carried out, there seem to be no studies made on the complexes of sarcosine with ... The ionization states of the sarcosine and oxalic acid molecules were ...
CIF access Acta Cryst. (1998). C54, IUC9800063
[ doi:10.1107/S0108270198099144 ]
Sarcosinium Oxalate Monohydrate R. V. Krishnakumar, M. S. Nandhini and S. Natarajan Abstract In the title compound, C3H8NO2+·C2HO4·H2O, the amino acid molecule exists with a protonated amino group and an uncharged carboxylic acid group. The oxalic acid molecule is found to exist in the mono-ionized state. The structure is stabilized by an extensive network of hydrogen bonds. Comment Sarcosine (N-methylglycine, CH3NH2+CH2COO−) is an α-amino acid found in many biological materials (Mostad & Natarajan, 1989). Although structural studies on the complexes of sarcosine with inorganic acids (Averbuch-Pouchot, 1988; Mostad & Natarajan, 1996) and metal ions (Krishnakumar et al., 1994, 1996; Krishnakumar & Natarajan, 1995) have been carried out, there seem to be no studies made on the complexes of sarcosine with carboxylic acids. In view of the biological and evolutionary importance of non-covalent interactions (Vijayan, 1988), the X-ray structure determination of this amino acid with oxalic acid has been taken up. The ionization states of the sarcosine and oxalic acid molecules were evident from the H atoms located near the relevant non-H atoms and the bond lengths and bond angles involving them. The amino acid molecule exists in the present structure in 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, thus maintaining the overall charge neutrality of the complex. There are no direct hydrogen-bonded interactions between the sarcosine molecules. The sarcosine layers are interconnected by interactions involving carboxylate ions. Unlike other oxalic acid complexes viz. D-tryptophan hydrogen oxalate (Bakke & Mostad, 1980) and L-histidine oxalate and DL-histidine oxalate (Prabu et al., 1996), the present complex has water of hydration. The presence of water of hydration may be to alleviate the numerical imbalance of donors and acceptors, since water molecules have two donors and frequently accept one bond.
Experimental Crystals of the title compound were grown by slow evaporation of an aqueous solution containing sarcosine and the oxalic acid in stoichiometric ratio, in 1:1 proportion. The density was determined by the flotation method using a mixture of carbon tetrachloride and xylene. Refinement All the H atoms were located experimentally from the difference Fourier map and refined isotropically.
CIF access Computing details Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS86 (Sheldrick, 1985); program(s) used to refine structure: SHELXL93 (Sheldrick, 1993); molecular graphics: SHELXL93; software used to prepare material for publication: SHELXL93.
(sarox) Crystal data C3H8N1O21+·C2HO41–·H2O1
V = 874.7 (2) Å3
Mr = 197.15
Z=4
Monoclinic, P21/n
Mo Kα
a = 5.5806 (7) Å
µ = 0.14 mm−1 T = 293 (2) K 0.30 × 0.25 × 0.20 mm
b = 22.641 (3) Å c = 7.0249 (3) Å β = 99.79 (1)º
Data collection Enraf Nonius CAD-4 diffractometer Absorption correction: none 1706 measured reflections 1543 independent reflections 1294 reflections with I > 2σ(I)
Rint = 0.021 2 standard reflections every 200 reflections intensity decay: 2%
Refinement R[F2 > 2σ(F2)] = 0.046 2
163 parameters
wR(F ) = 0.129
All H-atom parameters refined
S = 1.15
Δρmax = 0.51 e Å−3
1536 reflections
Δρmin = −0.36 e Å−3
Table 1 Hydrogen-bond geometry (Å, °) D—H···A
D—H
H···A
D···A
D—H···A
1.03 (4)
1.51 (4)
2.525 (3)
172 (3)
0.89 (3) 0.89 (3)
2.15 (3) 2.23 (3)
2.948 (2) 2.875 (3)
148 (3) 127 (3)
0.88 (3)
1.96 (3)
2.791 (3)
158 (3)
0.87 (4)
1.72 (4)
2.574 (3)
168 (4)
0.88 (4) 1.91 (4) 2.782 (2) O1W—H10···O6 Symmetry codes: (i) x−1/2, −y+1/2, z+1/2; (ii) x, y, z+1; (iii) x−1, y, z; (iv) −x+1/2, y−1/2, −z−1/2.
171 (3)
i
O1—H1···O5 N1—H4···O4 N1—H4···O5
N1—H5···O6ii O3—H9···O1W
iii iv
CIF access Acknowledgements The authors would like to thank the Council of Scientific and Industrial Research (CSIR), India, for financial support for the project and one of us (RVK) for a SRF. References Averbuch-Pouchot, M. T. (1988). Z. Kristallogr. 183, 285–291. Bakke, O. & Mostad, A. (1980). Acta Chem. Scand. Ser. B, 34, 559–570. Enraf-Nonius (1989). CAD-4 Software. Version 5. Enraf-Nonius, Delft, The Netherlands. Krishnakumar, R. V. & Natarajan, S. (1995). Cryst. Res. Technol. 30, 825–830. Krishnakumar, R. V., Natarajan, S., Asath Bahadur, S. & Cameron, T. S. (1994). Z. Kristallogr. 209, 443–444. Krishnakumar, R. V., Rameela, M. P. & Natarajan, S. (1996). Cryst. Res. Technol. 31, 203–207. Mostad, A. & Natarajan, S. (1989). Acta Chem. Scand. 43, 1004–1006. Mostad, A. & Natarajan, S. (1996). Cryst. Res. Technol. 31, 295–300. Prabu, M. M., Nagendra, H. G., Suresh, S. & Vijayan, M. (1996). J. Biomol. Struct. Dyn. 14, 387–392. Sheldrick, G. M. (1985). SHELXS86. Program for the Solution of Crystal Structures. Univ. of Göttingen, Germany. Sheldrick, G. M. (1993). SHELXL93. Program for the Refinement of Crystal Structures. University of Göttingen, Germany. Vijayan, M. (1988). Prog. Biophys. Mol. Biol. 52, 71–99.
CIF access Scheme 1
supplementary materials
supplementary materials (sarox) Crystal data C3H8N1O21+·C2HO41–·H2O1
F000 = 416 Dx = 1.497 Mg m−3
Mr = 197.15
Monoclinic, P21/n a = 5.5806 (7) Å b = 22.641 (3) Å c = 7.0249 (3) Å β = 99.79 (1)º V = 874.7 (2) Å3 Z=4
Dm = 1.50 Mg m−3 Dm measured by floatation in carbon tetrachloride/ xylene Mo Kα radiation λ = 0.71073 Å Cell parameters from 25 reflections θ = 5–12º µ = 0.14 mm−1 T = 293 (2) K Block cut from large plate, colourless 0.30 × 0.25 × 0.20 mm
Data collection Enraf Nonius CAD-4 diffractometer
Rint = 0.021
Radiation source: fine-focus sealed tube
θmax = 25º
Monochromator: graphite
θmin = 3º
T = 293(2) K ω–2θ scans Absorption correction: none 1706 measured reflections 1543 independent reflections 1294 reflections with I > 2σ(I)
h = 0→6 k = 0→26 l = −8→8 2 standard reflections every 200 reflections intensity decay: 2%
Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.046
Hydrogen site location: inferred from neighbouring sites All H-atom parameters refined Calculated w = 1/[σ2(Fo2) + (0.0829P)2 + 0.4545P] where P = (Fo2 + 2Fc2)/3 ?
wR(F2) = 0.129
(Δ/σ)max < 0.001
S = 1.15
Δρmax = 0.51 e Å−3
1536 reflections
Δρmin = −0.36 e Å−3
163 parameters
Extinction correction: SHELXL93, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct Extinction coefficient: 0.175 (17) methods Secondary atom site location: difference Fourier map
sup-1
supplementary materials Special details 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 on F2 for ALL reflections except for 7 with very negative F2 or flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > 2sigma(F2) is used only for calculating _R_factor_obs 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.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) O1 O2 C1 C2 N1 C3 O1W C4 C5 O3 O4 O5 O6 H1 H2 H3 H4 H5 H6 H7 H8 H10 H11 H9
x
y
z
Uiso*/Ueq
0.4438 (4) 0.2576 (4) 0.4306 (4) 0.6607 (4) 0.6251 (3) 0.8522 (5) 0.7475 (3) 0.2588 (4) 0.4406 (4) 0.0910 (3) 0.2776 (3) 0.5742 (3) 0.4383 (3) 0.287 (7) 0.704 (6) 0.785 (6) 0.523 (6) 0.549 (6) 0.810 (6) 0.964 (8) 0.932 (8) 0.701 (6) 0.758 (6) −0.010 (7)
0.30548 (8) 0.22266 (10) 0.24861 (10) 0.21693 (10) 0.15277 (8) 0.11760 (13) −0.00431 (8) 0.07596 (10) 0.11066 (10) 0.04981 (9) 0.07525 (8) 0.14540 (8) 0.10111 (8) 0.3250 (16) 0.2265 (13) 0.2295 (13) 0.1414 (13) 0.1460 (13) 0.0799 (16) 0.1293 (19) 0.1231 (18) −0.0346 (17) −0.0217 (14) 0.0298 (17)
0.6560 (3) 0.7082 (5) 0.6734 (3) 0.6533 (4) 0.6630 (3) 0.6840 (5) 0.2540 (3) 0.2423 (3) 0.1411 (3) 0.1227 (2) 0.4165 (2) 0.2494 (2) −0.0323 (2) 0.682 (5) 0.534 (5) 0.749 (5) 0.558 (5) 0.761 (5) 0.688 (5) 0.803 (6) 0.576 (6) 0.177 (5) 0.364 (5) 0.180 (5)
0.0502 (6) 0.0856 (10) 0.0315 (6) 0.0314 (6) 0.0280 (5) 0.0433 (7) 0.0388 (5) 0.0289 (5) 0.0293 (5) 0.0447 (6) 0.0425 (5) 0.0426 (5) 0.0398 (5) 0.068 (10)* 0.046 (8)* 0.046 (8)* 0.047 (8)* 0.045 (8)* 0.052 (9)* 0.082 (12)* 0.082 (12)* 0.059 (9)* 0.051 (9)* 0.072 (11)*
Atomic displacement parameters (Å2) O1 O2 C1
sup-2
U11 0.0475 (11) 0.0411 (12) 0.0288 (11)
U22 0.0338 (10) 0.0427 (13) 0.0333 (13)
U33 0.0764 (14) 0.185 (3) 0.0338 (12)
U12 0.0079 (8) 0.0013 (9) 0.0007 (9)
U13 0.0307 (10) 0.053 (2) 0.0091 (9)
U23 0.0039 (8) −0.0003 (14) −0.0002 (9)
supplementary materials C2 N1 C3 O1W C4 C5 O3 O4 O5 O6
0.0272 (12) 0.0267 (10) 0.0368 (14) 0.0476 (11) 0.0316 (11) 0.0304 (11) 0.0476 (11) 0.0444 (10) 0.0467 (10) 0.0449 (10)
0.0316 (12) 0.0316 (10) 0.0401 (15) 0.0372 (10) 0.0301 (11) 0.0318 (12) 0.0582 (12) 0.0603 (12) 0.0496 (11) 0.0503 (11)
0.0372 (13) 0.0268 (10) 0.054 (2) 0.0337 (10) 0.0261 (11) 0.0260 (11) 0.0298 (9) 0.0245 (9) 0.0331 (9) 0.0262 (9)
−0.0010 (9) 0.0015 (7) 0.0128 (11) −0.0115 (8) −0.0039 (9) −0.0053 (9) −0.0303 (9) −0.0171 (8) −0.0229 (8) −0.0190 (8)
0.0112 (10) 0.0078 (8) 0.0114 (12) 0.0127 (8) 0.0082 (8) 0.0061 (8) 0.0104 (8) 0.0109 (7) 0.0112 (8) 0.0120 (7)
−0.0001 (10) −0.0005 (8) 0.0052 (12) 0.0001 (8) −0.0012 (8) 0.0000 (8) −0.0039 (8) −0.0005 (7) −0.0067 (8) −0.0020 (7)
Geometric parameters (Å, °) O1—C1 O1—H1 O2—C1 C1—C2 C2—N1 C2—H2 C2—H3 N1—C3 N1—H4 N1—H5 C3—H6
1.297 (3) 1.03 (4) 1.190 (3) 1.498 (3) 1.469 (3) 0.94 (3) 0.92 (3) 1.482 (3) 0.89 (3) 0.88 (3) 0.89 (4)
C3—H7 C3—H8 O1W—H10 O1W—H11 C4—O4 C4—O3 C4—C5 C5—O6 C5—O5 O3—H9
0.99 (4) 0.95 (4) 0.89 (4) 0.86 (4) 1.211 (3) 1.290 (3) 1.548 (3) 1.235 (3) 1.249 (3) 0.87 (4)
C1—O1—H1 O2—C1—O1 O2—C1—C2 O1—C1—C2 N1—C2—C1 N1—C2—H2 C1—C2—H2 N1—C2—H3 C1—C2—H3 H2—C2—H3 C2—N1—C3 C2—N1—H4 C3—N1—H4 C2—N1—H5 C3—N1—H5
110.3 (20) 124.8 (2) 121.4 (2) 113.8 (2) 110.1 (2) 109.0 (18) 109.2 (18) 111.2 (18) 109.4 (19) 107.8 (26) 114.6 (2) 108.6 (19) 109.9 (19) 107.1 (20) 110.3 (19)
H4—N1—H5 N1—C3—H6 N1—C3—H7 H6—C3—H7 N1—C3—H8 H6—C3—H8 H7—C3—H8 H10—O1W—H11 O4—C4—O3 O4—C4—C5 O3—C4—C5 O6—C5—O5 O6—C5—C4 O5—C5—C4 C4—O3—H9
105.9 (28) 107.1 (22) 110.1 (25) 111.0 (32) 110.9 (24) 108.3 (33) 109.3 (34) 99.3 (29) 125.5 (2) 121.3 (2) 113.2 (2) 128.0 (2) 117.8 (2) 114.2 (2) 113.2 (24)
O2—C1—C2—N1 O1—C1—C2—N1 C1—C2—N1—C3 O4—C4—C5—O6
5.7 (4) −176.5 (2) −168.4 (2) 167.2 (2)
O3—C4—C5—O6 O4—C4—C5—O5 O3—C4—C5—O5
−13.6 (3) −12.5 (3) 166.7 (2)
Hydrogen-bond geometry (Å, °) D—H···A O1—H1···O5 N1—H4···O4
i
D—H
H···A
D···A
D—H···A
1.03 (4)
1.51 (4)
2.525 (3)
172 (3)
0.89 (3)
2.15 (3)
2.948 (2)
148 (3)
sup-3
supplementary materials N1—H4···O5
0.89 (3)
2.23 (3)
2.875 (3)
127 (3)
N1—H5···O6
0.88 (3)
1.96 (3)
2.791 (3)
158 (3)
O3—H9···O1Wiii
0.87 (4)
1.72 (4)
2.574 (3)
168 (4)
0.88 (4) 1.91 (4) 2.782 (2) O1W—H10···O6iv Symmetry codes: (i) x−1/2, −y+1/2, z+1/2; (ii) x, y, z+1; (iii) x−1, y, z; (iv) −x+1/2, y−1/2, −z−1/2.
171 (3)
ii
sup-4
