Non-covalent interactions in the multicomponent crystal of 1-amino­cyclo­pentane carb­oxy­lic acid, oxalic acid and water: a crystallographic and a theoretical approach

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.

Computing details

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).

(I)

Crystal data

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) Å^3	Rectangular, colourless
Z = 4	0.30 × 0.20 × 0.15 mm

Data collection

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

Refinement on F^2	88 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.062	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.164	w = 1/[σ^2(Fo^2) + (0.0662P)^2 + 0.7567P] where P = (Fo^2 + 2Fc^2)/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

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 (Ų)

	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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)