Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270101006965/jz1454sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270101006965/jz1454Isup2.hkl |
CCDC reference: 170183
A solution of glycine methyl ester hydrochloride (0.2 mol) and triethylamine (0.4 mol) in chloroform (250 ml) was treated with a solution of oxaloyl chloride (0.1 mol) in chloroform (150 ml), which was added slowly while maintaining the temperature at 273 K. After 1.5 h at room temperature, the solution was evaporated, yielding a white powder that was recrystallized from 2-propanol (yield 47%, m.p. 434 K). Colourless prismatic crystals were obtained by vapor diffusion (293 K) of a 46:54 (v/v) chloroform/carbon tetrachloride mixture, as precipitant, into a 56:44 (v/v) chloroform/carbon tetrachloride solution (concentration 2.6 mg ml-1).
H atoms were found in difference Fourier maps. However, those not linked to the amide nitrogen atoms were refined using constraints.
Data collection: CAD-4 Software (Kiers, 1994); cell refinement: SETANG and LS in CAD-4 Software; data reduction: local program; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: Word.
C8H12N2O6 | F(000) = 244 |
Mr = 232.20 | Dx = 1.403 Mg m−3 |
Monoclinic, P21/n | Cu Kα radiation, λ = 1.54178 Å |
a = 10.4122 (11) Å | Cell parameters from 25 reflections |
b = 4.7567 (8) Å | θ = 10.0–28.5° |
c = 11.6778 (16) Å | µ = 1.05 mm−1 |
β = 108.168 (10)° | T = 293 K |
V = 549.54 (13) Å3 | Prism, colourless |
Z = 2 | 0.24 × 0.14 × 0.12 mm |
Enraf-Nonius CAD4 diffractometer | Rint = 0.000 |
Radiation source: fine-focus sealed tube | θmax = 67.9°, θmin = 5.0° |
Graphite monochromator | h = −12→11 |
ω/2θ scans | k = 0→5 |
999 measured reflections | l = 0→14 |
999 independent reflections | 3 standard reflections every 120 min |
880 reflections with I > 2σ(I) | intensity decay: no decay |
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)] = 0.057 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.155 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | w = 1/[σ2(Fo2) + (0.1062P)2 + 0.110P] where P = (Fo2 + 2Fc2)/3 |
999 reflections | (Δ/σ)max = 0.015 |
83 parameters | Δρmax = 0.34 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
C8H12N2O6 | V = 549.54 (13) Å3 |
Mr = 232.20 | Z = 2 |
Monoclinic, P21/n | Cu Kα radiation |
a = 10.4122 (11) Å | µ = 1.05 mm−1 |
b = 4.7567 (8) Å | T = 293 K |
c = 11.6778 (16) Å | 0.24 × 0.14 × 0.12 mm |
β = 108.168 (10)° |
Enraf-Nonius CAD4 diffractometer | Rint = 0.000 |
999 measured reflections | 3 standard reflections every 120 min |
999 independent reflections | intensity decay: no decay |
880 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.057 | 0 restraints |
wR(F2) = 0.155 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | Δρmax = 0.34 e Å−3 |
999 reflections | Δρmin = −0.26 e Å−3 |
83 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Mean-plane data from final SHELXL refinement run: Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane) - 0.0561 (0.0088) x + 3.0911 (0.0037) y + 8.4502 (0.0084) z = 2.4459 (0.0052) * -0.0091 (0.0011) C1 * 0.0107 (0.0014) O1 * 0.0051 (0.0013) C2 * 0.0010 (0.0005) O2 * -0.0077 (0.0009) C3 Rms deviation of fitted atoms = 0.0075 3.2049 (0.0059) x - 3.3511 (0.0023) y + 5.9768 (0.0088) z = 6.1933 (0.0039) Angle to previous plane (with approximate e.s.d.) = 88.48 (0.06) * -0.0066 (0.0008) C3 * 0.0101 (0.0012) N1 * 0.0015 (0.0013) C4 * 0.0026 (0.0005) O3 * -0.0015 (0.0013) C4_$1 * -0.0026 (0.0005) O3_$1 * -0.0101 (0.0012) N1_$1 * 0.0066 (0.0008) C3_$1 Rms deviation of fitted atoms = 0.0062 |
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 | ||
C1 | 0.3982 (2) | −0.0991 (7) | 0.3273 (2) | 0.0652 (8) | |
H11C | 0.4169 | 0.0984 | 0.3384 | 0.085 (10)* | |
H12C | 0.3274 | −0.1483 | 0.3601 | 0.085 (9)* | |
H13C | 0.3702 | −0.1425 | 0.2428 | 0.074 (8)* | |
O1 | 0.51876 (12) | −0.2572 (3) | 0.38825 (12) | 0.0465 (5) | |
C2 | 0.62788 (15) | −0.1869 (3) | 0.36259 (12) | 0.0252 (5) | |
O2 | 0.63435 (13) | −0.0045 (3) | 0.29543 (13) | 0.0522 (5) | |
C4 | 0.93270 (14) | −0.0518 (3) | 0.50729 (12) | 0.0247 (5) | |
N1 | 0.87250 (14) | −0.2489 (3) | 0.43052 (13) | 0.0322 (5) | |
C3 | 0.74635 (17) | −0.3685 (4) | 0.42829 (15) | 0.0360 (5) | |
H31 | 0.7458 | −0.3966 | 0.5104 | 0.051 (6)* | |
H32 | 0.7367 | −0.5511 | 0.3895 | 0.035 (5)* | |
O3 | 0.89061 (13) | 0.0470 (3) | 0.58543 (11) | 0.0454 (5) | |
H1N | 0.911 (2) | −0.315 (4) | 0.3905 (19) | 0.036 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0252 (10) | 0.109 (2) | 0.0619 (13) | 0.0098 (11) | 0.0139 (9) | −0.0144 (14) |
O1 | 0.0297 (7) | 0.0678 (10) | 0.0468 (8) | −0.0104 (6) | 0.0192 (6) | 0.0068 (6) |
C2 | 0.0258 (9) | 0.0294 (9) | 0.0205 (7) | −0.0059 (6) | 0.0074 (6) | 0.0004 (6) |
O2 | 0.0373 (8) | 0.0585 (10) | 0.0623 (9) | 0.0065 (6) | 0.0177 (6) | 0.0316 (7) |
C4 | 0.0243 (8) | 0.0263 (8) | 0.0230 (8) | 0.0106 (6) | 0.0068 (6) | 0.0069 (6) |
N1 | 0.0233 (8) | 0.0374 (9) | 0.0355 (8) | 0.0043 (6) | 0.0085 (6) | −0.0028 (6) |
C3 | 0.0334 (9) | 0.0328 (10) | 0.0390 (9) | −0.0055 (7) | 0.0071 (7) | 0.0094 (7) |
O3 | 0.0398 (8) | 0.0632 (9) | 0.0421 (8) | −0.0032 (6) | 0.0258 (6) | −0.0122 (6) |
C1—O1 | 1.446 (3) | C4—O3 | 1.222 (2) |
C1—H11C | 0.9600 | C4—N1 | 1.313 (2) |
C1—H12C | 0.9600 | C4—C4i | 1.544 (3) |
C1—H13C | 0.9600 | N1—C3 | 1.424 (2) |
O1—C2 | 1.3058 (19) | N1—H1N | 0.77 (2) |
C2—O2 | 1.186 (2) | C3—H31 | 0.9700 |
C2—C3 | 1.506 (2) | C3—H32 | 0.9700 |
O1—C1—H11C | 109.5 | O3—C4—C4i | 120.57 (18) |
O1—C1—H12C | 109.5 | N1—C4—C4i | 114.14 (15) |
H11C—C1—H12C | 109.5 | C4—N1—C3 | 122.60 (15) |
O1—C1—H13C | 109.5 | C4—N1—H1N | 118.4 (16) |
H11C—C1—H13C | 109.5 | C3—N1—H1N | 118.5 (16) |
H12C—C1—H13C | 109.5 | N1—C3—C2 | 112.60 (13) |
C2—O1—C1 | 115.95 (16) | N1—C3—H31 | 109.1 |
O2—C2—O1 | 124.92 (15) | C2—C3—H31 | 109.1 |
O2—C2—C3 | 123.41 (15) | N1—C3—H32 | 109.1 |
O1—C2—C3 | 111.67 (13) | C2—C3—H32 | 109.1 |
O3—C4—N1 | 125.29 (15) | H31—C3—H32 | 107.8 |
C1—O1—C2—O2 | 0.9 (3) | C4—N1—C3—C2 | 80.54 (19) |
C1—O1—C2—C3 | −178.58 (17) | O2—C2—C3—N1 | 17.6 (2) |
O3—C4—N1—C3 | 1.4 (2) | O1—C2—C3—N1 | −162.85 (14) |
C4i—C4—N1—C3 | −179.01 (14) |
Symmetry code: (i) −x+2, −y, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O2ii | 0.77 (2) | 2.26 (2) | 2.886 (2) | 139 (2) |
N1—H1N···O3i | 0.77 (2) | 2.37 (2) | 2.707 (2) | 108 (2) |
Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+3/2, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C8H12N2O6 |
Mr | 232.20 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 293 |
a, b, c (Å) | 10.4122 (11), 4.7567 (8), 11.6778 (16) |
β (°) | 108.168 (10) |
V (Å3) | 549.54 (13) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 1.05 |
Crystal size (mm) | 0.24 × 0.14 × 0.12 |
Data collection | |
Diffractometer | Enraf-Nonius CAD4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 999, 999, 880 |
Rint | 0.000 |
(sin θ/λ)max (Å−1) | 0.601 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.057, 0.155, 1.10 |
No. of reflections | 999 |
No. of parameters | 83 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.34, −0.26 |
Computer programs: CAD-4 Software (Kiers, 1994), SETANG and LS in CAD-4 Software, local program, SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1976), Word.
C1—O1—C2—C3 | −178.58 (17) | C4—N1—C3—C2 | 80.54 (19) |
C4i—C4—N1—C3 | −179.01 (14) | O1—C2—C3—N1 | −162.85 (14) |
Symmetry code: (i) −x+2, −y, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O2ii | 0.77 (2) | 2.26 (2) | 2.886 (2) | 139 (2) |
N1—H1N···O3i | 0.77 (2) | 2.37 (2) | 2.707 (2) | 108 (2) |
Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+3/2, y−1/2, −z+1/2. |
Studies of the conformational preferences of the oxalamide group are nowadays interesting for the design of enzyme mimics and potential inhibitors (Karle et al., 1994), since it corresponds to a retrobispeptide unit. In addition, molecules with oxalamide groups are capable of forming two-dimensional networks, constituting significant targets for supramolecular synthesis (Coe et al., 1997). Polyoxalamides have also been widely studied in materials science because of the properties afforded by their stiff and hydrophilic units (Shalaby et al., 1973; Gaymans et al., 1984; Tirrell & Vogl, 1977). Our research has recently focused on the study of poly(ester amide)s derived from natural α-amino acids, and various diols and dicarboxylic acids, since a biodegradable behaviour is characteristic of this kind of polymer (Paredes et al., 1998). The title compound, (I), was chosen as the simplest model constituted by glycine residues in combination with oxalamide and ester groups. \sch
The title molecule is shown in Fig. 1, with selected torsion angles and hydrogen-bond geometry in Tables 1 and 2, respectively.
The amide and ester groups are planar within experimental accuracy, with a r.m.s. distance of the atoms from the best planes passing through them of 0.0062 and 0.0075 Å for C3/N1/C4/O3/C4'/O3'/N1'/C3' and C1/O1/C2/O2/C3, respectively. The planar conformation of the oxalamide group is also favoured by the establishment of an intramolecular NH···OC hydrogen bond (Table 2) of a pseudo C5 type (a five-membered ring characteristic of amino acids, where in this case a carbonyl C atom replaces the Cα atom; Karle et al., 1994). The torsion angles ϕ (O1—C2—C3—N1) and ψ (C2—C3—N1—C4), which define the glycine residue, are close to those found in the polyglycine II structure (75 and -145°, respectively; Crick & Rich, 1955). However, the ψ angle deviates towards 180° in agreement with theoretical studies (Momenteua et al., 1988) on polydepsipeptide chains and also with experimental data from model compounds of poly(ester amide)s (Urpí et al., 1998).
Molecules lie on inversion centers and the crystal structure is defined by a bilayered organization, as shown in Fig. 2. The packing is characterized by the establishment of a network of intermolecular hydrogen bonds that only involve the NH and CO moieties of the oxalamide and ester groups, respectively. This observation is also in agreement with theoretical investigations (Alemán et al., 1995) that indicated a similar strength for amide···ester and amide···amide interactions. Crystal structures of compounds with oxalamide units and neighbouring ester or acid groups show both possibilities: a) `like to like' amide-amide hydrogen bonds (Klaska et al., 1980; Yamaguchi et al., 1992; Bhattacharjee & Ammon, 1982) and b) `like to unlike' amide-acid (Coe et al., 1997; Karle & Ranganathan, 1995) or amide-ester (Karle et al., 1994) hydrogen bonds. The structure of the latter is similar to that found in the title compound. However,it should be pointed out that, in those cases, the `like to unlike' interactions would be favoured by the steric hindrance of lateral groups (compounds with amineisobutyryl or leucyl residues) or the capability to form additional hydrogen bonds between the oxalamide carbonyl and the hydroxyl of the acid groups.
Two C—H···O interactions found in the crystal may also be classified as hydrogen bonds (Table 2). One of these interactions involves the ester group, whereas the second one affects the oxalamide unit.