metal-organic compounds
{[1-(2-Aminoethylamino)-1-methylethyl]phosphonato-κ3N,N′,O}chloridopalladium(II) monohydrate
aInstitute of General and Inorganic Chemistry, NAS Ukraine, Kyiv, prosp. Palladina 32/34, 03680 Ukraine
*Correspondence e-mail: dudco_anatolij@ukr.net
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 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); Tromelin et al. (1986); Szabo et al. (2002). For related structures, see: Shkol'nikova et al. (1991).
Experimental
Crystal data
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Refinement
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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, 2010).
Supporting information
https://doi.org/10.1107/S1600536810001765/im2173sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810001765/im2173Isup2.hkl
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.
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
for restraining the O3—H3O distance to a reasonable value.Organic
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 (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 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).For general background to the use of organic
in as chelating agents in metal extraction and as drugs for the prevention of calcification and bone resorption, see: Matczak-Jon & Videnova-Adrabinska (2005); Tromelin et al. (1986); Szabo et al. (2002). For related structures, see: Shkol'nikova et al. (1991).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, 2010).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. |
[Pd(C5H14N2O3P)Cl]·H2O | Z = 2 |
Mr = 341.02 | F(000) = 340 |
Triclinic, P1 | Dx = 1.982 Mg m−3 |
Hall symbol: -P 1 | Melting point: 535 K |
a = 7.2158 (2) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 7.8981 (2) Å | Cell parameters from 2725 reflections |
c = 10.3179 (3) Å | θ = 2.9–26.2° |
α = 97.968 (2)° | µ = 1.99 mm−1 |
β = 98.403 (2)° | T = 100 K |
γ = 95.894 (2)° | Block, yellow |
V = 571.55 (3) Å3 | 0.38 × 0.12 × 0.10 mm |
Bruker APEXII CCD diffractometer | 2306 independent reflections |
Radiation source: fine-focus sealed tube | 1954 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.046 |
Detector resolution: 8.26 pixels mm-1 | θmax = 26.4°, θmin = 2.0° |
φ and ω scans | h = −8→8 |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | k = −9→9 |
Tmin = 0.519, Tmax = 0.832 | l = −12→12 |
8452 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)] = 0.032 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.076 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0351P)2 + 0.6204P] where P = (Fo2 + 2Fc2)/3 |
2306 reflections | (Δ/σ)max < 0.001 |
147 parameters | Δρmax = 0.75 e Å−3 |
1 restraint | Δρmin = −0.55 e Å−3 |
[Pd(C5H14N2O3P)Cl]·H2O | γ = 95.894 (2)° |
Mr = 341.02 | V = 571.55 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.2158 (2) Å | Mo Kα radiation |
b = 7.8981 (2) Å | µ = 1.99 mm−1 |
c = 10.3179 (3) Å | T = 100 K |
α = 97.968 (2)° | 0.38 × 0.12 × 0.10 mm |
β = 98.403 (2)° |
Bruker APEXII CCD diffractometer | 2306 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 1954 reflections with I > 2σ(I) |
Tmin = 0.519, Tmax = 0.832 | Rint = 0.046 |
8452 measured reflections |
R[F2 > 2σ(F2)] = 0.032 | 1 restraint |
wR(F2) = 0.076 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.05 | Δρmax = 0.75 e Å−3 |
2306 reflections | Δρmin = −0.55 e Å−3 |
147 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Pd1 | 0.22708 (4) | 0.52397 (4) | 0.07010 (3) | 0.01203 (11) | |
P1 | 0.15753 (15) | 0.54887 (16) | 0.35047 (10) | 0.0162 (3) | |
Cl1 | 0.27656 (14) | 0.26896 (14) | −0.05111 (10) | 0.0155 (2) | |
N1 | 0.1808 (5) | 0.7519 (4) | 0.1696 (3) | 0.0120 (7) | |
H1N | 0.060 (7) | 0.746 (6) | 0.150 (4) | 0.014* | |
N2 | 0.2614 (5) | 0.6578 (5) | −0.0782 (3) | 0.0126 (7) | |
H21N | 0.199 (6) | 0.594 (6) | −0.161 (4) | 0.015* | |
H22N | 0.368 (7) | 0.665 (6) | −0.078 (4) | 0.015* | |
O1 | 0.2068 (4) | 0.4194 (4) | 0.2400 (3) | 0.0184 (7) | |
O2 | 0.2368 (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* | |
O4 | 0.5268 (5) | 0.2409 (5) | 0.2944 (3) | 0.0249 (8) | |
H41O | 0.577 (8) | 0.316 (7) | 0.351 (5) | 0.030* | |
H42O | 0.428 (8) | 0.276 (7) | 0.281 (5) | 0.030* | |
C1 | 0.2460 (6) | 0.7633 (6) | 0.3169 (4) | 0.0158 (9) | |
C2 | 0.4630 (6) | 0.7880 (6) | 0.3480 (4) | 0.0214 (10) | |
H2A | 0.5114 | 0.9015 | 0.3301 | 0.032* | |
H2B | 0.5122 | 0.6982 | 0.2921 | 0.032* | |
H2C | 0.5036 | 0.7801 | 0.4416 | 0.032* | |
C3 | 0.1618 (7) | 0.9064 (6) | 0.3944 (4) | 0.0237 (10) | |
H3A | 0.2125 | 1.0182 | 0.3746 | 0.036* | |
H3B | 0.1944 | 0.9037 | 0.4896 | 0.036* | |
H3C | 0.0241 | 0.8895 | 0.3688 | 0.036* | |
C4 | 0.2573 (6) | 0.8907 (5) | 0.1007 (4) | 0.0157 (9) | |
H4A | 0.3965 | 0.9126 | 0.1242 | 0.019* | |
H4B | 0.2044 | 0.9989 | 0.1265 | 0.019* | |
C5 | 0.2000 (6) | 0.8285 (6) | −0.0464 (4) | 0.0168 (9) | |
H5A | 0.0613 | 0.8209 | −0.0712 | 0.020* | |
H5B | 0.2596 | 0.9106 | −0.0970 | 0.020* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.01212 (17) | 0.01164 (19) | 0.01225 (17) | 0.00112 (12) | 0.00298 (11) | 0.00076 (12) |
P1 | 0.0142 (5) | 0.0219 (7) | 0.0118 (5) | −0.0005 (5) | 0.0022 (4) | 0.0023 (5) |
Cl1 | 0.0142 (5) | 0.0136 (6) | 0.0183 (5) | 0.0028 (4) | 0.0027 (4) | 0.0002 (4) |
N1 | 0.0102 (17) | 0.0102 (19) | 0.0140 (17) | −0.0012 (15) | −0.0016 (13) | 0.0022 (14) |
N2 | 0.0097 (17) | 0.013 (2) | 0.0143 (18) | 0.0005 (15) | 0.0019 (14) | 0.0013 (15) |
O1 | 0.0237 (16) | 0.0159 (17) | 0.0148 (15) | −0.0016 (13) | 0.0046 (12) | 0.0013 (13) |
O2 | 0.0154 (15) | 0.033 (2) | 0.0141 (15) | −0.0006 (14) | 0.0034 (12) | 0.0062 (14) |
O3 | 0.0129 (15) | 0.0294 (19) | 0.0147 (15) | −0.0011 (14) | 0.0034 (11) | 0.0047 (14) |
O4 | 0.0216 (18) | 0.027 (2) | 0.0244 (18) | 0.0028 (16) | 0.0009 (14) | −0.0003 (15) |
C1 | 0.018 (2) | 0.016 (2) | 0.012 (2) | 0.0002 (18) | 0.0018 (16) | 0.0017 (17) |
C2 | 0.020 (2) | 0.028 (3) | 0.014 (2) | −0.003 (2) | 0.0005 (17) | 0.004 (2) |
C3 | 0.027 (3) | 0.023 (3) | 0.019 (2) | 0.003 (2) | 0.0066 (19) | −0.004 (2) |
C4 | 0.018 (2) | 0.009 (2) | 0.020 (2) | 0.0005 (18) | 0.0020 (17) | 0.0024 (18) |
C5 | 0.013 (2) | 0.014 (2) | 0.024 (2) | 0.0019 (18) | 0.0033 (17) | 0.0062 (19) |
Pd1—N2 | 2.006 (3) | O4—H41O | 0.79 (5) |
Pd1—N1 | 2.029 (3) | O4—H42O | 0.79 (6) |
Pd1—O1 | 2.056 (3) | C1—C3 | 1.523 (6) |
Pd1—Cl1 | 2.3083 (11) | C1—C2 | 1.538 (6) |
P1—O2 | 1.500 (3) | C2—H2A | 0.9800 |
P1—O1 | 1.530 (3) | C2—H2B | 0.9800 |
P1—O3 | 1.561 (3) | C2—H2C | 0.9800 |
P1—C1 | 1.844 (4) | C3—H3A | 0.9800 |
N1—C4 | 1.490 (5) | C3—H3B | 0.9800 |
N1—C1 | 1.511 (5) | C3—H3C | 0.9800 |
N1—H1N | 0.86 (5) | C4—C5 | 1.511 (6) |
N2—C5 | 1.471 (5) | C4—H4A | 0.9900 |
N2—H21N | 0.96 (5) | C4—H4B | 0.9900 |
N2—H22N | 0.76 (5) | C5—H5A | 0.9900 |
O3—H3O | 0.77 (3) | C5—H5B | 0.9900 |
N2—Pd1—N1 | 84.95 (14) | C3—C1—C2 | 111.8 (4) |
N2—Pd1—O1 | 171.76 (13) | N1—C1—P1 | 103.1 (3) |
N1—Pd1—O1 | 87.95 (12) | C3—C1—P1 | 111.8 (3) |
N2—Pd1—Cl1 | 92.89 (11) | C2—C1—P1 | 108.9 (3) |
N1—Pd1—Cl1 | 177.67 (10) | C1—C2—H2A | 109.5 |
O1—Pd1—Cl1 | 94.26 (9) | C1—C2—H2B | 109.5 |
O2—P1—O1 | 114.59 (18) | H2A—C2—H2B | 109.5 |
O2—P1—O3 | 112.56 (16) | C1—C2—H2C | 109.5 |
O1—P1—O3 | 107.83 (17) | H2A—C2—H2C | 109.5 |
O2—P1—C1 | 111.12 (19) | H2B—C2—H2C | 109.5 |
O1—P1—C1 | 105.66 (18) | C1—C3—H3A | 109.5 |
O3—P1—C1 | 104.36 (19) | C1—C3—H3B | 109.5 |
C4—N1—C1 | 118.5 (3) | H3A—C3—H3B | 109.5 |
C4—N1—Pd1 | 107.3 (2) | C1—C3—H3C | 109.5 |
C1—N1—Pd1 | 110.9 (3) | H3A—C3—H3C | 109.5 |
C4—N1—H1N | 105 (3) | H3B—C3—H3C | 109.5 |
C1—N1—H1N | 112 (3) | N1—C4—C5 | 106.8 (3) |
Pd1—N1—H1N | 101 (3) | N1—C4—H4A | 110.4 |
C5—N2—Pd1 | 108.9 (2) | C5—C4—H4A | 110.4 |
C5—N2—H21N | 114 (3) | N1—C4—H4B | 110.4 |
Pd1—N2—H21N | 111 (3) | C5—C4—H4B | 110.4 |
C5—N2—H22N | 111 (4) | H4A—C4—H4B | 108.6 |
Pd1—N2—H22N | 103 (3) | N2—C5—C4 | 108.7 (3) |
H21N—N2—H22N | 109 (4) | N2—C5—H5A | 109.9 |
P1—O1—Pd1 | 112.20 (17) | C4—C5—H5A | 109.9 |
P1—O3—H3O | 121 (4) | N2—C5—H5B | 109.9 |
H41O—O4—H42O | 97 (5) | C4—C5—H5B | 109.9 |
N1—C1—C3 | 110.7 (3) | H5A—C5—H5B | 108.3 |
N1—C1—C2 | 110.2 (3) | ||
N2—Pd1—N1—C4 | −18.0 (3) | C4—N1—C1—P1 | −168.6 (3) |
O1—Pd1—N1—C4 | 157.8 (3) | Pd1—N1—C1—P1 | −43.9 (3) |
N2—Pd1—N1—C1 | −148.9 (3) | O2—P1—C1—N1 | 170.2 (2) |
O1—Pd1—N1—C1 | 26.9 (3) | O1—P1—C1—N1 | 45.4 (3) |
N1—Pd1—N2—C5 | −10.8 (3) | O3—P1—C1—N1 | −68.2 (3) |
Cl1—Pd1—N2—C5 | 168.3 (3) | O2—P1—C1—C3 | −70.8 (3) |
O2—P1—O1—Pd1 | −149.06 (16) | O1—P1—C1—C3 | 164.3 (3) |
O3—P1—O1—Pd1 | 84.75 (19) | O3—P1—C1—C3 | 50.7 (3) |
C1—P1—O1—Pd1 | −26.4 (2) | O2—P1—C1—C2 | 53.2 (3) |
N1—Pd1—O1—P1 | 3.43 (18) | O1—P1—C1—C2 | −71.6 (3) |
Cl1—Pd1—O1—P1 | −175.86 (15) | O3—P1—C1—C2 | 174.8 (3) |
C4—N1—C1—C3 | 71.7 (5) | C1—N1—C4—C5 | 168.9 (3) |
Pd1—N1—C1—C3 | −163.6 (3) | Pd1—N1—C4—C5 | 42.4 (4) |
C4—N1—C1—C2 | −52.6 (5) | Pd1—N2—C5—C4 | 37.5 (4) |
Pd1—N1—C1—C2 | 72.2 (4) | N1—C4—C5—N2 | −53.3 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···Cl1i | 0.86 (5) | 2.48 (5) | 3.326 (4) | 169 (4) |
N2—H21N···O3i | 0.96 (5) | 1.98 (5) | 2.937 (5) | 177 (4) |
N2—H22N···Cl1ii | 0.76 (5) | 2.68 (5) | 3.365 (4) | 151 (4) |
O3—H3O···O2iii | 0.77 (3) | 1.75 (3) | 2.509 (4) | 168 (6) |
O4—H41O···O2iv | 0.79 (5) | 2.14 (6) | 2.911 (5) | 166 (5) |
O4—H42O···O1 | 0.79 (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. |
Experimental details
Crystal data | |
Chemical formula | [Pd(C5H14N2O3P)Cl]·H2O |
Mr | 341.02 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 100 |
a, b, c (Å) | 7.2158 (2), 7.8981 (2), 10.3179 (3) |
α, β, γ (°) | 97.968 (2), 98.403 (2), 95.894 (2) |
V (Å3) | 571.55 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.99 |
Crystal size (mm) | 0.38 × 0.12 × 0.10 |
Data collection | |
Diffractometer | Bruker APEXII CCD |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.519, 0.832 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8452, 2306, 1954 |
Rint | 0.046 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.032, 0.076, 1.05 |
No. of reflections | 2306 |
No. of parameters | 147 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.75, −0.55 |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), publCIF (Westrip, 2010).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···Cl1i | 0.86 (5) | 2.48 (5) | 3.326 (4) | 169 (4) |
N2—H21N···O3i | 0.96 (5) | 1.98 (5) | 2.937 (5) | 177 (4) |
N2—H22N···Cl1ii | 0.76 (5) | 2.68 (5) | 3.365 (4) | 151 (4) |
O3—H3O···O2iii | 0.77 (3) | 1.75 (3) | 2.509 (4) | 168 (6) |
O4—H41O···O2iv | 0.79 (5) | 2.14 (6) | 2.911 (5) | 166 (5) |
O4—H42O···O1 | 0.79 (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. |
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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).