μ-(2,2′-Bipyrimidine)-bis­[dichlorido­palladium(II)] dimethyl­formamide monosolvate

In the title compound, [Pd₂Cl₄(C₈H₆N₄)]·C₃H₇NO, the two Pd²⁺ cations have a distorted square-planar coordination sphere and are bridged by a bis-bidentate 2,2′-bipyrimidine ligand. Two terminal chloride anions are also bonded to each of the Pd²⁺ cations. The dinuclear complex and the dimethylformamide solvate molecule lie on the inter­section of a twofold rotation axis and a mirror plane, with disorder present in the solvate mol­ecule. There is a slight distortion from the square-planar metal geometry, as indicated by the bite angles of 81.77 (13)° and 91.63 (5)°. The C and O atoms of the solvent mol­ecule are disordered over two sets of sites of equal occupancy.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.005 Å
• H-atom completeness 47%
• Disorder in solvent or counterion
• R factor = 0.028
• wR factor = 0.059
• Data-to-parameter ratio = 16.3

checkCIF/PLATON results

No syntax errors found



Alert level C
CHEMW01_ALERT_1_C  The ratio of given/expected molecular weight as calculated
            from the _chemical_formula_sum lies outside
            the range 0.99 <> 1.01
            Calculated formula weight =   585.8686
            Formula weight given      =   578.8100
CHEMW01_ALERT_1_C  The difference between the given and expected weight for
            compound is greater 1 mass unit. Check that all hydrogen
            atoms have been taken into account.
PLAT041_ALERT_1_C Calc. and Reported SumFormula    Strings  Differ          ?
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors of         N22
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          2

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C11 H13 Cl4 N5 O1 Pd2
            Atom count from the _atom_site data:  C11 H6 Cl4 N5 O1 Pd2
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional?
           From the CIF: _cell_formula_units_Z    2
           From the CIF: _chemical_formula_sum  C11 H13 Cl4 N5 O Pd2
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C         22.00     22.00    0.00
           H         26.00     12.00   14.00
           Cl         8.00      8.00    0.00
           N         10.00     10.00    0.00
           O          2.00      2.00    0.00
           Pd         4.00      4.00    0.00
PLAT005_ALERT_5_G No _iucr_refine_instructions_details in CIF ....          ?
PLAT042_ALERT_1_G Calc. and Reported MoietyFormula Strings  Differ          ?
PLAT302_ALERT_4_G Note: Anion/Solvent Disorder ...................         80 Perc.
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          1
PLAT764_ALERT_4_G Overcomplete CIF Bond List Detected (Rep/Expd) .       1.24 Ratio
PLAT811_ALERT_5_G No ADDSYM Analysis: Too Many Excluded Atoms ....          !
PLAT960_ALERT_3_G Number of Intensities with I .LT. - 2*sig(I) ...          1

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   5 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  10 ALERT level G = General information/check it is not something unexpected

   6 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

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S1. Comment

Although a wide variety of metals are used in catalysis today, the platinum group metals show the most promising catalytic properties (Van Leeuwen (2004). Unfortunately, knowledge surrounding the actual catalysis process on a molecular level is minimal. Various platinum group metals which find application in heterogeneous catalysis are dispersed onto supports with little control. Consequently, this study was undertaken to explore the possibility of using bridging ligands ensure that metals are well dispersed in a controllable fashion. The insight gained by exploring bridged platinum group metals could contribute to ongoing homogeneous catalyst models of the metal complex. (Meij et al. (2005), Otto et al. (2003) Steyn et al. (1997)).

The compound crystallizes in a monoclinic C2/m space group with Z = 2. Both palladium atoms are situated on a twofold rotation axis and three carbon atoms, namely C11, C13 and C22 lie on a mirror plane. O22 of the DMF solvate molecule is situated on a twofold rotation axis and N22 on both a mirror plane and a rotation axis, which essentially gives N22 an occupation of 25%. As a result of the symmetry in the molecule there are only twelve atoms, including the hydrogen atoms, in the asymmetric unit. The geometry of the palladium centers is slightly distorted from the square planar geometry. This is illustrated by the N1—Pd01—N1c and Cl11—Pd01—Cl11c angles which are 81.77 (13)° and 91.63 (5)° respectively. The bond lengths and angles for the title compound are comparable to those in literature (Inagaki et al. (2007), Maekawa et al. (1994)). The palladium-nitrogen bonds of 2.05 Å are marginally longer than the mono-coordinated palladium complex (Hudgens et al. (1997)) which has a bond length of 1.99 Å. The Pd—Pd intra-molecular bond distances of 5.47 Å, is slightly shorter than the 5.62 Å for the platinum counterpart (Kawakami et al. (2006)).

Related literature

The title compound is structurally related to the mono-coordinated species reported by Hudgens et al. (1997). For background literature on homogenous catalytic catalyst models, see: Van Leeuwen (2004); Meij et al. (2005); Otto et al. (2003); Steyn et al. (1997). For related structures, see: Inagaki et al. (2007); Maekawa et al. (1994). The mono-coordinated platinum counterpart was reported by Kawakami et al. (2006). For the synthetic procedure, see: Boyle et al. (2004).

S2. Experimental

The title compound was prepared by the modification of the published procedure by Boyle et al. (2004). PdCl₂ (0.200 g, 1,13 x 10 ^-3 mol) was dissolved in boiling acetonitrile. 2,2-Bipyrimidine (0.092 g, 5.71 x 10 ^-4 mol) was added to the solution. Upon addition a yellow precipitate formed. Yield: 0.244 g (85%). ¹H NMR ((CD₃)₂SO): δ 7.9 (t, J = 5.2 Hz, 2H), 9.3 (dd, J = 5.1 Hz, 4H). IR (ATR): 1589 (v_C—H),1137 (v_C—N), 813 (v_Ar—H).

S3. Refinement

The aromatic, methine, and methyl H atoms were placed in geometrically idealized positions (C—H = 0.93–0.98) and constrained to ride on their parent atoms with U_ιso (H) = 1.2U_eq(C) for the aromatic protons. The highest residual electron density was located 0.55 Å from C13 and was essentially meaningless.

Computing details

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT-Plus (Bruker, 2008); data reduction: SAINT-Plus (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

Fig. 1. Diamond representation of the title compound, showing the numbering scheme and displacement ellipsoids (50% probability).

µ-(2,2'-Bipyrimidine)-bis[dichloridopalladium(II)] dimethylformamide monosolvate

Crystal data

[Pd2Cl4(C8H6N4)]·C3H7NO	F(000) = 550
Mr = 578.81	Dx = 2.231 Mg m^−3
Monoclinic, C2/m	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2y	Cell parameters from 1958 reflections
a = 10.7299 (6) Å	θ = 2.9–27.8°
b = 14.2399 (7) Å	µ = 2.71 mm^−1
c = 5.9381 (3) Å	T = 100 K
β = 108.229 (2)°	Cuboid, red
V = 861.76 (8) Å^3	0.09 × 0.09 × 0.08 mm
Z = 2

Data collection

Bruker APEXII diffractometer	1108 independent reflections
Radiation source: sealed tube	975 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.041
phi and ω scans	θmax = 28.3°, θmin = 3.6°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −12→14
Tmin = 0.785, Tmax = 0.814	k = −18→18
6102 measured reflections	l = −7→7

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.059	H-atom parameters constrained
S = 1.11	w = 1/[σ^2(Fo^2) + (0.0172P)^2 + 2.5414P] where P = (Fo^2 + 2Fc^2)/3
1108 reflections	(Δ/σ)max < 0.001
68 parameters	Δρmax = 0.75 e Å^−3
0 restraints	Δρmin = −0.79 e Å^−3

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
C11	0.5	0.4487 (3)	0.5	0.0149 (8)
C12	0.5694 (3)	0.3120 (2)	0.6987 (6)	0.0270 (8)
H12	0.6167	0.2793	0.8341	0.032*
C13	0.5	0.2637 (3)	0.5	0.0370 (13)
H13	0.5	0.1984	0.5	0.044*
N1	0.5696 (2)	0.40577 (17)	0.6995 (4)	0.0152 (5)
Cl11	0.72957 (8)	0.61422 (6)	1.23998 (14)	0.0303 (2)
Pd01	0.65034 (3)	0.5	0.96630 (6)	0.01736 (12)
N22	0.5	0	0	0.0288 (14)
O22	0.5	0.1536 (5)	0	0.052 (2)	0.5
C21	0.4476 (8)	0.0853 (5)	−0.1298 (13)	0.0356 (18)	0.5
C22	0.4325 (11)	0	−0.2451 (19)	0.053 (4)	0.5

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C11	0.013 (2)	0.015 (2)	0.018 (2)	0	0.0063 (17)	0
C12	0.0231 (18)	0.0158 (15)	0.035 (2)	0.0002 (13)	−0.0007 (15)	0.0069 (13)
C13	0.034 (3)	0.012 (2)	0.051 (3)	0	−0.008 (3)	0
N1	0.0112 (12)	0.0180 (12)	0.0155 (13)	0.0008 (10)	0.0027 (10)	0.0040 (10)
Cl11	0.0220 (4)	0.0488 (5)	0.0189 (4)	−0.0109 (4)	0.0045 (3)	−0.0137 (4)
Pd01	0.01263 (19)	0.0256 (2)	0.01300 (18)	0	0.00278 (13)	0
N22	0.052 (4)	0.016 (3)	0.026 (3)	0	0.025 (3)	0
O22	0.095 (7)	0.019 (4)	0.064 (6)	0	0.058 (6)	0
C21	0.037 (5)	0.038 (4)	0.041 (4)	−0.001 (3)	0.025 (4)	0.002 (4)
C22	0.015 (5)	0.123 (12)	0.018 (5)	0	0.003 (4)	0

Geometric parameters (Å, º)

C11—N1^i	1.335 (3)	N22—C22	1.408 (11)
C11—N1	1.335 (3)	N22—C22^iv	1.408 (11)
C11—C11^ii	1.462 (8)	N22—C21^v	1.454 (8)
C12—N1	1.336 (4)	N22—C21^vi	1.454 (8)
C12—C13	1.368 (4)	N22—C21	1.454 (8)
C12—H12	0.93	N22—C21^iv	1.454 (8)
C13—C12^i	1.368 (4)	O22—C21	1.258 (9)
C13—H13	0.93	O22—C21^v	1.258 (9)
N1—Pd01	2.050 (2)	C21—C22	1.379 (9)
Cl11—Pd01	2.2682 (8)	C21—C21^v	1.598 (16)
Pd01—N1^iii	2.050 (2)	C22—C21^vi	1.379 (9)
Pd01—Cl11^iii	2.2682 (8)
N1^i—C11—N1	125.5 (4)	C22^iv—N22—C21^vi	122.4 (3)
N1^i—C11—C11^ii	117.24 (18)	C21^v—N22—C21^vi	180.0 (3)
N1—C11—C11^ii	117.24 (18)	C22—N22—C21	57.6 (3)
N1—C12—C13	120.4 (3)	C22^iv—N22—C21	122.4 (3)
N1—C12—H12	119.8	C21^v—N22—C21	66.7 (6)
C13—C12—H12	119.8	C21^vi—N22—C21	113.3 (6)
C12—C13—C12^i	119.6 (4)	C22—N22—C21^iv	122.4 (3)
C12—C13—H13	120.2	C22^iv—N22—C21^iv	57.6 (3)
C12^i—C13—H13	120.2	C21^v—N22—C21^iv	113.3 (6)
C11—N1—C12	117.1 (3)	C21^vi—N22—C21^iv	66.7 (6)
C11—N1—Pd01	111.7 (2)	C21—N22—C21^iv	180.0 (6)
C12—N1—Pd01	131.1 (2)	C21—O22—C21^v	78.9 (8)
N1—Pd01—N1^iii	81.77 (13)	O22—C21—C22	160.9 (9)
N1—Pd01—Cl11	174.98 (7)	O22—C21—N22	107.2 (6)
N1^iii—Pd01—Cl11	93.29 (7)	C22—C21—N22	59.5 (5)
N1—Pd01—Cl11^iii	93.29 (7)	O22—C21—C21^v	50.6 (4)
N1^iii—Pd01—Cl11^iii	174.98 (7)	C22—C21—C21^v	114.6 (6)
Cl11—Pd01—Cl11^iii	91.63 (5)	N22—C21—C21^v	56.7 (3)
C22—N22—C22^iv	180.0000 (10)	C21—C22—C21^vi	123.5 (10)
C22—N22—C21^v	122.4 (3)	C21—C22—N22	62.9 (5)
C22^iv—N22—C21^v	57.6 (3)	C21^vi—C22—N22	62.9 (5)
C22—N22—C21^vi	57.6 (3)

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