Experimental. Crystal data

Transcription

1 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN N,N 0 -Dibenzyl-N 00 -(2,4-difluorobenzoyl)- N,N 0 -dimethylphosphoric triamide Mehrdad Pourayoubi, a Samad Shoghpour, a Laura Torre- Fernández b and Santiago García-Granda b * a Department of Chemistry, Ferdowsi University of Mashhad, Mashhad 91779, Iran, and b Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo CINN, C/ Julián Clavería, 8, Oviedo, Asturias, Spain Correspondence sgg@uniovi.es Received 25 November 2011; accepted 21 December 2011 Key indicators: single-crystal X-ray study; T = 300 K; mean (C C) = Å; R factor = 0.051; wr factor = 0.141; data-to-parameter ratio = In the title molecule, C 23 H 24 F 2 N 3 O 2 P, the P atom is in a distorted tetrahedral P( O)(N)(N) 2 environment, with the bond angles around the P atom in the range (11) (13). The phosphoryl and carbonyl groups, which are separated by an N atom, adopt an anti orientation relative to each other. In the C( O)NHP( O) fragment, the P N bond is longer [1.683 (2) Å] and the O P N angle is smaller [ (11) ] than the other P N bonds [1.613 (2) and (2) Å] and O P N bond angles [ (13) and (12) ], respectively. The N atoms have sp 2 character. In the crystal, pairs of P OH N hydrogen bonds form inversion dimers with R 2 2 (8) ring motifs. Experimental Crystal data C 23 H 24 F 2 N 3 O 2 P M r = Triclinic, P1 a = (6) Å b = (10) Å c = (8) Å = (7) = (5) Data collection Agilent Xcalibur Gemini R diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011) T min = 0.954, T max = Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections Table 1 Hydrogen-bond geometry (Å, ). = (7) V = (15) Å 3 Z =2 Cu K radiation = 1.44 mm 1 T = 300 K mm measured reflections 4209 independent reflections 2758 reflections with I > 2(I) R int = parameters H-atom parameters constrained max = 0.47 e Å 3 min = 0.27 e Å 3 Related literature For hydrogen-bond patterns in compounds with formula RC(O)NHP(O)[NR 1 R 2 ] 2 and RC(O)NHP(O)[NHR 1 ] 2 and for the discussion of different C( O) versus P( O) orientations in the C(O)NHP(O) fragment, see: Toghraee et al. (2011). For hydrogen-bond strengths in cyclic hydrogen-bond motifs and for bond lengths and angles, see: Pourayoubi et al. (2011). For graph-set analysis of hydrogen-bonds motifs, see: Bernstein et al. (1995). For the synthesis of the starting phosphorous chlorine compound, see: Pourayoubi et al. (2010). D HA D H HA DA D HA N2 H2O5 i (3) 171 Symmetry code: (i) x þ 1; y þ 1; z þ 1. Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 1999) and encifer (Allen et al., 2004). Financial support from the Spanish Ministerio de Educacion y Ciencia (MAT , MAT and the Factoría de Cristalización Consolider Ingenio 2010) and FEDER funding is acknowledged. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FY2035). o270 Pourayoubi et al. doi: /s

2 organic compounds References Agilent (2011). CrysAlis PRO. Agilent Technologies UK Ltd, Yarnton, England. Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst. 37, Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, Farrugia, L. J. (1999). J. Appl. Cryst. 32, 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, Pourayoubi, M., Tarahhomi, A., Rheingold, A. L. & Golen, J. A. (2010). Acta Cryst. E66, o3159. Pourayoubi, M., Tarahhomi, A., Saneei, A., Rheingold, A. L. & Golen, J. A. (2011). Acta Cryst. C67, o265 o272. Sheldrick, G. M. (2008). Acta Cryst. A64, Toghraee, M., Pourayoubi, M. & Divjakovic, V. (2011). Polyhedron, 30, Pourayoubi et al. C 23 H 24 F 2 N 3 O 2 P o271

3 [doi: /s ] N,N -Dibenzyl-N -(2,4-difluorobenzoyl)-N,N -dimethylphosphoric triamide Mehrdad Pourayoubi, Samad Shoghpour, Laura Torre-Fernández and Santiago García-Granda S1. Comment In a recently published paper, the collective behavior of hydrogen bonds (HBs) in the crystal packing of phosphoramidates having a C( O)NHP( O)(N) 2 and C( O)NHP( O)(NH) 2 skeletons were considered (Toghraee et al., 2011). The authors attempted to arrive at some empirical rules which are useful for predicting hydrogen-bond patterns in systems having "two H-acceptors and one H-donor site" and "two H-acceptors and three H-donor sites". As a continuation, the hydrogen bond strengths in such systems were analyzed based on hydrogen bond motifs (Pourayoubi et al., 2011). The structure determination of the title molecule, P(O)[NHC(O)C 6 H 3 (2,4-F 2 )][N(CH 3 )(CH 2 C 6 H 5 )] 2 (Fig. 1), was performed according to our interest in the collection of structural data related to new compounds having a C(O)NHP(O) skeleton. The phosphoryl and the carbonyl groups in the title molecule adopt an anti orientation relative to each other similarly to most of the carbacylamidophosphates. However, a few examples with a gauche orientation of these two groups were also reported (Toghraee et al., 2011). The phosphorus atom has a distorted tetrahedral configuration and the P O, C O, P N bond lengths and P N C bond angles are within the expected values. In the crystal structure, pairs of intermolecular P O H N hydrogen bonds (Table 1) form centrosymmetric dimers, see Figure 2, as R 22 (8) rings (Bernstein et al., 1995). S2. Experimental Synthesis of 2,4-F 2 C 6 H 3 C(O)NHP(O)Cl 2. 2,4-F 2 C 6 H 3 C(O)NHP(O)Cl 2 was prepared similarly to the procedure which was used for the preparation of 2,6-F 2 C 6 H 3 C(O)NHP(O)Cl 2 (Pourayoubi et al., 2010), but by using 2,4 F 2 C 6 H 3 C(O)NH 2 instead of 2,6 F 2 C 6 H 3 C(O)NH 2. Synthesis of title molecule. To a solution of 2,4-F 2 C 6 H 3 C(O)NHP(O)Cl 2 (2 mmol) in CHCl 3 (20 ml), a solution of N- methylbenzylamine (8 mmol) in CHCl 3 (5 ml) was added dropwise at 273 K. After 4 h stirring, the solvent was evaporated in vacuum and then the resulting solid was washed with distilled water. Single crystals of title compound were obtained from a mixture of CHCl 3 and n-c 7 H 16 (5 to 1 v/v) after slow evaporation at room temperature. IR (KBr, cm -1 ): 3064, 3043, 2872, 1683 (C O), 1615, 1453, 1343, 1265, 1215, 1175, 1155, 1128, 1088, 1017, 959, 877, 820, 791, 738, 714. S3. Refinement All H atoms were placed in geometrically calculated positions with N H = 0.86 Å and C H = 0.93 (aromatic C H), 0.96 (CH 3 ) or 0.97 Å (CH 2 ). H atoms were refined in riding mode with U iso (H) = 1.5 U eq (C) for methyl groups and U iso (H) = 1.2 U eq (C/N) for all other H atoms. sup-1

4 Figure 1 The molecular structure of the title compound with ellipsoids shown at the 30% probability level. Figure 2 A view of the centrosymmetric dimer formed by H-bonding. The H atoms not involved in the hydrogen bonding interaction have been omitted for clarity. sup-2

5 N,N -Dibenzyl-N -(2,4-difluorobenzoyl)- N,N -dimethylphosphoric triamide Crystal data C 23 H 24 F 2 N 3 O 2 P M r = Triclinic, P1 Hall symbol: -P 1 a = (6) Å b = (10) Å c = (8) Å α = (7) β = (5) γ = (7) V = (15) Å 3 Data collection Agilent Xcalibur Gemini R diffractometer Radiation source: Enhance (Cu) X-ray Source Graphite monochromator Detector resolution: pixels mm -1 ω scans Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011) T min = 0.954, T max = Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = S = reflections 268 parameters 0 restraints Primary atom site location: structure-invariant direct methods Z = 2 F(000) = 464 D x = Mg m 3 Cu Kα radiation, λ = Å Cell parameters from 2755 reflections θ = µ = 1.44 mm 1 T = 300 K Plate, colorless mm measured reflections 4209 independent reflections 2758 reflections with I > 2σ(I) R int = θ max = 70.7, θ min = 4.1 h = 8 12 k = l = Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ 2 (F o2 ) + (0.0585P) 2 ] where P = (F o 2 + 2F c2 )/3 (Δ/σ) max < Δρ max = 0.47 e Å 3 Δρ min = 0.27 e Å 3 Special details Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wr and goodness of fit S are based on F 2, conventional R-factors R are based on F, with F set to zero for negative F 2. The threshold expression of F 2 > σ(f 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 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 (Å 2 ) x y z U iso */U eq P (6) (7) (7) (2) N (2) (2) (2) (5) H * sup-3

6 N (2) (3) (2) (6) N (2) (2) (2) (6) O (18) (19) (2) (5) O (2) (2) (2) (6) F (2) (2) (2) (7) F (18) (2) (2) (7) C (3) (3) (3) (7) C (3) (3) (3) (7) H * C (3) (4) (3) (6) H * C (3) (4) (3) (6) C (3) (3) (3) (5) H * C (3) (3) (3) (5) C (3) (3) (3) (7) C (3) (3) (3) (9) H * C (4) (4) (4) (11) H * C (4) (5) (4) (12) H * C (3) (4) (3) (10) H * C (3) (3) (3) (7) H * C (3) (3) (3) (7) C (3) (3) (3) (8) H * C (4) (4) (4) (12) H * C (4) (5) (4) (14) H * C (4) (5) (4) (13) H * C (3) (4) (4) (10) H * C (3) (3) (3) (7) C (3) (3) (3) (8) H28A * H28B * C (3) (3) (3) (8) H29A * H29B * C (3) (4) (4) (12) H30A * H30B * H30C * sup-4

7 C (4) (4) (3) (13) H31A * H31B * H31C * Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 P (3) (4) (4) (3) (3) (3) N (10) (12) (15) (9) (10) (10) N (12) (16) (15) (11) (11) (12) N (12) (14) (14) (10) (11) (11) O (9) (11) (15) (8) (10) (10) O (11) (12) (18) (9) (11) (11) F (12) (14) (2) (10) (13) (14) F (9) (18) (19) (10) (10) (15) C (13) (16) (17) (12) (12) (13) C (15) (19) (2) (14) (13) (16) C (10) (16) (16) (10) (10) (13) C (10) (16) (16) (10) (10) (13) C (9) (13) (14) (9) (9) (11) C (9) (13) (14) (9) (9) (11) C (15) (18) (18) (13) (13) (14) C (2) (2) (2) (16) (17) (17) C (2) (2) (2) (2) (2) (2) C (2) (3) (2) (2) (18) (2) C (19) (3) (2) (19) (16) (2) C (15) (2) (19) (14) (14) (16) C (15) (17) (17) (13) (13) (14) C (17) (19) (2) (15) (15) (16) C (3) (3) (3) (2) (2) (2) C (2) (4) (3) (2) (2) (3) C (19) (4) (3) (2) (2) (3) C (18) (2) (3) (17) (17) (2) C (14) (16) (18) (12) (13) (13) C (19) (18) (19) (15) (15) (15) C (17) (17) (2) (14) (15) (15) C (18) (3) (3) (18) (17) (2) C (3) (3) (2) (2) (2) (2) Geometric parameters (Å, º) P1 O (19) C17 H P1 N (2) C18 C (5) P1 N (2) C18 H P1 N (2) C19 C (5) N2 C (3) C19 H N2 H C20 H sup-5

8 N3 C (4) C21 C (4) N3 C (4) C21 C (4) N4 C (4) C21 C (4) N4 C (4) C22 C (5) O6 C (3) C22 H F7 C (4) C23 C (6) F8 C (3) C23 H C9 C (4) C24 C (6) C9 C (4) C24 H C9 C (4) C25 C (5) C10 C (4) C25 H C10 H C26 H C11 C (5) C28 H28A C11 H C28 H28B C12 C (4) C29 H29A C13 C (4) C29 H29B C13 H C30 H30A C15 C (4) C30 H30B C15 C (4) C30 H30C C15 C (4) C31 H31A C16 C (5) C31 H31B C16 H C31 H31C C17 C (6) O5 P1 N (13) C15 C20 C (3) O5 P1 N (12) C15 C20 H N3 P1 N (13) C19 C20 H O5 P1 N (11) C22 C21 C (3) N3 P1 N (12) C22 C21 C (3) N4 P1 N (12) C26 C21 C (3) C27 N2 P (19) C23 C22 C (3) C27 N2 H C23 C22 H P1 N2 H C21 C22 H C28 N3 C (2) C22 C23 C (4) C28 N3 P (2) C22 C23 H C30 N3 P (2) C24 C23 H C31 N4 C (3) C25 C24 C (4) C31 N4 P (2) C25 C24 H C29 N4 P (2) C23 C24 H C14 C9 C (3) C24 C25 C (4) C14 C9 C (3) C24 C25 H C10 C9 C (2) C26 C25 H C11 C10 C (3) C25 C26 C (4) C11 C10 H C25 C26 H C9 C10 H C21 C26 H C12 C11 C (3) O6 C27 N (2) C12 C11 H O6 C27 C (2) C10 C11 H N2 C27 C (2) sup-6

9 C13 C12 F (3) N3 C28 C (2) C13 C12 C (3) N3 C28 H28A F8 C12 C (3) C15 C28 H28A C12 C13 C (3) N3 C28 H28B C12 C13 H C15 C28 H28B C14 C13 H H28A C28 H28B F7 C14 C (3) N4 C29 C (2) F7 C14 C (3) N4 C29 H29A C13 C14 C (3) C21 C29 H29A C16 C15 C (3) N4 C29 H29B C16 C15 C (3) C21 C29 H29B C20 C15 C (3) H29A C29 H29B C17 C16 C (3) N3 C30 H30A C17 C16 H N3 C30 H30B C15 C16 H H30A C30 H30B C16 C17 C (4) N3 C30 H30C C16 C17 H H30A C30 H30C C18 C17 H H30B C30 H30C C19 C18 C (4) N4 C31 H31A C19 C18 H N4 C31 H31B C17 C18 H H31A C31 H31B C18 C19 C (3) N4 C31 H31C C18 C19 H H31A C31 H31C C20 C19 H H31B C31 H31C O5 P1 N2 C (2) C28 C15 C16 C (3) N3 P1 N2 C (3) C15 C16 C17 C (6) N4 P1 N2 C (3) C16 C17 C18 C (6) O5 P1 N3 C (2) C17 C18 C19 C (6) N4 P1 N3 C (3) C16 C15 C20 C (4) N2 P1 N3 C (3) C28 C15 C20 C (3) O5 P1 N3 C (3) C18 C19 C20 C (5) N4 P1 N3 C (3) C26 C21 C22 C (5) N2 P1 N3 C (2) C29 C21 C22 C (3) O5 P1 N4 C (3) C21 C22 C23 C (6) N3 P1 N4 C (2) C22 C23 C24 C (7) N2 P1 N4 C (3) C23 C24 C25 C (7) O5 P1 N4 C (2) C24 C25 C26 C (6) N3 P1 N4 C (3) C22 C21 C26 C (5) N2 P1 N4 C (2) C29 C21 C26 C (3) C14 C9 C10 C (5) P1 N2 C27 O (4) C27 C9 C10 C (3) P1 N2 C27 C (2) C9 C10 C11 C (5) C14 C9 C27 O (5) C10 C11 C12 C (6) C10 C9 C27 O (3) C10 C11 C12 F (3) C14 C9 C27 N (3) F8 C12 C13 C (3) C10 C9 C27 N (4) C11 C12 C13 C (5) C30 N3 C28 C (4) C12 C13 C14 F (3) P1 N3 C28 C (3) sup-7

10 C12 C13 C14 C9 0.6 (5) C16 C15 C28 N (4) C10 C9 C14 F (3) C20 C15 C28 N (3) C27 C9 C14 F7 2.7 (5) C31 N4 C29 C (3) C10 C9 C14 C (5) P1 N4 C29 C (2) C27 C9 C14 C (3) C22 C21 C29 N (3) C20 C15 C16 C (5) C26 C21 C29 N (4) Hydrogen-bond geometry (Å, º) D H A D H H A D A D H A N2 H2 O5 i (3) 171 Symmetry code: (i) x+1, y+1, z+1. sup-8