PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actae2this articlesearchopen accesssubmitActa Crystallographica Section E: Crystallographic CommunicationsActa Crystallographica Section E: Crystallographic Communications
 
Acta Crystallogr E Crystallogr Commun. 2017 March 1; 73(Pt 3): 445–447.
Published online 2017 February 24. doi:  10.1107/S2056989017003024
PMCID: PMC5347073

Crystal structure of β-benzyl dl-aspartate N-carb­oxyanhydride

Abstract

In the title racemic compound, C12H11NO5 [systematic name: benzyl 2-(2,5-dioxooxazolidin-4-yl)acetate], the oxazolidine ring is planar, with an r.m.s. deviation of 0.03 Å. The benzyl ring is almost normal to the oxazolidine ring, making a dihedral angle of 80.11 (12)°. In the crystal, inversion dimers are formed between the l- and d-enanti­omers via pairs of N—H(...)O hydrogen bonds. This arrangement is favourable for the polymerization of the compound in the solid state. The dimers are linked by C—H(...)O hydrogen bonds, forming layers parallel to the ab plane.

Keywords: crystal structure, solid state polymerization, amino acid, N-carb­oxyanhydride, hydrogen bonding

Chemical context  

N-Carb­oxyanhydrides (NCAs) of amino acids are used ex­tensively as monomers for the preparation of high mol­ecular weight polypeptides (Kricheldorf, 2006  ). Amino acid NCAs are easily soluble but the resulting polypeptides are not soluble in general organic solvents. Only a few amino acid ester NCAs such as γ-benzyl l-glutamate NCA and γ-benzyl l-aspartate NCA are polymerized in solutions, because the resulting polypeptides are soluble in them. Thus, the polymerization of these amino acid ester NCAs has been investigated by many researchers. On the other hand, we found that every amino acid NCA crystal is polymerized in the solid state in hexane by the initiation of amines, and we have studied the solid-state polymerization of amino acid NCAs with reference to their crystal structures (Kanazawa, 1992  , 1998  ; Kanazawa et al., 1978  , 2006  ). We have studied the polymerization of γ-benzyl l-aspartate NCA (BLA NCA) initiated by butyl amine in solution and the solid state (Kanazawa & Sato, 1996  ), and determined the crystal structure of BLA NCA (Kanazawa & Magoshi, 2003  ), to consider the high reactivity in the solid state. In addition, we have attempted the preparation of single crystals of the title compound, β-benzyl dl-aspartate NCA (BDLA NCA). The BDLA NCA single crystals were obtained by a slow crystallization in solutions. The polymerization of BDLA NCA was carried out both in dioxane solution and in the solid state in hexane, using butyl amine as initiator. BDLA NCA is not so reactive in solutions; the existence of l- and d-enanti­omers in solution seems unfavourable for fast polymerization. On the other hand, the compound is very reactive in the solid state. It is therefore important to determine its crystal structure in order to consider the difference in the reactivity between the solution and the solid state.

An external file that holds a picture, illustration, etc.
Object name is e-73-00445-scheme1.jpg

Structural commentary  

The mol­ecular structure of the title compound is shown in Fig. 1  . The oxazolidine ring is planar, with a maximum deviation of 0.027 (2)Å for atom C1. The side chain has an extended conformation with the torsion angles C3—C4—C5—O5 and C4—C5—O5—C6 being 178.29 (14) and −179.29 (17)°, respectively. The benzyl ring is almost normal to the oxazolidine ring, making a dihedral angle of 80.11 (12)°.

Figure 1
The mol­ecular structure of the title compound, showing the atom labelling and 50% probability displacement ellipsoids.

Supra­molecular features  

In the crystal, β-benzyl l-aspartate NCA and β-benzyl d-aspartate NCA mol­ecules form a dimer structure around a crystallographic center of symmetry via a pair of N1—H1(...)O1i hydrogen bonds (Fig. 2  and Table 1  ). The dimers are linked by C—H(...)O hydrogen bonds, forming layers parallel to the ab plane (Fig. 2  and Table 1  ). The five-membered oxazolidine rings are packed in a layer and the –CH2COOCH2C6H5 groups are packed in another layer; these two different layers are stacked alternately. This sandwich structure is one of the important requirements for high reactivity in the solid state, because the five-membered rings can react with each other in the layer.

Figure 2
Crystal packing of the title compound, viewed along the c axis, showing the hydrogen bonds as dashed lines (see Table 1  ).
Table 1
Hydrogen-bond geometry (Å, °)

Synthesis and crystallization  

The synthesis of BDLA was carried out by the reaction of dl-aspartic acid with benzyl alcohol in a manner similar to that for γ-benzyl l-glutamate (BLG) (Kanazawa, 1992  ). The title compound was obtained by the reaction of BDLA with triphosgene in tetra­hydro­furan, as reported previously for BLA NCA (Kanazawa & Magoshi, 2003  ). The reaction product was recrystallized slowly in a mixture of ethyl acetate and hexane (1:50 v/v), avoiding moisture contamination, giving colourless prismatic crystals.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2  . The N-bound H atom was located in a difference Fourier map and refined with U iso(H) = 1.2U eq(N). The C-bound H atoms were positioned geometrically (C—H = 0.93–0.98 Å) and treated as riding with U iso(H) = 1.2U eq(C).

Table 2
Experimental details

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989017003024/su5349sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017003024/su5349Isup2.hkl

CCDC reference: 1534297

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

HK thanks Dr Hidehiro Uekusa of Tokyo Institute of Technology for assistance with the checking of the crystal structure analysis of the title compound.

supplementary crystallographic information

Crystal data

C12H11NO5F(000) = 1040
Mr = 249.22Dx = 1.328 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2ac 2abCell parameters from 15837 reflections
a = 8.6065 (8) Åθ = 3.0–27.6°
b = 12.1558 (12) ŵ = 0.11 mm1
c = 23.820 (2) ÅT = 293 K
V = 2492.0 (4) Å3Prism, colourless
Z = 80.43 × 0.23 × 0.03 mm

Data collection

Rigaku XtaLAB mini diffractometer2861 independent reflections
Radiation source: fine-focus sealed tube1520 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.084
Detector resolution: 6.849 pixels mm-1θmax = 27.5°, θmin = 3.0°
ω scansh = −11→11
Absorption correction: multi-scan (REQAB; Rigaku, 1998)k = −15→15
Tmin = 0.862, Tmax = 0.997l = −30→30
24433 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115H atoms treated by a mixture of independent and constrained refinement
S = 0.98w = 1/[σ2(Fo2) + (0.0503P)2] where P = (Fo2 + 2Fc2)/3
2861 reflections(Δ/σ)max = 0.020
166 parametersΔρmax = 0.13 e Å3
0 restraintsΔρmin = −0.16 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
Refinement. Refinement of F2 against ALL 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 > 2sigma(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)

xyzUiso*/Ueq
O1−0.15716 (18)−0.06365 (9)0.53169 (7)0.0695 (5)
O2−0.32140 (15)0.05348 (9)0.57507 (6)0.0558 (4)
O3−0.43399 (16)0.20638 (11)0.60784 (7)0.0696 (5)
O40.09214 (16)0.32273 (12)0.53621 (6)0.0675 (5)
O50.12154 (15)0.39128 (11)0.62231 (6)0.0592 (4)
N1−0.10097 (17)0.11990 (11)0.54204 (7)0.0428 (4)
C1−0.1845 (2)0.02906 (14)0.54691 (8)0.0475 (5)
C2−0.3277 (2)0.16511 (14)0.58457 (8)0.0476 (5)
C3−0.1816 (2)0.21622 (12)0.56219 (7)0.0392 (4)
H3−0.20660.26470.53060.047*
C4−0.0952 (2)0.28038 (14)0.60680 (8)0.0434 (5)
H4A−0.16280.33700.62190.052*
H4B−0.06700.23140.63730.052*
C50.0486 (2)0.33268 (14)0.58341 (9)0.0462 (5)
C60.2629 (3)0.44719 (19)0.60384 (10)0.0760 (7)
H6A0.23910.50050.57480.091*
H6B0.33690.39450.58900.091*
C70.3277 (2)0.50317 (18)0.65424 (9)0.0582 (6)
C80.2818 (2)0.60778 (18)0.66805 (10)0.0649 (6)
H80.21410.64550.64450.078*
C90.3345 (3)0.6578 (2)0.71624 (13)0.0841 (8)
H90.30190.72860.72530.101*
C100.4331 (4)0.6039 (3)0.75019 (13)0.1036 (10)
H100.46790.63750.78290.124*
C110.4824 (4)0.5014 (3)0.73727 (16)0.1274 (12)
H110.55160.46520.76090.153*
C120.4298 (3)0.4500 (2)0.68874 (14)0.1006 (10)
H120.46400.37960.67980.121*
H1−0.023 (2)0.1231 (14)0.5219 (8)0.051*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0806 (11)0.0323 (7)0.0957 (12)−0.0054 (7)0.0248 (9)−0.0072 (7)
O20.0549 (9)0.0408 (7)0.0716 (10)−0.0091 (6)0.0160 (7)−0.0024 (6)
O30.0517 (9)0.0652 (9)0.0918 (12)0.0024 (7)0.0223 (9)−0.0117 (8)
O40.0644 (10)0.0866 (11)0.0514 (10)−0.0233 (8)0.0137 (8)−0.0240 (8)
O50.0541 (8)0.0741 (9)0.0492 (9)−0.0240 (7)0.0029 (7)−0.0147 (7)
N10.0395 (9)0.0326 (8)0.0562 (11)−0.0019 (7)0.0074 (8)−0.0022 (7)
C10.0497 (12)0.0366 (10)0.0562 (14)−0.0024 (9)0.0075 (10)0.0014 (9)
C20.0462 (12)0.0437 (10)0.0529 (12)0.0010 (9)0.0015 (10)−0.0045 (9)
C30.0396 (10)0.0329 (9)0.0452 (11)0.0028 (8)0.0000 (9)−0.0027 (7)
C40.0432 (11)0.0428 (10)0.0441 (11)0.0005 (8)0.0016 (9)−0.0044 (8)
C50.0461 (11)0.0462 (10)0.0463 (12)−0.0027 (9)−0.0010 (10)−0.0087 (10)
C60.0619 (14)0.1002 (17)0.0660 (16)−0.0381 (13)0.0104 (13)−0.0191 (13)
C70.0450 (12)0.0712 (14)0.0583 (15)−0.0193 (11)0.0005 (11)−0.0107 (11)
C80.0487 (13)0.0744 (14)0.0714 (16)−0.0113 (11)0.0008 (12)0.0003 (12)
C90.0662 (17)0.0880 (17)0.098 (2)−0.0203 (14)0.0095 (16)−0.0349 (16)
C100.085 (2)0.144 (3)0.082 (2)−0.022 (2)−0.0167 (17)−0.041 (2)
C110.113 (3)0.141 (3)0.128 (3)0.009 (2)−0.070 (2)−0.019 (2)
C120.089 (2)0.0844 (18)0.128 (3)0.0070 (15)−0.035 (2)−0.0211 (18)

Geometric parameters (Å, º)

O1—C11.2070 (19)C4—H4B0.9700
O2—C21.377 (2)C6—C71.488 (3)
O2—C11.388 (2)C6—H6A0.9700
O3—C21.181 (2)C6—H6B0.9700
O4—C51.191 (2)C7—C121.365 (3)
O5—C51.327 (2)C7—C81.372 (3)
O5—C61.461 (2)C8—C91.376 (3)
N1—C11.323 (2)C8—H80.9300
N1—C31.443 (2)C9—C101.343 (4)
N1—H10.827 (19)C9—H90.9300
C2—C31.501 (2)C10—C111.352 (4)
C3—C41.513 (2)C10—H100.9300
C3—H30.9800C11—C121.390 (4)
C4—C51.499 (2)C11—H110.9300
C4—H4A0.9700C12—H120.9300
C2—O2—C1108.89 (14)O5—C5—C4111.02 (17)
C5—O5—C6115.67 (15)O5—C6—C7106.37 (17)
C1—N1—C3112.76 (15)O5—C6—H6A110.5
C1—N1—H1122.1 (12)C7—C6—H6A110.5
C3—N1—H1123.1 (12)O5—C6—H6B110.5
O1—C1—N1130.31 (19)C7—C6—H6B110.5
O1—C1—O2120.71 (16)H6A—C6—H6B108.6
N1—C1—O2108.98 (14)C12—C7—C8118.7 (2)
O3—C2—O2121.75 (18)C12—C7—C6120.7 (2)
O3—C2—C3129.78 (16)C8—C7—C6120.6 (2)
O2—C2—C3108.46 (15)C7—C8—C9121.0 (2)
N1—C3—C2100.67 (13)C7—C8—H8119.5
N1—C3—C4114.58 (15)C9—C8—H8119.5
C2—C3—C4112.05 (15)C10—C9—C8119.7 (3)
N1—C3—H3109.7C10—C9—H9120.2
C2—C3—H3109.7C8—C9—H9120.2
C4—C3—H3109.7C9—C10—C11120.7 (3)
C5—C4—C3111.29 (16)C9—C10—H10119.6
C5—C4—H4A109.4C11—C10—H10119.6
C3—C4—H4A109.4C10—C11—C12120.1 (3)
C5—C4—H4B109.4C10—C11—H11120.0
C3—C4—H4B109.4C12—C11—H11120.0
H4A—C4—H4B108.0C7—C12—C11119.8 (3)
O4—C5—O5124.41 (17)C7—C12—H12120.1
O4—C5—C4124.57 (17)C11—C12—H12120.1
C3—N1—C1—O1175.5 (2)C6—O5—C5—C4−179.29 (17)
C3—N1—C1—O2−5.3 (2)C3—C4—C5—O4−1.9 (3)
C2—O2—C1—O1−176.46 (19)C3—C4—C5—O5178.29 (14)
C2—O2—C1—N14.3 (2)C5—O5—C6—C7−177.72 (18)
C1—O2—C2—O3179.69 (19)O5—C6—C7—C1289.3 (3)
C1—O2—C2—C3−1.6 (2)O5—C6—C7—C8−88.3 (2)
C1—N1—C3—C24.1 (2)C12—C7—C8—C9−1.4 (3)
C1—N1—C3—C4124.47 (18)C6—C7—C8—C9176.3 (2)
O3—C2—C3—N1177.2 (2)C7—C8—C9—C100.4 (4)
O2—C2—C3—N1−1.29 (19)C8—C9—C10—C110.6 (5)
O3—C2—C3—C455.0 (3)C9—C10—C11—C12−0.7 (6)
O2—C2—C3—C4−123.50 (16)C8—C7—C12—C111.3 (4)
N1—C3—C4—C567.26 (19)C6—C7—C12—C11−176.4 (3)
C2—C3—C4—C5−178.86 (14)C10—C11—C12—C7−0.3 (5)
C6—O5—C5—O40.9 (3)

Hydrogen-bond geometry (Å, º)

D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.83 (2)2.13 (2)2.913 (3)157 (2)
C3—H3···O1ii0.982.393.101 (2)129

Symmetry codes: (i) −x, −y, −z+1; (ii) −x−1/2, y+1/2, z.

References

  • Kanazawa, H. (1992). Polymer, 33, 2557–2566.
  • Kanazawa, H. (1998). Mol. Cryst. Liq. Cryst. Sci. Technol. Sect. A, 313, 205–210.
  • Kanazawa, H., Inada, A. & Kawana, N. (2006). Macromol. Symp. 242, 104–112.
  • Kanazawa, H., Kawai, T., Ohashi, Y. & Sasada, Y. (1978). Bull. Chem. Soc. Jpn, 51, 2200–2204.
  • Kanazawa, H. & Magoshi, J. (2003). Acta Cryst. C59, o159–o161. [PubMed]
  • Kanazawa, H. & Sato, Y. (1996). Science Reports, Fukushima University. 59, 13–17.
  • Kricheldorf, H. R. (2006). Angew. Chem. Int. Ed. 45, 5752–5784. [PubMed]
  • 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.
  • Rigaku (1998). REQAB. Rigaku Corporation. Tokyo 196-8666, Japan.
  • Rigaku (2009). CrystalClear and CrystalStructure. Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography