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Acta Crystallogr Sect E Struct Rep Online. 2008 May 1; 64(Pt 5): o943.
Published online 2008 April 30. doi:  10.1107/S1600536808011835
PMCID: PMC2961324

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

Abstract

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.

Related literature

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

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Object name is e-64-0o943-scheme1.jpg

Experimental

Crystal data

  • C6H10N4O4
  • M r = 202.18
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o943-efi1.jpg
  • a = 6.9787 (14) Å
  • b = 15.233 (3) Å
  • c = 16.637 (3) Å
  • V = 1768.6 (6) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.13 mm−1
  • T = 293 (2) K
  • 0.20 × 0.17 × 0.14 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: none
  • 13278 measured reflections
  • 2211 independent reflections
  • 1509 reflections with I > 2σ(I)
  • R int = 0.046
  • 3 standard reflections every 400 reflections intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.114
  • S = 1.06
  • 2211 reflections
  • 255 parameters
  • H-atom parameters constraned
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.21 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808011835/bg2177sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808011835/bg2177Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Comment

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).

Experimental

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

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.

Figures

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.
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.

Crystal data

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

Enraf–Nonius CAD-4 diffractometerRint = 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

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

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 (Å2)

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)
H200.8344−0.00990.44910.047*
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)

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, °)

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—O4−171.5 (4)N4—N3—C6—N2174.4 (3)
C6—N3—N4—O311.6 (6)N4—N3—C6—N1−6.2 (5)
C12—N7—N8—O8176.6 (4)C12—N5—C8—C943.1 (5)
C12—N7—N8—O7−3.9 (6)C12—N5—C8—C7167.7 (4)
C6—N1—C2—C365.9 (5)O6—C7—C8—N53.5 (5)
C6—N1—C2—C1−169.6 (3)O5—C7—C8—N5−177.9 (3)
O2—C1—C2—N10.9 (5)O6—C7—C8—C9127.1 (4)
O1—C1—C2—N1−179.2 (3)O5—C7—C8—C9−54.3 (4)
O2—C1—C2—C3127.5 (4)N5—C8—C9—C10−80.9 (4)
O1—C1—C2—C3−52.6 (4)C7—C8—C9—C10158.7 (3)
N1—C2—C3—C4−72.3 (4)C8—C9—C10—C1130.0 (5)
C1—C2—C3—C4166.4 (3)C12—N6—C11—C10−69.0 (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—N2−69.2 (4)C8—N5—C12—N7−171.0 (3)
C5—N2—C6—N1−30.9 (6)C11—N6—C12—N512.6 (6)
C5—N2—C6—N3148.5 (3)C11—N6—C12—N7−168.3 (3)
C2—N1—C6—N2−25.9 (5)N8—N7—C12—N50.1 (5)
C2—N1—C6—N3154.8 (3)N8—N7—C12—N6−178.9 (3)

Hydrogen-bond geometry (Å, °)

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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BG2177).

References

  • 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.
  • Enraf–Nonius (1988). CAD-4 Manual. Enraf–Nonius, Delft, The Netherlands.
  • Karapetyan, H. A., Antipin, M. Yu., Sukiasyan, R. P. & Petrosyan, A. M. (2007). J. Mol. Struct.831, 90–96.
  • 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. [PubMed]
  • Spek, A. L. (1997). HELENA University of Utrecht, The Netherlands.

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