Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801010558/cf6092sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536801010558/cf6092Isup2.hkl |
CCDC reference: 170883
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.003 Å
- R factor = 0.044
- wR factor = 0.126
- Data-to-parameter ratio = 12.4
checkCIF results
No syntax errors found ADDSYM reports no extra symmetry
Alert Level C:
PLAT_369 Alert C Long C(sp2)-C(sp2) Bond C(4) - C(5) = 1.54 Ang.
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
1 Alert Level C = Please check
Crystals of (I) were grown from a saturated aqueous solution containing DL-alanine and oxalic acid in a 1:1 stoichiometric ratio.
H atoms were placed in calculated positions and were allowed to ride on their parent atoms with HFIX instructions using SHELXL97 defaults (Sheldrick, 1997).
Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1999); software used to prepare material for publication: SHELXL97.
Fig. 1. The molecular structure of (I) with atom-numbering scheme and 50% probability displacement ellipsoids. | |
Fig. 2. Packing diagram of the molecules of (I) in the unit cell viewed down the b axis. |
C3H8NO2+·C2HO4− | F(000) = 376 |
Mr = 179.13 | Dx = 1.499 Mg m−3 Dm = 1.50 Mg m−3 Dm measured by floatation in a mixture of xylene and bromoform |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 5.662 (2) Å | Cell parameters from 25 reflections |
b = 7.342 (2) Å | θ = 6–14° |
c = 19.157 (6) Å | µ = 0.14 mm−1 |
β = 94.48 (3)° | T = 293 K |
V = 793.9 (4) Å3 | Needle, colourless |
Z = 4 | 0.48 × 0.32 × 0.22 mm |
Enraf-Nonius CAD-4 diffractometer | 1103 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.011 |
Graphite monochromator | θmax = 24.9°, θmin = 2.1° |
ω–2θ scans | h = 0→6 |
Absorption correction: ψ scan (North et al., 1968) | k = 0→8 |
Tmin = 0.89, Tmax = 0.97 | l = −22→22 |
1542 measured reflections | 2 standard reflections every 60 min |
1390 independent reflections | intensity decay: 0.1% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.044 | H-atom parameters constrained |
wR(F2) = 0.126 | w = 1/[σ2(Fo2) + (0.0529P)2 + 0.5084P] where P = (Fo2 + 2Fc2)/3 |
S = 1.12 | (Δ/σ)max < 0.001 |
1390 reflections | Δρmax = 0.29 e Å−3 |
112 parameters | Δρmin = −0.21 e Å−3 |
0 restraints | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.016 (4) |
C3H8NO2+·C2HO4− | V = 793.9 (4) Å3 |
Mr = 179.13 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 5.662 (2) Å | µ = 0.14 mm−1 |
b = 7.342 (2) Å | T = 293 K |
c = 19.157 (6) Å | 0.48 × 0.32 × 0.22 mm |
β = 94.48 (3)° |
Enraf-Nonius CAD-4 diffractometer | 1103 reflections with I > 2σ(I) |
Absorption correction: ψ scan (North et al., 1968) | Rint = 0.011 |
Tmin = 0.89, Tmax = 0.97 | 2 standard reflections every 60 min |
1542 measured reflections | intensity decay: 0.1% |
1390 independent reflections |
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.126 | H-atom parameters constrained |
S = 1.12 | Δρmax = 0.29 e Å−3 |
1390 reflections | Δρmin = −0.21 e Å−3 |
112 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. |
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 | ||
O1 | 0.8597 (4) | 0.7994 (3) | 0.47437 (10) | 0.0640 (6) | |
H1 | 0.8872 | 0.7638 | 0.4353 | 0.096* | |
O2 | 0.7452 (3) | 0.5134 (2) | 0.48762 (8) | 0.0440 (5) | |
O3 | 0.0945 (3) | 0.7374 (3) | 0.81048 (8) | 0.0468 (5) | |
H3 | −0.0384 | 0.7229 | 0.7910 | 0.070* | |
O4 | 0.2081 (3) | 0.6750 (4) | 0.70572 (9) | 0.0749 (8) | |
O5 | 0.5443 (3) | 0.7832 (2) | 0.85896 (7) | 0.0424 (5) | |
O6 | 0.6636 (3) | 0.7056 (3) | 0.75614 (8) | 0.0479 (5) | |
N1 | 0.6243 (3) | 0.5701 (3) | 0.61814 (9) | 0.0395 (5) | |
H1A | 0.7135 | 0.4708 | 0.6161 | 0.059* | |
H1B | 0.4820 | 0.5490 | 0.5966 | 0.059* | |
H1C | 0.6090 | 0.5983 | 0.6627 | 0.059* | |
C1 | 0.7808 (4) | 0.6655 (4) | 0.50960 (12) | 0.0391 (6) | |
C2 | 0.7377 (5) | 0.7225 (3) | 0.58355 (12) | 0.0441 (6) | |
H2 | 0.8916 | 0.7462 | 0.6090 | 0.053* | |
C3 | 0.5910 (7) | 0.8905 (4) | 0.58644 (16) | 0.0766 (10) | |
H3A | 0.5698 | 0.9197 | 0.6344 | 0.115* | |
H3B | 0.4392 | 0.8701 | 0.5617 | 0.115* | |
H3C | 0.6695 | 0.9897 | 0.5651 | 0.115* | |
C4 | 0.5086 (3) | 0.7357 (3) | 0.79733 (10) | 0.0312 (5) | |
C5 | 0.2518 (3) | 0.7132 (3) | 0.76556 (10) | 0.0335 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0888 (16) | 0.0609 (12) | 0.0469 (11) | 0.0031 (11) | 0.0358 (11) | 0.0044 (9) |
O2 | 0.0367 (9) | 0.0617 (12) | 0.0341 (9) | −0.0010 (8) | 0.0068 (7) | −0.0080 (8) |
O3 | 0.0200 (8) | 0.0839 (13) | 0.0371 (9) | −0.0035 (8) | 0.0072 (6) | −0.0130 (8) |
O4 | 0.0291 (9) | 0.158 (2) | 0.0372 (10) | 0.0009 (11) | 0.0007 (7) | −0.0360 (12) |
O5 | 0.0285 (8) | 0.0726 (12) | 0.0267 (8) | −0.0081 (8) | 0.0053 (6) | −0.0110 (7) |
O6 | 0.0208 (7) | 0.0938 (14) | 0.0298 (8) | −0.0022 (8) | 0.0064 (6) | −0.0134 (8) |
N1 | 0.0435 (11) | 0.0528 (12) | 0.0228 (9) | 0.0063 (9) | 0.0063 (7) | −0.0019 (8) |
C1 | 0.0324 (12) | 0.0545 (15) | 0.0312 (11) | 0.0059 (11) | 0.0068 (9) | 0.0023 (11) |
C2 | 0.0462 (13) | 0.0568 (15) | 0.0298 (11) | −0.0030 (11) | 0.0072 (10) | −0.0041 (11) |
C3 | 0.121 (3) | 0.0573 (19) | 0.0565 (18) | 0.0166 (18) | 0.0382 (19) | −0.0017 (14) |
C4 | 0.0215 (10) | 0.0473 (13) | 0.0255 (10) | −0.0026 (9) | 0.0049 (8) | −0.0038 (9) |
C5 | 0.0215 (10) | 0.0499 (13) | 0.0293 (11) | −0.0014 (9) | 0.0043 (8) | −0.0082 (9) |
O1—C1 | 1.290 (3) | N1—H1B | 0.890 |
O1—H1 | 0.820 | N1—H1C | 0.890 |
O2—C1 | 1.205 (3) | C1—C2 | 1.516 (3) |
O3—C5 | 1.298 (2) | C2—C3 | 1.491 (4) |
O3—H3 | 0.820 | C2—H2 | 0.980 |
O4—C5 | 1.187 (3) | C3—H3A | 0.960 |
O5—C4 | 1.233 (2) | C3—H3B | 0.960 |
O6—C4 | 1.245 (2) | C3—H3C | 0.960 |
N1—C2 | 1.472 (3) | C4—C5 | 1.541 (3) |
N1—H1A | 0.890 | ||
C1—O1—H1 | 109.5 | C3—C2—H2 | 108.2 |
C5—O3—H3 | 109.5 | C1—C2—H2 | 108.2 |
C2—N1—H1A | 109.5 | C2—C3—H3A | 109.5 |
C2—N1—H1B | 109.5 | C2—C3—H3B | 109.5 |
H1A—N1—H1B | 109.5 | H3A—C3—H3B | 109.5 |
C2—N1—H1C | 109.5 | C2—C3—H3C | 109.5 |
H1A—N1—H1C | 109.5 | H3A—C3—H3C | 109.5 |
H1B—N1—H1C | 109.5 | H3B—C3—H3C | 109.5 |
O2—C1—O1 | 125.3 (2) | O5—C4—O6 | 125.93 (19) |
O2—C1—C2 | 123.3 (2) | O5—C4—C5 | 119.18 (17) |
O1—C1—C2 | 111.4 (2) | O6—C4—C5 | 114.88 (17) |
N1—C2—C3 | 110.3 (2) | O4—C5—O3 | 124.8 (2) |
N1—C2—C1 | 108.5 (2) | O4—C5—C4 | 121.69 (18) |
C3—C2—C1 | 113.3 (2) | O3—C5—C4 | 113.49 (17) |
N1—C2—H2 | 108.2 | ||
O2—C1—C2—N1 | −6.2 (3) | O5—C4—C5—O4 | 176.9 (3) |
O1—C1—C2—N1 | 174.0 (2) | O6—C4—C5—O4 | −2.1 (4) |
O2—C1—C2—C3 | −129.1 (3) | O5—C4—C5—O3 | −4.0 (3) |
O1—C1—C2—C3 | 51.0 (3) | O6—C4—C5—O3 | 177.1 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O5i | 0.82 | 1.80 | 2.591 (2) | 161 |
O3—H3···O6ii | 0.82 | 1.77 | 2.587 (2) | 174 |
N1—H1A···O5iii | 0.89 | 1.98 | 2.834 (3) | 161 |
N1—H1B···O2iv | 0.89 | 2.03 | 2.863 (3) | 154 |
N1—H1C···O6 | 0.89 | 1.96 | 2.818 (2) | 162 |
C2—H2···O4v | 0.98 | 2.53 | 3.423 (3) | 152 |
Symmetry codes: (i) x+1/2, −y+3/2, z−1/2; (ii) x−1, y, z; (iii) −x+3/2, y−1/2, −z+3/2; (iv) −x+1, −y+1, −z+1; (v) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C3H8NO2+·C2HO4− |
Mr | 179.13 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 293 |
a, b, c (Å) | 5.662 (2), 7.342 (2), 19.157 (6) |
β (°) | 94.48 (3) |
V (Å3) | 793.9 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.48 × 0.32 × 0.22 |
Data collection | |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | ψ scan (North et al., 1968) |
Tmin, Tmax | 0.89, 0.97 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1542, 1390, 1103 |
Rint | 0.011 |
(sin θ/λ)max (Å−1) | 0.593 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.126, 1.12 |
No. of reflections | 1390 |
No. of parameters | 112 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.29, −0.21 |
Computer programs: CAD-4 Software (Enraf-Nonius, 1989), CAD-4 Software, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 1999), SHELXL97.
O2—C1—C2—N1 | −6.2 (3) | O2—C1—C2—C3 | −129.1 (3) |
O1—C1—C2—N1 | 174.0 (2) | O1—C1—C2—C3 | 51.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O5i | 0.82 | 1.80 | 2.591 (2) | 160.6 |
O3—H3···O6ii | 0.82 | 1.77 | 2.587 (2) | 174.0 |
N1—H1A···O5iii | 0.89 | 1.98 | 2.834 (3) | 161.1 |
N1—H1B···O2iv | 0.89 | 2.03 | 2.863 (3) | 154.2 |
N1—H1C···O6 | 0.89 | 1.96 | 2.818 (2) | 162.0 |
C2—H2···O4v | 0.98 | 2.53 | 3.423 (3) | 151.6 |
Symmetry codes: (i) x+1/2, −y+3/2, z−1/2; (ii) x−1, y, z; (iii) −x+3/2, y−1/2, −z+3/2; (iv) −x+1, −y+1, −z+1; (v) x+1, y, z. |
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X-ray crystallographic investigations of the complexes of amino acids with carboxylic acids are expected to throw light on the nature of intermolecular interactions and biomolecular aggregation patterns that might have occurred in prebiotic polymerization (Vijayan, 1988; Prasad & Vijayan, 1993). Recently, an accurate determination of the crystal structures of DL-alanine (Subha Nandhini et al., 2001b) was carried out in our laboratory. The present study reports the crystal structure of the title salt, (I), a complex of DL-alanine with oxalic acid.
Fig. 1 shows the molecular numbering scheme. The amino acid molecule exists in the cationic form with a neutral carboxylic acid group and a protonated amino group. The oxalic acid molecule exists in the mono-ionized state. In the asymmetric unit, the DL-alaninium cation and the semi-oxalate anion are linked to each other through a N—H···O hydrogen bond. The conformation of the DL-alaninium ions in the present structure is significantly different from the values observed for DL-alanine. The N atom deviates by 0.148 (4) Å from the carboxylate plane and the methyl C atom deviates by 1.063 (5) Å in the opposite direction. The corresponding values observed in DL-alanine are 0.392 (5) and 1.356 (4) Å, respectively. The conformation of the semi-oxalate ion remains essentially planar as observed in the crystal structures of other complexes of amino acids with oxalic acid.
In the crystal structure of (I), the alanine molecules dimerize across inversion centres through head-to-tail N - H···O hydrogen bonds, as observed in many other amino acid racemates (Soman & Vijayan, 1989). The hydrogen-bonded alanine dimers form columns along the b axis and each such column is connected to others through semi-oxalate ions (Fig. 2). The semi-oxalate ions aggregate into hydrogen-bonded strings along the shortest cell axis, generated by translation as observed in glycinium oxalate (Subha Nandhini et al., 2001a) and L-alaninium oxalate (Subha Nandhini et al., 2001c). The crystal structure is also characterized by the presence of a C—H···O hydrogen bond and a short C···O contact [C1···O2(-x + 2,-y + 1,-z + 1) = 2.987 (6) Å] between amino acids. While the aggregation pattern of the semi-oxalate ions is identical in the crystal structures of oxalic acid complexes of glycine, L-alanine and the title compound, (I), the aggregation of amino acid molecules shows no common pattern.