The asymmetric unit of the
DL-lysine complex of adipic acid [bis(
DL-lysinium) adipate], 2C
6H
15N
2O
2+·C
6H
8O
42−, contains a zwitterionic singly charged lysinium cation and half a doubly charged adipate anion (the complete anion has inversion symmetry). That of the
L-lysine complex (lysinium hydrogen adipate), C
6H
15N
2O
2+·C
6H
9O
4−, consists of a lysinium cation and a singly charged hydrogen adipate anion. In both structures, the lysinium cations organize into layers interconnected by adipate or hydrogen adipate anions. However, the arrangement of the molecular ions in the layer is profoundly different in the
DL- and
L-lysine complexes. The hydrogen adipate anions in the
L-lysine complex form linear arrays in which adjacent ions are interconnected by a symmetric O
H
O hydrogen bond.
Supporting information
CCDC references: 603201; 603202
In both cases, aqueous solutions of amino acid (Sigma) and adipic acid in 1:1 molar ratio were used to grow the crystals of the complexes, employing the liquid diffusion method with acetonitrile as the precipitant.
The structure of the L-lysine complex was determined using DIRDIF99 (Beurskens et al., 1999) employing the ORIENT option, in which the coordinates of the lysinium cation taken from Saraswathi et al. (2001) were used as input. In both cases, H atoms were located in differnece Fourier maps with the aid of geometrical considerations. The amino H atoms were constrained, except for rotation about their respective C—N bonds. All remaining H atoms were treated as riding on their parent atoms. The C—H and N—H distances were constrained at 0.97–0.98 and 0.89 Å, respectively. The lone carboxyl H atom in (II) was refined freely. In the case of (II), Friedel opposite reflections were merged, although the space group is non-centrosymmetric. An absolute configuration consistent with natural L-lysine was assumed.
For both compounds, data collection: SMART (Bruker, 2001); cell refinement: SMART; data reduction: SAINT (Bruker, 2001). Program(s) used to solve structure: SHELXS97 (Sheldrick, 1997) for (I); DIRDIF99 (Beurskens et al., 1999) for (II). For both compounds, program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: PLATON (Spek, 2003).
(I) bis(DL-lysinium) adipate
top
Crystal data top
2C6H15N2O2+·C6H8O42− | Z = 1 |
Mr = 438.52 | F(000) = 238 |
Triclinic, P1 | Dx = 1.366 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.4730 (15) Å | Cell parameters from 1582 reflections |
b = 7.773 (2) Å | θ = 1.0–28.0° |
c = 13.011 (4) Å | µ = 0.11 mm−1 |
α = 100.112 (4)° | T = 298 K |
β = 93.292 (4)° | Plate, colourless |
γ = 100.744 (4)° | 0.69 × 0.60 × 0.20 mm |
V = 533.0 (3) Å3 | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2494 independent reflections |
Radiation source: fine-focus sealed tube | 2269 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.014 |
ω scans | θmax = 28.0°, θmin = 2.7° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −7→7 |
Tmin = 0.912, Tmax = 0.983 | k = −10→10 |
6254 measured reflections | l = −16→17 |
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)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.120 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0641P)2 + 0.1692P] where P = (Fo2 + 2Fc2)/3 |
2494 reflections | (Δ/σ)max < 0.001 |
138 parameters | Δρmax = 0.45 e Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
Crystal data top
2C6H15N2O2+·C6H8O42− | γ = 100.744 (4)° |
Mr = 438.52 | V = 533.0 (3) Å3 |
Triclinic, P1 | Z = 1 |
a = 5.4730 (15) Å | Mo Kα radiation |
b = 7.773 (2) Å | µ = 0.11 mm−1 |
c = 13.011 (4) Å | T = 298 K |
α = 100.112 (4)° | 0.69 × 0.60 × 0.20 mm |
β = 93.292 (4)° | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2494 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 2269 reflections with I > 2σ(I) |
Tmin = 0.912, Tmax = 0.983 | Rint = 0.014 |
6254 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.120 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.45 e Å−3 |
2494 reflections | Δρmin = −0.27 e Å−3 |
138 parameters | |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 1.12680 (17) | 0.87726 (14) | 0.36247 (9) | 0.0408 (3) | |
O2 | 1.14608 (18) | 0.78844 (13) | 0.51564 (8) | 0.0388 (3) | |
N1 | 0.63059 (17) | 0.87197 (13) | 0.36834 (8) | 0.0244 (2) | |
H1A | 0.6550 | 0.8519 | 0.3006 | 0.037* | |
H1B | 0.7001 | 0.9843 | 0.3971 | 0.037* | |
H1C | 0.4674 | 0.8533 | 0.3753 | 0.037* | |
C1 | 1.0308 (2) | 0.81182 (15) | 0.43531 (10) | 0.0264 (3) | |
C2 | 0.7466 (2) | 0.74863 (15) | 0.42207 (9) | 0.0235 (2) | |
H2 | 0.6846 | 0.7490 | 0.4913 | 0.028* | |
C3 | 0.6865 (2) | 0.55891 (16) | 0.35872 (10) | 0.0288 (3) | |
H3A | 0.7632 | 0.4836 | 0.3972 | 0.035* | |
H3B | 0.7630 | 0.5586 | 0.2933 | 0.035* | |
C4 | 0.4089 (2) | 0.47602 (16) | 0.33339 (10) | 0.0288 (3) | |
H4A | 0.3277 | 0.4781 | 0.3978 | 0.035* | |
H4B | 0.3308 | 0.5446 | 0.2905 | 0.035* | |
C5 | 0.3782 (2) | 0.28451 (16) | 0.27502 (10) | 0.0294 (3) | |
H5A | 0.4785 | 0.2829 | 0.2159 | 0.035* | |
H5B | 0.4417 | 0.2147 | 0.3214 | 0.035* | |
C6 | 0.1110 (2) | 0.19761 (16) | 0.23543 (10) | 0.0295 (3) | |
H6A | 0.0161 | 0.1755 | 0.2941 | 0.035* | |
H6B | 0.0355 | 0.2768 | 0.1995 | 0.035* | |
N7 | 0.1041 (2) | 0.02726 (15) | 0.16255 (9) | 0.0358 (3) | |
H7A | 0.2005 | 0.0469 | 0.1113 | 0.054* | |
H7B | −0.0522 | −0.0187 | 0.1353 | 0.054* | |
H7C | 0.1599 | −0.0488 | 0.1972 | 0.054* | |
O11 | 0.4879 (2) | 0.19082 (19) | −0.15658 (8) | 0.0565 (4) | |
O12 | 0.29642 (18) | 0.14007 (14) | −0.01797 (8) | 0.0413 (3) | |
C13 | 0.4775 (2) | 0.21272 (16) | −0.06041 (10) | 0.0284 (3) | |
C14 | 0.6995 (2) | 0.32779 (18) | 0.01104 (10) | 0.0308 (3) | |
H14A | 0.7828 | 0.2499 | 0.0448 | 0.037* | |
H14B | 0.6361 | 0.4049 | 0.0657 | 0.037* | |
C15 | 0.8943 (2) | 0.44398 (17) | −0.03955 (10) | 0.0294 (3) | |
H15A | 0.8139 | 0.5226 | −0.0739 | 0.035* | |
H15B | 0.9638 | 0.3684 | −0.0928 | 0.035* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0205 (4) | 0.0493 (6) | 0.0558 (6) | 0.0041 (4) | 0.0058 (4) | 0.0211 (5) |
O2 | 0.0334 (5) | 0.0362 (5) | 0.0415 (5) | 0.0064 (4) | −0.0154 (4) | 0.0004 (4) |
N1 | 0.0170 (4) | 0.0266 (5) | 0.0275 (5) | 0.0015 (4) | −0.0005 (3) | 0.0033 (4) |
C1 | 0.0202 (5) | 0.0194 (5) | 0.0363 (6) | 0.0034 (4) | −0.0035 (4) | −0.0012 (4) |
C2 | 0.0203 (5) | 0.0244 (5) | 0.0241 (5) | 0.0017 (4) | 0.0003 (4) | 0.0036 (4) |
C3 | 0.0242 (6) | 0.0239 (6) | 0.0346 (6) | 0.0009 (4) | −0.0006 (5) | 0.0010 (5) |
C4 | 0.0254 (6) | 0.0250 (6) | 0.0324 (6) | −0.0007 (5) | −0.0015 (5) | 0.0033 (5) |
C5 | 0.0257 (6) | 0.0266 (6) | 0.0315 (6) | −0.0007 (5) | −0.0014 (5) | 0.0012 (5) |
C6 | 0.0261 (6) | 0.0264 (6) | 0.0324 (6) | −0.0014 (5) | −0.0013 (5) | 0.0041 (5) |
N7 | 0.0289 (6) | 0.0309 (6) | 0.0400 (6) | −0.0007 (4) | −0.0093 (5) | −0.0024 (5) |
O11 | 0.0443 (6) | 0.0823 (9) | 0.0288 (5) | −0.0105 (6) | −0.0063 (4) | 0.0005 (5) |
O12 | 0.0274 (5) | 0.0442 (6) | 0.0453 (6) | −0.0090 (4) | −0.0005 (4) | 0.0087 (5) |
C13 | 0.0229 (6) | 0.0273 (6) | 0.0314 (6) | 0.0009 (4) | −0.0031 (4) | 0.0023 (5) |
C14 | 0.0259 (6) | 0.0344 (6) | 0.0267 (6) | −0.0057 (5) | −0.0028 (5) | 0.0059 (5) |
C15 | 0.0241 (6) | 0.0304 (6) | 0.0294 (6) | −0.0032 (5) | −0.0004 (5) | 0.0044 (5) |
Geometric parameters (Å, º) top
O1—C1 | 1.2489 (16) | C5—H5B | 0.9700 |
O2—C1 | 1.2479 (16) | C6—N7 | 1.4800 (16) |
N1—C2 | 1.4907 (15) | C6—H6A | 0.9700 |
N1—H1A | 0.8900 | C6—H6B | 0.9700 |
N1—H1B | 0.8900 | N7—H7A | 0.8900 |
N1—H1C | 0.8900 | N7—H7B | 0.8900 |
C1—C2 | 1.5313 (16) | N7—H7C | 0.8900 |
C2—C3 | 1.5243 (16) | O11—C13 | 1.2388 (17) |
C2—H2 | 0.9800 | O12—C13 | 1.2529 (16) |
C3—C4 | 1.5277 (16) | C13—C14 | 1.5212 (16) |
C3—H3A | 0.9700 | C14—C15 | 1.5216 (17) |
C3—H3B | 0.9700 | C14—H14A | 0.9700 |
C4—C5 | 1.5218 (17) | C14—H14B | 0.9700 |
C4—H4A | 0.9700 | C15—C15i | 1.526 (2) |
C4—H4B | 0.9700 | C15—H15A | 0.9700 |
C5—C6 | 1.5111 (17) | C15—H15B | 0.9700 |
C5—H5A | 0.9700 | | |
| | | |
C2—N1—H1A | 109.5 | C6—C5—H5B | 108.8 |
C2—N1—H1B | 109.5 | C4—C5—H5B | 108.8 |
H1A—N1—H1B | 109.5 | H5A—C5—H5B | 107.7 |
C2—N1—H1C | 109.5 | N7—C6—C5 | 109.84 (10) |
H1A—N1—H1C | 109.5 | N7—C6—H6A | 109.7 |
H1B—N1—H1C | 109.5 | C5—C6—H6A | 109.7 |
O2—C1—O1 | 125.91 (12) | N7—C6—H6B | 109.7 |
O2—C1—C2 | 117.52 (11) | C5—C6—H6B | 109.7 |
O1—C1—C2 | 116.53 (10) | H6A—C6—H6B | 108.2 |
N1—C2—C3 | 111.42 (9) | C6—N7—H7A | 109.5 |
N1—C2—C1 | 109.36 (9) | C6—N7—H7B | 109.5 |
C3—C2—C1 | 108.17 (9) | H7A—N7—H7B | 109.5 |
N1—C2—H2 | 109.3 | C6—N7—H7C | 109.5 |
C3—C2—H2 | 109.3 | H7A—N7—H7C | 109.5 |
C1—C2—H2 | 109.3 | H7B—N7—H7C | 109.5 |
C2—C3—C4 | 115.65 (10) | O11—C13—O12 | 123.52 (12) |
C2—C3—H3A | 108.4 | O11—C13—C14 | 118.83 (11) |
C4—C3—H3A | 108.4 | O12—C13—C14 | 117.60 (11) |
C2—C3—H3B | 108.4 | C13—C14—C15 | 117.08 (11) |
C4—C3—H3B | 108.4 | C13—C14—H14A | 108.0 |
H3A—C3—H3B | 107.4 | C15—C14—H14A | 108.0 |
C5—C4—C3 | 109.65 (10) | C13—C14—H14B | 108.0 |
C5—C4—H4A | 109.7 | C15—C14—H14B | 108.0 |
C3—C4—H4A | 109.7 | H14A—C14—H14B | 107.3 |
C5—C4—H4B | 109.7 | C14—C15—C15i | 112.61 (13) |
C3—C4—H4B | 109.7 | C14—C15—H15A | 109.1 |
H4A—C4—H4B | 108.2 | C15i—C15—H15A | 109.1 |
C6—C5—C4 | 113.64 (11) | C14—C15—H15B | 109.1 |
C6—C5—H5A | 108.8 | C15i—C15—H15B | 109.1 |
C4—C5—H5A | 108.8 | H15A—C15—H15B | 107.8 |
| | | |
O2—C1—C2—N1 | 145.95 (11) | C3—C4—C5—C6 | −173.34 (10) |
O1—C1—C2—N1 | −36.27 (14) | C4—C5—C6—N7 | 168.81 (10) |
O2—C1—C2—C3 | −92.53 (13) | O11—C13—C14—C15 | 14.11 (19) |
O1—C1—C2—C3 | 85.25 (13) | O12—C13—C14—C15 | −168.24 (12) |
N1—C2—C3—C4 | −57.19 (14) | C13—C14—C15—C15i | 178.96 (13) |
C1—C2—C3—C4 | −177.43 (10) | C14—C15—C15i—C14i | 180.0 |
C2—C3—C4—C5 | −177.16 (10) | | |
Symmetry code: (i) −x+2, −y+1, −z. |
Hydrogen-bond geometry (Å, º) top
D—H···A | H···A | D···A | D—H···A |
N1—H1A···O11ii | 1.94 | 2.730 (2) | 148 |
N1—H1B···O2iii | 1.94 | 2.815 (2) | 169 |
N1—H1C···O1iv | 1.91 | 2.762 (2) | 160 |
N7—H7A···O12 | 2.00 | 2.838 (2) | 156 |
N7—H7B···O12v | 1.95 | 2.764 (2) | 152 |
N7—H7C···O1vi | 2.33 | 3.037 (2) | 137 |
N7—H7C···O11vii | 2.43 | 3.042 (2) | 126 |
Symmetry codes: (ii) −x+1, −y+1, −z; (iii) −x+2, −y+2, −z+1; (iv) x−1, y, z; (v) −x, −y, −z; (vi) x−1, y−1, z; (vii) −x+1, −y, −z. |
(II)
L-lysine hydrogen adipate
top
Crystal data top
C6H15N2O2+·C6H9O4− | F(000) = 316 |
Mr = 292.33 | Dx = 1.301 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 2077 reflections |
a = 10.532 (3) Å | θ = 1.0–26.0° |
b = 7.2834 (17) Å | µ = 0.10 mm−1 |
c = 10.599 (3) Å | T = 298 K |
β = 113.352 (3)° | Prism, colourless |
V = 746.5 (3) Å3 | 0.91 × 0.65 × 0.17 mm |
Z = 2 | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1481 independent reflections |
Radiation source: fine-focus sealed tube | 1329 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.017 |
ω scans | θmax = 25.3°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −12→12 |
Tmin = 0.891, Tmax = 0.981 | k = −8→8 |
6202 measured reflections | l = −12→12 |
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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.135 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0766P)2 + 0.245P] where P = (Fo2 + 2Fc2)/3 |
2701 reflections | (Δ/σ)max < 0.001 |
187 parameters | Δρmax = 0.27 e Å−3 |
1 restraint | Δρmin = −0.21 e Å−3 |
Crystal data top
C6H15N2O2+·C6H9O4− | V = 746.5 (3) Å3 |
Mr = 292.33 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 10.532 (3) Å | µ = 0.10 mm−1 |
b = 7.2834 (17) Å | T = 298 K |
c = 10.599 (3) Å | 0.91 × 0.65 × 0.17 mm |
β = 113.352 (3)° | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1481 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 1329 reflections with I > 2σ(I) |
Tmin = 0.891, Tmax = 0.981 | Rint = 0.017 |
6202 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.051 | 1 restraint |
wR(F2) = 0.135 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.27 e Å−3 |
2701 reflections | Δρmin = −0.21 e Å−3 |
187 parameters | |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.3280 (3) | −0.1297 (7) | 0.3506 (4) | 0.1199 (19) | |
O2 | 0.3483 (3) | 0.1277 (5) | 0.4558 (4) | 0.0816 (11) | |
N1 | 0.0681 (3) | −0.0957 (6) | 0.1887 (3) | 0.0550 (9) | |
H1A | 0.0812 | −0.2099 | 0.2212 | 0.083* | |
H1B | 0.1128 | −0.0799 | 0.1338 | 0.083* | |
H1C | −0.0218 | −0.0762 | 0.1415 | 0.083* | |
C1 | 0.2794 (3) | 0.0107 (6) | 0.3761 (4) | 0.0470 (8) | |
C2 | 0.1221 (3) | 0.0369 (5) | 0.3057 (3) | 0.0439 (9) | |
H2 | 0.1019 | 0.1625 | 0.2703 | 0.053* | |
C3 | 0.0502 (3) | 0.0004 (6) | 0.4032 (3) | 0.0409 (8) | |
H3A | 0.0565 | −0.1297 | 0.4244 | 0.049* | |
H3B | 0.0995 | 0.0658 | 0.4885 | 0.049* | |
C4 | −0.1013 (3) | 0.0571 (6) | 0.3474 (3) | 0.0455 (9) | |
H4A | −0.1079 | 0.1897 | 0.3385 | 0.055* | |
H4B | −0.1493 | 0.0044 | 0.2567 | 0.055* | |
C5 | −0.1702 (3) | −0.0063 (6) | 0.4411 (3) | 0.0460 (8) | |
H5A | −0.1681 | −0.1394 | 0.4446 | 0.055* | |
H5B | −0.1166 | 0.0383 | 0.5333 | 0.055* | |
C6 | −0.3175 (3) | 0.0562 (7) | 0.3987 (4) | 0.0558 (11) | |
H6A | −0.3219 | 0.1886 | 0.3878 | 0.067* | |
H6B | −0.3741 | 0.0019 | 0.3107 | 0.067* | |
N7 | −0.3734 (3) | 0.0035 (5) | 0.5017 (3) | 0.0500 (8) | |
H7A | −0.3630 | −0.1169 | 0.5169 | 0.075* | |
H7B | −0.4628 | 0.0320 | 0.4702 | 0.075* | |
H7C | −0.3279 | 0.0635 | 0.5798 | 0.075* | |
O11 | 0.7984 (3) | −0.0598 (9) | 1.0006 (3) | 0.1135 (19) | |
O12 | 0.8095 (2) | −0.0023 (5) | 0.8049 (2) | 0.0649 (9) | |
C13 | 0.7443 (3) | −0.0196 (6) | 0.8818 (3) | 0.0467 (9) | |
C14 | 0.5913 (3) | 0.0121 (8) | 0.8157 (3) | 0.0569 (11) | |
H14A | 0.5753 | 0.1396 | 0.7874 | 0.068* | |
H14B | 0.5535 | −0.0626 | 0.7333 | 0.068* | |
C15 | 0.5130 (3) | −0.0296 (6) | 0.9034 (3) | 0.0473 (9) | |
H15A | 0.5563 | 0.0347 | 0.9902 | 0.057* | |
H15B | 0.5193 | −0.1601 | 0.9229 | 0.057* | |
C16 | 0.3625 (3) | 0.0242 (6) | 0.8382 (3) | 0.0470 (9) | |
H16A | 0.3210 | −0.0311 | 0.7477 | 0.056* | |
H16B | 0.3559 | 0.1564 | 0.8265 | 0.056* | |
C17 | 0.2819 (3) | −0.0340 (7) | 0.9217 (3) | 0.0499 (10) | |
H17A | 0.2917 | −0.1657 | 0.9361 | 0.060* | |
H17B | 0.3220 | 0.0246 | 1.0111 | 0.060* | |
C18 | 0.1315 (3) | 0.0120 (6) | 0.8571 (3) | 0.0450 (9) | |
O19 | 0.0800 (2) | 0.0972 (5) | 0.7517 (3) | 0.0588 (8) | |
O20 | 0.0609 (2) | −0.0525 (6) | 0.9238 (3) | 0.0720 (11) | |
H20 | −0.062 (5) | −0.035 (8) | 0.868 (4) | 0.086 (15)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0345 (16) | 0.140 (4) | 0.158 (4) | 0.014 (2) | 0.009 (2) | −0.072 (3) |
O2 | 0.0387 (15) | 0.076 (2) | 0.108 (3) | −0.0007 (16) | 0.0056 (16) | −0.026 (2) |
N1 | 0.0344 (15) | 0.090 (2) | 0.0390 (14) | −0.0010 (16) | 0.0132 (12) | 0.0016 (16) |
C1 | 0.0280 (16) | 0.059 (2) | 0.0551 (18) | −0.0007 (18) | 0.0181 (14) | −0.0025 (19) |
C2 | 0.0256 (15) | 0.059 (2) | 0.0469 (17) | −0.0017 (15) | 0.0139 (13) | 0.0047 (16) |
C3 | 0.0287 (15) | 0.052 (2) | 0.0418 (15) | −0.0010 (15) | 0.0141 (12) | 0.0015 (16) |
C4 | 0.0297 (15) | 0.061 (2) | 0.0482 (17) | 0.0045 (15) | 0.0176 (13) | 0.0049 (16) |
C5 | 0.0289 (15) | 0.059 (2) | 0.0511 (17) | 0.0023 (17) | 0.0171 (13) | 0.0057 (18) |
C6 | 0.0324 (17) | 0.081 (3) | 0.0568 (19) | 0.0096 (19) | 0.0204 (15) | 0.020 (2) |
N7 | 0.0265 (12) | 0.068 (2) | 0.0588 (16) | −0.0007 (15) | 0.0206 (12) | 0.0054 (16) |
O11 | 0.0268 (12) | 0.253 (6) | 0.0573 (16) | 0.015 (2) | 0.0128 (12) | 0.028 (3) |
O12 | 0.0277 (11) | 0.117 (3) | 0.0565 (13) | 0.0076 (16) | 0.0234 (10) | 0.0098 (17) |
C13 | 0.0244 (15) | 0.071 (3) | 0.0443 (17) | 0.0000 (17) | 0.0135 (13) | −0.0011 (18) |
C14 | 0.0226 (15) | 0.105 (3) | 0.0445 (16) | 0.006 (2) | 0.0143 (13) | 0.012 (2) |
C15 | 0.0246 (15) | 0.072 (3) | 0.0489 (16) | 0.0026 (16) | 0.0184 (13) | 0.0071 (18) |
C16 | 0.0253 (14) | 0.072 (3) | 0.0475 (16) | 0.0049 (17) | 0.0182 (13) | 0.0050 (18) |
C17 | 0.0256 (15) | 0.077 (3) | 0.0492 (17) | 0.0052 (17) | 0.0172 (13) | 0.0115 (19) |
C18 | 0.0256 (15) | 0.070 (2) | 0.0406 (16) | 0.0027 (18) | 0.0145 (13) | 0.0023 (18) |
O19 | 0.0317 (12) | 0.093 (2) | 0.0533 (14) | 0.0143 (14) | 0.0181 (11) | 0.0184 (15) |
O20 | 0.0287 (12) | 0.134 (3) | 0.0601 (14) | 0.0093 (16) | 0.0250 (11) | 0.0311 (19) |
Geometric parameters (Å, º) top
O1—C1 | 1.221 (6) | C4—C5 | 1.517 (4) |
O2—C1 | 1.217 (5) | C4—H4A | 0.9700 |
O11—C13 | 1.195 (4) | C4—H4B | 0.9700 |
O12—C13 | 1.264 (4) | C5—C6 | 1.505 (4) |
O19—C18 | 1.203 (4) | C5—H5A | 0.9700 |
O20—C18 | 1.300 (4) | C5—H5B | 0.9700 |
O20—H20 | 1.20 (5) | C6—H6A | 0.9700 |
N1—C2 | 1.495 (5) | C6—H6B | 0.9700 |
N1—H1A | 0.8900 | C13—C14 | 1.499 (4) |
N1—H1B | 0.8900 | C14—C15 | 1.498 (4) |
N1—H1C | 0.8900 | C14—H14A | 0.9700 |
N7—C6 | 1.482 (4) | C14—H14B | 0.9700 |
N7—H7A | 0.8900 | C15—C16 | 1.508 (4) |
N7—H7B | 0.8900 | C15—H15A | 0.9700 |
N7—H7C | 0.8900 | C15—H15B | 0.9700 |
C1—C2 | 1.535 (4) | C16—C17 | 1.509 (4) |
C2—C3 | 1.527 (4) | C16—H16A | 0.9700 |
C2—H2 | 0.9800 | C16—H16B | 0.9700 |
C3—C4 | 1.523 (4) | C17—C18 | 1.494 (4) |
C3—H3A | 0.9700 | C17—H17A | 0.9700 |
C3—H3B | 0.9700 | C17—H17B | 0.9700 |
| | | |
C2—N1—H1A | 109.5 | H5A—C5—H5B | 107.6 |
C2—N1—H1B | 109.5 | N7—C6—C5 | 111.4 (3) |
H1A—N1—H1B | 109.5 | N7—C6—H6A | 109.4 |
C2—N1—H1C | 109.5 | C5—C6—H6A | 109.4 |
H1A—N1—H1C | 109.5 | N7—C6—H6B | 109.4 |
H1B—N1—H1C | 109.5 | C5—C6—H6B | 109.4 |
C6—N7—H7A | 109.5 | H6A—C6—H6B | 108.0 |
C6—N7—H7B | 109.5 | O11—C13—O12 | 123.4 (3) |
H7A—N7—H7B | 109.5 | O11—C13—C14 | 120.4 (3) |
C6—N7—H7C | 109.5 | O12—C13—C14 | 116.2 (3) |
H7A—N7—H7C | 109.5 | C15—C14—C13 | 115.7 (3) |
H7B—N7—H7C | 109.5 | C15—C14—H14A | 108.4 |
O2—C1—O1 | 123.6 (3) | C13—C14—H14A | 108.4 |
O2—C1—C2 | 118.8 (4) | C15—C14—H14B | 108.4 |
O1—C1—C2 | 117.6 (4) | C13—C14—H14B | 108.4 |
N1—C2—C3 | 108.7 (3) | H14A—C14—H14B | 107.4 |
N1—C2—C1 | 107.8 (3) | C14—C15—C16 | 113.6 (3) |
C3—C2—C1 | 112.3 (3) | C14—C15—H15A | 108.9 |
N1—C2—H2 | 109.3 | C16—C15—H15A | 108.9 |
C3—C2—H2 | 109.3 | C14—C15—H15B | 108.9 |
C1—C2—H2 | 109.3 | C16—C15—H15B | 108.9 |
C4—C3—C2 | 114.5 (3) | H15A—C15—H15B | 107.7 |
C4—C3—H3A | 108.6 | C15—C16—C17 | 113.0 (3) |
C2—C3—H3A | 108.6 | C15—C16—H16A | 109.0 |
C4—C3—H3B | 108.6 | C17—C16—H16A | 109.0 |
C2—C3—H3B | 108.6 | C15—C16—H16B | 109.0 |
H3A—C3—H3B | 107.6 | C17—C16—H16B | 109.0 |
C5—C4—C3 | 111.3 (3) | H16A—C16—H16B | 107.8 |
C5—C4—H4A | 109.4 | C18—C17—C16 | 114.2 (3) |
C3—C4—H4A | 109.4 | C18—C17—H17A | 108.7 |
C5—C4—H4B | 109.4 | C16—C17—H17A | 108.7 |
C3—C4—H4B | 109.4 | C18—C17—H17B | 108.7 |
H4A—C4—H4B | 108.0 | C16—C17—H17B | 108.7 |
C6—C5—C4 | 114.6 (3) | H17A—C17—H17B | 107.6 |
C6—C5—H5A | 108.6 | O19—C18—O20 | 123.2 (3) |
C4—C5—H5A | 108.6 | O19—C18—C17 | 123.2 (3) |
C6—C5—H5B | 108.6 | O20—C18—C17 | 113.7 (3) |
C4—C5—H5B | 108.6 | C18—O20—H20 | 116 (2) |
| | | |
O2—C1—C2—N1 | 165.4 (4) | C4—C5—C6—N7 | −174.8 (3) |
O1—C1—C2—N1 | −16.2 (5) | O11—C13—C14—C15 | −6.3 (7) |
O2—C1—C2—C3 | −74.9 (5) | O12—C13—C14—C15 | 173.3 (4) |
O1—C1—C2—C3 | 103.6 (5) | C13—C14—C15—C16 | 173.6 (4) |
N1—C2—C3—C4 | −71.3 (4) | C14—C15—C16—C17 | 174.8 (4) |
C1—C2—C3—C4 | 169.5 (3) | C15—C16—C17—C18 | −178.1 (4) |
C2—C3—C4—C5 | 172.4 (3) | C16—C17—C18—O19 | −4.0 (6) |
C3—C4—C5—C6 | 175.7 (4) | C16—C17—C18—O20 | 174.4 (4) |
Hydrogen-bond geometry (Å, º) top
D—H···A | H···A | D···A | D—H···A |
N1—H1A···O19i | 2.31 | 2.935 (5) | 128 |
N1—H1A···O12ii | 2.49 | 3.220 (6) | 140 |
N1—H1B···O20iii | 2.08 | 2.796 (4) | 137 |
N1—H1C···O11iv | 1.89 | 2.761 (4) | 164 |
N7—H7A···O2i | 1.88 | 2.770 (5) | 178 |
N7—H7B···O2v | 2.06 | 2.918 (4) | 163 |
N7—H7B···O1v | 2.37 | 3.066 (4) | 135 |
N7—H7C···O12v | 2.30 | 3.022 (4) | 139 |
N7—H7C···O1vi | 2.35 | 3.037 (7) | 134 |
O20—H20···O12v | 1.27 (5) | 2.467 (3) | 175 (5) |
Symmetry codes: (i) −x, y−1/2, −z+1; (ii) −x+1, y−1/2, −z+1; (iii) x, y, z−1; (iv) x−1, y, z−1; (v) x−1, y, z; (vi) −x, y+1/2, −z+1. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | 2C6H15N2O2+·C6H8O42− | C6H15N2O2+·C6H9O4− |
Mr | 438.52 | 292.33 |
Crystal system, space group | Triclinic, P1 | Monoclinic, P21 |
Temperature (K) | 298 | 298 |
a, b, c (Å) | 5.4730 (15), 7.773 (2), 13.011 (4) | 10.532 (3), 7.2834 (17), 10.599 (3) |
α, β, γ (°) | 100.112 (4), 93.292 (4), 100.744 (4) | 90, 113.352 (3), 90 |
V (Å3) | 533.0 (3) | 746.5 (3) |
Z | 1 | 2 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.11 | 0.10 |
Crystal size (mm) | 0.69 × 0.60 × 0.20 | 0.91 × 0.65 × 0.17 |
|
Data collection |
Diffractometer | Bruker SMART CCD area-detector diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.912, 0.983 | 0.891, 0.981 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6254, 2494, 2269 | 6202, 1481, 1329 |
Rint | 0.014 | 0.017 |
(sin θ/λ)max (Å−1) | 0.660 | 0.602 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.120, 1.04 | 0.051, 0.135, 1.04 |
No. of reflections | 2494 | 2701 |
No. of parameters | 138 | 187 |
No. of restraints | 0 | 1 |
H-atom treatment | H-atom parameters constrained | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.45, −0.27 | 0.27, −0.21 |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | H···A | D···A | D—H···A |
N1—H1A···O11i | 1.94 | 2.730 (2) | 148 |
N1—H1B···O2ii | 1.94 | 2.815 (2) | 169 |
N1—H1C···O1iii | 1.91 | 2.762 (2) | 160 |
N7—H7A···O12 | 2.00 | 2.838 (2) | 156 |
N7—H7B···O12iv | 1.95 | 2.764 (2) | 152 |
N7—H7C···O1v | 2.33 | 3.037 (2) | 137 |
N7—H7C···O11vi | 2.43 | 3.042 (2) | 126 |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+2, −y+2, −z+1; (iii) x−1, y, z; (iv) −x, −y, −z; (v) x−1, y−1, z; (vi) −x+1, −y, −z. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | H···A | D···A | D—H···A |
N1—H1A···O19i | 2.31 | 2.935 (5) | 128 |
N1—H1A···O12ii | 2.49 | 3.220 (6) | 140 |
N1—H1B···O20iii | 2.08 | 2.796 (4) | 137 |
N1—H1C···O11iv | 1.89 | 2.761 (4) | 164 |
N7—H7A···O2i | 1.88 | 2.770 (5) | 178 |
N7—H7B···O2v | 2.06 | 2.918 (4) | 163 |
N7—H7B···O1v | 2.37 | 3.066 (4) | 135 |
N7—H7C···O12v | 2.30 | 3.022 (4) | 139 |
N7—H7C···O1vi | 2.35 | 3.037 (7) | 134 |
O20—H20···O12v | 1.27 (5) | 2.467 (3) | 175 (5) |
Symmetry codes: (i) −x, y−1/2, −z+1; (ii) −x+1, y−1/2, −z+1; (iii) x, y, z−1; (iv) x−1, y, z−1; (v) x−1, y, z; (vi) −x, y+1/2, −z+1. |
Torsion angles (°) defining the molecular conformations of (I) and (II) topTorsion | (I) | (II) |
N1-C2-C1-O1(ψ1) | -36.3 (1) | -16.2 (5) |
N1-C2-C3-C4(χ1) | -57.2 (1) | -71.3 (4) |
C2-C3-C4-C5(χ2) | -177.2 (1) | 172.4 (3) |
C3-C4-C5-C6(χ3) | -173.3 (1) | 175.7 (4) |
C4-C5-C6-N7(χ4) | 168.8 (1) | -174.8 (3) |
O11-C13-C14-C15 | 14.1 (1) | -6.3 (7) |
C13-C14-C15-C16 | 179.0 (1) | 173.6 (4) |
C14-C15-C16-C17 | 180.0 (1) | 174.8 (4) |
C15-C16-C17-C18 | | -178.1 (4) |
C16-C17-C18-O19 | | -4.0 (6) |
In (I), atoms C16 and C17 correspond to the centrosymmetric equivalents of atoms C15 and C14, respectively. |
In a long-term programme, we have been investigating the supramolecular association of amino acids and peptides using an approach involving the preparation and X-ray analysis of crystalline complexes of amino acids and peptides among themselves and with other molecules (Vijayan, 1988; Roy et al., 2005). The patterns of association observed in the course of these investigations were found to be of possible relevance to chemical evolution and the origin of life (Vijayan, 1980, 1988). For more than a decade, the focus of the programme has been on complexes of amino acids and peptides, particularly the basic amino acids arginine, lysine and histidine, with carboxylic acids that are believed to have existed in the prebiotic milieu, and with related compounds. The results obtained from the study of complexes involving dicarboxylic acids have been particularly interesting in relation to common features of association, their variability, and the effect of chirality on ionization state, stoichiometry and aggregation patterns. Many of the complexes reported by us have been those of DL- and L-lysine with monocarboxylic acids (Suresh et al., 1994; Suresh & Vijayan, 1983b, 1995) and dicarboxylic acids (Prasad & Vijayan, 1991; Venkatraman et al., 1997; Pratap et al., 2000; Saraswathi et al., 2001, 2003) with varying length. They also often exhibit common features of supramolecular association, despite differences in crystal their structures. The effect of reversing the chirality of half the amino acid molecules, as happens when comparing the crystal structures involving DL and L forms of the same amino acid, is manifested in two different ways in amino acid–carboxylic acid complexes. In some instances, the pattern of aggregation remains the same; the effect is absorbed by small alterations. In other instances, the effect is profound and leads to an entirely different pattern. The latter is true in the lysine complexes. Among the lysine complexes studied by us so far, one conspicuous absence was that of complexes involving adipic acid. Here, we report the crystal structures of the adipic acid complexes of DL-lysine, (I), and L-lysine, (II).
In both complexes, the amino acid exists as a positively charged zwitterion, with protonated amino groups and a deprotonated carboxyl group. Both the carboxyl groups in the adipic acid molecule are deprotonated in the DL-lysine complex, (I). The stoichiometry between the singly charged lysinium cation and the doubly charged adipate anion is 2:1. The lysinium cation occupies a general position, while the adipate ion is located across an inversion centre. In the L-lysine complex, (II), one carboxyl group in the adipic acid molecule is deprotonated and negatively charged while the other is neutral. The stoichiometry between the components is 1:1. The lysinium cation has the most sterically favourable conformation, with an all-trans extended side chain trans to the α-carboxylate group in both complexes (Prasad & Vijayan, 1991) (Fig. 1, Table 1). The adipate and hydrogen adipate anions have nearly fully extended conformations.
The crystal structures of the complexes are illustrated in Figs. 2 and 3, and the parameters of the hydrogen bonds that stabilize them are listed in Tables 2 and 3. The tables include a full description of the three-centred hydrogen bonds, but these are asymmetric and only the shorter branches are given in the figures. Atom N7 in the DL-lysine complex, and atoms N1 and N7 in the L-lysine complex, are involved in these hydrogen bonds. They are characterized by large deviations of the N—H···O angles from 180°.
In (I), the lysinium cations aggregate into layers parallel to the ab plane, as illustrated in Fig. 4. The molecular ions first form hydrogen-bonded dimers across inversion centres, stabilized by a pair of N1···O2 hydrogen bonds. These dimers then form ribbons parallel to a. Neighbouring dimers, related by translation in the ribbon, are interconnected by a pair of N1···O1 hydrogen bonds. We had earlier demonstrated, particularly in the context of prebiotic polymerization, that amino acids almost invariably aggregate in head-to-tail sequences of the type ···NH3+—CHR—COO−···NH3+—CHR—COO−···, in which the α-amino and the α-carboxylate groups are brought into periodic hydrogen-bonded proximity in a peptide-like arrangement. The adjacent molecules in this sequence are often related by a translation (an S sequence), a 21 screw (Z) or a glide plane (DL). When the O atom involved in the hydrogen bonds is cis to the amino group (conventionally referred to O1), then `1' is added as a suffix to S, Z or DL in the description of the sequence. If the O atom is trans to the amino group, then `2' is added (Suresh & Vijayan, 1983a). The N1···O1 hydrogen bonds referred to above form part of two S1 head-to-tail sequences. Neighbouring ribbons interact through a hydrogen bond between the side-chain terminal amino N atom (N7) from one and a carboxylate O atom (O1) from the other.
The lysinium layers are interconnected by adipate anions. A carboxylate O atom at one end of the adipate anion directly interacts with atom N1 of a lysinium cation in one layer, while its centrosymmetric equivalent interacts with a centrosymmetrically related atom N1 in the adjacent layer. This O atom also has a weak interaction with a side-chain amino group. The other O atom forms hydrogen bonds with the side-chain amino N atoms of two separate lysinium cations at both ends of the adipate anion. The adipate anions do not interact with each other. They are situated in interstitial spaces between packed lysinium cations.
In the present case, the effect of chirality on molecular aggregation is profound. The crystal structure of the L-lysine complex (Fig. 3) is different from that of the DL-lysine complex, except that in the L-lysine complex the lysinium cations also aggregate in layers. In each layer (Fig. 5), the most prominent feature is linear arrays of lysinium cations stabilized by intermolecular hydrogen bonds between side-chain amino groups and α-carboxylate O atoms. The molecules in the array are related by a translation. Adjacent arrays, related by a 21 screw axis, run in opposite directions. They are again interconnected by hydrogen bonds involving the side-chain amino group and carboxylate O atoms. This structure presents a very rare case in which the α-amino group is not involved in intermolecular interactions with the α-carboxylate group. In most cases, such interactions lead to one or more head-to-tail sequences in which the α-amino and α-carboxylate groups are brought into periodic hydrogen-bonded proximity in a peptide-like arrangement (Suresh & Vijayan, 1983a).
The hydrogen adipate anions are also arranged in linear arrays along a. The arrays form corrugated layers parallel to the ab plane (Fig. 6). In each array, adjacent hydrogen adipate anions are connected by a symmetric O···H···O hydrogen bond, in which the H atom can be described as being shared by the two anions (Fig. 7). Adjacent arrays in each layer are related by a 21 screw parallel to b. The arrays in each layer are interconnected by hydrogen bonds involving α-amino groups.