trans-Bis[2-(pyrimidin-2-yl)ethyn­yl]bis­(tri­phenylphosphine)palladium

Bosch, E.

doi:10.1107/S2414314625006364

metal-organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 10| Part 8| August 2025| x250636

https://doi.org/10.1107/S2414314625006364

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trans-Bis[2-(pyrimidin-2-yl)ethynyl]bis(triphenylphosphine)palladium

Eric Bosch ^a ^*

^aChemistry and Biochemistry Department, Missouri State University, 901 South National Avenue, Springfield MO 65897, USA
^*Correspondence e-mail: [email protected]

Edited by L. Van Meervelt, Katholieke Universiteit Leuven, Belgium (Received 14 July 2025; accepted 16 July 2025; online 5 August 2025)

The title palladium complex, [Pd(C₆H₃N₂)₂(C₁₈H₁₅P)₂], was isolated as an impurity that co-eluted with the organic product of a palladium-catalyzed Sonogashira coupling. It crystallizes in the monoclinic space group C2/c with one half of the complex in the asymmetric unit. The palladium atom (site symmetry $[\overline{1}]$ ) has a square-planar geometry with trans phosphine ligands. The P—Pd—C angle is 95.19 (9)°.

Keywords: crystal structure; Sonogashira coupling reaction; bis alkynylpalladium complex.

CCDC reference: 2473412

Structure description

The Sonogashira reaction is a palladium-catalyzed cross-coupling reaction of aryl- and vinylhalides with terminal alkynes to form alkynylbenzenes (Sonogashira et al., 1975 ). The mechanism involves a transient intermediate in which the aryl and alkynyl moieties are both bound to the palladium atom. Subsequently, reductive elimination yields the aryl alkyne. The intentional formation of mono- and bis-arylethynyl palladium complexes has separately been exploited in a variety of fields, including self-assembled metallocycles (Sepehrpour et al., 2019 ) and nonlinear optical materials (Yang et al., 1995 ). Herein we describe the structure of the title bis-alkynyl palladium complex, [Pd(C₆H₃N₂)₂(C₁₈H₁₅P)₂], fortuitously isolated during the workup of a Sonogashira coupling reaction performed with a slight excess of 2-ethynylpyrimidine.

The asymmetric unit contains one half of the complex as shown in Fig. 1. The palladium atom adopts square-planar geometry with symmetry-constrained linear P—Pd—P and C—Pd—C bonds and a P1—Pd1—C1 angle of 95.19 (9)°. The pyrimidine rings are twisted by 28.42 (9)° relative to the plane defined by the four atoms directly bonded to palladium. The Pd1—C1 distance is 2.008 (3) Å. A search of the Cambridge Structural Database (CSD, version 2025.1.1; Groom et al., 2016 ) for related bis-ethynyl bis-phosphino palladium complexes yielded 14 unique structures. In these structures, the Pd—C distance ranges from 1.986 to 2.069 Å with an average of 2.012 Å.

Figure 1
Partially labeled asymmetric unit of the the title palladium complex, [Pd(C₆H₃N₂)₂(C₁₈H₁₅P)₂], including the symmetry-generated half of the complex (symmetry operation: $[{3\over 2}]$ − x, $[{3\over 2}]$ − y, 1 − z).

The crystal packing (Fig. 2) along with a view of the Hirshfeld surface (Fig. 3; Spackman et al., 2021 ) show that, as expected, the major inter-complex interactions involve interdigitation of the aromatic moieties. Accordingly, element-to-element analysis of these interactions shows that major interactions are H⋯H, C⋯H/H⋯C and N⋯H/H⋯N interactions corresponding to 52.3, 34.1 and 10.4% of the surface area, respectively.

Figure 2
View along the b axis of the crystal packing of the title palladium complex [Pd(C₆H₃N₂)₂(C₁₈H₁₅P)₂].

Figure 3
Hirshfeld surface of the title palladium complex [Pd(C₆H₃N₂)₂(C₁₈H₁₅P)₂], with two adjacent interacting complexes. C⋯H and C⋯C intermolecular interactions are shown as red and yellow dashed lines, respectively, and labelled X and Y.

We recently described the structures of arylpalladium iodide complexes also incidentally isolated from Sonogashira reaction products where the reactions were performed with a slight excess of the aryl iodide (Bosch, 2025 ). These results provide some insight into the fate of the palladium catalyst in the Sonogashira coupling reaction provided that one of the organic reagents is initially in slight excess.

Synthesis and crystallization

The complex was isolated after a Sonogashira coupling reaction between 1,3,5-trifluoro-2-iodobenzene and 2-ethynylpyrimidine. The reaction was performed with a slight excess, 1.05 molar equiv., of the ethynylpyrimidine. The product was detected as an orange crystalline impurity in the bulk product 2-(2,4,6-trifluorophenylethynyl)pyrimidine isolated after flash chromatography with mixtures of hexane and ethyl acetate. Manual separation afforded small amounts of the complex in crystalline form suitable for single-crystal X-ray crystallography.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1.

Table 1
Experimental details

Crystal data
Chemical formula	[Pd(C₆H₃N₂)₂(C₁₈H₁₅P)₂]
M_r	837.15
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	100
a, b, c (Å)	22.1529 (13), 13.7110 (13), 12.3853 (9)
β (°)	90.690 (2)
V (Å³)	3761.6 (5)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.62
Crystal size (mm)	0.35 × 0.20 × 0.02

Data collection
Diffractometer	Bruker APEXI CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.564, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	24110, 4171, 3041
R_int	0.079
(sin θ/λ)_max (Å⁻¹)	0.642

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.091, 1.02
No. of reflections	4171
No. of parameters	250
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.59, −0.66
Computer programs: APEX2 and SAINT (Bruker, 2014 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2019/2 (Sheldrick, 2015b ) and X-SEED-4 (Barbour, 2020 ).

Structural data

CCDC reference: 2473412

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314625006364/vm4069sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314625006364/vm4069Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314625006364/vm4069Isup3.cdx

checkCIF report

Computing details top

(I) top

Crystal data top

[Pd(C₆H₃N₂)₂(C₁₈H₁₅P)₂]	F(000) = 1712
M_r = 837.15	D_x = 1.478 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 22.1529 (13) Å	Cell parameters from 3308 reflections
b = 13.7110 (13) Å	θ = 2.4–23.5°
c = 12.3853 (9) Å	µ = 0.62 mm⁻¹
β = 90.690 (2)°	T = 100 K
V = 3761.6 (5) Å³	Plate, orange
Z = 4	0.35 × 0.20 × 0.02 mm

Data collection top

Bruker APEXI CCD diffractometer	3041 reflections with I > 2σ(I)
Detector resolution: 8.3660 pixels mm^-1	R_int = 0.079
φ and ω scans	θ_max = 27.1°, θ_min = 1.8°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −28→28
T_min = 0.564, T_max = 0.746	k = −17→17
24110 measured reflections	l = −15→15
4171 independent reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H-atom parameters constrained
wR(F²) = 0.091	w = 1/[σ²(F_o²) + (0.034P)² + 7.3694P] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max < 0.001
4171 reflections	Δρ_max = 0.59 e Å⁻³
250 parameters	Δρ_min = −0.66 e Å⁻³
0 restraints

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.

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

	x	y	z	U_iso*/U_eq
Pd1	0.750000	0.750000	0.500000	0.01796 (10)
P1	0.66798 (4)	0.66217 (6)	0.56457 (6)	0.01975 (18)
N1	0.58722 (14)	0.9407 (2)	0.2463 (3)	0.0449 (9)
C1	0.70247 (14)	0.8220 (2)	0.3862 (2)	0.0209 (7)
N2	0.67884 (15)	0.9460 (2)	0.1481 (2)	0.0372 (8)
C2	0.67628 (14)	0.8677 (2)	0.3173 (2)	0.0211 (7)
C3	0.64549 (15)	0.9208 (2)	0.2336 (3)	0.0252 (7)
C4	0.5602 (2)	0.9855 (3)	0.1602 (4)	0.0638 (15)
H4	0.518332	1.000109	0.163862	0.077*
C5	0.5901 (2)	1.0098 (3)	0.0706 (4)	0.0581 (14)
H5	0.569826	1.038911	0.010696	0.070*
C6	0.6500 (2)	0.9914 (3)	0.0683 (3)	0.0473 (11)
H6	0.672319	1.011791	0.007286	0.057*
C7	0.59797 (15)	0.6599 (3)	0.4845 (2)	0.0253 (7)
C8	0.56959 (17)	0.5749 (3)	0.4499 (3)	0.0372 (9)
H8	0.587809	0.513304	0.463157	0.045*
C9	0.51444 (19)	0.5807 (4)	0.3958 (3)	0.0513 (12)
H9	0.495113	0.522482	0.372235	0.062*
C10	0.48739 (17)	0.6689 (4)	0.3759 (3)	0.0456 (11)
H10	0.449183	0.671727	0.340330	0.055*
C11	0.51582 (16)	0.7524 (4)	0.4074 (3)	0.0444 (10)
H11	0.497736	0.813819	0.392644	0.053*
C12	0.57103 (15)	0.7480 (3)	0.4611 (3)	0.0351 (8)
H12	0.590602	0.806847	0.482071	0.042*
C13	0.68175 (14)	0.5330 (2)	0.5896 (2)	0.0213 (7)
C14	0.67023 (15)	0.4879 (2)	0.6875 (3)	0.0252 (7)
H14	0.658594	0.525676	0.748053	0.030*
C15	0.67578 (15)	0.3873 (3)	0.6965 (3)	0.0304 (8)
H15	0.668344	0.356419	0.763764	0.036*
C16	0.69201 (16)	0.3318 (3)	0.6085 (3)	0.0338 (8)
H16	0.694506	0.262872	0.614631	0.041*
C17	0.70460 (17)	0.3766 (3)	0.5118 (3)	0.0344 (9)
H17	0.716307	0.338504	0.451546	0.041*
C18	0.70025 (16)	0.4772 (3)	0.5021 (3)	0.0306 (8)
H18	0.709901	0.508013	0.435808	0.037*
C19	0.64234 (14)	0.7144 (2)	0.6911 (3)	0.0216 (7)
C20	0.58997 (16)	0.6818 (3)	0.7404 (3)	0.0329 (8)
H20	0.567433	0.630066	0.708617	0.039*
C21	0.57048 (17)	0.7238 (3)	0.8348 (3)	0.0387 (10)
H21	0.535143	0.700015	0.868562	0.046*
C22	0.60193 (17)	0.8000 (3)	0.8802 (3)	0.0372 (9)
H22	0.588364	0.828918	0.945278	0.045*
C23	0.65326 (16)	0.8344 (3)	0.8313 (3)	0.0309 (8)
H23	0.674524	0.888152	0.861690	0.037*
C24	0.67402 (15)	0.7907 (2)	0.7374 (3)	0.0256 (7)
H24	0.710074	0.813407	0.705116	0.031*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Pd1	0.01900 (17)	0.01846 (16)	0.01646 (16)	−0.00124 (16)	0.00149 (12)	0.00134 (15)
P1	0.0215 (4)	0.0208 (4)	0.0170 (4)	−0.0020 (3)	0.0017 (3)	−0.0003 (3)
N1	0.0306 (18)	0.041 (2)	0.062 (2)	−0.0024 (15)	−0.0102 (16)	0.0225 (17)
C1	0.0194 (16)	0.0203 (16)	0.0232 (16)	−0.0026 (13)	0.0048 (13)	−0.0031 (13)
N2	0.058 (2)	0.0295 (17)	0.0238 (16)	0.0020 (15)	0.0020 (15)	0.0012 (13)
C2	0.0240 (17)	0.0203 (16)	0.0192 (16)	−0.0004 (13)	0.0023 (13)	−0.0015 (13)
C3	0.0289 (19)	0.0192 (17)	0.0275 (18)	−0.0030 (14)	−0.0054 (15)	0.0005 (14)
C4	0.036 (3)	0.059 (3)	0.096 (4)	−0.007 (2)	−0.025 (3)	0.032 (3)
C5	0.075 (4)	0.040 (3)	0.059 (3)	−0.015 (2)	−0.034 (3)	0.023 (2)
C6	0.080 (4)	0.032 (2)	0.029 (2)	−0.005 (2)	−0.010 (2)	0.0017 (17)
C7	0.0255 (18)	0.0334 (19)	0.0172 (16)	−0.0029 (15)	0.0028 (13)	0.0026 (14)
C8	0.040 (2)	0.040 (2)	0.031 (2)	−0.0081 (18)	−0.0111 (17)	0.0007 (17)
C9	0.043 (3)	0.067 (3)	0.043 (2)	−0.023 (2)	−0.016 (2)	0.002 (2)
C10	0.024 (2)	0.083 (3)	0.029 (2)	−0.006 (2)	−0.0055 (16)	0.014 (2)
C11	0.0243 (18)	0.064 (3)	0.045 (2)	0.006 (2)	0.0011 (16)	0.018 (2)
C12	0.0238 (17)	0.0376 (19)	0.044 (2)	0.0008 (19)	0.0023 (15)	0.003 (2)
C13	0.0206 (16)	0.0220 (16)	0.0213 (16)	−0.0035 (13)	−0.0001 (13)	0.0007 (13)
C14	0.0284 (19)	0.0279 (18)	0.0192 (16)	−0.0017 (15)	0.0011 (14)	0.0012 (14)
C15	0.0291 (19)	0.031 (2)	0.0306 (19)	−0.0011 (16)	0.0002 (15)	0.0108 (16)
C16	0.033 (2)	0.0231 (18)	0.046 (2)	−0.0005 (15)	0.0032 (17)	0.0059 (17)
C17	0.043 (2)	0.0261 (19)	0.034 (2)	0.0026 (17)	0.0046 (17)	−0.0057 (16)
C18	0.039 (2)	0.0305 (19)	0.0221 (17)	−0.0024 (16)	0.0057 (15)	0.0009 (15)
C19	0.0204 (16)	0.0213 (15)	0.0230 (16)	0.0003 (13)	0.0018 (13)	−0.0026 (13)
C20	0.031 (2)	0.040 (2)	0.0282 (19)	−0.0098 (17)	0.0043 (15)	−0.0097 (16)
C21	0.030 (2)	0.049 (3)	0.038 (2)	−0.0066 (17)	0.0128 (17)	−0.0106 (17)
C22	0.034 (2)	0.046 (2)	0.031 (2)	0.0018 (18)	0.0061 (17)	−0.0159 (18)
C23	0.030 (2)	0.034 (2)	0.0289 (19)	−0.0009 (16)	−0.0002 (15)	−0.0095 (16)
C24	0.0235 (18)	0.0278 (17)	0.0254 (17)	0.0002 (14)	0.0017 (14)	−0.0020 (14)

Geometric parameters (Å, º) top

Pd1—C1	2.008 (3)	C8—C9	1.389 (5)
Pd1—C1ⁱ	2.008 (3)	C9—C10	1.371 (6)
Pd1—P1ⁱ	2.3293 (8)	C10—C11	1.362 (6)
Pd1—P1	2.3294 (8)	C11—C12	1.386 (5)
P1—C19	1.820 (3)	C13—C14	1.387 (4)
P1—C13	1.823 (3)	C13—C18	1.392 (4)
P1—C7	1.831 (3)	C14—C15	1.390 (5)
N1—C3	1.331 (5)	C15—C16	1.380 (5)
N1—C4	1.362 (5)	C16—C17	1.378 (5)
C1—C2	1.202 (4)	C17—C18	1.388 (5)
N2—C6	1.325 (5)	C19—C24	1.381 (4)
N2—C3	1.344 (4)	C19—C20	1.391 (5)
C2—C3	1.433 (4)	C20—C21	1.378 (5)
C4—C5	1.342 (6)	C21—C22	1.372 (5)
C5—C6	1.352 (6)	C22—C23	1.379 (5)
C7—C12	1.377 (5)	C23—C24	1.391 (5)
C7—C8	1.389 (5)

C1—Pd1—C1ⁱ	180.0	C12—C7—P1	117.5 (3)
C1—Pd1—P1ⁱ	84.81 (9)	C8—C7—P1	124.0 (3)
C1ⁱ—Pd1—P1ⁱ	95.19 (9)	C9—C8—C7	119.6 (4)
C1—Pd1—P1	95.19 (9)	C10—C9—C8	121.1 (4)
C1ⁱ—Pd1—P1	84.81 (9)	C11—C10—C9	119.3 (4)
P1ⁱ—Pd1—P1	180.0	C10—C11—C12	120.3 (4)
C19—P1—C13	106.82 (14)	C7—C12—C11	121.1 (4)
C19—P1—C7	101.63 (15)	C14—C13—C18	119.6 (3)
C13—P1—C7	102.39 (15)	C14—C13—P1	123.3 (2)
C19—P1—Pd1	110.17 (11)	C18—C13—P1	116.9 (2)
C13—P1—Pd1	115.53 (11)	C13—C14—C15	119.8 (3)
C7—P1—Pd1	118.82 (11)	C16—C15—C14	120.4 (3)
C3—N1—C4	114.7 (4)	C17—C16—C15	119.9 (3)
C2—C1—Pd1	177.0 (3)	C16—C17—C18	120.3 (3)
C6—N2—C3	116.4 (4)	C17—C18—C13	120.0 (3)
C1—C2—C3	178.9 (4)	C24—C19—C20	118.9 (3)
N1—C3—N2	125.7 (3)	C24—C19—P1	119.6 (2)
N1—C3—C2	118.2 (3)	C20—C19—P1	121.4 (2)
N2—C3—C2	116.1 (3)	C21—C20—C19	120.6 (3)
C5—C4—N1	122.8 (4)	C22—C21—C20	120.2 (3)
C4—C5—C6	117.7 (4)	C21—C22—C23	119.8 (3)
N2—C6—C5	122.5 (4)	C22—C23—C24	120.2 (3)
C12—C7—C8	118.5 (3)	C19—C24—C23	120.1 (3)

Symmetry code: (i) −x+3/2, −y+3/2, −z+1.

Acknowledgements

We thank the Missouri State University Provost Incentive Fund that funded the purchase of the X-ray diffractometer.

Funding information

Funding for this research was provided by: Funding for this research was provided by: National Science Foundation, Directorate for Mathematical and Physical Sciences (grant No. CHE1606556).

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