metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

(1,4,8,11-Tetra­aza­cyclo­tetra­deca­ne)palladium(II) diiodide monohydrate

aChonnam National University, School of Chemical Engineering, Research Institute of Catalysis, Gwangju, Republic of Korea
*Correspondence e-mail: hakwang@chonnam.ac.kr

Edited by M. Weil, Vienna University of Technology, Austria (Received 18 July 2019; accepted 19 July 2019; online 23 July 2019)

In the title compound, [Pd(C10H24N4)]I2·H2O, the PdII ion is four-coordinated in a slightly distorted square-planar coordination environment defined by four N atoms from a 1,4,8,11-tetra­aza­cyclo­tetra­decane ligand. The cationic complex, two I anions and the solvent water mol­ecule are linked through inter­molecular hydrogen bonds into a three-dimensional network structure.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

With reference to the title compound, [Pd(cyclam)]I2·H2O (cyclam = 1,4,8,11-tetra­aza­cyclo­tetra­deca­ne), the crystal structures of related cyclam-PdII complexes, viz. [Pd(cyclam)]Cl2·2CH3OH (Hunter et al., 2004[Hunter, T. M., Paisey, S. J., Park, H., Cleghorn, L., Parkin, A., Parsons, S. & Sadler, P. J. (2004). J. Inorg. Biochem. 98, 713-719.]) and [Pd(cyclam)](CH3CO2)2·2H2O (Liang et al., 2002[Liang, X., Parkinson, J. A., Weishäupl, M., Gould, R. O., Paisey, S. J., Park, H., Hunter, T. M., Blindauer, C. A., Parsons, S. & Sadler, P. J. (2002). J. Am. Chem. Soc. 124, 9105-9112.]), have been determined previously.

The title compound consists of a cationic [Pd(cyclam)]2+ complex, two I counter-anions and a solvent water mol­ecule. In the cationic complex, the central PdII ion is four-coordinated in a slightly distorted square-planar coordination environment defined by four N atoms from the tetra­dentate cyclam ligand (Fig. 1[link]). The Pd—N bond lengths are almost equal with Pd—N = 2.0307 (19)-2.044 (2) Å. The six-membered chelate rings are in the stable chair conformations, and the torsion angles N1—C1—C2—N2 = 55.7 (3)° and N3—C6—C7—N4 = −57.1 (3)° reflect the gauche conformation for the group within the five-membered chelate rings. In the crystal, the complex mol­ecules are stacked in columns parallel to the b axis. In the crystal structure, the complex cations, anions and solvent water mol­ecule are linked through inter­molecular O—H⋯I, N—H⋯O and N—H⋯I hydrogen bonds into a three-dimensional network structure (Table 1[link]; Fig. 2[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H2O⋯I1 0.79 (4) 2.63 (5) 3.405 (3) 169 (4)
O1—H1O⋯I2 0.65 (4) 2.91 (4) 3.549 (3) 168 (5)
N2—H2⋯O1i 0.78 (3) 2.22 (3) 2.993 (3) 173 (3)
N3—H3⋯I2ii 0.82 (3) 3.02 (3) 3.656 (2) 137 (2)
N4—H4⋯O1iii 0.78 (3) 2.29 (3) 3.035 (3) 161 (3)
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iii) -x+1, -y+1, -z+1.
[Figure 1]
Figure 1
The mol­ecular entities in the crystal structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 40% probability level for non-H atoms.
[Figure 2]
Figure 2
The packing in the crystal structure of the title compound, viewed approximately along the b axis. Hydrogen-bonding inter­actions are drawn as dashed lines.

Synthesis and crystallization

To a solution of [PdI2(pyridine)2] (0.3322 g, 0.641 mmol) in acetone (30 ml) was added 1,4,8,11-tetra­aza­cyclo­tetra­decane (0.1296 g, 0.647 mmol) in MeOH (20 ml) and refluxed for 1 h. The formed dark-brown precipitate was removed by filtration. After evaporation of the solvent of the filtrate, the residue was washed with acetone, and dried at 323 K, to give a pale-yellow powder (0.3166 g). Yellow crystals suitable for X-ray analysis were obtained by slow evaporation from an MeOH/2-butanone solution at room temperature.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The highest peak (0.49 e Å−3) and the deepest hole (−0.72 e Å−3) in the difference Fourier map are located 0.79 and 0.77 Å, respectively, from the atoms I2 and I1.

Table 2
Experimental details

Crystal data
Chemical formula [Pd(C10H24N4)]I2·H2O
Mr 578.55
Crystal system, space group Monoclinic, P21/n
Temperature (K) 223
a, b, c (Å) 9.3993 (4), 13.7266 (5), 13.8797 (6)
β (°) 93.9017 (14)
V3) 1786.61 (13)
Z 4
Radiation type Mo Kα
μ (mm−1) 4.49
Crystal size (mm) 0.23 × 0.18 × 0.11
 
Data collection
Diffractometer PHOTON 100 CMOS detector
Absorption correction Multi-scan (SADABS; Bruker, 2016[Bruker (2016). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.595, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections 48072, 3544, 3307
Rint 0.043
(sin θ/λ)max−1) 0.619
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.017, 0.041, 1.12
No. of reflections 3544
No. of parameters 188
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.49, −0.72
Computer programs: APEX2 and SAINT (Bruker, 2016[Bruker (2016). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014/7 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]) and ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014/7 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXL2014/7 (Sheldrick, 2015b).

(1,4,8,11-Tetraazacyclotetradecane)palladium(II) diiodide monohydrate top
Crystal data top
[Pd(C10H24N4)]I2·H2OF(000) = 1096
Mr = 578.55Dx = 2.151 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 9.3993 (4) ÅCell parameters from 9932 reflections
b = 13.7266 (5) Åθ = 2.5–28.3°
c = 13.8797 (6) ŵ = 4.49 mm1
β = 93.9017 (14)°T = 223 K
V = 1786.61 (13) Å3Block, yellow
Z = 40.23 × 0.18 × 0.11 mm
Data collection top
PHOTON 100 CMOS detector
diffractometer
3307 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.043
φ and ω scansθmax = 26.1°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
h = 1111
Tmin = 0.595, Tmax = 0.745k = 1616
48072 measured reflectionsl = 1717
3544 independent reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.017H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.041 w = 1/[σ2(Fo2) + (0.0147P)2 + 1.4653P]
where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max = 0.001
3544 reflectionsΔρmax = 0.49 e Å3
188 parametersΔρmin = 0.72 e Å3
0 restraintsExtinction correction: SHELXL2014/7 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.00940 (16)
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Hydrogen atoms on C atoms were positioned geometrically and allowed to ride on their respective parent atoms: C—H = 0.98 Å and Uiso(H) = 1.2Ueq(C). Hydrogen atoms bonded to N and O atoms were located from Fourier difference maps and refined isotropically.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Pd10.25793 (2)0.38024 (2)0.72122 (2)0.02194 (6)
I10.74413 (2)0.36724 (2)0.35324 (2)0.04099 (7)
I20.19189 (2)0.37008 (2)0.21133 (2)0.03941 (6)
N10.0680 (2)0.42530 (15)0.76680 (16)0.0329 (4)
H10.068 (3)0.482 (2)0.7613 (18)0.029 (7)*
N20.1427 (3)0.34020 (17)0.59789 (16)0.0402 (5)
H20.123 (3)0.286 (2)0.6050 (18)0.029 (7)*
N30.4495 (2)0.33712 (17)0.6762 (2)0.0458 (6)
H30.456 (3)0.279 (2)0.687 (2)0.042 (8)*
N40.3719 (3)0.42382 (16)0.84436 (18)0.0449 (6)
H40.381 (3)0.480 (2)0.837 (2)0.048 (9)*
C10.0451 (3)0.3835 (2)0.6988 (3)0.0572 (9)
H1A0.06220.31530.71540.069*
H1B0.13420.41970.70330.069*
C20.0026 (3)0.3900 (2)0.5994 (3)0.0578 (9)
H2A0.01170.45840.58060.069*
H2B0.06720.35860.55380.069*
C30.2129 (5)0.3580 (2)0.5075 (2)0.0687 (11)
H3A0.22550.42830.49900.082*
H3B0.15160.33390.45270.082*
C40.3572 (5)0.3081 (3)0.5081 (3)0.0863 (15)
H4A0.34600.24000.52740.104*
H4B0.38860.30830.44220.104*
C50.4711 (5)0.3539 (3)0.5739 (3)0.0800 (14)
H5A0.56400.32740.55920.096*
H5B0.47270.42420.56170.096*
C60.5594 (3)0.3852 (2)0.7434 (4)0.0789 (14)
H6A0.65180.35290.73930.095*
H6B0.56990.45370.72540.095*
C70.5134 (4)0.3782 (2)0.8436 (3)0.0702 (12)
H7A0.50850.30980.86340.084*
H7B0.58150.41210.88850.084*
C80.3033 (4)0.4087 (2)0.9361 (2)0.0646 (10)
H8A0.36380.43700.98920.078*
H8B0.29550.33860.94810.078*
C90.1575 (5)0.4538 (2)0.9350 (2)0.0707 (11)
H9A0.12560.45211.00080.085*
H9B0.16480.52240.91630.085*
C100.0464 (4)0.4057 (2)0.8686 (2)0.0572 (9)
H10A0.04920.33520.87970.069*
H10B0.04810.42920.88340.069*
O10.5464 (3)0.36267 (15)0.13842 (18)0.0472 (5)
H1O0.478 (5)0.365 (3)0.144 (3)0.061 (15)*
H2O0.587 (5)0.356 (3)0.189 (3)0.077 (14)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02275 (9)0.02002 (9)0.02342 (9)0.00007 (6)0.00437 (6)0.00080 (6)
I10.04594 (11)0.03372 (10)0.04233 (11)0.00799 (7)0.00412 (7)0.00678 (7)
I20.04463 (11)0.03331 (10)0.04076 (11)0.00051 (6)0.00623 (7)0.00246 (6)
N10.0341 (11)0.0208 (10)0.0455 (12)0.0008 (8)0.0143 (9)0.0006 (8)
N20.0591 (15)0.0290 (11)0.0312 (11)0.0031 (10)0.0070 (10)0.0049 (9)
N30.0349 (12)0.0260 (11)0.0794 (18)0.0015 (9)0.0249 (11)0.0021 (11)
N40.0533 (14)0.0213 (10)0.0564 (15)0.0045 (9)0.0226 (11)0.0058 (10)
C10.0233 (13)0.0366 (14)0.112 (3)0.0024 (10)0.0032 (15)0.0162 (16)
C20.0521 (18)0.0468 (16)0.069 (2)0.0100 (13)0.0336 (16)0.0153 (15)
C30.133 (3)0.0510 (17)0.0224 (13)0.0114 (19)0.0033 (17)0.0005 (12)
C40.159 (4)0.059 (2)0.048 (2)0.025 (3)0.065 (3)0.0053 (17)
C50.087 (3)0.058 (2)0.103 (3)0.0159 (19)0.074 (3)0.016 (2)
C60.0208 (13)0.0350 (15)0.181 (5)0.0028 (11)0.007 (2)0.017 (2)
C70.0479 (18)0.0402 (17)0.116 (3)0.0065 (13)0.041 (2)0.0198 (18)
C80.123 (3)0.0407 (15)0.0269 (14)0.0178 (18)0.0203 (17)0.0052 (12)
C90.138 (3)0.0493 (18)0.0264 (14)0.036 (2)0.0204 (18)0.0019 (13)
C100.077 (2)0.0404 (15)0.0597 (19)0.0200 (15)0.0493 (17)0.0140 (14)
O10.0459 (14)0.0437 (12)0.0510 (14)0.0005 (10)0.0045 (11)0.0059 (9)
Geometric parameters (Å, º) top
Pd1—N12.0307 (19)C3—H3A0.9800
Pd1—N32.034 (2)C3—H3B0.9800
Pd1—N22.038 (2)C4—C51.498 (6)
Pd1—N42.044 (2)C4—H4A0.9800
N1—C101.466 (3)C4—H4B0.9800
N1—C11.487 (4)C5—H5A0.9800
N1—H10.78 (3)C5—H5B0.9800
N2—C31.477 (4)C6—C71.487 (6)
N2—C21.485 (4)C6—H6A0.9800
N2—H20.78 (3)C6—H6B0.9800
N3—C51.467 (5)C7—H7A0.9800
N3—C61.497 (5)C7—H7B0.9800
N3—H30.82 (3)C8—C91.503 (5)
N4—C71.471 (4)C8—H8A0.9800
N4—C81.480 (4)C8—H8B0.9800
N4—H40.78 (3)C9—C101.499 (5)
C1—C21.482 (5)C9—H9A0.9800
C1—H1A0.9800C9—H9B0.9800
C1—H1B0.9800C10—H10A0.9800
C2—H2A0.9800C10—H10B0.9800
C2—H2B0.9800O1—H1O0.65 (4)
C3—C41.518 (6)O1—H2O0.79 (4)
N1—Pd1—N3179.11 (9)C4—C3—H3B109.3
N1—Pd1—N285.15 (9)H3A—C3—H3B107.9
N3—Pd1—N295.45 (10)C5—C4—C3114.5 (3)
N1—Pd1—N494.14 (10)C5—C4—H4A108.6
N3—Pd1—N485.24 (11)C3—C4—H4A108.6
N2—Pd1—N4178.61 (9)C5—C4—H4B108.6
C10—N1—C1113.6 (3)C3—C4—H4B108.6
C10—N1—Pd1115.25 (18)H4A—C4—H4B107.6
C1—N1—Pd1106.87 (16)N3—C5—C4112.6 (3)
C10—N1—H1106.2 (18)N3—C5—H5A109.1
C1—N1—H1109.3 (19)C4—C5—H5A109.1
Pd1—N1—H1105.2 (19)N3—C5—H5B109.1
C3—N2—C2112.6 (3)C4—C5—H5B109.1
C3—N2—Pd1115.2 (2)H5A—C5—H5B107.8
C2—N2—Pd1106.56 (17)C7—C6—N3108.8 (3)
C3—N2—H2113.1 (19)C7—C6—H6A109.9
C2—N2—H2103 (2)N3—C6—H6A109.9
Pd1—N2—H2105.7 (19)C7—C6—H6B109.9
C5—N3—C6113.5 (3)N3—C6—H6B109.9
C5—N3—Pd1115.8 (2)H6A—C6—H6B108.3
C6—N3—Pd1105.6 (2)N4—C7—C6107.5 (3)
C5—N3—H3109 (2)N4—C7—H7A110.2
C6—N3—H3106 (2)C6—C7—H7A110.2
Pd1—N3—H3106 (2)N4—C7—H7B110.2
C7—N4—C8113.2 (3)C6—C7—H7B110.2
C7—N4—Pd1107.0 (2)H7A—C7—H7B108.5
C8—N4—Pd1116.4 (2)N4—C8—C9112.6 (2)
C7—N4—H4108 (2)N4—C8—H8A109.1
C8—N4—H4108 (2)C9—C8—H8A109.1
Pd1—N4—H4104 (2)N4—C8—H8B109.1
C2—C1—N1108.6 (2)C9—C8—H8B109.1
C2—C1—H1A110.0H8A—C8—H8B107.8
N1—C1—H1A110.0C10—C9—C8114.9 (2)
C2—C1—H1B110.0C10—C9—H9A108.5
N1—C1—H1B110.0C8—C9—H9A108.5
H1A—C1—H1B108.4C10—C9—H9B108.5
C1—C2—N2108.1 (2)C8—C9—H9B108.5
C1—C2—H2A110.1H9A—C9—H9B107.5
N2—C2—H2A110.1N1—C10—C9112.1 (3)
C1—C2—H2B110.1N1—C10—H10A109.2
N2—C2—H2B110.1C9—C10—H10A109.2
H2A—C2—H2B108.4N1—C10—H10B109.2
N2—C3—C4111.8 (3)C9—C10—H10B109.2
N2—C3—H3A109.3H10A—C10—H10B107.9
C4—C3—H3A109.3H1O—O1—H2O109 (5)
N2—C3—H3B109.3
C10—N1—C1—C2168.5 (2)C5—N3—C6—C7170.2 (3)
Pd1—N1—C1—C240.3 (2)Pd1—N3—C6—C742.3 (3)
N1—C1—C2—N255.7 (3)C8—N4—C7—C6171.1 (2)
C3—N2—C2—C1169.2 (3)Pd1—N4—C7—C641.7 (3)
Pd1—N2—C2—C142.0 (3)N3—C6—C7—N457.1 (3)
C2—N2—C3—C4178.9 (3)C7—N4—C8—C9178.7 (3)
Pd1—N2—C3—C456.5 (3)Pd1—N4—C8—C954.2 (3)
N2—C3—C4—C572.1 (4)N4—C8—C9—C1068.8 (4)
C6—N3—C5—C4178.0 (3)C1—N1—C10—C9176.7 (2)
Pd1—N3—C5—C455.7 (3)Pd1—N1—C10—C959.6 (3)
C3—C4—C5—N371.6 (4)C8—C9—C10—N172.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H2O···I10.79 (4)2.63 (5)3.405 (3)169 (4)
O1—H1O···I20.65 (4)2.91 (4)3.549 (3)168 (5)
N2—H2···O1i0.78 (3)2.22 (3)2.993 (3)173 (3)
N3—H3···I2ii0.82 (3)3.02 (3)3.656 (2)137 (2)
N4—H4···O1iii0.78 (3)2.29 (3)3.035 (3)161 (3)
Symmetry codes: (i) x1/2, y+1/2, z+1/2; (ii) x+1/2, y+1/2, z+1/2; (iii) x+1, y+1, z+1.
 

Acknowledgements

The author thanks the KBSI, Seoul Center, for the X-ray data collection.

Funding information

This study was supported financially by Chonnam National University (grant No. 2018–3317).

References

First citationBruker (2016). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationHunter, T. M., Paisey, S. J., Park, H., Cleghorn, L., Parkin, A., Parsons, S. & Sadler, P. J. (2004). J. Inorg. Biochem. 98, 713–719.  CSD CrossRef PubMed CAS Google Scholar
First citationLiang, X., Parkinson, J. A., Weishäupl, M., Gould, R. O., Paisey, S. J., Park, H., Hunter, T. M., Blindauer, C. A., Parsons, S. & Sadler, P. J. (2002). J. Am. Chem. Soc. 124, 9105–9112.  CSD CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar

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