Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536803009164/na6224sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536803009164/na6224Isup2.hkl |
CCDC reference: 214804
Colorless prismatic single crystals of (I) were obtained during an attempt to grow the complex of L-proline with oxalic acid, in the presence of a few drops of pyridine, from a saturated aqueous solution containing proline and oxalic acid in a stoichiometric ratio. Unexpectedly, instead of L-prolinium oxalate, only the title compound, (I), was obtained.
All the H atoms except those of the water molecules were generated geometrically and were allowed to ride on their respective parent atoms. The water H atoms were located from the difference Fourier map and allowed to refine isotropically.
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, 1990); 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 the atom-numbering scheme and ellipsoids at the 50% probability level. | |
Fig. 2. The packing of the molecules of (I), viewed down the a axis. |
C5H6N+·C2H2O4−·C2HO4·2H2O | Z = 2 |
Mr = 295.20 | F(000) = 308 |
Triclinic, P1 | Dx = 1.537 Mg m−3 Dm = 1.55 Mg m−3 Dm measured by flotation in a mixture of xylene and bromoform |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.992 (7) Å | Cell parameters from 25 reflections |
b = 9.539 (2) Å | θ = 2.0–25.0° |
c = 10.098 (2) Å | µ = 0.14 mm−1 |
α = 84.36 (2)° | T = 293 K |
β = 79.54 (4)° | Prismatic, colourless |
γ = 74.71 (6)° | 0.40 × 0.35 × 0.17 mm |
V = 638.0 (7) Å3 |
Enraf-Nonius CAD-4 diffractometer | 1946 reflections with I > 2s(I) |
Radiation source: fine-focus sealed tube | Rint = 0.006 |
Graphite monochromator | θmax = 25.0°, θmin = 2.1° |
ω–2θ scans | h = 0→8 |
Absorption correction: ψ scan (North et al., 1968) | k = −10→11 |
Tmin = 0.948, Tmax = 0.971 | l = −11→11 |
2451 measured reflections | 2 standard reflections every 200 reflections |
2250 independent reflections | intensity decay: <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)] = 0.037 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.113 | w = 1/[σ2(Fo2) + (0.0645P)2 + 0.1652P] where P = (Fo2 + 2Fc2)/3 |
S = 1.09 | (Δ/σ)max < 0.001 |
2250 reflections | Δρmax = 0.26 e Å−3 |
198 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: 0.017 (5) |
C5H6N+·C2H2O4−·C2HO4·2H2O | γ = 74.71 (6)° |
Mr = 295.20 | V = 638.0 (7) Å3 |
Triclinic, P1 | Z = 2 |
a = 6.992 (7) Å | Mo Kα radiation |
b = 9.539 (2) Å | µ = 0.14 mm−1 |
c = 10.098 (2) Å | T = 293 K |
α = 84.36 (2)° | 0.40 × 0.35 × 0.17 mm |
β = 79.54 (4)° |
Enraf-Nonius CAD-4 diffractometer | 1946 reflections with I > 2s(I) |
Absorption correction: ψ scan (North et al., 1968) | Rint = 0.006 |
Tmin = 0.948, Tmax = 0.971 | 2 standard reflections every 200 reflections |
2451 measured reflections | intensity decay: <1% |
2250 independent reflections |
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.113 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.09 | Δρmax = 0.26 e Å−3 |
2250 reflections | Δρmin = −0.21 e Å−3 |
198 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 | 0.2512 (2) | −0.37241 (12) | 0.15703 (13) | 0.0503 (4) | |
O2 | 0.30716 (18) | −0.18041 (12) | 0.02663 (12) | 0.0425 (3) | |
H2A | 0.3941 | −0.2417 | −0.0171 | 0.064* | |
O3 | −0.02042 (17) | −0.19127 (11) | 0.32664 (11) | 0.0367 (3) | |
H3A | −0.0939 | −0.1280 | 0.3752 | 0.055* | |
O4 | 0.04479 (18) | −0.00249 (11) | 0.19387 (12) | 0.0397 (3) | |
O5 | 0.45749 (18) | −0.16978 (11) | 0.32184 (11) | 0.0388 (3) | |
O6 | 0.55016 (18) | 0.01715 (11) | 0.20116 (11) | 0.0390 (3) | |
H6A | 0.6140 | −0.0456 | 0.1488 | 0.058* | |
O7 | 0.24706 (17) | 0.01413 (12) | 0.51304 (11) | 0.0377 (3) | |
O8 | 0.28745 (19) | 0.20154 (12) | 0.36944 (12) | 0.0433 (3) | |
O9 | 0.62884 (18) | −0.32827 (13) | −0.11797 (12) | 0.0400 (3) | |
H7 | 0.653 (3) | −0.290 (2) | −0.201 (2) | 0.049 (5)* | |
H8 | 0.663 (4) | −0.415 (3) | −0.129 (2) | 0.067 (7)* | |
O10 | 0.19735 (19) | 0.15999 (14) | 0.97140 (12) | 0.0391 (3) | |
H9 | 0.156 (3) | 0.099 (2) | 1.038 (2) | 0.055 (6)* | |
H10 | 0.238 (4) | 0.214 (3) | 1.014 (2) | 0.066 (7)* | |
N1 | 0.2595 (2) | 0.70956 (15) | 0.57175 (16) | 0.0450 (4) | |
H1 | 0.2813 | 0.7850 | 0.5236 | 0.054* | |
C2 | 0.2537 (3) | 0.5940 (2) | 0.50914 (18) | 0.0459 (4) | |
H2 | 0.2737 | 0.5955 | 0.4155 | 0.055* | |
C3 | 0.2181 (3) | 0.47385 (18) | 0.58428 (19) | 0.0445 (4) | |
H3 | 0.2125 | 0.3929 | 0.5421 | 0.053* | |
C4 | 0.1909 (3) | 0.47313 (19) | 0.72162 (19) | 0.0463 (4) | |
H4 | 0.1682 | 0.3913 | 0.7735 | 0.056* | |
C5 | 0.1972 (3) | 0.5944 (2) | 0.78308 (19) | 0.0516 (5) | |
H5 | 0.1774 | 0.5958 | 0.8766 | 0.062* | |
C6 | 0.2332 (3) | 0.71304 (18) | 0.7038 (2) | 0.0477 (5) | |
H6 | 0.2390 | 0.7956 | 0.7433 | 0.057* | |
C7 | 0.2200 (2) | −0.24363 (15) | 0.13065 (15) | 0.0303 (3) | |
C8 | 0.0676 (2) | −0.13161 (15) | 0.22227 (14) | 0.0279 (3) | |
C9 | 0.4514 (2) | −0.04164 (15) | 0.30302 (14) | 0.0278 (3) | |
C10 | 0.3170 (2) | 0.07087 (15) | 0.40268 (14) | 0.0292 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0652 (8) | 0.0209 (6) | 0.0537 (8) | −0.0061 (5) | 0.0134 (6) | −0.0043 (5) |
O2 | 0.0475 (7) | 0.0294 (6) | 0.0386 (7) | −0.0038 (5) | 0.0145 (5) | −0.0011 (5) |
O3 | 0.0438 (6) | 0.0246 (6) | 0.0352 (6) | −0.0071 (5) | 0.0088 (5) | −0.0023 (4) |
O4 | 0.0452 (7) | 0.0209 (6) | 0.0448 (7) | −0.0047 (5) | 0.0080 (5) | −0.0009 (5) |
O5 | 0.0478 (7) | 0.0222 (6) | 0.0420 (6) | −0.0079 (5) | 0.0026 (5) | −0.0018 (4) |
O6 | 0.0501 (7) | 0.0262 (6) | 0.0338 (6) | −0.0093 (5) | 0.0117 (5) | −0.0041 (4) |
O7 | 0.0468 (7) | 0.0282 (6) | 0.0321 (6) | −0.0091 (5) | 0.0079 (5) | −0.0006 (4) |
O8 | 0.0620 (8) | 0.0222 (6) | 0.0376 (6) | −0.0077 (5) | 0.0087 (5) | −0.0027 (4) |
O9 | 0.0520 (7) | 0.0238 (6) | 0.0367 (7) | −0.0045 (5) | 0.0059 (5) | −0.0036 (5) |
O10 | 0.0486 (7) | 0.0346 (7) | 0.0337 (6) | −0.0142 (5) | −0.0001 (5) | −0.0022 (5) |
N1 | 0.0466 (8) | 0.0280 (7) | 0.0604 (10) | −0.0131 (6) | −0.0123 (7) | 0.0146 (6) |
C2 | 0.0516 (10) | 0.0442 (10) | 0.0412 (10) | −0.0108 (8) | −0.0110 (8) | 0.0038 (7) |
C3 | 0.0506 (10) | 0.0288 (9) | 0.0571 (11) | −0.0116 (7) | −0.0126 (8) | −0.0050 (7) |
C4 | 0.0538 (10) | 0.0319 (9) | 0.0539 (11) | −0.0187 (8) | −0.0048 (8) | 0.0091 (7) |
C5 | 0.0647 (12) | 0.0486 (11) | 0.0412 (10) | −0.0180 (9) | −0.0009 (8) | −0.0048 (8) |
C6 | 0.0513 (10) | 0.0256 (9) | 0.0668 (13) | −0.0085 (7) | −0.0093 (9) | −0.0093 (8) |
C7 | 0.0341 (8) | 0.0240 (8) | 0.0318 (8) | −0.0073 (6) | −0.0022 (6) | −0.0024 (6) |
C8 | 0.0300 (7) | 0.0246 (7) | 0.0288 (7) | −0.0088 (6) | −0.0017 (6) | −0.0002 (6) |
C9 | 0.0314 (7) | 0.0244 (7) | 0.0277 (7) | −0.0086 (6) | −0.0036 (6) | 0.0003 (6) |
C10 | 0.0330 (8) | 0.0254 (8) | 0.0287 (7) | −0.0090 (6) | −0.0009 (6) | −0.0021 (6) |
O1—C7 | 1.201 (2) | N1—C6 | 1.315 (2) |
O2—C7 | 1.294 (2) | N1—C2 | 1.336 (2) |
O2—H2A | 0.8200 | N1—H1 | 0.8600 |
O3—C8 | 1.283 (2) | C2—C3 | 1.365 (3) |
O3—H3A | 0.8200 | C2—H2 | 0.9300 |
O4—C8 | 1.212 (2) | C3—C4 | 1.365 (3) |
O5—C9 | 1.209 (2) | C3—H3 | 0.9300 |
O6—C9 | 1.297 (2) | C4—C5 | 1.380 (3) |
O6—H6A | 0.8200 | C4—H4 | 0.9300 |
O7—C10 | 1.264 (2) | C5—C6 | 1.373 (3) |
O8—C10 | 1.231 (2) | C5—H5 | 0.9300 |
O9—H7 | 0.88 (2) | C6—H6 | 0.9300 |
O9—H8 | 0.81 (3) | C7—C8 | 1.539 (2) |
O10—H9 | 0.90 (2) | C9—C10 | 1.544 (2) |
O10—H10 | 0.83 (3) | ||
C7—O2—H2A | 109.5 | C6—C5—H5 | 120.6 |
C8—O3—H3A | 109.5 | C4—C5—H5 | 120.6 |
C9—O6—H6A | 109.5 | N1—C6—C5 | 119.76 (16) |
H7—O9—H8 | 103 (2) | N1—C6—H6 | 120.1 |
H9—O10—H10 | 102 (2) | C5—C6—H6 | 120.1 |
C6—N1—C2 | 122.9 (2) | O1—C7—O2 | 126.3 (1) |
C6—N1—H1 | 118.6 | O1—C7—C8 | 122.4 (1) |
C2—N1—H1 | 118.6 | O2—C7—C8 | 111.3 (1) |
N1—C2—C3 | 119.2 (2) | O4—C8—O3 | 127.0 (1) |
N1—C2—H2 | 120.4 | O4—C8—C7 | 120.3 (1) |
C3—C2—H2 | 120.4 | O3—C8—C7 | 112.7 (1) |
C2—C3—C4 | 119.60 (16) | O5—C9—O6 | 125.8 (1) |
C2—C3—H3 | 120.2 | O5—C9—C10 | 121.3 (1) |
C4—C3—H3 | 120.2 | O6—C9—C10 | 112.8 (1) |
C3—C4—C5 | 119.70 (16) | O8—C10—O7 | 127.0 (1) |
C3—C4—H4 | 120.1 | O8—C10—C9 | 119.4 (1) |
C5—C4—H4 | 120.1 | O7—C10—C9 | 113.6 (1) |
C6—C5—C4 | 118.82 (18) | ||
C6—N1—C2—C3 | 0.3 (3) | O2—C7—C8—O4 | −1.3 (2) |
N1—C2—C3—C4 | −0.6 (3) | O1—C7—C8—O3 | −0.5 (2) |
C2—C3—C4—C5 | 0.8 (3) | O2—C7—C8—O3 | −179.7 (1) |
C3—C4—C5—C6 | −0.7 (3) | O5—C9—C10—O8 | −167.5 (2) |
C2—N1—C6—C5 | −0.3 (3) | O6—C9—C10—O8 | 11.9 (2) |
C4—C5—C6—N1 | 0.5 (3) | O5—C9—C10—O7 | 12.1 (2) |
O1—C7—C8—O4 | 178.0 (2) | O6—C9—C10—O7 | −168.5 (1) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2A···O9 | 0.82 | 1.80 | 2.592 (3) | 161 |
O3—H3A···O7i | 0.82 | 1.67 | 2.486 (2) | 174 |
O6—H6A···O10ii | 0.82 | 1.82 | 2.626 (2) | 166 |
O9—H7···O8iii | 0.88 (2) | 1.85 (2) | 2.735 (2) | 176 (2) |
O9—H8···O1iv | 0.81 (3) | 1.99 (3) | 2.802 (2) | 179 (3) |
O10—H9···O4v | 0.90 (2) | 1.92 (2) | 2.811 (2) | 171 (2) |
O10—H10···O9ii | 0.83 (3) | 2.07 (3) | 2.897 (2) | 173 (2) |
N1—H1···O7vi | 0.86 | 2.13 | 2.889 (2) | 147 |
N1—H1···O5vi | 0.86 | 2.25 | 2.934 (2) | 137 |
Symmetry codes: (i) −x, −y, −z+1; (ii) −x+1, −y, −z+1; (iii) −x+1, −y, −z; (iv) −x+1, −y−1, −z; (v) x, y, z+1; (vi) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C5H6N+·C2H2O4−·C2HO4·2H2O |
Mr | 295.20 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 293 |
a, b, c (Å) | 6.992 (7), 9.539 (2), 10.098 (2) |
α, β, γ (°) | 84.36 (2), 79.54 (4), 74.71 (6) |
V (Å3) | 638.0 (7) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.40 × 0.35 × 0.17 |
Data collection | |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | ψ scan (North et al., 1968) |
Tmin, Tmax | 0.948, 0.971 |
No. of measured, independent and observed [I > 2s(I)] reflections | 2451, 2250, 1946 |
Rint | 0.006 |
(sin θ/λ)max (Å−1) | 0.594 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.113, 1.09 |
No. of reflections | 2250 |
No. of parameters | 198 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.26, −0.21 |
Computer programs: CAD-4 Software (Enraf-Nonius, 1989), CAD-4 Software, SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 1999), SHELXL97.
O1—C7 | 1.201 (2) | O8—C10 | 1.231 (2) |
O2—C7 | 1.294 (2) | N1—C6 | 1.315 (2) |
O3—C8 | 1.283 (2) | N1—C2 | 1.336 (2) |
O4—C8 | 1.212 (2) | C2—C3 | 1.365 (3) |
O5—C9 | 1.209 (2) | C3—C4 | 1.365 (3) |
O6—C9 | 1.297 (2) | C4—C5 | 1.380 (3) |
O7—C10 | 1.264 (2) | ||
C6—N1—C2 | 122.9 (2) | O3—C8—C7 | 112.7 (1) |
N1—C2—C3 | 119.2 (2) | O5—C9—O6 | 125.8 (1) |
O1—C7—O2 | 126.3 (1) | O5—C9—C10 | 121.3 (1) |
O1—C7—C8 | 122.4 (1) | O6—C9—C10 | 112.8 (1) |
O2—C7—C8 | 111.3 (1) | O8—C10—O7 | 127.0 (1) |
O4—C8—O3 | 127.0 (1) | O8—C10—C9 | 119.4 (1) |
O4—C8—C7 | 120.3 (1) | O7—C10—C9 | 113.6 (1) |
C6—N1—C2—C3 | 0.3 (3) | O2—C7—C8—O3 | −179.7 (1) |
N1—C2—C3—C4 | −0.6 (3) | O5—C9—C10—O8 | −167.5 (2) |
O1—C7—C8—O4 | 178.0 (2) | O6—C9—C10—O8 | 11.9 (2) |
O2—C7—C8—O4 | −1.3 (2) | O5—C9—C10—O7 | 12.1 (2) |
O1—C7—C8—O3 | −0.5 (2) | O6—C9—C10—O7 | −168.5 (1) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2A···O9 | 0.82 | 1.80 | 2.592 (3) | 161 |
O3—H3A···O7i | 0.82 | 1.67 | 2.486 (2) | 174 |
O6—H6A···O10ii | 0.82 | 1.82 | 2.626 (2) | 166 |
O9—H7···O8iii | 0.88 (2) | 1.85 (2) | 2.735 (2) | 176 (2) |
O9—H8···O1iv | 0.81 (3) | 1.99 (3) | 2.802 (2) | 179 (3) |
O10—H9···O4v | 0.90 (2) | 1.92 (2) | 2.811 (2) | 171 (2) |
O10—H10···O9ii | 0.83 (3) | 2.07 (3) | 2.897 (2) | 173 (2) |
N1—H1···O7vi | 0.86 | 2.13 | 2.889 (2) | 147 |
N1—H1···O5vi | 0.86 | 2.25 | 2.934 (2) | 137 |
Symmetry codes: (i) −x, −y, −z+1; (ii) −x+1, −y, −z+1; (iii) −x+1, −y, −z; (iv) −x+1, −y−1, −z; (v) x, y, z+1; (vi) x, y+1, z. |
The present study reports the crystal structure of pyridinium oxalate oxalic acid dihydrate, (I), as part of a series of investigations being carried out to observe conformational changes in carboxylic acid molecules and characteristic hydrogen-bonding patterns in their crystal structures.
Fig. 1 shows the molecular structure of (I) with the atom-numbering scheme. The pyridine molecule exists in the cationic form with a protonated ring N atom. One of the oxalic acid molecules exists in a mono-ionized state while the other molecule in the uncharged state. The oxalic acid molecule is more planar [the largest displacements from the plane are by 0.012 (2) Å for O1 and 0.011 (1) Å for O4, on the same side] than the hydrogen oxalate ion [the largest displacements from the plane are by 0.017 (2) Å for O6 and 0.123 (2) Å for O8, on opposite sides]. The geometric parameters of the pyridinium ion are in agreement with those of the pyridinium ions of other structures, viz. bisthiourea pyridinium bromide (Truter & Vickery, 1972) and pyridinium dichloroiodide (Tucker & Kroon, 1973). The C—C bond lengths of the oxalate ion and oxalic acid molecules [C7—C8 = 1.539 (2) Å and C9—C10 = 1.544 (2) Å] are longer than accepted values. Perhaps the abnormally long C—C distance found in the oxalic acid molecule and oxalate ion can be justified by intramolecular O···O steric hindrance, shown by the following contacts: O1···O3 = 2.682 (2), O2···O4 = 2.626 (2), O5···O7 = 2.691 (2) and O2···O4 = 2.666 (2) Å, all significantly shorter than the sum of the van der Waals radii of 3.04 Å (Bondi, 1964). This steric interaction not only causes an enlargement of about 0.04 Å of the C—C central bond in both oxalic acid residues, but also some twisting of the two carboxylic acid groups about it, twisting that is significant only in the anion, as shown by the values of the torsion angles O1—C7—C8—O3 = −0.5 (2)° and O5—C9—C10—O7 = 12.1 (2)°. However, such large deviations in bond lengths are also observed in the case of oxalic acid dihydrate, with C—C = 1.537 Å (Ahmed & Cruickshank, 1953), and in the crystal structures of anhydrous α- and β-oxalic acids, with values of 1.537 (1) and 1.537 (1) Å, respectively (Derrissen & Smith, 1974). A slight increase in the C10—O7 bond length [1.264 (2) Å] compared to C10—O8 [1.231 (2) Å] may be attributed to atom O7 participating in two hydrogen bonds and O8 in only one hydrogen bond in the structure. The other geometrical parameters of the oxalic acid molecules are found to be in agreement with those of other similar structures (oxalic acid dihydrate, anhydrous α- and β-oxalic acids, etc.).
Fig. 2 shows the packing pattern of (I), viewed down the a axis. The oxalate and oxalic acid residues related by a center of inversion are alternately linked along the diagonal of the ac plane. Pyridinium ions link the oxalate ion layers through bifurcated N—H···O hydrogen bonds, leading to a characteristic three-dimensional aggregation pattern. One of the water molecules (O10) as donor, mediates O—H···O interactions with the oxalic acid residue. The other water molecule (O9) links the uncharged oxalic acid molecules and the oxalate ions through O—H···O hydrogen bonds. Short carbonyl contacts [C7···O5 = 3.004 (4) Å, C8···O5 = 2.995 (3) Å and C8···O10(-x, −y, −z + 1) = 3.002 (3) Å] are also observed (Allen et al., 1998). Thus the structure is stabilized by O—H···O and N—H···O hydrogen bonds in addition to short contacts and van der Waals interactions. The complex can be described as an inclusion compound with the oxalate ion and oxalic acid molecule as hosts and the pyridinium ion as the guest.