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Acta Crystallogr Sect E Struct Rep Online. 2010 February 1; 66(Pt 2): m182.
Published online 2010 January 20. doi:  10.1107/S1600536810001765
PMCID: PMC2979859

{[1-(2-Amino­ethyl­amino)-1-methyl­ethyl]phospho­nato-κ3 N,N′,O}chloridopalladium(II) monohydrate

Abstract

In the title compound, [Pd(C5H14N2O3P)Cl]·H2O, the Pd(II) atom shows a slightly distorted square-planar geometry and forms two five-membered metallacycles, which both exhibit half-chair conformations. The crystal structure consists of layers propogating in the [100] direction which are connected into a three-dimensional network by strong N—H(...)Cl, N—H(...)O and O—H(...)O hydrogen bonds.

Related literature

For general background to the use of organic phospho­nic acids as chelating agents in metal extraction and as drugs for the prevention of calcification and bone resorption, see: Matczak-Jon & Videnova-Adrabinska (2005 [triangle]); Tromelin et al. (1986 [triangle]); Szabo et al. (2002 [triangle]). For related structures, see: Shkol’nikova et al. (1991 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0m182-scheme1.jpg

Experimental

Crystal data

  • [Pd(C5H14N2O3P)Cl]·H2O
  • M r = 341.02
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0m182-efi1.jpg
  • a = 7.2158 (2) Å
  • b = 7.8981 (2) Å
  • c = 10.3179 (3) Å
  • α = 97.968 (2)°
  • β = 98.403 (2)°
  • γ = 95.894 (2)°
  • V = 571.55 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 1.99 mm−1
  • T = 100 K
  • 0.38 × 0.12 × 0.10 mm

Data collection

  • Bruker APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.519, T max = 0.832
  • 8452 measured reflections
  • 2306 independent reflections
  • 1954 reflections with I > 2σ(I)
  • R int = 0.046

Refinement

  • R[F 2 > 2σ(F 2)] = 0.032
  • wR(F 2) = 0.076
  • S = 1.05
  • 2306 reflections
  • 147 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.75 e Å−3
  • Δρmin = −0.55 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; 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: publCIF (Westrip, 2010 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810001765/im2173sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810001765/im2173Isup2.hkl

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

supplementary crystallographic information

Comment

Organic phosphonic acids are potentially very powerful chelating agents used in metal extractions and they are also tested by 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 molecular structure of the title compound contains one molecule of the complex per asymmetric unit (Fig.1). The palladium atom shows a slightly distorted square-planar geometry. Mean average deviation from the respective plane is 0.040 (1) Å with a maximum deviation for O1 of 0.048 (1) Å. The bond lengths have a good correlation with reference data (Shkol'nikova et al., 1991). The ligand molecule coordinated to the palladium atom in a tridentate manner via phosphonic oxygen and two amino nitrogen atoms creating two five-membered metallacyclic subunits in half-chair conformation. Torsion angles C1–P1–O1–Pd1 = -26.4 (2)° and Pd1–N1–C1–P1 = -43.9 (3)° of the metallacycle [Pd1O1P1C1N1] slightly differ from the corresponding angles Pd1–N1–C4–C5 = 42.4 (4)° and Pd1–N2–C5–C4 = 37.5 (4)° of the second metallacycle [PdN1C4C5N2] because of different stereochemical environments. The crystal structure of the title compound forms a layered supramolecular structure, stabilized by strong N–H···Cl, N–H···O and O–H···O hydrogen bonds (Fig.2, Table 1).

Experimental

2-(2-aminoethyl)aminopropan-2-yl-phosphonic acid hydrochloride (0.219 g, 1 mmol) in water (10 ml) was mixed together with a solution of palladium diacetate (0.224 g, 1 mmol, Merck ≥ 99%) in benzene (10 ml). The color of the aqueous phase of the reaction mixture slowly turned to pale yellow. After stirring for 12 h, the aqueous phase of the solution was separated. Suitable single crystals of the title compound were produced by slow evaporation of water from an aqueous solution at room temperature (yield: 76%). A pale yellow needle-shaped crystal was used for data collection.

Refinement

H atoms bonded to N and O atoms were located in a difference map and refined with constrained Uiso(H) = 1.2Ueq(N,O). Other H atoms were positioned geometrically and refined using riding model with C–H = 0.99 Å for CH2 [Uiso(H) = 1.2Ueq(C)] and C–H = 0.98 Å for CH3 [Uiso(H) = 1.5Ueq(C)]. The DFIX instruction was used in the final refinement for restraining the O3—H3O distance to a reasonable value.

Figures

Fig. 1.
The title compound showing 50% probability displacement ellipsoids for non-hydrogen atoms.
Fig. 2.
Crystal packing of the title compound, projection down the a axis. Dashed lines indicate hydrogen bonds.

Crystal data

[Pd(C5H14N2O3P)Cl]·H2OZ = 2
Mr = 341.02F(000) = 340
Triclinic, P1Dx = 1.982 Mg m3
Hall symbol: -P 1Melting point: 535 K
a = 7.2158 (2) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.8981 (2) ÅCell parameters from 2725 reflections
c = 10.3179 (3) Åθ = 2.9–26.2°
α = 97.968 (2)°µ = 1.99 mm1
β = 98.403 (2)°T = 100 K
γ = 95.894 (2)°Block, yellow
V = 571.55 (3) Å30.38 × 0.12 × 0.10 mm

Data collection

Bruker APEXII CCD diffractometer2306 independent reflections
Radiation source: fine-focus sealed tube1954 reflections with I > 2σ(I)
graphiteRint = 0.046
Detector resolution: 8.26 pixels mm-1θmax = 26.4°, θmin = 2.0°
[var phi] and ω scansh = −8→8
Absorption correction: multi-scan (SADABS; Bruker, 2005)k = −9→9
Tmin = 0.519, Tmax = 0.832l = −12→12
8452 measured reflections

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)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.076H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0351P)2 + 0.6204P] where P = (Fo2 + 2Fc2)/3
2306 reflections(Δ/σ)max < 0.001
147 parametersΔρmax = 0.75 e Å3
1 restraintΔρmin = −0.55 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
Pd10.22708 (4)0.52397 (4)0.07010 (3)0.01203 (11)
P10.15753 (15)0.54887 (16)0.35047 (10)0.0162 (3)
Cl10.27656 (14)0.26896 (14)−0.05111 (10)0.0155 (2)
N10.1808 (5)0.7519 (4)0.1696 (3)0.0120 (7)
H1N0.060 (7)0.746 (6)0.150 (4)0.014*
N20.2614 (5)0.6578 (5)−0.0782 (3)0.0126 (7)
H21N0.199 (6)0.594 (6)−0.161 (4)0.015*
H22N0.368 (7)0.665 (6)−0.078 (4)0.015*
O10.2068 (4)0.4194 (4)0.2400 (3)0.0184 (7)
O20.2368 (4)0.5237 (4)0.4882 (3)0.0209 (7)
O3−0.0616 (4)0.5451 (4)0.3289 (3)0.0190 (7)
H3O−0.117 (6)0.538 (7)0.387 (4)0.023*
O40.5268 (5)0.2409 (5)0.2944 (3)0.0249 (8)
H41O0.577 (8)0.316 (7)0.351 (5)0.030*
H42O0.428 (8)0.276 (7)0.281 (5)0.030*
C10.2460 (6)0.7633 (6)0.3169 (4)0.0158 (9)
C20.4630 (6)0.7880 (6)0.3480 (4)0.0214 (10)
H2A0.51140.90150.33010.032*
H2B0.51220.69820.29210.032*
H2C0.50360.78010.44160.032*
C30.1618 (7)0.9064 (6)0.3944 (4)0.0237 (10)
H3A0.21251.01820.37460.036*
H3B0.19440.90370.48960.036*
H3C0.02410.88950.36880.036*
C40.2573 (6)0.8907 (5)0.1007 (4)0.0157 (9)
H4A0.39650.91260.12420.019*
H4B0.20440.99890.12650.019*
C50.2000 (6)0.8285 (6)−0.0464 (4)0.0168 (9)
H5A0.06130.8209−0.07120.020*
H5B0.25960.9106−0.09700.020*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Pd10.01212 (17)0.01164 (19)0.01225 (17)0.00112 (12)0.00298 (11)0.00076 (12)
P10.0142 (5)0.0219 (7)0.0118 (5)−0.0005 (5)0.0022 (4)0.0023 (5)
Cl10.0142 (5)0.0136 (6)0.0183 (5)0.0028 (4)0.0027 (4)0.0002 (4)
N10.0102 (17)0.0102 (19)0.0140 (17)−0.0012 (15)−0.0016 (13)0.0022 (14)
N20.0097 (17)0.013 (2)0.0143 (18)0.0005 (15)0.0019 (14)0.0013 (15)
O10.0237 (16)0.0159 (17)0.0148 (15)−0.0016 (13)0.0046 (12)0.0013 (13)
O20.0154 (15)0.033 (2)0.0141 (15)−0.0006 (14)0.0034 (12)0.0062 (14)
O30.0129 (15)0.0294 (19)0.0147 (15)−0.0011 (14)0.0034 (11)0.0047 (14)
O40.0216 (18)0.027 (2)0.0244 (18)0.0028 (16)0.0009 (14)−0.0003 (15)
C10.018 (2)0.016 (2)0.012 (2)0.0002 (18)0.0018 (16)0.0017 (17)
C20.020 (2)0.028 (3)0.014 (2)−0.003 (2)0.0005 (17)0.004 (2)
C30.027 (3)0.023 (3)0.019 (2)0.003 (2)0.0066 (19)−0.004 (2)
C40.018 (2)0.009 (2)0.020 (2)0.0005 (18)0.0020 (17)0.0024 (18)
C50.013 (2)0.014 (2)0.024 (2)0.0019 (18)0.0033 (17)0.0062 (19)

Geometric parameters (Å, °)

Pd1—N22.006 (3)O4—H41O0.79 (5)
Pd1—N12.029 (3)O4—H42O0.79 (6)
Pd1—O12.056 (3)C1—C31.523 (6)
Pd1—Cl12.3083 (11)C1—C21.538 (6)
P1—O21.500 (3)C2—H2A0.9800
P1—O11.530 (3)C2—H2B0.9800
P1—O31.561 (3)C2—H2C0.9800
P1—C11.844 (4)C3—H3A0.9800
N1—C41.490 (5)C3—H3B0.9800
N1—C11.511 (5)C3—H3C0.9800
N1—H1N0.86 (5)C4—C51.511 (6)
N2—C51.471 (5)C4—H4A0.9900
N2—H21N0.96 (5)C4—H4B0.9900
N2—H22N0.76 (5)C5—H5A0.9900
O3—H3O0.77 (3)C5—H5B0.9900
N2—Pd1—N184.95 (14)C3—C1—C2111.8 (4)
N2—Pd1—O1171.76 (13)N1—C1—P1103.1 (3)
N1—Pd1—O187.95 (12)C3—C1—P1111.8 (3)
N2—Pd1—Cl192.89 (11)C2—C1—P1108.9 (3)
N1—Pd1—Cl1177.67 (10)C1—C2—H2A109.5
O1—Pd1—Cl194.26 (9)C1—C2—H2B109.5
O2—P1—O1114.59 (18)H2A—C2—H2B109.5
O2—P1—O3112.56 (16)C1—C2—H2C109.5
O1—P1—O3107.83 (17)H2A—C2—H2C109.5
O2—P1—C1111.12 (19)H2B—C2—H2C109.5
O1—P1—C1105.66 (18)C1—C3—H3A109.5
O3—P1—C1104.36 (19)C1—C3—H3B109.5
C4—N1—C1118.5 (3)H3A—C3—H3B109.5
C4—N1—Pd1107.3 (2)C1—C3—H3C109.5
C1—N1—Pd1110.9 (3)H3A—C3—H3C109.5
C4—N1—H1N105 (3)H3B—C3—H3C109.5
C1—N1—H1N112 (3)N1—C4—C5106.8 (3)
Pd1—N1—H1N101 (3)N1—C4—H4A110.4
C5—N2—Pd1108.9 (2)C5—C4—H4A110.4
C5—N2—H21N114 (3)N1—C4—H4B110.4
Pd1—N2—H21N111 (3)C5—C4—H4B110.4
C5—N2—H22N111 (4)H4A—C4—H4B108.6
Pd1—N2—H22N103 (3)N2—C5—C4108.7 (3)
H21N—N2—H22N109 (4)N2—C5—H5A109.9
P1—O1—Pd1112.20 (17)C4—C5—H5A109.9
P1—O3—H3O121 (4)N2—C5—H5B109.9
H41O—O4—H42O97 (5)C4—C5—H5B109.9
N1—C1—C3110.7 (3)H5A—C5—H5B108.3
N1—C1—C2110.2 (3)
N2—Pd1—N1—C4−18.0 (3)C4—N1—C1—P1−168.6 (3)
O1—Pd1—N1—C4157.8 (3)Pd1—N1—C1—P1−43.9 (3)
N2—Pd1—N1—C1−148.9 (3)O2—P1—C1—N1170.2 (2)
O1—Pd1—N1—C126.9 (3)O1—P1—C1—N145.4 (3)
N1—Pd1—N2—C5−10.8 (3)O3—P1—C1—N1−68.2 (3)
Cl1—Pd1—N2—C5168.3 (3)O2—P1—C1—C3−70.8 (3)
O2—P1—O1—Pd1−149.06 (16)O1—P1—C1—C3164.3 (3)
O3—P1—O1—Pd184.75 (19)O3—P1—C1—C350.7 (3)
C1—P1—O1—Pd1−26.4 (2)O2—P1—C1—C253.2 (3)
N1—Pd1—O1—P13.43 (18)O1—P1—C1—C2−71.6 (3)
Cl1—Pd1—O1—P1−175.86 (15)O3—P1—C1—C2174.8 (3)
C4—N1—C1—C371.7 (5)C1—N1—C4—C5168.9 (3)
Pd1—N1—C1—C3−163.6 (3)Pd1—N1—C4—C542.4 (4)
C4—N1—C1—C2−52.6 (5)Pd1—N2—C5—C437.5 (4)
Pd1—N1—C1—C272.2 (4)N1—C4—C5—N2−53.3 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···Cl1i0.86 (5)2.48 (5)3.326 (4)169 (4)
N2—H21N···O3i0.96 (5)1.98 (5)2.937 (5)177 (4)
N2—H22N···Cl1ii0.76 (5)2.68 (5)3.365 (4)151 (4)
O3—H3O···O2iii0.77 (3)1.75 (3)2.509 (4)168 (6)
O4—H41O···O2iv0.79 (5)2.14 (6)2.911 (5)166 (5)
O4—H42O···O10.79 (6)2.08 (6)2.854 (5)167 (5)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IM2173).

References

  • 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]
  • Shkol’nikova, L. M., Porai-Koshits, M. A., Fundamenskii, V. S., Poznyak, A. L. & Kalugina, E. V. (1991). Koord. Khim.17, 954–963.
  • Szabo, Ch. 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.
  • Westrip, S. P. (2010). publCIF. In preparation.

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