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Acta Cryst. (2008). E64, m1369    [ doi:10.1107/S1600536808023817 ]

Potassium L-2-nitrimino-1,3-diazepane-4-carboxylate monohydrate

H. A. Karapetyan

Abstract top

The title compound, K+·C6H9N4O4-·H2O, crystallizes with the K atoms located on special positions related by pseudocentres of symmetry. Each K atom is coordinated by six O-atom donors. The N and water H atoms are involved in inter- and intramolecular N-H...O, N-H...N and O-H...O hydrogen bonding. The data indicate inversion twinning.

Comment top

Cyclic L-2-nitrimino-1,3-diazepane-4-carboxylic acid (L-NIDCA), produced by elimination of amine from L-nitroarginine (Paul et al., 1961) , may generate new non-linear optical materials like L-nitroarginine itself [Apreyan et al. (2008a, 2008b); Karapetyan et al.(2007); Petrosyan et al. (2005); the crystal structures of L-NIDCA and its monohydrate have been recently reported [Karapetyan (2008a, 2008b)].

This paper presents a structural study of the potassium salt of L-NIDCA monohydrate. The structure was solved and refined in the orthorhombic unit cell with I222 space group. The choice of the non-centric space group was based on the generation of second harmonic observed on a powder sample (YAG:Nd laser, Kurtz-Perry method [Kurtz & Perry,1968]). In this structure, two independent potassium cations occupy special positions. These potassium atoms are located about pseudo-inversion centers, which is most likely the reason for the presence of high level pseudosymmetry in the structure. Both potassium cations are coordinated by six oxygen atoms with K···O bond lengths in the ranges 2.712 (5)-2.815 (7) Å for K1 and 2.642 (5)-2.783 (6) Å for K2.

A view of the asymmetric unit is shown in Fig. 1. The high value of Ueq of atom C3 of the 1,3-diazepane ring compared to those of its neighbors indicates potential disorder of this atom. In the crystal structure, the nitrogen-bound H atoms and the water H atoms are involved in N—H···O, N—H···N and O—H···O hydrogen bonding (Table 1), one of them being intra- and the other three intermolecular, linking anions and water molecules in infinite layers parallel to the bc plane (Fig. 2).

Related literature top

For related literature, see: Apreyan & Petrosyan (2008); Apreyan et al. (2008a,b); Karapetyan (2008a,b); Karapetyan et al. (2007); Kurtz & Perry (1968); Paul et al. (1961); Petrosyan et al. (2005).

Experimental top

The title compound was synthesized from a mixture of aqueous solutions containing L-nitroarginine (2 g, Sigma-Aldrich) and KOH (0.512 g) at room temperature. Single crystals of the title compound were obtained by slow evaporation of the solution. At 97° C decomposition of the crystals was observed.

Refinement top

The data set was collected in a full sphere of reciprocal space. Space group I222 was chosen on the basis of the powder second harmonic of YAG:Nb laser generation property of the crystals of the title compound. In spite of the fact that all H atoms appear in difference Fourier maps in reasonable positions, they became unacceptable after refinement. Because of this, all the H atoms except those belonging to the water molecule were placed in geometrically calculated positions and included in the refinement in a riding model approximation, with Uiso(H) = 1.2Ueq(carrier atom). The positions of the H atoms of the water molecule were located in difference Fourier maps and included in the refinement with fixed O—H (0.85 Å), H···H (1.35 Å) distances and isotropic temperature parameters Uiso(H) = 1.4Ueq(O). The absolute configuration has been determined using L-nitroarginine of known absolute configuration.

Computing details top

Data collection: Datcol in CAD-4 Software (Enraf–Nonius, 1988); cell refinement: LS in CAD-4 Software (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 asymmetric unit, showing the atomic numbering and displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. Packing of the molecules. For clarity, only the donors in the original molecule and their corresponding acceptors are labelled. Symmetry codes are: (i) x, y - 1, z; (ii)-x + 1/2, y - 1/2, -z + 1/2; (iii) x, 2 - y, 1 - z. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted.
Potassium L-2-nitrimino-1,3-diazepane-4-carboxylate monohydrate top
Crystal data top
K+·C6H9N4O4−·H2OF(000) = 1072
Mr = 258.29Dx = 1.586 Mg m−3
Orthorhombic, I222Mo Kα radiation, λ = 0.71073 Å
Hall symbol: I 2 2Cell parameters from 24 reflections
a = 7.3883 (15) Åθ = 14–16°
b = 10.087 (2) ŵ = 0.51 mm−1
c = 29.031 (6) ÅT = 293 K
V = 2163.5 (8) Å3Prism, yellow
Z = 80.21 × 0.14 × 0.11 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer		Rint = 0.030
Radiation source: fine-focus sealed tubeθmax = 30.0°, θmin = 2.1°
graphiteh = −10→10
ω/2θ scansk = −13→13
5030 measured reflectionsl = −38→38
3141 independent reflections3 standard reflections every 400 reflections
1726 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)] = 0.065H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.193 w = 1/[σ2(Fo2) + (0.0676P)2 + 6.1136P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
3141 reflectionsΔρmax = 0.43 e Å−3
154 parametersΔρmin = −0.39 e Å−3
3 restraintsAbsolute structure: Flack (1983), 1350 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.48 (20)
Crystal data top
K+·C6H9N4O4−·H2OV = 2163.5 (8) Å3
Mr = 258.29Z = 8
Orthorhombic, I222Mo Kα radiation
a = 7.3883 (15) ŵ = 0.51 mm−1
b = 10.087 (2) ÅT = 293 K
c = 29.031 (6) Å0.21 × 0.14 × 0.11 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer		Rint = 0.030
5030 measured reflectionsθmax = 30.0°
3141 independent reflections3 standard reflections every 400 reflections
1726 reflections with I > 2σ(I) intensity decay: none
Refinement top
R[F2 > 2σ(F2)] = 0.065H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.193Δρmax = 0.43 e Å−3
S = 1.04Δρmin = −0.39 e Å−3
3141 reflectionsAbsolute structure: Flack (1983), 1350 Friedel pairs
154 parametersFlack parameter: 0.48 (20)
3 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
K10.50000.50000.26313 (7)0.0481 (5)
K20.00000.50000.26268 (8)0.0536 (5)
O10.2429 (10)0.6833 (3)0.28276 (9)0.0510 (8)
O20.2513 (10)0.8993 (3)0.29658 (9)0.0618 (10)
O30.2476 (15)1.1286 (3)0.37039 (10)0.0905 (16)
O40.2389 (10)1.2557 (3)0.42935 (11)0.0723 (12)
O50.2461 (12)0.3267 (3)0.30317 (11)0.0644 (10)
N10.2755 (14)0.8784 (3)0.38382 (11)0.0630 (19)
H20.33730.93200.36700.076*
N20.2659 (10)0.8275 (3)0.46137 (11)0.0583 (14)
H90.32240.85260.48580.070*
N30.2516 (11)1.0441 (3)0.44244 (10)0.0490 (10)
N40.2478 (12)1.1416 (3)0.41290 (11)0.0526 (10)
C10.2419 (12)0.7820 (4)0.30906 (13)0.0433 (11)
C20.2101 (7)0.7544 (4)0.36059 (14)0.0397 (12)
H10.07940.74700.36570.048*
C30.294 (2)0.6381 (6)0.37834 (19)0.118 (5)
H40.42400.65140.37930.142*
H30.26970.56450.35780.142*
C40.2262 (15)0.6022 (4)0.42740 (17)0.069 (2)
H50.11500.55260.42320.082*
H60.31390.54040.43990.082*
C50.1931 (9)0.6894 (5)0.46054 (17)0.0601 (19)
H70.23190.64810.48910.072*
H80.06240.69740.46240.072*
C60.2498 (15)0.9152 (4)0.42687 (13)0.0475 (10)
H100.288 (8)0.279 (5)0.3251 (13)0.07 (2)*
H110.288 (14)0.287 (8)0.2790 (13)0.16 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
K10.0547 (12)0.0388 (11)0.0507 (11)0.0026 (10)0.0000.000
K20.0566 (12)0.0404 (12)0.0637 (13)−0.0021 (11)0.0000.000
O10.070 (2)0.0423 (15)0.0409 (14)0.000 (3)0.008 (3)−0.0129 (13)
O20.115 (3)0.0374 (15)0.0326 (13)0.013 (4)−0.002 (4)0.0002 (11)
O30.202 (5)0.0350 (16)0.0343 (15)−0.001 (5)−0.009 (5)0.0075 (12)
O40.136 (4)0.0279 (13)0.0534 (18)0.006 (4)−0.007 (4)−0.0024 (13)
O50.103 (3)0.0470 (17)0.0436 (17)−0.009 (4)−0.003 (4)0.0143 (15)
N10.134 (6)0.0286 (16)0.0266 (16)−0.021 (4)0.012 (3)−0.0014 (12)
N20.115 (4)0.0309 (16)0.0291 (15)−0.017 (3)0.012 (4)−0.0006 (13)
N30.087 (3)0.0286 (14)0.0312 (15)0.007 (4)0.006 (4)0.0001 (12)
N40.088 (3)0.0310 (16)0.0393 (17)0.005 (4)0.014 (4)0.0017 (13)
C10.057 (3)0.039 (2)0.0339 (18)0.007 (4)−0.010 (3)−0.0022 (15)
C20.049 (3)0.0352 (19)0.0344 (19)0.004 (2)−0.002 (2)−0.0046 (16)
C30.267 (17)0.043 (3)0.043 (3)0.046 (7)−0.002 (6)0.008 (2)
C40.125 (6)0.029 (2)0.052 (2)−0.013 (4)−0.008 (5)0.0091 (18)
C50.098 (6)0.037 (2)0.045 (3)0.001 (3)0.004 (3)0.011 (2)
C60.079 (3)0.0335 (17)0.0298 (17)−0.002 (5)0.001 (5)−0.0016 (14)
Geometric parameters (Å, °) top
K1—O12.712 (5)O4—N41.247 (4)
K1—O1i2.712 (5)O5—H100.856 (19)
K1—O2ii2.736 (6)O5—H110.87 (2)
K1—O2iii2.736 (6)N1—C61.318 (5)
K1—O5i2.815 (7)N1—C21.502 (6)
K1—O52.815 (7)N1—H20.8600
K1—C1ii3.524 (5)N2—C61.342 (5)
K1—C1iii3.524 (5)N2—C51.494 (7)
K1—K23.6942 (8)N2—H90.8600
K1—K2iv3.6942 (8)N3—N41.305 (4)
K1—H112.70 (11)N3—C61.377 (5)
K2—O12.642 (5)C1—C21.540 (6)
K2—O1v2.642 (5)C1—K1viii3.524 (5)
K2—O2vi2.714 (6)C2—C31.423 (9)
K2—O2ii2.714 (6)C2—H10.9800
K2—O52.783 (6)C3—C41.552 (9)
K2—O5v2.783 (6)C3—H40.9700
K2—K1vii3.6942 (8)C3—H30.9700
K2—H113.06 (6)C4—C51.326 (7)
O1—C11.255 (4)C4—H50.9700
O2—C11.239 (5)C4—H60.9700
O2—K2viii2.714 (6)C5—H70.9700
O2—K1viii2.736 (6)C5—H80.9700
O3—N41.241 (4)
O1—K1—O1i155.74 (15)O2ii—K2—K1vii132.78 (15)
O1—K1—O2ii84.89 (16)O5—K2—K1vii130.69 (16)
O1i—K1—O2ii110.81 (14)O5v—K2—K1vii49.08 (15)
O1—K1—O2iii110.81 (14)O1—K2—K147.16 (12)
O1i—K1—O2iii84.89 (16)O1v—K2—K1132.72 (12)
O2ii—K1—O2iii101.4 (2)O2vi—K2—K1132.78 (15)
O1—K1—O5i87.51 (15)O2ii—K2—K147.57 (13)
O1i—K1—O5i82.52 (14)O5—K2—K149.08 (15)
O2ii—K1—O5i160.81 (11)O5v—K2—K1130.69 (16)
O2iii—K1—O5i65.09 (14)K1vii—K2—K1179.60 (13)
O1—K1—O582.52 (14)O1—K2—H1189 (2)
O1i—K1—O587.51 (15)O1v—K2—H1187 (2)
O2ii—K1—O565.09 (14)O2vi—K2—H11146.2 (10)
O2iii—K1—O5160.81 (11)O2ii—K2—H1150.6 (8)
O5i—K1—O5131.23 (19)O5—K2—H1116.1 (6)
O1—K1—C1ii101.25 (17)O5v—K2—H11146.1 (6)
O1i—K1—C1ii93.15 (14)K1vii—K2—H11134 (2)
O2ii—K1—C1ii17.69 (15)K1—K2—H1146 (2)
O2iii—K1—C1ii101.48 (14)C1—O1—K2133.3 (6)
O5i—K1—C1ii166.12 (17)C1—O1—K1132.3 (5)
O5—K1—C1ii61.33 (12)K2—O1—K187.26 (8)
O1—K1—C1iii93.15 (14)C1—O2—K2viii125.5 (5)
O1i—K1—C1iii101.25 (17)C1—O2—K1viii120.1 (6)
O2ii—K1—C1iii101.48 (14)K2viii—O2—K1viii85.34 (8)
O2iii—K1—C1iii17.69 (15)K2—O5—K182.59 (8)
O5i—K1—C1iii61.33 (12)K2—O5—H10155 (4)
O5—K1—C1iii166.12 (17)K1—O5—H10114 (5)
C1ii—K1—C1iii107.02 (17)K2—O5—H11101 (5)
O1—K1—K245.59 (12)K1—O5—H1174 (7)
O1i—K1—K2134.53 (12)H10—O5—H11102 (3)
O2ii—K1—K247.09 (13)C6—N1—C2127.9 (6)
O2iii—K1—K2132.56 (15)C6—N1—H2116.0
O5i—K1—K2131.90 (15)C2—N1—H2116.0
O5—K1—K248.33 (15)C6—N2—C5124.8 (5)
C1ii—K1—K259.38 (14)C6—N2—H9117.6
C1iii—K1—K2120.34 (15)C5—N2—H9117.6
O1—K1—K2iv134.53 (12)N4—N3—C6119.7 (3)
O1i—K1—K2iv45.59 (12)O3—N4—O4118.6 (3)
O2ii—K1—K2iv132.56 (15)O3—N4—N3125.0 (3)
O2iii—K1—K2iv47.09 (13)O4—N4—N3116.4 (3)
O5i—K1—K2iv48.33 (15)O2—C1—O1125.4 (4)
O5—K1—K2iv131.90 (15)O2—C1—C2117.8 (3)
C1ii—K1—K2iv120.34 (15)O1—C1—C2116.6 (4)
C1iii—K1—K2iv59.38 (14)O2—C1—K1viii42.2 (4)
K2—K1—K2iv179.60 (13)O1—C1—K1viii97.8 (3)
O1—K1—H1195.8 (12)C2—C1—K1viii127.8 (4)
O1i—K1—H1180.1 (15)C3—C2—N1112.6 (5)
O2ii—K1—H1154.4 (13)C3—C2—C1115.8 (5)
O2iii—K1—H11142.9 (4)N1—C2—C1103.6 (4)
O5i—K1—H11144.2 (12)C3—C2—H1108.2
O5—K1—H1117.9 (4)N1—C2—H1108.2
C1ii—K1—H1146.4 (10)C1—C2—H1108.2
C1iii—K1—H11153.2 (8)C2—C3—C4112.6 (8)
K2—K1—H1154.5 (15)C2—C3—H4109.1
K2iv—K1—H11125.5 (15)C4—C3—H4109.1
O1—K2—O1v154.51 (16)C2—C3—H3109.1
O1—K2—O2vi109.73 (14)C4—C3—H3109.1
O1v—K2—O2vi86.68 (16)H4—C3—H3107.8
O1—K2—O2ii86.68 (16)C5—C4—C3124.8 (4)
O1v—K2—O2ii109.73 (14)C5—C4—H5106.1
O2vi—K2—O2ii101.3 (2)C3—C4—H5106.1
O1—K2—O584.41 (15)C5—C4—H6106.1
O1v—K2—O584.89 (16)C3—C4—H6106.1
O2vi—K2—O5160.93 (12)H5—C4—H6106.3
O2ii—K2—O565.81 (15)C4—C5—N2124.3 (5)
O1—K2—O5v84.89 (16)C4—C5—H7106.3
O1v—K2—O5v84.41 (15)N2—C5—H7106.3
O2vi—K2—O5v65.81 (15)C4—C5—H8106.3
O2ii—K2—O5v160.93 (12)N2—C5—H8106.3
O5—K2—O5v130.0 (2)H7—C5—H8106.4
O1—K2—K1vii132.72 (12)N1—C6—N2120.6 (4)
O1v—K2—K1vii47.16 (12)N1—C6—N3125.2 (4)
O2vi—K2—K1vii47.57 (13)N2—C6—N3112.1 (3)
O1v—K2—O1—C1−49.9 (4)O2ii—K1—O5—K2−53.73 (14)
O2vi—K2—O1—C177.6 (4)O2iii—K1—O5—K2−101.4 (5)
O2ii—K2—O1—C1178.5 (4)O5i—K1—O5—K2114.12 (11)
O5—K2—O1—C1−115.5 (4)C1ii—K1—O5—K2−73.12 (16)
O5v—K2—O1—C115.6 (4)C1iii—K1—O5—K2−38.4 (6)
K1vii—K2—O1—C127.7 (5)K2iv—K1—O5—K2−179.55 (14)
K1—K2—O1—C1−151.7 (4)C6—N3—N4—O3−2.1 (16)
O1v—K2—O1—K1101.82 (8)C6—N3—N4—O4175.9 (10)
O2vi—K2—O1—K1−130.65 (16)K2viii—O2—C1—O1−49.8 (12)
O2ii—K2—O1—K1−29.78 (10)K1viii—O2—C1—O157.6 (12)
O5—K2—O1—K136.21 (12)K2viii—O2—C1—C2135.8 (5)
O5v—K2—O1—K1167.33 (12)K1viii—O2—C1—C2−116.8 (5)
K1vii—K2—O1—K1179.47 (16)K2viii—O2—C1—K1viii−107.4 (3)
O1i—K1—O1—C149.8 (4)K2—O1—C1—O2−114.3 (9)
O2ii—K1—O1—C1−178.2 (4)K1—O1—C1—O2105.4 (9)
O2iii—K1—O1—C1−77.9 (4)K2—O1—C1—C260.2 (8)
O5i—K1—O1—C1−15.8 (4)K1—O1—C1—C2−80.1 (8)
O5—K1—O1—C1116.3 (4)K2—O1—C1—K1viii−79.4 (3)
C1ii—K1—O1—C1175.0 (4)K1—O1—C1—K1viii140.3 (2)
C1iii—K1—O1—C1−76.9 (5)C6—N1—C2—C3−67.0 (11)
K2—K1—O1—C1152.2 (4)C6—N1—C2—C1167.2 (9)
K2iv—K1—O1—C1−28.3 (5)O2—C1—C2—C3−146.7 (9)
O1i—K1—O1—K2−102.45 (8)O1—C1—C2—C338.4 (11)
O2ii—K1—O1—K229.60 (10)K1viii—C1—C2—C3164.0 (6)
O2iii—K1—O1—K2129.84 (15)O2—C1—C2—N1−22.9 (10)
O5i—K1—O1—K2−168.04 (12)O1—C1—C2—N1162.2 (8)
O5—K1—O1—K2−35.89 (12)K1viii—C1—C2—N1−72.2 (6)
C1ii—K1—O1—K222.82 (11)N1—C2—C3—C472.2 (10)
C1iii—K1—O1—K2130.87 (14)C1—C2—C3—C4−168.9 (7)
K2iv—K1—O1—K2179.46 (17)C2—C3—C4—C5−39.8 (16)
O1—K2—O5—K1−34.97 (11)C3—C4—C5—N2−19.3 (15)
O1v—K2—O5—K1168.20 (12)C6—N2—C5—C452.9 (12)
O2vi—K2—O5—K1104.1 (5)C2—N1—C6—N242.7 (16)
O2ii—K2—O5—K153.89 (13)C2—N1—C6—N3−154.9 (9)
O5v—K2—O5—K1−113.49 (10)C5—N2—C6—N1−43.0 (15)
K1vii—K2—O5—K1−179.56 (14)C5—N2—C6—N3152.5 (8)
O1—K1—O5—K234.09 (11)N4—N3—C6—N112.3 (17)
O1i—K1—O5—K2−168.08 (12)N4—N3—C6—N2176.0 (9)
Symmetry codes: (i) −x+1, −y+1, z; (ii) −x+1/2, y−1/2, −z+1/2; (iii) x+1/2, −y+3/2, −z+1/2; (iv) x+1, y, z; (v) −x, −y+1, z; (vi) x−1/2, −y+3/2, −z+1/2; (vii) x−1, y, z; (viii) −x+1/2, y+1/2, −z+1/2.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O5—H11···O1ii0.87 (2)2.09 (5)2.885 (5)153 (10)
O5—H10···O3ix0.86 (2)2.03 (4)2.793 (4)148 (6)
N2—H9···N3x0.862.393.080 (4)138
N1—H2···O30.862.092.561 (5)114
Symmetry codes: (ii) −x+1/2, y−1/2, −z+1/2; (ix) x, y−1, z; (x) x, −y+2, −z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O5—H11···O1i0.87 (2)2.09 (5)2.885 (5)153 (10)
O5—H10···O3ii0.86 (2)2.03 (4)2.793 (4)148 (6)
N2—H9···N3iii0.862.393.080 (4)138
N1—H2···O30.862.092.561 (5)114
Symmetry codes: (i) −x+1/2, y−1/2, −z+1/2; (ii) x, y−1, z; (iii) x, −y+2, −z+1.
Acknowledgements top

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

references
References top

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