Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100015456/vj1115sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270100015456/vj1115Isup2.hkl |
CCDC reference: 158278
Colourless single crystals of the above complex were grown as transparent plates, from a saturated aqueous solution containing glycine and oxalic acid in stoichiometric ratio, 1:1 proportion. The density was determined by the flotation method using a liquid mixture of carbon tetrachloride and xylene.
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 atom-numbering scheme and 50% probability displacement ellipsoids. | |
Fig. 2. Packing diagram of the molecule viewed down the b axis. |
C2H6NO2+·C2HO4− | F(000) = 344 |
Mr = 165.11 | Dx = 1.658 Mg m−3 Dm = 1.66 Mg m−3 Dm measured by flotation method |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54180 Å |
a = 10.5807 (15) Å | Cell parameters from 25 reflections |
b = 5.650 (2) Å | θ = 16–29° |
c = 12.093 (3) Å | µ = 1.43 mm−1 |
β = 113.83 (1)° | T = 293 K |
V = 661.3 (3) Å3 | Plates, colourless |
Z = 4 | 0.45 × 0.32 × 0.22 mm |
Enraf-Nonius CAD4 diffractometer | 1183 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.013 |
Graphite monochromator | θmax = 70.0°, θmin = 4.6° |
ω–2θ scans | h = 0→12 |
Absorption correction: ψ scan (North et al., 1968) | k = 0→6 |
Tmin = 0.555, Tmax = 0.730 | l = −14→13 |
1280 measured reflections | 2 standard reflections every 200 reflections |
1212 independent reflections | intensity decay: 0.1% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: located |
R[F2 > 2σ(F2)] = 0.036 | All H-atom parameters refined |
wR(F2) = 0.106 | Calculated w = 1/[σ2(Fo2) + (0.058P)2 + 0.2023P] where P = (Fo2 + 2Fc2)/3 |
S = 1.21 | (Δ/σ)max < 0.001 |
1212 reflections | Δρmax = 0.28 e Å−3 |
129 parameters | Δρmin = −0.21 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.069 (4) |
C2H6NO2+·C2HO4− | V = 661.3 (3) Å3 |
Mr = 165.11 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 10.5807 (15) Å | µ = 1.43 mm−1 |
b = 5.650 (2) Å | T = 293 K |
c = 12.093 (3) Å | 0.45 × 0.32 × 0.22 mm |
β = 113.83 (1)° |
Enraf-Nonius CAD4 diffractometer | 1183 reflections with I > 2σ(I) |
Absorption correction: ψ scan (North et al., 1968) | Rint = 0.013 |
Tmin = 0.555, Tmax = 0.730 | 2 standard reflections every 200 reflections |
1280 measured reflections | intensity decay: 0.1% |
1212 independent reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.106 | All H-atom parameters refined |
S = 1.21 | Δρmax = 0.28 e Å−3 |
1212 reflections | Δρmin = −0.21 e Å−3 |
129 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 | ||
N1 | −0.27816 (15) | 0.2485 (3) | 0.79503 (13) | 0.0355 (4) | |
O1 | −0.60285 (13) | 0.1930 (2) | 0.54347 (12) | 0.0468 (4) | |
O2 | −0.50188 (13) | 0.5083 (2) | 0.65663 (11) | 0.0418 (4) | |
O3 | −0.09956 (12) | 0.0715 (2) | 0.58171 (12) | 0.0378 (4) | |
O4 | 0.11644 (11) | 0.2165 (2) | 0.66801 (10) | 0.0343 (3) | |
O5 | −0.20401 (11) | 0.49360 (19) | 0.55030 (12) | 0.0396 (4) | |
O6 | 0.00490 (11) | 0.65912 (17) | 0.62212 (10) | 0.0320 (3) | |
C1 | −0.49894 (15) | 0.3073 (3) | 0.62413 (13) | 0.0301 (4) | |
C2 | −0.36952 (16) | 0.1594 (3) | 0.67389 (14) | 0.0319 (4) | |
C3 | −0.00764 (15) | 0.2399 (2) | 0.62010 (12) | 0.0249 (4) | |
C4 | −0.07662 (15) | 0.4867 (2) | 0.59528 (12) | 0.0247 (4) | |
H1 | −0.671 (3) | 0.289 (5) | 0.510 (3) | 0.076 (8)* | |
H2 | −0.320 (2) | 0.174 (4) | 0.6224 (18) | 0.046 (5)* | |
H3 | −0.390 (2) | 0.006 (4) | 0.6808 (17) | 0.035 (5)* | |
H4 | −0.261 (2) | 0.407 (5) | 0.797 (2) | 0.058 (6)* | |
H5 | −0.313 (3) | 0.217 (4) | 0.851 (2) | 0.066 (7)* | |
H6 | −0.191 (2) | 0.174 (4) | 0.8206 (19) | 0.047 (5)* | |
H7 | −0.060 (2) | −0.071 (5) | 0.597 (2) | 0.062 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0241 (8) | 0.0347 (8) | 0.0426 (8) | 0.0004 (6) | 0.0081 (6) | 0.0036 (6) |
O1 | 0.0292 (7) | 0.0396 (7) | 0.0549 (8) | 0.0067 (5) | −0.0005 (6) | −0.0092 (6) |
O2 | 0.0315 (7) | 0.0369 (7) | 0.0507 (7) | 0.0057 (5) | 0.0102 (5) | −0.0073 (5) |
O3 | 0.0294 (7) | 0.0187 (6) | 0.0606 (8) | −0.0004 (4) | 0.0132 (5) | −0.0001 (5) |
O4 | 0.0251 (7) | 0.0285 (6) | 0.0442 (6) | 0.0043 (4) | 0.0088 (5) | 0.0028 (4) |
O5 | 0.0220 (7) | 0.0272 (6) | 0.0613 (8) | 0.0036 (4) | 0.0083 (5) | 0.0031 (5) |
O6 | 0.0270 (6) | 0.0187 (6) | 0.0472 (6) | −0.0012 (4) | 0.0117 (5) | 0.0004 (4) |
C1 | 0.0249 (8) | 0.0315 (8) | 0.0341 (7) | 0.0021 (6) | 0.0121 (6) | 0.0003 (6) |
C2 | 0.0249 (8) | 0.0323 (9) | 0.0384 (8) | 0.0034 (6) | 0.0127 (7) | 0.0013 (6) |
C3 | 0.0258 (9) | 0.0195 (8) | 0.0292 (7) | 0.0012 (5) | 0.0109 (6) | 0.0018 (5) |
C4 | 0.0247 (9) | 0.0206 (7) | 0.0281 (7) | 0.0008 (5) | 0.0098 (6) | 0.0011 (5) |
N1—C2 | 1.480 (2) | O3—H7 | 0.89 (3) |
N1—H4 | 0.91 (3) | O4—C3 | 1.2092 (19) |
N1—H5 | 0.90 (3) | O5—C4 | 1.234 (2) |
N1—H6 | 0.94 (2) | O6—C4 | 1.2540 (18) |
O1—C1 | 1.308 (2) | C1—C2 | 1.506 (2) |
O1—H1 | 0.86 (3) | C2—H2 | 0.96 (2) |
O2—C1 | 1.207 (2) | C2—H3 | 0.90 (2) |
O3—C3 | 1.3047 (19) | C3—C4 | 1.546 (2) |
C2—N1—H4 | 113.8 (15) | N1—C2—H2 | 107.8 (13) |
C2—N1—H5 | 111.7 (16) | C1—C2—H2 | 109.7 (12) |
H4—N1—H5 | 108 (2) | N1—C2—H3 | 108.6 (12) |
C2—N1—H6 | 109.4 (13) | C1—C2—H3 | 110.8 (12) |
H4—N1—H6 | 106 (2) | H2—C2—H3 | 110.6 (17) |
H5—N1—H6 | 108 (2) | O4—C3—O3 | 126.84 (13) |
C1—O1—H1 | 110 (2) | O4—C3—C4 | 121.87 (13) |
C3—O3—H7 | 111.5 (16) | O3—C3—C4 | 111.29 (12) |
O2—C1—O1 | 125.66 (15) | O5—C4—O6 | 127.17 (13) |
O2—C1—C2 | 122.07 (14) | O5—C4—C3 | 117.42 (13) |
O1—C1—C2 | 112.26 (14) | O6—C4—C3 | 115.41 (12) |
N1—C2—C1 | 109.37 (13) | ||
O2—C1—C2—N1 | 24.7 (2) | O3—C3—C4—O5 | 3.57 (18) |
O1—C1—C2—N1 | −155.86 (14) | O4—C3—C4—O6 | 3.73 (19) |
O4—C3—C4—O5 | −177.25 (13) | O3—C3—C4—O6 | −175.44 (12) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O5i | 0.86 (3) | 1.73 (3) | 2.593 (2) | 174 (3) |
N1—H4···O4ii | 0.91 (3) | 2.25 (3) | 3.082 (2) | 152 (2) |
N1—H5···O2iii | 0.90 (3) | 2.26 (3) | 2.949 (2) | 133 (2) |
N1—H5···O5iv | 0.90 (3) | 2.51 (2) | 3.172 (2) | 130 (2) |
N1—H6···O6v | 0.94 (2) | 1.81 (2) | 2.698 (2) | 156 (2) |
O3—H7···O6vi | 0.89 (3) | 1.65 (3) | 2.540 (2) | 177 (2) |
C2—H2···O5 | 0.96 (2) | 2.53 (2) | 3.314 (2) | 139 (2) |
Symmetry codes: (i) −x−1, −y+1, −z+1; (ii) −x, y+1/2, −z+3/2; (iii) −x−1, y−1/2, −z+3/2; (iv) x, −y+1/2, z+1/2; (v) −x, y−1/2, −z+3/2; (vi) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | C2H6NO2+·C2HO4− |
Mr | 165.11 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 10.5807 (15), 5.650 (2), 12.093 (3) |
β (°) | 113.83 (1) |
V (Å3) | 661.3 (3) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 1.43 |
Crystal size (mm) | 0.45 × 0.32 × 0.22 |
Data collection | |
Diffractometer | Enraf-Nonius CAD4 diffractometer |
Absorption correction | ψ scan (North et al., 1968) |
Tmin, Tmax | 0.555, 0.730 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1280, 1212, 1183 |
Rint | 0.013 |
(sin θ/λ)max (Å−1) | 0.610 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.106, 1.21 |
No. of reflections | 1212 |
No. of parameters | 129 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.28, −0.21 |
Computer programs: CAD-4 Software (Enraf-Nonius, 1989), CAD-4 Software, SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 1999), SHELXL97.
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O5i | 0.86 (3) | 1.73 (3) | 2.593 (2) | 174 (3) |
N1—H4···O4ii | 0.91 (3) | 2.25 (3) | 3.082 (2) | 152 (2) |
N1—H5···O2iii | 0.90 (3) | 2.26 (3) | 2.949 (2) | 133 (2) |
N1—H5···O5iv | 0.90 (3) | 2.51 (2) | 3.172 (2) | 130 (2) |
N1—H6···O6v | 0.94 (2) | 1.81 (2) | 2.698 (2) | 156 (2) |
O3—H7···O6vi | 0.89 (3) | 1.65 (3) | 2.540 (2) | 177 (2) |
C2—H2···O5 | 0.96 (2) | 2.53 (2) | 3.314 (2) | 139 (2) |
Symmetry codes: (i) −x−1, −y+1, −z+1; (ii) −x, y+1/2, −z+3/2; (iii) −x−1, y−1/2, −z+3/2; (iv) x, −y+1/2, z+1/2; (v) −x, y−1/2, −z+3/2; (vi) x, y−1, z. |
Structural data on the complexes of amino acids with carboxylic acids seem to be very limited. Single crystal X-ray investigations on such complexes are expected to throw light on the geometrical features of biomolecular interactions and aggregation patterns that might well have occurred in prebiotic polymerization (Vijayan, 1988; Prasad & Vijayan, 1993). The present study reports the crystal structure of a complex of glycine, the simplest of amino acids commonly found in proteins, with oxalic acid, (I). \sch
The glycine molecule exists in the cationic form with a positively charged amino group and an uncharged carboxylic group. The oxalic acid molecule exists in a mono ionized state in the crystals. The crystal structure of the complex is illustrated in Figure 2 and the hydrogen bonds that stabilize it are listed in Table 1. The glycine molecules form columns around 21 screw axes parallel to b. The molecules in each column are interconnected by a hydrogen bond between the amino and carboxyl groups of adjacent molecules, in a head-to-tail arrangement. Semi-oxalate ions also form columns parallel to b. The adjacent molecules are related by a cell translation and interconnected by a O—H···O hydrogen bond. Each such column and its equivalent generated by a centre of inversion connect two glycine columns giving rise to a double layer parallel to (102). In each layer, the unlike molecules are connected through an O—H···O hydrogen bond between the carboxyl group of the amino acid and the carboxylate group of the semi-oxalate ion, and their symmetry equivalents. The double layer is further stabilized by hydrogen bonds of the amino group of glycine with the semi-oxalate ion. The double layers are held together by possible C—H···O and van der Waals interactions. The mode of aggregation in the structure is different from those observed so far in amino acid- oxalic acid complexes (Bakke & Mostad, 1980; Prabu et al., 1996; Chandra et al., 1998; Krishnakumar et al., 1999).