A model compound for poly(ester amide)s: Diethyl-3,9-diaza-4,8-dioxoundecanedioate

Article abstract of DOI:10.1023/A:1009533102931

The compound diethyl-3,9-diaza-4,8-dioxoundecanedioate (EtGGGEt) has crystallized in the space group P2₁ with cell parameters a = 8.267(2), b = 4.853(4), c = 20.361(6) A, β = 97.96(2)°. The crystal structure has been solved by direct methods and refined using the full matrix least squares methodology. There is one molecule in the asymmetric unit, in spite of its symmetric constitution. The central part of the molecule, the glutaramide moiety, has a partial folded conformation (TSTTST), which differs from the all trans conformation found in related moieties but with an even number of carbon atoms. The two flanking glycine residues have a different conformation one from each other; the first one adopts the standard conformation (ψ = -156.5°, φ = 73°), while the second one has an unusual conformation. In this glycine the oxygen atom has a big temperature factor and it is disordered in two positions. Both facts, conformation and disorder of the second glycine, seem to be due to improvement of contacts with neighboring molecules. The molecules are hydrogen bonded along the b axis, forming infinite rows with the same sense of orientation, so the crystal has a polar structure.

Full text of DOI:10.1023/A:1009533102931

Journal of Chemical Crystallography, Vol. 29, No. 9, 1999
A model compound for poly(ester amide)s: diethyl-3,9-
diaza-4,8-dioxoundecanedioate
Lourdes Urpı,(1)* Alfonso Rodrıguez-Galan,(1) and Jordi Puiggalı(1)
´
´
´
´
Received October 1, 1998
The compound diethyl-3,9-diaza-4,8-dioxoundecanedioate (EtGGGEt) has crystallized in
˚
the space group P21 with cell parameters a ϭ 8.267(2), b ϭ 4.853(4), c ϭ 20.361(6) A, ͱ ϭ
97.96(2)Њ. The crystal structure has been solved by direct methods and refined using the full
matrix least squares methodology. There is one molecule in the asymmetric unit, in spite of
its symmetric constitution. The central part of the molecule, the glutaramide moiety, has a
partial folded conformation (TSTTST), which differs from the all trans conformation found
in related moieties but with an even number of carbon atoms. The two flanking glycine
residues have a different conformation one from each other; the first one adopts the standard
conformation (␺ ϭ Ϫ156.5Њ, ␸ ϭ 73Њ), while the second one has an unusual conformation.
In this glycine the oxygen atom has a big temperature factor and it is disordered in two
positions. Both facts, conformation and disorder of the second glycine, seem to be due to
improvement of contacts with neighboring molecules. The molecules are hydrogen bonded
along the b axis, forming infinite rows with the same sense of orientation, so the crystal has
a polar structure.
KEY WORDS: Poly(ester amide)s; glycine; glutaric acid; model compound; nylons; X-ray diffraction.
Introduction
Experimental
There has been an increasing interest in the
study of poly(ester amide)s due to their potential
biodegradability and adequate mechanical proper-
ties.1 In particular, those polymers derived from
natural amino acids appear to have an enhanced sus-
ceptibility to degradation. As part of our work on
the structural study of new poly(ester amide)s,2–4
we report here the structure of the model com-
Synthesis
For the preparation of the title compound, 3.6
mmol of glutaryl dichloride were poured into a chlo-
roform solution of 7.2 mmol of glycine ethyl ester
hydrochloride and 14.4 mmol of triethylamine. After
two hours of stirring, the solution was evaporated to
dryness. The solution was extracted with ethyl acetate
and the product was recovered by evaporation of
solvent. For purification, it was twice recrystallized
from toluene (m.p. 364-365 K, yield 80%).
pound
diethyl-3,9-diaza-4,8-dioxoundecanedioate
(EtGGGEt), (see Scheme 1).
X-ray diffraction
Scheme 1
Crystals were obtained by vapor diffusion from
a dibutylether–acetonitrile (7:3, relation in volume)
solution (concentration 3.33 mg/ml) equilibrated
(1) Departament d’Enginyeria Qu´ımica, Universitat Polite`cnica de
Catalunya, Av. Diagonal 647, E-08028 Barcelona, Spain.
* To whom correspondence should be addressed.
1049
1074-1542/99/0900-1049$16.00/0  1999 Plenum Publishing Corporation

1050
Urpı, Rodrıguez-Galan, and Puiggalı
´ ´ ´
´
Table 1. Crystal Data and Structure Refinement
Compound
CH3CH2OC(O)CH2NHC(O)U(CH2)3U
C(O)NHCH2C(O)OCH2CH3
CCDC-1003/5668
Colorless/needle
C13H22N2O6
302.33
293(2)
CCDC deposit no.
Color/shape
Chemical formula
Formula weight
Temperature, K
Crystal system
Monoclinic
Space group
P21
Unit cell dimensions
˚
a ϭ 8.267(2) A
˚
b ϭ 4.853(4) A ͱ ϭ 97.96(2)Њ
˚
c ϭ 20.861(6) A
Volume, A
3
˚
809.0(7)
Z
2
Density (calculated), mg/m3
Absorption coefficient, mmϪ1
Diffractometer/scan
1.241
0.829
CAD4-Enraf Nonius/Ͷ-␪
2.19–56.96
2526
␪ range for data collection, deg
Reflections measured
Independent/observed reflections
Data/restraints/parameters
Goodness of fit on F2
Final R indices [F Ͼ 4␴(F)]
R indices (all data)
1245 (Rint ϭ 0.0475)/1245 [F Ͼ 2␴(F)]
1245/9/202
1.160
R1 ϭ 0.0665, wR2 ϭ 0.1566
R1 ϭ 0.1186, wR2 ϭ 0.1967
˚
Table 3. Selected Geometric Parameters [A, Њ] for EtGGGEt
Table 2. Fractional Atomic Coordinates and Equivalent Isotropic
Displacement Parameter (A ) of Non-Hydrogen Atoms for
(a) Selected torsional angles
2
˚
ClUC2UO3UC4
C2UO3UC4UC5
O3UC4UC5UN6
C4UC5UN6UC7
C5UN6UC7UC8
N6UC7UC8UC9
C7UC8UC9UCЈ8
C8UC9UCЈ8UCЈ7
C9UCЈ8UCЈ7UNЈ6
CЈ8UCЈ7UNЈ6UCЈ5
CЈ7UNЈ6UCЈ5UCЈ4
NЈ6UCЈ5UCЈ4UOЈ3
CЈ5UCЈ4UOЈ3UCЈ2
CЈ4UOЈ3UCЈ2UCЈ1
(b) Hydrogen-bonding geometry
DUHиииA
N6UH6иииO7(i)
NЈ6UHЈ6иииOЈ7(i)
(c) Contact distances
OЈ4AиииC8(ii)
Ϫ177.3(8)
Ϫ176.6(8)
Ϫ156.5(7)
73(1)
179.8(7)
Ϫ137.3(8)
Ϫ177.2(7)
179.9(8)
134.0(9)
175.8(8)
Ϫ129(1)
174(1)
EtGGGEt
x
y
z
Ueq
C1
C2
O3
C4
O4
C5
N6
C7
0.704(1)
0.835(1)
0.7843(6)
0.894(1)
1.0286(8)
0.8230(9)
0.9428(8)
1.022(1)
0.9953(9)
1.143(1)
1.140(1)
1.270(1)
1.274(1)
1.260(1)
1.2888(9)
1.304(1)
1.440(1)
1.557(3)
1.480(3)
1.4668(8)
1.604(1)
1.628(2)
0.663(3)
0.483(2)
0.365(1)
0.206(2)
0.170(2)
0.080(2)
0.002(1)
0.188(2)
0.433(1)
0.087(2)
0.229(2)
0.126(2)
0.258(2)
0.507(1)
0.093(1)
0.191(2)
0.074(2)
0.02(1)
0.0055(4)
0.0382(4)
0.0961(2)
0.1322(4)
0.1206(3)
0.1894(4)
0.2435(3)
0.2836(4)
0.2730(3)
0.3381(3)
0.4040(4)
0.4562(3)
0.5220(4)
0.5294(3)
0.5745(3)
0.6409(4)
0.6840(5)
0.654(1)
0.113(4)
0.103(3)
0.083(2)
0.073(2)
0.112(3)
0.075(2)
0.072(2)
0.067(2)
0.101(2)
0.078(2)
0.084(2)
0.083(2)
0.075(2)
0.121(3)
0.082(2)
0.101(3)
0.089(3)
0.14(2)
Ϫ179(1)
176(1)
O7
C8
C9
D---H
2.847(9)
2.98(1)
HиииA
1.991(9) 173.8(3)
2.14(1) 166.3(3)
D---HиииA
CЈ8
CЈ7
OЈ7
NЈ6
CЈ5
CЈ4
OЈ4A
OЈ4B
OЈ3
CЈ2
CЈ1
3.25(3)
3.25(2)
3.42(2)
3.38(2)
3.45(3)
3.36(1)
OЈ4AиииC9(ii)
OЈ4AиииCЈ8(ii)
OЈ4BиииC8(ii)
OЈ4BиииCЈ5(i)
Ϫ0.172(4)
0.178(2)
0.067(3)
0.215(4)
0.679(1)
0.126(9)
0.104(2)
0.144(6)
0.161(6)
0.7433(3)
0.7872(5)
0.8493(5)
OЈ7иииCЈ8(iii)
Symmetry codes:
(i) x, y Ϫ 1, z; (ii) 1 Ϫ x, Ϫ0.5 ϩ y, 1 Ϫ z; (iii) x, 1 ϩ y, z.

Diethyl-3,9-diaza-4,8-dioxoundecanedioate
1051
against a reservoir with dibutylether–acetonitrile
(9:1, relation in volume).
refined with a rigid bond restraint for the components
of the anisotropic displacement parameters of the
two positions.
The relatively high R value and the not
very high resolution are related to the small dimen-
sions of the crystal. The drawings were made with
molecular graphics programs ORTEP-II8 and
CERIUS 3.1.9
The main characteristics of data collection are
indicated in Table 1. The software used for cell re-
finement and for data collection was the software of
CAD4 in UNIX version.5 Data reduction was carried
out with a local program.
The solution of the structure has been obtained
by direct methods, with a standard run of the program
SHELXS-86.6 The refinement was carried out with
the program SHELXL-937 and the main parameters
about refinement are summarized in Table 1. After
doing 10 cycles of isotropic refinement and 30 cycles
of anisotropic refinement of all non-hydrogen atoms,
the hydrogen atoms were placed at calculated posi-
tions. Some of the H atoms were possible to be lo-
cated in the difference Fourier map, but not all. We
decided to place all H atoms at calculated positions
to increase the reflections/parameters ratio. All H
atoms were thus located at ideal positions and were
refined riding on their bonded atoms with a fixed
isotropic displacement parameter 1.5 (for methyl H
atoms) or 1.2 (for all other H atoms) times the value
of the equivalent isotropic displacement parameter
of the atom to which they were attached.
Discussion
The values of bond distances and bond angles
found in the studied compound agree with current
values found in the literature for methylene, esther,
and amide groups. The conformation of the central
part of the molecule, the glutaramide moiety, is
TSTTST (Table 3a). This result differs from the all
trans conformation expected for even-even nylons10
and also found in the even suberamide unit of the
related model compound diethyl-3,12-diaza-4,11-di-
oxotetradecanedioate (EtGSGEt).4 However, the
skew torsion angles are in full agreement with the Ͳ
conformation characteristic of nylons derived from
odd diacids.10
In spite of its chemical symmetry, the molecule
is asymmetric and so the conformation of the two
glycine residues is different (Fig. 2 and Table 3a).
Whereas, the torsion angles ␺ (OUCOUCH2UNH)
and ␸ (COUCH2UNHUCO) of one residue are
A bond length restraint was necessary to be ap-
plied to the terminal ethyl bonds. The OЈ4 atom is
disordered in two positions (61% in the main position
(B) and 39% in the secondary position (A)). This
atom has a big temperature factor, so it has been
Fig. 1. An ORTEP-II8 (25% probability ellipsoids) view of the title compound (EtGGGEt) showing the numbering scheme. H atoms
are shown as isotropic spheres of arbitrary radii. Two equivalent molecules interacting through two hydrogen bonds (thinner lines)
are represented.

1052
Urpı, Rodrıguez-Galan, and Puiggalı
´ ´ ´
´
although they still have close contacts with glutaryl
carbon atoms of a neighbor molecule as it is shown
in Table 3c. In fact, all the atoms of the second glycine
residue (CЈ1 to NЈ6) have a bigger temperature factor
than the chemically related atoms of the first glycine
residue (C1 to N6) (Table 2). Slight differences have
also been found in the hydrogen bond geometry that
involves both halves of the molecule (Table 3b). The
amide groups are planar, with a root-mean square
distance of the atoms from the best planes defined
˚
by them of 0.005 and 0.023 A for C5UN6U
C7(O7)UC8 and CЈ5UNЈ6UCЈ7(OЈ7)UCЈ8, re-
spectively.
The molecular packing is characterized by the
establishment of a single hydrogen bond direction
between molecules (Fig. 1), in a similar way to that
postulated for the Ͳ-form12 of nylons derived from
odd diacids. A twofold screw axis parallel to the hy-
drogen bond direction relates the non-hydrogen
bonded molecules of the unit cell. Thus, all amide
groups result with the same orientation and so the
crystal has a polar structure (Fig. 2).
Acknowledgments
The authors express their gratitude to Dr. L.J.
Campos for help with X-ray data collection. This
investigation was supported by a research grant from
CICYT (MAT97-1013).
References
Fig. 2. Crystal packing of the studied compound (EtGGGEt)
drawn with the CERIUS 3.1 software package.9 Molecules are
hydrogen bonded along the b axis direction. Note the different
environment of the two halves of the molecule.
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close to that found in EtGSGEt (Ϫ156.5 and 73Њ,
respectively to Ϫ162 and 72Њ), the ␸ torsion angle of
the second residue has a deviation toward a skew
conformation (Ϫ129Њ). This observation shows a
slight deviation from the reported values (68–
94Њ interval) on the UOCOCH2NHU derivatives
that are available in the Cambridge Structure Data
Base.11 In fact, this distortion may be due to the im-
provement of contacts with the glutaryl residue of a
neighboring molecule. Note that this is not the case
for the former glycine unit. In the same way, the OЈ4
carbonyl oxygen atom is disordered in two positions,
10. Kohan, M.I., Ed. Nylon Plastics Handbook; Hanser Publish-
ers: Mu¨nchen, 1995; pp 108-150.
11. Allen, F.H.; Kennard, O.; Taylor, R. Acc. Chem. Res. 1983,
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