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Acta Cryst. (2009). E65, o2606-o2607    [ doi:10.1107/S1600536809037611 ]

N-(Fluoren-9-ylmethoxycarbonyl)-L-aspartic acid 4-tert-butyl ester

K. Yamada, D. Hashizume and T. Shimizu

Abstract top

The bond distances and bond angles of the title compound, C23H25NO6, 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 two-dimensional sheet structure parallel to the ab plane.

Comment top

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-α-protecting 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 -60.3 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 21 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.

Related literature top

For related literature on 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 related literature on the crystal structures of N-α-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 top

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.

Refinement top

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 Uiso's of the H atoms were fixed to be 1.2Ueq(C/N) for methyne, methylene, phenyl and amino, or 1.5Ueq(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.

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2005); cell refinement: HKL-2000 (Otwinowski & Minor, 1997); data reduction: HKL-2000 (Otwinowski & Minor, 1997); 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 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of (I), showing the atom labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 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 top
Crystal data top
C23H25NO6F(000) = 872
Mr = 411.44Dx = 1.340 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 15181 reflections
a = 5.7166 (4) Åθ = 1.8–27.6°
b = 11.1175 (10) ŵ = 0.10 mm−1
c = 32.083 (3) ÅT = 90 K
V = 2039.0 (3) Å3Needle, colourless
Z = 40.11 × 0.05 × 0.04 mm
Data collection top
Rigaku AFC-8
diffractometer with Saturn70 CCD detector		2167 reflections with I > 2σ(I)
Radiation source: fine-focus rotating anodeRint = 0.077
confocalθmax = 27.6°, θmin = 1.9°
Detector resolution: 28.5714 pixels mm-1h = −7→6
ω scansk = −14→10
15110 measured reflectionsl = −41→41
2722 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.148H-atom parameters constrained
S = 1.13 w = 1/[σ2(Fo2) + (0.0694P)2 + 0.981P]
where P = (Fo2 + 2Fc2)/3
2722 reflections(Δ/σ)max < 0.001
286 parametersΔρmax = 0.29 e Å−3
0 restraintsΔρmin = −0.27 e Å−3
Crystal data top
C23H25NO6V = 2039.0 (3) Å3
Mr = 411.44Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.7166 (4) ŵ = 0.10 mm−1
b = 11.1175 (10) ÅT = 90 K
c = 32.083 (3) Å0.11 × 0.05 × 0.04 mm
Data collection top
Rigaku AFC-8
diffractometer with Saturn70 CCD detector		2167 reflections with I > 2σ(I)
15110 measured reflectionsRint = 0.077
2722 independent reflectionsθmax = 27.6°
Refinement top
R[F2 > 2σ(F2)] = 0.059H-atom parameters constrained
wR(F2) = 0.148Δρmax = 0.29 e Å−3
S = 1.13Δρmin = −0.27 e Å−3
2722 reflectionsAbsolute structure: ?
286 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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 F2 against al reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 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 (Å2) top
xyzUiso*/Ueq
O10.6301 (5)0.4494 (2)0.15286 (8)0.0271 (6)
O20.7666 (5)0.3298 (2)0.10086 (7)0.0237 (6)
O31.1545 (5)0.4557 (2)0.20322 (8)0.0254 (6)
H31.20640.52450.20890.038*
O40.8720 (5)0.5069 (2)0.24884 (8)0.0267 (6)
O50.6813 (5)0.1857 (2)0.28643 (7)0.0230 (6)
O60.3240 (5)0.2717 (2)0.27449 (7)0.0207 (6)
N10.6108 (6)0.3053 (3)0.22971 (9)0.0221 (7)
H10.50040.33950.21470.027*
C10.8504 (7)0.3115 (3)0.21511 (11)0.0203 (8)
H1A0.94310.25110.23130.024*
C20.8711 (7)0.2786 (3)0.16889 (11)0.0221 (8)
H2A1.03850.27870.16100.027*
H2B0.81060.19610.16480.027*
C30.7406 (7)0.3629 (3)0.14049 (11)0.0205 (8)
C40.9549 (7)0.4366 (3)0.22432 (11)0.0215 (8)
C50.6574 (8)0.4001 (3)0.06656 (11)0.0254 (9)
C60.7397 (9)0.3306 (4)0.02814 (12)0.0363 (11)
H6A0.68390.24740.02980.054*
H6B0.91100.33120.02700.054*
H6C0.67680.36870.00300.054*
C70.7598 (8)0.5265 (3)0.06653 (13)0.0309 (9)
H7A0.93080.52160.06760.046*
H7B0.70240.57060.09090.046*
H7C0.71200.56850.04110.046*
C80.3951 (8)0.3978 (4)0.07039 (14)0.0333 (10)
H8A0.34810.43960.09590.050*
H8B0.34100.31420.07150.050*
H8C0.32530.43810.04620.050*
C90.5502 (7)0.2491 (3)0.26529 (11)0.0180 (7)
C100.2379 (7)0.2366 (3)0.31542 (10)0.0206 (8)
H10A0.36630.20150.33220.025*
H10B0.11250.17580.31260.025*
C110.1424 (7)0.3503 (3)0.33673 (11)0.0199 (8)
H110.02320.39010.31850.024*
C120.0379 (7)0.3219 (3)0.37912 (11)0.0231 (8)
C13−0.1547 (8)0.2505 (3)0.38905 (11)0.0243 (8)
H13−0.23970.20990.36790.029*
C14−0.2195 (7)0.2401 (3)0.43060 (12)0.0263 (9)
H14−0.35070.19180.43780.032*
C15−0.0960 (8)0.2990 (3)0.46202 (12)0.0284 (9)
H15−0.14330.29030.49020.034*
C160.0969 (7)0.3707 (3)0.45224 (12)0.0261 (9)
H160.18300.41030.47350.031*
C170.1598 (8)0.3825 (3)0.41070 (11)0.0227 (8)
C180.3500 (7)0.4533 (3)0.39111 (11)0.0220 (8)
C190.5228 (8)0.5253 (3)0.40880 (12)0.0286 (9)
H190.53060.53650.43810.034*
C200.6843 (8)0.5807 (3)0.38242 (13)0.0302 (10)
H200.80670.62790.39400.036*
C210.6685 (8)0.5678 (3)0.33946 (13)0.0289 (9)
H210.77880.60720.32200.035*
C220.4919 (8)0.4973 (3)0.32146 (12)0.0250 (8)
H220.47920.49010.29200.030*
C230.3357 (7)0.4382 (3)0.34766 (11)0.0230 (8)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0316 (17)0.0205 (13)0.0293 (14)0.0069 (13)0.0030 (13)0.0004 (10)
O20.0291 (16)0.0162 (12)0.0258 (13)0.0015 (12)−0.0022 (12)0.0003 (10)
O30.0280 (16)0.0139 (12)0.0342 (14)−0.0014 (12)0.0038 (13)0.0000 (10)
O40.0299 (17)0.0195 (12)0.0306 (13)0.0004 (13)0.0039 (13)−0.0027 (11)
O50.0225 (14)0.0157 (12)0.0307 (13)0.0032 (11)0.0002 (12)0.0030 (10)
O60.0205 (14)0.0179 (12)0.0237 (12)−0.0001 (11)−0.0007 (11)0.0004 (9)
N10.0208 (18)0.0186 (15)0.0269 (15)0.0018 (14)−0.0007 (13)0.0030 (12)
C10.0191 (19)0.0139 (16)0.0279 (18)0.0013 (16)−0.0016 (16)0.0020 (13)
C20.024 (2)0.0115 (16)0.0305 (18)0.0027 (15)0.0019 (17)0.0004 (13)
C30.0168 (19)0.0160 (17)0.0286 (19)−0.0019 (15)0.0021 (16)0.0032 (14)
C40.023 (2)0.0199 (17)0.0212 (17)0.0022 (16)−0.0020 (16)0.0023 (14)
C50.029 (2)0.0225 (18)0.0248 (18)−0.0006 (17)−0.0020 (19)0.0034 (14)
C60.041 (3)0.037 (2)0.031 (2)0.003 (2)−0.001 (2)−0.0055 (18)
C70.031 (2)0.0233 (19)0.039 (2)0.0000 (18)−0.003 (2)0.0060 (16)
C80.024 (2)0.031 (2)0.045 (2)−0.0005 (18)−0.007 (2)0.0090 (19)
C90.0171 (18)0.0119 (16)0.0249 (17)−0.0016 (14)−0.0015 (15)−0.0022 (13)
C100.0212 (19)0.0169 (16)0.0236 (17)0.0028 (15)0.0000 (16)0.0004 (13)
C110.021 (2)0.0133 (16)0.0260 (17)0.0008 (16)0.0001 (17)0.0016 (13)
C120.028 (2)0.0135 (16)0.0278 (18)0.0033 (16)0.0004 (17)0.0006 (14)
C130.025 (2)0.0162 (17)0.0316 (19)0.0022 (17)−0.0024 (18)−0.0024 (14)
C140.024 (2)0.0176 (17)0.037 (2)0.0013 (16)0.0061 (18)−0.0002 (15)
C150.038 (3)0.0202 (19)0.0270 (19)0.0022 (18)0.0056 (18)0.0016 (14)
C160.030 (2)0.0175 (18)0.031 (2)0.0028 (17)−0.0008 (18)−0.0040 (14)
C170.024 (2)0.0139 (16)0.0305 (19)0.0019 (16)−0.0001 (17)−0.0002 (13)
C180.020 (2)0.0140 (16)0.0317 (19)0.0006 (16)0.0002 (17)−0.0017 (13)
C190.034 (3)0.0188 (18)0.033 (2)−0.0009 (17)−0.0024 (19)−0.0046 (15)
C200.030 (2)0.0152 (18)0.045 (2)−0.0057 (17)−0.001 (2)−0.0088 (15)
C210.030 (2)0.0138 (17)0.043 (2)−0.0010 (17)0.008 (2)−0.0010 (15)
C220.029 (2)0.0131 (16)0.0326 (19)−0.0014 (17)0.0021 (18)−0.0015 (14)
C230.022 (2)0.0122 (16)0.035 (2)0.0020 (16)0.0013 (18)0.0005 (13)
Geometric parameters (Å, °) top
O1—C31.218 (4)C8—H8C0.9800
O2—C31.332 (4)C10—C111.537 (5)
O2—C51.487 (4)C10—H10A0.9900
O3—C41.344 (5)C10—H10B0.9900
O3—H30.8400C11—C231.516 (5)
O4—C41.206 (4)C11—C121.518 (5)
O5—C91.232 (4)C11—H111.0000
O6—C91.350 (5)C12—C131.395 (6)
O6—C101.456 (4)C12—C171.402 (5)
N1—C91.346 (4)C13—C141.388 (5)
N1—C11.450 (5)C13—H130.9500
N1—H10.8800C14—C151.394 (6)
C1—C21.532 (5)C14—H140.9500
C1—C41.542 (5)C15—C161.397 (6)
C1—H1A1.0000C15—H150.9500
C2—C31.504 (5)C16—C171.387 (5)
C2—H2A0.9900C16—H160.9500
C2—H2B0.9900C17—C181.482 (5)
C5—C81.504 (6)C18—C191.392 (5)
C5—C71.522 (5)C18—C231.407 (5)
C5—C61.529 (5)C19—C201.395 (6)
C6—H6A0.9800C19—H190.9500
C6—H6B0.9800C20—C211.389 (6)
C6—H6C0.9800C20—H200.9500
C7—H7A0.9800C21—C221.402 (6)
C7—H7B0.9800C21—H210.9500
C7—H7C0.9800C22—C231.392 (5)
C8—H8A0.9800C22—H220.9500
C8—H8B0.9800
C3—O2—C5120.9 (3)N1—C9—O6110.2 (3)
C4—O3—H3109.5O6—C10—C11107.5 (3)
C9—O6—C10118.1 (3)O6—C10—H10A110.2
C9—N1—C1122.6 (3)C11—C10—H10A110.2
C9—N1—H1118.7O6—C10—H10B110.2
C1—N1—H1118.7C11—C10—H10B110.2
N1—C1—C2112.0 (3)H10A—C10—H10B108.5
N1—C1—C4110.3 (3)C23—C11—C12102.3 (3)
C2—C1—C4111.7 (3)C23—C11—C10112.0 (3)
N1—C1—H1A107.5C12—C11—C10111.5 (3)
C2—C1—H1A107.5C23—C11—H11110.3
C4—C1—H1A107.5C12—C11—H11110.3
C3—C2—C1113.6 (3)C10—C11—H11110.3
C3—C2—H2A108.9C13—C12—C17120.1 (3)
C1—C2—H2A108.9C13—C12—C11129.3 (3)
C3—C2—H2B108.9C17—C12—C11110.6 (3)
C1—C2—H2B108.9C14—C13—C12118.5 (4)
H2A—C2—H2B107.7C14—C13—H13120.7
O1—C3—O2126.0 (3)C12—C13—H13120.7
O1—C3—C2123.5 (3)C13—C14—C15121.3 (4)
O2—C3—C2110.5 (3)C13—C14—H14119.3
O4—C4—O3124.1 (3)C15—C14—H14119.3
O4—C4—C1123.8 (4)C14—C15—C16120.4 (4)
O3—C4—C1112.0 (3)C14—C15—H15119.8
O2—C5—C8110.4 (3)C16—C15—H15119.8
O2—C5—C7108.9 (3)C17—C16—C15118.4 (4)
C8—C5—C7113.5 (4)C17—C16—H16120.8
O2—C5—C6101.6 (3)C15—C16—H16120.8
C8—C5—C6111.3 (4)C16—C17—C12121.3 (4)
C7—C5—C6110.3 (3)C16—C17—C18130.4 (4)
C5—C6—H6A109.5C12—C17—C18108.3 (3)
C5—C6—H6B109.5C19—C18—C23120.9 (4)
H6A—C6—H6B109.5C19—C18—C17130.8 (3)
C5—C6—H6C109.5C23—C18—C17108.3 (3)
H6A—C6—H6C109.5C18—C19—C20118.4 (4)
H6B—C6—H6C109.5C18—C19—H19120.8
C5—C7—H7A109.5C20—C19—H19120.8
C5—C7—H7B109.5C21—C20—C19120.9 (4)
H7A—C7—H7B109.5C21—C20—H20119.6
C5—C7—H7C109.5C19—C20—H20119.6
H7A—C7—H7C109.5C20—C21—C22120.9 (4)
H7B—C7—H7C109.5C20—C21—H21119.6
C5—C8—H8A109.5C22—C21—H21119.6
C5—C8—H8B109.5C23—C22—C21118.5 (4)
H8A—C8—H8B109.5C23—C22—H22120.7
C5—C8—H8C109.5C21—C22—H22120.7
H8A—C8—H8C109.5C22—C23—C18120.3 (4)
H8B—C8—H8C109.5C22—C23—C11129.2 (3)
O5—C9—N1125.1 (4)C18—C23—C11110.4 (3)
O5—C9—O6124.7 (3)
C9—N1—C1—C2132.6 (3)C12—C13—C14—C15−0.2 (6)
C9—N1—C1—C4−102.3 (4)C13—C14—C15—C160.2 (6)
N1—C1—C2—C362.5 (4)C14—C15—C16—C170.7 (6)
C4—C1—C2—C3−61.9 (4)C15—C16—C17—C12−1.6 (6)
C5—O2—C3—O10.3 (6)C15—C16—C17—C18178.6 (4)
C5—O2—C3—C2−179.0 (3)C13—C12—C17—C161.7 (6)
C1—C2—C3—O10.5 (5)C11—C12—C17—C16−179.9 (4)
C1—C2—C3—O2179.7 (3)C13—C12—C17—C18−178.5 (3)
N1—C1—C4—O417.0 (5)C11—C12—C17—C18−0.1 (4)
C2—C1—C4—O4142.3 (4)C16—C17—C18—C191.9 (7)
N1—C1—C4—O3−165.8 (3)C12—C17—C18—C19−177.9 (4)
C2—C1—C4—O3−40.5 (4)C16—C17—C18—C23−178.1 (4)
C3—O2—C5—C8−63.1 (4)C12—C17—C18—C232.1 (4)
C3—O2—C5—C762.2 (5)C23—C18—C19—C20−1.0 (6)
C3—O2—C5—C6178.7 (3)C17—C18—C19—C20178.9 (4)
C1—N1—C9—O5−9.2 (5)C18—C19—C20—C212.2 (6)
C1—N1—C9—O6171.1 (3)C19—C20—C21—C22−1.0 (6)
C10—O6—C9—O510.9 (5)C20—C21—C22—C23−1.5 (6)
C10—O6—C9—N1−169.3 (3)C21—C22—C23—C182.6 (6)
C9—O6—C10—C11122.3 (3)C21—C22—C23—C11−175.1 (4)
O6—C10—C11—C23−68.6 (4)C19—C18—C23—C22−1.4 (6)
O6—C10—C11—C12177.4 (3)C17—C18—C23—C22178.7 (3)
C23—C11—C12—C13176.5 (4)C19—C18—C23—C11176.7 (3)
C10—C11—C12—C13−63.7 (5)C17—C18—C23—C11−3.2 (4)
C23—C11—C12—C17−1.7 (4)C12—C11—C23—C22−179.1 (4)
C10—C11—C12—C17118.1 (4)C10—C11—C23—C2261.3 (5)
C17—C12—C13—C14−0.8 (5)C12—C11—C23—C183.0 (4)
C11—C12—C13—C14−178.8 (4)C10—C11—C23—C18−116.5 (3)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O5i0.841.912.744 (3)172
N1—H1···O3ii0.882.393.213 (4)156
Symmetry codes: (i) −x+2, y+1/2, −z+1/2; (ii) x−1, y, z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O5i0.841.912.744 (3)172
N1—H1···O3ii0.882.393.213 (4)156
Symmetry codes: (i) −x+2, y+1/2, −z+1/2; (ii) x−1, y, z.
Acknowledgements top

KY thanks the Ministry of Education, Science, Sports, Culture and Technology (MEXT) of Japan for funding this work [Young Scientists (B), grant No. 20750022]. TS appreciates support from the World Premier International Research Center Initiative (WPI Initiative) on Materials Nanoarchitronics (MANA) at NIMS, from MEXT.

references
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