Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104020943/ob1197sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270104020943/ob1197Isup2.hkl |
CCDC reference: 254951
A sample of cis-4-aminocyclohexanecarboxylic acid (500 mg, Aldrich, 98%) was dissolved in an ethanol/water mixture (1:8, 2 ml). Crystals of (I) suitable for X-ray diffraction analysis were grown by slow evaporation. 13C NMR (100.6 MHz, D2O): δ 24.8 (C-3 = C-7), 27.3 (C-4 = C-6), 41.4 (C-7), 49.0 (C-3), 183.6 (C-1); 1H NMR (400 MHz, D2O): δ 2.37 (1H, m, H-1eq), 1.90 (2H, m, H-2eq = H-6eq), 1.61 (2H, m, H-2ax = H-6ax), 1.58 (2H, m, H-3ax = H-5ax), 1.83 (2H, dc, J = 10, 4 Hz, H-3eq = H-5eq), 3.29 (1H, q, J = 4 Hz, H-4ax).
The H atoms of the NH3+ group and that of the water molecule were located in difference Fourier maps and refined isotropically. The H atoms of the cyclohexane ring were placed geometrically and their positions were fixed, with Uiso(H) values of 1.2Ueq(parent).
Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Branderburg, 1998); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 1990).
C7H13NO2·0.5H2O | F(000) = 664 |
Mr = 152.19 | Dx = 1.265 Mg m−3 |
Monoclinic, C2/c | Melting point: 543.7(2) K |
Hall symbol: -C 2yc | Mo Kα radiation, λ = 0.71073 Å |
a = 19.871 (4) Å | Cell parameters from 3462 reflections |
b = 6.1614 (11) Å | θ = 2.1–28.3° |
c = 13.475 (2) Å | µ = 0.10 mm−1 |
β = 104.452 (3)° | T = 293 K |
V = 1597.6 (5) Å3 | Plate, colourless |
Z = 8 | 0.30 × 0.30 × 0.20 mm |
Siemens SMART CCD area-detector diffractometer | 1880 independent reflections |
Radiation source: fine-focus sealed tube | 1100 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.060 |
ϕ and ω scans | θmax = 28.3°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −26→26 |
Tmin = 0.890, Tmax = 0.980 | k = −8→8 |
7982 measured reflections | l = −17→17 |
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)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.102 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.97 | w = 1/[σ2(Fo2) + (0.0496)2] where P = (Fo2 + 2Fc2)/3 |
1880 reflections | (Δ/σ)max < 0.001 |
118 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.18 e Å−3 |
C7H13NO2·0.5H2O | V = 1597.6 (5) Å3 |
Mr = 152.19 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 19.871 (4) Å | µ = 0.10 mm−1 |
b = 6.1614 (11) Å | T = 293 K |
c = 13.475 (2) Å | 0.30 × 0.30 × 0.20 mm |
β = 104.452 (3)° |
Siemens SMART CCD area-detector diffractometer | 1880 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 1100 reflections with I > 2σ(I) |
Tmin = 0.890, Tmax = 0.980 | Rint = 0.060 |
7982 measured reflections |
R[F2 > 2σ(F2)] = 0.047 | 0 restraints |
wR(F2) = 0.102 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.97 | Δρmax = 0.19 e Å−3 |
1880 reflections | Δρmin = −0.18 e Å−3 |
118 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 | ||
O1 | 0.19125 (6) | 0.1498 (2) | 0.82728 (9) | 0.0444 (4) | |
O2 | 0.12833 (7) | 0.4494 (2) | 0.80900 (10) | 0.0535 (4) | |
N1 | 0.18569 (8) | 0.2275 (3) | 1.21393 (11) | 0.0341 (4) | |
H1N | 0.1893 (9) | 0.114 (3) | 1.2563 (14) | 0.046 (5)* | |
H2N | 0.2277 (11) | 0.258 (3) | 1.2017 (15) | 0.056 (6)* | |
H3N | 0.1689 (9) | 0.346 (3) | 1.2427 (15) | 0.057 (6)* | |
C1 | 0.13990 (8) | 0.2585 (3) | 0.83866 (12) | 0.0318 (4) | |
C2 | 0.08859 (8) | 0.1499 (3) | 0.89015 (13) | 0.0347 (4) | |
H2 | 0.0506 | 0.1009 | 0.8364 | 0.042* | |
C3 | 0.05855 (9) | 0.3107 (3) | 0.95420 (14) | 0.0444 (5) | |
H3A | 0.0439 | 0.4382 | 0.9150 | 0.053* | |
H3B | 0.0189 | 0.2480 | 0.9706 | 0.053* | |
C4 | 0.11137 (9) | 0.3711 (3) | 1.05225 (13) | 0.0393 (5) | |
H4A | 0.1515 | 0.4422 | 1.0357 | 0.047* | |
H4B | 0.0905 | 0.4737 | 1.0918 | 0.047* | |
C5 | 0.13517 (9) | 0.1698 (3) | 1.11559 (12) | 0.0328 (4) | |
H5 | 0.0952 | 0.1033 | 1.1313 | 0.039* | |
C6 | 0.16715 (9) | 0.0077 (3) | 1.05560 (13) | 0.0365 (4) | |
H6A | 0.2092 | 0.0691 | 1.0426 | 0.044* | |
H6B | 0.1799 | −0.1232 | 1.0961 | 0.044* | |
C7 | 0.11691 (9) | −0.0496 (3) | 0.95459 (13) | 0.0400 (5) | |
H7A | 0.0784 | −0.1307 | 0.9681 | 0.048* | |
H7B | 0.1403 | −0.1423 | 0.9158 | 0.048* | |
O1W | 0.5000 | 0.2077 (4) | 0.7500 | 0.0651 (6) | |
H1W | 0.5343 (12) | 0.117 (4) | 0.768 (2) | 0.090 (9)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0404 (7) | 0.0414 (7) | 0.0590 (8) | −0.0057 (6) | 0.0267 (6) | −0.0124 (6) |
O2 | 0.0597 (8) | 0.0443 (8) | 0.0650 (9) | 0.0026 (6) | 0.0317 (7) | 0.0197 (7) |
N1 | 0.0390 (9) | 0.0319 (9) | 0.0353 (8) | 0.0002 (7) | 0.0167 (7) | 0.0010 (7) |
C1 | 0.0362 (9) | 0.0333 (9) | 0.0275 (8) | −0.0068 (8) | 0.0107 (7) | −0.0045 (7) |
C2 | 0.0304 (8) | 0.0400 (10) | 0.0338 (9) | −0.0089 (8) | 0.0083 (7) | 0.0015 (8) |
C3 | 0.0361 (9) | 0.0586 (12) | 0.0436 (11) | 0.0108 (9) | 0.0195 (8) | 0.0137 (9) |
C4 | 0.0483 (11) | 0.0358 (10) | 0.0395 (10) | 0.0128 (8) | 0.0219 (9) | 0.0031 (8) |
C5 | 0.0334 (9) | 0.0337 (9) | 0.0350 (9) | −0.0017 (8) | 0.0153 (7) | 0.0019 (7) |
C6 | 0.0478 (10) | 0.0252 (9) | 0.0379 (10) | 0.0043 (7) | 0.0130 (8) | 0.0015 (7) |
C7 | 0.0495 (10) | 0.0342 (10) | 0.0402 (10) | −0.0121 (8) | 0.0184 (9) | −0.0012 (8) |
O1W | 0.0641 (14) | 0.0496 (13) | 0.0725 (16) | 0.000 | 0.0002 (12) | 0.000 |
C1—O1 | 1.261 (2) | C3—H3B | 0.9509 |
C1—O2 | 1.245 (2) | C4—C5 | 1.513 (2) |
C5—N1 | 1.492 (2) | C4—H4A | 0.9833 |
N1—H1N | 0.89 (2) | C4—H4B | 0.9833 |
N1—H2N | 0.91 (2) | C5—C6 | 1.520 (2) |
N1—H3N | 0.93 (2) | C5—H5 | 0.9625 |
C1—C2 | 1.524 (2) | C6—C7 | 1.515 (2) |
C2—C7 | 1.529 (2) | C6—H6A | 0.9712 |
C2—C3 | 1.530 (2) | C6—H6B | 0.9712 |
C2—H2 | 0.9559 | C7—H7A | 0.9681 |
C3—C4 | 1.515 (3) | C7—H7B | 0.9681 |
C3—H3A | 0.9509 | O1W—H1W | 0.87 (2) |
C5—N1—H1N | 108.1 (11) | C3—C4—H4A | 109.7 |
C5—N1—H2N | 109.4 (12) | C5—C4—H4B | 109.7 |
H1N—N1—H2N | 110.3 (16) | C3—C4—H4B | 109.7 |
C5—N1—H3N | 109.1 (11) | H4A—C4—H4B | 108.2 |
H1N—N1—H3N | 109.2 (17) | N1—C5—C4 | 110.6 (1) |
H2N—N1—H3N | 110.8 (16) | N1—C5—C6 | 110.5 (1) |
O2—C1—O1 | 123.6 (2) | C4—C5—C6 | 110.6 (1) |
O2—C1—C2 | 118.0 (2) | N1—C5—H5 | 108.3 |
O1—C1—C2 | 118.4 (2) | C4—C5—H5 | 108.3 |
C1—C2—C7 | 114.7 (1) | C6—C5—H5 | 108.3 |
C1—C2—C3 | 111.9 (1) | C7—C6—C5 | 111.20 (15) |
C7—C2—C3 | 109.9 (1) | C7—C6—H6A | 109.4 |
C1—C2—H2 | 106.6 | C5—C6—H6A | 109.4 |
C7—C2—H2 | 106.6 | C7—C6—H6B | 109.4 |
C3—C2—H2 | 106.6 | C5—C6—H6B | 109.4 |
C4—C3—C2 | 111.6 (1) | H6A—C6—H6B | 108.0 |
C4—C3—H3A | 109.3 | C6—C7—C2 | 112.92 (14) |
C2—C3—H3A | 109.3 | C6—C7—H7A | 109.0 |
C4—C3—H3B | 109.3 | C2—C7—H7A | 109.0 |
C2—C3—H3B | 109.3 | C6—C7—H7B | 109.0 |
H3A—C3—H3B | 108.0 | C2—C7—H7B | 109.0 |
C5—C4—C3 | 109.98 (15) | H7A—C7—H7B | 107.8 |
C5—C4—H4A | 109.7 | H1W—O1W—H1Wi | 100 (2) |
Symmetry code: (i) −x+1, y, −z+3/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H2N···O1ii | 0.91 (2) | 1.84 (2) | 2.745 (2) | 174 (2) |
O1W—H1W···O2iii | 0.87 (2) | 2.09 (2) | 2.942 (2) | 169 (2) |
N1—H3N···O2iv | 0.93 (2) | 1.84 (2) | 2.763 (2) | 171 (2) |
N1—H1N···O1v | 0.89 (2) | 1.88 (2) | 2.769 (2) | 171 (2) |
Symmetry codes: (ii) −x+1/2, −y+1/2, −z+2; (iii) x+1/2, y−1/2, z; (iv) x, −y+1, z+1/2; (v) x, −y, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C7H13NO2·0.5H2O |
Mr | 152.19 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 293 |
a, b, c (Å) | 19.871 (4), 6.1614 (11), 13.475 (2) |
β (°) | 104.452 (3) |
V (Å3) | 1597.6 (5) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.30 × 0.30 × 0.20 |
Data collection | |
Diffractometer | Siemens SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.890, 0.980 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7982, 1880, 1100 |
Rint | 0.060 |
(sin θ/λ)max (Å−1) | 0.667 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.102, 0.97 |
No. of reflections | 1880 |
No. of parameters | 118 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.19, −0.18 |
Computer programs: SMART (Bruker, 1998), SAINT (Bruker, 1998), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), DIAMOND (Branderburg, 1998), SHELXL97 and PLATON (Spek, 1990).
C1—O1 | 1.261 (2) | C2—C3 | 1.530 (2) |
C1—O2 | 1.245 (2) | C3—C4 | 1.515 (3) |
C5—N1 | 1.492 (2) | C4—C5 | 1.513 (2) |
C1—C2 | 1.524 (2) | C5—C6 | 1.520 (2) |
C2—C7 | 1.529 (2) | C6—C7 | 1.515 (2) |
O2—C1—O1 | 123.6 (2) | N1—C5—C4 | 110.6 (1) |
O2—C1—C2 | 118.0 (2) | N1—C5—C6 | 110.5 (1) |
O1—C1—C2 | 118.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H2N···O1i | 0.91 (2) | 1.84 (2) | 2.745 (2) | 174 (2) |
O1W—H1W···O2ii | 0.87 (2) | 2.09 (2) | 2.942 (2) | 169 (2) |
N1—H3N···O2iii | 0.93 (2) | 1.84 (2) | 2.763 (2) | 171 (2) |
N1—H1N···O1iv | 0.89 (2) | 1.88 (2) | 2.769 (2) | 171 (2) |
Symmetry codes: (i) −x+1/2, −y+1/2, −z+2; (ii) x+1/2, y−1/2, z; (iii) x, −y+1, z+1/2; (iv) x, −y, z+1/2. |
Amino acids often cocrystallize with water molecules (Görbitz & Hersleth, 2000). In these simple biological systems, the role played by the water molecule is diverse, ranging from just occupying void space in the structure to being involved in cooperative effects associated with the conformation of the extended hydrogen-bonding patterns (Jeffrey & Maluszynska, 1982; Dannenberg, 2002). These effects are most relevant in the crystalline solid state, where the periodicity allows the development of interactions between neighboring molecules with redistribution of charge density among functional groups, producing effects similar to resonance, in which hydrogen bonds shorten and the energy gain is not additive (Steiner, 2002). We are currently investigating the energetic character and arrangement of hydrogen-bonding patterns in structurally related amino acid hydrates, in which the flexibility of the carbon skeleton and the orientation of the amino and carboxylic acid groups can dictate the way individual molecules aggregate to form supramolecular structures. In particular, the structures of the isomers 2-, 3- and 4-piperidinecarboxylic acid have been assessed by means of ab-initio density-functional and semi-empirical calculations (Delgado et al., 2001; Cuervo et al. 2002; Mora et al. 2002). Continuing these studies, we report here the structure of the title compound, (I), which differs from 4-piperidiniumcarboxylate, (II), in that the ammonium group is positioned outside the six-membered ring, enabling the ammonium group to donate three H atoms for hydrogen bonding.
Fig. 1 shows the molecular structure and the atom-labeling scheme. Water atom O1W lies on a twofold axis parallel to the b axis. The C1—O1 and C1—O2 distances are equal within 3σ (see Table 1), indicating an almost symmetrical carboxylate group. On the other hand, the three H atoms bonded to atom N1 were found in a difference Fourier map, which confirms the zwitterionic nature of the molecule. The asymmetry parameters ΔCs [maximum +4.6 (2)° and minimum +0.9 (2)°] and ΔC2 [maximum +6.0 (2)° and minimum +2.3 (2)°] (Griffin et al., 1984) and the Cremer & Pople (1975) puckering parameters [Cs(C2) = 3.9 (2)°, Cs(C3) = 4.6 (2)°, Cs(C4) = 0.9 (2)°, C2(C2—C3) = 6.0 (2)°, C2(C3—C4) = 3.8 (2)° and C2(C4—C5) = 2.3 (2)°] reveal the presence of three local mirror planes and three local twofold axes, confirming that the cyclohexane ring adopts the more stable chair conformation, as seen in the trans- and cis- isomers of 4-aminomethylcyclohexanecarboxylic acid (Yamazaki et al., 1981; Groth, 1968), and their hydrohalides (Kadoya et al., 1966). This conformation is also adopted in the liquid state, as revealed by 1H and 13C NMR spectra taken in D2O.
This conformation favors the joining of two amino acid units by head-to-tail hydrogen bonding (Table 2), thus forming a sandwich-like 16-atom macrocycle (Fig. 2). In this sandwich structure there are three hydrogen bonds of the type +N—H···OCO−, two of which are bifurcated, with? acceptor O1. Neighboring sandwich structures connect via their polar ends through hydrogen bonds, giving rise to helicoidally extended chains running along the c axis. These chains are held together by intercalated water molecules interacting through −OCO···HW—OW hydrogen bonds. This additional hydrogen bond makes carboxylate atom O2 a bifurcated acceptor. The neighboring chains have intermolecular hydrophobic H···H contacts that are close to the sum of their van der Waals radii (2.40 Å).