organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

(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

(Received 29 December 2009; accepted 14 January 2010; online 23 January 2010)

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[Herbert, R. H. & Kelleher, F. (1994). Tetrahedron Lett. 35, 5497-5500.]); Ciajolo et al. (1995[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.]); Morley et al. (1981[Morley, J. E., Levine, A. S. & Prasad, C. (1981). Brain Res. 210, 475-478.]); Kazuharu et al. (1990[Kazuharu, I., Nakamura, K., Kurohashi, M., Nakanishi, T. & Ichii, T. (1990). Phytochemistry, 29, 35-39.]); Funabashi et al. (1994[Funabashi, Y., Horiguchi, T., Iinuma, S., Tanida, S. & Harada, S. (1994). J. Antibiot. 47, 1202-1218.]); Moyroud et al. (1996[Moyroud, J., Gelin, J., Chêne, A. & Mortier, J. (1996). Tetrahedron, 52, 8525-8534.]); Caballero et al. (2003[Caballero, E., Avendano, C. & Menendez, J. C. (2003). J. Org. Chem. 68, 6944-6951.]); Onishi et al. (2003[Onishi, T., Sebahar, P. R. & Williams, R. M. (2003). Org. Lett. 5, 3135-3137.]); Alberch et al. (2004[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.]); von Nussbaum et al. (2003[Nussbaum, F. von (2003). Angew. Chem. Int. Ed. 42, 3068-3071.]). For related structures, see: Hendea et al. (2006[Hendea, D., Laschat, S., Baro, A. & Frey, W. (2006). Helv. Chim. Acta, 89, 1894-1909.]).

[Scheme 1]

Experimental

Crystal data
  • C9H14N2O2

  • Mr = 182.22

  • Monoclinic, P 21

  • a = 6.8657 (4) Å

  • b = 9.9258 (17) Å

  • c = 7.0040 (5) Å

  • β = 90.892 (6)°

  • V = 477.25 (9) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 293 K

  • 0.46 × 0.40 × 0.33 mm

Data collection
  • Enraf–Nonius CAD-4 diffractometer

  • 1290 measured reflections

  • 1200 independent reflections

  • 937 reflections with I > 2σ(I)

  • Rint = 0.032

  • 3 standard reflections every 200 reflections intensity decay: 1%

Refinement
  • R[F2 > 2σ(F2)] = 0.044

  • wR(F2) = 0.120

  • S = 1.09

  • 1200 reflections

  • 119 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.15 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯O4i 0.87 1.98 2.817 (3) 161
Symmetry code: (i) [-x+2, y+{\script{1\over 2}}, -z].

Data collection: CAD-4 Software (Enraf–Nonius, 1989[Enraf-Nonius (1989). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Software; data reduction: HELENA (Spek, 1996[Spek, A. L. (1996). HELENA. University of Utrecht, The Netherlands.]); program(s) used to solve structure: SIR97 (Altomare et al., 1999[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.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and Mercury (Macrae et al., 2006[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.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

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).

Related literature top

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 top

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 column chromatography 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.

Refinement top

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.

Structure description top

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).

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).

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. Synthetic route.
[Figure 2] Fig. 2. The molecular structure of the title compound with labeling scheme. Displacement ellipsoids are shown at the 40% probability level.
[Figure 3] Fig. 3. Polymeric chain along b axis formed by intermolecular hydrogen bonding. Symmetry code: -x + 2, y + 1/2, -z
[Figure 4] Fig. 4. Partial packing of the title compound showing the stacking of the molecules along [100] (top) and along [010] (bottom).
(3R,8aS)-3-Ethylperhydropyrrolo[1,2-a]pyrazine-1,4-dione top
Crystal data top
C9H14N2O2F(000) = 196
Mr = 182.22Dx = 1.268 Mg m3
Monoclinic, P21Melting point: 407 K
Hall symbol: P 2ybMo Kα radiation, λ = 0.71073 Å
a = 6.8657 (4) ÅCell parameters from 25 reflections
b = 9.9258 (17) Åθ = 3.6–15.6°
c = 7.0040 (5) ŵ = 0.09 mm1
β = 90.892 (6)°T = 293 K
V = 477.25 (9) Å3Prism, colorless
Z = 20.46 × 0.40 × 0.33 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.032
Radiation source: fine-focus sealed tubeθmax = 27.9°, θmin = 3.0°
Graphite monochromatorh = 99
ω–2θ scansk = 130
1290 measured reflectionsl = 90
1200 independent reflections3 standard reflections every 200 reflections
937 reflections with I > 2σ(I) intensity decay: 1%
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)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.120H-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 parametersΔρmax = 0.17 e Å3
1 restraintΔρmin = 0.15 e Å3
0 constraints
Crystal data top
C9H14N2O2V = 477.25 (9) Å3
Mr = 182.22Z = 2
Monoclinic, P21Mo Kα radiation
a = 6.8657 (4) ŵ = 0.09 mm1
b = 9.9258 (17) ÅT = 293 K
c = 7.0040 (5) Å0.46 × 0.40 × 0.33 mm
β = 90.892 (6)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.032
1290 measured reflections3 standard reflections every 200 reflections
1200 independent reflections intensity decay: 1%
937 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0441 restraint
wR(F2) = 0.120H-atom parameters constrained
S = 1.09Δρmax = 0.17 e Å3
1200 reflectionsΔρmin = 0.15 e Å3
119 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.6671 (5)0.5429 (3)0.1100 (4)0.0446 (7)
C30.8672 (4)0.3662 (3)0.0490 (4)0.0446 (7)
H31.00830.35190.04000.054*
C40.7726 (4)0.2617 (3)0.0781 (4)0.0428 (7)
C60.5113 (5)0.2151 (3)0.3021 (5)0.0481 (7)
H6A0.59120.19660.41450.058*
H6B0.47320.13040.24350.058*
C70.3339 (5)0.2985 (4)0.3527 (5)0.0646 (10)
H7A0.30150.28670.48600.077*
H7B0.22230.27320.27410.077*
C80.3944 (5)0.4437 (4)0.3131 (5)0.0603 (9)
H8A0.28160.50010.28780.072*
H8B0.46810.48100.41990.072*
C8A0.5200 (4)0.4315 (3)0.1373 (4)0.0415 (6)
H8AA0.43530.42630.02370.050*
C90.8066 (5)0.3439 (4)0.2576 (5)0.0572 (9)
H9A0.83510.25140.29240.069*
H9B0.66700.35680.27050.069*
C100.9082 (6)0.4374 (5)0.3946 (5)0.0691 (11)
H10A1.04660.43070.37530.104*
H10B0.86730.52840.37200.104*
H10C0.87510.41240.52350.104*
N20.8290 (4)0.5027 (2)0.0198 (4)0.0486 (7)
H20.91290.56290.01710.058*
N50.6154 (3)0.3007 (2)0.1667 (3)0.0396 (6)
O10.6391 (4)0.6573 (2)0.1630 (4)0.0643 (7)
O40.8399 (4)0.1481 (2)0.0937 (4)0.0655 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0549 (17)0.0338 (15)0.0452 (15)0.0027 (13)0.0003 (13)0.0037 (13)
C30.0380 (15)0.0432 (17)0.0528 (16)0.0016 (12)0.0064 (13)0.0008 (14)
C40.0405 (15)0.0384 (15)0.0494 (16)0.0032 (13)0.0012 (13)0.0032 (13)
C60.0556 (18)0.0402 (16)0.0486 (16)0.0063 (14)0.0040 (14)0.0026 (14)
C70.061 (2)0.067 (2)0.066 (2)0.0009 (19)0.0250 (16)0.005 (2)
C80.065 (2)0.050 (2)0.067 (2)0.0113 (17)0.0253 (16)0.0011 (17)
C8A0.0415 (14)0.0351 (14)0.0480 (15)0.0053 (13)0.0043 (12)0.0018 (12)
C90.066 (2)0.055 (2)0.0507 (17)0.0062 (16)0.0063 (16)0.0058 (15)
C100.077 (2)0.079 (3)0.0526 (19)0.003 (2)0.0156 (17)0.0057 (19)
N20.0534 (15)0.0378 (14)0.0549 (15)0.0127 (12)0.0085 (12)0.0031 (11)
N50.0416 (13)0.0317 (12)0.0457 (13)0.0024 (10)0.0051 (10)0.0018 (11)
O10.0847 (18)0.0346 (12)0.0737 (16)0.0033 (12)0.0073 (14)0.0050 (12)
O40.0627 (14)0.0468 (14)0.0875 (17)0.0208 (12)0.0180 (12)0.0095 (13)
Geometric parameters (Å, º) top
C1—O11.210 (4)C7—H7A0.9700
C1—N21.347 (4)C7—H7B0.9700
C1—C8A1.512 (4)C8—C8A1.519 (4)
C3—N21.464 (4)C8—H8A0.9700
C3—C41.519 (4)C8—H8B0.9700
C3—C91.529 (4)C8A—N51.468 (4)
C3—H30.9800C8A—H8AA0.9800
C4—O41.223 (4)C9—C101.513 (5)
C4—N51.312 (4)C9—H9A0.9700
C6—N51.467 (4)C9—H9B0.9700
C6—C71.519 (5)C10—H10A0.9600
C6—H6A0.9700C10—H10B0.9600
C6—H6B0.9700C10—H10C0.9600
C7—C81.527 (6)N2—H20.8717
O1—C1—N2123.9 (3)C8A—C8—H8B111.1
O1—C1—C8A122.5 (3)C7—C8—H8B111.1
N2—C1—C8A113.6 (3)H8A—C8—H8B109.0
N2—C3—C4111.0 (2)N5—C8A—C1111.6 (2)
N2—C3—C9113.7 (3)N5—C8A—C8102.4 (2)
C4—C3—C9110.4 (3)C1—C8A—C8115.7 (3)
N2—C3—H3107.1N5—C8A—H8AA109.0
C4—C3—H3107.1C1—C8A—H8AA109.0
C9—C3—H3107.1C8—C8A—H8AA109.0
O4—C4—N5122.8 (3)C10—C9—C3113.3 (3)
O4—C4—C3121.2 (3)C10—C9—H9A108.9
N5—C4—C3116.0 (3)C3—C9—H9A108.9
N5—C6—C7103.6 (3)C10—C9—H9B108.9
N5—C6—H6A111.0C3—C9—H9B108.9
C7—C6—H6A111.0H9A—C9—H9B107.7
N5—C6—H6B111.0C9—C10—H10A109.5
C7—C6—H6B111.0C9—C10—H10B109.5
H6A—C6—H6B109.0H10A—C10—H10B109.5
C6—C7—C8104.5 (3)C9—C10—H10C109.5
C6—C7—H7A110.8H10A—C10—H10C109.5
C8—C7—H7A110.8H10B—C10—H10C109.5
C6—C7—H7B110.8C1—N2—C3125.6 (3)
C8—C7—H7B110.8C1—N2—H2119.3
H7A—C7—H7B108.9C3—N2—H2114.5
C8A—C8—C7103.4 (3)C4—N5—C6123.2 (3)
C8A—C8—H8A111.1C4—N5—C8A124.3 (2)
C7—C8—H8A111.1C6—N5—C8A112.5 (2)
N2—C3—C4—O4152.4 (3)O1—C1—N2—C3179.1 (3)
C9—C3—C4—O480.6 (4)C8A—C1—N2—C30.2 (4)
N2—C3—C4—N528.2 (4)C4—C3—N2—C131.8 (4)
C9—C3—C4—N598.8 (3)C9—C3—N2—C193.3 (3)
N5—C6—C7—C823.9 (4)O4—C4—N5—C63.8 (5)
C6—C7—C8—C8A36.4 (4)C3—C4—N5—C6176.8 (3)
O1—C1—C8A—N5147.5 (3)O4—C4—N5—C8A173.9 (3)
N2—C1—C8A—N533.2 (3)C3—C4—N5—C8A5.4 (4)
O1—C1—C8A—C831.1 (4)C7—C6—N5—C4175.5 (3)
N2—C1—C8A—C8149.7 (3)C7—C6—N5—C8A2.5 (3)
C7—C8—C8A—N533.9 (3)C1—C8A—N5—C437.8 (4)
C7—C8—C8A—C1155.4 (3)C8—C8A—N5—C4162.1 (3)
N2—C3—C9—C1059.2 (4)C1—C8A—N5—C6144.3 (3)
C4—C3—C9—C10175.3 (3)C8—C8A—N5—C620.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O4i0.871.982.817 (3)161
Symmetry code: (i) x+2, y+1/2, z.

Experimental details

Crystal data
Chemical formulaC9H14N2O2
Mr182.22
Crystal system, space groupMonoclinic, P21
Temperature (K)293
a, b, c (Å)6.8657 (4), 9.9258 (17), 7.0040 (5)
β (°) 90.892 (6)
V3)477.25 (9)
Z2
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.46 × 0.40 × 0.33
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
1290, 1200, 937
Rint0.032
(sin θ/λ)max1)0.659
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.120, 1.09
No. of reflections1200
No. of parameters119
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O4i0.871.982.817 (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

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