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Single-crystal X-ray diffraction and quantum mechanical theories were used to examine in detail the subtle nature of non-covalent interactions in the [2:1:1] multicomponent crystal of 1,1-aminocyclopentanecarboxylic acid:oxalic acid:water. The crystal, which is a hydrate salt of the amino acid with the hydrogen-oxalate ion, also contains the zwitterion of the amino acid in equal proportions. It was found that a dimeric cation [Acc5(Z)
Acc5(C)]
+ bonded by an O—H
O hydrogen bond exists due to a charge transfer between acid and carboxylate groups. The three-dimensional crystal is built by blocks stacked along the [101] direction by dispersion interactions, with each block growing along two directions: a hydrogen oxalate HOX
−HOX
− catameric supramolecular structure along the [010] direction; and double
HOX
−—
W—[Acc5(Z)
Acc5(C)]
+ chains related by inversion centers along the
direction. A PBE-DFT optimization, under periodic boundary conditions, was carried out. The fully optimized structure obtained was used to extract the coordinates to calculate the stabilization energy between the dimers under the crystal field, employing the M062X/aug-cc-pVTZ level of theory. The non-covalent index isosurfaces employed here allow the visualization of where the hydrogen bond and dispersion interactions contribute within the crystal. The crystal atomic arrangements are analyzed by employing the Atoms in Molecules and electron localization function theories. Within this context, the presence of density bond critical points is employed as a criterion for proving the existence of the hydrogen bond and it was found that these results agree with those rendered by the crystallographic geometrical analysis, with only three exceptions, for which bond critical points were not found.
Supporting information
CCDC reference: 1568826
Data collection: CrystalClear (Rigaku/MSC Inc., 2000); cell refinement: CrystalClear (Rigaku/MSC Inc., 2000); data reduction: CrystalStructure 3.6.0 (Rigaku/MSC Inc., 2004); program(s) used to solve structure: SHELXS2016/6 (Sheldrick, 2016); program(s) used to refine structure: SHELXL2016/6 (Sheldrick, 2016); molecular graphics: DIAMOND (Brandenburg & Putz, 2006); software used to prepare material for publication: SHELXL2016/6 (Sheldrick, 2016).
Crystal data top
C14H26N2O9 | F(000) = 784 |
Mr = 366.37 | Dx = 1.393 Mg m−3 Dm = 1.393 Mg m−3 Dm measured by not measured |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.7107 Å |
a = 17.283 (3) Å | Cell parameters from 19530 reflections |
b = 5.7371 (8) Å | θ = 1.4–28.1° |
c = 18.561 (3) Å | µ = 0.12 mm−1 |
β = 108.274 (4)° | T = 291 K |
V = 1747.5 (5) Å3 | Rectangular, colourless |
Z = 4 | 0.30 × 0.20 × 0.15 mm |
Data collection top
RIGAKU AFC7S Mercury diffractometer | 3558 independent reflections |
Radiation source: normal-focus sealed tube | 2320 reflections with I > 2σ(I) |
Detector resolution: 14.6306 pixels mm-1 | Rint = 0.062 |
ω scans | θmax = 28.1°, θmin = 1.4° |
Absorption correction: multi-scan Jacobson, R. (1998) | h = −20→20 |
Tmin = 0.937, Tmax = 0.948 | k = −7→5 |
19530 measured reflections | l = −22→22 |
Refinement top
Refinement on F2 | 88 restraints |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.062 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.164 | w = 1/[σ2(Fo2) + (0.0662P)2 + 0.7567P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max < 0.001 |
3558 reflections | Δρmax = 0.29 e Å−3 |
312 parameters | Δρmin = −0.29 e Å−3 |
Special details top
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | Occ. (<1) |
N1 | 0.71589 (14) | 0.4390 (4) | 0.35067 (15) | 0.0375 (5) | |
H11 | 0.706 (2) | 0.367 (6) | 0.302 (2) | 0.071 (10)* | |
H12 | 0.6919 (19) | 0.590 (6) | 0.3442 (17) | 0.062 (9)* | |
H13 | 0.6902 (18) | 0.374 (5) | 0.3777 (17) | 0.048 (9)* | |
O2 | 0.79780 (12) | 0.7041 (3) | 0.28638 (11) | 0.0531 (5) | |
O1 | 0.91798 (13) | 0.6401 (4) | 0.37413 (13) | 0.0684 (7) | |
H1 | 0.950 (3) | 0.763 (8) | 0.346 (3) | 0.127 (15)* | |
C1 | 0.84098 (17) | 0.6130 (5) | 0.34402 (16) | 0.0413 (7) | |
C2 | 0.80528 (15) | 0.4531 (4) | 0.39079 (14) | 0.0349 (6) | |
C3 | 0.84390 (18) | 0.2095 (5) | 0.40022 (17) | 0.0509 (8) | |
H3A | 0.803089 | 0.090831 | 0.397460 | 0.061* | |
H3B | 0.868400 | 0.179987 | 0.360702 | 0.061* | |
C4 | 0.9083 (5) | 0.2074 (15) | 0.4776 (4) | 0.061 (2) | 0.678 (18) |
H4A | 0.958 (2) | 0.289 (4) | 0.4774 (4) | 0.074* | 0.678 (18) |
H4B | 0.9219 (8) | 0.049 (7) | 0.4970 (9) | 0.074* | 0.678 (18) |
C5 | 0.8611 (6) | 0.3424 (19) | 0.5223 (6) | 0.073 (3) | 0.678 (18) |
H5A | 0.820 (2) | 0.242 (5) | 0.5328 (7) | 0.088* | 0.678 (18) |
H5B | 0.8982 (16) | 0.399 (3) | 0.571 (2) | 0.088* | 0.678 (18) |
C4B | 0.8718 (18) | 0.180 (3) | 0.4868 (7) | 0.079 (6) | 0.322 (18) |
H4B1 | 0.830 (5) | 0.100 (9) | 0.5015 (16) | 0.095* | 0.322 (18) |
H4B2 | 0.920 (5) | 0.086 (10) | 0.5022 (17) | 0.095* | 0.322 (18) |
C5B | 0.8889 (14) | 0.413 (3) | 0.5265 (13) | 0.074 (6) | 0.322 (18) |
H5B1 | 0.8834 (13) | 0.407 (3) | 0.584 (5) | 0.089* | 0.322 (18) |
H5B2 | 0.949 (5) | 0.482 (7) | 0.5290 (13) | 0.089* | 0.322 (18) |
C6 | 0.82099 (19) | 0.5444 (5) | 0.47241 (15) | 0.0491 (7) | |
H6A | 0.856654 | 0.679165 | 0.481995 | 0.059* | |
H6B | 0.770278 | 0.586859 | 0.481004 | 0.059* | |
N2 | 1.01369 (17) | 1.0784 (5) | 0.14719 (14) | 0.0463 (6) | |
H21 | 0.966 (2) | 1.192 (6) | 0.1395 (19) | 0.074 (10)* | |
H22 | 0.996 (3) | 0.939 (8) | 0.127 (2) | 0.109 (15)* | |
H23 | 1.047 (2) | 1.130 (5) | 0.1202 (18) | 0.062 (9)* | |
O3 | 0.94629 (12) | 0.7709 (3) | 0.20984 (12) | 0.0509 (5) | |
O4 | 0.99939 (14) | 0.9130 (4) | 0.32631 (12) | 0.0673 (7) | |
C7 | 0.99324 (16) | 0.8976 (4) | 0.25728 (16) | 0.0398 (6) | |
C8 | 1.05297 (15) | 1.0480 (4) | 0.23084 (14) | 0.0373 (6) | |
C9 | 1.07420 (18) | 1.2831 (5) | 0.27099 (17) | 0.0482 (7) | |
H9A | 1.065199 | 1.407492 | 0.233892 | 0.058* | |
H9B | 1.039890 | 1.311083 | 0.302640 | 0.058* | |
C10 | 1.1632 (7) | 1.278 (3) | 0.3195 (11) | 0.080 (5) | 0.52 (2) |
H10A | 1.1678 (8) | 1.311 (4) | 0.361 (3) | 0.096* | 0.52 (2) |
H10B | 1.189 (2) | 1.365 (7) | 0.3039 (17) | 0.096* | 0.52 (2) |
C11 | 1.1916 (8) | 1.028 (3) | 0.3147 (9) | 0.077 (4) | 0.48 (2) |
H11A | 1.242 (4) | 1.028 (3) | 0.3110 (9) | 0.092* | 0.48 (2) |
H11B | 1.1922 (8) | 0.949 (6) | 0.356 (3) | 0.092* | 0.48 (2) |
C10B | 1.1578 (9) | 1.240 (4) | 0.3264 (12) | 0.087 (6) | 0.48 (2) |
H10C | 1.1543 (9) | 1.135 (8) | 0.378 (3) | 0.104* | 0.48 (2) |
H10D | 1.192 (2) | 1.413 (11) | 0.3469 (17) | 0.104* | 0.48 (2) |
C11B | 1.1989 (4) | 1.1000 (17) | 0.2783 (9) | 0.058 (3) | 0.52 (2) |
H11C | 1.2084 (7) | 1.195 (5) | 0.238 (2) | 0.070* | 0.52 (2) |
H11D | 1.250 (3) | 1.031 (4) | 0.3093 (17) | 0.070* | 0.52 (2) |
C12 | 1.13470 (17) | 0.9188 (5) | 0.24734 (19) | 0.0524 (8) | |
H12A | 1.127897 | 0.754947 | 0.256729 | 0.063* | |
H12B | 1.155128 | 0.931891 | 0.204429 | 0.063* | |
C13 | 0.60324 (16) | −0.0480 (4) | 0.54309 (15) | 0.0382 (6) | |
C14 | 0.62234 (16) | 0.1935 (4) | 0.51573 (16) | 0.0399 (6) | |
O5 | 0.63155 (14) | −0.2189 (3) | 0.51124 (12) | 0.0544 (6) | |
H55 | 0.621 (2) | −0.349 (6) | 0.5271 (19) | 0.067 (10)* | |
O6 | 0.56691 (13) | −0.0716 (3) | 0.58792 (11) | 0.0520 (5) | |
O7 | 0.60949 (14) | 0.3630 (3) | 0.55320 (12) | 0.0596 (6) | |
O8 | 0.64709 (14) | 0.2030 (3) | 0.46069 (12) | 0.0559 (6) | |
O1W | 0.37498 (14) | 0.1441 (4) | 0.65001 (14) | 0.0499 (5) | |
H2W | 0.397 (3) | 0.035 (8) | 0.682 (2) | 0.106 (16)* | |
H1W | 0.363 (2) | 0.064 (7) | 0.607 (2) | 0.095 (14)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0368 (14) | 0.0379 (14) | 0.0417 (14) | −0.0034 (10) | 0.0177 (11) | −0.0011 (11) |
O2 | 0.0491 (13) | 0.0630 (13) | 0.0456 (12) | −0.0036 (10) | 0.0125 (10) | 0.0179 (10) |
O1 | 0.0377 (13) | 0.0950 (17) | 0.0679 (15) | −0.0131 (11) | 0.0101 (11) | 0.0324 (13) |
C1 | 0.0392 (17) | 0.0408 (15) | 0.0451 (17) | −0.0018 (12) | 0.0148 (14) | 0.0043 (12) |
C2 | 0.0348 (15) | 0.0337 (13) | 0.0365 (14) | −0.0015 (10) | 0.0115 (11) | 0.0022 (10) |
C3 | 0.0511 (18) | 0.0391 (16) | 0.063 (2) | 0.0043 (13) | 0.0193 (16) | 0.0035 (13) |
C4 | 0.043 (4) | 0.052 (3) | 0.080 (4) | 0.006 (3) | 0.006 (3) | 0.014 (3) |
C5 | 0.074 (6) | 0.092 (6) | 0.038 (4) | 0.005 (4) | −0.007 (4) | 0.005 (4) |
C4B | 0.093 (14) | 0.060 (8) | 0.060 (9) | 0.026 (9) | −0.009 (9) | 0.008 (6) |
C5B | 0.056 (10) | 0.083 (10) | 0.059 (8) | 0.020 (8) | −0.019 (8) | −0.023 (8) |
C6 | 0.0579 (19) | 0.0511 (17) | 0.0379 (16) | −0.0066 (14) | 0.0146 (14) | −0.0036 (13) |
N2 | 0.0533 (17) | 0.0464 (15) | 0.0446 (15) | −0.0053 (13) | 0.0231 (13) | 0.0013 (11) |
O3 | 0.0444 (12) | 0.0472 (11) | 0.0598 (13) | −0.0130 (9) | 0.0145 (10) | −0.0049 (9) |
O4 | 0.0663 (15) | 0.0935 (17) | 0.0427 (13) | −0.0334 (12) | 0.0178 (11) | 0.0037 (11) |
C7 | 0.0345 (15) | 0.0387 (15) | 0.0459 (17) | 0.0005 (12) | 0.0120 (13) | 0.0070 (12) |
C8 | 0.0368 (15) | 0.0358 (14) | 0.0413 (15) | −0.0019 (11) | 0.0153 (12) | 0.0007 (11) |
C9 | 0.0548 (19) | 0.0361 (15) | 0.0562 (19) | −0.0041 (13) | 0.0210 (15) | −0.0032 (13) |
C10 | 0.050 (7) | 0.069 (9) | 0.100 (10) | −0.003 (5) | −0.006 (6) | −0.018 (6) |
C11 | 0.058 (5) | 0.084 (7) | 0.077 (7) | 0.012 (5) | 0.004 (5) | 0.004 (6) |
C10B | 0.105 (12) | 0.050 (7) | 0.087 (9) | −0.016 (6) | 0.002 (8) | −0.039 (7) |
C11B | 0.031 (4) | 0.055 (5) | 0.082 (7) | −0.007 (3) | 0.007 (4) | 0.002 (4) |
C12 | 0.0382 (17) | 0.0465 (17) | 0.074 (2) | 0.0005 (12) | 0.0196 (16) | −0.0058 (14) |
C13 | 0.0419 (16) | 0.0360 (14) | 0.0382 (15) | 0.0020 (12) | 0.0150 (13) | 0.0005 (11) |
C14 | 0.0439 (16) | 0.0362 (15) | 0.0425 (16) | −0.0001 (12) | 0.0175 (13) | 0.0030 (12) |
O5 | 0.0816 (16) | 0.0323 (11) | 0.0664 (14) | 0.0038 (10) | 0.0478 (12) | 0.0041 (10) |
O6 | 0.0708 (15) | 0.0443 (11) | 0.0561 (13) | 0.0021 (9) | 0.0419 (12) | 0.0061 (9) |
O7 | 0.0944 (17) | 0.0328 (11) | 0.0712 (15) | −0.0004 (10) | 0.0540 (13) | −0.0021 (9) |
O8 | 0.0865 (16) | 0.0414 (11) | 0.0553 (13) | −0.0116 (10) | 0.0448 (12) | −0.0020 (9) |
O1W | 0.0617 (14) | 0.0387 (11) | 0.0494 (13) | 0.0060 (10) | 0.0175 (11) | −0.0020 (10) |
Geometric parameters (Å, º) top
N1—C2 | 1.492 (3) | O3—C7 | 1.230 (3) |
N1—H11 | 0.96 (4) | O4—C7 | 1.255 (3) |
N1—H12 | 0.95 (3) | O4—H1 | 1.35 (5) |
N1—H13 | 0.85 (3) | C7—C8 | 1.539 (4) |
O2—C1 | 1.214 (3) | C8—C9 | 1.529 (4) |
O1—C1 | 1.281 (3) | C8—C12 | 1.538 (4) |
O1—H1 | 1.11 (5) | C9—C10B | 1.507 (13) |
C1—C2 | 1.521 (4) | C9—C10 | 1.520 (10) |
C2—C3 | 1.535 (4) | C9—H9A | 0.9700 |
C2—C6 | 1.544 (4) | C9—H9B | 0.9700 |
C3—C4 | 1.517 (7) | C10—C11 | 1.526 (15) |
C3—C4B | 1.536 (13) | C10—H10A | 0.78 (6) |
C3—H3A | 0.9700 | C10—H10B | 0.78 (6) |
C3—H3B | 0.9700 | C11—C12 | 1.466 (9) |
C4—C5 | 1.542 (11) | C11—H11A | 0.89 (6) |
C4—H4A | 0.98 (4) | C11—H11B | 0.89 (6) |
C4—H4B | 0.98 (4) | C10B—C11B | 1.533 (15) |
C5—C6 | 1.509 (8) | C10B—H10C | 1.15 (7) |
C5—H5A | 0.98 (4) | C10B—H10D | 1.15 (7) |
C5—H5B | 0.98 (4) | C11B—C12 | 1.498 (7) |
C4B—C5B | 1.512 (16) | C11B—H11C | 0.98 (5) |
C4B—H4B1 | 0.96 (9) | C11B—H11D | 0.98 (5) |
C4B—H4B2 | 0.96 (9) | C12—H12A | 0.9700 |
C5B—C6 | 1.489 (13) | C12—H12B | 0.9700 |
C5B—H5B1 | 1.09 (9) | C13—O6 | 1.197 (3) |
C5B—H5B2 | 1.09 (9) | C13—O5 | 1.316 (3) |
C6—H6A | 0.9700 | C13—C14 | 1.546 (4) |
C6—H6B | 0.9700 | C14—O8 | 1.226 (3) |
N2—C8 | 1.497 (4) | C14—O7 | 1.255 (3) |
N2—H21 | 1.03 (4) | O5—H55 | 0.84 (4) |
N2—H22 | 0.90 (5) | O1W—H2W | 0.86 (5) |
N2—H23 | 0.92 (3) | O1W—H1W | 0.89 (4) |
| | | |
C2—N1—H11 | 110 (2) | H21—N2—H23 | 109 (3) |
C2—N1—H12 | 110.8 (19) | H22—N2—H23 | 104 (3) |
H11—N1—H12 | 109 (3) | C7—O4—H1 | 112 (2) |
C2—N1—H13 | 112 (2) | O3—C7—O4 | 126.7 (3) |
H11—N1—H13 | 113 (3) | O3—C7—C8 | 117.4 (2) |
H12—N1—H13 | 101 (3) | O4—C7—C8 | 115.8 (2) |
C1—O1—H1 | 118 (2) | N2—C8—C9 | 111.4 (2) |
O2—C1—O1 | 126.9 (3) | N2—C8—C12 | 110.6 (2) |
O2—C1—C2 | 121.0 (2) | C9—C8—C12 | 105.2 (2) |
O1—C1—C2 | 112.1 (2) | N2—C8—C7 | 105.3 (2) |
N1—C2—C1 | 106.8 (2) | C9—C8—C7 | 114.9 (2) |
N1—C2—C3 | 110.7 (2) | C12—C8—C7 | 109.4 (2) |
C1—C2—C3 | 112.0 (2) | C10B—C9—C8 | 102.8 (8) |
N1—C2—C6 | 110.1 (2) | C10—C9—C8 | 108.3 (6) |
C1—C2—C6 | 112.2 (2) | C10—C9—H9A | 110.0 |
C3—C2—C6 | 105.1 (2) | C8—C9—H9A | 110.0 |
C4—C3—C2 | 106.2 (4) | C10—C9—H9B | 110.0 |
C2—C3—C4B | 101.7 (7) | C8—C9—H9B | 110.0 |
C4—C3—H3A | 110.5 | H9A—C9—H9B | 108.4 |
C2—C3—H3A | 110.5 | C9—C10—C11 | 105.6 (10) |
C4—C3—H3B | 110.5 | C9—C10—H10A | 110.6 |
C2—C3—H3B | 110.5 | C11—C10—H10A | 110.6 |
H3A—C3—H3B | 108.7 | C9—C10—H10B | 110.6 |
C3—C4—C5 | 98.6 (6) | C11—C10—H10B | 110.6 |
C3—C4—H4A | 112.0 | H10A—C10—H10B | 108.8 |
C5—C4—H4A | 112.0 | C12—C11—C10 | 108.0 (8) |
C3—C4—H4B | 112.0 | C12—C11—H11A | 110.1 |
C5—C4—H4B | 112.0 | C10—C11—H11A | 110.1 |
H4A—C4—H4B | 109.7 | C12—C11—H11B | 110.1 |
C6—C5—C4 | 105.9 (7) | C10—C11—H11B | 110.1 |
C6—C5—H5A | 110.6 | H11A—C11—H11B | 108.4 |
C4—C5—H5A | 110.6 | C9—C10B—C11B | 102.0 (10) |
C6—C5—H5B | 110.6 | C9—C10B—H10C | 111.4 |
C4—C5—H5B | 110.6 | C11B—C10B—H10C | 111.4 |
H5A—C5—H5B | 108.7 | C9—C10B—H10D | 111.4 |
C5B—C4B—C3 | 111.1 (15) | C11B—C10B—H10D | 111.4 |
C5B—C4B—H4B1 | 109.4 | H10C—C10B—H10D | 109.2 |
C3—C4B—H4B1 | 109.4 | C12—C11B—C10B | 99.5 (9) |
C5B—C4B—H4B2 | 109.4 | C12—C11B—H11C | 111.9 |
C3—C4B—H4B2 | 109.4 | C10B—C11B—H11C | 111.9 |
H4B1—C4B—H4B2 | 108.0 | C12—C11B—H11D | 111.9 |
C6—C5B—C4B | 97.3 (12) | C10B—C11B—H11D | 111.9 |
C6—C5B—H5B1 | 112.3 | H11C—C11B—H11D | 109.6 |
C4B—C5B—H5B1 | 112.3 | C11—C12—C8 | 107.0 (5) |
C6—C5B—H5B2 | 112.3 | C11B—C12—C8 | 105.4 (4) |
C4B—C5B—H5B2 | 112.3 | C11—C12—H12A | 110.3 |
H5B1—C5B—H5B2 | 109.9 | C8—C12—H12A | 110.3 |
C5B—C6—C2 | 110.4 (9) | C11—C12—H12B | 110.3 |
C5—C6—C2 | 104.3 (5) | C8—C12—H12B | 110.3 |
C5—C6—H6A | 110.9 | H12A—C12—H12B | 108.6 |
C2—C6—H6A | 110.9 | O6—C13—O5 | 125.3 (2) |
C5—C6—H6B | 110.9 | O6—C13—C14 | 122.8 (2) |
C2—C6—H6B | 110.9 | O5—C13—C14 | 111.9 (2) |
H6A—C6—H6B | 108.9 | O8—C14—O7 | 126.6 (2) |
C8—N2—H21 | 107.6 (19) | O8—C14—C13 | 118.7 (2) |
C8—N2—H22 | 109 (3) | O7—C14—C13 | 114.8 (2) |
H21—N2—H22 | 111 (3) | C13—O5—H55 | 111 (2) |
C8—N2—H23 | 116 (2) | H2W—O1W—H1W | 100 (4) |
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