b = (10) Å c = (3) Å V = (3) Å 3 Z =4 Data collection Refinement

Transcription

1 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN N-(Fluoren-9-ylmethoxycarbonyl)-Laspartic acid 4-tert-butyl ester Kazuhiko Yamada, a * Daisuke Hashizume b and Tadashi Shimizu a a National Institute for Materials Science, 3-13 Sakura, Tsukuba , Japan, and b Advanced Technology Support Division, RIKEN, 2-1 Hirosawa, Wako, Saitama , Japan Correspondence yamada.kazuhiko@nims.go.jp Received 10 September 2009; accepted 17 September 2009 b = (10) Å c = (3) Å V = (3) Å 3 Z =4 Data collection Rigaku AFC-8 diffractometer with Saturn70 CCD detector Absorption correction: none measured reflections Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections Table 1 Hydrogen-bond geometry (Å, ). Mo K radiation = 0.10 mm 1 T =90K mm 2722 independent reflections 2167 reflections with I > 2(I) R int = parameters H-atom parameters constrained max = 0.29 e Å 3 min = 0.27 e Å 3 Key indicators: single-crystal X-ray study; T = 90 K; mean (C C) = Å; R factor = 0.059; wr factor = 0.148; data-to-parameter ratio = 9.5. The bond distances and bond angles of the title compound, C 23 H 25 NO 6, are consistent with values typically found for fluoren-9-ylmethoxycarbonyl-protected amino acids. The conformations of the backbone and the side chain are slightly different from those of l-aspartic acid. The crystal structure exhibits two intermolecular hydrogen bonds, forming a twodimensional sheet structure parallel to the ab plane. Related literature For the crystal structures of aspartic acids, see: Dawson (1977); Sequeira et al. (1989); Flaig et al. (1998); Rao (1973); Wang et al. (2007); Umadevi et al. (2003); Derissen et al. (1968); Bendeif & Jelsch (2007). For the crystal structures of N-fluoren-9-ylmethoxycarbonyl-protected amino acids, see: Valle et al. (1984); Yamada, Hashizume & Shimizu (2008); Yamada, Hashizume, Shimizu & Deguchi (2008); Yamada, Hashizume, Shimizu, Ohiki & Yokoyama (2008). Experimental Crystal data C 23 H 25 NO 6 M r = Orthorhombic, P a = (4) Å Present address: Department of Chemistry and Materials Science, Graduate School of Science and Engineering, Tokyo Institute of Technology, Japan. D HA D H HA DA D HA O3 H3O5 i (3) 172 N1 H1O3 ii (4) 156 Symmetry codes: (i) x þ 2; y þ 1 2 ; z þ 1 2 ; (ii) x 1; y; z. Data collection: CrystalClear (Rigaku/MSC, 2005); cell refinement: HKL-2000 (Otwinowski & Minor, 1997); data reduction: HKL-2000; program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97. KY thanks the Ministry of Education, Science, Sports, Culture and Technology (MEXT) of Japan for funding this work [Young Scientists (B), grant No ]. TS appreciates support from the World Premier International Research Center Initiative (WPI Initiative) on Materials Nanoarchitronics (MANA) at NIMS, from MEXT. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FJ2243). References Bendeif, E. & Jelsch, C. (2007). Acta Cryst. C63, o361 o364. Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, Dawson, B. (1977). Acta Cryst. B33, Derissen, J. L., Endeman, H. J. & Peerdeman, A. F. (1968). Acta Cryst. B24, Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. Flaig, R., Koritsanszky, T., Zobel, D. & Luger, P. (1998). J. Am. Chem. Soc. 120, Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp New York: Academic Press. Rao, S. T. (1973). Acta Cryst. B29, Rigaku/MSC (2005). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA. Sequeira, A., Rajagopal, H. & Ramanadham, M. (1989). Acta Cryst. C45, Sheldrick, G. M. (2008). Acta Cryst. A64, Umadevi, K., Anitha, K., Sridhar, B., Srinivasan, N. & Rajaram, R. K. (2003). Acta Cryst. E59, o1073 o1075. Valle, G., Bonora, G. M. & Toniolo, C. (1984). Can. J. Chem. 62, o2606 Yamada et al. doi: /s

2 organic compounds Wang, G.-M., Li, Z.-X., Duan, C.-S. & Li, H. (2007). Acta Cryst. E63, o4003. Yamada, K., Hashizume, D. & Shimizu, T. (2008). Acta Cryst. E64, o1112. Yamada, K., Hashizume, D., Shimizu, T. & Deguchi, K. (2008). Acta Cryst. E64, o1533. Yamada, K., Hashizume, D., Shimizu, T., Ohiki, S. & Yokoyama, S. (2008). J. Mol. Struct. 888, Yamada et al. C 23 H 25 NO 6 o2607

3 supporting information [ N-(Fluoren-9-ylmethoxycarbonyl)-L-aspartic acid 4-tert-butyl ester Kazuhiko Yamada, Daisuke Hashizume and Tadashi Shimizu S1. Comment L-Aspartic acid is one of the 20 building blocks of proteins, and, in mammals, can be produced from oxaloacetate by transamination. As for the related compounds of an aspartic acid, the crystal structures of L-aspartic acid (Derissen et al.,1968; Bendeif & Jelsch, 2007), L-aspartic acid monohydrate (Umadevi et al., 2003), DL-aspartic acid (Sequeira et al., 1989; Flaig et al., 1998; Rao, 1973; Wang et al., 2007), and DL-aspartic acid hydrochloride (Dawson, 1977) have been reported so far. Fluoren-9-ylmethoxycarbonyl (Fmoc) group is widely used for solid-phase peptide synthesis protocols as an N-αprotecting group. To our best knowledge, however,there have been only four literatures reporting crystal structures of Fmoc-protected amino acids (Valle et al., 1984; Yamada, Hashizume & Shimizu, 2008; Yamada, Hashizume, Shimizu & Deguchi, 2008; Yamada, Hashizume, Shimizu, Ohiki & Yokoyama, 2008). In this communication, the crystal structure of N-Fmoc-protected aspartic acid 4-tert-butyl ester (I) is reported. The molecular structure of (I) is shown in Fig. 1 together with the atom labeling. The bond lengths and angles of the present molecule are in reasonable agreement with typical values found in L-aspartic acids and the related compounds. The conformations of the backbone and the side-chain, however, are slightly different from those of L-aspartic acid. The torsion angles, N1 C1 C2 C3 and N1 C1 C4 O4, are found to be 62.5 (4) and 17.0 (5), respectively. For L-aspartic acid, the corresponding angles are and -39.2, respectively. In the Fmoc-protected amino acids, the fluoren moiety takes various conformations as shown in the available literatures. In this case, the conformation of the Fmoc moiety is similar to those of Fmoc-protected isoleucine and serine. Fig. 2 shows the crystal structure of (I). The molecules are linked via intermolecular hydrogen bonds between carboxyl and Fmoc moieties, O3 H3 O5 to form the column around the 2 1 screw axis parallel to the b axis. The columns, related by translation symmeties along the a axis each other, are joined together through weak hydrogen bonds between the amino and carboxyl groups, N1 H1 O3, two-dimensional sheet structures are formed paralell to the ab plane consequentry. The geometries of the hydrogen bonds are listed in Table 2. S2. Experimental A powdered sample of the title compound was purchased from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). Single crystals suitable for X-ray structure analysis could be obtained by recrystallization from ethyl acetate-dichloromethane (80:20) solution, which afforded white needle-like crystals. S3. Refinement All H atoms were located on the difference maps, and were treated as riding atoms with C/N/O H distances of 1.00, 0.99, 0.98, 0.95, 0.88 and 0.84 Å, for methyne, methylene, methyl, phenyl, amino and hydroxyl groups, respectively, on the refinements. The U iso 's of the H atoms were fixed to be 1.2U eq (C/N) for methyne, methylene, phenyl and amino, or sup-1

4 1.5U eq (C/O) for methyl and hydroxyl of the parent atoms. All Friedel pairs were merged, and all f"s of containing atoms were set to zero. Figure 1 A view of the molecular structure of (I), showing the atom labeling scheme. Displacement ellipsoids are drawn at the 50% probability level. sup-2

5 Figure 2 A packing diagram of (I) viewed from the c axis. Broken lines indicate the hydrogen bonds. The molecules in the region of 0 < z < 1/2 were plotted. The atoms of the fluoren-9-yl moiety and H atoms, except for H1 and H3, were omitted for clarity. N-(Fluoren-9-ylmethoxycarbonyl)-L-aspartic acid 4-tert-butyl ester Crystal data C 23 H 25 NO 6 M r = Orthorhombic, P Hall symbol: P 2ac 2ab a = (4) Å b = (10) Å c = (3) Å V = (3) Å 3 Z = 4 Data collection Rigaku AFC-8 diffractometer with Saturn70 CCD detector Radiation source: fine-focus rotating anode Confocal monochromator F(000) = 872 D x = Mg m 3 Mo Kα radiation, λ = Å Cell parameters from reflections θ = µ = 0.10 mm 1 T = 90 K Needle, colourless mm Detector resolution: pixels mm -1 ω scans measured reflections 2722 independent reflections sup-3

6 2167 reflections with I > 2σ(I) R int = θ max = 27.6, θ min = 1.9 Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = S = reflections 286 parameters 0 restraints Primary atom site location: structure-invariant direct methods h = 7 6 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 ) + (0.0694P) P] where P = (F o 2 + 2F c2 )/3 (Δ/σ) max < Δρ max = 0.29 e Å 3 Δρ min = 0.27 e Å 3 Special details Experimental. All Friedel pairs were merged, and all f"s of containing atoms were set to zero. 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 al 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 > 2σ(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 O (5) (2) (8) (6) O (5) (2) (7) (6) O (5) (2) (8) (6) H * O (5) (2) (8) (6) O (5) (2) (7) (6) O (5) (2) (7) (6) N (6) (3) (9) (7) H * C (7) (3) (11) (8) H1A * C (7) (3) (11) (8) H2A * H2B * C (7) (3) (11) (8) C (7) (3) (11) (8) C (8) (3) (11) (9) C (9) (4) (12) (11) H6A * H6B * H6C * sup-4

7 C (8) (3) (13) (9) H7A * H7B * H7C * C (8) (4) (14) (10) H8A * H8B * H8C * C (7) (3) (11) (7) C (7) (3) (10) (8) H10A * H10B * C (7) (3) (11) (8) H * C (7) (3) (11) (8) C (8) (3) (11) (8) H * C (7) (3) (12) (9) H * C (8) (3) (12) (9) H * C (7) (3) (12) (9) H * C (8) (3) (11) (8) C (7) (3) (11) (8) C (8) (3) (12) (9) H * C (8) (3) (13) (10) H * C (8) (3) (13) (9) H * C (8) (3) (12) (8) H * C (7) (3) (11) (8) Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 O (17) (13) (14) (13) (13) (10) O (16) (12) (13) (12) (12) (10) O (16) (12) (14) (12) (13) (10) O (17) (12) (13) (13) (13) (11) O (14) (12) (13) (11) (12) (10) O (14) (12) (12) (11) (11) (9) N (18) (15) (15) (14) (13) (12) C (19) (16) (18) (16) (16) (13) C (2) (16) (18) (15) (17) (13) C (19) (17) (19) (15) (16) (14) sup-5

8 C (2) (17) (17) (16) (16) (14) C (2) (18) (18) (17) (19) (14) C (3) (2) (2) (2) (2) (18) C (2) (19) (2) (18) (2) (16) C (2) (2) (2) (18) (2) (19) C (18) (16) (17) (14) (15) (13) C (19) (16) (17) (15) (16) (13) C (2) (16) (17) (16) (17) (13) C (2) (16) (18) (16) (17) (14) C (2) (17) (19) (17) (18) (14) C (2) (17) (2) (16) (18) (15) C (3) (19) (19) (18) (18) (14) C (2) (18) (2) (17) (18) (14) C (2) (16) (19) (16) (17) (13) C (2) (16) (19) (16) (17) (13) C (3) (18) (2) (17) (19) (15) C (2) (18) (2) (17) (2) (15) C (2) (17) (2) (17) (2) (15) C (2) (16) (19) (17) (18) (14) C (2) (16) (2) (16) (18) (13) Geometric parameters (Å, º) O1 C (4) C8 H8C O2 C (4) C10 C (5) O2 C (4) C10 H10A O3 C (5) C10 H10B O3 H C11 C (5) O4 C (4) C11 C (5) O5 C (4) C11 H O6 C (5) C12 C (6) O6 C (4) C12 C (5) N1 C (4) C13 C (5) N1 C (5) C13 H N1 H C14 C (6) C1 C (5) C14 H C1 C (5) C15 C (6) C1 H1A C15 H C2 C (5) C16 C (5) C2 H2A C16 H C2 H2B C17 C (5) C5 C (6) C18 C (5) C5 C (5) C18 C (5) C5 C (5) C19 C (6) C6 H6A C19 H C6 H6B C20 C (6) C6 H6C C20 H C7 H7A C21 C (6) sup-6

9 C7 H7B C21 H C7 H7C C22 C (5) C8 H8A C22 H C8 H8B C3 O2 C (3) N1 C9 O (3) C4 O3 H O6 C10 C (3) C9 O6 C (3) O6 C10 H10A C9 N1 C (3) C11 C10 H10A C9 N1 H O6 C10 H10B C1 N1 H C11 C10 H10B N1 C1 C (3) H10A C10 H10B N1 C1 C (3) C23 C11 C (3) C2 C1 C (3) C23 C11 C (3) N1 C1 H1A C12 C11 C (3) C2 C1 H1A C23 C11 H C4 C1 H1A C12 C11 H C3 C2 C (3) C10 C11 H C3 C2 H2A C13 C12 C (3) C1 C2 H2A C13 C12 C (3) C3 C2 H2B C17 C12 C (3) C1 C2 H2B C14 C13 C (4) H2A C2 H2B C14 C13 H O1 C3 O (3) C12 C13 H O1 C3 C (3) C13 C14 C (4) O2 C3 C (3) C13 C14 H O4 C4 O (3) C15 C14 H O4 C4 C (4) C14 C15 C (4) O3 C4 C (3) C14 C15 H O2 C5 C (3) C16 C15 H O2 C5 C (3) C17 C16 C (4) C8 C5 C (4) C17 C16 H O2 C5 C (3) C15 C16 H C8 C5 C (4) C16 C17 C (4) C7 C5 C (3) C16 C17 C (4) C5 C6 H6A C12 C17 C (3) C5 C6 H6B C19 C18 C (4) H6A C6 H6B C19 C18 C (3) C5 C6 H6C C23 C18 C (3) H6A C6 H6C C18 C19 C (4) H6B C6 H6C C18 C19 H C5 C7 H7A C20 C19 H C5 C7 H7B C21 C20 C (4) H7A C7 H7B C21 C20 H C5 C7 H7C C19 C20 H H7A C7 H7C C20 C21 C (4) H7B C7 H7C C20 C21 H C5 C8 H8A C22 C21 H sup-7

10 C5 C8 H8B C23 C22 C (4) H8A C8 H8B C23 C22 H C5 C8 H8C C21 C22 H H8A C8 H8C C22 C23 C (4) H8B C8 H8C C22 C23 C (3) O5 C9 N (4) C18 C23 C (3) O5 C9 O (3) C9 N1 C1 C (3) C12 C13 C14 C (6) C9 N1 C1 C (4) C13 C14 C15 C (6) N1 C1 C2 C (4) C14 C15 C16 C (6) C4 C1 C2 C (4) C15 C16 C17 C (6) C5 O2 C3 O1 0.3 (6) C15 C16 C17 C (4) C5 O2 C3 C (3) C13 C12 C17 C (6) C1 C2 C3 O1 0.5 (5) C11 C12 C17 C (4) C1 C2 C3 O (3) C13 C12 C17 C (3) N1 C1 C4 O (5) C11 C12 C17 C (4) C2 C1 C4 O (4) C16 C17 C18 C (7) N1 C1 C4 O (3) C12 C17 C18 C (4) C2 C1 C4 O (4) C16 C17 C18 C (4) C3 O2 C5 C (4) C12 C17 C18 C (4) C3 O2 C5 C (5) C23 C18 C19 C (6) C3 O2 C5 C (3) C17 C18 C19 C (4) C1 N1 C9 O5 9.2 (5) C18 C19 C20 C (6) C1 N1 C9 O (3) C19 C20 C21 C (6) C10 O6 C9 O (5) C20 C21 C22 C (6) C10 O6 C9 N (3) C21 C22 C23 C (6) C9 O6 C10 C (3) C21 C22 C23 C (4) O6 C10 C11 C (4) C19 C18 C23 C (6) O6 C10 C11 C (3) C17 C18 C23 C (3) C23 C11 C12 C (4) C19 C18 C23 C (3) C10 C11 C12 C (5) C17 C18 C23 C (4) C23 C11 C12 C (4) C12 C11 C23 C (4) C10 C11 C12 C (4) C10 C11 C23 C (5) C17 C12 C13 C (5) C12 C11 C23 C (4) C11 C12 C13 C (4) C10 C11 C23 C (3) Hydrogen-bond geometry (Å, º) D H A D H H A D A D H A O3 H3 O5 i (3) 172 N1 H1 O3 ii (4) 156 Symmetry codes: (i) x+2, y+1/2, z+1/2; (ii) x 1, y, z. sup-8