DL-Norleucine (2-aminohexanoic acid, C6H13NO2) forms a double-layer structure in all known phases (α, β, γ). The crystal structure of the β-phase was redetermined at 173 K. Diffraction patterns of the α- and β-phases frequently show diffuse streaks parallel to c*, which indicates a stacking disorder of the layers. A symmetry analysis was carried out to derive possible stacking sequences. Lattice-energy minimizations by force fields and by dispersion-corrected density functional theory (DFT-D) were performed on a set of ordered model structures with Z = 4, 8 and 16 with different stacking sequences. The calculated energies depend not only on the arrangement of neighbouring double layers, but also of next-neighbouring double layers. Stacking probabilities were calculated from the DFT-D energies. According to the calculated stacking probabilities large models containing 100 double layers were constructed. Their simulated diffraction patterns show sharp reflections for h + k = 2n and diffuse streaks parallel to c* through all reflections with h + k = 2n + 1. Experimental single-crystal X-ray diffraction revealed that at 173 K norleucine exists in the β-phase with stacking disorder. After reheating to room temperature, the investigated crystal showed a diffraction pattern with strong diffuse scattering parallel to c* through all reflections with h + k = 2n + 1, which is in good agreement with the simulated disordered structure.
Supporting information
CCDC reference: 1570080
Program(s) used to refine structure: SHELXL2016/6 (Sheldrick, 2016).
Crystal data top
C6H13NO2 | F(000) = 576 |
Mr = 131.17 | Dx = 1.195 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
a = 31.2310 (18) Å | Cell parameters from 8204 reflections |
b = 4.7296 (4) Å | θ = 2.1–26.5° |
c = 9.8739 (5) Å | µ = 0.09 mm−1 |
β = 91.719 (5)° | T = 173 K |
V = 1457.82 (17) Å3 | Plate, colourless |
Z = 8 | 0.28 × 0.26 × 0.09 mm |
Data collection top
STOE IPDS II two-circle- diffractometer | 1326 reflections with I > 2σ(I) |
Radiation source: Genix 3D IµS microfocus X-ray source | Rint = 0.037 |
ω scans | θmax = 26.1°, θmin = 2.6° |
Absorption correction: multi-scan X-Area (Stoe & Cie, 2001) | h = −38→38 |
Tmin = 0.370, Tmax = 1.000 | k = −5→5 |
8204 measured reflections | l = −12→12 |
1451 independent reflections | |
Refinement top
Refinement on F2 | 17 restraints |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.038 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.117 | w = 1/[σ2(Fo2) + (0.0743P)2 + 0.9606P] where P = (Fo2 + 2Fc2)/3 |
S = 0.97 | (Δ/σ)max = 0.001 |
1451 reflections | Δρmax = 0.20 e Å−3 |
131 parameters | Δρmin = −0.19 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) |
O1 | 0.71594 (3) | −0.07663 (19) | 0.80083 (9) | 0.0273 (3) | 0.950 (4) |
O2 | 0.68563 (4) | 0.2049 (3) | 0.95311 (9) | 0.0308 (3) | 0.950 (4) |
N1 | 0.70227 (4) | 0.2984 (4) | 0.60003 (12) | 0.0236 (3) | 0.950 (4) |
H1N | 0.6947 (5) | 0.443 (4) | 0.5384 (18) | 0.034 (4)* | 0.950 (4) |
H2N | 0.7296 (7) | 0.325 (4) | 0.6260 (18) | 0.037 (4)* | 0.950 (4) |
H3N | 0.7000 (6) | 0.112 (5) | 0.553 (2) | 0.046 (6)* | 0.950 (4) |
C1 | 0.69433 (4) | 0.1340 (3) | 0.83407 (12) | 0.0228 (3) | 0.950 (4) |
C2 | 0.67414 (4) | 0.3110 (3) | 0.71923 (12) | 0.0231 (3) | 0.950 (4) |
H2 | 0.671506 | 0.511703 | 0.749761 | 0.028* | 0.950 (4) |
C3 | 0.62962 (4) | 0.1938 (4) | 0.68334 (14) | 0.0275 (4) | 0.950 (4) |
H3A | 0.611142 | 0.222502 | 0.761901 | 0.033* | 0.950 (4) |
H3B | 0.632126 | −0.012559 | 0.668684 | 0.033* | 0.950 (4) |
C4 | 0.60742 (4) | 0.3243 (4) | 0.55838 (14) | 0.0321 (4) | 0.950 (4) |
H4A | 0.605438 | 0.531494 | 0.570993 | 0.039* | 0.950 (4) |
H4B | 0.625003 | 0.288853 | 0.478358 | 0.039* | 0.950 (4) |
C5 | 0.56276 (6) | 0.2057 (8) | 0.5316 (2) | 0.0409 (6) | 0.950 (4) |
H5A | 0.564447 | −0.003153 | 0.528131 | 0.049* | 0.950 (4) |
H5B | 0.544440 | 0.257430 | 0.607842 | 0.049* | 0.950 (4) |
C6 | 0.54197 (6) | 0.3129 (5) | 0.40014 (18) | 0.0489 (5) | 0.950 (4) |
H6A | 0.513360 | 0.229781 | 0.388218 | 0.073* | 0.950 (4) |
H6B | 0.539564 | 0.519350 | 0.403630 | 0.073* | 0.950 (4) |
H6C | 0.559582 | 0.258628 | 0.323876 | 0.073* | 0.950 (4) |
O1' | 0.7160 (8) | 0.583 (5) | 0.800 (2) | 0.058 (9)* | 0.050 (4) |
O2' | 0.6849 (12) | 0.313 (8) | 0.952 (3) | 0.071 (15)* | 0.050 (4) |
N1' | 0.7010 (8) | 0.191 (8) | 0.593 (3) | 0.019 (8)* | 0.050 (4) |
C1' | 0.6939 (9) | 0.372 (6) | 0.830 (2) | 0.048 (9)* | 0.050 (4) |
C2' | 0.6739 (9) | 0.198 (7) | 0.717 (3) | 0.057 (16)* | 0.050 (4) |
C3' | 0.6288 (10) | 0.297 (12) | 0.681 (4) | 0.08 (2)* | 0.050 (4) |
C4' | 0.6072 (11) | 0.180 (11) | 0.554 (4) | 0.062 (13)* | 0.050 (4) |
C5' | 0.5617 (14) | 0.278 (15) | 0.525 (6) | 0.06 (3)* | 0.050 (4) |
C6' | 0.545 (2) | 0.176 (18) | 0.387 (6) | 0.12 (3)* | 0.050 (4) |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0342 (5) | 0.0236 (5) | 0.0239 (5) | 0.0040 (4) | −0.0018 (4) | 0.0007 (3) |
O2 | 0.0500 (7) | 0.0253 (7) | 0.0171 (5) | 0.0020 (5) | 0.0002 (4) | −0.0007 (4) |
N1 | 0.0301 (8) | 0.0213 (8) | 0.0191 (6) | −0.0026 (5) | −0.0017 (4) | 0.0010 (5) |
C1 | 0.0292 (6) | 0.0187 (6) | 0.0203 (6) | −0.0033 (5) | −0.0018 (5) | 0.0001 (5) |
C2 | 0.0310 (7) | 0.0200 (8) | 0.0181 (6) | 0.0004 (5) | −0.0003 (5) | −0.0008 (5) |
C3 | 0.0299 (8) | 0.0277 (9) | 0.0249 (7) | 0.0000 (5) | −0.0010 (5) | 0.0021 (5) |
C4 | 0.0343 (8) | 0.0303 (9) | 0.0313 (8) | −0.0003 (6) | −0.0069 (6) | 0.0033 (6) |
C5 | 0.0341 (11) | 0.0453 (15) | 0.0425 (12) | −0.0020 (7) | −0.0096 (6) | 0.0045 (9) |
C6 | 0.0391 (9) | 0.0632 (14) | 0.0435 (10) | 0.0015 (8) | −0.0147 (7) | −0.0008 (9) |
Geometric parameters (Å, º) top
O1—C1 | 1.2526 (16) | C5—C6 | 1.521 (3) |
O2—C1 | 1.2597 (15) | C5—H5A | 0.9900 |
N1—C2 | 1.4908 (16) | C5—H5B | 0.9900 |
N1—H1N | 0.939 (19) | C6—H6A | 0.9800 |
N1—H2N | 0.89 (2) | C6—H6B | 0.9800 |
N1—H3N | 1.00 (2) | C6—H6C | 0.9800 |
C1—C2 | 1.5302 (17) | O1'—C1' | 1.257 (18) |
C2—C3 | 1.5286 (18) | O2'—C1' | 1.270 (18) |
C2—H2 | 1.0000 | N1'—C2' | 1.509 (19) |
C3—C4 | 1.5275 (18) | C1'—C2' | 1.506 (18) |
C3—H3A | 0.9900 | C2'—C3' | 1.515 (19) |
C3—H3B | 0.9900 | C3'—C4' | 1.512 (19) |
C4—C5 | 1.519 (2) | C4'—C5' | 1.51 (2) |
C4—H4A | 0.9900 | C5'—C6' | 1.52 (2) |
C4—H4B | 0.9900 | | |
| | | |
C2—N1—H1N | 109.9 (10) | C5—C4—H4B | 109.1 |
C2—N1—H2N | 110.4 (11) | C3—C4—H4B | 109.1 |
H1N—N1—H2N | 107.7 (15) | H4A—C4—H4B | 107.8 |
C2—N1—H3N | 111.5 (12) | C6—C5—C4 | 113.1 (2) |
H1N—N1—H3N | 109.2 (15) | C6—C5—H5A | 109.0 |
H2N—N1—H3N | 108.1 (16) | C4—C5—H5A | 109.0 |
O1—C1—O2 | 126.09 (12) | C6—C5—H5B | 109.0 |
O1—C1—C2 | 117.02 (11) | C4—C5—H5B | 109.0 |
O2—C1—C2 | 116.76 (12) | H5A—C5—H5B | 107.8 |
N1—C2—C3 | 110.85 (11) | C5—C6—H6A | 109.5 |
N1—C2—C1 | 108.89 (11) | C5—C6—H6B | 109.5 |
C3—C2—C1 | 108.97 (12) | H6A—C6—H6B | 109.5 |
N1—C2—H2 | 109.4 | C5—C6—H6C | 109.5 |
C3—C2—H2 | 109.4 | H6A—C6—H6C | 109.5 |
C1—C2—H2 | 109.4 | H6B—C6—H6C | 109.5 |
C2—C3—C4 | 115.37 (13) | O1'—C1'—O2' | 123 (2) |
C2—C3—H3A | 108.4 | O1'—C1'—C2' | 118 (2) |
C4—C3—H3A | 108.4 | O2'—C1'—C2' | 119 (2) |
C2—C3—H3B | 108.4 | N1'—C2'—C1' | 113 (2) |
C4—C3—H3B | 108.4 | N1'—C2'—C3' | 111 (2) |
H3A—C3—H3B | 107.5 | C1'—C2'—C3' | 112 (2) |
C5—C4—C3 | 112.57 (16) | C2'—C3'—C4' | 118 (2) |
C5—C4—H4A | 109.1 | C5'—C4'—C3' | 116 (3) |
C3—C4—H4A | 109.1 | C6'—C5'—C4' | 112 (3) |
| | | |
O1—C1—C2—N1 | −31.26 (17) | O1'—C1'—C2'—N1' | 33 (4) |
O2—C1—C2—N1 | 152.63 (13) | O2'—C1'—C2'—N1' | −153 (3) |
O1—C1—C2—C3 | 89.76 (14) | O1'—C1'—C2'—C3' | −93 (4) |
O2—C1—C2—C3 | −86.35 (15) | O2'—C1'—C2'—C3' | 82 (4) |
N1—C2—C3—C4 | −52.8 (2) | N1'—C2'—C3'—C4' | 43 (6) |
C1—C2—C3—C4 | −172.65 (13) | C1'—C2'—C3'—C4' | 170 (4) |
C2—C3—C4—C5 | −177.94 (17) | C2'—C3'—C4'—C5' | 178 (5) |
C3—C4—C5—C6 | −174.50 (19) | C3'—C4'—C5'—C6' | 173 (6) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O2i | 0.939 (19) | 1.886 (19) | 2.801 (2) | 164.3 (15) |
N1—H2N···O1ii | 0.89 (2) | 1.89 (2) | 2.7717 (16) | 171.1 (17) |
N1—H3N···O1iii | 1.00 (2) | 2.56 (2) | 3.1759 (16) | 119.7 (15) |
N1—H3N···O2iii | 1.00 (2) | 1.84 (2) | 2.828 (2) | 168.6 (18) |
C2—H2···O1iv | 1.00 | 2.43 | 3.2677 (18) | 140 |
Symmetry codes: (i) x, −y+1, z−1/2; (ii) −x+3/2, y+1/2, −z+3/2; (iii) x, −y, z−1/2; (iv) x, y+1, z. |