X-ray studies on crystalline complexes involving amino acids and peptides. XXXVII. Novel aggregation patterns and effect of chirality in the complexes of DL- and L-lysine with glutaric acid

The complexes of glutaric acid with DL-lysine contain singly positively charged zwitterionic lysinium ions and singly negatively charged semi-glutarate ions. Both the ions exhibit different conformations in the two complexes. The structures contain head-to-tail sequences of amino acids. However, the aggregation patterns in the two complexes are entirely different, demonstrating the effect of chirality on molecular aggregation. These patterns also turn out to be different from those so far observed, in structures containing amino acids. The structures contain characteristic interaction patterns involving linear arrays of alternating amino and carboxylate groups.

Computing details

For both compounds, data collection: CAD4; cell refinement: CAD4; data reduction: CAD4; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP III. Software used to prepare material for publication: MS Word for (I); MS WORD for (II).

Figures

(I)

Crystal data

C6H15N2O2·C5H7O4	F(000) = 600
Mr = 278.31	Dx = 1.335 Mg m^−3
Monoclinic, Ia	Cu Kα radiation, λ = 1.54180 Å
a = 10.398 (6) Å	Cell parameters from 25 reflections
b = 8.662 (2) Å	θ = 10–30°
c = 15.393 (6) Å	µ = 0.92 mm^−1
β = 93.06 (2)°	T = 293 K
V = 1384.4 (10) Å^3	Rectangular, colourless
Z = 4	0.8 × 0.5 × 0.2 mm

Data collection

CAD4 diffractometer	1382 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.020
Graphite monochromator	θmax = 75.2°, θmin = 5.8°
ω–2/q scans	h = 0→13
Absorption correction: for a cylinder mounted on the ϕ axis Dwiggins JR Acta.Cryst 1975, A31,146	k = 0→10
Tmin = 0.714, Tmax = 0.728	l = −19→19
2138 measured reflections	3 standard reflections every 60 min
1426 independent reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.040	w = 1/[σ^2(Fo^2) + (0.0986P)^2 + 0.2437P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.152	(Δ/σ)max < 0.001
S = 1.30	Δρmax = 0.28 e Å^−3
1426 reflections	Δρmin = −0.25 e Å^−3
174 parameters	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
2 restraints	Extinction coefficient: 0.0038 (10)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack H D (1983), Acta Cryst. A39, 876-881
Secondary atom site location: difference Fourier map

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.8492 (3)	0.0830 (3)	0.28982 (18)	0.0388 (6)
H1C	0.8393	0.0667	0.2328	0.058*
H1B	0.9038	0.0137	0.3134	0.058*
H1A	0.8803	0.1775	0.2996	0.058*
O1	0.6747 (3)	0.2904 (4)	0.2421 (2)	0.0621 (8)
O2	0.5131 (2)	0.1704 (3)	0.3029 (2)	0.0508 (6)
C1	0.6300 (3)	0.1872 (3)	0.2858 (2)	0.0361 (6)
C2	0.7230 (3)	0.0680 (3)	0.32933 (19)	0.0326 (6)
H2	0.6890	−0.0361	0.3182	0.039*
C3	0.7365 (3)	0.0953 (4)	0.4275 (2)	0.0383 (7)
H3A	0.7702	0.1985	0.4376	0.046*
H3B	0.6513	0.0919	0.4502	0.046*
C4	0.8218 (4)	−0.0175 (4)	0.4788 (2)	0.0439 (7)
H4A	0.9106	−0.0024	0.4644	0.053*
H4B	0.7972	−0.1222	0.4630	0.053*
C5	0.8107 (3)	0.0046 (4)	0.5762 (2)	0.0425 (7)
H5A	0.8295	0.1114	0.5910	0.051*
H5B	0.7228	−0.0165	0.5907	0.051*
C6	0.9004 (4)	−0.0984 (4)	0.6298 (2)	0.0441 (7)
H6A	0.8830	−0.2051	0.6140	0.053*
H6B	0.9884	−0.0756	0.6163	0.053*
N7	0.8870 (3)	−0.0794 (4)	0.7241 (2)	0.0458 (7)
H7A	0.9417	−0.1422	0.7530	0.069*
H7B	0.8068	−0.1023	0.7370	0.069*
H7C	0.9044	0.0179	0.7391	0.069*
O11	0.4743 (3)	0.6461 (4)	0.3567 (2)	0.0556 (7)
O12	0.6622 (3)	0.6816 (3)	0.29923 (17)	0.0515 (6)
C13	0.5933 (3)	0.6281 (4)	0.3572 (2)	0.0386 (7)
C14	0.6633 (3)	0.5360 (4)	0.4289 (2)	0.0432 (7)
H14A	0.7171	0.6060	0.4640	0.052*
H14B	0.7198	0.4626	0.4024	0.052*
C15	0.5770 (4)	0.4483 (4)	0.4886 (3)	0.0480 (8)
H15A	0.5134	0.3913	0.4531	0.058*
H15B	0.6290	0.3737	0.5218	0.058*
C16	0.5078 (4)	0.5492 (5)	0.5512 (2)	0.0460 (8)
H16A	0.4663	0.6333	0.5189	0.055*
H16B	0.4408	0.4887	0.5766	0.055*
C17	0.5935 (3)	0.6157 (4)	0.6233 (2)	0.0387 (7)
O18	0.7053 (3)	0.5818 (4)	0.63856 (19)	0.0591 (8)
O19	0.5326 (3)	0.7166 (4)	0.66971 (18)	0.0542 (7)
H19	0.5735	0.7313	0.7160	0.081*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0354 (14)	0.0474 (14)	0.0338 (12)	0.0027 (10)	0.0035 (10)	−0.0001 (10)
O1	0.0501 (16)	0.0596 (16)	0.076 (2)	0.0030 (12)	0.0016 (13)	0.0320 (14)
O2	0.0307 (11)	0.0565 (14)	0.0645 (16)	0.0005 (10)	−0.0046 (10)	0.0095 (12)
C1	0.0329 (14)	0.0408 (14)	0.0341 (14)	−0.0034 (11)	−0.0043 (10)	0.0007 (11)
C2	0.0279 (13)	0.0356 (13)	0.0341 (14)	−0.0023 (10)	−0.0011 (10)	0.0002 (10)
C3	0.0388 (15)	0.0427 (14)	0.0334 (14)	0.0057 (12)	0.0018 (11)	0.0019 (11)
C4	0.0520 (18)	0.0464 (17)	0.0328 (15)	0.0133 (14)	−0.0039 (13)	0.0001 (12)
C5	0.0421 (16)	0.0486 (17)	0.0366 (15)	0.0082 (13)	−0.0005 (12)	0.0022 (12)
C6	0.0423 (17)	0.0519 (17)	0.0378 (16)	0.0098 (13)	−0.0002 (13)	0.0020 (13)
N7	0.0393 (15)	0.0569 (17)	0.0403 (15)	0.0062 (12)	−0.0056 (11)	0.0068 (12)
O11	0.0413 (13)	0.0697 (17)	0.0558 (15)	0.0114 (12)	0.0024 (11)	0.0151 (13)
O12	0.0487 (14)	0.0611 (14)	0.0452 (14)	0.0046 (11)	0.0066 (10)	0.0179 (11)
C13	0.0408 (16)	0.0367 (14)	0.0380 (15)	0.0030 (12)	0.0001 (12)	0.0002 (11)
C14	0.0456 (17)	0.0469 (16)	0.0371 (15)	0.0095 (13)	0.0031 (13)	0.0024 (13)
C15	0.066 (2)	0.0391 (15)	0.0393 (15)	−0.0006 (15)	0.0057 (15)	0.0014 (13)
C16	0.0427 (17)	0.0558 (18)	0.0397 (17)	−0.0033 (14)	0.0041 (13)	−0.0030 (14)
C17	0.0386 (16)	0.0467 (15)	0.0314 (13)	0.0014 (12)	0.0062 (11)	0.0043 (12)
O18	0.0478 (15)	0.088 (2)	0.0415 (13)	0.0161 (14)	−0.0003 (10)	−0.0026 (13)
O19	0.0455 (14)	0.0676 (17)	0.0492 (15)	0.0099 (12)	0.0002 (11)	−0.0149 (12)

Geometric parameters (Å, º)

N1—C2	1.481 (4)	O11—C13	1.246 (4)
O1—C1	1.226 (4)	O12—C13	1.262 (4)
O2—C1	1.266 (4)	C13—C14	1.517 (4)
C1—C2	1.543 (4)	C14—C15	1.521 (5)
C2—C3	1.528 (4)	C15—C16	1.512 (5)
C3—C4	1.514 (4)	C16—C17	1.500 (5)
C4—C5	1.521 (4)	C17—O18	1.210 (5)
C5—C6	1.505 (4)	C17—O19	1.313 (4)
C6—N7	1.475 (5)
O1—C1—O2	126.5 (3)	O11—C13—O12	123.4 (3)
O1—C1—C2	118.6 (3)	O11—C13—C14	120.6 (3)
O2—C1—C2	114.8 (3)	O12—C13—C14	116.1 (3)
N1—C2—C3	110.9 (2)	C13—C14—C15	115.2 (3)
N1—C2—C1	108.1 (2)	C16—C15—C14	114.4 (3)
C3—C2—C1	110.4 (2)	C17—C16—C15	114.2 (3)
C4—C3—C2	115.9 (3)	O18—C17—O19	122.9 (3)
C3—C4—C5	111.1 (3)	O18—C17—C16	125.2 (3)
C6—C5—C4	112.8 (3)	O19—C17—C16	111.9 (3)
N7—C6—C5	112.6 (3)

(II)

Crystal data

C6H15N2O2·C5H7O4	Dx = 1.310 Mg m^−3
Mr = 278.31	Cu Kα radiation, λ = 1.54180 Å
Trigonal, P31	Cell parameters from 25 reflections
a = 9.044 (1) Å	θ = 10–30°
c = 14.943 (3) Å	µ = 0.90 mm^−1
V = 1058.5 (3) Å^3	T = 293 K
Z = 3	Needle, colourless
F(000) = 450	1 × 0.44 × 0.31 mm

Data collection

CAD4 diffractometer	1387 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.050
Graphite monochromator	θmax = 75.6°, θmin = 5.7°
ω–2/q scans	h = 0→9
Absorption correction: empirical North et al ., 1968	k = 0→9
Tmin = 0.945, Tmax = 1.000	l = −17→18
1745 measured reflections	3 standard reflections every 60 min
1452 independent reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.063	w = 1/[σ^2(Fo^2) + (0.0208P)^2 + 1.5074P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.142	(Δ/σ)max < 0.001
S = 1.19	Δρmax = 0.31 e Å^−3
1452 reflections	Δρmin = −0.31 e Å^−3
174 parameters	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.035 (2)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack H D (1983), Acta Cryst. A39, 876-881
Secondary atom site location: difference Fourier map

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.6198 (6)	0.3550 (6)	0.6881 (3)	0.0365 (10)
H1C	0.6612	0.3020	0.7211	0.055*
H1B	0.6984	0.4230	0.6487	0.055*
H1A	0.5271	0.2780	0.6591	0.055*
O1	0.3256 (5)	0.1988 (5)	0.7860 (2)	0.0408 (9)
O2	0.4578 (5)	0.3893 (5)	0.8954 (2)	0.0434 (10)
C1	0.4429 (6)	0.3382 (7)	0.8160 (3)	0.0327 (11)
C2	0.5742 (6)	0.4590 (6)	0.7475 (3)	0.0321 (11)
H2	0.6766	0.5447	0.7788	0.038*
C3	0.5037 (8)	0.5484 (8)	0.6898 (4)	0.0407 (12)
H3A	0.4096	0.4629	0.6545	0.049*
H3B	0.5921	0.6238	0.6484	0.049*
C4	0.4413 (8)	0.6522 (7)	0.7414 (4)	0.0414 (12)
H4A	0.3624	0.5812	0.7877	0.050*
H4B	0.5378	0.7477	0.7704	0.050*
C5	0.3536 (8)	0.7185 (8)	0.6813 (4)	0.0462 (14)
H5A	0.2707	0.6257	0.6444	0.055*
H5B	0.4376	0.8047	0.6417	0.055*
C6	0.2643 (8)	0.7947 (8)	0.7328 (4)	0.0436 (13)
H6A	0.1930	0.7150	0.7787	0.052*
H6B	0.3488	0.8985	0.7622	0.052*
N7	0.1576 (6)	0.8343 (6)	0.6737 (3)	0.0402 (11)
H7A	0.1069	0.8789	0.7060	0.060*
H7B	0.0787	0.7389	0.6474	0.060*
H7C	0.2231	0.9089	0.6321	0.060*
O11	0.5053 (6)	0.3213 (5)	0.4835 (3)	0.0561 (12)
O12	0.3790 (7)	0.1100 (6)	0.5797 (3)	0.0656 (15)
C13	0.4068 (7)	0.1673 (8)	0.5009 (4)	0.0412 (12)
C14	0.3183 (8)	0.0438 (7)	0.4251 (4)	0.0417 (13)
H14A	0.2193	−0.0572	0.4485	0.050*
H14B	0.3953	0.0088	0.4004	0.050*
C15	0.2610 (8)	0.1187 (8)	0.3501 (4)	0.0442 (13)
H15A	0.1888	0.1597	0.3747	0.053*
H15B	0.3602	0.2150	0.3234	0.053*
C16	0.1637 (7)	−0.0138 (7)	0.2789 (4)	0.0403 (13)
H16A	0.2384	−0.0490	0.2514	0.048*
H16B	0.0690	−0.1134	0.3063	0.048*
C17	0.0968 (7)	0.0567 (8)	0.2081 (4)	0.0390 (12)
O18	0.1561 (7)	0.0931 (7)	0.1335 (3)	0.0634 (14)
O19	−0.0300 (6)	0.0744 (7)	0.2349 (3)	0.0592 (13)
H19	−0.0498	0.1286	0.1975	0.089*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.040 (2)	0.047 (3)	0.025 (2)	0.024 (2)	0.0012 (17)	−0.0008 (18)
O1	0.0302 (18)	0.042 (2)	0.035 (2)	0.0064 (16)	0.0021 (15)	−0.0037 (16)
O2	0.050 (2)	0.050 (2)	0.0277 (19)	0.0233 (19)	0.0027 (16)	−0.0015 (16)
C1	0.032 (2)	0.045 (3)	0.024 (2)	0.021 (2)	0.0024 (19)	0.005 (2)
C2	0.027 (2)	0.033 (3)	0.029 (2)	0.010 (2)	0.0044 (19)	0.0022 (19)
C3	0.047 (3)	0.048 (3)	0.033 (3)	0.028 (3)	0.005 (2)	0.008 (2)
C4	0.048 (3)	0.046 (3)	0.037 (3)	0.029 (3)	−0.004 (2)	0.002 (2)
C5	0.057 (4)	0.054 (3)	0.036 (3)	0.034 (3)	−0.001 (3)	0.006 (3)
C6	0.056 (4)	0.045 (3)	0.033 (3)	0.028 (3)	−0.008 (2)	0.001 (2)
N7	0.049 (3)	0.046 (3)	0.030 (2)	0.028 (2)	−0.002 (2)	−0.0001 (19)
O11	0.062 (3)	0.047 (3)	0.035 (2)	0.010 (2)	−0.001 (2)	−0.0024 (19)
O12	0.080 (3)	0.055 (3)	0.028 (2)	0.007 (2)	−0.010 (2)	0.0029 (19)
C13	0.042 (3)	0.050 (3)	0.032 (3)	0.023 (3)	−0.001 (2)	−0.004 (2)
C14	0.051 (3)	0.040 (3)	0.032 (3)	0.022 (3)	−0.011 (2)	−0.001 (2)
C15	0.049 (3)	0.046 (3)	0.036 (3)	0.022 (3)	−0.009 (2)	−0.001 (2)
C16	0.044 (3)	0.049 (3)	0.035 (3)	0.029 (3)	−0.011 (2)	−0.001 (2)
C17	0.043 (3)	0.050 (3)	0.026 (2)	0.025 (3)	−0.007 (2)	0.002 (2)
O18	0.077 (3)	0.100 (4)	0.038 (2)	0.062 (3)	0.013 (2)	0.021 (2)
O19	0.060 (3)	0.100 (4)	0.036 (2)	0.054 (3)	0.007 (2)	0.014 (2)

Geometric parameters (Å, º)

N1—C2	1.494 (6)	O11—C13	1.249 (7)
O1—C1	1.256 (6)	O12—C13	1.261 (7)
O2—C1	1.256 (6)	C13—C14	1.509 (7)
C1—C2	1.535 (6)	C14—C15	1.527 (7)
C2—C3	1.523 (7)	C15—C16	1.512 (8)
C3—C4	1.525 (8)	C16—C17	1.510 (7)
C4—C5	1.508 (7)	C17—O18	1.209 (7)
C5—C6	1.509 (8)	C17—O19	1.298 (7)
C6—N7	1.478 (7)
O2—C1—O1	126.0 (5)	O11—C13—O12	122.5 (5)
O2—C1—C2	117.8 (5)	O11—C13—C14	119.2 (5)
O1—C1—C2	116.2 (4)	O12—C13—C14	118.3 (5)
N1—C2—C3	108.6 (4)	C13—C14—C15	113.2 (5)
N1—C2—C1	107.9 (4)	C16—C15—C14	110.9 (5)
C3—C2—C1	112.1 (4)	C17—C16—C15	110.8 (5)
C2—C3—C4	115.0 (4)	O18—C17—O19	123.4 (5)
C5—C4—C3	111.9 (5)	O18—C17—C16	122.9 (5)
C4—C5—C6	112.7 (5)	O19—C17—C16	113.7 (5)
N7—C6—C5	111.6 (5)