S)[NH][N]2 and P(S)[NH]2[N] segments and one example for each of the P(S)[N–NH]3 (CSD Pourayoubi et al.
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research papers the LEP orientation on this pyramidal N atom is on the opposite side of the P S bond vector. The P1—O1—C7 bond angle of 120.67 (9) is similar to the P—O—C angles in compounds with a P(S)—O—R segment. The O2/O20 atoms of the ethoxy group in (II) indicate disorder over two sites. In the crystal structure, molecules are linked via ˚ ] and N—H O N—H S P [N S = 3.4420 (15) A ˚ [N O = 3.1301 (16) A] hydrogen bonds into a one-dimensional chain parallel to the c axis (Fig. 9 and Table 5). The N S distance in (II) is shorter than in (I) and this may be because of the anti co-operativity (Steiner, 2002) of the three hydrogen bonds received by one acceptor in (I); the collective tendency of N—H S distances in structures with a P(S)[O]2[N] segment (Fig. 10) shows more population in the longer distances for N S interactions relative to the collective tendency for structures with a P(S)[N]3 skeleton (due to the differences in the electron densities on S atoms in the mentioned skeletons being reflected in differences in the corresponding P S bond lengths). Figure 10 Histogram of the N S distances of N—H S P hydrogen bonds in compounds with a P(S)[O]2[N] segment deposited in the CSD (Allen, 2002). The number of hits in each region is given above the column.
Michal Dusˇek acknowledges Czech Science Foundation (grant No. GACR 14–03276S).
References refcode JAQMOE; Chandrasekhar & Azhakar, 2005) and P(S)[NH]3 segments (CSD refcode ICEDEZ; Pinkas & Verkade, 1998) (Fig. 6); the 30 entries of N S distances in compounds with a P(S)[N]3 skeleton were found in the CSD}. Compound (II) was synthesized from the reaction of P(S)[OC2H5]2Cl with phenylhydrazine (1:2 molar ratio) in dry CH3CN. Selected bond lengths and angles for (II) are given in Table 4. The P atom is bonded in a distorted tetrahedral P(S)[O]2[N] ˚] environment (Fig. 7) and the P S bond length [1.9302 (6) A is shorter than the P S bond length of (I). A CSD analysis of P S bond lengths for compounds with a P(S)[N]3 skeleton shows the maximum population to be in the ˚ , which is populated by 70 bond lengths out range 1.92–1.94 A of 143 (about 49% of bonds found in the CSD); a similar analysis for compounds with a P(S)[O]2[N] skeleton shows the maximum population shift to shorter bond lengths and to be in ˚ (about 57%, 147 bonds from the total the range 1.90–1.92 A bonds of 260) (Fig. 8). This is an expected result because of the higher electronegativity of the two O atoms in the P(S)[O]2[N] segment with respect to the atoms of the P(S)[N]3 segment. It should be noted that the exact prediction of bond length (or the exact prediction of increasing/lowering of bond lengths with changing the groups) is impossible as electronegativity is only one of the factors affecting bond lengths and the effects of different factors and the overall tendency may not be predicted exactly. Of the two N atoms in the C6H5NHNH segment, atom N2 is significantly shifted towards sp3-hybridization relative to atom N1, which is almost perfectly planar (the bond-angle sums are 345.1 and 359.1 , respectively). Atom N2 is separated by the other N atom from the P S group and the vector introducing
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