b = (17) Å c = (18) Å = (4) = (4) = (4) V = (3) Å 3 Data collection Refinement

Transcription

1 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN (Z)-N-tert-Butyl-2-(4-methoxyanilino)- N 0 -(4-methoxyphenyl)-2-phenylacetimidamide Sue A. Roberts, a * Biswajit Saha, b,c Brendan Frett b,c and Hong-Yu Li b,c a Department of Chemistry and Biochemistry, 1306 E University Boulevard, The University of Arizona, Tucson, AZ 85721, USA, b College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ 85721, USA, and c Bio5 Oro Valley, The University of Arizona, Oro Valley, AZ 85737, USA Correspondence suer@ .arizona.edu b = (17) Å c = (18) Å = (4) = (4) = (4) V = (3) Å 3 Data collection Bruker Kappa APEXII DUO CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009) T min = 0.89, T max = 0.99 Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections 289 parameters Z =2 Mo K radiation = 0.08 mm 1 T = 100 K mm measured reflections 6607 independent reflections 5476 reflections with I > 2(I) R int = H atoms treated by a mixture of independent and constrained refinement max = 0.36 e Å 3 min = 0.38 e Å 3 Received 10 April 2013; accepted 9 May 2013 Key indicators: single-crystal X-ray study; T = 100 K; mean (C C) = Å; R factor = 0.043; wr factor = 0.106; data-to-parameter ratio = In the crystal of the title compound, C 26 H 31 N 3 O 2, pairs of N HO hydrogen bonds link molecules, forming inversion dimers, which enclose an R 2 2 (20) ring motif. One N atom does not form hydrogen bonds and lies in a hydrophobic pocket with closest intermolecular contacts of (2) and (2) Å. Related literature For the synthesis of the title compound, and a discussion of the use of the three-component Ugi reaction to synthesize amidines, see: Saha et al. (2013). Table 1 Hydrogen-bond geometry (Å, ). D HA D H HA DA D HA N2 H2O1 i (15) (15) (13) (12) Symmetry code: (i) x þ 1; y þ 2; z þ 2. Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) and OLEX2 (Dolomanov et al., 2009); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2006); software used to prepare material for publication: publcif (Westrip, 2010). The Bruker Kappa APEXII DUO was purchased with funding from NSF grant CHE The work was supported by start-up funds from the University of Arizona to HYL. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: PK2477). Experimental Crystal data C 26 H 31 N 3 O 2 M r = Triclinic, P1 a = (17) Å References Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, Farrugia, L. J. (2012). J. Appl. Cryst. 45, Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, Saha, B., Frett, B., Wang, Y. & Li, H.-Y. (2013). Tetrahedron Lett. 54, Sheldrick, G. M. (2008). Acta Cryst. A64, Westrip, S. P. (2010). J. Appl. Cryst. 43, o902 Roberts et al. doi: /s

2 supporting information [doi: /s ] (Z)-N-tert-Butyl-2-(4-methoxyanilino)-N -(4-methoxyphenyl)-2-phenylacetimidamide Sue A. Roberts, Biswajit Saha, Brendan Frett and Hong-Yu Li S1. Comment The title compound was prepared as a secondary product of the three component Ugi reaction (Saha et al., 2013). The central C1 C22 single bond has four bulky substituents arranged, roughly, as if pointing at the corners of a tetrahedron. The angle between the planes containing the substituents, defined by N1 C22 N3 and C2 C1 C20, is (1). Pairs of hydrogen bonds between N2 and O1 [3.170 (1) Å] connect two molecules across an inversion center, creating a cavity around the inversion center with a diameter of about 5 Å. The closest contact across the inversion center involving atoms not involved in the hydrogen bonding is (3) Å between the hydrogen bonded to C3 and its symmetry equivalent (symmetry transformation -x + 1, -y + 2, -z + 2). The hydrogen bonding graph set is R 2 2(20). Nitrogen N3 is unusual in that, although protonated, it does not form hydrogen bonds with acceptor atoms. Instead, it lies in a hydrophobic cavity with closest intermolecular contacts of (2) Å and (2) Å to C15 and C16 respectively. S2. Experimental The compound was synthesized as previously reported [compound 5a in (Saha et al., 2013)]. The crude residue was purified by silica gel column chromatography using (10 30%) ethylacetate-hexane to obtain the pure product. The pure compound was dissolved in 50% ethylacetate-hexane and kept at room temperature for 2 days during which crystals formed. S3. Refinement All hydrogen atoms were visible in a difference Fourier map and, except for H2 were added at calculated positions. Bond distances are set to 0.95 Å for aromatic carbon-hydrogen bonds, 0.98 Å for methyl group carbon-hydrogen bonds and 0.88 Å for nitrogen-hydrogen bonds. Thermal parameters for hydrogen atoms were set to 1.2 times the isotropic equivalent thermal parameter of the atom to which the hydrogen atom is bonded, except for methyl group hydrogen atoms where the thermal parameter was set to 1.5 times the isotropic equivalent thermal parameter of the carbon atom the hydrogen atom is bonded to. The positional and isotropic thermal parameters of H2 were refined. sup-1

3 Figure 1 The molecular structure of the title compound. Non-hydrogen atoms are shown as 50% probability ellipsoids. sup-2

4 Figure 2 View showing unit cell packing. Unit cell axes are labeled in the figure. (Z)-N-tert-Butyl-2-(4-methoxyanilino)-N -(4-methoxyphenyl)-2-phenylacetimidamide Crystal data C 26 H 31 N 3 O 2 M r = Triclinic, P1 a = (17) Å b = (17) Å c = (18) Å α = (4) β = (4) γ = (4) V = (3) Å 3 Data collection Bruker Kappa APEXII DUO CCD diffractometer Radiation source: fine-focus sealed tube Graphite monochromator Detector resolution: pixels mm -1 φ and ω scans Z = 2 F(000) = 448 D x = Mg m 3 Mo Kα radiation, λ = Å Cell parameters from 9952 reflections θ = µ = 0.08 mm 1 T = 100 K Block, colourless mm Absorption correction: multi-scan (SADABS; Bruker, 2009) T min = 0.89, T max = measured reflections 6607 independent reflections 5476 reflections with I > 2σ(I) R int = sup-3

5 θ max = 29.9, θ min = 1.9 h = Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = S = reflections 289 parameters 0 restraints Primary atom site location: structure-invariant direct methods k = l = Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H atoms treated by a mixture of independent and constrained refinement w = 1/[σ 2 (F o2 ) + (0.0397P) P] where P = (F o 2 + 2F c2 )/3 (Δ/σ) max = Δρ max = 0.36 e Å 3 Δρ min = 0.38 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 C (10) (9) (9) (19) C (10) (10) (9) (2) H * C (11) (10) (10) (2) H * C (11) (10) (9) (19) H * C (11) (10) (9) (2) H * C (10) (9) (9) (19) C (11) (11) (9) (2) H * C (10) (10) (9) (2) H * C (11) (10) (10) (2) H * C (10) (10) (9) (19) C (10) (9) (9) (18) H * C (10) (10) (9) (2) C (11) (10) (9) (2) H * sup-4

6 C (10) (10) (9) (2) C (11) (10) (9) (2) C (12) (11) (11) (2) H * C (12) (13) (12) (3) H24A * H24B * H24C * C (13) (12) (12) (3) H * C (13) (12) (10) (2) H25A * H25B * H25C * C (13) (13) (12) (3) H * C (12) (12) (12) (3) H21A * H21B * H21C * C (12) (13) (12) (3) H14A * H14B * H14C * C (12) (13) (12) (3) H * C (16) (12) (12) (3) H23A * H23B * H23C * C (14) (14) (13) (3) H * O (8) (7) (7) (17) O (8) (8) (7) (17) N (9) (8) (8) (17) N (9) (9) (8) (18) H3A * N (9) (9) (8) (18) C (10) (10) (9) (2) H (15) (14) (13) (3)* Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 C (4) (4) (4) (4) (3) (3) C (4) (5) (5) (4) (4) (4) C (5) (5) (5) (4) (4) (4) C (5) (5) (4) (4) (4) (3) sup-5

7 C (5) (5) (4) (4) (4) (3) C (4) (4) (4) (3) (3) (3) C (5) (5) (4) (4) (4) (4) C (4) (5) (4) (4) (4) (4) C (5) (5) (5) (4) (4) (4) C (5) (5) (4) (4) (4) (3) C (4) (4) (4) (3) (3) (3) C (5) (5) (4) (4) (4) (4) C (5) (5) (4) (4) (4) (4) C (4) (5) (4) (4) (4) (4) C (5) (5) (4) (4) (4) (4) C (5) (5) (6) (4) (4) (4) C (5) (7) (6) (5) (4) (5) C (6) (6) (6) (5) (5) (5) C (6) (6) (5) (5) (4) (4) C (6) (6) (6) (5) (5) (5) C (5) (6) (7) (4) (5) (5) C (5) (7) (6) (5) (5) (5) C (5) (7) (6) (5) (5) (5) C (8) (6) (6) (6) (6) (4) C (7) (7) (7) (5) (6) (6) O (4) (4) (4) (3) (3) (3) O (4) (4) (4) (3) (3) (3) N (4) (4) (4) (3) (3) (3) N (4) (4) (4) (3) (3) (3) N (4) (4) (4) (3) (3) (3) C (5) (5) (4) (4) (4) (4) Geometric parameters (Å, º) C20 C (14) C26 C (15) C20 C (14) C26 C (16) C20 N (13) C26 N (13) C11 H C3 H C11 C (14) C3 C (17) C11 C (15) C24 H24A C18 H C24 H24B C18 C (15) C24 H24C C18 C (14) C7 H C15 H C7 C (18) C15 C (15) C25 H25A C16 H C25 H25B C16 C (15) C25 H25C C22 C (14) C4 H C22 N (12) C4 C (19) C22 N (13) C21 H21A C10 H C21 H21B C10 C (14) C21 H21C sup-6

8 C10 C (15) C21 O (15) C12 H C14 H14A C12 C (15) C14 H14B C19 H C14 H14C C8 C (14) C14 O (14) C8 N (13) C5 H C1 H C5 C (2) C1 C (14) C23 H23A C1 N (13) C23 H23B C17 O (12) C23 H23C C9 H C6 H C2 C (15) O1 C (12) C2 C (16) N2 H (15) C26 C (16) N3 H3A C15 C20 N (9) C26 C24 H24A C19 C20 C (9) C26 C24 H24B C19 C20 N (9) C26 C24 H24C C12 C11 H H24A C24 H24B C13 C11 H H24A C24 H24C C13 C11 C (9) H24B C24 H24C C19 C18 H C2 C7 H C17 C18 H C6 C7 C (12) C17 C18 C (10) C6 C7 H C20 C15 H C26 C25 H25A C16 C15 C (10) C26 C25 H25B C16 C15 H C26 C25 H25C C15 C16 H H25A C25 H25B C15 C16 C (9) H25A C25 H25C C17 C16 H H25B C25 H25C N3 C22 C (8) C3 C4 H N1 C22 C (9) C5 C4 C (12) N1 C22 N (9) C5 C4 H C9 C10 H H21A C21 H21B C9 C10 C (10) H21A C21 H21C C13 C10 H H21B C21 H21C C11 C12 H O2 C21 H21A C11 C12 C (10) O2 C21 H21B C8 C12 H O2 C21 H21C C20 C19 C (9) H14A C14 H14B C20 C19 H H14A C14 H14C C18 C19 H H14B C14 H14C C12 C8 C (9) O1 C14 H14A C12 C8 N (9) O1 C14 H14B C9 C8 N (9) O1 C14 H14C C22 C1 H C4 C5 H C2 C1 C (8) C4 C5 C (11) C2 C1 H C6 C5 H sup-7

9 N2 C1 C (8) C26 C23 H23A N2 C1 H C26 C23 H23B N2 C1 C (8) C26 C23 H23C C18 C17 C (9) H23A C23 H23B O2 C17 C (10) H23A C23 H23C O2 C17 C (9) H23B C23 H23C C10 C9 C (10) C7 C6 H C10 C9 H C5 C6 C (12) C8 C9 H C5 C6 H C3 C2 C (9) C17 O2 C (8) C3 C2 C (10) C13 O1 C (9) C7 C2 C (10) C20 N2 C (8) C25 C26 C (9) C20 N2 H (9) C23 C26 C (10) C1 N2 H (9) C23 C26 C (10) C22 N3 C (9) N3 C26 C (9) C22 N3 H3A N3 C26 C (9) C26 N3 H3A N3 C26 C (9) C22 N1 C (9) C2 C3 H C11 C13 C (9) C2 C3 C (11) O1 C13 C (9) C4 C3 H O1 C13 C (9) C20 C15 C16 C (16) C9 C8 N1 C (14) C11 C12 C8 C (15) C2 C1 N2 C (9) C11 C12 C8 N (9) C2 C3 C4 C (19) C18 C17 O2 C (15) C2 C7 C6 C5 0.7 (2) C15 C20 C19 C (16) C3 C2 C7 C (19) C15 C20 N2 C (9) C3 C4 C5 C6 1.7 (2) C15 C16 C17 C (16) C24 C26 N3 C (14) C15 C16 C17 O (9) C7 C2 C3 C (17) C16 C17 O2 C (10) C25 C26 N3 C (10) C22 C1 C2 C (10) C4 C5 C6 C7 2.1 (2) C22 C1 C2 C (14) C14 O1 C13 C (15) C22 C1 N2 C (11) C14 O1 C13 C (10) C12 C11 C13 C (15) C23 C26 N3 C (14) C12 C11 C13 O (9) N2 C20 C15 C (9) C12 C8 C9 C (15) N2 C20 C19 C (10) C12 C8 N1 C (12) N2 C1 C2 C (11) C19 C20 C15 C (15) N2 C1 C2 C (12) C19 C20 N2 C (14) N3 C22 C1 C (10) C19 C18 C17 C (16) N3 C22 C1 N (11) C19 C18 C17 O (10) N3 C22 N1 C (9) C1 C22 N3 C (9) N1 C22 C1 C (12) C1 C22 N1 C (15) N1 C22 C1 N (10) C1 C2 C3 C (10) N1 C22 N3 C (16) C1 C2 C7 C (11) N1 C8 C9 C (10) C17 C18 C19 C (16) C13 C11 C12 C (15) C9 C10 C13 C (16) C13 C10 C9 C (16) sup-8

10 C9 C10 C13 O (9) Hydrogen-bond geometry (Å, º) D H A D H H A D A D H A N2 H2 O1 i (15) (15) (13) (12) Symmetry code: (i) x+1, y+2, z+2. sup-9