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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2436.
Published online 2008 November 26. doi:  10.1107/S1600536808038968
PMCID: PMC2959911

1-Ammonio-1-phosphono­pentane-1-phospho­nic acid

Abstract

The title compound, C5H15NO6P2, was obtained by the reaction of penta­nenitrile with PCl3 followed by the dropwise addition of water. The asymmetric unit contains one mol­ecule, which exists as a zwitterion with a positive charge on the –NH3 group and a negative charge on one of the phospho­nic O atoms. The crystal structure displays N—H(...)O and O—H(...)O hydrogen bonding, which creates a three-dimensional network.

Related literature

For the biological activity of organic disphospho­nic acids, see: Matczak-Jon & Videnova-Adrabinska (2005 [triangle]); Szabo et al. (2002 [triangle]); Tromelin et al. (1986 [triangle]). For comparable bond lengths, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o2436-scheme1.jpg

Experimental

Crystal data

  • C5H15NO6P2
  • M r = 247.12
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2436-efi1.jpg
  • a = 14.5502 (3) Å
  • b = 7.1896 (1) Å
  • c = 9.4855 (2) Å
  • β = 96.938 (1)°
  • V = 985.01 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.45 mm−1
  • T = 100 (2) K
  • 0.38 × 0.36 × 0.09 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.848, T max = 0.961
  • 23409 measured reflections
  • 2471 independent reflections
  • 2225 reflections with I > 2σ(I)
  • R int = 0.043

Refinement

  • R[F 2 > 2σ(F 2)] = 0.028
  • wR(F 2) = 0.072
  • S = 1.06
  • 2471 reflections
  • 152 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.44 e Å−3
  • Δρmin = −0.32 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808038968/ez2151sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808038968/ez2151Isup2.hkl

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

supplementary crystallographic information

Comment

Organic diphosphonic acids are potentially very powerful chelating agents used in metal extractions and have been tested by the pharmaceutical industry for use as efficient drugs preventing calcification and inhibiting bone resorption (Tromelin et al., 1986, Matczak-Jon & Videnova-Adrabinska, 2005). Diphosphonic acids are used in the treatment of Paget disease, osteoporosis and tumoral osteolysis (Szabo et al., 2002).

The asymmetric unit of the title compound contains one molecule, which exists as a zwitterion with positive and negative charges on the NH3 group and one of the phosphonic oxygen atoms, respectively. The phosphorus atoms display slightly distorted tetrahedral geometries, each provided by three oxygen atoms and one carbon atom. Bond lengths and angles have normal values (Allen et al., 1987).

There are no solvent water molecules in the asymmetric unit, which is unusual for α-aminodiphosphonic acids. This fact can be explained by the presence of the hydrophobic alkyl group. The structure is stabilized by a three-dimensional O—H···O and N—H···O hydrogen bonding network (Fig. 1, Table 1).

Experimental

Dry hydrogen chloride at about 278 K was brought into contact with the surface of a mixture of pentanenitrile (83.13 g, 1 mol) and PCl3 (87.4 ml, 1 mol). After an hour water (54 ml, 3 mol) was added to the mixture dropwise. After a day the solution was treated by an excess amount of water and then vacuum distilled. The obtained solution was treated by a mixture of acetone and diethyl ether, yielding colourless crystals of the title compound.

Refinement

H atoms bonded to O and N atoms were located in a difference map. Other H atoms bonded to C atoms were positioned geometrically and refined using a riding model with C—H = 0.98 Å for CH3 [Uiso(H) = 1.5Ueq(C)] and C—H = 0.99 Å for CH2 [Uiso(H) = 1.2Ueq(C)]

Figures

Fig. 1.
The asymmetric unit of the title compound showing the atom-labelling scheme and 50% probability displacement ellipsoids for the non-hydrogen atoms.
Fig. 2.
Crystal packing of the title compound; projection along b axis. Dashed lines indicate hydrogen bonds.

Crystal data

C5H15NO6P2F000 = 520
Mr = 247.12Dx = 1.666 Mg m3
Monoclinic, P21/cMelting point: 562 K
Hall symbol: -P 2ybcMo Kα radiation λ = 0.71073 Å
a = 14.5502 (3) ÅCell parameters from 8806 reflections
b = 7.1896 (1) Åθ = 2.8–28.4º
c = 9.4855 (2) ŵ = 0.45 mm1
β = 96.938 (1)ºT = 100 (2) K
V = 985.01 (3) Å3Plate, colourless
Z = 40.38 × 0.36 × 0.09 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2471 independent reflections
Radiation source: fine-focus sealed tube2225 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.043
T = 100(2) Kθmax = 28.4º
[var phi] and ω scansθmin = 2.8º
Absorption correction: multi-scan(SADABS; Bruker, 2005)h = −19→19
Tmin = 0.848, Tmax = 0.961k = −9→9
23409 measured reflectionsl = −12→12

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.028H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.072  w = 1/[σ2(Fo2) + (0.0317P)2 + 0.8863P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2471 reflectionsΔρmax = 0.44 e Å3
152 parametersΔρmin = −0.32 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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
P10.39648 (2)0.07886 (5)0.68586 (4)0.00647 (9)
P20.28775 (2)−0.24846 (5)0.54892 (4)0.00680 (9)
C10.30732 (9)0.00397 (19)0.54146 (14)0.0067 (3)
C20.21901 (10)0.1205 (2)0.55184 (15)0.0100 (3)
H2A0.19140.07780.63660.012*
H2B0.23830.25140.56920.012*
C30.14290 (10)0.1183 (2)0.42611 (16)0.0139 (3)
H3A0.16980.14890.33800.017*
H3B0.1157−0.00790.41530.017*
C40.06761 (12)0.2576 (3)0.4478 (2)0.0239 (4)
H4A0.04850.23810.54340.029*
H4B0.09390.38440.44570.029*
C5−0.01700 (12)0.2475 (3)0.3401 (2)0.0238 (4)
H5A0.00050.27140.24520.036*
H5B−0.06200.34110.36240.036*
H5C−0.04470.12340.34240.036*
N10.34540 (9)0.04748 (18)0.40433 (12)0.0075 (2)
O10.20552 (7)−0.29755 (15)0.43309 (11)0.0103 (2)
O20.26347 (7)−0.29945 (15)0.69151 (10)0.0105 (2)
O30.37688 (7)−0.33350 (15)0.50568 (11)0.0102 (2)
O40.48097 (7)−0.03933 (15)0.68442 (11)0.0106 (2)
O50.35286 (7)0.08211 (14)0.82242 (10)0.0092 (2)
O60.41170 (7)0.28091 (15)0.63361 (11)0.0103 (2)
H1N0.4006 (14)0.015 (3)0.406 (2)0.015 (5)*
H2N0.3439 (14)0.172 (3)0.387 (2)0.022 (5)*
H3N0.3141 (13)−0.009 (3)0.331 (2)0.014 (5)*
H1O0.2192 (17)−0.283 (4)0.356 (3)0.032 (6)*
H3O0.3713 (18)−0.416 (4)0.450 (3)0.040 (7)*
H6O0.4518 (18)0.340 (4)0.684 (3)0.046 (8)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
P10.00764 (16)0.00625 (17)0.00532 (16)−0.00016 (12)−0.00004 (12)−0.00001 (12)
P20.00865 (17)0.00661 (17)0.00509 (16)−0.00071 (12)0.00064 (12)−0.00014 (12)
C10.0075 (6)0.0081 (6)0.0045 (6)0.0003 (5)0.0007 (5)0.0000 (5)
C20.0085 (6)0.0107 (7)0.0107 (6)0.0022 (5)0.0010 (5)−0.0017 (5)
C30.0119 (7)0.0176 (8)0.0114 (7)0.0050 (6)−0.0014 (5)−0.0005 (6)
C40.0146 (8)0.0292 (10)0.0264 (9)0.0094 (7)−0.0043 (7)−0.0081 (7)
C50.0140 (7)0.0316 (10)0.0249 (9)0.0078 (7)−0.0024 (6)0.0026 (7)
N10.0082 (6)0.0087 (6)0.0058 (5)−0.0007 (4)0.0011 (4)−0.0002 (4)
O10.0113 (5)0.0123 (5)0.0070 (5)−0.0025 (4)0.0002 (4)−0.0008 (4)
O20.0142 (5)0.0105 (5)0.0068 (4)−0.0006 (4)0.0018 (4)0.0006 (4)
O30.0116 (5)0.0083 (5)0.0109 (5)0.0009 (4)0.0022 (4)−0.0026 (4)
O40.0095 (5)0.0122 (5)0.0096 (5)0.0026 (4)−0.0004 (4)−0.0001 (4)
O50.0123 (5)0.0087 (5)0.0067 (4)−0.0001 (4)0.0016 (4)−0.0003 (4)
O60.0134 (5)0.0079 (5)0.0089 (5)−0.0031 (4)−0.0007 (4)0.0013 (4)

Geometric parameters (Å, °)

P1—O41.4959 (10)C3—H3A0.9900
P1—O51.5099 (10)C3—H3B0.9900
P1—O61.5593 (11)C4—C51.504 (2)
P1—C11.8492 (14)C4—H4A0.9900
P2—O21.4846 (10)C4—H4B0.9900
P2—O31.5337 (11)C5—H5A0.9800
P2—O11.5639 (10)C5—H5B0.9800
P2—C11.8398 (14)C5—H5C0.9800
C1—N11.5070 (17)N1—H1N0.84 (2)
C1—C21.5471 (19)N1—H2N0.91 (2)
C2—C31.5264 (19)N1—H3N0.88 (2)
C2—H2A0.9900O1—H1O0.79 (2)
C2—H2B0.9900O3—H3O0.79 (3)
C3—C41.517 (2)O6—H6O0.83 (3)
O4—P1—O5116.59 (6)C2—C3—H3A109.5
O4—P1—O6112.20 (6)C4—C3—H3B109.5
O5—P1—O6110.42 (6)C2—C3—H3B109.5
O4—P1—C1109.37 (6)H3A—C3—H3B108.1
O5—P1—C1108.06 (6)C5—C4—C3114.90 (15)
O6—P1—C198.61 (6)C5—C4—H4A108.5
O2—P2—O3116.57 (6)C3—C4—H4A108.5
O2—P2—O1109.77 (6)C5—C4—H4B108.5
O3—P2—O1108.78 (6)C3—C4—H4B108.5
O2—P2—C1109.49 (6)H4A—C4—H4B107.5
O3—P2—C1104.08 (6)C4—C5—H5A109.5
O1—P2—C1107.72 (6)C4—C5—H5B109.5
N1—C1—C2109.71 (11)H5A—C5—H5B109.5
N1—C1—P2108.22 (9)C4—C5—H5C109.5
C2—C1—P2113.48 (10)H5A—C5—H5C109.5
N1—C1—P1106.30 (9)H5B—C5—H5C109.5
C2—C1—P1107.99 (9)C1—N1—H1N112.5 (13)
P2—C1—P1110.90 (7)C1—N1—H2N111.0 (13)
C3—C2—C1118.31 (12)H1N—N1—H2N106.4 (19)
C3—C2—H2A107.7C1—N1—H3N112.3 (12)
C1—C2—H2A107.7H1N—N1—H3N106.5 (18)
C3—C2—H2B107.7H2N—N1—H3N107.9 (18)
C1—C2—H2B107.7P2—O1—H1O111.4 (17)
H2A—C2—H2B107.1P2—O3—H3O117.1 (19)
C4—C3—C2110.76 (13)P1—O6—H6O114.5 (19)
C4—C3—H3A109.5
O2—P2—C1—N1171.72 (8)O4—P1—C1—C2176.54 (9)
O3—P2—C1—N146.42 (10)O5—P1—C1—C248.68 (11)
O1—P2—C1—N1−68.96 (10)O6—P1—C1—C2−66.19 (10)
O2—P2—C1—C2−66.27 (11)O4—P1—C1—P251.62 (9)
O3—P2—C1—C2168.44 (9)O5—P1—C1—P2−76.24 (8)
O1—P2—C1—C253.05 (11)O6—P1—C1—P2168.90 (7)
O2—P2—C1—P155.49 (9)N1—C1—C2—C350.75 (17)
O3—P2—C1—P1−69.81 (8)P2—C1—C2—C3−70.43 (15)
O1—P2—C1—P1174.81 (7)P1—C1—C2—C3166.21 (11)
O4—P1—C1—N1−65.79 (10)C1—C2—C3—C4−173.11 (14)
O5—P1—C1—N1166.35 (9)C2—C3—C4—C5−171.76 (15)
O6—P1—C1—N151.49 (10)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···O4i0.84 (2)2.02 (2)2.7584 (16)146.7 (19)
N1—H2N···O5ii0.91 (2)1.88 (2)2.7799 (16)169.4 (19)
N1—H3N···O2iii0.88 (2)1.99 (2)2.8451 (16)162.9 (18)
O1—H1O···O2iii0.79 (2)1.85 (3)2.6297 (15)167 (3)
O3—H3O···O5iii0.79 (3)1.70 (3)2.4884 (15)175 (3)
O6—H6O···O4iv0.83 (3)1.72 (3)2.5372 (14)168 (3)

Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, −y+1/2, z−1/2; (iii) x, −y−1/2, z−1/2; (iv) −x+1, y+1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: EZ2151).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Matczak-Jon, E. & Videnova-Adrabinska, V. (2005). Coord. Chem. Rev.249, 2458–2488.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Szabo, C. M., Martin, M. B. & Oldfield, E. (2002). J. Med. Chem.45, 2894–2903. [PubMed]
  • Tromelin, A., El Manouni, D. & Burgada, R. (1986). Phosphorus Sulfur Relat. Elem.27, 301–312.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography