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metal-organic compounds
trans-Chlorido[6-chloro-4-(4-methoxybenzyl)-3-oxo-3,4-dihydropyrazin-2-yl]bis(triphenylphosphine)palladium(II)
aBiomolecular Architecture, Katholieke Universiteit Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven (Heverlee), Belgium, and bMolecular Design and Synthesis, Katholieke Universiteit Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven (Heverlee), Belgium
*Correspondence e-mail: luc.vanmeervelt@chem.kuleuven.be
The title compound, [Pd(C12H10ClN2O2)Cl(C18H15P)2], is the intermediate of the reduction of a 3,5-dichloropyrazinone [Loosen, Tutonda, Khorasani, Compernolle & Hoornaert (1991). Tetrahedron, 47, 9259–9268]. This species is formed by of coordinatively unsaturated Pd0 to the reactive 3-position of the heterocycle. The coordination around the Pd atom is square planar, with two trans PPh3 ligands. π–π interactions are observed between the centroid of the pyrazinone ring and planes of two adjacent phenyl rings, one from each PPh3 group (3.25 and 3.078 Å), stabilizing the intermediate structure. This could explain the reduced reactivity towards substitution of the Cl atom by the formate anion, resulting in poor yield of the reduced compound. 3-Substituted pyrazinones are important precursors in the synthesis of 5-aminopiperidinone-2-carboxylate (APC) systems.
Related literature
For related literature on the reduction of 3,5-dichloropyrazinones, see: Loosen et al. (1991). For related literature on 3,5-dichloropyrazinones, see: Pawar & De Borggraeve (2006
). For related literature on APC systems, see: De Borggraeve et al. (2004
); Alen et al. (2007
). For the Cambridge Structural Database (Version 5.28), see: Allen (2002
).
Experimental
Crystal data
|
Data collection: SMART (Bruker, 1997); cell SAINT (Bruker, 1997
); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997
); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997
); molecular graphics: ORTEPIII (Burnett & Johnson, 1996
) and ORTEP-3 for Windows (Farrugia, 1997
); software used to prepare material for publication: PLATON (Spek, 2003
).
Supporting information
https://doi.org/10.1107/S1600536807063441/dn2294sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807063441/dn2294Isup2.hkl
To a solution of 570 mg (2 mmol) 3,5-dichloropyrazinone in 20 ml DMF, 204 mg (3 mmol) sodium formate and 115 mg Pd(PPh3)4 are added. The solution is stirred for 4 h at 110 °C under inert atmosphere. After removal of the solvent, the residue is treated with 50 ml of water and extracted with 3x 50 ml dichloromethane. After drying over magnesium sulfate and evaporation of the solvent, the product was chromatographically purified (Heptane/EtOAc 50:50). The title compound was formed as a by-product with a yield of 45% and spontaneously crystallized from the Heptane/EtOAc mixture.
Hydrogen atoms were positioned geometrically; Uiso(H) = xUeq(C), where x = 1.5 for methyl and 1.2 for all other H atoms.
The
contains a solvent accessible void (164.3 Å3). The contribution of the disordered solvent atoms were taken into acount by the squeeze algorithm implemented in the PLATON program (Spek, 2003) for a total of 52.4 electrons.The target structure 5-chloro-1-(4-methoxybenzyl)-2(1H)-pyrazinone) was synthesized as a starting product for the synthesis of dipeptide mimics (Alen et al., 2007; De Borggraeve et al., 2004). This compound can be formed by reduction of a 3,5-dichloropyrazinone with sodium formate using Pd(PPh3)4 as a catalyst. Surprisingly, the title compound (I) was isolated as an intermediate (Scheme 1, Fig. 1). This means that substitution of the chlorine atom with sodium formate and subsequent proton shift leading to the desired compound, did not occur. In similar reactions the yields are high and no traces of the intermediate substance are found. However, the presence of a hydrogen atom para to the palladium atom and a para-methoxybenzyl substituent on the N-1 nitrogen atom of the pyrazinone scaffold, seem to increase the stability of the intermediate. This stability might arise from the π–π interactions between the pyrazinone and two phenyl rings of the PPh3 groups. The centroid of the pyrazinone makes a distance of 3.25 Å and 3.078 Å with the planes formed by the two adjacent phenyl rings. Searches in the CSD database (Version 5.28) (Allen, 2002) for similar structures (59 hits in 50 crystal structures) revealed that the angle between the pyrazinone ring and an adjacent phenyl ring is on average 27.6° (range 13.0° - 65.2°). As fragment for the CSD search a Pd atom with only four substituents (2 PPh3 groups, any halogen and an aromatic ring consisting of any atom type) was used. In the represented structure the angles are 15.4° and 13.9°, resulting in almost parallel pyrazinone and adjacent phenyl rings.
For related literature on the reduction of 3,5-dichloropyrazinones, see: Loosen et al. (1991). For related literature on 3,5-dichloropyrazinones, see: Pawar & De Borggraeve (2006). For related literature on APC systems, see: De Borggraeve et al. (2004); Alen et al. (2007). For the Cambridge Structural Database, see: Allen (2002).
Data collection: SMART (Bruker, 1997); cell
SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: PLATON (Spek, 2003).[Pd(C12H10ClN2O2)Cl(C18H15P)2] | Z = 2 |
Mr = 916.06 | F(000) = 936 |
Triclinic, P1 | Dx = 1.284 Mg m−3 |
Hall symbol: -P 1 | Cu Kα radiation, λ = 1.54178 Å |
a = 10.7544 (1) Å | Cell parameters from 6414 reflections |
b = 13.1526 (1) Å | θ = 2.6–70.6° |
c = 16.9967 (1) Å | µ = 5.13 mm−1 |
α = 91.811 (1)° | T = 100 K |
β = 94.39 (1)° | Block, transparent |
γ = 98.451 (1)° | 0.5 × 0.24 × 0.24 mm |
V = 2368.83 (3) Å3 |
Bruker SMART 6000 diffractometer | 8422 independent reflections |
Radiation source: fine-focus sealed tube | 7879 reflections with I > 2σ(I) |
Crossed Goebel mirrors monochromator | Rint = 0.041 |
ω and φ scans | θmax = 68.8°, θmin = 2.6° |
Absorption correction: multi-scan (SADABS; Bruker, 1997) | h = −12→12 |
Tmin = 0.175, Tmax = 0.292 | k = −15→15 |
23121 measured reflections | l = −20→20 |
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)] = 0.029 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.073 | H-atom parameters constrained |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0381P)2 + 0.3456P] where P = (Fo2 + 2Fc2)/3 |
8422 reflections | (Δ/σ)max = 0.002 |
515 parameters | Δρmax = 0.58 e Å−3 |
318 restraints | Δρmin = −0.58 e Å−3 |
[Pd(C12H10ClN2O2)Cl(C18H15P)2] | γ = 98.451 (1)° |
Mr = 916.06 | V = 2368.83 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 10.7544 (1) Å | Cu Kα radiation |
b = 13.1526 (1) Å | µ = 5.13 mm−1 |
c = 16.9967 (1) Å | T = 100 K |
α = 91.811 (1)° | 0.5 × 0.24 × 0.24 mm |
β = 94.39 (1)° |
Bruker SMART 6000 diffractometer | 8422 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1997) | 7879 reflections with I > 2σ(I) |
Tmin = 0.175, Tmax = 0.292 | Rint = 0.041 |
23121 measured reflections |
R[F2 > 2σ(F2)] = 0.029 | 318 restraints |
wR(F2) = 0.073 | H-atom parameters constrained |
S = 1.08 | Δρmax = 0.58 e Å−3 |
8422 reflections | Δρmin = −0.58 e Å−3 |
515 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 | 0.882642 (11) | 0.283301 (9) | 0.798987 (7) | 0.00908 (6) | |
P2 | 0.83318 (4) | 0.22202 (3) | 0.92192 (2) | 0.00951 (10) | |
C3 | 0.84174 (17) | 0.08526 (14) | 0.92756 (11) | 0.0124 (3) | |
C4 | 0.83393 (19) | 0.02691 (15) | 0.85665 (11) | 0.0177 (4) | |
H4 | 0.8301 | 0.0594 | 0.8076 | 0.021* | |
C5 | 0.8318 (2) | −0.07905 (15) | 0.85853 (12) | 0.0221 (4) | |
H5 | 0.8258 | −0.1189 | 0.8104 | 0.027* | |
C6 | 0.83855 (19) | −0.12702 (15) | 0.93000 (13) | 0.0210 (4) | |
H6 | 0.8377 | −0.1993 | 0.9308 | 0.025* | |
C7 | 0.84646 (18) | −0.06874 (15) | 1.00047 (12) | 0.0184 (4) | |
H7 | 0.8512 | −0.1013 | 1.0495 | 0.022* | |
C8 | 0.84748 (17) | 0.03648 (15) | 0.99934 (11) | 0.0152 (4) | |
H8 | 0.8521 | 0.0758 | 1.0476 | 0.018* | |
C9 | 0.93153 (18) | 0.28969 (14) | 1.00503 (11) | 0.0141 (4) | |
C10 | 0.8973 (2) | 0.28020 (16) | 1.08230 (12) | 0.0196 (4) | |
H10 | 0.8211 | 0.2379 | 1.0921 | 0.023* | |
C11 | 0.9737 (2) | 0.33190 (17) | 1.14494 (12) | 0.0255 (4) | |
H11 | 0.9503 | 0.3243 | 1.1974 | 0.031* | |
C12 | 1.0844 (2) | 0.39479 (16) | 1.13073 (13) | 0.0272 (5) | |
H12 | 1.1367 | 0.4303 | 1.1736 | 0.033* | |
C13 | 1.1187 (2) | 0.40580 (15) | 1.05453 (14) | 0.0252 (5) | |
H13 | 1.1943 | 0.4493 | 1.0452 | 0.030* | |
C14 | 1.0431 (2) | 0.35355 (14) | 0.99098 (12) | 0.0188 (4) | |
H14 | 1.0672 | 0.3613 | 0.9386 | 0.023* | |
C15 | 0.67328 (18) | 0.23049 (15) | 0.94789 (10) | 0.0139 (4) | |
C16 | 0.6417 (2) | 0.32462 (15) | 0.97354 (12) | 0.0196 (4) | |
H16 | 0.7061 | 0.3821 | 0.9845 | 0.023* | |
C17 | 0.5173 (2) | 0.33501 (17) | 0.98318 (13) | 0.0265 (5) | |
H17 | 0.4970 | 0.3993 | 1.0010 | 0.032* | |
C18 | 0.4222 (2) | 0.25182 (18) | 0.96699 (13) | 0.0264 (5) | |
H18 | 0.3368 | 0.2594 | 0.9725 | 0.032* | |
C19 | 0.4529 (2) | 0.15776 (17) | 0.94274 (13) | 0.0238 (4) | |
H19 | 0.3883 | 0.1003 | 0.9326 | 0.029* | |
C20 | 0.5775 (2) | 0.14669 (16) | 0.93306 (11) | 0.0186 (4) | |
H20 | 0.5975 | 0.0819 | 0.9163 | 0.022* | |
P21 | 0.90967 (4) | 0.34277 (3) | 0.67295 (2) | 0.00962 (10) | |
C22 | 1.06025 (17) | 0.42371 (13) | 0.66477 (11) | 0.0123 (3) | |
O22 | 0.63099 (13) | 0.14734 (10) | 0.74606 (8) | 0.0164 (3) | |
C23 | 1.11981 (18) | 0.47685 (15) | 0.73317 (11) | 0.0162 (4) | |
H23 | 1.0858 | 0.4651 | 0.7826 | 0.019* | |
C24 | 1.2293 (2) | 0.54722 (16) | 0.72865 (13) | 0.0234 (4) | |
H24 | 1.2687 | 0.5846 | 0.7749 | 0.028* | |
C25 | 1.2805 (2) | 0.56260 (17) | 0.65720 (14) | 0.0265 (5) | |
H25 | 1.3551 | 0.6105 | 0.6544 | 0.032* | |
C26 | 1.2236 (2) | 0.50845 (17) | 0.58949 (13) | 0.0242 (4) | |
H26 | 1.2601 | 0.5182 | 0.5406 | 0.029* | |
C27 | 1.1130 (2) | 0.43986 (15) | 0.59306 (11) | 0.0187 (4) | |
H27 | 1.0732 | 0.4038 | 0.5464 | 0.022* | |
C28 | 0.89390 (18) | 0.23888 (15) | 0.59781 (11) | 0.0155 (4) | |
C29 | 0.9105 (2) | 0.14114 (15) | 0.62008 (12) | 0.0191 (4) | |
H29 | 0.9347 | 0.1297 | 0.6736 | 0.023* | |
C30 | 0.8916 (2) | 0.05938 (17) | 0.56403 (14) | 0.0278 (5) | |
H30 | 0.9043 | −0.0074 | 0.5793 | 0.033* | |
C31 | 0.8544 (2) | 0.07548 (17) | 0.48620 (14) | 0.0293 (5) | |
H31 | 0.8393 | 0.0193 | 0.4485 | 0.035* | |
C32 | 0.8392 (2) | 0.17322 (19) | 0.46310 (13) | 0.0295 (5) | |
H32 | 0.8152 | 0.1842 | 0.4094 | 0.035* | |
C33 | 0.8591 (2) | 0.25544 (17) | 0.51857 (12) | 0.0226 (4) | |
H33 | 0.8491 | 0.3226 | 0.5027 | 0.027* | |
C34 | 0.79522 (19) | 0.42356 (15) | 0.63620 (10) | 0.0153 (4) | |
C35 | 0.8235 (2) | 0.53018 (15) | 0.64354 (11) | 0.0192 (4) | |
H35 | 0.9064 | 0.5619 | 0.6616 | 0.023* | |
C36 | 0.7301 (2) | 0.59064 (18) | 0.62441 (12) | 0.0274 (5) | |
H36 | 0.7494 | 0.6635 | 0.6294 | 0.033* | |
C37 | 0.6096 (2) | 0.5446 (2) | 0.59829 (13) | 0.0304 (5) | |
H37 | 0.5464 | 0.5860 | 0.5850 | 0.037* | |
C38 | 0.5802 (2) | 0.4381 (2) | 0.59132 (12) | 0.0274 (5) | |
H38 | 0.4969 | 0.4067 | 0.5738 | 0.033* | |
C39 | 0.67304 (19) | 0.37767 (17) | 0.61004 (11) | 0.0197 (4) | |
H39 | 0.6533 | 0.3048 | 0.6050 | 0.024* | |
Cl40 | 1.08823 (4) | 0.23058 (3) | 0.81045 (3) | 0.01784 (10) | |
C41 | 0.71073 (17) | 0.32121 (14) | 0.78835 (10) | 0.0112 (3) | |
N42 | 0.68875 (15) | 0.41388 (12) | 0.80409 (9) | 0.0134 (3) | |
C43 | 0.56729 (19) | 0.43210 (15) | 0.79552 (11) | 0.0155 (4) | |
Cl45 | 0.54465 (5) | 0.55731 (4) | 0.82009 (3) | 0.02764 (12) | |
C46 | 0.46835 (18) | 0.36031 (15) | 0.77103 (10) | 0.0156 (4) | |
H46 | 0.3853 | 0.3772 | 0.7655 | 0.019* | |
N47 | 0.49052 (15) | 0.26179 (12) | 0.75423 (9) | 0.0136 (3) | |
C48 | 0.61075 (17) | 0.23561 (14) | 0.76109 (10) | 0.0122 (3) | |
C49 | 0.38425 (18) | 0.18064 (15) | 0.72664 (11) | 0.0168 (4) | |
H49A | 0.3067 | 0.1955 | 0.7497 | 0.020* | |
H49B | 0.4025 | 0.1135 | 0.7456 | 0.020* | |
C50 | 0.36165 (18) | 0.17346 (14) | 0.63773 (12) | 0.0157 (4) | |
C51 | 0.25756 (19) | 0.20966 (15) | 0.60036 (12) | 0.0185 (4) | |
H51 | 0.2003 | 0.2384 | 0.6312 | 0.022* | |
C52 | 0.2369 (2) | 0.20408 (15) | 0.51874 (12) | 0.0222 (4) | |
H52 | 0.1656 | 0.2287 | 0.4939 | 0.027* | |
C53 | 0.3206 (2) | 0.16237 (14) | 0.47317 (12) | 0.0188 (4) | |
C54 | 0.4253 (2) | 0.12637 (16) | 0.50919 (12) | 0.0216 (4) | |
H54 | 0.4831 | 0.0986 | 0.4782 | 0.026* | |
C55 | 0.44411 (19) | 0.13164 (16) | 0.59098 (12) | 0.0203 (4) | |
H55 | 0.5148 | 0.1062 | 0.6157 | 0.024* | |
O56 | 0.29196 (16) | 0.15893 (12) | 0.39257 (9) | 0.0268 (3) | |
C57 | 0.3688 (3) | 0.1064 (3) | 0.34498 (15) | 0.0500 (8) | |
H57A | 0.4568 | 0.1394 | 0.3539 | 0.075* | |
H57B | 0.3399 | 0.1095 | 0.2891 | 0.075* | |
H57C | 0.3623 | 0.0344 | 0.3594 | 0.075* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.00829 (8) | 0.01200 (8) | 0.00741 (8) | 0.00311 (5) | −0.00019 (5) | 0.00213 (5) |
P2 | 0.0098 (2) | 0.0118 (2) | 0.0068 (2) | 0.00126 (16) | −0.00014 (16) | 0.00116 (15) |
C3 | 0.0102 (8) | 0.0130 (8) | 0.0138 (8) | 0.0015 (6) | −0.0006 (7) | 0.0018 (6) |
C4 | 0.0197 (10) | 0.0199 (9) | 0.0136 (9) | 0.0042 (8) | −0.0006 (7) | −0.0001 (7) |
C5 | 0.0253 (11) | 0.0175 (9) | 0.0228 (10) | 0.0045 (8) | −0.0016 (8) | −0.0062 (8) |
C6 | 0.0152 (10) | 0.0148 (9) | 0.0331 (11) | 0.0028 (7) | 0.0002 (8) | 0.0028 (8) |
C7 | 0.0127 (9) | 0.0197 (9) | 0.0240 (10) | 0.0034 (7) | 0.0024 (7) | 0.0111 (8) |
C8 | 0.0119 (9) | 0.0201 (9) | 0.0140 (9) | 0.0030 (7) | 0.0020 (7) | 0.0034 (7) |
C9 | 0.0169 (9) | 0.0120 (8) | 0.0130 (8) | 0.0033 (7) | −0.0029 (7) | −0.0008 (6) |
C10 | 0.0210 (10) | 0.0233 (10) | 0.0141 (9) | 0.0049 (8) | −0.0014 (8) | −0.0048 (7) |
C11 | 0.0313 (12) | 0.0287 (11) | 0.0164 (9) | 0.0097 (9) | −0.0030 (8) | −0.0093 (8) |
C12 | 0.0332 (12) | 0.0202 (10) | 0.0261 (11) | 0.0063 (9) | −0.0110 (9) | −0.0099 (8) |
C13 | 0.0246 (11) | 0.0121 (9) | 0.0351 (12) | −0.0028 (8) | −0.0104 (9) | 0.0000 (8) |
C14 | 0.0210 (10) | 0.0130 (9) | 0.0214 (9) | 0.0010 (7) | −0.0030 (8) | 0.0026 (7) |
C15 | 0.0134 (9) | 0.0203 (9) | 0.0085 (8) | 0.0034 (7) | 0.0021 (7) | 0.0026 (7) |
C16 | 0.0204 (10) | 0.0184 (9) | 0.0212 (10) | 0.0038 (8) | 0.0068 (8) | 0.0043 (7) |
C17 | 0.0295 (12) | 0.0243 (10) | 0.0305 (11) | 0.0142 (9) | 0.0121 (9) | 0.0066 (9) |
C18 | 0.0175 (10) | 0.0363 (12) | 0.0292 (11) | 0.0101 (9) | 0.0110 (8) | 0.0110 (9) |
C19 | 0.0159 (10) | 0.0311 (11) | 0.0235 (10) | 0.0000 (8) | 0.0033 (8) | 0.0020 (8) |
C20 | 0.0186 (10) | 0.0222 (10) | 0.0149 (9) | 0.0026 (8) | 0.0021 (7) | −0.0007 (7) |
P21 | 0.0116 (2) | 0.0115 (2) | 0.0060 (2) | 0.00296 (16) | 0.00008 (15) | 0.00123 (15) |
C22 | 0.0127 (9) | 0.0123 (8) | 0.0132 (8) | 0.0056 (7) | 0.0013 (7) | 0.0035 (6) |
O22 | 0.0156 (7) | 0.0142 (6) | 0.0195 (7) | 0.0057 (5) | −0.0031 (5) | −0.0020 (5) |
C23 | 0.0150 (9) | 0.0175 (9) | 0.0166 (9) | 0.0036 (7) | 0.0022 (7) | 0.0000 (7) |
C24 | 0.0184 (10) | 0.0245 (10) | 0.0260 (10) | 0.0012 (8) | −0.0012 (8) | −0.0028 (8) |
C25 | 0.0173 (10) | 0.0242 (10) | 0.0378 (12) | −0.0003 (8) | 0.0061 (9) | 0.0037 (9) |
C26 | 0.0244 (11) | 0.0248 (10) | 0.0264 (10) | 0.0058 (8) | 0.0133 (8) | 0.0086 (8) |
C27 | 0.0238 (10) | 0.0193 (9) | 0.0147 (9) | 0.0074 (8) | 0.0046 (8) | 0.0021 (7) |
C28 | 0.0149 (9) | 0.0177 (9) | 0.0131 (9) | 0.0014 (7) | −0.0012 (7) | −0.0030 (7) |
C29 | 0.0220 (10) | 0.0165 (9) | 0.0182 (9) | 0.0018 (8) | 0.0010 (8) | −0.0001 (7) |
C30 | 0.0356 (13) | 0.0178 (10) | 0.0287 (11) | 0.0012 (9) | 0.0024 (9) | −0.0059 (8) |
C31 | 0.0334 (12) | 0.0241 (11) | 0.0271 (11) | −0.0026 (9) | 0.0006 (9) | −0.0140 (9) |
C32 | 0.0353 (13) | 0.0362 (12) | 0.0164 (10) | 0.0093 (10) | −0.0047 (9) | −0.0081 (9) |
C33 | 0.0300 (11) | 0.0242 (10) | 0.0139 (9) | 0.0084 (9) | −0.0033 (8) | −0.0028 (8) |
C34 | 0.0176 (9) | 0.0231 (9) | 0.0071 (8) | 0.0078 (7) | 0.0019 (7) | 0.0044 (7) |
C35 | 0.0248 (11) | 0.0214 (10) | 0.0141 (9) | 0.0106 (8) | 0.0032 (8) | 0.0055 (7) |
C36 | 0.0380 (13) | 0.0315 (11) | 0.0195 (10) | 0.0230 (10) | 0.0087 (9) | 0.0100 (8) |
C37 | 0.0315 (12) | 0.0505 (14) | 0.0181 (10) | 0.0291 (11) | 0.0081 (9) | 0.0154 (9) |
C38 | 0.0177 (10) | 0.0545 (14) | 0.0128 (9) | 0.0131 (10) | 0.0009 (8) | 0.0125 (9) |
C39 | 0.0162 (10) | 0.0343 (11) | 0.0094 (8) | 0.0045 (8) | 0.0014 (7) | 0.0074 (7) |
Cl40 | 0.0125 (2) | 0.0251 (2) | 0.0184 (2) | 0.00943 (17) | 0.00230 (16) | 0.00715 (17) |
C41 | 0.0136 (9) | 0.0156 (8) | 0.0045 (7) | 0.0024 (7) | 0.0010 (6) | 0.0010 (6) |
N42 | 0.0158 (8) | 0.0163 (7) | 0.0084 (7) | 0.0048 (6) | −0.0007 (6) | −0.0007 (5) |
C43 | 0.0191 (10) | 0.0169 (9) | 0.0119 (8) | 0.0091 (7) | −0.0011 (7) | −0.0025 (7) |
Cl45 | 0.0266 (3) | 0.0223 (2) | 0.0346 (3) | 0.01454 (19) | −0.0088 (2) | −0.0137 (2) |
C46 | 0.0155 (9) | 0.0230 (9) | 0.0102 (8) | 0.0104 (7) | 0.0004 (7) | −0.0016 (7) |
N47 | 0.0116 (8) | 0.0176 (7) | 0.0113 (7) | 0.0026 (6) | −0.0003 (6) | −0.0008 (6) |
C48 | 0.0134 (9) | 0.0166 (9) | 0.0069 (8) | 0.0038 (7) | −0.0010 (6) | 0.0015 (6) |
C49 | 0.0108 (9) | 0.0197 (9) | 0.0190 (9) | 0.0002 (7) | 0.0004 (7) | 0.0008 (7) |
C50 | 0.0133 (9) | 0.0126 (8) | 0.0200 (9) | −0.0002 (7) | −0.0013 (7) | 0.0011 (7) |
C51 | 0.0166 (10) | 0.0176 (9) | 0.0213 (10) | 0.0046 (7) | −0.0013 (8) | −0.0006 (7) |
C52 | 0.0257 (11) | 0.0180 (9) | 0.0230 (10) | 0.0090 (8) | −0.0087 (8) | 0.0016 (8) |
C53 | 0.0254 (10) | 0.0131 (8) | 0.0163 (9) | 0.0009 (7) | −0.0040 (8) | −0.0005 (7) |
C54 | 0.0220 (10) | 0.0233 (10) | 0.0196 (10) | 0.0055 (8) | 0.0003 (8) | −0.0052 (8) |
C55 | 0.0172 (10) | 0.0227 (10) | 0.0211 (10) | 0.0080 (8) | −0.0056 (8) | −0.0018 (8) |
O56 | 0.0393 (9) | 0.0273 (8) | 0.0151 (7) | 0.0131 (7) | −0.0047 (6) | −0.0004 (6) |
C57 | 0.0578 (19) | 0.084 (2) | 0.0150 (11) | 0.0361 (17) | −0.0002 (11) | −0.0048 (12) |
Pd1—C41 | 1.9812 (19) | C26—C27 | 1.389 (3) |
Pd1—P21 | 2.3280 (4) | C26—H26 | 0.9500 |
Pd1—P2 | 2.3343 (4) | C27—H27 | 0.9500 |
Pd1—Cl40 | 2.4084 (4) | C28—C29 | 1.384 (3) |
P2—C3 | 1.8198 (18) | C28—C33 | 1.402 (3) |
P2—C9 | 1.8225 (18) | C29—C30 | 1.395 (3) |
P2—C15 | 1.8259 (19) | C29—H29 | 0.9500 |
C3—C4 | 1.398 (3) | C30—C31 | 1.384 (3) |
C3—C8 | 1.398 (3) | C30—H30 | 0.9500 |
C4—C5 | 1.392 (3) | C31—C32 | 1.385 (4) |
C4—H4 | 0.9500 | C31—H31 | 0.9500 |
C5—C6 | 1.388 (3) | C32—C33 | 1.393 (3) |
C5—H5 | 0.9500 | C32—H32 | 0.9500 |
C6—C7 | 1.392 (3) | C33—H33 | 0.9500 |
C6—H6 | 0.9500 | C34—C35 | 1.390 (3) |
C7—C8 | 1.383 (3) | C34—C39 | 1.396 (3) |
C7—H7 | 0.9500 | C35—C36 | 1.396 (3) |
C8—H8 | 0.9500 | C35—H35 | 0.9500 |
C9—C10 | 1.395 (3) | C36—C37 | 1.381 (4) |
C9—C14 | 1.401 (3) | C36—H36 | 0.9500 |
C10—C11 | 1.388 (3) | C37—C38 | 1.390 (4) |
C10—H10 | 0.9500 | C37—H37 | 0.9500 |
C11—C12 | 1.388 (4) | C38—C39 | 1.390 (3) |
C11—H11 | 0.9500 | C38—H38 | 0.9500 |
C12—C13 | 1.380 (4) | C39—H39 | 0.9500 |
C12—H12 | 0.9500 | C41—N42 | 1.299 (2) |
C13—C14 | 1.398 (3) | C41—C48 | 1.474 (3) |
C13—H13 | 0.9500 | N42—C43 | 1.360 (3) |
C14—H14 | 0.9500 | C43—C46 | 1.345 (3) |
C15—C20 | 1.396 (3) | C43—Cl45 | 1.7423 (19) |
C15—C16 | 1.396 (3) | C46—N47 | 1.377 (2) |
C16—C17 | 1.387 (3) | C46—H46 | 0.9500 |
C16—H16 | 0.9500 | N47—C48 | 1.384 (2) |
C17—C18 | 1.388 (3) | N47—C49 | 1.481 (2) |
C17—H17 | 0.9500 | C49—C50 | 1.510 (3) |
C18—C19 | 1.385 (3) | C49—H49A | 0.9900 |
C18—H18 | 0.9500 | C49—H49B | 0.9900 |
C19—C20 | 1.391 (3) | C50—C55 | 1.394 (3) |
C19—H19 | 0.9500 | C50—C51 | 1.397 (3) |
C20—H20 | 0.9500 | C51—C52 | 1.386 (3) |
P21—C22 | 1.8199 (19) | C51—H51 | 0.9500 |
P21—C28 | 1.8208 (19) | C52—C53 | 1.392 (3) |
P21—C34 | 1.8283 (19) | C52—H52 | 0.9500 |
C22—C27 | 1.393 (3) | C53—O56 | 1.379 (2) |
C22—C23 | 1.398 (3) | C53—C54 | 1.391 (3) |
O22—C48 | 1.235 (2) | C54—C55 | 1.387 (3) |
C23—C24 | 1.395 (3) | C54—H54 | 0.9500 |
C23—H23 | 0.9500 | C55—H55 | 0.9500 |
C24—C25 | 1.380 (3) | O56—C57 | 1.432 (3) |
C24—H24 | 0.9500 | C57—H57A | 0.9800 |
C25—C26 | 1.385 (3) | C57—H57B | 0.9800 |
C25—H25 | 0.9500 | C57—H57C | 0.9800 |
C41—Pd1—P21 | 87.89 (5) | C26—C27—C22 | 120.32 (18) |
C41—Pd1—P2 | 86.59 (5) | C26—C27—H27 | 119.8 |
P21—Pd1—P2 | 174.088 (16) | C22—C27—H27 | 119.8 |
C41—Pd1—Cl40 | 177.83 (5) | C29—C28—C33 | 119.68 (18) |
P21—Pd1—Cl40 | 92.403 (15) | C29—C28—P21 | 119.31 (15) |
P2—Pd1—Cl40 | 93.033 (15) | C33—C28—P21 | 120.94 (15) |
C3—P2—C9 | 108.29 (8) | C28—C29—C30 | 120.10 (19) |
C3—P2—C15 | 102.83 (9) | C28—C29—H29 | 119.9 |
C9—P2—C15 | 103.12 (9) | C30—C29—H29 | 119.9 |
C3—P2—Pd1 | 111.86 (6) | C31—C30—C29 | 120.1 (2) |
C9—P2—Pd1 | 114.02 (6) | C31—C30—H30 | 120.0 |
C15—P2—Pd1 | 115.72 (6) | C29—C30—H30 | 120.0 |
C4—C3—C8 | 119.60 (17) | C32—C31—C30 | 120.24 (19) |
C4—C3—P2 | 117.83 (14) | C32—C31—H31 | 119.9 |
C8—C3—P2 | 122.43 (14) | C30—C31—H31 | 119.9 |
C5—C4—C3 | 119.52 (18) | C31—C32—C33 | 120.0 (2) |
C5—C4—H4 | 120.2 | C31—C32—H32 | 120.0 |
C3—C4—H4 | 120.2 | C33—C32—H32 | 120.0 |
C6—C5—C4 | 120.65 (19) | C32—C33—C28 | 119.9 (2) |
C6—C5—H5 | 119.7 | C32—C33—H33 | 120.1 |
C4—C5—H5 | 119.7 | C28—C33—H33 | 120.1 |
C5—C6—C7 | 119.69 (18) | C35—C34—C39 | 119.60 (18) |
C5—C6—H6 | 120.2 | C35—C34—P21 | 120.60 (15) |
C7—C6—H6 | 120.2 | C39—C34—P21 | 119.27 (15) |
C8—C7—C6 | 120.18 (18) | C34—C35—C36 | 120.0 (2) |
C8—C7—H7 | 119.9 | C34—C35—H35 | 120.0 |
C6—C7—H7 | 119.9 | C36—C35—H35 | 120.0 |
C7—C8—C3 | 120.35 (18) | C37—C36—C35 | 120.0 (2) |
C7—C8—H8 | 119.8 | C37—C36—H36 | 120.0 |
C3—C8—H8 | 119.8 | C35—C36—H36 | 120.0 |
C10—C9—C14 | 119.27 (17) | C36—C37—C38 | 120.4 (2) |
C10—C9—P2 | 121.40 (15) | C36—C37—H37 | 119.8 |
C14—C9—P2 | 119.33 (15) | C38—C37—H37 | 119.8 |
C11—C10—C9 | 120.6 (2) | C37—C38—C39 | 119.7 (2) |
C11—C10—H10 | 119.7 | C37—C38—H38 | 120.2 |
C9—C10—H10 | 119.7 | C39—C38—H38 | 120.2 |
C12—C11—C10 | 119.9 (2) | C38—C39—C34 | 120.3 (2) |
C12—C11—H11 | 120.1 | C38—C39—H39 | 119.9 |
C10—C11—H11 | 120.1 | C34—C39—H39 | 119.9 |
C13—C12—C11 | 120.12 (19) | N42—C41—C48 | 123.17 (17) |
C13—C12—H12 | 119.9 | N42—C41—Pd1 | 122.49 (13) |
C11—C12—H12 | 119.9 | C48—C41—Pd1 | 114.33 (13) |
C12—C13—C14 | 120.6 (2) | C41—N42—C43 | 118.09 (16) |
C12—C13—H13 | 119.7 | C46—C43—N42 | 124.11 (17) |
C14—C13—H13 | 119.7 | C46—C43—Cl45 | 120.40 (15) |
C13—C14—C9 | 119.5 (2) | N42—C43—Cl45 | 115.49 (14) |
C13—C14—H14 | 120.2 | C43—C46—N47 | 118.31 (17) |
C9—C14—H14 | 120.2 | C43—C46—H46 | 120.8 |
C20—C15—C16 | 118.82 (18) | N47—C46—H46 | 120.8 |
C20—C15—P2 | 120.50 (15) | C46—N47—C48 | 121.92 (16) |
C16—C15—P2 | 120.19 (15) | C46—N47—C49 | 119.99 (16) |
C17—C16—C15 | 120.59 (19) | C48—N47—C49 | 118.08 (15) |
C17—C16—H16 | 119.7 | O22—C48—N47 | 122.10 (17) |
C15—C16—H16 | 119.7 | O22—C48—C41 | 123.50 (17) |
C16—C17—C18 | 120.3 (2) | N47—C48—C41 | 114.40 (16) |
C16—C17—H17 | 119.9 | N47—C49—C50 | 112.06 (15) |
C18—C17—H17 | 119.9 | N47—C49—H49A | 109.2 |
C19—C18—C17 | 119.5 (2) | C50—C49—H49A | 109.2 |
C19—C18—H18 | 120.3 | N47—C49—H49B | 109.2 |
C17—C18—H18 | 120.3 | C50—C49—H49B | 109.2 |
C18—C19—C20 | 120.6 (2) | H49A—C49—H49B | 107.9 |
C18—C19—H19 | 119.7 | C55—C50—C51 | 118.42 (18) |
C20—C19—H19 | 119.7 | C55—C50—C49 | 121.16 (18) |
C19—C20—C15 | 120.24 (19) | C51—C50—C49 | 120.43 (18) |
C19—C20—H20 | 119.9 | C52—C51—C50 | 120.69 (19) |
C15—C20—H20 | 119.9 | C52—C51—H51 | 119.7 |
C22—P21—C28 | 107.68 (9) | C50—C51—H51 | 119.7 |
C22—P21—C34 | 102.95 (9) | C51—C52—C53 | 119.96 (19) |
C28—P21—C34 | 103.53 (9) | C51—C52—H52 | 120.0 |
C22—P21—Pd1 | 113.86 (6) | C53—C52—H52 | 120.0 |
C28—P21—Pd1 | 112.69 (6) | O56—C53—C54 | 123.74 (19) |
C34—P21—Pd1 | 115.12 (6) | O56—C53—C52 | 115.97 (18) |
C27—C22—C23 | 119.38 (18) | C54—C53—C52 | 120.28 (18) |
C27—C22—P21 | 122.84 (14) | C55—C54—C53 | 119.10 (19) |
C23—C22—P21 | 117.63 (14) | C55—C54—H54 | 120.5 |
C24—C23—C22 | 119.85 (18) | C53—C54—H54 | 120.5 |
C24—C23—H23 | 120.1 | C54—C55—C50 | 121.55 (19) |
C22—C23—H23 | 120.1 | C54—C55—H55 | 119.2 |
C25—C24—C23 | 120.17 (19) | C50—C55—H55 | 119.2 |
C25—C24—H24 | 119.9 | C53—O56—C57 | 116.97 (18) |
C23—C24—H24 | 119.9 | O56—C57—H57A | 109.5 |
C24—C25—C26 | 120.3 (2) | O56—C57—H57B | 109.5 |
C24—C25—H25 | 119.9 | H57A—C57—H57B | 109.5 |
C26—C25—H25 | 119.9 | O56—C57—H57C | 109.5 |
C25—C26—C27 | 120.0 (2) | H57A—C57—H57C | 109.5 |
C25—C26—H26 | 120.0 | H57B—C57—H57C | 109.5 |
C27—C26—H26 | 120.0 |
Experimental details
Crystal data | |
Chemical formula | [Pd(C12H10ClN2O2)Cl(C18H15P)2] |
Mr | 916.06 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 100 |
a, b, c (Å) | 10.7544 (1), 13.1526 (1), 16.9967 (1) |
α, β, γ (°) | 91.811 (1), 94.39 (1), 98.451 (1) |
V (Å3) | 2368.83 (3) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 5.13 |
Crystal size (mm) | 0.5 × 0.24 × 0.24 |
Data collection | |
Diffractometer | Bruker SMART 6000 |
Absorption correction | Multi-scan (SADABS; Bruker, 1997) |
Tmin, Tmax | 0.175, 0.292 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23121, 8422, 7879 |
Rint | 0.041 |
(sin θ/λ)max (Å−1) | 0.605 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.029, 0.073, 1.08 |
No. of reflections | 8422 |
No. of parameters | 515 |
No. of restraints | 318 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.58, −0.58 |
Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 for Windows (Farrugia, 1997), PLATON (Spek, 2003).
Acknowledgements
The Katholieke Universiteit Leuven is gratefully acknowledged for financial support. The authors thank the FWO [Fund for Scientific Research–Flanders (Belgium)] for financial support. JA and WMDB (Postdoctoral Fellows of the FWO–Flanders) thank the FWO for Fellowships received. WMDB also thanks the FWO for a `Krediet aan Navorsers'.
References
Alen, J., Smets, W. J., Dobrzańska, L., De Borggraeve, W. M., Compernolle, F. & Hoornaert, G. J. (2007). Eur. J. Org. Chem. 6, 965–971. Web of Science CSD CrossRef Google Scholar
Allen, F. H. (2002). Acta Cryst. B58, 380–388. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Bruker (1997). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA. Google Scholar
De Borggraeve, W. M., Verbist, B. M. P., Rombouts, F. J. R., Pawar, V. G., Smets, W. J., Kamoune, L., Alen, J., Van der Eycken, E. V., Compernolle, F. & Hoornaert, G. J. (2004). Tetrahedron, 60, 11597–11612. CrossRef CAS Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Loosen, P. K., Tutonda, M. G., Khorasani, M. F., Compernolle, F. & Hoornaert, G. J. (1991). Tetrahedron, 47, 9259–9268. CrossRef CAS Web of Science Google Scholar
Pawar, V. G. & De Borggraeve, W. M. (2006). Synthesis, 17, 2799–2814. Google Scholar
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany. Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar
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The target structure 5-chloro-1-(4-methoxybenzyl)-2(1H)-pyrazinone) was synthesized as a starting product for the synthesis of dipeptide mimics (Alen et al., 2007; De Borggraeve et al., 2004). This compound can be formed by reduction of a 3,5-dichloropyrazinone with sodium formate using Pd(PPh3)4 as a catalyst. Surprisingly, the title compound (I) was isolated as an intermediate (Scheme 1, Fig. 1). This means that substitution of the chlorine atom with sodium formate and subsequent proton shift leading to the desired compound, did not occur. In similar reactions the yields are high and no traces of the intermediate substance are found. However, the presence of a hydrogen atom para to the palladium atom and a para-methoxybenzyl substituent on the N-1 nitrogen atom of the pyrazinone scaffold, seem to increase the stability of the intermediate. This stability might arise from the π–π interactions between the pyrazinone and two phenyl rings of the PPh3 groups. The centroid of the pyrazinone makes a distance of 3.25 Å and 3.078 Å with the planes formed by the two adjacent phenyl rings. Searches in the CSD database (Version 5.28) (Allen, 2002) for similar structures (59 hits in 50 crystal structures) revealed that the angle between the pyrazinone ring and an adjacent phenyl ring is on average 27.6° (range 13.0° - 65.2°). As fragment for the CSD search a Pd atom with only four substituents (2 PPh3 groups, any halogen and an aromatic ring consisting of any atom type) was used. In the represented structure the angles are 15.4° and 13.9°, resulting in almost parallel pyrazinone and adjacent phenyl rings.