supplementary materials


bg2177 scheme

Acta Cryst. (2008). E64, o943    [ doi:10.1107/S1600536808011835 ]

L-2-Nitrimino-1,3-diazepane-4-carboxylic acid

H. A. Karapetyan

Abstract top

The cyclic form of L-nitroarginine, C6H10N4O4, crystallizes with two independent molecules in the asymmetric unit. According to the geometrical parameters, similar in both molecules, the structure corresponds to that of L-2-nitrimino-1,3-diazepane-4-carboxylic acid; there are, however, conformational differences between the independent molecules, one of them being close to a twisted chair while the other might be described as a rather flattened boat. All six active H atoms in the two molecules are involved in hydrogen bonds, two of which are intramolecular and four intermolecular, forming an infinite chain of molecules along the b axis.

Comment top

The salts of the L-arginine have been intensively investigated as non-linear optical materials [Petrosyan et al.(2005) and Karapetyan et al.(2007)]. Recently, reports about L-nitroarginine [Apreyan et al.(2008)] and its crystalline salts [Apreyan et al.(2007)] (a promising line of non-linear optical materials) have appeared.

We present herein a structural study of the cyclic form of L-nitroarginine, C6H10N4O4 (I), which crystallizes with two independent molecules in the unit cell. The molecule was reported for the first time by (Paul et al., 1961) where it was suggested to be 2-nitro-4-carboxy-1,3- -diazacycloheptane, on the basis of chemical properties and IR spectra. According to the present single-crystal X-ray diffraction results the L-2-nitrimino-1,3-diazepane-4-carboxylic acid (L-NIDCA) form is suggested instead. A view of the H-bonded pair of crystallographically independent molecules is shown in Fig. 1. The values of bond distances and angles are in agreement with common accepted values which lead to the proposed structural interpretation. In spite of the metric similarities there are conformational differences between the independent moieties, one of them being close to a twist-chair while the other may be described as an essentially flattened boat. All six active H atoms in the crystal are involved in hydrogen bonding (Table 1), two of them being intra- and four inter-molecular, linking crystallographically independent units and by way of which an infinite chain of molecules along the b axis is formed (Fig. 2).

Related literature top

For the crystal structures of some analogs of the title compound, see: Apreyan et al. (2007, 2008); Karapetyan et al. (2007); Petrosyan et al. (2005). For related literature, see: Paul et al. (1961); Apreyan & Petrosyan (2008).

Experimental top

The obtainement of crystals of the title compound consisted of a two step process.First of all, the potassium salt of (I) was obtained by the reaction of L-nitroarginine with KOH. Afterwards, by the interaction of this potassium salt with HBF4 and further separation of the poorly soluble KBF4 salt, single crystals of (I) were obtained by slow evaporation at room temperature. The compound obtained is more correctly named L-2-nitrimino-1,3-diazepane-4-carboxylic acid (L-NIDCA). Details of the obtainment of L-NIDCA and L-NIDCA.H2O, as well as vibrational spectra, thermal properties and SHG will be reported soon separately [Apreyan and Petrosyan, 2008].

Refinement top

In spite of a pronounced centrosymmetric statistics of intensities, non-centrosymmetric P2(1)2(1)2(1) was chosen as the space group, on the basis of second harmonic generation. The statistics was latter justified by the structure resolution, which presents a strong pseudo centrosymmetric character. All the H atoms were placed in geometrically calculated positions and included in the refinement in a riding model approximation, with Uiso(H): 1.5Ueq(of hydroxyl O atoms) and 1.2Ueq (other carrier atoms). The positional as well as anisotropic thermal parameters of non-hydrogen atoms were refined without restraints. In the absense of any significant anomalous effect, Friedel pairs were merged.

Computing details top

Data collection: CAD-4 Manual (Enraf–Nonius, 1988); cell refinement: CAD-4 Manual (Enraf–Nonius, 1988); data reduction: HELENA (Spek, (1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A perspective view of the crystallographically independent molecules paired via intermolecular H-bonds showing atomic numbering and displacement ellipsoids at the 50% probability.
[Figure 2] Fig. 2. Packing of the molecules (without non-active H atoms). For clarity the non-hydrogen atoms of the crystallographically independent molecules participating in H-bonds are numbered only.
L-2-Nitrimino-1,3-diazepane-4-carboxylic acid top
Crystal data top
C6H10N4O4F000 = 848
Mr = 202.18Dx = 1.519 Mg m3
Orthorhombic, P212121Mo Kα radiation
λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 24 reflections
a = 6.9787 (14) Åθ = 14–16º
b = 15.233 (3) ŵ = 0.13 mm1
c = 16.637 (3) ÅT = 293 (2) K
V = 1768.6 (6) Å3Block, colourless
Z = 80.20 × 0.17 × 0.14 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.046
Radiation source: fine-focus sealed tubeθmax = 27.0º
Monochromator: graphiteθmin = 2.5º
T = 293(2) Kh = 7→8
ω/2θ scansk = 19→19
Absorption correction: nonel = 21→21
13278 measured reflections3 standard reflections
2211 independent reflections every 400 reflections
1509 reflections with I > 2σ(I) intensity decay: none
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.041H-atom parameters constrained
wR(F2) = 0.114  w = 1/[σ2(Fo2) + (0.0543P)2 + 0.5039P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
2211 reflectionsΔρmax = 0.25 e Å3
255 parametersΔρmin = 0.21 e Å3
Primary atom site location: structure-invariant direct methods
Crystal data top
C6H10N4O4V = 1768.6 (6) Å3
Mr = 202.18Z = 8
Orthorhombic, P212121Mo Kα
a = 6.9787 (14) ŵ = 0.13 mm1
b = 15.233 (3) ÅT = 293 (2) K
c = 16.637 (3) Å0.20 × 0.17 × 0.14 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.046
Absorption correction: none3 standard reflections
13278 measured reflections every 400 reflections
2211 independent reflections intensity decay: none
1509 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.041Δρmax = 0.25 e Å3
wR(F2) = 0.114Δρmin = 0.21 e Å3
S = 1.06Absolute structure: ?
2211 reflectionsFlack parameter: ?
255 parametersRogers parameter: ?
H-atom parameters constrained
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
xyzUiso*/Ueq
O10.7754 (5)0.88281 (14)0.60814 (15)0.0563 (8)
H10.77960.93370.59220.085*
O20.8669 (4)0.85314 (15)0.48298 (16)0.0472 (7)
O30.8340 (4)0.67954 (15)0.34868 (15)0.0530 (8)
O40.7646 (6)0.55602 (18)0.29427 (15)0.0723 (10)
O50.8340 (6)0.38278 (15)0.38570 (16)0.0659 (10)
H110.82100.43360.40090.099*
O60.8143 (4)0.35371 (15)0.51572 (15)0.0442 (7)
O70.8020 (5)0.17963 (15)0.64914 (14)0.0525 (8)
O80.7484 (6)0.05314 (16)0.70190 (15)0.0632 (9)
N10.8515 (4)0.68230 (16)0.50423 (17)0.0333 (7)
H30.90300.71030.46490.040*
N20.8213 (5)0.54128 (18)0.55682 (17)0.0392 (8)
H100.75180.49520.55060.047*
N30.8130 (5)0.55431 (18)0.42317 (17)0.0384 (8)
N40.8015 (5)0.59993 (18)0.35350 (18)0.0426 (8)
N50.8587 (4)0.18391 (17)0.49647 (17)0.0366 (7)
H130.86000.21320.54070.044*
N60.8668 (5)0.04394 (18)0.44140 (17)0.0393 (7)
H200.83440.00990.44910.047*
N70.8136 (4)0.05420 (18)0.57390 (16)0.0356 (7)
N80.7869 (5)0.09867 (18)0.64405 (18)0.0405 (7)
C10.8179 (5)0.8301 (2)0.5493 (2)0.0348 (9)
C20.7977 (5)0.73407 (19)0.57448 (18)0.0313 (8)
H20.66190.72300.58540.038*
C30.9090 (6)0.7139 (2)0.6508 (2)0.0442 (9)
H51.04500.71330.63880.053*
H40.88570.75980.69000.053*
C40.8511 (6)0.6259 (2)0.6862 (2)0.0429 (9)
H60.90560.62020.73960.052*
H70.71280.62360.69120.052*
C50.9179 (6)0.5504 (2)0.6348 (2)0.0428 (9)
H81.05420.55710.62530.051*
H90.90000.49640.66490.051*
C60.8289 (5)0.5961 (2)0.4948 (2)0.0313 (8)
C70.8343 (5)0.3309 (2)0.4473 (2)0.0343 (8)
C80.8689 (5)0.2356 (2)0.42267 (19)0.0336 (8)
H120.99920.23100.40110.040*
C90.7300 (6)0.2026 (2)0.3592 (2)0.0455 (9)
H150.61010.18700.38490.055*
H140.70390.24960.32140.055*
C100.8042 (6)0.1241 (2)0.3135 (2)0.0483 (10)
H170.69590.08930.29550.058*
H160.87160.14460.26610.058*
C110.9367 (6)0.0661 (2)0.36141 (19)0.0437 (9)
H190.95780.01220.33170.052*
H181.05940.09550.36670.052*
C120.8479 (5)0.09769 (19)0.5036 (2)0.0306 (8)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.107 (2)0.0200 (12)0.0418 (15)0.0005 (15)0.0200 (17)0.0027 (11)
O20.0777 (19)0.0213 (11)0.0427 (15)0.0003 (12)0.0161 (14)0.0023 (11)
O30.093 (2)0.0271 (13)0.0389 (15)0.0039 (13)0.0023 (15)0.0058 (12)
O40.137 (3)0.0472 (18)0.0325 (15)0.009 (2)0.009 (2)0.0075 (14)
O50.137 (3)0.0214 (13)0.0387 (15)0.0028 (16)0.0074 (17)0.0042 (11)
O60.0735 (18)0.0234 (12)0.0357 (13)0.0021 (12)0.0036 (13)0.0026 (11)
O70.096 (2)0.0264 (12)0.0353 (14)0.0023 (14)0.0031 (15)0.0035 (12)
O80.115 (3)0.0393 (15)0.0347 (15)0.0006 (19)0.0091 (18)0.0087 (13)
N10.0498 (18)0.0193 (13)0.0307 (16)0.0017 (13)0.0056 (14)0.0026 (13)
N20.064 (2)0.0215 (13)0.0319 (15)0.0086 (13)0.0034 (15)0.0008 (13)
N30.062 (2)0.0205 (14)0.0325 (16)0.0005 (14)0.0049 (15)0.0004 (13)
N40.067 (2)0.0277 (14)0.0334 (17)0.0067 (15)0.0013 (17)0.0016 (15)
N50.063 (2)0.0188 (13)0.0278 (16)0.0042 (14)0.0032 (15)0.0005 (13)
N60.064 (2)0.0198 (13)0.0339 (16)0.0009 (14)0.0020 (15)0.0001 (13)
N70.0563 (19)0.0212 (14)0.0294 (15)0.0001 (13)0.0012 (15)0.0011 (12)
N80.063 (2)0.0258 (14)0.0332 (17)0.0007 (14)0.0005 (17)0.0020 (14)
C10.042 (2)0.0233 (18)0.039 (2)0.0016 (14)0.0035 (17)0.0020 (17)
C20.0437 (19)0.0193 (14)0.0310 (17)0.0004 (14)0.0016 (16)0.0015 (13)
C30.063 (2)0.0331 (16)0.0363 (18)0.0035 (17)0.0063 (19)0.0031 (14)
C40.067 (2)0.0336 (18)0.0278 (18)0.0030 (17)0.0058 (17)0.0015 (15)
C50.061 (2)0.0317 (17)0.036 (2)0.0055 (18)0.0003 (19)0.0027 (15)
C60.037 (2)0.0225 (16)0.0344 (19)0.0017 (13)0.0061 (15)0.0002 (15)
C70.050 (2)0.0197 (17)0.0335 (19)0.0037 (14)0.0001 (16)0.0014 (15)
C80.046 (2)0.0205 (14)0.0345 (18)0.0019 (14)0.0019 (16)0.0002 (13)
C90.061 (2)0.0350 (17)0.0401 (19)0.0117 (17)0.0133 (19)0.0061 (15)
C100.078 (3)0.0290 (18)0.038 (2)0.0057 (18)0.006 (2)0.0030 (16)
C110.069 (3)0.0296 (17)0.0326 (19)0.0080 (17)0.0094 (19)0.0046 (15)
C120.041 (2)0.0198 (15)0.0309 (18)0.0005 (13)0.0014 (15)0.0023 (14)
Geometric parameters (Å, °) top
O1—C11.300 (4)N7—N81.362 (4)
O1—H10.8200N7—C121.365 (4)
O2—C11.207 (4)C1—C21.528 (4)
O3—N41.236 (3)C2—C31.519 (4)
O4—N41.219 (4)C2—H20.9800
O5—C71.294 (4)C3—C41.519 (5)
O5—H110.8200C3—H50.9700
O6—C71.199 (4)C3—H40.9700
O7—N81.241 (3)C4—C51.507 (5)
O8—N81.216 (3)C4—H60.9700
N1—C61.332 (4)C4—H70.9700
N1—C21.459 (4)C5—H80.9700
N1—H30.8600C5—H90.9700
N2—C61.328 (4)C7—C81.527 (4)
N2—C51.469 (4)C8—C91.520 (5)
N2—H100.8600C8—H120.9800
N3—N41.354 (4)C9—C101.508 (5)
N3—C61.356 (4)C9—H150.9700
N5—C121.321 (4)C9—H140.9700
N5—C81.460 (4)C10—C111.506 (5)
N5—H130.8600C10—H170.9700
N6—C121.327 (4)C10—H160.9700
N6—C111.457 (4)C11—H190.9700
N6—H200.8600C11—H180.9700
C1—O1—H1109.5C3—C4—H7109.2
C7—O5—H11109.5H6—C4—H7107.9
C6—N1—C2126.6 (3)N2—C5—C4115.5 (3)
C6—N1—H3116.7N2—C5—H8108.4
C2—N1—H3116.7C4—C5—H8108.4
C6—N2—C5127.5 (3)N2—C5—H9108.4
C6—N2—H10116.3C4—C5—H9108.4
C5—N2—H10116.3H8—C5—H9107.5
N4—N3—C6121.1 (3)N2—C6—N1122.2 (3)
O4—N4—O3121.6 (3)N2—C6—N3112.6 (3)
O4—N4—N3115.0 (3)N1—C6—N3125.2 (3)
O3—N4—N3123.2 (3)O6—C7—O5125.1 (3)
C12—N5—C8127.9 (3)O6—C7—C8123.3 (3)
C12—N5—H13116.0O5—C7—C8111.6 (3)
C8—N5—H13116.0N5—C8—C9112.0 (3)
C12—N6—C11127.1 (3)N5—C8—C7106.2 (3)
C12—N6—H20116.5C9—C8—C7113.6 (3)
C11—N6—H20116.5N5—C8—H12108.3
N8—N7—C12121.1 (3)C9—C8—H12108.3
O8—N8—O7122.1 (3)C7—C8—H12108.3
O8—N8—N7115.1 (3)C10—C9—C8113.2 (3)
O7—N8—N7122.8 (3)C10—C9—H15108.9
O2—C1—O1125.0 (3)C8—C9—H15108.9
O2—C1—C2123.7 (3)C10—C9—H14108.9
O1—C1—C2111.4 (3)C8—C9—H14108.9
N1—C2—C3115.4 (3)H15—C9—H14107.8
N1—C2—C1105.9 (3)C11—C10—C9114.1 (3)
C3—C2—C1112.0 (3)C11—C10—H17108.7
N1—C2—H2107.7C9—C10—H17108.7
C3—C2—H2107.7C11—C10—H16108.7
C1—C2—H2107.7C9—C10—H16108.7
C4—C3—C2111.5 (3)H17—C10—H16107.6
C4—C3—H5109.3N6—C11—C10114.5 (3)
C2—C3—H5109.3N6—C11—H19108.6
C4—C3—H4109.3C10—C11—H19108.6
C2—C3—H4109.3N6—C11—H18108.6
H5—C3—H4108.0C10—C11—H18108.6
C5—C4—C3111.9 (3)H19—C11—H18107.6
C5—C4—H6109.2N5—C12—N6122.5 (3)
C3—C4—H6109.2N5—C12—N7124.8 (3)
C5—C4—H7109.2N6—C12—N7112.7 (3)
C6—N3—N4—O4171.5 (4)N4—N3—C6—N2174.4 (3)
C6—N3—N4—O311.6 (6)N4—N3—C6—N16.2 (5)
C12—N7—N8—O8176.6 (4)C12—N5—C8—C943.1 (5)
C12—N7—N8—O73.9 (6)C12—N5—C8—C7167.7 (4)
C6—N1—C2—C365.9 (5)O6—C7—C8—N53.5 (5)
C6—N1—C2—C1169.6 (3)O5—C7—C8—N5177.9 (3)
O2—C1—C2—N10.9 (5)O6—C7—C8—C9127.1 (4)
O1—C1—C2—N1179.2 (3)O5—C7—C8—C954.3 (4)
O2—C1—C2—C3127.5 (4)N5—C8—C9—C1080.9 (4)
O1—C1—C2—C352.6 (4)C7—C8—C9—C10158.7 (3)
N1—C2—C3—C472.3 (4)C8—C9—C10—C1130.0 (5)
C1—C2—C3—C4166.4 (3)C12—N6—C11—C1069.0 (5)
C2—C3—C4—C569.8 (4)C9—C10—C11—N647.6 (5)
C6—N2—C5—C466.1 (5)C8—N5—C12—N68.0 (6)
C3—C4—C5—N269.2 (4)C8—N5—C12—N7171.0 (3)
C5—N2—C6—N130.9 (6)C11—N6—C12—N512.6 (6)
C5—N2—C6—N3148.5 (3)C11—N6—C12—N7168.3 (3)
C2—N1—C6—N225.9 (5)N8—N7—C12—N50.1 (5)
C2—N1—C6—N3154.8 (3)N8—N7—C12—N6178.9 (3)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H10···O6i0.862.272.938 (4)134
N6—H20···O2i0.862.172.988 (4)158
N1—H3···O2i0.862.212.629 (3)110
N1—H3···O3i0.862.052.591 (4)121
N5—H13···O6i0.862.202.625 (4)110
N5—H13···O7i0.861.922.571 (4)132
O5—H11···N3i0.821.882.690 (4)172
O5—H11···O4i0.822.603.084 (4)119
O1—H1···N7i0.821.882.685 (3)169
O1—H1···O8i0.822.593.033 (3)116
Symmetry codes: i; i; i.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
N2—H10···O6i0.862.272.938 (4)134
N6—H20···O2i0.862.172.988 (4)158
N1—H3···O3i0.862.052.591 (4)121
N5—H13···O7i0.861.922.571 (4)132
O5—H11···N3i0.821.882.690 (4)172
O1—H1···N7i0.821.882.685 (3)169
Symmetry codes: i; i; i.
Acknowledgements top

The author expresses his thanks to Dr R. A. Apreyan and Dr A. M. Petrosyan for providing the crystals and for valuable discussion of the results.

references
References top

Apreyan, R. A., Karapetyan, H. A. & Petrosyan, A. M. (2007). J. Mol. Struct. 875, 272–281.

Apreyan, R. A., Karapetyan, H. A. & Petrosyan, A. M. (2008). J. Mol. Struct. 874, 187–193.

Apreyan, R. A. & Petrosyan, A. M. (2008). In preparation.

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Paul, R., Anderson, G. W. & Callahan, F. M. (1961). J. Org. Chem. 26, 3347–3350.

Petrosyan, A. M., Sukiasyan, R. P., Karapetyan, H. A., Antipin, M. Yu. & Apreyan, R. A. (2005). J. Cryst. Growth, 275, e1927–e1933.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (1997). HELENA. University of Utrecht, The Netherlands.