organic compounds
Ammonium dihydrogen (1-ammoniopentane-1,1-diyl)diphosphonate
aInstitute of General and Inorganic Chemistry, NAS Ukraine Kyiv, Prosp. Palladina 32/34, 03680 Ukraine
*Correspondence e-mail: dudco_anatolij@ukr.net
The title compound, NH4+·C5H14NO6P2−, was obtained from 1-ammonio-1-phosphonopentane-1-phosphonic acid and ammonium hydroxide in aqueous solution. The of title compound contains one molecule, which consists of an ammonium cation and an aminodiphosphonic anion with the H atoms transferred from the phosphonic acid group to the amino group. The shows a three-dimensional network of O—H⋯O and N—H⋯O hydrogen bonds which stabilize the structure.
Related literature
For general background to the use of organic diphosphonic acids as chelating agents in metal extraction and as drugs to prevent calcification and inhibit bone resorption, see: Matczak-Jon & Videnova-Adrabinska (2005); Tromelin et al. (1986); Szabo et al. (2002). For related structures, see: Bon et al. (2008). For bond–length data, see: Allen et al. (1987).
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2005); cell SAINT (Bruker, 2005); data reduction: SAINT; 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: publCIF (Westrip, 2009).
Supporting information
10.1107/S1600536809028323/rk2155sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809028323/rk2155Isup2.hkl
The title compound was obtained by the reaction of 1–ammonio–1–phosphonopentane–1–phosphonic acid and ammonium hydroxide (1:1) in the aqueous solution. The solution was left at room temperature. Colourless crystals of the title compound were obtained after 5 days staying.
The H atoms bonded to O and N atoms were located in a difference map and refined freely. Other H atoms which bonded to C were positioned geometrically and refined using a riding model with C—H = 0.96 Å for CH3 with Uiso(H) = 1.5Ueq(C) and C—H = 0.97 Å for CH2 with Uiso(H) = 1.2Ueq(C).
Data collection: APEX2 (Bruker, 2005); cell
SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); 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: publCIF (Westrip, 2009).Fig. 1. The asymmetric unit of title compound with the atom numbering scheme. Displacement ellipsoids are drawn at 50% probability level. Hydrogen atoms are presented as a small spheres of arbitrary rAdius. | |
Fig. 2. Crystal packing of title compound, projection along b axis. Dashed lines indicate hydrogen bonds. |
NH4+·C5H14NO6P2− | F(000) = 560 |
Mr = 264.15 | Dx = 1.587 Mg m−3 |
Monoclinic, P21/c | Melting point: 495 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 9.6007 (6) Å | Cell parameters from 824 reflections |
b = 5.7239 (4) Å | θ = 2.7–21.1° |
c = 20.3259 (15) Å | µ = 0.41 mm−1 |
β = 98.100 (3)° | T = 296 K |
V = 1105.84 (13) Å3 | Needle, colourless |
Z = 4 | 0.50 × 0.12 × 0.04 mm |
Bruker APEXII CCD diffractometer | 2256 independent reflections |
Radiation source: fine–focus sealed tube | 1532 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.056 |
Detector resolution: 8.26 pixels mm-1 | θmax = 26.4°, θmin = 2.0° |
ϕ and ω scans | h = −11→11 |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | k = −7→5 |
Tmin = 0.824, Tmax = 0.982 | l = −24→25 |
5297 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.122 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0435P)2 + 0.4298P] where P = (Fo2 + 2Fc2)/3 |
2256 reflections | (Δ/σ)max < 0.001 |
173 parameters | Δρmax = 0.37 e Å−3 |
0 restraints | Δρmin = −0.38 e Å−3 |
NH4+·C5H14NO6P2− | V = 1105.84 (13) Å3 |
Mr = 264.15 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.6007 (6) Å | µ = 0.41 mm−1 |
b = 5.7239 (4) Å | T = 296 K |
c = 20.3259 (15) Å | 0.50 × 0.12 × 0.04 mm |
β = 98.100 (3)° |
Bruker APEXII CCD diffractometer | 2256 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 1532 reflections with I > 2σ(I) |
Tmin = 0.824, Tmax = 0.982 | Rint = 0.056 |
5297 measured reflections |
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.122 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.37 e Å−3 |
2256 reflections | Δρmin = −0.38 e Å−3 |
173 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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. |
x | y | z | Uiso*/Ueq | ||
P1 | 0.22481 (10) | 0.43513 (17) | 0.29915 (4) | 0.0195 (3) | |
P2 | 0.00587 (9) | 0.47871 (16) | 0.39608 (4) | 0.0184 (2) | |
C1 | 0.1590 (3) | 0.3149 (6) | 0.37310 (16) | 0.0161 (7) | |
C2 | 0.2832 (4) | 0.3109 (7) | 0.43011 (17) | 0.0243 (8) | |
H2A | 0.3635 | 0.2439 | 0.4129 | 0.029* | |
H2B | 0.3070 | 0.4715 | 0.4421 | 0.029* | |
C3 | 0.2649 (4) | 0.1806 (7) | 0.49344 (17) | 0.0295 (9) | |
H3A | 0.1787 | 0.2316 | 0.5088 | 0.035* | |
H3B | 0.2567 | 0.0146 | 0.4841 | 0.035* | |
C4 | 0.3877 (4) | 0.2227 (8) | 0.54735 (18) | 0.0374 (11) | |
H4A | 0.3885 | 0.3860 | 0.5602 | 0.045* | |
H4B | 0.4745 | 0.1909 | 0.5297 | 0.045* | |
C5 | 0.3827 (5) | 0.0731 (9) | 0.6084 (2) | 0.0506 (13) | |
H5A | 0.2985 | 0.1074 | 0.6271 | 0.076* | |
H5B | 0.4634 | 0.1059 | 0.6407 | 0.076* | |
H5C | 0.3831 | −0.0889 | 0.5962 | 0.076* | |
N1 | 0.1106 (3) | 0.0689 (5) | 0.35619 (16) | 0.0200 (7) | |
N2 | 0.3682 (4) | 0.9144 (7) | 0.2109 (2) | 0.0297 (8) | |
O1 | 0.3514 (2) | 0.2924 (4) | 0.28929 (11) | 0.0247 (6) | |
O2 | 0.2493 (3) | 0.6898 (4) | 0.31012 (12) | 0.0279 (6) | |
O3 | 0.1056 (3) | 0.3928 (5) | 0.23993 (12) | 0.0282 (7) | |
O4 | −0.0725 (3) | 0.2932 (4) | 0.43385 (13) | 0.0263 (6) | |
O5 | −0.0902 (2) | 0.5374 (5) | 0.33383 (12) | 0.0280 (6) | |
O6 | 0.0601 (3) | 0.6800 (4) | 0.43945 (11) | 0.0237 (6) | |
H3O | 0.107 (5) | 0.279 (9) | 0.217 (2) | 0.065 (18)* | |
H4O | −0.061 (5) | 0.303 (9) | 0.475 (2) | 0.070 (18)* | |
H11N | 0.180 (4) | −0.059 (7) | 0.3428 (19) | 0.047 (12)* | |
H12N | 0.078 (5) | −0.001 (8) | 0.392 (2) | 0.060 (14)* | |
H13N | 0.038 (4) | 0.063 (7) | 0.321 (2) | 0.040 (12)* | |
H21N | 0.336 (5) | 0.810 (9) | 0.247 (3) | 0.083 (18)* | |
H22N | 0.449 (5) | 0.874 (7) | 0.2012 (19) | 0.040 (13)* | |
H23N | 0.295 (6) | 0.919 (10) | 0.176 (3) | 0.10 (2)* | |
H24N | 0.377 (5) | 1.058 (8) | 0.231 (2) | 0.048 (14)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
P1 | 0.0216 (5) | 0.0158 (5) | 0.0220 (5) | −0.0005 (4) | 0.0066 (4) | 0.0005 (4) |
P2 | 0.0181 (5) | 0.0165 (5) | 0.0213 (5) | 0.0008 (4) | 0.0054 (4) | 0.0007 (4) |
C1 | 0.0180 (17) | 0.0085 (18) | 0.0212 (17) | −0.0008 (15) | 0.0006 (14) | 0.0005 (13) |
C2 | 0.0189 (18) | 0.026 (2) | 0.0263 (19) | −0.0043 (17) | −0.0025 (15) | −0.0006 (16) |
C3 | 0.028 (2) | 0.034 (3) | 0.0250 (19) | −0.002 (2) | 0.0005 (17) | 0.0037 (17) |
C4 | 0.037 (2) | 0.043 (3) | 0.029 (2) | 0.004 (2) | −0.0054 (19) | 0.0001 (19) |
C5 | 0.052 (3) | 0.068 (4) | 0.030 (2) | 0.011 (3) | 0.000 (2) | 0.007 (2) |
N1 | 0.0237 (16) | 0.0152 (17) | 0.0211 (16) | −0.0026 (14) | 0.0028 (14) | −0.0007 (13) |
N2 | 0.026 (2) | 0.026 (2) | 0.040 (2) | 0.0035 (18) | 0.0115 (18) | 0.0002 (17) |
O1 | 0.0194 (13) | 0.0244 (15) | 0.0314 (13) | 0.0026 (12) | 0.0074 (11) | −0.0023 (11) |
O2 | 0.0360 (15) | 0.0154 (15) | 0.0347 (14) | −0.0015 (13) | 0.0132 (12) | −0.0007 (11) |
O3 | 0.0297 (15) | 0.0329 (18) | 0.0216 (13) | 0.0049 (14) | 0.0019 (12) | −0.0045 (13) |
O4 | 0.0315 (15) | 0.0229 (16) | 0.0265 (15) | −0.0089 (12) | 0.0108 (12) | −0.0013 (12) |
O5 | 0.0198 (12) | 0.0329 (17) | 0.0305 (14) | 0.0030 (12) | 0.0002 (11) | 0.0063 (12) |
O6 | 0.0317 (14) | 0.0131 (14) | 0.0278 (13) | −0.0043 (12) | 0.0097 (11) | −0.0040 (10) |
P1—O2 | 1.488 (3) | C4—C5 | 1.514 (5) |
P1—O1 | 1.501 (2) | C4—H4A | 0.9700 |
P1—O3 | 1.559 (3) | C4—H4B | 0.9700 |
P1—C1 | 1.844 (3) | C5—H5A | 0.9600 |
P2—O5 | 1.495 (2) | C5—H5B | 0.9600 |
P2—O6 | 1.499 (2) | C5—H5C | 0.9600 |
P2—O4 | 1.564 (3) | N1—H11N | 1.05 (4) |
P2—C1 | 1.858 (3) | N1—H12N | 0.93 (5) |
C1—N1 | 1.507 (4) | N1—H13N | 0.93 (4) |
C1—C2 | 1.541 (5) | N2—H21N | 1.02 (6) |
C2—C3 | 1.519 (5) | N2—H22N | 0.86 (4) |
C2—H2A | 0.9700 | N2—H23N | 0.93 (6) |
C2—H2B | 0.9700 | N2—H24N | 0.92 (5) |
C3—C4 | 1.511 (5) | O3—H3O | 0.80 (5) |
C3—H3A | 0.9700 | O4—H4O | 0.82 (5) |
C3—H3B | 0.9700 | ||
O2—P1—O1 | 116.04 (14) | C2—C3—H3B | 109.4 |
O2—P1—O3 | 110.56 (16) | H3A—C3—H3B | 108.0 |
O1—P1—O3 | 109.44 (15) | C3—C4—C5 | 113.1 (4) |
O2—P1—C1 | 107.97 (15) | C3—C4—H4A | 109.0 |
O1—P1—C1 | 106.42 (15) | C5—C4—H4A | 109.0 |
O3—P1—C1 | 105.83 (15) | C3—C4—H4B | 109.0 |
O5—P2—O6 | 116.53 (15) | C5—C4—H4B | 109.0 |
O5—P2—O4 | 106.61 (15) | H4A—C4—H4B | 107.8 |
O6—P2—O4 | 112.60 (14) | C4—C5—H5A | 109.5 |
O5—P2—C1 | 108.42 (14) | C4—C5—H5B | 109.5 |
O6—P2—C1 | 108.33 (14) | H5A—C5—H5B | 109.5 |
O4—P2—C1 | 103.51 (14) | C4—C5—H5C | 109.5 |
N1—C1—C2 | 109.8 (3) | H5A—C5—H5C | 109.5 |
N1—C1—P1 | 107.0 (2) | H5B—C5—H5C | 109.5 |
C2—C1—P1 | 107.5 (2) | C1—N1—H11N | 122 (2) |
N1—C1—P2 | 107.4 (2) | C1—N1—H12N | 110 (3) |
C2—C1—P2 | 112.0 (2) | H11N—N1—H12N | 101 (3) |
P1—C1—P2 | 113.01 (17) | C1—N1—H13N | 113 (2) |
C3—C2—C1 | 118.3 (3) | H11N—N1—H13N | 102 (3) |
C3—C2—H2A | 107.7 | H12N—N1—H13N | 107 (4) |
C1—C2—H2A | 107.7 | H21N—N2—H22N | 112 (4) |
C3—C2—H2B | 107.7 | H21N—N2—H23N | 107 (4) |
C1—C2—H2B | 107.7 | H22N—N2—H23N | 116 (4) |
H2A—C2—H2B | 107.1 | H21N—N2—H24N | 103 (4) |
C4—C3—C2 | 111.4 (3) | H22N—N2—H24N | 108 (4) |
C4—C3—H3A | 109.4 | H23N—N2—H24N | 109 (4) |
C2—C3—H3A | 109.4 | P1—O3—H3O | 120 (4) |
C4—C3—H3B | 109.4 | P2—O4—H4O | 116 (4) |
O2—P1—C1—N1 | 170.1 (2) | O5—P2—C1—C2 | 162.9 (2) |
O1—P1—C1—N1 | −64.7 (2) | O6—P2—C1—C2 | 35.6 (3) |
O3—P1—C1—N1 | 51.7 (3) | O4—P2—C1—C2 | −84.2 (3) |
O2—P1—C1—C2 | −72.0 (3) | O5—P2—C1—P1 | 41.3 (2) |
O1—P1—C1—C2 | 53.2 (3) | O6—P2—C1—P1 | −86.01 (19) |
O3—P1—C1—C2 | 169.6 (2) | O4—P2—C1—P1 | 154.25 (17) |
O2—P1—C1—P2 | 52.1 (2) | N1—C1—C2—C3 | −53.3 (4) |
O1—P1—C1—P2 | 177.27 (16) | P1—C1—C2—C3 | −169.4 (3) |
O3—P1—C1—P2 | −66.4 (2) | P2—C1—C2—C3 | 65.9 (4) |
O5—P2—C1—N1 | −76.5 (2) | C1—C2—C3—C4 | −171.9 (3) |
O6—P2—C1—N1 | 156.2 (2) | C2—C3—C4—C5 | −172.9 (3) |
O4—P2—C1—N1 | 36.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H11N···O2i | 1.05 (4) | 1.75 (4) | 2.777 (4) | 163 (3) |
N1—H13N···O3ii | 0.93 (4) | 1.98 (4) | 2.828 (4) | 152 (3) |
N1—H12N···O6i | 0.93 (5) | 2.08 (5) | 2.879 (4) | 143 (4) |
O3—H3O···O5ii | 0.80 (5) | 1.72 (5) | 2.519 (4) | 174 (5) |
O4—H4O···O6iii | 0.82 (5) | 1.75 (5) | 2.566 (3) | 173 (5) |
N2—H22N···O1iv | 0.86 (4) | 1.95 (4) | 2.781 (4) | 161 (4) |
N2—H21N···O2 | 1.02 (6) | 1.77 (6) | 2.769 (4) | 165 (4) |
N2—H23N···O5v | 0.93 (6) | 2.07 (6) | 2.787 (5) | 134 (5) |
N2—H24N···O1vi | 0.92 (5) | 1.83 (5) | 2.705 (5) | 159 (4) |
Symmetry codes: (i) x, y−1, z; (ii) −x, y−1/2, −z+1/2; (iii) −x, −y+1, −z+1; (iv) −x+1, y+1/2, −z+1/2; (v) −x, y+1/2, −z+1/2; (vi) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | NH4+·C5H14NO6P2− |
Mr | 264.15 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 296 |
a, b, c (Å) | 9.6007 (6), 5.7239 (4), 20.3259 (15) |
β (°) | 98.100 (3) |
V (Å3) | 1105.84 (13) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.41 |
Crystal size (mm) | 0.50 × 0.12 × 0.04 |
Data collection | |
Diffractometer | Bruker APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.824, 0.982 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5297, 2256, 1532 |
Rint | 0.056 |
(sin θ/λ)max (Å−1) | 0.626 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.122, 1.02 |
No. of reflections | 2256 |
No. of parameters | 173 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.37, −0.38 |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), publCIF (Westrip, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H11N···O2i | 1.05 (4) | 1.75 (4) | 2.777 (4) | 163 (3) |
N1—H13N···O3ii | 0.93 (4) | 1.98 (4) | 2.828 (4) | 152 (3) |
N1—H12N···O6i | 0.93 (5) | 2.08 (5) | 2.879 (4) | 143 (4) |
O3—H3O···O5ii | 0.80 (5) | 1.72 (5) | 2.519 (4) | 174 (5) |
O4—H4O···O6iii | 0.82 (5) | 1.75 (5) | 2.566 (3) | 173 (5) |
N2—H22N···O1iv | 0.86 (4) | 1.95 (4) | 2.781 (4) | 161 (4) |
N2—H21N···O2 | 1.02 (6) | 1.77 (6) | 2.769 (4) | 165 (4) |
N2—H23N···O5v | 0.93 (6) | 2.07 (6) | 2.787 (5) | 134 (5) |
N2—H24N···O1vi | 0.92 (5) | 1.83 (5) | 2.705 (5) | 159 (4) |
Symmetry codes: (i) x, y−1, z; (ii) −x, y−1/2, −z+1/2; (iii) −x, −y+1, −z+1; (iv) −x+1, y+1/2, −z+1/2; (v) −x, y+1/2, −z+1/2; (vi) x, y+1, z. |
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. CrossRef Web of Science Google Scholar
Bon, V. V., Dudko, A. V., Kozachkova, A. N. & Pekhnyo, V. I. (2008). Acta Cryst. E64, o2436. Web of Science CSD CrossRef IUCr Journals Google Scholar
Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Matczak-Jon, E. & Videnova-Adrabinska, V. (2005). Coord. Chem. Rev. 249, 2458–2488. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Szabo, Ch. M., Martin, M. B. & Oldfield, E. (2002). J. Med. Chem. 45, 2894–2903. Web of Science CSD CrossRef PubMed CAS Google Scholar
Tromelin, A., El Manouni, D. & Burgada, R. (1986). Phosphorus Sulfur Relat. Elem. 27, 301–312. CrossRef CAS Web of Science Google Scholar
Westrip, S. P. (2009). publCIF. In preparation. Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
The organic diphosphonic acids are potentially very powerful chelating agents used in metal extractions and are 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 title compound (Fig. 1) contains one molecule, which exists as anion with protons transferred from the phosphonic group to the amino group. The ammonium cation attendant in structure neutralizes the negatively charged phosphonic acid residual. The phosphorus atom displays a slightly distorted tetrahedral geometry provided by three oxygen atoms and one carbon atom. Bond lengths and angles have normal values (Allen et al., 1987). The crystal structure of title compound shows three–dimensional network of O—H···O and N—H···O hydrogen bonds which additionally stabilized the structure (Table 1, Fig. 2).