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Logo of actae2this articlesearchopen accesssubmitActa Crystallographica Section E: Crystallographic CommunicationsActa Crystallographica Section E: Crystallographic Communications
 
Acta Crystallogr E Crystallogr Commun. 2017 April 1; 73(Pt 4): 528–530.
Published online 2017 March 17. doi:  10.1107/S2056989017003929
PMCID: PMC5382614

Crystal structure of trans-di­chloridobis­[N-(5,5-di­methyl-4,5-di­hydro-3H-pyrrol-2-yl-κN)acetamide]palladium(II) dihydrate

Abstract

The title complex, [PdCl2(C8H14N2O)2]·2H2O, was obtained by N–O bond cleavage of the oxa­diazo­line rings of the trans-[di­chlorido-bis­(2,5,5-trimethyl-5,6,7,7a-tetra­hydro­pyrrolo­[1,2-b][1,2,4]oxa­diazole-N 1)]palladium(II) complex. The palladium(II) atom exhibits an almost square-planar coordination provided by two trans-arranged chloride anions and a nitro­gen atom from each of the two neutral organic ligands. In the crystal, N—H(...)O, O—H(...)O and O—H(...)Cl hydrogen bonds link complex mol­ecules into double layers parallel to the bc plane.

Keywords: crystal structure, palladium, nitrile, nitrone, cyclo­addition, N—O bond cleavage

Chemical context  

The [2 + 3]-cyclo­addition of nitro­nes with nitriles is one of the most important routes for the synthesis of 1,2,4-oxa­diazo­lines (Bokach et al., 2011  ). However, there are some limitations for this method, as only electrophilically activated nitriles react with nitro­nes under harsh conditions and/or long reaction times (Eberson et al., 1998  ; Lasri et al., 2008  ). The coordination of nitriles to a suitable metal atom becomes a convenient methodology and facile metal-mediated route for the synthesis of a large number of compounds, inaccessible directly by pure organic chemistry (Bokach et al., 2011  ). The N—O bond cleavage of oxa­diazo­line rings can be promoted by thermal heating to furnish the derived keto­imine complexes (Lasri et al., 2011  ). Moreover, the oxa­diazo­line ligands are opened by N—O bond cleavage to form pyrrolylbenzamide derivatives in which the N atoms of the pyrrolyl moieties coordinate to the palladium atom in the trans positions (Lasri et al., 2009  ).

In this work, we report the synthesis and crystal structure of the title complex trans-[di­chlorido-bis­(N-(4,5-di­hydro-5,5-dimethyl-3H-pyrrol-2-yl)acetamide)]palladium(II) dihydrate, 2.

The fused bicyclic 1,2,4-oxa­diazo­line palladium(II) complex trans-[PdCl2{N=C(Me)ONC(H)CH2CH2CMe2}2] (1) was previously synthesized by one of us (Lasri et al., 2009  ), in good yield (ca 75%), by treatment of trans-[PdCl2(NCMe)2] with pyrroline N-oxide O+N=CHCH2CH2CMe2 (Scheme, reaction a). Inter­estingly, refluxing complex 1 in CHCl3 for one week affords a mixture of compounds from which the title compound 2 was isolated by mechanical separation of the crystals obtained from slow evaporation of an acetone/toluene (30:1 v/v) solution. Compound 2 was characterized by IR spectroscopy and also by X-ray diffraction, which shows that the oxa­diazo­line ligands of 1 have opened by N—O bond cleavage to form a pyrrolylacetamide derivative, i.e. N-(4,5-di­hydro-5,5-dimethyl-3H-pyrrol-2-yl)acetamide, in which the N-atoms of the pyrrolyl moieties coordinate to palladium in the trans position (Scheme, reaction b).

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Object name is e-73-00528-scheme1.jpg

Structural commentary  

The slightly distorted square-planar coordination sphere around the PdII atom comprises two chloride anions and two nitro­gen atoms from two neutral organic ligands (Fig. 1  ). The Cl—Pd—Cl, N—Pd—N, and Cl—Pd—N angles all deviate by less that 5° from the ideal 90° or 180° angles. The Pd—N [mean value 2.0783 (16) Å] and Pd—Cl [mean value 2.336 (12) Å] bond lengths fall in the range of typical distances found in similar types of PdII complexes. The five-membered heterocyclic rings each have a twist conformation, with puckering parameters Q = 0.238 (4) Å, [var phi] = −108.8 (8)° and Q = 0.245 (4) Å, [var phi] = 69.9 (8)° for N1/C1–C4 and N3/C9–C12, respectively. The crystal structures of the 2-ethyl and 2-(4-bromo­phen­yl) analogues of the title compounds have been reported elsewhere (Lasri et al., 2009  ).

Figure 1
The mol­ecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. Dashed lines indicate hydrogen bonds

Supra­molecular features  

In the asymmetric unit, both the N2 and N4 atoms act as hydrogen-bond donors for the O3 atom of a water mol­ecule (Table 1  ). The water mol­ecule including the O3 atom also acts as a hydrogen-bond donor to Cl2 and to a second water mol­ecule (O4) which, in turn, forms hydrogen bonds with the Cl1 and O3 atoms of neighboring metal complexes. A view of the crystal packing (Fig. 2  ) shows that the mol­ecules are organized in such a way that hydrogen bonds form double layers of metal complexes parallel to the bc plane, mainly connected by weak van der Waals inter­actions.

Figure 2
Packing diagram of the title compound viewed down the c axis.
Table 1
Hydrogen-bond geometry (Å, °)

Synthesis and crystallization  

A solution of bis­(1,2,4-oxa­diazo­line) palladium(II) (complex 1; 100 mg, 0.206 mmol; Lasri et al., 2009  ) in CHCl3 (10 mL) was refluxed for one week. The solvent was then removed in vacuo and the resulting solid was washed with three 10 mL portions of diethyl ether and dried under air to give a yellow solid. The 1H and 13C NMR spectra in CDCl3 of the obtained solid show the presence of a mixture of compounds. However, the pyrrolylacetamide product 2 was isolated by mechanical separation of the crystals obtained from slow evaporation of an acetone/toluene (30:1 v/v) solution. The IR spectrum of 2 shows strong ν(NC=O) and ν(N=C) vibrations at 1729 and 1644 cm−1, respectively, and ν(NH) at 3300 cm−1.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2  . The amine and water hydrogen atoms were located in a difference-Fourier map and refined isotropically. All other hydrogen atoms were positioned geometrically and constrained to ride on their parent atoms, with C—H = 0.96–0.97 Å, and with U iso = 1.2 U eq(C) or 1.5U eq(C) for methyl H atoms. A rotating model was applied to the methyl groups. The maximum electron density is located 0.97 Å from atom Pd1 and the minimum electron density is located 0.95 Å from atom Pd1. Two outliers (An external file that holds a picture, illustration, etc.
Object name is e-73-00528-efi1.jpg02 and 002) were omitted in the last cycles of refinement.

Table 2
Experimental details

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989017003929/rz5207sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017003929/rz5207Isup2.hkl

CCDC reference: 1537327

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors acknowledge with thanks the Deanship of Scientific Research (DSR) at King Abdulaziz University, Jeddah, for technical and financial support.

supplementary crystallographic information

Crystal data

[PdCl2(C8H14N2O)2]·2H2OF(000) = 1072
Mr = 521.75Dx = 1.498 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 15.945 (12) ÅCell parameters from 9661 reflections
b = 8.765 (6) Åθ = 2.5–25.4°
c = 16.894 (13) ŵ = 1.06 mm1
β = 101.481 (19)°T = 293 K
V = 2314 (3) Å3Block, yellow
Z = 40.24 × 0.20 × 0.05 mm

Data collection

Bruker D8 Quest diffractometer3546 reflections with I > 2σ(I)
Radiation source: sealed X-Ray tubeRint = 0.050
[var phi] and ω scansθmax = 26.9°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2016); additional spherical absorption correction applied with µ*r = 0.2000h = −20→20
Tmin = 0.594, Tmax = 0.745k = −10→10
30712 measured reflectionsl = −18→19
4239 independent reflections

Refinement

Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.032H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.071w = 1/[σ2(Fo2) + (0.0253P)2 + 2.688P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
4239 reflectionsΔρmax = 0.56 e Å3
274 parametersΔρmin = −0.50 e Å3

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
Pd10.21183 (2)0.43221 (3)0.41558 (2)0.02882 (8)
Cl10.15431 (6)0.28686 (10)0.50868 (5)0.0475 (2)
Cl20.27918 (6)0.56600 (11)0.32714 (6)0.0523 (2)
O10.3558 (2)−0.0129 (5)0.2615 (2)0.1043 (13)
O20.46851 (17)0.6655 (3)0.6391 (2)0.0817 (10)
O30.6085 (3)0.6187 (6)0.7839 (2)0.0918 (13)
O40.6653 (2)0.6870 (4)0.9547 (2)0.0641 (8)
N10.18404 (15)0.2675 (3)0.32579 (15)0.0330 (6)
N20.30573 (19)0.1373 (3)0.3545 (2)0.0458 (7)
N30.23602 (16)0.6039 (3)0.50208 (15)0.0330 (6)
N40.36553 (17)0.5252 (4)0.56263 (18)0.0438 (7)
C10.1043 (2)0.2662 (4)0.2637 (2)0.0432 (8)
C20.1062 (3)0.1119 (5)0.2189 (2)0.0575 (10)
H2A0.07400.03500.24150.069*
H2B0.08160.12330.16190.069*
C30.1936 (3)0.0699 (4)0.2301 (2)0.0528 (9)
H3A0.21860.10030.18470.063*
H3B0.2016−0.03880.23930.063*
C40.2301 (2)0.1634 (4)0.30675 (19)0.0368 (7)
C50.3638 (3)0.0430 (5)0.3314 (3)0.0642 (11)
C60.4363 (3)0.0199 (6)0.4007 (3)0.0914 (17)
H6A0.43980.10530.43680.137*
H6B0.48870.01140.38120.137*
H6C0.4271−0.07180.42880.137*
C70.0348 (2)0.2747 (5)0.3112 (3)0.0652 (12)
H7A−0.01980.26420.27540.098*
H7B0.03740.37140.33830.098*
H7C0.04200.19400.35040.098*
C80.1026 (3)0.3988 (5)0.2027 (2)0.0623 (11)
H8A0.05000.39570.16360.093*
H8B0.14990.38840.17570.093*
H8C0.10700.49440.23090.093*
C90.1786 (2)0.7343 (4)0.5045 (2)0.0430 (8)
C100.2181 (3)0.8178 (5)0.5865 (3)0.0696 (12)
H10A0.21180.92750.58080.084*
H10B0.19040.78410.62970.084*
C110.3071 (2)0.7748 (4)0.6028 (2)0.0557 (10)
H11A0.32840.75640.65990.067*
H11B0.34230.85150.58390.067*
C120.3034 (2)0.6287 (4)0.55392 (19)0.0363 (7)
C130.4437 (2)0.5445 (5)0.6085 (2)0.0547 (10)
C140.4948 (2)0.4047 (5)0.6150 (3)0.0798 (15)
H14A0.47390.34030.56930.120*
H14B0.49050.35190.66380.120*
H14C0.55350.43030.61600.120*
C150.0952 (3)0.6747 (5)0.5097 (3)0.0810 (14)
H15A0.05710.75780.51390.121*
H15B0.10020.61070.55650.121*
H15C0.07290.61620.46210.121*
C160.1746 (3)0.8313 (5)0.4258 (3)0.0782 (14)
H16A0.13520.91430.42530.117*
H16B0.15560.76800.37930.117*
H16C0.23040.87090.42450.117*
H10.727 (6)0.706 (10)0.968 (5)0.23 (4)*
H20.647 (2)0.669 (4)0.915 (2)0.036 (12)*
H30.641 (4)0.588 (8)0.765 (4)0.12 (3)*
H40.570 (5)0.644 (8)0.747 (4)0.15 (3)*
H50.353 (2)0.434 (4)0.544 (2)0.036 (9)*
H60.316 (2)0.186 (4)0.401 (2)0.044 (10)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Pd10.02776 (12)0.02964 (13)0.02942 (14)0.00102 (10)0.00656 (9)−0.00173 (11)
Cl10.0576 (5)0.0483 (5)0.0396 (5)−0.0088 (4)0.0168 (4)0.0040 (4)
Cl20.0484 (5)0.0583 (5)0.0565 (5)−0.0123 (4)0.0260 (4)−0.0003 (5)
O10.101 (3)0.116 (3)0.101 (3)0.047 (2)0.034 (2)−0.027 (2)
O20.0476 (16)0.064 (2)0.125 (3)−0.0168 (15)−0.0023 (17)−0.0192 (19)
O30.076 (3)0.122 (3)0.072 (2)0.015 (2)0.002 (2)−0.035 (2)
O40.063 (2)0.065 (2)0.058 (2)0.0002 (15)−0.0035 (16)−0.0105 (17)
N10.0315 (13)0.0333 (14)0.0344 (14)−0.0017 (11)0.0070 (11)−0.0043 (12)
N20.0457 (17)0.0401 (17)0.0516 (19)0.0085 (13)0.0100 (15)−0.0064 (15)
N30.0363 (14)0.0281 (14)0.0359 (14)0.0023 (11)0.0102 (12)−0.0004 (11)
N40.0343 (15)0.0404 (18)0.0538 (19)−0.0045 (13)0.0018 (13)−0.0087 (14)
C10.0386 (18)0.050 (2)0.0368 (18)−0.0045 (15)−0.0020 (14)−0.0042 (16)
C20.062 (2)0.057 (2)0.050 (2)−0.0137 (19)0.0011 (18)−0.0125 (19)
C30.074 (3)0.044 (2)0.041 (2)0.0026 (19)0.0120 (18)−0.0076 (17)
C40.0472 (19)0.0310 (17)0.0346 (18)−0.0012 (15)0.0139 (15)0.0006 (14)
C50.061 (3)0.048 (2)0.089 (3)0.016 (2)0.030 (2)0.002 (2)
C60.053 (3)0.079 (3)0.140 (5)0.027 (2)0.014 (3)0.007 (3)
C70.0337 (19)0.087 (3)0.071 (3)−0.003 (2)0.0012 (18)−0.006 (2)
C80.060 (2)0.059 (3)0.058 (2)0.001 (2)−0.0113 (19)0.006 (2)
C90.048 (2)0.0326 (18)0.050 (2)0.0088 (15)0.0162 (16)−0.0012 (15)
C100.081 (3)0.050 (2)0.077 (3)0.013 (2)0.015 (2)−0.021 (2)
C110.064 (3)0.039 (2)0.061 (2)−0.0030 (18)0.0060 (19)−0.0127 (18)
C120.0408 (18)0.0303 (16)0.0384 (18)−0.0032 (14)0.0088 (15)−0.0016 (14)
C130.0393 (19)0.057 (3)0.066 (3)−0.0099 (18)0.0078 (18)−0.003 (2)
C140.036 (2)0.074 (3)0.122 (4)0.003 (2)0.000 (2)−0.010 (3)
C150.053 (3)0.066 (3)0.130 (4)0.020 (2)0.034 (3)−0.001 (3)
C160.099 (3)0.061 (3)0.080 (3)0.039 (3)0.029 (3)0.025 (2)

Geometric parameters (Å, º)

Pd1—N12.077 (3)C5—C61.486 (6)
Pd1—N32.080 (3)C6—H6A0.9600
Pd1—Cl22.3238 (14)C6—H6B0.9600
Pd1—Cl12.3478 (14)C6—H6C0.9600
O1—C51.262 (5)C7—H7A0.9600
O2—C131.211 (5)C7—H7B0.9600
O3—H30.71 (6)C7—H7C0.9600
O3—H40.81 (7)C8—H8A0.9600
O4—H10.98 (9)C8—H8B0.9600
O4—H20.70 (4)C8—H8C0.9600
N1—C41.253 (4)C9—C151.448 (5)
N1—C11.478 (4)C9—C161.569 (5)
N2—C41.330 (4)C9—C101.583 (5)
N2—C51.355 (5)C10—C111.442 (5)
N2—H60.88 (3)C10—H10A0.9700
N3—C121.263 (4)C10—H10B0.9700
N3—C91.470 (4)C11—C121.518 (5)
N4—C121.329 (4)C11—H11A0.9700
N4—C131.341 (5)C11—H11B0.9700
N4—H50.87 (3)C13—C141.463 (6)
C1—C71.494 (5)C14—H14A0.9600
C1—C81.551 (5)C14—H14B0.9600
C1—C21.553 (5)C14—H14C0.9600
C2—C31.417 (5)C15—H15A0.9600
C2—H2A0.9700C15—H15B0.9600
C2—H2B0.9700C15—H15C0.9600
C3—C41.545 (5)C16—H16A0.9600
C3—H3A0.9700C16—H16B0.9600
C3—H3B0.9700C16—H16C0.9600
N1—Pd1—N3177.41 (10)H7A—C7—H7B109.5
N1—Pd1—Cl286.56 (9)C1—C7—H7C109.5
N3—Pd1—Cl292.39 (9)H7A—C7—H7C109.5
N1—Pd1—Cl193.26 (9)H7B—C7—H7C109.5
N3—Pd1—Cl187.97 (9)C1—C8—H8A109.5
Cl2—Pd1—Cl1175.38 (3)C1—C8—H8B109.5
H3—O3—H4105 (7)H8A—C8—H8B109.5
H1—O4—H2117 (6)C1—C8—H8C109.5
C4—N1—C1106.2 (3)H8A—C8—H8C109.5
C4—N1—Pd1130.0 (2)H8B—C8—H8C109.5
C1—N1—Pd1123.5 (2)C15—C9—N3107.8 (3)
C4—N2—C5121.3 (4)C15—C9—C16111.3 (4)
C4—N2—H6117 (2)N3—C9—C16108.5 (3)
C5—N2—H6122 (2)C15—C9—C10108.9 (3)
C12—N3—C9107.2 (3)N3—C9—C10104.0 (3)
C12—N3—Pd1128.7 (2)C16—C9—C10115.7 (3)
C9—N3—Pd1123.6 (2)C11—C10—C9104.5 (3)
C12—N4—C13124.3 (3)C11—C10—H10A110.8
C12—N4—H5119 (2)C9—C10—H10A110.8
C13—N4—H5116 (2)C11—C10—H10B110.8
N1—C1—C7104.1 (3)C9—C10—H10B110.8
N1—C1—C8111.4 (3)H10A—C10—H10B108.9
C7—C1—C8113.8 (3)C10—C11—C12100.8 (3)
N1—C1—C2104.7 (3)C10—C11—H11A111.6
C7—C1—C2113.1 (3)C12—C11—H11A111.6
C8—C1—C2109.2 (3)C10—C11—H11B111.6
C3—C2—C1106.0 (3)C12—C11—H11B111.6
C3—C2—H2A110.5H11A—C11—H11B109.4
C1—C2—H2A110.5N3—C12—N4118.2 (3)
C3—C2—H2B110.5N3—C12—C11117.2 (3)
C1—C2—H2B110.5N4—C12—C11124.6 (3)
H2A—C2—H2B108.7O2—C13—N4123.0 (4)
C2—C3—C499.8 (3)O2—C13—C14124.9 (4)
C2—C3—H3A111.8N4—C13—C14112.1 (3)
C4—C3—H3A111.8C13—C14—H14A109.5
C2—C3—H3B111.8C13—C14—H14B109.5
C4—C3—H3B111.8H14A—C14—H14B109.5
H3A—C3—H3B109.5C13—C14—H14C109.5
N1—C4—N2118.5 (3)H14A—C14—H14C109.5
N1—C4—C3117.3 (3)H14B—C14—H14C109.5
N2—C4—C3124.2 (3)C9—C15—H15A109.5
O1—C5—N2124.0 (4)C9—C15—H15B109.5
O1—C5—C6127.1 (4)H15A—C15—H15B109.5
N2—C5—C6109.0 (4)C9—C15—H15C109.5
C5—C6—H6A109.5H15A—C15—H15C109.5
C5—C6—H6B109.5H15B—C15—H15C109.5
H6A—C6—H6B109.5C9—C16—H16A109.5
C5—C6—H6C109.5C9—C16—H16B109.5
H6A—C6—H6C109.5H16A—C16—H16B109.5
H6B—C6—H6C109.5C9—C16—H16C109.5
C1—C7—H7A109.5H16A—C16—H16C109.5
C1—C7—H7B109.5H16B—C16—H16C109.5
C4—N1—C1—C7133.6 (3)C12—N3—C9—C15−130.9 (3)
Pd1—N1—C1—C7−52.9 (4)Pd1—N3—C9—C1557.0 (4)
C4—N1—C1—C8−103.4 (3)C12—N3—C9—C16108.4 (4)
Pd1—N1—C1—C870.2 (3)Pd1—N3—C9—C16−63.7 (4)
C4—N1—C1—C214.5 (3)C12—N3—C9—C10−15.3 (4)
Pd1—N1—C1—C2−171.9 (2)Pd1—N3—C9—C10172.5 (2)
N1—C1—C2—C3−24.4 (4)C15—C9—C10—C11139.3 (4)
C7—C1—C2—C3−137.2 (3)N3—C9—C10—C1124.6 (4)
C8—C1—C2—C395.0 (4)C16—C9—C10—C11−94.4 (4)
C1—C2—C3—C422.3 (4)C9—C10—C11—C12−22.5 (4)
C1—N1—C4—N2−178.3 (3)C9—N3—C12—N4−179.9 (3)
Pd1—N1—C4—N28.7 (5)Pd1—N3—C12—N4−8.3 (5)
C1—N1—C4—C3−0.2 (4)C9—N3—C12—C110.9 (4)
Pd1—N1—C4—C3−173.2 (2)Pd1—N3—C12—C11172.4 (2)
C5—N2—C4—N1−169.9 (3)C13—N4—C12—N3172.2 (3)
C5—N2—C4—C312.1 (5)C13—N4—C12—C11−8.6 (6)
C2—C3—C4—N1−15.3 (4)C10—C11—C12—N315.3 (4)
C2—C3—C4—N2162.7 (3)C10—C11—C12—N4−163.9 (4)
C4—N2—C5—O18.2 (7)C12—N4—C13—O2−8.9 (6)
C4—N2—C5—C6−172.4 (4)C12—N4—C13—C14172.6 (4)

Hydrogen-bond geometry (Å, º)

D—H···AD—HH···AD···AD—H···A
O4—H1···Cl1i0.98 (10)1.99 (9)2.952 (4)169 (8)
O4—H2···O30.69 (3)2.22 (3)2.909 (5)171 (3)
O3—H3···Cl2ii0.71 (6)2.58 (7)3.269 (5)163 (8)
O3—H4···O20.81 (7)2.19 (7)2.994 (6)169 (7)
N4—H5···O4iii0.87 (3)2.19 (4)3.010 (5)159 (3)
N2—H6···O4iii0.88 (3)2.40 (3)3.194 (5)151 (3)

Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) −x+1, −y+1, −z+1; (iii) −x+1, y−1/2, −z+3/2.

References

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Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography