organic compounds
(3R,8aS)-3-Ethylperhydropyrrolo[1,2-a]pyrazine-1,4-dione
aDepto. de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
*Correspondence e-mail: adajb@qmc.ufsc.br
In the title compound, C9H14N2O2, the pyrrolidine and piperazine rings adopt envelope and boat conformations, respectively. The chiral centers were assigned on the basis of the known stereogenic center of an enantiomerically pure starting material and the trans relationship between the H atoms attached to these centers. The crystal packing is stabilized by an intermolecular hydrogen bond between the N—H group and a carbonyl O atom of the diketopiperazine group, forming zigzag C(5) chains along [010].
Related literature
For general background to the chemistry and biological properties of diketopiperazines, see: Herbert & Kelleher (1994); Ciajolo et al. (1995); Morley et al. (1981); Kazuharu et al. (1990); Funabashi et al. (1994); Moyroud et al. (1996); Caballero et al. (2003); Onishi et al. (2003); Alberch et al. (2004); von Nussbaum et al. (2003). For related structures, see: Hendea et al. (2006).
Experimental
Crystal data
|
Data collection
|
Refinement
|
Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell CAD-4 Software; data reduction: HELENA (Spek, 1996); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97.
Supporting information
https://doi.org/10.1107/S1600536810001856/bh2268sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810001856/bh2268Isup2.hkl
To a solution of L-proline methyl ester derivative (II) (0.084 mmol) in methanol (6 ml) was added Pd/C (10%, 18 mg, three portions of 6 mg of the catalyst were added each 10 h) and the mixture was shaken under 40 psi of hydrogen at room temperature for 28 h and 30 min [TLC control, alumina, ethyl acetate/hexane (1:3 v/v)]. After filtration of the catalyst, the solvent was evaporated under reduced pressure and
of the residue over alumina with ethyl acetate afforded compound (I) as a white solid, with 84% yield. A careful crystallization from ethyl acetate/hexane (1:3 v/v) provided crystals (mp. 133.5–134.5°C) suitable for X-ray analysis.All non-H atoms were refined with anisotropic displacement parameters. H atoms were placed at their idealized positions with distances of 0.98, 0.97 and 0.96 Å for CH, CH2 and CH3, respectively. Uiso of the H atoms were fixed at 1.2 times for methine and methylene and 1.5 times for methyl of the Ueq of the carrier C atom. Hydrogen atom of the cyclic piperazine amine group was found in a difference map and treated with a riding model and its Uiso was also fixed at 1.2 times Ueq of the parent N atom.
Diketopiperazine (DKP) backbone is an important pharmacophore in medicinal chemistry, which is conformationally restrained by six-membered ring with side chains that are oriented in a spatially defined manner (Herbert & Kelleher, 1994; Ciajolo et al., 1995). DKPs are quite common in nature and many natural products with the DKP scaffold have been isolated encompassing a wide range of biological activities (Morley et al., 1981; Kazuharu et al., 1990; Funabashi et al., 1994; Moyroud et al., 1996). Several
of microorganisms with interesting biological properties contain a proline-derived diketopiperazine as part of their molecular skeleton (Caballero et al., 2003; Onishi et al., 2003; Alberch et al., 2004; von Nussbaum et al., 2003). During our work on the synthesis of L-proline-based DKPs, we prepared L-proline methyl ester derivative (II) which, under hydrogenolysis condition, led to the title compound (I, Fig. 1). Despite its full chemical characterization and the known configuration of the starting material L-proline, the at C3 was tentatively assigned as being R due to the trans relationship of the hydrogen atoms attached to carbons C3 and C8a based on 1H-NMR and NOE experiments. The crystallographic data unambiguously confirmed the trans relationship of the above mentioned hydrogen atoms and consequently the R configuration of the chiral center at C3 (Fig. 2).The molecular structure of (I) consists of a bicycle system formed by pyrrolidine and piperazine fused rings (Hendea et al., 2006). The five-membered pyrrolidine ring shows an
which is enveloped at C8. Piperazine ring shows perfect boat conformation, where N2, C1, C4 and N5 atoms lie on the basal plane (r.m.s. deviation: 0.0016 Å) and C3 and C8a are out of the basal mean plane by 0.39 Å (average) toward the same direction.Strong intermolecular hydrogen bonds between the N—H group and the carbonyl O atom of the diketopiperazine neighboring groups contribute to the stabilization of the
N2—H2···O4i [symmetry code: (i) -x + 2, y + 1/2, -z] interactions promote the formation of parallel one-dimensional zigzag C(5) chains running on the 21 screw axis along [010] (Fig. 3). Furthermore, the molecules of (I) are stacked viewing in perpendicular projection of the chains, along [100], and viewing in parallel projection of the chains, along [010] (Fig. 4).For general background to the chemistry and biological properties of diketopiperazines, see: Herbert & Kelleher (1994); Ciajolo et al. (1995); Morley et al. (1981); Kazuharu et al. (1990); Funabashi et al. (1994); Moyroud et al. (1996); Caballero et al. (2003); Onishi et al. (2003); Alberch et al. (2004); von Nussbaum et al. (2003). For related structures, see: Hendea et al. (2006).
Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell
CAD-4 Software (Enraf–Nonius, 1989); data reduction: HELENA (Spek, 1996); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C9H14N2O2 | F(000) = 196 |
Mr = 182.22 | Dx = 1.268 Mg m−3 |
Monoclinic, P21 | Melting point: 407 K |
Hall symbol: P 2yb | Mo Kα radiation, λ = 0.71073 Å |
a = 6.8657 (4) Å | Cell parameters from 25 reflections |
b = 9.9258 (17) Å | θ = 3.6–15.6° |
c = 7.0040 (5) Å | µ = 0.09 mm−1 |
β = 90.892 (6)° | T = 293 K |
V = 477.25 (9) Å3 | Prism, colorless |
Z = 2 | 0.46 × 0.40 × 0.33 mm |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.032 |
Radiation source: fine-focus sealed tube | θmax = 27.9°, θmin = 3.0° |
Graphite monochromator | h = −9→9 |
ω–2θ scans | k = −13→0 |
1290 measured reflections | l = −9→0 |
1200 independent reflections | 3 standard reflections every 200 reflections |
937 reflections with I > 2σ(I) | intensity decay: 1% |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.120 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0525P)2 + 0.0801P] where P = (Fo2 + 2Fc2)/3 |
1200 reflections | (Δ/σ)max < 0.001 |
119 parameters | Δρmax = 0.17 e Å−3 |
1 restraint | Δρmin = −0.15 e Å−3 |
0 constraints |
C9H14N2O2 | V = 477.25 (9) Å3 |
Mr = 182.22 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 6.8657 (4) Å | µ = 0.09 mm−1 |
b = 9.9258 (17) Å | T = 293 K |
c = 7.0040 (5) Å | 0.46 × 0.40 × 0.33 mm |
β = 90.892 (6)° |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.032 |
1290 measured reflections | 3 standard reflections every 200 reflections |
1200 independent reflections | intensity decay: 1% |
937 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.044 | 1 restraint |
wR(F2) = 0.120 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.17 e Å−3 |
1200 reflections | Δρmin = −0.15 e Å−3 |
119 parameters |
x | y | z | Uiso*/Ueq | ||
C1 | 0.6671 (5) | 0.5429 (3) | 0.1100 (4) | 0.0446 (7) | |
C3 | 0.8672 (4) | 0.3662 (3) | −0.0490 (4) | 0.0446 (7) | |
H3 | 1.0083 | 0.3519 | −0.0400 | 0.054* | |
C4 | 0.7726 (4) | 0.2617 (3) | 0.0781 (4) | 0.0428 (7) | |
C6 | 0.5113 (5) | 0.2151 (3) | 0.3021 (5) | 0.0481 (7) | |
H6A | 0.5912 | 0.1966 | 0.4145 | 0.058* | |
H6B | 0.4732 | 0.1304 | 0.2435 | 0.058* | |
C7 | 0.3339 (5) | 0.2985 (4) | 0.3527 (5) | 0.0646 (10) | |
H7A | 0.3015 | 0.2867 | 0.4860 | 0.077* | |
H7B | 0.2223 | 0.2732 | 0.2741 | 0.077* | |
C8 | 0.3944 (5) | 0.4437 (4) | 0.3131 (5) | 0.0603 (9) | |
H8A | 0.2816 | 0.5001 | 0.2878 | 0.072* | |
H8B | 0.4681 | 0.4810 | 0.4199 | 0.072* | |
C8A | 0.5200 (4) | 0.4315 (3) | 0.1373 (4) | 0.0415 (6) | |
H8AA | 0.4353 | 0.4263 | 0.0237 | 0.050* | |
C9 | 0.8066 (5) | 0.3439 (4) | −0.2576 (5) | 0.0572 (9) | |
H9A | 0.8351 | 0.2514 | −0.2924 | 0.069* | |
H9B | 0.6670 | 0.3568 | −0.2705 | 0.069* | |
C10 | 0.9082 (6) | 0.4374 (5) | −0.3946 (5) | 0.0691 (11) | |
H10A | 1.0466 | 0.4307 | −0.3753 | 0.104* | |
H10B | 0.8673 | 0.5284 | −0.3720 | 0.104* | |
H10C | 0.8751 | 0.4124 | −0.5235 | 0.104* | |
N2 | 0.8290 (4) | 0.5027 (2) | 0.0198 (4) | 0.0486 (7) | |
H2 | 0.9129 | 0.5629 | −0.0171 | 0.058* | |
N5 | 0.6154 (3) | 0.3007 (2) | 0.1667 (3) | 0.0396 (6) | |
O1 | 0.6391 (4) | 0.6573 (2) | 0.1630 (4) | 0.0643 (7) | |
O4 | 0.8399 (4) | 0.1481 (2) | 0.0937 (4) | 0.0655 (7) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0549 (17) | 0.0338 (15) | 0.0452 (15) | 0.0027 (13) | −0.0003 (13) | 0.0037 (13) |
C3 | 0.0380 (15) | 0.0432 (17) | 0.0528 (16) | 0.0016 (12) | 0.0064 (13) | 0.0008 (14) |
C4 | 0.0405 (15) | 0.0384 (15) | 0.0494 (16) | 0.0032 (13) | 0.0012 (13) | −0.0032 (13) |
C6 | 0.0556 (18) | 0.0402 (16) | 0.0486 (16) | −0.0063 (14) | 0.0040 (14) | 0.0026 (14) |
C7 | 0.061 (2) | 0.067 (2) | 0.066 (2) | 0.0009 (19) | 0.0250 (16) | 0.005 (2) |
C8 | 0.065 (2) | 0.050 (2) | 0.067 (2) | 0.0113 (17) | 0.0253 (16) | 0.0011 (17) |
C8A | 0.0415 (14) | 0.0351 (14) | 0.0480 (15) | 0.0053 (13) | 0.0043 (12) | 0.0018 (12) |
C9 | 0.066 (2) | 0.055 (2) | 0.0507 (17) | −0.0062 (16) | 0.0063 (16) | −0.0058 (15) |
C10 | 0.077 (2) | 0.079 (3) | 0.0526 (19) | −0.003 (2) | 0.0156 (17) | −0.0057 (19) |
N2 | 0.0534 (15) | 0.0378 (14) | 0.0549 (15) | −0.0127 (12) | 0.0085 (12) | −0.0031 (11) |
N5 | 0.0416 (13) | 0.0317 (12) | 0.0457 (13) | 0.0024 (10) | 0.0051 (10) | 0.0018 (11) |
O1 | 0.0847 (18) | 0.0346 (12) | 0.0737 (16) | 0.0033 (12) | 0.0073 (14) | −0.0050 (12) |
O4 | 0.0627 (14) | 0.0468 (14) | 0.0875 (17) | 0.0208 (12) | 0.0180 (12) | 0.0095 (13) |
C1—O1 | 1.210 (4) | C7—H7A | 0.9700 |
C1—N2 | 1.347 (4) | C7—H7B | 0.9700 |
C1—C8A | 1.512 (4) | C8—C8A | 1.519 (4) |
C3—N2 | 1.464 (4) | C8—H8A | 0.9700 |
C3—C4 | 1.519 (4) | C8—H8B | 0.9700 |
C3—C9 | 1.529 (4) | C8A—N5 | 1.468 (4) |
C3—H3 | 0.9800 | C8A—H8AA | 0.9800 |
C4—O4 | 1.223 (4) | C9—C10 | 1.513 (5) |
C4—N5 | 1.312 (4) | C9—H9A | 0.9700 |
C6—N5 | 1.467 (4) | C9—H9B | 0.9700 |
C6—C7 | 1.519 (5) | C10—H10A | 0.9600 |
C6—H6A | 0.9700 | C10—H10B | 0.9600 |
C6—H6B | 0.9700 | C10—H10C | 0.9600 |
C7—C8 | 1.527 (6) | N2—H2 | 0.8717 |
O1—C1—N2 | 123.9 (3) | C8A—C8—H8B | 111.1 |
O1—C1—C8A | 122.5 (3) | C7—C8—H8B | 111.1 |
N2—C1—C8A | 113.6 (3) | H8A—C8—H8B | 109.0 |
N2—C3—C4 | 111.0 (2) | N5—C8A—C1 | 111.6 (2) |
N2—C3—C9 | 113.7 (3) | N5—C8A—C8 | 102.4 (2) |
C4—C3—C9 | 110.4 (3) | C1—C8A—C8 | 115.7 (3) |
N2—C3—H3 | 107.1 | N5—C8A—H8AA | 109.0 |
C4—C3—H3 | 107.1 | C1—C8A—H8AA | 109.0 |
C9—C3—H3 | 107.1 | C8—C8A—H8AA | 109.0 |
O4—C4—N5 | 122.8 (3) | C10—C9—C3 | 113.3 (3) |
O4—C4—C3 | 121.2 (3) | C10—C9—H9A | 108.9 |
N5—C4—C3 | 116.0 (3) | C3—C9—H9A | 108.9 |
N5—C6—C7 | 103.6 (3) | C10—C9—H9B | 108.9 |
N5—C6—H6A | 111.0 | C3—C9—H9B | 108.9 |
C7—C6—H6A | 111.0 | H9A—C9—H9B | 107.7 |
N5—C6—H6B | 111.0 | C9—C10—H10A | 109.5 |
C7—C6—H6B | 111.0 | C9—C10—H10B | 109.5 |
H6A—C6—H6B | 109.0 | H10A—C10—H10B | 109.5 |
C6—C7—C8 | 104.5 (3) | C9—C10—H10C | 109.5 |
C6—C7—H7A | 110.8 | H10A—C10—H10C | 109.5 |
C8—C7—H7A | 110.8 | H10B—C10—H10C | 109.5 |
C6—C7—H7B | 110.8 | C1—N2—C3 | 125.6 (3) |
C8—C7—H7B | 110.8 | C1—N2—H2 | 119.3 |
H7A—C7—H7B | 108.9 | C3—N2—H2 | 114.5 |
C8A—C8—C7 | 103.4 (3) | C4—N5—C6 | 123.2 (3) |
C8A—C8—H8A | 111.1 | C4—N5—C8A | 124.3 (2) |
C7—C8—H8A | 111.1 | C6—N5—C8A | 112.5 (2) |
N2—C3—C4—O4 | −152.4 (3) | O1—C1—N2—C3 | −179.1 (3) |
C9—C3—C4—O4 | 80.6 (4) | C8A—C1—N2—C3 | 0.2 (4) |
N2—C3—C4—N5 | 28.2 (4) | C4—C3—N2—C1 | −31.8 (4) |
C9—C3—C4—N5 | −98.8 (3) | C9—C3—N2—C1 | 93.3 (3) |
N5—C6—C7—C8 | −23.9 (4) | O4—C4—N5—C6 | 3.8 (5) |
C6—C7—C8—C8A | 36.4 (4) | C3—C4—N5—C6 | −176.8 (3) |
O1—C1—C8A—N5 | −147.5 (3) | O4—C4—N5—C8A | −173.9 (3) |
N2—C1—C8A—N5 | 33.2 (3) | C3—C4—N5—C8A | 5.4 (4) |
O1—C1—C8A—C8 | −31.1 (4) | C7—C6—N5—C4 | −175.5 (3) |
N2—C1—C8A—C8 | 149.7 (3) | C7—C6—N5—C8A | 2.5 (3) |
C7—C8—C8A—N5 | −33.9 (3) | C1—C8A—N5—C4 | −37.8 (4) |
C7—C8—C8A—C1 | −155.4 (3) | C8—C8A—N5—C4 | −162.1 (3) |
N2—C3—C9—C10 | 59.2 (4) | C1—C8A—N5—C6 | 144.3 (3) |
C4—C3—C9—C10 | −175.3 (3) | C8—C8A—N5—C6 | 20.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O4i | 0.87 | 1.98 | 2.817 (3) | 161 |
Symmetry code: (i) −x+2, y+1/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C9H14N2O2 |
Mr | 182.22 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 293 |
a, b, c (Å) | 6.8657 (4), 9.9258 (17), 7.0040 (5) |
β (°) | 90.892 (6) |
V (Å3) | 477.25 (9) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.46 × 0.40 × 0.33 |
Data collection | |
Diffractometer | Enraf–Nonius CAD-4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1290, 1200, 937 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.659 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.120, 1.09 |
No. of reflections | 1200 |
No. of parameters | 119 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.17, −0.15 |
Computer programs: CAD-4 Software (Enraf–Nonius, 1989), HELENA (Spek, 1996), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and Mercury (Macrae et al., 2006).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O4i | 0.87 | 1.98 | 2.817 (3) | 161 |
Symmetry code: (i) −x+2, y+1/2, −z. |
Acknowledgements
The authors are grateful to the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), the Fundação de Apoio à Pesquisa Científica e Tecnológica do Estado de Santa Catarina (FAPESC) and the Instituto Nacional de Ciência e Tecnologia (INCT)–Catálise for financial assistance.
References
Alberch, L., Bailey, P. D., Clingan, P. D., Mills, T. J., Price, R. A. & Pritchard, R. G. (2004). Eur. J. Org. Chem. pp. 1887–1890. Web of Science CSD CrossRef Google Scholar
Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119. Web of Science CrossRef CAS IUCr Journals Google Scholar
Caballero, E., Avendano, C. & Menendez, J. C. (2003). J. Org. Chem. 68, 6944–6951. Web of Science CrossRef PubMed CAS Google Scholar
Ciajolo, M. R., Balboni, G., Picone, D., Salvadori, S., Tancredi, T., Temussi, P. A. & Tuzi, A. (1995). Int. J. Pept. Protein Res. 46, 134–138. CrossRef CAS PubMed Web of Science Google Scholar
Enraf–Nonius (1989). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands. Google Scholar
Funabashi, Y., Horiguchi, T., Iinuma, S., Tanida, S. & Harada, S. (1994). J. Antibiot. 47, 1202–1218. CrossRef CAS PubMed Web of Science Google Scholar
Hendea, D., Laschat, S., Baro, A. & Frey, W. (2006). Helv. Chim. Acta, 89, 1894–1909. Web of Science CSD CrossRef CAS Google Scholar
Herbert, R. H. & Kelleher, F. (1994). Tetrahedron Lett. 35, 5497–5500. CrossRef CAS Web of Science Google Scholar
Kazuharu, I., Nakamura, K., Kurohashi, M., Nakanishi, T. & Ichii, T. (1990). Phytochemistry, 29, 35–39. Google Scholar
Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453–457. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Morley, J. E., Levine, A. S. & Prasad, C. (1981). Brain Res. 210, 475–478. CrossRef CAS PubMed Web of Science Google Scholar
Moyroud, J., Gelin, J., Chêne, A. & Mortier, J. (1996). Tetrahedron, 52, 8525–8534. CrossRef CAS Web of Science Google Scholar
Nussbaum, F. von (2003). Angew. Chem. Int. Ed. 42, 3068–3071. Google Scholar
Onishi, T., Sebahar, P. R. & Williams, R. M. (2003). Org. Lett. 5, 3135–3137. Web of Science CrossRef PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (1996). HELENA. University of Utrecht, The Netherlands. Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Diketopiperazine (DKP) backbone is an important pharmacophore in medicinal chemistry, which is conformationally restrained by six-membered ring with side chains that are oriented in a spatially defined manner (Herbert & Kelleher, 1994; Ciajolo et al., 1995). DKPs are quite common in nature and many natural products with the DKP scaffold have been isolated encompassing a wide range of biological activities (Morley et al., 1981; Kazuharu et al., 1990; Funabashi et al., 1994; Moyroud et al., 1996). Several secondary metabolites of microorganisms with interesting biological properties contain a proline-derived diketopiperazine as part of their molecular skeleton (Caballero et al., 2003; Onishi et al., 2003; Alberch et al., 2004; von Nussbaum et al., 2003). During our work on the synthesis of L-proline-based DKPs, we prepared L-proline methyl ester derivative (II) which, under hydrogenolysis condition, led to the title compound (I, Fig. 1). Despite its full chemical characterization and the known configuration of the starting material L-proline, the absolute configuration at C3 was tentatively assigned as being R due to the trans relationship of the hydrogen atoms attached to carbons C3 and C8a based on 1H-NMR and NOE experiments. The crystallographic data unambiguously confirmed the trans relationship of the above mentioned hydrogen atoms and consequently the R configuration of the chiral center at C3 (Fig. 2).
The molecular structure of (I) consists of a bicycle system formed by pyrrolidine and piperazine fused rings (Hendea et al., 2006). The five-membered pyrrolidine ring shows an envelope conformation, which is enveloped at C8. Piperazine ring shows perfect boat conformation, where N2, C1, C4 and N5 atoms lie on the basal plane (r.m.s. deviation: 0.0016 Å) and C3 and C8a are out of the basal mean plane by 0.39 Å (average) toward the same direction.
Strong intermolecular hydrogen bonds between the N—H group and the carbonyl O atom of the diketopiperazine neighboring groups contribute to the stabilization of the crystal structure. N2—H2···O4i [symmetry code: (i) -x + 2, y + 1/2, -z] interactions promote the formation of parallel one-dimensional zigzag C(5) chains running on the 21 screw axis along [010] (Fig. 3). Furthermore, the molecules of (I) are stacked viewing in perpendicular projection of the chains, along [100], and viewing in parallel projection of the chains, along [010] (Fig. 4).