X-ray studies on crystalline complexes involving amino acids and peptides. XL. Conformational variability, recurring and new features of aggregation, and effect of chirality in the malonic acid complexes of DL- and L-arginine

The crystal structures of the complexes of malonic acid with DL- and L-arginine, which contain positively charged argininium ions and negatively charged semimalonate ions, further demonstrate the conformational flexibility of amino acids. A larger proportion of folded conformations than would be expected on the basis of steric consideration appears to occur in arginine, presumably because of the requirements of hydrogen bonding. The aggregation pattern in the DL-arginine complex bears varying degrees of resemblance to patterns observed in other similar structures. An antiparallel hydrogen-bonded dimeric arrangement of arginine, and to a lesser extent lysine, is a recurring motif. Similarities also exist among the structures in the interactions with this motif and its assembly into larger features of aggregation. However, the aggregation pattern observed in the L-arginine complex differs from any observed so far, which demonstrates that all the general patterns of amino-acid aggregation have not yet been elucidated. The two complexes represent cases where the reversal of the chirality of half the amino-acid molecules leads to a fundamentally different aggregation pattern.

Computing details

For both compounds, data collection: SMART; cell refinement: SAINT; data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997). Molecular graphics: ORTEP-3 for DL; ORTEP 3 for L. Software used to prepare material for publication: MS Word 2000 for DL; MS WORD 2000 for L.

Figures

(DL)

Crystal data

C9H20N4O7	Z = 8
Mr = 296.29	F(000) = 1264
Monoclinic, C2/c	Dx = 1.409 Mg m^−3
a = 19.559 (2) Å	Mo Kα radiation, λ = 0.71073 Å
b = 5.0296 (6) Å	µ = 0.12 mm^−1
c = 28.407 (4) Å	T = 293 K
β = 90.553 (2)°	Platy, colourless
V = 2794.3 (6) Å^3	0.47 × 0.07 × 0.05 mm

Data collection

CCD diffractometer	1471 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.086
Graphite monochromator	θmax = 23.5°, θmin = 1.4°
ω–2/q scans	h = −21→21
11194 measured reflections	k = −5→5
2077 independent reflections	l = −31→31

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.069	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.141	H atoms treated by a mixture of independent and constrained refinement
S = 1.12
2077 reflections	(Δ/σ)max < 0.001
193 parameters	Δρmax = 0.21 e Å^−3
0 restraints	Δρmin = −0.22 e Å^−3

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	0.28733 (14)	−0.1220 (5)	0.55565 (10)	0.0297 (7)
H1B	0.2899	−0.1872	0.5847	0.045*
H1A	0.3000	−0.2463	0.5352	0.045*
H1C	0.2445	−0.0725	0.5494	0.045*
O1	0.31441 (13)	0.0729 (5)	0.46927 (9)	0.0383 (7)
O2	0.34037 (12)	0.4715 (4)	0.49770 (8)	0.0322 (6)
C1	0.32865 (16)	0.2247 (7)	0.50207 (12)	0.0242 (8)
C2	0.33368 (16)	0.1131 (6)	0.55164 (12)	0.0256 (8)
H2	0.3194	0.2497	0.5741	0.031*
C3	0.40648 (16)	0.0236 (7)	0.56387 (13)	0.0333 (9)
H3A	0.4064	−0.0579	0.5948	0.040*
H3B	0.4203	−0.1109	0.5414	0.040*
C4	0.45910 (17)	0.2484 (7)	0.56372 (13)	0.0321 (9)
H4A	0.4632	0.3185	0.5321	0.039*
H4B	0.4437	0.3912	0.5840	0.039*
C5	0.52843 (17)	0.1495 (7)	0.58082 (13)	0.0366 (10)
H5A	0.5233	0.0708	0.6118	0.044*
H5B	0.5441	0.0114	0.5597	0.044*
N6	0.57996 (14)	0.3573 (6)	0.58350 (11)	0.0381 (8)
H6	0.6030	0.3873	0.5584	0.046*
C7	0.59484 (18)	0.5041 (7)	0.62061 (13)	0.0324 (9)
N8	0.56127 (16)	0.4749 (7)	0.66077 (11)	0.0516 (10)
H8A	0.5292	0.3586	0.6628	0.062*
H8B	0.5716	0.5724	0.6847	0.062*
N9	0.64452 (14)	0.6826 (6)	0.61870 (10)	0.0388 (8)
H9A	0.6672	0.7030	0.5932	0.047*
H9B	0.6541	0.7781	0.6430	0.047*
O11	0.55248 (16)	1.0852 (7)	0.80604 (13)	0.0757 (11)
H11	0.559 (3)	0.963 (10)	0.773 (2)	0.12 (2)*
O12	0.60831 (17)	1.4232 (7)	0.83521 (12)	0.0782 (11)
C13	0.6036 (2)	1.2478 (10)	0.80574 (16)	0.0507 (12)
C14	0.6558 (2)	1.2140 (8)	0.76781 (13)	0.0456 (11)
H14A	0.6994	1.1761	0.7829	0.055*
H14B	0.6604	1.3831	0.7518	0.055*
C15	0.6433 (2)	1.0026 (8)	0.73083 (15)	0.0433 (10)
O16	0.59218 (16)	0.8539 (6)	0.73578 (10)	0.0624 (9)
O17	0.68318 (15)	0.9889 (6)	0.69784 (11)	0.0643 (9)
OW	−0.2144 (2)	0.2606 (8)	0.65004 (11)	0.0701 (11)
HWA	−0.249 (2)	0.193 (9)	0.6645 (17)	0.068 (17)*
HWB	−0.182 (3)	0.118 (12)	0.657 (2)	0.12 (2)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0309 (18)	0.0306 (16)	0.0276 (17)	−0.0026 (14)	−0.0018 (13)	0.0044 (14)
O1	0.0555 (18)	0.0322 (15)	0.0272 (15)	−0.0089 (13)	0.0011 (13)	−0.0011 (12)
O2	0.0382 (15)	0.0228 (14)	0.0356 (15)	−0.0013 (12)	0.0031 (12)	0.0033 (11)
C1	0.017 (2)	0.023 (2)	0.032 (2)	0.0020 (16)	0.0026 (16)	0.0013 (18)
C2	0.026 (2)	0.0205 (18)	0.030 (2)	−0.0006 (16)	−0.0002 (16)	0.0020 (16)
C3	0.029 (2)	0.034 (2)	0.037 (2)	−0.0038 (18)	−0.0022 (18)	0.0056 (18)
C4	0.026 (2)	0.035 (2)	0.035 (2)	−0.0003 (18)	−0.0008 (17)	0.0058 (17)
C5	0.030 (2)	0.043 (2)	0.037 (2)	−0.0004 (19)	−0.0014 (18)	0.0000 (19)
N6	0.0256 (18)	0.061 (2)	0.0281 (19)	−0.0142 (17)	0.0050 (14)	−0.0023 (17)
C7	0.023 (2)	0.047 (2)	0.027 (2)	0.000 (2)	−0.0037 (18)	0.0035 (19)
N8	0.049 (2)	0.071 (2)	0.035 (2)	−0.0271 (19)	0.0111 (18)	−0.0079 (18)
N9	0.0316 (19)	0.054 (2)	0.0306 (19)	−0.0137 (17)	0.0021 (15)	−0.0018 (16)
O11	0.057 (2)	0.095 (3)	0.077 (3)	−0.020 (2)	0.0326 (19)	−0.027 (2)
O12	0.084 (3)	0.086 (3)	0.065 (2)	−0.010 (2)	0.030 (2)	−0.031 (2)
C13	0.048 (3)	0.061 (3)	0.043 (3)	0.006 (3)	0.008 (2)	−0.003 (2)
C14	0.039 (3)	0.057 (3)	0.041 (3)	−0.001 (2)	0.004 (2)	−0.002 (2)
C15	0.038 (3)	0.053 (3)	0.039 (3)	−0.001 (2)	−0.001 (2)	−0.001 (2)
O16	0.060 (2)	0.070 (2)	0.058 (2)	−0.0224 (19)	0.0146 (17)	−0.0158 (17)
O17	0.057 (2)	0.087 (2)	0.050 (2)	−0.0143 (18)	0.0219 (17)	−0.0257 (17)
OW	0.063 (2)	0.095 (3)	0.052 (2)	−0.003 (2)	0.0099 (19)	0.032 (2)

Geometric parameters (Å, º)

N1—C2	1.495 (4)	C7—N9	1.325 (4)
O1—C1	1.234 (4)	C7—N8	1.330 (4)
O2—C1	1.269 (4)	O11—C13	1.292 (5)
C1—C2	1.518 (5)	O12—C13	1.219 (5)
C2—C3	1.530 (4)	C13—C14	1.501 (6)
C3—C4	1.529 (4)	C14—C15	1.513 (5)
C4—C5	1.520 (5)	C15—O17	1.227 (5)
C5—N6	1.453 (4)	C15—O16	1.257 (5)
N6—C7	1.317 (4)
O1—C1—O2	124.8 (3)	N6—C7—N9	120.2 (3)
O1—C1—C2	118.9 (3)	N6—C7—N8	121.2 (4)
O2—C1—C2	116.2 (3)	N9—C7—N8	118.6 (3)
N1—C2—C1	109.2 (3)	O12—C13—O11	120.5 (4)
N1—C2—C3	108.3 (2)	O12—C13—C14	121.8 (5)
C1—C2—C3	111.8 (3)	O11—C13—C14	117.7 (4)
C4—C3—C2	114.0 (3)	C13—C14—C15	118.1 (4)
C5—C4—C3	110.9 (3)	O17—C15—O16	124.3 (4)
N6—C5—C4	113.4 (3)	O17—C15—C14	118.0 (4)
C7—N6—C5	126.3 (3)	O16—C15—C14	117.7 (4)
O1—C1—C2—N1	−28.9 (4)	H1A—N1—C2—H2	179.8
O2—C1—C2—N1	151.8 (3)	H1B—N1—C2—H2	−60.2
O1—C1—C2—C3	90.9 (4)	H1C—N1—C2—H2	59.8
O2—C1—C2—C3	−88.4 (3)	H1A—N1—C2—C1	60.5
N1—C2—C3—C4	−177.0 (3)	H1B—N1—C2—C1	−179.5
C1—C2—C3—C4	62.7 (4)	H1C—N1—C2—C1	−59.5
C2—C3—C4—C5	174.4 (3)	H1A—N1—C2—C3	−61.5
C3—C4—C5—N6	−177.4 (3)	H1B—N1—C2—C3	58.5
C4—C5—N6—C7	92.1 (4)	H1C—N1—C2—C3	178.5
C5—N6—C7—N9	178.1 (3)	O1—C1—C2—N1	−28.9 (4)
C5—N6—C7—N8	−1.0 (6)	O2—C1—C2—N1	151.8 (3)
O12—C13—C14—C15	−176.0 (4)	O11—C13—C14—C15	3.4 (6)
O11—C13—C14—C15	3.4 (6)	O12—C13—C14—C15	−176.0 (4)
C13—C14—C15—O17	174.5 (4)	O16—C15—C14—C13	−4.9 (6)
C13—C14—C15—O16	−4.9 (6)	O17—C15—C14—C13	174.5 (4)

(L)

Crystal data

C9H18N4O6	V = 324.4 (6) Å^3
Mr = 278.27	Z = 1
Triclinic, P1	F(000) = 148
a = 5.353 (6) Å	Dx = 1.425 Mg m^−3
b = 6.931 (8) Å	Mo Kα radiation, λ = 0.71073 Å
c = 9.922 (11) Å	µ = 0.12 mm^−1
α = 69.530 (16)°	T = 293 K
β = 89.035 (17)°	Platy, colourless
γ = 71.128 (16)°	0.42 × 0.27 × 0.15 mm

Data collection

CCD diffractometer	2415 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.030
Graphite monochromator	θmax = 27.3°, θmin = 2.2°
ω–2/q scans	h = −6→6
3424 measured reflections	k = −8→8
2525 independent reflections	l = −12→12

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.038	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.107
S = 0.98	(Δ/σ)max < 0.001
2525 reflections	Δρmax = 0.30 e Å^−3
176 parameters	Δρmin = −0.17 e Å^−3
3 restraints	Absolute structure: Flack H D (1983), Acta Cryst. A39, 876-881
Primary atom site location: structure-invariant direct methods

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	0.0671 (3)	1.0348 (3)	0.49646 (16)	0.0311 (3)
H1B	−0.0761	0.9954	0.5156	0.047*
H1A	0.1673	0.9608	0.4461	0.047*
H1C	0.0173	1.1776	0.4451	0.047*
O1	0.5550 (3)	1.0450 (3)	0.48354 (16)	0.0495 (4)
O2	0.5629 (3)	1.1103 (3)	0.68440 (17)	0.0483 (4)
C1	0.4655 (3)	1.0556 (3)	0.59818 (19)	0.0309 (4)
C2	0.2225 (3)	0.9854 (3)	0.63455 (18)	0.0318 (4)
H2	0.1130	1.0668	0.6903	0.038*
C3	0.3101 (4)	0.7358 (3)	0.7235 (2)	0.0402 (4)
H3A	0.4140	0.6566	0.6664	0.048*
H3B	0.4228	0.7023	0.8099	0.048*
C4	0.0764 (4)	0.6583 (3)	0.7670 (3)	0.0445 (5)
H4A	−0.0226	0.7335	0.8274	0.053*
H4B	−0.0405	0.6991	0.6805	0.053*
C5	0.1533 (4)	0.4141 (3)	0.8479 (2)	0.0421 (4)
H5A	−0.0052	0.3738	0.8544	0.051*
H5B	0.2710	0.3384	0.7931	0.051*
N6	0.2836 (3)	0.3416 (3)	0.99219 (18)	0.0385 (4)
H6	0.1951	0.3964	1.0511	0.046*
C7	0.5245 (3)	0.1997 (3)	1.04230 (19)	0.0317 (4)
N8	0.6912 (3)	0.1245 (3)	0.95796 (18)	0.0380 (4)
H8A	0.6437	0.1681	0.8669	0.046*
H8B	0.8471	0.0320	0.9942	0.046*
N9	0.6075 (4)	0.1328 (3)	1.18205 (18)	0.0451 (4)
H9A	0.5041	0.1821	1.2386	0.054*
H9B	0.7644	0.0403	1.2157	0.054*
O11	0.7053 (3)	0.6196 (3)	0.06034 (16)	0.0506 (4)
H11	0.523 (14)	0.705 (10)	0.055 (6)	0.145 (19)*
O12	1.0040 (3)	0.4097 (2)	0.24880 (17)	0.0467 (4)
C13	0.7776 (4)	0.5358 (3)	0.1979 (2)	0.0371 (4)
C14	0.5744 (4)	0.5978 (3)	0.2955 (2)	0.0403 (4)
H14A	0.6458	0.6598	0.3530	0.048*
H14B	0.5524	0.4647	0.3618	0.048*
C15	0.3006 (4)	0.7584 (3)	0.2241 (2)	0.0401 (4)
O16	0.2553 (3)	0.8193 (3)	0.08737 (17)	0.0512 (4)
O17	0.1349 (3)	0.8216 (3)	0.3008 (2)	0.0573 (4)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0204 (6)	0.0406 (7)	0.0290 (7)	−0.0118 (6)	0.0027 (5)	−0.0072 (6)
O1	0.0312 (6)	0.0954 (12)	0.0333 (7)	−0.0330 (7)	0.0104 (5)	−0.0264 (7)
O2	0.0365 (7)	0.0697 (10)	0.0536 (9)	−0.0215 (7)	0.0049 (6)	−0.0368 (8)
C1	0.0226 (7)	0.0368 (9)	0.0295 (8)	−0.0076 (6)	0.0002 (6)	−0.0096 (7)
C2	0.0262 (8)	0.0457 (10)	0.0261 (8)	−0.0146 (7)	0.0079 (6)	−0.0141 (7)
C3	0.0304 (9)	0.0491 (11)	0.0316 (9)	−0.0102 (8)	0.0006 (7)	−0.0066 (8)
C4	0.0302 (9)	0.0412 (10)	0.0493 (11)	−0.0076 (8)	0.0042 (8)	−0.0056 (9)
C5	0.0336 (9)	0.0383 (10)	0.0493 (11)	−0.0099 (8)	−0.0009 (8)	−0.0119 (8)
N6	0.0358 (8)	0.0373 (8)	0.0374 (8)	−0.0080 (7)	0.0096 (7)	−0.0120 (7)
C7	0.0369 (9)	0.0293 (8)	0.0296 (9)	−0.0151 (7)	0.0060 (7)	−0.0083 (7)
N8	0.0332 (8)	0.0425 (8)	0.0310 (8)	−0.0044 (6)	0.0011 (6)	−0.0125 (7)
N9	0.0500 (10)	0.0513 (10)	0.0299 (8)	−0.0127 (8)	0.0045 (7)	−0.0143 (7)
O11	0.0540 (9)	0.0478 (8)	0.0363 (8)	−0.0078 (7)	0.0107 (6)	−0.0081 (6)
O12	0.0404 (8)	0.0383 (7)	0.0495 (8)	−0.0074 (6)	0.0102 (7)	−0.0078 (6)
C13	0.0372 (10)	0.0296 (9)	0.0414 (10)	−0.0110 (8)	0.0069 (8)	−0.0095 (8)
C14	0.0414 (10)	0.0359 (9)	0.0387 (11)	−0.0094 (8)	0.0056 (8)	−0.0112 (8)
C15	0.0382 (10)	0.0363 (9)	0.0484 (12)	−0.0116 (8)	0.0059 (8)	−0.0195 (9)
O16	0.0452 (8)	0.0513 (9)	0.0462 (8)	−0.0054 (7)	−0.0041 (7)	−0.0144 (7)
O17	0.0420 (8)	0.0653 (10)	0.0676 (12)	−0.0061 (7)	0.0055 (7)	−0.0386 (9)

Geometric parameters (Å, º)

N1—C2	1.487 (3)	C7—N8	1.322 (3)
O1—C1	1.243 (3)	C7—N9	1.331 (3)
O2—C1	1.232 (2)	O11—C13	1.291 (3)
C1—C2	1.526 (3)	O12—C13	1.231 (3)
C2—C3	1.554 (3)	C13—C14	1.503 (3)
C3—C4	1.515 (3)	C14—C15	1.522 (3)
C4—C5	1.513 (3)	C15—O17	1.232 (3)
C5—N6	1.447 (3)	C15—O16	1.273 (3)
N6—C7	1.318 (3)
O2—C1—O1	125.10 (18)	N6—C7—N8	122.36 (18)
O2—C1—C2	118.90 (17)	N6—C7—N9	119.34 (17)
O1—C1—C2	115.95 (15)	N8—C7—N9	118.28 (18)
N1—C2—C1	108.20 (14)	O12—C13—O11	121.92 (19)
N1—C2—C3	109.25 (15)	O12—C13—C14	120.5 (2)
C1—C2—C3	110.19 (15)	O11—C13—C14	117.60 (18)
C4—C3—C2	112.47 (15)	C13—C14—C15	117.32 (18)
C5—C4—C3	114.03 (17)	O17—C15—O16	123.5 (2)
N6—C5—C4	113.40 (18)	O17—C15—C14	118.7 (2)
C7—N6—C5	126.40 (16)	O16—C15—C14	117.78 (17)
O2—C1—C2—N1	152.13 (16)	H1A—N1—C2—C1	60.3
O1—C1—C2—N1	−30.3 (2)	H1B—N1—C2—C1	−179.7
O2—C1—C2—C3	−88.5 (2)	H1C—N1—C2—C1	−59.7
O1—C1—C2—C3	89.1 (2)	H1A—N1—C2—H2	179.9
N1—C2—C3—C4	−63.2 (2)	H1B—N1—C2—H2	−60.1
C1—C2—C3—C4	178.09 (16)	H1C—N1—C2—H2	59.9
C2—C3—C4—C5	177.33 (17)	H1A—N1—C2—C3	−59.7
C3—C4—C5—N6	70.1 (2)	H1B—N1—C2—C3	60.3
C4—C5—N6—C7	−120.1 (2)	H1C—N1—C2—C3	−179.7
C5—N6—C7—N8	8.3 (3)	O1—C1—C2—N1	−30.3 (2)
C5—N6—C7—N9	−173.36 (18)	O2—C1—C2—N1	152.13 (16)
O12—C13—C14—C15	178.72 (18)	O11—C13—C14—C15	−1.2 (3)
O11—C13—C14—C15	−1.2 (3)	O12—C13—C14—C15	178.72 (18)
C13—C14—C15—O17	−175.94 (19)	O16—C15—C14—C13	4.4 (3)
C13—C14—C15—O16	4.4 (3)	O17—C15—C14—C13	−175.94 (19)