R44(30) rectangular rings in 2,5-dioxopiperazine-1,4-diacetic acid

Article abstract of DOI:10.1107/S0108270103017803

Molecules of the title 2,5-dioxopiperazinedione derivative, C ₈H₁₀N₂O₆, occupy centres of symmetry in the crystal structure. The six-membered ring has an almost planar conformation, with the substituent on nitrogen nearly perpendicular to the ring. The ideal geometry of the isolated molecule, as determined by ab initio HF-LCAO quantum-mechanical calculations, is slightly more puckered than that observed in the solid state. In the crystal structure, a strong hydrogen bond joins neighbouring molecules, thus forming a network of rectangular R ₄⁴(30) rings.

Full text of DOI:10.1107/S0108270103017803

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
ISSN 0108-2701
R44(30) rectangular rings in 2,5-dioxo-
piperazine-1,4-diacetic acid
Figure 1
An ORTEPII plot (Johnson, 1976) of (I). Displacement ellipsoids are
drawn at the 50% probability level.
Manuela Ramos Silva,a* Ana Matos Beja,a Jose Antonio
PaixÄao,a Abilio J. F. N. Sobral,b Lucia M. L. Cabralb and
A. M. d'A. Rocha Gonsalvesb
chair), with a weighted average torsion angle of 7.63 (12)ꢀ and
a
Â
Ã
CEMDRX, Departamento de Fõsica, Faculdade de Ciencias e Tecnologia,
Universidade de Coimbra, P-3004-516 Coimbra, Portugal, and bDepartamento
puckering parametꢀers (Cremer & Pople, 1975) Q, ꢀ and ' of
ꢀ
Ê
Ã
Â
de Quõmica, Faculdade de Ciencias e Tecnologia, Universidade de Coimbra,
0.067 (2) A, 7.5 (2) and 0 , respectively (Fig. 1 and Table 1).
The ideal geometry of the isolated molecule as determined by
an ab initio HF±LCAO (Hartree±Fock linear combination of
atomic orbitals) quantum-mechanical calculation using the
GAMESS program (Schmidt et al., 1993) and a 631(d,p) basis
set, shows a slightly more puckered conformation, with an
average torsion angle within the ring of 13.09ꢀ. N,N0-Di-
methyldiketopiperazine (Groth, 1969) exhibits a ring confor-
mation close to that of (I), with a weighted average torsion
angle of 6.9 (4)ꢀ; however, greater degrees of puckering have
been found, for example, in 1,6-bis(methoxycarbonylmethyl)-
2,5-piperazinedione, for which a weighted average torsion
angle of 18.1 (2)ꢀ was reported (Tapia-Benavides et al., 1997).
Atoms O3 and C2 share the plane of the ring atoms, their
deviations from the least-squares plane being 0.087 (4) and
P-3004-535 Coimbra, Portugal
Correspondence e-mail: manuela@pollux.fis.uc.pt
Received 15 July 2003
Accepted 11 August 2003
Online 23 September 2003
Molecules of the title 2,5-dioxopiperazinedione derivative,
C8H10N2O6, occupy centres of symmetry in the crystal
structure. The six-membered ring has an almost planar
conformation, with the substituent on nitrogen nearly
perpendicular to the ring. The ideal geometry of the isolated
molecule, as determined by ab initio HF±LCAO quantum-
mechanical calculations, is slightly more puckered than that
observed in the solid state. In the crystal structure, a strong
hydrogen bond joins neighbouring molecules, thus forming a
network of rectangular R44(30) rings.
Ê
0.086 (4) A, respectively. The substituent on nitrogen is also
planar and is almost perpendicular to the ring, the angle
between the two least-squares planes being 89.55 (8)ꢀ. The
C4ÐN1ÐC2ÐC1 and C3ÐN1ÐC2ÐC1 torsion angles are
84.4 (2) and 85.7 (3)ꢀ, respectively; the corresponding ideal
values for the isolated molecule are 84.76 and 81.04ꢀ, and the
corresponding torsion angles in 1,6-bis(methoxycarbonyl-
Comment
The condensation of amino acids or their esters leads to 2,5-
piperazinediones, an important class of nitrogen-containing
organic compounds. These cyclic compounds are found in
nature as the result of protein degradation (Bray et al., 1991;
Steinberg & Lada, 1983) and are also described as antibiotics
(Nakatsuka et al., 1983), antitumorals (Arison & Beck, 1973)
and models for protein studies (Benedetti et al., 1976; Radding
et al., 1980). The dimerization of iminodiacetic acid or its
esters leads naturally to N-substituted 2,5-piperazinediones,
although the synthesis is generally a low-yield process (Jong-
kees, 1908; Dubsky & Granacher, 1917; Tapia-Benavides et al.,
1997). We have synthesized the title compound, (I), by the
cyclization of iminodiacetic acid dimethyl ester in the presence
of NiCl2.
Figure 2
The title N-substituted 2,5-piperazinedione molecule occu-
pies a crystallographic centre of symmetry. The six-membered
ring has an almost planar conformation (extremely ¯attened
A view of the extended structure of (I), with hydrogen bonds shown as
dashed lines. H atoms not participating in hydrogen bonding have been
omitted for clarity.
o562 # 2003 International Union of Crystallography
DOI: 10.1107/S0108270103017803
Acta Cryst. (2003). C59, o562±o563

organic compounds
Table 1
Selected geometric parameters (A, ).
methyl)-2,5-piperazinedione (Tapia-Benavides et al., 1997) are
78.04 and 84.94ꢀ.
The large asymmetry in the two carboxy CÐO distances
ꢀ
Ê
O1ÐC1
O2ÐC1
O3ÐC3
1.192 (3)
1.317 (3)
1.236 (3)
N1ÐC3
N1ÐC2
1.329 (3)
1.455 (3)
Ê
Ê
[O1ÐC1 = 1.192 (3) A and O2ÐC1 = 1.317 (3) A] re¯ects the
fact that the H atom is retained by the carboxy group. This H
1
atom is involved in a strong O2ÐH2Á Á ÁO3(x 1,
y
,
2
C3ÐN1ÐC4
C2ÐN1ÐC4
124.31 (18)
115.65 (17)
O1ÐC1ÐO2
N1ÐC2ÐC1
124.1 (2)
110.26 (18)
z
12 ) hydrogen bond that links the molecules, with a donor±
Ê
acceptor distance of 2.726 (3) A and a DÐHÁ Á ÁA angle of
166 (3)ꢀ (Table 2). Using graph-set analysis (Bernstein et al.,
1995) to describe patterns in the hydrogen-bond network, we
®nd rectangular-shaped R44(30) rings (Fig. 2).
C3ÐN1ÐC2ÐC1
O1ÐC1ÐC2ÐN1
O2ÐC1ÐC2ÐN1
85.7 (3)
5.0 (4)
176.95 (19)
C2ÐN1ÐC3ÐO3
C4ÐN1ÐC3ÐO3
4.8 (3)
174.0 (2)
Table 2
Hydrogen-bonding geometry (A, ).
Experimental
ꢀ
Ê
Iminodiacetic acid was mixed with NiCl2 in a solution of ethanol and
water and heated at 333 K overnight. The solution was left to cool and
evaporate slowly at room temperature; after a few months, small
single crystals had grown (with a slight green super®cial tint caused
by impurities). Prior to data collection, Laue photographs of the
crystal were taken in order to appraise its quality.
DÐHÁ Á ÁA
O2ÐH2Á Á ÁO3i
DÐH
HÁ Á ÁA
1.85 (4)
DÁ Á ÁA
DÐHÁ Á ÁA
0.89 (4)
2.726 (3)
166 (3)
1
2
1
Symmetry code: (i) x 1;
y; z
.
2
program(s) used to re®ne structure: SHELXL97 (Sheldrick, 1997);
molecular graphics: ORTEPII (Johnson, 1976); software used to
prepare material for publication: SHELXL97.
Crystal data
3
C8H10N2O6
Mr = 230.18
Dx = 1.618 Mg m
Mo Kꢂ radiation
Cell parameters from 14
re¯ections
Ã
Monoclinic, P21=c
Ä
Financial assistance from FundacËao para a Ciencia e a
Tecnologia (Sapiens POCTI/QUI/42536) and Chymiotechnon,
Portugal, is acknowledged.
Ê
a = 5.5322 (6) A
ꢀ = 7.7±13.6ꢀ
ꢃ = 0.14 mm
T = 293 (2) K
Ê
b = 9.1505 (13) A
1
Ê
c = 9.8235 (8) A
ꢁ = 108.189 (7)ꢀ
3
Ê
V = 472.44 (9) A
Z = 2
Plate, colourless
0.27 Â 0.23 Â 0.09 mm
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: FA1026). Services for accessing these data are
described at the back of the journal.
Data collection
Enraf±Nonius CAD-4
diffractometer
!±2ꢀ scans
2943 measured re¯ections
872 independent re¯ections
604 re¯ections with I > 2ꢄ(I)
Rint = 0.045
ꢀ
max = 25.5ꢀ
h = 6 ! 6
References
k = 11 ! 11
l = 11 ! 11
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3 standard re¯ections
frequency: 180 min
intensity decay: 3%
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Re®nement on F2
R[F2 > 2ꢄ(F2)] = 0.042
wR(F2) = 0.117
S = 1.05
872 re¯ections
76 parameters
H atoms treated by a mixture of
independent and constrained
re®nement
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3
Ê
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Ê
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Áꢅmin
=
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Data collection: CAD-4 Software (Enraf±Nonius, 1989); cell
re®nement: CAD-4 Software; data reduction: HELENA (Spek, 1997);
program(s) used to solve structure: SHELXS97 (Sheldrick, 1997);
ꢁ
Acta Cryst. (2003). C59, o562±o563
Manuela Ramos Silva et al. C8H10N2O6 o563