Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104018682/sk1752sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270104018682/sk1752Isup2.hkl |
CCDC reference: 251339
The title compound was prepared from piperazine (0.5 g, 5.8 mmol) and ethyl chlorooxoacetate (1.3 ml, 11.6 mmol) in tetrahydrofuran, in the presence of triethyl amine (1.6 ml, 11.6 mmol). After filtering, evaporation of the solvent, several washings with distilled water and drying, compound (I) was obtained as a colourless solid (1.33 g, 80% yield; m.p. 393–394 K). IR spectroscopy (neat solid, ν, cm−1): 3286 (NH), 1780 (CO); 1H NMR (300.08 MHz, DMSO-d6, δ, p.p.m.): 4.29, 4.28 (q, 2H each, 2CH2), 3.55, 3.42 (m, 4H each, 4NCH2), 1.26 (t, 6H, 2CH3); 13C NMR (75.46 MHz, DMSO-d6, δ, p.p.m.): 162.4, 159.8 (4CO), 62.0 (2CH2), 45.5, 44.7, 40.7, 40.0 (4NCH2), 13.8 (2CH3). Crystals of (I) suitable for X-ray analysis were obtained after slow crystallization from a solution in ethyl alcohol.
All H atoms were refined as riding on their parent atoms, with C—H distances in the range 0.96–0.97 Å and with Uiso(H) = 1.2Ueq(C). Please check added text.
Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2000); software used to prepare material for publication: SHELXL97 and WinGX2003 (Farrugia, 1999).
C12H18N2O6 | F(000) = 304 |
Mr = 286.28 | Dx = 1.311 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 600 reflections |
a = 6.2258 (15) Å | θ = 20–25° |
b = 13.660 (3) Å | µ = 0.11 mm−1 |
c = 8.656 (2) Å | T = 293 K |
β = 99.807 (4)° | Block, colourless |
V = 725.4 (3) Å3 | 0.42 × 0.36 × 0.30 mm |
Z = 2 |
Bruker SMART CCD area-detector diffractometer | 1473 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.032 |
Graphite monochromator | θmax = 27.2°, θmin = 2.8° |
ϕ and ω scans | h = −7→7 |
7773 measured reflections | k = −17→17 |
1581 independent reflections | l = −10→10 |
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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.11 | w = 1/[σ2(Fo2) + (0.0466P)2 + 0.4689P] where P = (Fo2 + 2Fc2)/3 |
1581 reflections | (Δ/σ)max < 0.001 |
91 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.21 e Å−3 |
C12H18N2O6 | V = 725.4 (3) Å3 |
Mr = 286.28 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 6.2258 (15) Å | µ = 0.11 mm−1 |
b = 13.660 (3) Å | T = 293 K |
c = 8.656 (2) Å | 0.42 × 0.36 × 0.30 mm |
β = 99.807 (4)° |
Bruker SMART CCD area-detector diffractometer | 1473 reflections with I > 2σ(I) |
7773 measured reflections | Rint = 0.032 |
1581 independent reflections |
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.11 | Δρmax = 0.35 e Å−3 |
1581 reflections | Δρmin = −0.21 e Å−3 |
91 parameters |
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles |
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 > σ(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. |
x | y | z | Uiso*/Ueq | ||
O2 | 0.06263 (19) | 0.45470 (8) | 0.21364 (15) | 0.0260 (4) | |
O3 | 0.3298 (2) | 0.24711 (9) | 0.23533 (16) | 0.0311 (4) | |
O4 | 0.01101 (17) | 0.26405 (8) | 0.06638 (14) | 0.0198 (3) | |
N1 | 0.3783 (2) | 0.45017 (9) | 0.10382 (16) | 0.0174 (4) | |
C2 | 0.2040 (2) | 0.40967 (11) | 0.15561 (18) | 0.0176 (4) | |
C3 | 0.1934 (2) | 0.29694 (11) | 0.15493 (18) | 0.0182 (4) | |
C5 | −0.0192 (3) | 0.15697 (11) | 0.0696 (2) | 0.0216 (5) | |
C6 | −0.2481 (3) | 0.13523 (12) | −0.0141 (2) | 0.0251 (5) | |
C7 | 0.5456 (3) | 0.39694 (11) | 0.03207 (19) | 0.0185 (4) | |
C8 | 0.4227 (3) | 0.55547 (11) | 0.12582 (19) | 0.0197 (4) | |
H5A | −0.00004 | 0.13379 | 0.17694 | 0.0259* | |
H5B | 0.08678 | 0.12447 | 0.01702 | 0.0259* | |
H6A | −0.27423 | 0.06602 | −0.01211 | 0.0377* | |
H6B | −0.26395 | 0.15708 | −0.12082 | 0.0377* | |
H6C | −0.35125 | 0.16881 | 0.03769 | 0.0377* | |
H7A | 0.50096 | 0.32929 | 0.01391 | 0.0278* | |
H7B | 0.68316 | 0.39749 | 0.10415 | 0.0278* | |
H8A | 0.55302 | 0.56492 | 0.20342 | 0.0295* | |
H8B | 0.30191 | 0.58678 | 0.16390 | 0.0295* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O2 | 0.0222 (6) | 0.0208 (6) | 0.0384 (7) | −0.0022 (5) | 0.0145 (5) | −0.0034 (5) |
O3 | 0.0227 (6) | 0.0215 (6) | 0.0447 (8) | −0.0029 (5) | −0.0068 (5) | 0.0117 (5) |
O4 | 0.0178 (6) | 0.0136 (5) | 0.0270 (6) | −0.0004 (4) | 0.0006 (5) | 0.0012 (4) |
N1 | 0.0165 (7) | 0.0134 (6) | 0.0228 (7) | −0.0013 (5) | 0.0050 (5) | −0.0009 (5) |
C2 | 0.0167 (7) | 0.0168 (7) | 0.0189 (8) | −0.0015 (6) | 0.0022 (6) | 0.0008 (6) |
C3 | 0.0156 (7) | 0.0181 (8) | 0.0215 (8) | −0.0012 (6) | 0.0049 (6) | 0.0020 (6) |
C5 | 0.0206 (8) | 0.0140 (7) | 0.0300 (9) | −0.0005 (6) | 0.0041 (7) | 0.0006 (6) |
C6 | 0.0247 (9) | 0.0183 (8) | 0.0309 (10) | −0.0028 (7) | 0.0008 (7) | −0.0027 (7) |
C7 | 0.0164 (7) | 0.0133 (7) | 0.0267 (9) | 0.0013 (5) | 0.0061 (6) | 0.0005 (6) |
C8 | 0.0211 (8) | 0.0148 (7) | 0.0246 (8) | −0.0026 (6) | 0.0082 (6) | −0.0040 (6) |
O2—C2 | 1.2474 (18) | C5—H5A | 0.9695 |
O3—C3 | 1.211 (2) | C5—H5B | 0.9705 |
O4—C3 | 1.3350 (18) | C6—H6A | 0.9600 |
O4—C5 | 1.4756 (19) | C6—H6B | 0.9597 |
N1—C2 | 1.3603 (19) | C6—H6C | 0.9601 |
N1—C7 | 1.490 (2) | C7—H7A | 0.9701 |
N1—C8 | 1.471 (2) | C7—H7B | 0.9699 |
C2—C3 | 1.541 (2) | C8—H8A | 0.9698 |
C5—C6 | 1.514 (3) | C8—H8B | 0.9703 |
C7—C8i | 1.556 (2) | ||
O2···O4 | 2.8932 (17) | C7···O3 | 3.146 (2) |
O2···C5ii | 3.376 (2) | C7···O3viii | 3.332 (2) |
O3···C8iii | 3.169 (2) | C8···O3ix | 3.169 (2) |
O3···C7 | 3.146 (2) | C3···H7A | 2.4795 |
O3···N1 | 3.0328 (19) | H5A···O3 | 2.5524 |
O3···C7iv | 3.332 (2) | H5A···O2vi | 2.6757 |
O4···O2 | 2.8932 (17) | H5A···H8Bvi | 2.5932 |
O4···C7v | 3.389 (2) | H5B···O3 | 2.7736 |
O2···H8B | 2.4245 | H5B···O2viii | 2.8203 |
O2···H5Biv | 2.8203 | H6B···H7Bx | 2.4626 |
O2···H7Bv | 2.5155 | H6C···H7Av | 2.3728 |
O2···H5Aii | 2.6757 | H7A···O3 | 2.6009 |
O3···H8Aiii | 2.6221 | H7A···C3 | 2.4795 |
O3···H7A | 2.6009 | H7A···H6Cvii | 2.3728 |
O3···H7Aiv | 2.6766 | H7A···O3viii | 2.6766 |
O3···H5A | 2.5524 | H7B···O2vii | 2.5155 |
O3···H5B | 2.7736 | H7B···O4vii | 2.7970 |
O4···H7Bv | 2.7970 | H7B···H6Bxi | 2.4626 |
N1···O3 | 3.0328 (19) | H8A···O3ix | 2.6221 |
N1···N1i | 2.882 (2) | H8B···O2 | 2.4245 |
C5···O2vi | 3.376 (2) | H8B···H5Aii | 2.5932 |
C7···O4vii | 3.389 (2) | ||
C3—O4—C5 | 114.92 (12) | H5A—C5—H5B | 108.51 |
C2—N1—C7 | 126.33 (12) | C5—C6—H6A | 109.46 |
C2—N1—C8 | 119.86 (13) | C5—C6—H6B | 109.49 |
C7—N1—C8 | 113.70 (13) | C5—C6—H6C | 109.44 |
O2—C2—N1 | 126.11 (14) | H6A—C6—H6B | 109.49 |
O2—C2—C3 | 117.49 (12) | H6A—C6—H6C | 109.47 |
N1—C2—C3 | 116.18 (12) | H6B—C6—H6C | 109.48 |
O3—C3—O4 | 125.82 (14) | N1—C7—H7A | 109.34 |
O3—C3—C2 | 122.26 (13) | N1—C7—H7B | 109.36 |
O4—C3—C2 | 111.72 (12) | H7A—C7—H7B | 107.99 |
O4—C5—C6 | 107.34 (13) | C8i—C7—H7A | 109.35 |
N1—C7—C8i | 111.39 (13) | C8i—C7—H7B | 109.34 |
N1—C8—C7i | 110.12 (13) | N1—C8—H8A | 109.66 |
O4—C5—H5A | 110.28 | N1—C8—H8B | 109.61 |
O4—C5—H5B | 110.22 | H8A—C8—H8B | 108.14 |
C6—C5—H5A | 110.28 | C7i—C8—H8A | 109.66 |
C6—C5—H5B | 110.22 | C7i—C8—H8B | 109.62 |
C3—O4—C5—C6 | 170.75 (13) | C8—N1—C2—C3 | −169.32 (13) |
C5—O4—C3—O3 | −0.5 (2) | C7—N1—C2—C3 | 6.7 (2) |
C5—O4—C3—C2 | −175.47 (12) | C8—N1—C2—O2 | 5.1 (2) |
C2—N1—C7—C8i | 128.91 (16) | O2—C2—C3—O3 | −111.34 (17) |
C7—N1—C2—O2 | −178.94 (15) | O2—C2—C3—O4 | 63.85 (18) |
C2—N1—C8—C7i | −129.30 (16) | N1—C2—C3—O3 | 63.5 (2) |
C8—N1—C7—C8i | −54.87 (18) | N1—C2—C3—O4 | −121.26 (14) |
C7—N1—C8—C7i | 54.22 (18) | N1—C7—C8i—N1i | 52.85 (18) |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x, y+1/2, −z+1/2; (iii) −x+1, y−1/2, −z+1/2; (iv) x, −y+1/2, z+1/2; (v) x−1, y, z; (vi) −x, y−1/2, −z+1/2; (vii) x+1, y, z; (viii) x, −y+1/2, z−1/2; (ix) −x+1, y+1/2, −z+1/2; (x) x−1, −y+1/2, z−1/2; (xi) x+1, −y+1/2, z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
C7—H7B···O2vii | 0.97 | 2.52 | 3.425 (2) | 156 |
C8—H8B···O2 | 0.97 | 2.42 | 2.842 (2) | 106 |
Symmetry code: (vii) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C12H18N2O6 |
Mr | 286.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 6.2258 (15), 13.660 (3), 8.656 (2) |
β (°) | 99.807 (4) |
V (Å3) | 725.4 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.42 × 0.36 × 0.30 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7773, 1581, 1473 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.644 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.118, 1.11 |
No. of reflections | 1581 |
No. of parameters | 91 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.35, −0.21 |
Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 2000), SHELXL97 and WinGX2003 (Farrugia, 1999).
O2—C2 | 1.2474 (18) | N1—C7 | 1.490 (2) |
O3—C3 | 1.211 (2) | N1—C8 | 1.471 (2) |
O4—C3 | 1.3350 (18) | C2—C3 | 1.541 (2) |
O4—C5 | 1.4756 (19) | C5—C6 | 1.514 (3) |
N1—C2 | 1.3603 (19) | C7—C8i | 1.556 (2) |
C2—N1—C7 | 126.33 (12) | O3—C3—C2 | 122.26 (13) |
C2—N1—C8 | 119.86 (13) | O4—C3—C2 | 111.72 (12) |
C7—N1—C8 | 113.70 (13) | O4—C5—C6 | 107.34 (13) |
O2—C2—N1 | 126.11 (14) | N1—C7—C8i | 111.39 (13) |
O2—C2—C3 | 117.49 (12) | N1—C8—C7i | 110.12 (13) |
N1—C2—C3 | 116.18 (12) | ||
C7—N1—C2—O2 | −178.94 (15) | N1—C2—C3—O3 | 63.5 (2) |
O2—C2—C3—O3 | −111.34 (17) |
Symmetry code: (i) −x+1, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
C7—H7B···O2ii | 0.97 | 2.52 | 3.425 (2) | 156 |
C8—H8B···O2 | 0.97 | 2.42 | 2.842 (2) | 106 |
Symmetry code: (ii) x+1, y, z. |
Alkyl oxamates have been used as intermediates in the synthesis of oxamides (Toda et al., 1986) and oxamic acid derivatives which exhibit inhibitory protein tyrosine phosphatase activity (Andersen et al., 2002). Recently, oxamates derived from primary amines have been used as molecular models for the study of three-centred hydrogen bonding (Martínez-Martínez et al., 1998; Padilla-Martínez et al., 2001) and in the design of molecular clefts (Martin et al., 2002; Padilla-Martínez et al., 2003). However, oxamates derived from secondary amines are scarce in the literature (Cambridge Structural Database, Version of April 2004; Allen, 2002). In this context, the molecular and supramolecular structures of the title compound, (I), are reported. \sch
Compound (I) forms monoclinic centrosymmetric crystals (P21/c, Z = 2). Thus, only one half of the molecule is found in the asymmetric unit and the other half is generated by symmetry. The molecular structure of (I) and the atom-numbering scheme are shown in Figure 1. Selected bond lengths and angles are listed in Table 1.
The piperazine ring exhibits a chair conformation, with bond lengths and angles in the standard ranges, with a mean N—C bond length of 1.48 (2) Å. The angles around the N atom sum to almost 360° and the N1—C2 bond length is 1.3603 (19) Å, in accordance with Nsp2—Csp2 amide character [1.355 (14) Å; Allen et al., 1987]. The oxalyl C2—C3 bond length is exactly 1.541 (2) Å, the value usually assumed for a Csp3—Csp3 single bond (Dewar & Schmeizing, 1968). Therefore, the ethyl oxamate moiety, –N—C(O)—C(O)-OCH2CH3, can be considered as composed of two singly bonded functionalities, an amide [–N1—C2(O2)] and an ester [–C3(O3)—O4—Et]. The ethyl oxamate group in (I) is not planar. The two carbonyl groups are almost perpendicular, with an O2—C2—C3—O3 torsion angle of −111.37 (17)°.
The steric hindrance between the amide carbonyl and the ethoxy O atom is released by the adoption of the conformation exhibited by compound (I), in which the O2···O4 contact distance of 2.893 (2) Å is longer than the equivalent distance of 2.640 (2) Å observed in the antiperiplanar conformation (Padilla-Martínez et al., 2003), but is nevertheless shorter than the sum of the van der Waals radii (3.04 Å; Bondi, 1964).
It is worth noting that the almost perpendicular conformation between the two carbonyl groups in (I) seems to be preferred in oxamates derived from secondary amines (Venkatramani et al., 1994), in contrast with the antiperiplanar arrangement usually found in those derived from primary amines, probably due to its stabilization by strong intramolecular hydrogen-bonding interactions (Padilla-Martínez et al., 2001; García-Báez et al., 2003).
An intramolecular soft C—H···O hydrogen-bonding interaction (Desiraju, 1996) exists between C8—H8B and the amidic carbonyl O2 atom [C8···O2 2.42 Å 2.842 (2) Å in Table 2? and C8—H8B···O2 106°], forming an S(5) ring motif, according to graph-set notation (Bernstein et al., 1995). The hydrogen-bonding geometry is listed in Table 2. Infinite supramolecular tapes, which propagate along the b direction (Fig. 2), are formed through a second soft hydrogen-bonding interaction along C7—H7B···O2i [C7···O2 3.425 (2) Å and C7—H7B···O2 156°; symmetry code: (i) 1 + x, y, z], which forms a twelve-membered ring described by the graph-set descriptor R22(12). The rotation energy barrier around the oxalyl C2—C3 bond should be low enough that these two hydrogen bonds fix the molecule of (I) in a symmetrical conformation in the solid state. On the other hand, the four C atoms of the piperazine ring are observed as four different signals, at 45.5, 44.7, 40.7 and 40.0 p.p.m. by 13C NMR, revealing the predominance of a non-symmetrical conformation in solution.