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

Bon, V.V.; Dudko, A.V.; Kozachkova, A.N.; Pekhnyo, V.I.

doi:10.1107/S1600536808038968

organic compounds

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Volume 64| Part 12| December 2008| Page o2436

doi:10.1107/S1600536808038968

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

V. V. Bon,^a ^* A. V. Dudko,^a A. N. Kozachkova ^a and V. I. Pekhnyo ^a

^aV.I. Vernadskii Institute of General and Inorganic Chemistry, Kyiv 03680, Ukraine
^*Correspondence e-mail: bon@ionc.kiev.ua

(Received 7 November 2008; accepted 20 November 2008; online 26 November 2008)

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 ); Szabo et al. (2002 ); Tromelin et al. (1986 ). For comparable bond lengths, see: Allen et al. (1987 ).

Experimental

Crystal data

C₅H₁₅NO₆P₂
M_r = 247.12
Monoclinic, P 2₁ /c
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 ) 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[F² > 2σ(F²)] = 0.028
wR(F²) = 0.072
S = 1.06
2471 reflections
152 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.44 e Å⁻³
Δρ_min = −0.32 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯O4ⁱ	0.84 (2)	2.02 (2)	2.7584 (16)	146.7 (19)
N1—H2N⋯O5ⁱⁱ	0.91 (2)	1.88 (2)	2.7799 (16)	169.4 (19)
N1—H3N⋯O2ⁱⁱⁱ	0.88 (2)	1.99 (2)	2.8451 (16)	162.9 (18)
O1—H1O⋯O2ⁱⁱⁱ	0.79 (2)	1.85 (3)	2.6297 (15)	167 (3)
O3—H3O⋯O5ⁱⁱⁱ	0.79 (3)	1.70 (3)	2.4884 (15)	175 (3)
O6—H6O⋯O4^iv	0.83 (3)	1.72 (3)	2.5372 (14)	168 (3)
Symmetry codes: (i) -x+1, -y, -z+1; (ii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iii) $[x, -y-{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iv) $[-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

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

Supporting information

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

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

checkCIF report

Comment top

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).

Related literature top

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

Experimental top

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.

Computing details top

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

Figures top

	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.

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

Crystal data top

C₅H₁₅NO₆P₂	F(000) = 520
M_r = 247.12	D_x = 1.666 Mg m⁻³
Monoclinic, P2₁/c	Melting point: 562 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 14.5502 (3) Å	Cell parameters from 8806 reflections
b = 7.1896 (1) Å	θ = 2.8–28.4°
c = 9.4855 (2) Å	µ = 0.45 mm⁻¹
β = 96.938 (1)°	T = 100 K
V = 985.01 (3) Å³	Plate, colourless
Z = 4	0.38 × 0.36 × 0.09 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2471 independent reflections
Radiation source: fine-focus sealed tube	2225 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.043
ϕ and ω scans	θ_max = 28.4°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −19→19
T_min = 0.848, T_max = 0.961	k = −9→9
23409 measured reflections	l = −12→12

Refinement top

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)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.072	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0317P)² + 0.8863P] where P = (F_o² + 2F_c²)/3
2471 reflections	(Δ/σ)_max < 0.001
152 parameters	Δρ_max = 0.44 e Å⁻³
0 restraints	Δρ_min = −0.32 e Å⁻³

Crystal data top

C₅H₁₅NO₆P₂	V = 985.01 (3) Å³
M_r = 247.12	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 14.5502 (3) Å	µ = 0.45 mm⁻¹
b = 7.1896 (1) Å	T = 100 K
c = 9.4855 (2) Å	0.38 × 0.36 × 0.09 mm
β = 96.938 (1)°

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2471 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	2225 reflections with I > 2σ(I)
T_min = 0.848, T_max = 0.961	R_int = 0.043
23409 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.028	0 restraints
wR(F²) = 0.072	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	Δρ_max = 0.44 e Å⁻³
2471 reflections	Δρ_min = −0.32 e Å⁻³
152 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
P1	0.39648 (2)	0.07886 (5)	0.68586 (4)	0.00647 (9)
P2	0.28775 (2)	−0.24846 (5)	0.54892 (4)	0.00680 (9)
C1	0.30732 (9)	0.00397 (19)	0.54146 (14)	0.0067 (3)
C2	0.21901 (10)	0.1205 (2)	0.55184 (15)	0.0100 (3)
H2A	0.1914	0.0778	0.6366	0.012*
H2B	0.2383	0.2514	0.5692	0.012*
C3	0.14290 (10)	0.1183 (2)	0.42611 (16)	0.0139 (3)
H3A	0.1698	0.1489	0.3380	0.017*
H3B	0.1157	−0.0079	0.4153	0.017*
C4	0.06761 (12)	0.2576 (3)	0.4478 (2)	0.0239 (4)
H4A	0.0485	0.2381	0.5434	0.029*
H4B	0.0939	0.3844	0.4457	0.029*
C5	−0.01700 (12)	0.2475 (3)	0.3401 (2)	0.0238 (4)
H5A	0.0005	0.2714	0.2452	0.036*
H5B	−0.0620	0.3411	0.3624	0.036*
H5C	−0.0447	0.1234	0.3424	0.036*
N1	0.34540 (9)	0.04748 (18)	0.40433 (12)	0.0075 (2)
O1	0.20552 (7)	−0.29755 (15)	0.43309 (11)	0.0103 (2)
O2	0.26347 (7)	−0.29945 (15)	0.69151 (10)	0.0105 (2)
O3	0.37688 (7)	−0.33350 (15)	0.50568 (11)	0.0102 (2)
O4	0.48097 (7)	−0.03933 (15)	0.68442 (11)	0.0106 (2)
O5	0.35286 (7)	0.08211 (14)	0.82242 (10)	0.0092 (2)
O6	0.41170 (7)	0.28091 (15)	0.63361 (11)	0.0103 (2)
H1N	0.4006 (14)	0.015 (3)	0.406 (2)	0.015 (5)*
H2N	0.3439 (14)	0.172 (3)	0.387 (2)	0.022 (5)*
H3N	0.3141 (13)	−0.009 (3)	0.331 (2)	0.014 (5)*
H1O	0.2192 (17)	−0.283 (4)	0.356 (3)	0.032 (6)*
H3O	0.3713 (18)	−0.416 (4)	0.450 (3)	0.040 (7)*
H6O	0.4518 (18)	0.340 (4)	0.684 (3)	0.046 (8)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
P1	0.00764 (16)	0.00625 (17)	0.00532 (16)	−0.00016 (12)	−0.00004 (12)	−0.00001 (12)
P2	0.00865 (17)	0.00661 (17)	0.00509 (16)	−0.00071 (12)	0.00064 (12)	−0.00014 (12)
C1	0.0075 (6)	0.0081 (6)	0.0045 (6)	0.0003 (5)	0.0007 (5)	0.0000 (5)
C2	0.0085 (6)	0.0107 (7)	0.0107 (6)	0.0022 (5)	0.0010 (5)	−0.0017 (5)
C3	0.0119 (7)	0.0176 (8)	0.0114 (7)	0.0050 (6)	−0.0014 (5)	−0.0005 (6)
C4	0.0146 (8)	0.0292 (10)	0.0264 (9)	0.0094 (7)	−0.0043 (7)	−0.0081 (7)
C5	0.0140 (7)	0.0316 (10)	0.0249 (9)	0.0078 (7)	−0.0024 (6)	0.0026 (7)
N1	0.0082 (6)	0.0087 (6)	0.0058 (5)	−0.0007 (4)	0.0011 (4)	−0.0002 (4)
O1	0.0113 (5)	0.0123 (5)	0.0070 (5)	−0.0025 (4)	0.0002 (4)	−0.0008 (4)
O2	0.0142 (5)	0.0105 (5)	0.0068 (4)	−0.0006 (4)	0.0018 (4)	0.0006 (4)
O3	0.0116 (5)	0.0083 (5)	0.0109 (5)	0.0009 (4)	0.0022 (4)	−0.0026 (4)
O4	0.0095 (5)	0.0122 (5)	0.0096 (5)	0.0026 (4)	−0.0004 (4)	−0.0001 (4)
O5	0.0123 (5)	0.0087 (5)	0.0067 (4)	−0.0001 (4)	0.0016 (4)	−0.0003 (4)
O6	0.0134 (5)	0.0079 (5)	0.0089 (5)	−0.0031 (4)	−0.0007 (4)	0.0013 (4)

Geometric parameters (Å, º) top

P1—O4	1.4959 (10)	C3—H3A	0.9900
P1—O5	1.5099 (10)	C3—H3B	0.9900
P1—O6	1.5593 (11)	C4—C5	1.504 (2)
P1—C1	1.8492 (14)	C4—H4A	0.9900
P2—O2	1.4846 (10)	C4—H4B	0.9900
P2—O3	1.5337 (11)	C5—H5A	0.9800
P2—O1	1.5639 (10)	C5—H5B	0.9800
P2—C1	1.8398 (14)	C5—H5C	0.9800
C1—N1	1.5070 (17)	N1—H1N	0.84 (2)
C1—C2	1.5471 (19)	N1—H2N	0.91 (2)
C2—C3	1.5264 (19)	N1—H3N	0.88 (2)
C2—H2A	0.9900	O1—H1O	0.79 (2)
C2—H2B	0.9900	O3—H3O	0.79 (3)
C3—C4	1.517 (2)	O6—H6O	0.83 (3)

O4—P1—O5	116.59 (6)	C2—C3—H3A	109.5
O4—P1—O6	112.20 (6)	C4—C3—H3B	109.5
O5—P1—O6	110.42 (6)	C2—C3—H3B	109.5
O4—P1—C1	109.37 (6)	H3A—C3—H3B	108.1
O5—P1—C1	108.06 (6)	C5—C4—C3	114.90 (15)
O6—P1—C1	98.61 (6)	C5—C4—H4A	108.5
O2—P2—O3	116.57 (6)	C3—C4—H4A	108.5
O2—P2—O1	109.77 (6)	C5—C4—H4B	108.5
O3—P2—O1	108.78 (6)	C3—C4—H4B	108.5
O2—P2—C1	109.49 (6)	H4A—C4—H4B	107.5
O3—P2—C1	104.08 (6)	C4—C5—H5A	109.5
O1—P2—C1	107.72 (6)	C4—C5—H5B	109.5
N1—C1—C2	109.71 (11)	H5A—C5—H5B	109.5
N1—C1—P2	108.22 (9)	C4—C5—H5C	109.5
C2—C1—P2	113.48 (10)	H5A—C5—H5C	109.5
N1—C1—P1	106.30 (9)	H5B—C5—H5C	109.5
C2—C1—P1	107.99 (9)	C1—N1—H1N	112.5 (13)
P2—C1—P1	110.90 (7)	C1—N1—H2N	111.0 (13)
C3—C2—C1	118.31 (12)	H1N—N1—H2N	106.4 (19)
C3—C2—H2A	107.7	C1—N1—H3N	112.3 (12)
C1—C2—H2A	107.7	H1N—N1—H3N	106.5 (18)
C3—C2—H2B	107.7	H2N—N1—H3N	107.9 (18)
C1—C2—H2B	107.7	P2—O1—H1O	111.4 (17)
H2A—C2—H2B	107.1	P2—O3—H3O	117.1 (19)
C4—C3—C2	110.76 (13)	P1—O6—H6O	114.5 (19)
C4—C3—H3A	109.5

O2—P2—C1—N1	171.72 (8)	O4—P1—C1—C2	176.54 (9)
O3—P2—C1—N1	46.42 (10)	O5—P1—C1—C2	48.68 (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—P2	51.62 (9)
O3—P2—C1—C2	168.44 (9)	O5—P1—C1—P2	−76.24 (8)
O1—P2—C1—C2	53.05 (11)	O6—P1—C1—P2	168.90 (7)
O2—P2—C1—P1	55.49 (9)	N1—C1—C2—C3	50.75 (17)
O3—P2—C1—P1	−69.81 (8)	P2—C1—C2—C3	−70.43 (15)
O1—P2—C1—P1	174.81 (7)	P1—C1—C2—C3	166.21 (11)
O4—P1—C1—N1	−65.79 (10)	C1—C2—C3—C4	−173.11 (14)
O5—P1—C1—N1	166.35 (9)	C2—C3—C4—C5	−171.76 (15)
O6—P1—C1—N1	51.49 (10)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O4ⁱ	0.84 (2)	2.02 (2)	2.7584 (16)	146.7 (19)
N1—H2N···O5ⁱⁱ	0.91 (2)	1.88 (2)	2.7799 (16)	169.4 (19)
N1—H3N···O2ⁱⁱⁱ	0.88 (2)	1.99 (2)	2.8451 (16)	162.9 (18)
O1—H1O···O2ⁱⁱⁱ	0.79 (2)	1.85 (3)	2.6297 (15)	167 (3)
O3—H3O···O5ⁱⁱⁱ	0.79 (3)	1.70 (3)	2.4884 (15)	175 (3)
O6—H6O···O4^iv	0.83 (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.

Experimental details

Crystal data
Chemical formula	C₅H₁₅NO₆P₂
M_r	247.12
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	100
a, b, c (Å)	14.5502 (3), 7.1896 (1), 9.4855 (2)
β (°)	96.938 (1)
V (Å³)	985.01 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.45
Crystal size (mm)	0.38 × 0.36 × 0.09

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.848, 0.961
No. of measured, independent and observed [I > 2σ(I)] reflections	23409, 2471, 2225
R_int	0.043
(sin θ/λ)_max (Å⁻¹)	0.670

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.028, 0.072, 1.06
No. of reflections	2471
No. of parameters	152
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.32

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O4ⁱ	0.84 (2)	2.02 (2)	2.7584 (16)	146.7 (19)
N1—H2N···O5ⁱⁱ	0.91 (2)	1.88 (2)	2.7799 (16)	169.4 (19)
N1—H3N···O2ⁱⁱⁱ	0.88 (2)	1.99 (2)	2.8451 (16)	162.9 (18)
O1—H1O···O2ⁱⁱⁱ	0.79 (2)	1.85 (3)	2.6297 (15)	167 (3)
O3—H3O···O5ⁱⁱⁱ	0.79 (3)	1.70 (3)	2.4884 (15)	175 (3)
O6—H6O···O4^iv	0.83 (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.

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
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, C. 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

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