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The title bis(glycyl-L-aspartic acid) oxalate complex {systematic name: bis[2-(2-ammonioacetamido)butanedioic acid] oxalate 0.4-hydrate}, 2C6H11N2O5+·C2O42−·4H2O, crystallizes in a triclinic space group with the planar peptide unit in a trans conformation. The asymmetric unit consists of two glycyl-L-aspartic acid molecules with positively charged amino groups and neutral carboxyl groups, and an oxalate dianion. The twist around the C—Cα bond indicates that both the peptide molecules adopt extended conformations, while the twist around the N—Cα bond shows that one has a folded and the other a semi-extended state. The present complex can be described as an inclusion compound with the dipeptide molecule as the host and the oxalate anion as the guest. The usual head-to-tail sequence of aggregation is not observed in this complex, as is also the case with the glycyl-L-aspartic acid dihydrate molecule. The study of aggregation and interaction patterns in binary systems is the first step towards understanding more complex phenomena. This further leads to results that are of general interest in bimolecular aggregation.
Supporting information
CCDC reference: 634884
Crystals of bis(glycyl-L-aspartic acid) oxalate were grown by slow evaporation from a saturated aqueous solution containing stoichiometric quantities of glycyl-L-aspartic acid and oxalic acid.
All H atoms were fixed using geometrical constraints and were considered as riding on the atoms to which they are attached, with C—H, N—H and O—H distances of 0.97–0.98, 0.86–0.89 and 0.82 Å, respectively. At this stage, the maximum difference density of 0.60 e Å−3 indicated the presence of a possible atom site. In addition, a check for solvent-accessible volume using PLATON (Spek, 2003) showed a void of 128 Å3. An attempt to refine this peak as a water atom with full occupancy resulted in a high Uiso value. An alternative strategy, the SQUEEZE function of PLATON (van der Sluis & Spek, 1990: Spek, 2003) was used to eliminate the contribution of the electron density in the solvent region form the intensity data. PLATON total Potential Solvent Area Vol 29.4 Å3 [please clarify meaning of this] estimated that the cavity contained four electrons, which is equivalent to one partially occupied solvent water molecule. The PLATON suite was used to generate the reflection file and the refinement was carried out using this file.
Data collection: SMART (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
bis[2-(2-ammonioacetamido)butanedioic acid] oxalate 0.4-hydrate
top
Crystal data top
2C6H11N2O5+·C2O42−·0.4H2O | Z = 1 |
Mr = 477.56 | F(000) = 246 |
Triclinic, P1 | Dx = 1.519 Mg m−3 |
Hall symbol: P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 4.8100 (8) Å | Cell parameters from 2081 reflections |
b = 10.7760 (18) Å | θ = 2.0–26.4° |
c = 10.8756 (18) Å | µ = 0.14 mm−1 |
α = 69.325 (3)° | T = 300 K |
β = 85.792 (3)° | Irregular, colourless |
γ = 81.946 (3)° | 0.24 × 0.19 × 0.13 mm |
V = 522.03 (15) Å3 | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1732 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.028 |
Graphite monochromator | θmax = 26.4°, θmin = 2.0° |
ϕ and ω scans | h = −6→5 |
5499 measured reflections | k = −13→13 |
2081 independent reflections | l = −13→13 |
Refinement top
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)] = 0.059 | Hydrogen site location: constr |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.11 | w = 1/[σ2(Fo2) + (0.0749P)2] where P = (Fo2 + 2Fc2)/3 |
2081 reflections | (Δ/σ)max < 0.001 |
297 parameters | Δρmax = 0.28 e Å−3 |
3 restraints | Δρmin = −0.19 e Å−3 |
Crystal data top
2C6H11N2O5+·C2O42−·0.4H2O | γ = 81.946 (3)° |
Mr = 477.56 | V = 522.03 (15) Å3 |
Triclinic, P1 | Z = 1 |
a = 4.8100 (8) Å | Mo Kα radiation |
b = 10.7760 (18) Å | µ = 0.14 mm−1 |
c = 10.8756 (18) Å | T = 300 K |
α = 69.325 (3)° | 0.24 × 0.19 × 0.13 mm |
β = 85.792 (3)° | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1732 reflections with I > 2σ(I) |
5499 measured reflections | Rint = 0.028 |
2081 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.059 | 3 restraints |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.11 | Δρmax = 0.28 e Å−3 |
2081 reflections | Δρmin = −0.19 e Å−3 |
297 parameters | |
Special details top
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles |
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O4 | 0.0104 (7) | 0.4777 (4) | 0.3705 (4) | 0.0488 (14) | |
O8 | 0.3237 (9) | 0.3465 (4) | 0.1545 (4) | 0.0510 (16) | |
O9 | 0.1254 (8) | 0.5107 (3) | −0.0168 (3) | 0.0446 (14) | |
O12 | 0.3319 (10) | 0.8424 (4) | 0.1311 (5) | 0.0655 (16) | |
O13 | 0.7000 (9) | 0.8660 (4) | −0.0103 (4) | 0.0596 (16) | |
N1 | 0.2079 (9) | 0.3927 (4) | 0.6125 (4) | 0.0378 (12) | |
N5 | 0.4292 (8) | 0.5234 (4) | 0.2696 (4) | 0.0316 (14) | |
C2 | 0.4128 (12) | 0.4195 (6) | 0.5026 (5) | 0.0431 (19) | |
C3 | 0.2647 (10) | 0.4768 (5) | 0.3739 (5) | 0.0299 (17) | |
C6 | 0.3133 (10) | 0.5768 (4) | 0.1387 (4) | 0.0268 (16) | |
C7 | 0.2577 (10) | 0.4624 (5) | 0.0941 (5) | 0.0297 (17) | |
C10 | 0.4976 (11) | 0.6692 (5) | 0.0415 (5) | 0.0343 (16) | |
C11 | 0.4956 (12) | 0.8009 (5) | 0.0618 (5) | 0.0389 (17) | |
O17 | 1.2525 (8) | 1.0291 (5) | 0.4262 (4) | 0.0607 (14) | |
O21 | 0.9577 (10) | 1.1712 (4) | 0.6203 (5) | 0.0697 (18) | |
O22 | 1.2008 (8) | 1.0048 (4) | 0.7744 (4) | 0.0521 (16) | |
O25 | 1.0426 (12) | 0.6538 (5) | 0.5892 (5) | 0.083 (2) | |
O26 | 0.7376 (8) | 0.6641 (4) | 0.7483 (4) | 0.0462 (12) | |
N14 | 1.0929 (9) | 1.1014 (4) | 0.1719 (4) | 0.0385 (16) | |
N18 | 0.8189 (8) | 0.9927 (4) | 0.5108 (4) | 0.0334 (14) | |
C15 | 0.8765 (13) | 1.0801 (8) | 0.2765 (6) | 0.056 (2) | |
C16 | 1.0034 (11) | 1.0304 (6) | 0.4127 (5) | 0.0421 (17) | |
C19 | 0.8926 (10) | 0.9466 (5) | 0.6496 (5) | 0.0345 (17) | |
C20 | 1.0259 (11) | 1.0540 (5) | 0.6792 (6) | 0.0389 (17) | |
C23 | 1.0769 (11) | 0.8122 (5) | 0.6907 (6) | 0.0427 (17) | |
C24 | 0.9524 (12) | 0.7022 (5) | 0.6697 (5) | 0.0407 (18) | |
O27 | 0.9036 (9) | 0.3279 (4) | 0.9456 (4) | 0.0545 (16) | |
O28 | 0.6271 (8) | 0.4250 (4) | 0.7740 (4) | 0.0453 (14) | |
O29 | 0.4371 (9) | 0.1874 (4) | 0.8223 (4) | 0.0577 (14) | |
O30 | 0.6904 (10) | 0.1015 (4) | 0.9994 (4) | 0.0590 (16) | |
C27 | 0.7228 (11) | 0.3286 (5) | 0.8712 (5) | 0.0337 (16) | |
C28 | 0.6043 (10) | 0.1932 (5) | 0.9011 (5) | 0.0320 (17) | |
H1A | 0.09197 | 0.33874 | 0.60422 | 0.0561* | |
H1B | 0.29750 | 0.35372 | 0.68790 | 0.0561* | |
H1C | 0.10981 | 0.46920 | 0.61220 | 0.0561* | |
H2A | 0.53017 | 0.33727 | 0.50696 | 0.0514* | |
H2B | 0.53291 | 0.48216 | 0.50888 | 0.0514* | |
H5 | 0.60558 | 0.52221 | 0.27902 | 0.0381* | |
H6 | 0.13203 | 0.62915 | 0.14414 | 0.0319* | |
H9 | 0.07579 | 0.44930 | −0.03446 | 0.0668* | |
H10A | 0.43572 | 0.68651 | −0.04660 | 0.0411* | |
H10B | 0.68876 | 0.62497 | 0.04792 | 0.0411* | |
H13 | 0.69884 | 0.93695 | 0.00181 | 0.0897* | |
H14A | 1.20442 | 1.15745 | 0.17949 | 0.0578* | |
H14B | 1.01185 | 1.13594 | 0.09411 | 0.0578* | |
H14C | 1.19416 | 1.02365 | 0.17852 | 0.0578* | |
H15A | 0.76179 | 1.01519 | 0.27090 | 0.0676* | |
H15B | 0.75576 | 1.16336 | 0.26421 | 0.0676* | |
H18 | 0.64690 | 0.99544 | 0.49228 | 0.0401* | |
H19 | 0.71716 | 0.93370 | 0.70172 | 0.0417* | |
H22 | 1.25466 | 1.06578 | 0.79121 | 0.0780* | |
H23A | 1.25417 | 0.82330 | 0.64180 | 0.0514* | |
H23B | 1.11704 | 0.78580 | 0.78316 | 0.0514* | |
H26 | 0.72258 | 0.58622 | 0.75844 | 0.0689* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O4 | 0.027 (2) | 0.075 (3) | 0.039 (2) | −0.0149 (19) | −0.0008 (17) | −0.010 (2) |
O8 | 0.064 (3) | 0.032 (2) | 0.057 (3) | −0.0070 (19) | −0.025 (2) | −0.0103 (19) |
O9 | 0.067 (3) | 0.0296 (19) | 0.041 (2) | −0.0147 (18) | −0.0257 (19) | −0.0088 (17) |
O12 | 0.082 (3) | 0.044 (2) | 0.083 (3) | −0.024 (2) | 0.022 (3) | −0.036 (2) |
O13 | 0.071 (3) | 0.044 (2) | 0.071 (3) | −0.034 (2) | 0.004 (2) | −0.020 (2) |
N1 | 0.043 (2) | 0.037 (2) | 0.036 (2) | −0.0133 (19) | −0.005 (2) | −0.012 (2) |
N5 | 0.019 (2) | 0.046 (3) | 0.033 (2) | −0.0090 (18) | −0.0089 (18) | −0.014 (2) |
C2 | 0.036 (3) | 0.059 (4) | 0.030 (3) | −0.009 (3) | −0.005 (2) | −0.008 (3) |
C3 | 0.026 (3) | 0.031 (3) | 0.031 (3) | −0.006 (2) | −0.005 (2) | −0.007 (2) |
C6 | 0.028 (3) | 0.023 (2) | 0.029 (3) | −0.0042 (19) | −0.0081 (19) | −0.0066 (19) |
C7 | 0.031 (3) | 0.025 (3) | 0.035 (3) | −0.013 (2) | −0.001 (2) | −0.009 (2) |
C10 | 0.042 (3) | 0.032 (3) | 0.029 (2) | −0.010 (2) | −0.010 (2) | −0.007 (2) |
C11 | 0.052 (3) | 0.030 (3) | 0.035 (3) | −0.014 (2) | −0.018 (3) | −0.005 (2) |
O17 | 0.031 (2) | 0.092 (3) | 0.043 (2) | −0.027 (2) | −0.0127 (18) | 0.006 (2) |
O21 | 0.087 (3) | 0.028 (2) | 0.096 (4) | −0.008 (2) | −0.046 (3) | −0.015 (2) |
O22 | 0.059 (3) | 0.040 (2) | 0.065 (3) | −0.0190 (19) | −0.026 (2) | −0.018 (2) |
O25 | 0.131 (5) | 0.050 (3) | 0.079 (3) | −0.036 (3) | 0.045 (3) | −0.035 (3) |
O26 | 0.055 (2) | 0.038 (2) | 0.055 (2) | −0.0221 (19) | 0.001 (2) | −0.0221 (19) |
N14 | 0.044 (3) | 0.033 (2) | 0.037 (3) | −0.0081 (19) | −0.016 (2) | −0.006 (2) |
N18 | 0.023 (2) | 0.036 (2) | 0.036 (3) | −0.0096 (17) | −0.0092 (19) | −0.0023 (19) |
C15 | 0.037 (3) | 0.078 (4) | 0.046 (4) | −0.017 (3) | −0.011 (3) | −0.007 (3) |
C16 | 0.033 (3) | 0.049 (3) | 0.041 (3) | −0.014 (2) | −0.012 (3) | −0.006 (3) |
C19 | 0.024 (3) | 0.035 (3) | 0.050 (3) | −0.009 (2) | −0.008 (2) | −0.018 (2) |
C20 | 0.034 (3) | 0.041 (3) | 0.051 (3) | −0.010 (2) | −0.009 (2) | −0.024 (3) |
C23 | 0.040 (3) | 0.035 (3) | 0.054 (3) | −0.011 (2) | −0.013 (2) | −0.012 (2) |
C24 | 0.063 (4) | 0.016 (2) | 0.040 (3) | −0.004 (2) | 0.002 (3) | −0.007 (2) |
O27 | 0.072 (3) | 0.036 (2) | 0.061 (3) | −0.025 (2) | −0.037 (2) | −0.010 (2) |
O28 | 0.065 (3) | 0.035 (2) | 0.038 (2) | −0.0283 (19) | −0.0119 (19) | −0.0047 (19) |
O29 | 0.081 (3) | 0.041 (2) | 0.054 (2) | −0.034 (2) | −0.028 (2) | −0.005 (2) |
O30 | 0.087 (3) | 0.031 (2) | 0.056 (3) | −0.027 (2) | −0.037 (2) | 0.003 (2) |
C27 | 0.043 (3) | 0.027 (2) | 0.036 (3) | −0.014 (2) | 0.003 (2) | −0.014 (2) |
C28 | 0.041 (3) | 0.034 (3) | 0.029 (3) | −0.021 (2) | −0.009 (2) | −0.013 (2) |
Geometric parameters (Å, º) top
O4—C3 | 1.225 (6) | N18—C19 | 1.467 (7) |
O8—C7 | 1.197 (7) | N18—C16 | 1.322 (7) |
O9—C7 | 1.307 (6) | N14—H14A | 0.8899 |
O12—C11 | 1.200 (7) | N14—H14C | 0.8903 |
O13—C11 | 1.329 (7) | N14—H14B | 0.8897 |
O9—H9 | 0.8199 | N18—H18 | 0.8598 |
O13—H13 | 0.8196 | C2—C3 | 1.504 (7) |
O17—C16 | 1.215 (7) | C6—C10 | 1.504 (7) |
O21—C20 | 1.207 (8) | C6—C7 | 1.536 (7) |
O22—C20 | 1.295 (7) | C10—C11 | 1.510 (8) |
O25—C24 | 1.196 (8) | C2—H2A | 0.9697 |
O26—C24 | 1.307 (7) | C2—H2B | 0.9706 |
O22—H22 | 0.8197 | C6—H6 | 0.9799 |
O26—H26 | 0.8199 | C10—H10A | 0.9703 |
O27—C27 | 1.228 (7) | C10—H10B | 0.9698 |
O28—C27 | 1.253 (7) | C15—C16 | 1.528 (8) |
O29—C28 | 1.240 (7) | C19—C23 | 1.525 (8) |
O30—C28 | 1.223 (7) | C19—C20 | 1.535 (8) |
N1—C2 | 1.465 (7) | C23—C24 | 1.492 (8) |
N5—C6 | 1.455 (6) | C15—H15A | 0.9698 |
N5—C3 | 1.320 (6) | C15—H15B | 0.9700 |
N1—H1C | 0.8897 | C19—H19 | 0.9797 |
N1—H1A | 0.8901 | C23—H23A | 0.9702 |
N1—H1B | 0.8902 | C23—H23B | 0.9698 |
N5—H5 | 0.8598 | C27—C28 | 1.559 (8) |
N14—C15 | 1.463 (8) | | |
| | | |
O4···N1 | 2.663 (6) | N14···O30iv | 2.793 (6) |
O4···N5i | 2.991 (5) | N14···O8vi | 2.947 (6) |
O4···C2i | 3.160 (7) | N14···O12v | 3.035 (7) |
O4···C7 | 3.201 (7) | N14···O17 | 2.733 (6) |
O8···N14ii | 2.947 (6) | N14···O27iv | 2.882 (6) |
O8···C3 | 3.146 (7) | N18···O21 | 2.767 (6) |
O8···O27iii | 3.224 (6) | N18···O17i | 2.870 (6) |
O8···N5 | 2.740 (6) | C2···O28 | 3.220 (7) |
O9···O26iii | 3.097 (5) | C2···O4v | 3.160 (7) |
O9···O27iii | 2.531 (6) | C2···O25i | 3.257 (9) |
O9···C24iii | 3.397 (6) | C3···O8 | 3.146 (7) |
O9···C10i | 3.388 (7) | C7···O4 | 3.201 (7) |
O12···N5 | 3.210 (7) | C7···O27iii | 3.218 (7) |
O12···N14i | 3.035 (7) | C10···O9v | 3.388 (7) |
O13···C28iv | 3.284 (7) | C10···O26xii | 3.327 (7) |
O13···O30iv | 2.571 (6) | C11···O22iii | 3.396 (7) |
O17···C23 | 3.146 (7) | C11···O30iv | 3.322 (7) |
O17···N14 | 2.733 (6) | C15···O17i | 3.328 (7) |
O17···C15v | 3.328 (7) | C15···O30iv | 3.128 (8) |
O17···O21 | 3.170 (7) | C16···O21 | 3.115 (8) |
O17···C20 | 2.972 (7) | C20···O17 | 2.972 (7) |
O17···N18v | 2.870 (6) | C20···O29vi | 3.351 (7) |
O21···N18 | 2.767 (6) | C23···O26v | 3.347 (7) |
O21···C16 | 3.115 (8) | C23···O17 | 3.146 (7) |
O21···N1vi | 2.793 (7) | C24···O28 | 3.364 (7) |
O21···O17 | 3.170 (7) | C24···O9viii | 3.397 (6) |
O21···O29vii | 3.235 (7) | C27···O26 | 3.392 (7) |
O22···C11viii | 3.396 (7) | C28···O13x | 3.284 (7) |
O22···O29vi | 2.622 (6) | C7···H10Bi | 3.0079 |
O25···N1v | 2.741 (7) | C11···H5 | 3.0997 |
O25···C2v | 3.257 (9) | C16···H23A | 2.8989 |
O26···C23i | 3.347 (7) | C20···H1Avi | 2.9409 |
O26···C10ix | 3.327 (7) | C24···H1Cv | 2.7884 |
O26···C27 | 3.392 (7) | C27···H9viii | 2.7284 |
O26···O28 | 2.618 (6) | C27···H14Bx | 2.8727 |
O26···O9viii | 3.097 (5) | C27···H1B | 2.8800 |
O27···N14x | 2.882 (6) | C27···H26 | 2.6088 |
O27···O8viii | 3.224 (6) | C28···H13x | 2.5724 |
O27···O30 | 2.636 (6) | C28···H1B | 2.7388 |
O27···C7viii | 3.218 (7) | C28···H22ii | 2.8710 |
O27···O9viii | 2.531 (6) | C28···H14Bx | 2.8249 |
O28···C2 | 3.220 (7) | H1A···O29 | 2.8511 |
O28···N1 | 2.902 (6) | H1A···O21ii | 1.9479 |
O28···N1v | 3.233 (6) | H1A···C20ii | 2.9409 |
O28···O26 | 2.618 (6) | H1A···O4 | 2.4802 |
O28···O29 | 2.702 (6) | H1B···C27 | 2.8800 |
O28···C24 | 3.364 (7) | H1B···C28 | 2.7388 |
O29···N1 | 2.727 (6) | H1B···O29 | 1.9382 |
O29···O28 | 2.702 (6) | H1B···O28 | 2.2466 |
O29···O21xi | 3.235 (7) | H1C···C24i | 2.7884 |
O29···O22ii | 2.622 (6) | H1C···O25i | 1.8986 |
O29···C20ii | 3.351 (7) | H1C···O28i | 2.7987 |
O30···O13x | 2.571 (6) | H1C···O4 | 2.6737 |
O30···N14x | 2.793 (6) | H2A···O21xi | 2.5950 |
O30···O27 | 2.636 (6) | H2B···O28 | 2.7853 |
O30···C11x | 3.322 (7) | H2B···O4v | 2.6561 |
O30···C15x | 3.128 (8) | H2B···H5 | 2.3896 |
O4···H6 | 2.5071 | H5···H2B | 2.3896 |
O4···H1A | 2.4802 | H5···C11 | 3.0997 |
O4···H1C | 2.6737 | H5···H10B | 2.3905 |
O4···H2Bi | 2.6561 | H5···O4v | 2.1673 |
O4···H5i | 2.1673 | H6···H10Bi | 2.4557 |
O8···H14Aii | 2.1135 | H6···O12 | 2.5679 |
O8···H15Bxi | 2.6813 | H6···O4 | 2.5071 |
O9···H10Bi | 2.4684 | H9···O27iii | 1.7247 |
O9···H10A | 2.4920 | H9···C27iii | 2.7284 |
O12···H14Ci | 2.1950 | H10A···H23Biii | 2.3410 |
O12···H6 | 2.5679 | H10A···O9 | 2.4920 |
O17···H23A | 2.5966 | H10A···O26xii | 2.6361 |
O17···H15Av | 2.8887 | H10B···H6v | 2.4557 |
O17···H18v | 2.0174 | H10B···H5 | 2.3905 |
O17···H14A | 2.5586 | H10B···O9v | 2.4684 |
O17···H14C | 2.7505 | H10B···C7v | 3.0079 |
O21···H2Avii | 2.5950 | H13···C28iv | 2.5724 |
O21···H1Avi | 1.9479 | H13···O30iv | 1.7589 |
O22···H19v | 2.6433 | H13···O29iv | 2.8928 |
O22···H23A | 2.7870 | H14A···O8vi | 2.1135 |
O22···H23B | 2.4172 | H14A···O27iv | 2.9041 |
O25···H1Cv | 1.8986 | H14A···O17 | 2.5586 |
O26···H10Aix | 2.6361 | H14B···O30iv | 2.0625 |
O26···H23Ai | 2.7506 | H14B···O27iv | 2.1497 |
O26···H19 | 2.7558 | H14B···C28iv | 2.8249 |
O27···H14Ax | 2.9041 | H14B···C27iv | 2.8727 |
O27···H14Bx | 2.1497 | H14C···O12v | 2.1950 |
O27···H26 | 2.8688 | H14C···O17 | 2.7505 |
O27···H9viii | 1.7247 | H15A···H18 | 2.3713 |
O28···H26 | 1.8062 | H15A···O30iv | 2.7967 |
O28···H1B | 2.2466 | H15A···O17i | 2.8887 |
O28···H2B | 2.7853 | H15B···O8vii | 2.6813 |
O28···H1Cv | 2.7987 | H15B···H18 | 2.5703 |
O29···H1B | 1.9382 | H18···O17i | 2.0174 |
O29···H13x | 2.8928 | H18···H15A | 2.3713 |
O29···H1A | 2.8511 | H18···H15B | 2.5703 |
O29···H22ii | 1.8113 | H19···O22i | 2.6433 |
O30···H15Ax | 2.7967 | H19···O26 | 2.7558 |
O30···H14Bx | 2.0625 | H22···O29vi | 1.8113 |
O30···H13x | 1.7589 | H22···C28vi | 2.8710 |
N1···O21ii | 2.793 (7) | H23A···O17 | 2.5966 |
N1···O4 | 2.663 (6) | H23A···O22 | 2.7870 |
N1···O25i | 2.741 (7) | H23A···O26v | 2.7506 |
N1···O28i | 3.233 (6) | H23A···C16 | 2.8989 |
N1···O28 | 2.902 (6) | H23B···O22 | 2.4172 |
N1···O29 | 2.727 (6) | H23B···H10Aviii | 2.3410 |
N5···O4v | 2.991 (5) | H26···O27 | 2.8688 |
N5···O8 | 2.740 (6) | H26···O28 | 1.8062 |
N5···O12 | 3.210 (7) | H26···C27 | 2.6088 |
| | | |
C7—O9—H9 | 109.48 | C7—C6—H6 | 107.55 |
C11—O13—H13 | 109.48 | N5—C6—H6 | 107.52 |
C20—O22—H22 | 109.49 | C10—C6—H6 | 107.52 |
C24—O26—H26 | 109.46 | C6—C10—H10B | 108.86 |
C3—N5—C6 | 120.3 (4) | C11—C10—H10A | 108.84 |
C2—N1—H1A | 109.44 | C11—C10—H10B | 108.87 |
C2—N1—H1B | 109.48 | H10A—C10—H10B | 107.69 |
C2—N1—H1C | 109.51 | C6—C10—H10A | 108.82 |
H1A—N1—H1B | 109.43 | N14—C15—C16 | 111.9 (5) |
H1A—N1—H1C | 109.49 | O17—C16—C15 | 121.4 (5) |
H1B—N1—H1C | 109.48 | O17—C16—N18 | 124.5 (5) |
C3—N5—H5 | 119.89 | N18—C16—C15 | 114.1 (5) |
C6—N5—H5 | 119.84 | N18—C19—C23 | 111.9 (4) |
C16—N18—C19 | 123.3 (4) | N18—C19—C20 | 110.6 (4) |
C15—N14—H14C | 109.44 | C20—C19—C23 | 112.4 (4) |
H14B—N14—H14C | 109.47 | O22—C20—C19 | 113.1 (5) |
H14A—N14—H14B | 109.51 | O21—C20—C19 | 120.8 (5) |
C15—N14—H14B | 109.47 | O21—C20—O22 | 126.0 (6) |
C15—N14—H14A | 109.48 | C19—C23—C24 | 114.8 (5) |
H14A—N14—H14C | 109.46 | O25—C24—O26 | 123.8 (6) |
C19—N18—H18 | 118.35 | O25—C24—C23 | 122.9 (6) |
C16—N18—H18 | 118.32 | O26—C24—C23 | 113.3 (5) |
N1—C2—C3 | 110.3 (4) | N14—C15—H15A | 109.26 |
N5—C3—C2 | 114.9 (4) | N14—C15—H15B | 109.23 |
O4—C3—C2 | 120.6 (5) | C16—C15—H15A | 109.22 |
O4—C3—N5 | 124.5 (5) | C16—C15—H15B | 109.20 |
N5—C6—C7 | 110.3 (4) | H15A—C15—H15B | 107.94 |
C7—C6—C10 | 111.9 (4) | N18—C19—H19 | 107.21 |
N5—C6—C10 | 111.8 (4) | C20—C19—H19 | 107.26 |
O9—C7—C6 | 110.0 (4) | C23—C19—H19 | 107.21 |
O8—C7—O9 | 125.9 (5) | C19—C23—H23A | 108.57 |
O8—C7—C6 | 124.1 (5) | C19—C23—H23B | 108.57 |
C6—C10—C11 | 113.6 (4) | C24—C23—H23A | 108.55 |
O12—C11—C10 | 125.4 (5) | C24—C23—H23B | 108.60 |
O13—C11—C10 | 110.0 (5) | H23A—C23—H23B | 107.55 |
O12—C11—O13 | 124.6 (5) | O27—C27—O28 | 127.3 (5) |
N1—C2—H2A | 109.62 | O27—C27—C28 | 115.7 (5) |
C3—C2—H2B | 109.59 | O28—C27—C28 | 117.1 (5) |
N1—C2—H2B | 109.54 | O29—C28—O30 | 126.1 (5) |
C3—C2—H2A | 109.66 | O29—C28—C27 | 117.4 (5) |
H2A—C2—H2B | 108.11 | O30—C28—C27 | 116.4 (5) |
| | | |
C6—N5—C3—C2 | 177.6 (5) | C6—C10—C11—O13 | 168.3 (4) |
C3—N5—C6—C10 | 158.4 (5) | C6—C10—C11—O12 | −12.7 (8) |
C3—N5—C6—C7 | −76.3 (6) | N14—C15—C16—O17 | 9.8 (10) |
C6—N5—C3—O4 | −2.1 (8) | N14—C15—C16—N18 | −171.4 (6) |
C19—N18—C16—C15 | −177.5 (6) | N18—C19—C20—O22 | −151.3 (5) |
C19—N18—C16—O17 | 1.2 (10) | C23—C19—C20—O21 | 157.5 (5) |
C16—N18—C19—C20 | 57.7 (7) | N18—C19—C20—O21 | 31.6 (7) |
C16—N18—C19—C23 | −68.4 (7) | N18—C19—C23—C24 | −57.5 (6) |
N1—C2—C3—O4 | −10.2 (8) | C23—C19—C20—O22 | −25.4 (7) |
N1—C2—C3—N5 | 170.1 (5) | C20—C19—C23—C24 | 177.4 (5) |
C10—C6—C7—O9 | −61.8 (5) | C19—C23—C24—O25 | 111.2 (7) |
C10—C6—C7—O8 | 119.2 (6) | C19—C23—C24—O26 | −69.2 (6) |
N5—C6—C7—O8 | −5.9 (7) | O27—C27—C28—O29 | −174.7 (5) |
C7—C6—C10—C11 | 164.7 (4) | O27—C27—C28—O30 | 3.9 (7) |
N5—C6—C7—O9 | 173.0 (4) | O28—C27—C28—O29 | 4.5 (7) |
N5—C6—C10—C11 | −71.0 (5) | O28—C27—C28—O30 | −177.0 (5) |
Symmetry codes: (i) x−1, y, z; (ii) x−1, y−1, z; (iii) x−1, y, z−1; (iv) x, y+1, z−1; (v) x+1, y, z; (vi) x+1, y+1, z; (vii) x, y+1, z; (viii) x+1, y, z+1; (ix) x, y, z+1; (x) x, y−1, z+1; (xi) x, y−1, z; (xii) x, y, z−1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O21ii | 0.89 | 1.95 | 2.793 (7) | 158 |
N1—H1B···O28 | 0.89 | 2.25 | 2.902 (6) | 130 |
N1—H1B···O29 | 0.89 | 1.94 | 2.727 (6) | 147 |
N1—H1C···O25i | 0.89 | 1.90 | 2.741 (7) | 157 |
N5—H5···O4v | 0.86 | 2.170 | 2.991 (5) | 160 |
O9—H9···O27iii | 0.82 | 1.72 | 2.531 (6) | 167 |
O13—H13···O30iv | 0.82 | 1.76 | 2.571 (6) | 170 |
N14—H14A···O8vi | 0.89 | 2.11 | 2.947 (6) | 156 |
N14—H14B···O27iv | 0.89 | 2.15 | 2.882 (6) | 139 |
N14—H14B···O30iv | 0.89 | 2.06 | 2.793 (6) | 139 |
N14—H14C···O12v | 0.89 | 2.20 | 3.035 (7) | 157 |
N18—H18···O17i | 0.86 | 2.02 | 2.870 (6) | 171 |
O22—H22···O29vi | 0.82 | 1.81 | 2.622 (6) | 170 |
O26—H26···O28 | 0.82 | 1.81 | 2.618 (6) | 170 |
C2—H2A···O21xi | 0.97 | 2.59 | 3.432 (8) | 145 |
C10—H10B···O9v | 0.97 | 2.47 | 3.388 (7) | 158 |
Symmetry codes: (i) x−1, y, z; (ii) x−1, y−1, z; (iii) x−1, y, z−1; (iv) x, y+1, z−1; (v) x+1, y, z; (vi) x+1, y+1, z; (xi) x, y−1, z. |
Experimental details
Crystal data |
Chemical formula | 2C6H11N2O5+·C2O42−·0.4H2O |
Mr | 477.56 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 300 |
a, b, c (Å) | 4.8100 (8), 10.7760 (18), 10.8756 (18) |
α, β, γ (°) | 69.325 (3), 85.792 (3), 81.946 (3) |
V (Å3) | 522.03 (15) |
Z | 1 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.24 × 0.19 × 0.13 |
|
Data collection |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5499, 2081, 1732 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.625 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.059, 0.133, 1.11 |
No. of reflections | 2081 |
No. of parameters | 297 |
No. of restraints | 3 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.28, −0.19 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O21i | 0.89 | 1.95 | 2.793 (7) | 158 |
N1—H1B···O28 | 0.89 | 2.25 | 2.902 (6) | 130 |
N1—H1B···O29 | 0.89 | 1.94 | 2.727 (6) | 147 |
N1—H1C···O25ii | 0.89 | 1.90 | 2.741 (7) | 157 |
N5—H5···O4iii | 0.86 | 2.170 | 2.991 (5) | 160 |
O9—H9···O27iv | 0.82 | 1.72 | 2.531 (6) | 167 |
O13—H13···O30v | 0.82 | 1.76 | 2.571 (6) | 170 |
N14—H14A···O8vi | 0.89 | 2.11 | 2.947 (6) | 156 |
N14—H14B···O27v | 0.89 | 2.15 | 2.882 (6) | 139 |
N14—H14B···O30v | 0.89 | 2.06 | 2.793 (6) | 139 |
N14—H14C···O12iii | 0.89 | 2.20 | 3.035 (7) | 157 |
N18—H18···O17ii | 0.86 | 2.02 | 2.870 (6) | 171 |
O22—H22···O29vi | 0.82 | 1.81 | 2.622 (6) | 170 |
O26—H26···O28 | 0.82 | 1.81 | 2.618 (6) | 170 |
C2—H2A···O21vii | 0.97 | 2.59 | 3.432 (8) | 145 |
C10—H10B···O9iii | 0.97 | 2.47 | 3.388 (7) | 158 |
Symmetry codes: (i) x−1, y−1, z; (ii) x−1, y, z; (iii) x+1, y, z; (iv) x−1, y, z−1; (v) x, y+1, z−1; (vi) x+1, y+1, z; (vii) x, y−1, z. |
1. Comparision of the torsion angles between bis(glycyl-L aspartic acid) oxalate and glycyl-L-aspartic acid dihydrate topAtoms | bis (glycyl-L aspartic acid) oxalate | | Glycyl-L aspartic acid |
| Torsion angles (°) | | Torsion angles(°) |
| Molecule 1 | Molecule 2 | |
N1-C2-C3-N5(ψ) | 170.1 (5) | -171.4 (6) | -164.40 |
C2-C3-N5-C6(ω) | 177.6 (5) | -177.5 (6) | -175.90 |
C3-N5-C6-C7 (ϕ) | -76.3 (6) | 57.7 (7) | -133.24 |
N5-C6-C10-C11(ψ1) | -71.0 (5) | -57.5 (6) | 56.43 |
'N5-C6-C7-O8(ψ2') ' | -5.9 (7) | 31.6 (7) | 1.04 |
'N5-C6-C7-O9(ψ2'') ' | 173.0 (4) | -151.3 (5) | -179.46 |
C7-C6-C10-C11(ψ2) | 164.7 (4) | 177.4 (5) | -68.02 |
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X-ray analysis of complexes of amino acids and peptides among themselves as well as with relevant molecules helps in understanding the geometrical features of elementary patterns of these complexes (Vijayan, 1988). The aggregation pattern of biological molecules largely depends on the non-covalent interactions. In these complexes there is always an extensive network of hydrogen bonds. The aggregation pattern can divulge information relating to chemical evolution and the origin of life. In addition, structural and conformational studies of peptides that contain acidic residues have shown that these compounds are implicated in the binding of calcium and similar metals to proteins (Wasserman et al., 1977). It has been observed that these residues are involved in the complexation of calcium in all calcium proteins of known structure (Kretsinger & Nelson, 1976). Most of the calcium-specific site sequences contain glycine adjacent to one or more of the coordinating acid peptide residues (Potter et al., 1977). The acidic side chain of these peptides offers unique possibilities of hydrogen bonding, which may result in unusual conformational properties. The crystal structure of the peptide glycyl-L-aspartic acid has been determined using single-crystal X-ray diffraction (Eggleston & Hodgson, 1982: Pichon-Pesme et al., 2000). Oxalic acid is the simplest dicarboxylic acid and it can, in principle, exist in three ionization states, viz. singly charged (semi-oxalate), doubly charged (oxalate) and neutral (oxalic acid). Oxalic acid has also been complexed with the peptides glycyl glycine (Ejsmont et al., 2003), glycyl-L-histidine and L-histidyl-L-alanine (Manoj & Vijayan, 2000). We present here the crystal structure of a bis(glycyl-L-aspartic acid) oxalate complex, (I), solved using single-crystal X-ray diffraction. Using the Cambridge Structural Database (CSD; update 5.26 of November 2004; Allen, 2002) an analysis of geometry in the salts of the peptide and oxalic acid has been carried out.
A displacement ellipsoid representation of the complex is given in Fig. 1. The asymmetric unit consists of two glycyl-L-aspartic acid molecules with positively charged amino groups and neutral carboxyl groups, and an oxalate ion, which is doubly negatively charged. A comparison of the bond parameters of the peptide unit in the complex and in the pure structure showed that only the bond parameters involving the main chain COOH group differ, as a result of the zwitterionic nature of the pure glycyl-L-aspartic acid. The peptide plane is defined by atoms C1, C2, O1, N2 and H6 for the first molecule and C7, C8, O6, N4 and H17 for the second molecule of peptide. The maximum deviations from the least-squares plane through these atoms occur for C3 [−0.023 (3) Å] and C7 [0.022 (4) Å].
The torsion angles of the two molecules of (I) and that of glycyl-L-aspartic acid are compared in Table 3. The planarity of the peptide unit is defined by the torsion angle ω, which characterizes the rotation around the C—N peptide bond. An ω value of 180° corresponds to a planar peptide unit (trans conformation). In the present complex the deviation of ω (C1—C2—N2—C3 and C7—C8—N4—C9) for both the peptide residues is about 3°, and hence they adopt trans conformations. The full conformation of a peptide chain is described by two additional torsion angles, ψ and ϕ, which characterize the twist around the C—Cα and N—Cα bonds, respectively (Suresh & Vijayan, 1985; Vijayan, 1988). The ψ angle around C—Cα is also extended in the present structure, which is also true for pure glycyl-L-aspartic acid molecule. As a rough guide, the confirmation may be considered as extended if the magnitude of ϕ is between 60 and 180°; otherwise it may be considered folded. According to this guide, one of the peptide molecules (molecule 2) is in a folded state and the other (molecule 1) is in a semi-extended state in the complex, unlike the molecule of pure glycyl-L-aspartic acid, which is extended, having a value of −133.3°. The aspartic acid residue has ψ1 of around 60° with the side chain trans to the carboxyl group in both the peptide molecules, unlike the case in pure glycyl-L-aspartic acid, which has a side chain having a cis conformation to the carboxyl group.
Comparison of the oxalate bond parameters for the three above-mentioned peptide–oxalate complexes shows that in all cases, with the exception of glycyl-L-histidine oxalate, the oxalate unit exists as doubly ionized oxalate anion. The stochiometery in the case of the present complex and bis(glycyl glycinium) oxalate is 2:1. The other two have 1:1 stochiometery. In all the complexes the oxalate ion is essentially planar, the O—C—C—O torsion angle having deviation of around 6° from planarity. Table 2 gives the hydrogen-bonding parameters in the present complex. The peptide molecule has a number of potential H-atom donors and acceptors in the structures. As observed previously (Eggleston & Hodgson, 1982) and in the present complex, intramolecular hydrogen bonding is absent. An arrangement in which the terminal amino group and the carboxylate group are brought into periodic hydrogen-bonded proximity is called a head-to-tail sequence. In the present complex, the terminal amine groups (i.e. N3/H12 and N1/H3) are hydrogen bonded to atoms O4 and O9 respectively, which are the main-chain alpha carboxyl O atoms. However, the arrangement is not the usual head-to-tail arrangement. Rather the two molecules are related by a pseudo-inversion center. It is also seen that the amine N atoms of each peptide molecule (N3—H14 and N1—H1) are hydrogen bonded to atoms O3 and O8, respectively, which are the side-chain carboxyl O atoms. Amine atoms H2 and H13 also form bifurcated hydrogen bonds to the oxalate O atoms (O13/O12 and O14/O11, respectively). The O-bound H atoms of the carboxyl groups of the main chain and the side chain act as hydrogen-bond donors to the oxalate O atom. Each oxalate O atom, in turn, acts as an acceptor of two hydrogen bonds (one to the amino N atom and the other to the OH group of the carboxyl group). Another interesting observation is that the peptide N atom forms a hydrogen bond to the peptide carbonyl (i.e. N2—H6···O1iii and N4—H17···O6i; Table 2) of the same molecule but in different asymmetric unit resulting in an S5–4 (Vijayan, 1988) sequence. Adjacent molecules are parallel. A hydrogen bond between the peptide N atom and the peptide carbonyl group is also observed in the pure glycyl-L-aspartic acid, bis(glycyl-L-histidine) oxalate and glycyl-L-histidine–oxalic acid complexes, but the same is not true for the L-histidyl-L-alanine complex. Hence it can be said that this might be due to the fact that the glycyl residue occupying the amine terminal position does not cause steric hindrance to allow this type of hydrogen bond to be formed in these kind of complexes. Of course, a systematic study of complexes of oxalic acid with peptides involving a glycyl residue at the amine terminal position is required to prove this point. In terms of graph-set notation (Bernstein et al., 1995), the largest motif has the first-level graph set N1 = DDD, the binary level being R24 (22). The next level graph set is N1 = DD, the binary level being R21 (5) and C4. The dipeptide and oxalate molecules are arranged parallel to the ab plane. Fig. 2 shows the packing as viewed down the crystallographic a axis. It is observed that the dipeptide molecules are stacked in such a way that the oxalate molecules are enclosed in the voids created during stacking. The present complex can be described as an inclusion compound with the dipeptide molecule as the host and the oxalate as the guest.