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Acta Crystallogr Sect E Struct Rep Online. 2008 July 1; 64(Pt 7): o1222.
Published online 2008 June 7. doi:  10.1107/S1600536808015146
PMCID: PMC2961828

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

Abstract

The title compound, C6H10N4O4·H2O, crystallizes with two independent formula units in the asymmetric unit, their geometric parameters being quite similar. The conformations of the 1,3-diazepane rings are also similar and close to a twist-boat. All ten O- and N-bound H atoms are involved in hydrogen bonds, two of which are intra- and eight inter­molecular linking crystallographically independent mol­ecules, into a three-dimensional hydrogen-bonded network.

Related literature

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

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Object name is e-64-o1222-scheme1.jpg

Experimental

Crystal data

  • C6H10N4O4·H2O
  • M r = 220.20
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1222-efi1.jpg
  • a = 9.0115 (18) Å
  • b = 14.729 (3) Å
  • c = 15.257 (3) Å
  • V = 2025.0 (7) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.13 mm−1
  • T = 293 (2) K
  • 0.22 × 0.17 × 0.12 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: none
  • 6714 measured reflections
  • 2512 independent reflections
  • 1583 reflections with I > 2σ(I)
  • R int = 0.040
  • 3 standard reflections every 400 reflections intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.045
  • wR(F 2) = 0.132
  • S = 1.02
  • 2512 reflections
  • 286 parameters
  • 6 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.44 e Å−3
  • Δρmin = −0.27 e Å−3

Data collection: DATCOL in CAD-4 Manual (Enraf–Nonius, 1988 [triangle]); cell refinement: LS in CAD-4 Manual (Enraf–Nonius, 1988 [triangle]); 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/S1600536808015146/bg2187sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808015146/bg2187Isup2.hkl

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

Acknowledgments

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

supplementary crystallographic information

Comment

The L-nitroarginine and its crystaline salts have been investigated as a promising line of non-linear optical materials [Apreyan et al.(2008a) and Apreyan et al.(2008b)]. The cyclic form of L-nitroarginine was reported for the first time in Paul et al., 1961, where it was suggested to be 2-nitro-4-carboxy-1,3-diazacycloheptane. Recently, on the basis of the crystal structure of the cyclic form of L-nitroarginine [Karapetyan, 2008] it was shown to be L-2-nitrimino-1,3-diazepane-4-carboxylic acid (L-NIDCA).

We present herein a structural study of the L-NIDCA monohydrate, C6H10N4O4 × H2O (I), which crystallizes with two independent formulas in the asymmetric unit, shown in Fig. 1. The metric parameters of independent L-NIDCA molecules are in agreement with commonly accepted values and their conformations are the same, being close to that of a 7-membered ring twist-boat . All ten active H atoms in the crystal are involved in hydrogen bonding (Table 1), two of them being intra- and eight inter-molecular, linking crystallographically independent units and by way of which a tree-dimensional H bonded network results (Fig. 2).

Experimental

By the reaction of L-nitroarginine with KOH the potassium salt was obtained. 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 below room temperature. 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

The positions of all hydrogen atoms clearly revealed in a difference Fourier map. Foillowing common practice, however, all H atoms except those belonging to water molecules were placed in geometrically calculated positions and included in the refinement in a riding model approximation (O-H: 0.85Å, C-H: 0.97-0.98Å, N-H:0.86Å). The positions of H atoms of both independent water molecules were determined from the difference Fourier maps and refined with restrained O-H: 0.85 (4)Å distances. Displacement parameters were taken as Uiso(H): 1.2Ueq(carrier atom).

In the absense of any significant anomalous effect, Friedel pairs were merged, which explains the rather low parameters/reflections ratio.

Figures

Fig. 1.
View of the asymmetric unit of (I) showing atomic numbering and displacement ellipsoids at the 50% probability. Only active H atoms are presented for clarity. H-bonds drawn in broken lines.
Fig. 2.
Packing view of the structure ( non-active H atoms not shown). H-bonds drawn in broken lines. Symmetry codes: (i) -x + 2, y - 1/2, -z + 3/2; (ii) -x + 2, y + 1/2, -z + 3/2; (iii) -x + 1, y - 1/2, -z + 3/2; (iv) -x + 1, y + 1/2, -z + 3/2.

Crystal data

C6H10N4O4·H2OF(000) = 928
Mr = 220.20Dx = 1.445 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 24 reflections
a = 9.0115 (18) Åθ = 14–16°
b = 14.729 (3) ŵ = 0.13 mm1
c = 15.257 (3) ÅT = 293 K
V = 2025.0 (7) Å3Prismatic, yellow
Z = 80.22 × 0.17 × 0.12 mm

Data collection

Enraf–Nonius CAD-4 diffractometerRint = 0.040
Radiation source: fine-focus sealed tubeθmax = 27.0°, θmin = 2.6°
graphiteh = 0→11
ω/2θ scansk = −17→18
6714 measured reflectionsl = −19→19
2512 independent reflections3 standard reflections every 400 reflections
1583 reflections with I > 2σ(I) intensity decay: none

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.132H atoms treated by a mixture of independent and constrained refinement
S = 1.02w = 1/[σ2(Fo2) + (0.0704P)2 + 0.3433P] where P = (Fo2 + 2Fc2)/3
2512 reflections(Δ/σ)max = 0.014
286 parametersΔρmax = 0.44 e Å3
6 restraintsΔρmin = −0.27 e Å3

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
O10.8550 (4)0.81385 (17)0.6510 (2)0.0559 (8)
H10.86480.76050.66530.084*
O21.0592 (4)0.83261 (16)0.7324 (2)0.0556 (8)
O31.2651 (4)1.00838 (17)0.83155 (19)0.0592 (8)
O41.2868 (4)1.1299 (2)0.90927 (18)0.0591 (8)
N11.0627 (4)1.00945 (18)0.7113 (2)0.0421 (7)
H31.14040.97890.72560.051*
N20.9663 (4)1.1533 (2)0.6923 (2)0.0507 (9)
H100.94371.20180.72070.061*
N31.1385 (4)1.13746 (18)0.7971 (2)0.0407 (7)
N41.2311 (4)1.0889 (2)0.8470 (2)0.0431 (8)
C10.9593 (5)0.8623 (2)0.6876 (2)0.0399 (9)
C20.9446 (5)0.9624 (2)0.6654 (2)0.0409 (9)
H20.84920.98430.68790.049*
C30.9495 (6)0.9789 (3)0.5664 (2)0.0561 (11)
H41.02830.94280.54060.067*
H50.85630.96010.54030.067*
C40.9765 (8)1.0790 (3)0.5471 (3)0.0733 (16)
H61.08221.09070.55120.088*
H70.94671.09110.48720.088*
C50.8980 (6)1.1435 (3)0.6055 (3)0.0688 (15)
H90.89511.20260.57740.083*
H80.79641.12310.61290.083*
C61.0582 (5)1.0969 (2)0.7326 (2)0.0382 (8)
O50.2203 (4)0.6209 (2)0.6113 (2)0.0681 (9)
H110.19920.56670.61120.102*
O60.3842 (4)0.5793 (2)0.7134 (2)0.0702 (9)
O70.6264 (5)0.6721 (2)0.8634 (2)0.0816 (12)
O80.7679 (5)0.7592 (2)0.9383 (2)0.0785 (11)
N50.5019 (4)0.7416 (2)0.7264 (2)0.0474 (8)
H130.54670.69200.73990.057*
N60.5183 (5)0.8983 (2)0.7299 (2)0.0581 (10)
H200.53270.94340.76460.070*
N70.6483 (5)0.8224 (2)0.8311 (2)0.0564 (10)
N80.6787 (5)0.7483 (3)0.8780 (2)0.0594 (10)
C70.3282 (5)0.6353 (3)0.6665 (3)0.0518 (10)
C80.3764 (5)0.7345 (2)0.6670 (3)0.0479 (10)
H120.29490.77100.69080.057*
C90.4115 (6)0.7691 (3)0.5742 (3)0.0577 (12)
H140.47180.72440.54410.069*
H150.31950.77570.54190.069*
C100.4921 (8)0.8586 (4)0.5744 (3)0.0860 (17)
H160.59770.84620.57610.103*
H170.47170.88880.51910.103*
C110.4585 (9)0.9205 (3)0.6433 (3)0.0859 (19)
H180.35150.92500.64820.103*
H190.49530.97990.62670.103*
C120.5530 (5)0.8170 (2)0.7613 (2)0.0453 (9)
O90.8626 (5)0.9582 (3)0.8857 (4)0.0980 (13)
H210.799 (5)0.918 (3)0.883 (4)0.118*
H220.927 (6)0.944 (4)0.923 (4)0.118*
O101.1127 (6)0.9147 (4)0.9685 (4)0.134 (2)
H231.132 (9)0.882 (5)1.014 (3)0.161*
H241.170 (9)0.893 (6)0.929 (4)0.161*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.063 (2)0.0304 (13)0.0741 (19)−0.0079 (14)−0.0175 (17)0.0017 (13)
O20.0548 (17)0.0305 (13)0.081 (2)0.0015 (13)−0.0159 (18)0.0023 (14)
O30.0668 (19)0.0344 (13)0.0765 (18)0.0104 (14)−0.0205 (18)−0.0031 (13)
O40.070 (2)0.0534 (16)0.0541 (16)0.0008 (17)−0.0194 (16)−0.0042 (14)
N10.0486 (19)0.0241 (13)0.0536 (17)0.0017 (14)−0.0098 (16)−0.0009 (13)
N20.065 (2)0.0289 (15)0.058 (2)0.0053 (16)−0.0198 (19)−0.0017 (14)
N30.0478 (19)0.0276 (14)0.0467 (16)0.0026 (15)−0.0085 (16)−0.0011 (13)
N40.051 (2)0.0338 (15)0.0446 (16)−0.0019 (16)−0.0056 (17)0.0014 (13)
C10.042 (2)0.0301 (16)0.047 (2)0.0002 (18)0.0023 (19)−0.0020 (16)
C20.048 (2)0.0291 (17)0.0456 (19)−0.0018 (17)−0.008 (2)−0.0025 (15)
C30.082 (3)0.042 (2)0.045 (2)−0.008 (2)−0.006 (2)−0.0004 (17)
C40.117 (5)0.057 (3)0.047 (2)−0.008 (3)−0.011 (3)0.008 (2)
C50.099 (4)0.040 (2)0.068 (3)0.006 (3)−0.031 (3)0.007 (2)
C60.046 (2)0.0289 (16)0.0402 (18)−0.0023 (17)0.0028 (18)−0.0001 (15)
O50.072 (2)0.0556 (18)0.077 (2)−0.0083 (17)−0.010 (2)0.0005 (17)
O60.086 (2)0.0405 (15)0.085 (2)0.0007 (16)−0.015 (2)0.0082 (16)
O70.123 (3)0.0527 (19)0.069 (2)−0.007 (2)−0.022 (2)0.0136 (16)
O80.111 (3)0.074 (2)0.0512 (16)0.024 (2)−0.021 (2)−0.0030 (15)
N50.060 (2)0.0358 (15)0.0461 (18)0.0087 (16)−0.0062 (19)−0.0002 (14)
N60.082 (3)0.0379 (17)0.055 (2)0.0094 (18)−0.006 (2)−0.0026 (15)
N70.081 (3)0.0446 (18)0.0435 (17)0.0112 (19)−0.010 (2)−0.0004 (15)
N80.082 (3)0.057 (2)0.0387 (17)0.018 (2)−0.003 (2)−0.0031 (17)
C70.053 (3)0.047 (2)0.056 (2)0.005 (2)0.000 (2)−0.003 (2)
C80.050 (2)0.039 (2)0.055 (2)0.0087 (19)0.001 (2)−0.0025 (18)
C90.069 (3)0.055 (3)0.049 (2)0.000 (2)−0.011 (2)0.0107 (19)
C100.114 (5)0.084 (4)0.059 (3)−0.012 (4)−0.005 (3)0.017 (3)
C110.140 (6)0.040 (2)0.078 (3)0.008 (3)−0.035 (4)0.013 (2)
C120.059 (2)0.0377 (19)0.0396 (19)0.009 (2)0.006 (2)0.0003 (16)
O90.082 (3)0.059 (2)0.152 (4)0.013 (2)−0.013 (3)0.009 (2)
O100.110 (4)0.172 (5)0.120 (4)0.017 (4)−0.016 (3)0.082 (4)

Geometric parameters (Å, °)

O1—C11.306 (5)O6—C71.203 (5)
O1—H10.8200O7—N81.238 (5)
O2—C11.212 (5)O8—N81.232 (5)
O3—N41.247 (4)N5—C121.316 (5)
O4—N41.232 (4)N5—C81.453 (5)
N1—C61.329 (4)N5—H130.8600
N1—C21.450 (5)N6—C121.326 (5)
N1—H30.8600N6—C111.463 (6)
N2—C61.324 (5)N6—H200.8600
N2—C51.467 (5)N7—N81.334 (5)
N2—H100.8600N7—C121.371 (6)
N3—N41.338 (4)C7—C81.525 (6)
N3—C61.359 (5)C8—C91.536 (6)
C1—C21.518 (5)C8—H120.9800
C2—C31.531 (5)C9—C101.505 (7)
C2—H20.9800C9—H140.9700
C3—C41.523 (6)C9—H150.9700
C3—H40.9700C10—C111.424 (7)
C3—H50.9700C10—H160.9700
C4—C51.482 (7)C10—H170.9700
C4—H60.9700C11—H180.9700
C4—H70.9700C11—H190.9700
C5—H90.9700O9—H210.83 (4)
C5—H80.9700O9—H220.84 (4)
O5—C71.304 (5)O10—H230.86 (4)
O5—H110.8200O10—H240.86 (4)
C1—O1—H1109.5C12—N5—C8125.8 (3)
C6—N1—C2124.0 (3)C12—N5—H13117.1
C6—N1—H3118.0C8—N5—H13117.1
C2—N1—H3118.0C12—N6—C11127.9 (3)
C6—N2—C5128.3 (3)C12—N6—H20116.1
C6—N2—H10115.9C11—N6—H20116.1
C5—N2—H10115.9N8—N7—C12119.9 (3)
N4—N3—C6120.6 (3)O8—N8—O7120.1 (4)
O4—N4—O3120.8 (3)O8—N8—N7115.3 (4)
O4—N4—N3115.5 (3)O7—N8—N7124.6 (4)
O3—N4—N3123.6 (3)O6—C7—O5125.8 (4)
O2—C1—O1125.4 (3)O6—C7—C8122.4 (4)
O2—C1—C2122.7 (4)O5—C7—C8111.8 (4)
O1—C1—C2111.9 (3)N5—C8—C7107.0 (3)
N1—C2—C1107.0 (3)N5—C8—C9113.0 (3)
N1—C2—C3112.3 (3)C7—C8—C9111.9 (3)
C1—C2—C3111.8 (3)N5—C8—H12108.3
N1—C2—H2108.5C7—C8—H12108.3
C1—C2—H2108.5C9—C8—H12108.3
C3—C2—H2108.5C10—C9—C8112.9 (4)
C4—C3—C2110.4 (3)C10—C9—H14109.0
C4—C3—H4109.6C8—C9—H14109.0
C2—C3—H4109.6C10—C9—H15109.0
C4—C3—H5109.6C8—C9—H15109.0
C2—C3—H5109.6H14—C9—H15107.8
H4—C3—H5108.1C11—C10—C9117.3 (5)
C5—C4—C3115.4 (4)C11—C10—H16108.0
C5—C4—H6108.4C9—C10—H16108.0
C3—C4—H6108.4C11—C10—H17108.0
C5—C4—H7108.4C9—C10—H17108.0
C3—C4—H7108.4H16—C10—H17107.2
H6—C4—H7107.5C10—C11—N6116.5 (4)
N2—C5—C4113.9 (4)C10—C11—H18108.2
N2—C5—H9108.8N6—C11—H18108.2
C4—C5—H9108.8C10—C11—H19108.2
N2—C5—H8108.8N6—C11—H19108.2
C4—C5—H8108.8H18—C11—H19107.3
H9—C5—H8107.7N5—C12—N6122.2 (4)
N2—C6—N1120.9 (4)N5—C12—N7125.7 (3)
N2—C6—N3113.2 (3)N6—C12—N7112.1 (3)
N1—C6—N3125.9 (3)H21—O9—H22109 (5)
C7—O5—H11109.5H23—O10—H24104 (5)
C6—N3—N4—O4−172.7 (4)C12—N7—N8—O8178.5 (4)
C6—N3—N4—O39.7 (6)C12—N7—N8—O70.0 (7)
C6—N1—C2—C1−156.2 (3)C12—N5—C8—C7−162.6 (4)
C6—N1—C2—C380.7 (5)C12—N5—C8—C973.8 (5)
O2—C1—C2—N1−3.2 (5)O6—C7—C8—N54.4 (6)
O1—C1—C2—N1178.4 (3)O5—C7—C8—N5−176.7 (3)
O2—C1—C2—C3120.1 (4)O6—C7—C8—C9128.7 (5)
O1—C1—C2—C3−58.3 (5)O5—C7—C8—C9−52.4 (5)
N1—C2—C3—C4−44.5 (6)N5—C8—C9—C10−45.9 (5)
C1—C2—C3—C4−164.7 (4)C7—C8—C9—C10−166.7 (4)
C2—C3—C4—C5−39.4 (7)C8—C9—C10—C11−32.6 (7)
C6—N2—C5—C4−20.4 (7)C9—C10—C11—N673.8 (8)
C3—C4—C5—N277.0 (6)C12—N6—C11—C10−26.1 (9)
C5—N2—C6—N1−22.8 (7)C8—N5—C12—N6−16.8 (7)
C5—N2—C6—N3159.5 (4)C8—N5—C12—N7164.7 (4)
C2—N1—C6—N2−19.6 (6)C11—N6—C12—N5−18.4 (8)
C2—N1—C6—N3157.9 (4)C11—N6—C12—N7160.3 (5)
N4—N3—C6—N2176.6 (3)N8—N7—C12—N5−10.4 (6)
N4—N3—C6—N1−1.0 (6)N8—N7—C12—N6170.9 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1···N3i0.821.902.716 (4)173.
N1—H3···O3i0.862.022.586 (4)123.
N2—H10···O2i0.862.052.889 (4)163.
O5—H11···O9i0.821.692.510 (5)174.
N5—H13···O7i0.862.042.584 (5)121.
N6—H20···O6i0.862.162.937 (5)150.
O9—H21···N7i0.83 (4)2.11 (3)2.902 (6)160 (7)
O9—H22···O10i0.84 (4)1.86 (3)2.662 (7)159 (7)
O10—H23···O7i0.86 (4)2.04 (4)2.869 (6)163 (6)
O10—H24···O3i0.86 (4)2.41 (8)2.856 (6)113 (5)

Symmetry codes: i; i; i; i; i; i.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BG2187).

References

  • Apreyan, R. A., Karapetyan, H. A. & Petrosyan, A. M. (2008a). J. Mol. Struct.874, 187–193.
  • Apreyan, R. A., Karapetyan, H. A. & Petrosyan, A. M. (2008b). J. Mol. Struct.875, 272–281.
  • Apreyan, R. A. & Petrosyan, A. M. (2008). In preparation.
  • Enraf–Nonius (1988). CAD-4 Manual. Enraf–Nonius, Delft, The Netherlands.
  • Karapetyan, H. A. (2008). Acta Cryst. E64, o943. [PMC free article] [PubMed]
  • 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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