Startseite Redetermination of crystal structure of [bis(pyridin-2-ylmethyl)amine-κ 3 N,Nʹ,Nʺ]chloridopalladium(II) chloride monohydrate
Artikel Open Access

Redetermination of crystal structure of [bis(pyridin-2-ylmethyl)amine-κ 3 N,,]chloridopalladium(II) chloride monohydrate

  • Kwang Ha ORCID logo EMAIL logo
Veröffentlicht/Copyright: 20. Februar 2023

Abstract

C12H13Cl2N3Pd·H2O, triclinic, P1̄ (no. 2), a = 7.0698(4) Å, b = 8.5546(6) Å, c = 12.8539(9) Å, α = 106.541(2)°, β = 102.510(2)°, γ = 91.572(2)°, V = 724.23(8) Å3, Z = 2, R gt (F) = 0.0199, wR ref (F 2) = 0.0438, T = 223 K.

CCDC no.: 2240090

The title crystal structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Yellow rod
Size: 0.60 × 0.60 × 0.06 mm
Wavelength:

μ:
Mo Kα radiation (0.71073 Å)

1.64 mm−1
Diffractometer, scan mode:

θ max, completeness:
Bruker APEX-II, φ and ω

28.3°, >99%
N(hkl)measured , N(hkl)unique, R int: 24317, 3612, 0.036
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 3354
N(param)refined: 232
Programs: Bruker [1], SHELX [2], ORTEP-III [3], PLATON [4]
Table 2:

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

Atom x y z U iso*/U eq
Pd1 0.18329 (2) 0.47625 (2) 0.41472 (2) 0.02368 (5)
Cl1 0.22208 (7) 0.26532 (6) 0.49396 (4) 0.03540 (11)
Cl2 0.45300 (8) 0.62868 (6) 0.18328 (4) 0.03726 (11)
O1 0.6865 (3) 0.7159 (3) 0.0123 (2) 0.0569 (5)
H1A 0.628 (4) 0.710 (4) 0.056 (3) 0.063 (10)*
H1B 0.660 (5) 0.642 (4) −0.037 (3) 0.065 (10)*
N1 0.0347 (2) 0.3392 (2) 0.26184 (13) 0.0300 (3)
N2 0.1702 (3) 0.6540 (2) 0.34080 (14) 0.0310 (3)
H2N 0.285 (4) 0.640 (3) 0.309 (2) 0.060 (8)*
N3 0.3083 (2) 0.65980 (18) 0.55242 (12) 0.0249 (3)
C1 0.0056 (3) 0.1748 (3) 0.22164 (19) 0.0372 (5)
H1 0.057 (3) 0.118 (3) 0.2725 (19) 0.039 (6)*
C2 −0.0999 (3) 0.0969 (3) 0.1144 (2) 0.0460 (6)
H2 −0.120 (4) −0.015 (3) 0.093 (2) 0.061 (8)*
C3 −0.1731 (4) 0.1899 (3) 0.0468 (2) 0.0525 (6)
H3 −0.243 (4) 0.141 (3) −0.026 (2) 0.061 (8)*
C4 −0.1417 (3) 0.3587 (3) 0.08649 (19) 0.0453 (5)
H4 −0.184 (4) 0.423 (3) 0.043 (2) 0.054 (8)*
C5 −0.0383 (3) 0.4317 (3) 0.19513 (16) 0.0325 (4)
C6 −0.0078 (3) 0.6137 (3) 0.24837 (18) 0.0346 (4)
H6A 0.002 (3) 0.668 (3) 0.196 (2) 0.043 (6)*
H6B −0.116 (4) 0.649 (3) 0.280 (2) 0.048 (7)*
C7 0.1923 (3) 0.8166 (2) 0.42369 (17) 0.0310 (4)
H7A 0.064 (3) 0.853 (3) 0.4302 (17) 0.032 (6)*
H7B 0.252 (3) 0.898 (3) 0.4028 (18) 0.034 (6)*
C8 0.2972 (3) 0.8102 (2) 0.53739 (16) 0.0261 (4)
C9 0.3725 (3) 0.9496 (2) 0.62468 (18) 0.0341 (4)
H9 0.362 (3) 1.047 (3) 0.6107 (18) 0.034 (6)*
C10 0.4606 (3) 0.9356 (3) 0.72816 (18) 0.0386 (5)
H10 0.504 (3) 1.027 (3) 0.786 (2) 0.047 (7)*
C11 0.4739 (3) 0.7821 (3) 0.74253 (17) 0.0346 (4)
H11 0.530 (3) 0.774 (3) 0.813 (2) 0.042 (6)*
C12 0.3971 (3) 0.6467 (2) 0.65318 (16) 0.0285 (4)
H12 0.402 (3) 0.546 (3) 0.6594 (18) 0.034 (6)*

1 Source of materials

To a solution of bis(pyridin-2-ylmethyl)amine (0.1274 g, 0.639 mmol) in acetone (10 mL) was added Na2PdCl4 (0.1921 g, 0.653 mmol) in H2O (5 mL) and stirred for 2 h at room temperature. The formed precipitate was separated by filtration, washed with acetone, and dried at 60 °C, to give a yellow powder (0.1448 g). Crystals were obtained by slow evaporation from MeOH at room temperature.

2 Experimental details

All H atoms were located from Fourier difference maps and refined isotropically: C–H = 0.89(2)–0.98(2) Å, N–H = 0.98(3) Å and O–H = 0.74(3), 0.78(3) Å.

3 Comment

The crystal structures of the related bis(pyridin-2-ylmethyl)amine (bpa) metal complexes [Cu(bpa) (NCS) (ClO4)] [5], [Re(bpa)(CO)3]Br·0.5H2O [6] and [Fe(bpa)Cl3] [7] have been determined previously. The X-ray structure analysis of the title compound was previously carried out by Bugarčić et al. [8], but they did not give a complete description of the hydrogen atoms. The structure presented herein is essentially the same as the published structure, however, the geometric properties and parameters here presented are slightly different and more accurate, respectively.

The title compound consists of a cationic Pd(II) complex [Pd(bpa)Cl]+, a Cl anion and one water molecule. In the complex, the central Pd2+ cation is four-coordinated in a distorted square-planar coordination geometry defined by three N atoms of the tridentate bpa ligand and one anionic Cl ligand. The tight N–Pd–N chelating angles of <N1–Pd1–N2 = 82.88(7)° and <N2–Pd1–N3 = 83.35(6)° contribute the distortion of the square-plane. The three Pd-N bond lengths are almost equal with d(Pd–N) = 2.0037(16)–2.0163(16) Å. In the crystal, the complex is nearly planar: the dihedral angles between the pyridine ring and the least-squares plane of the PdClN3 unit [maximum deviation = 0.0955(9) Å] are 10.85(6)° (ring N1–C5) and 7.23(5)° (ring N3–C12). The dihedral angle between the pyridine ring planes is 4.54(7)°. The Pd-complex, the anion and the solvent molecule are connected by O/N–H⃛Cl and C–H⃛Cl/O hydrogen bonds with distances of 3.110(2)–3.635(2) Å between the donor and acceptor atoms [4]. The cationic complexes are stacked in columns along [100]. In the columns, several π–π interactions between adjacent pyridine rings are present. The shortest distance between Cg1 (the centroid of ring N1–C5) and Cg2 i (ring N3–C12; symmetry code i: −x, 1−y, 1−z) is 3.948(1) Å, and the dihedral angle between the ring planes is 4.5(1)° [4].


Corresponding author: Kwang Ha, School of Chemical Engineering, Research Institute of Catalysis, Chonnam National University, Gwangju 61186, Republic of Korea, E-mail:

Funding source: Chonnam National University

Award Identifier / Grant number: 2022–0170

Acknowledgements

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

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: Chonnam National University (Grant number: 2022–0170).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

1. Bruker. APEX2, SAINT and SADABS; Bruker AXS Inc.: Madison, WI, USA, 2016.Suche in Google Scholar

2. Sheldrick, G. M. Crystal structure refinement with SHELXL. Acta Crystallogr. 2015, C71, 3–8; https://doi.org/10.1107/s2053229614024218.Suche in Google Scholar

3. Farrugia, L. J. ORTEP-3 for Windows-a version of ORTEP–III with a graphical user interface (GUI). J. Appl. Crystallogr. 1997, 30, 565; https://doi.org/10.1107/s0021889897003117.Suche in Google Scholar

4. Spek, A. L. Single-crystal structure validation with the program PLATON. J. Appl. Crystallogr. 2003, 36, 7–13; https://doi.org/10.1107/s0021889802022112.Suche in Google Scholar

5. Mautner, F. A., Albering, J. H., Harrelson, E. V., Gallo, A. A., Massoud, S. S. N-bonding vs. S-bonding in thiocyanato-copper(II) complexes. J. Mol. Struct. 2011, 1006, 570–575; https://doi.org/10.1016/j.molstruc.2011.10.005.Suche in Google Scholar

6. Schutte, M., Muller, T. J., Visser, H. G., Roodt, A. [Bis(pyridin-2-ylmethyl)amine-κ3N,Nʹ,Nʺ]tricarbonylrhenium(I) bromide hemihydrate. Acta Crystallogr. 2012, E68, m741–m742.10.1107/S1600536812019654Suche in Google Scholar PubMed PubMed Central

7. Viswanathan, R., Palaniandavar, M., Balasubramanian, T., Muthiah, P. T. Synthesis, structure, spectra and redox chemistry of iron(III) complexes of tridentate pyridyl and benzimidazolyl ligands. J. Chem. Soc., Dalton Trans. 1996, 2519–2525; https://doi.org/10.1039/dt9960002519.Suche in Google Scholar

8. Bugarčić, Ž. D., Liehr, G., van Eldik, R. Kinetics and mechanism of the reaction of chelated Pd(II) complexes with thiols in acidic aqueous solution. Synthesis and crystal structure of [Pd(bpma)Cl]Cl.H2O (bpma = bis(2-pyridylmethyl)amine). J. Chem. Soc., Dalton Trans. 2002, 951–956; https://doi.org/10.1039/b106038b.Suche in Google Scholar

Received: 2023-01-25
Accepted: 2023-02-06
Published Online: 2023-02-20
Published in Print: 2023-06-27

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of phenyl(3,3-dichloro-1,3-dihydro-2H-pyrrolo[2,3-b]pyridin-2-one)methanone, C7H4Cl2N2O
  4. Crystal structure of poly[diaqua-bis(μ 2-1,4-diaminobutane-N:N′)cobalt(II)] dichloride, C8H28Cl2CoN4O2
  5. Synthesis and crystal structure of (4aR,7S)-7-hydroxy-7-isopropyl-1,1-dimethyldecahydro-2H,6H-8a,4a-(epoxymethano)phenanthren-12-one, C20H32O3
  6. The crystal structure of 1-(2-chlorobenzyl)-3-(3,5-dichlorophenyl)urea, C14H11Cl3N2O
  7. Crystal structure of tetrapropylammonium-1,3,5-thiadiazole-5-amido-2-carbamate – 1,2,4-thiadiazole-3,5-diamine – water (1/1/1), C17H37N9O3S2
  8. Tetrabutylammonium 1,3,5-thiadiazole-5-amido-2-carbamate—1,2,4-thiadiazole-3,5-diamine— water (1/1/1), C21H45N9O3S2
  9. The crystal structure of ((E)-2,4-dichloro-6-(((2-hydroxy-5-nitrophenyl)imino)methyl)phenolato-κ 3 N,O,O′)tris(pyridine-κN)manganese(II), C28H21Cl2MnN5O4
  10. The crystal structure of aqua-bis{2-bromo-6-((2-(2-phenylacetyl)hydrazineylidene)methyl)phenolato-κ3 N,O,O′}-dimethylformamide-κ1 O-erbium(III) chloride – dimethylformamide – water (1/2/1), C39H49N7O9Br2ClEr
  11. Crystal structure of (diaqua-bis(phenanthroline-K 2 N,N′)-tetrakis(m 2-3,4,5,6-tetrafluorophthalato-K 4 O,O:O′:O″;K 2 O:O′)dierbium (III) phenanthroline (1/2), C80H38Er2F16N8O18
  12. Crystal structure of (E)-7-methoxy-2-(4-methoxy-2-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C20H17F3O3
  13. The crystal structure of 4–(4,4,5,5–tetramethyl–1,3,2–dioxaborolan–2–yl)morpholine, C10H20BNO3
  14. The crystal structure of catena–poly[aqua(1-naphthoato-κ 2 O,O′)-(μ-1-naphthoato-κ 4 O:O,O′:O′)lead(II)], C22H16O5Pb
  15. The crystal structure of 1-(4-chlorophenyl)-3-cycloheptylurea, C14H19ClN2O
  16. The crystal structure of 4-(pyren-1-yl)butyl-4-nitrobenzoate, C27H21NO4
  17. Crystal structure of cyclo-(bis(µ2-3,3′-(1H-imidazole-3-ium-1,3-diyl)dipropionato-κ4 O,O′:O″,O″′)-dinitrato-κ2 O,O′-tetraoxido-diuranium(VI) C18H22N6O18U2
  18. The crystal structure of catena-[nitrato-κ 2 O,O′-(μ 3-3-iodobenzene-1,2-dicarboxylato-κ 4 O:O′:O″,O‴)-(2,2′:6′,2″-terpyridine-κ 3 N,N′,N″)lanthanum(III)], C23H14IN4O7La
  19. Redetermination of crystal structure of [bis(pyridin-2-ylmethyl)amine-κ 3 N,,]chloridopalladium(II) chloride monohydrate
  20. Crystal structure of catena-poly[triaqua-[bis(m2-4-(1H-1,2,4-triazol-1-yl)benzoato-k2O:O')-(4-(1H-1,2,4-triazol-1-yl)benzoato-k1O)-praseodymium (III) monohydrate], C27H26N9O10Pr
  21. Crystal structure of trans-diaqua-bis(methyl methylcarbamohydrazonothioato-κ2 N,N′) nickel(II) iodide semihydrate, C6H22N6O2NiS2I2·0.5H2O
  22. The crystal structure of 2-(2-fluoro-4-methyl-5-((2,2,2-trifluoroethyl)thio)phenyl)isoindolin-1-one, C17H13F4NOS
  23. The crystal structure of di-μ-1-naphthylacetato-κ 3 O,O′:O;κ 3 O:O,O′-bis[(1-naphthylacetato-κ 2 O,O′)(2,2′-bipyridine-κ 2 N,N′)lead(II)] monohydrate, C68H54N4O9Pb2
  24. Crystal structure of tetrapropylammonium guanidinium 4,4′-sulfonyldibenzoate monohydrate, C27H44N4O7S
  25. Crystal structure of bis(tetrapropylammonium) terephthalate – 1-(diaminomethylene)thiourea – water (1/2/4) C18H40N5O4S
  26. Crystal structure of (E)-7-fluoro-2-(4-morpholinobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C21H20FNO2
  27. The crystal structure of poly[diaqua-bis(μ 3-5-bromobenzene-1,3-dicarboxylato-κ 3 O,O,O′)-(μ 2-1,3-bis-(4-pyridyl)-propane-κ 2 N,N′)-dizinc(II))] – 5-bromobenzene-1,3-dicarboxylic acid [2/1], C37H29Br3N2O14Zn2
  28. The crystal structure of 2-bromo-1,3-phenylene bis(4-methylbenzenesulfonate), C20H17BrO6S2
  29. Crystal structure of europium dichromium icosaaluminum, EuCr2Al20
  30. The crystal structure of N1,N3-di((E)-benzylidene) isophthalohydrazide dihydrate, C 22 H 22 N 4 O 4
  31. Crystal structure of 7α,11α-dihydroxy-15-oxo-ent-kauran-16-en-19,6β-olide, C20H26O5
  32. Crystal structure of 4-chloro-N′-[(1E)-pyridin-3-ylmethylidene]benzohydrazide, C13H10ClN3O
  33. The crystal structure of (Z)-3-(1-(2-((E)-4-isopropylbenzylidene)hydrazinyl)ethylidene) chroman-2,4-dione, C21H20N2O3
  34. Crystal structure of E-7-fluoro-2-(2-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C18H12F4O
  35. Crystal structure of bis(6-aminopyridine-2-carboxylato–k2O,N)-bis(N,N-dimethylformamide-k1 O)zinc(II), C18H24N6O6Zn
  36. Crystal structure of 5-(adamantan-1-yl)-3-[(4-{[2-(trifluoromethyl)phenyl]-methyl}piperazin-1-yl)methyl]-1,3,4-oxadiazole-2(3H)-thione, C25H31F3N4OS
  37. Crystal structure of tetrapropylammonium bicarbonate–1-(diaminomethylene)thiourea – water (2/2/1), C30H72N10O7S2
  38. Crystal structure of tris(2,2′-bipyridine-κ2 N,N′)iron(II) triiodide – dichloromethane (2/1), C61H50Cl2Fe2I12N12
  39. Crystal structure of 2-amino-3-[2-(1,3,3-trimethyl-1,3-dihydro-indol-2-ylidene)-ethylideneamino]-but-2-enedinitrile, C17H17N5
  40. The crystal structure of 1-(2-chlorophenyl)-3-cycloheptylurea, C14H19ClN2O
  41. Crystal structure of potassium bis(pentaselenido-κ 2 Se 1,Se 5)palladate(II), K2[Pd(Se5)2]
  42. The crystal structure of 5,10-bis(2-methoxyethyl)-5,10-dihydro-[1,2,3,4]tetrathiocino[5,6-b:8, 7-b′]diindole, C22H22N2O2S4
  43. The crystal structure of 4-(4-iodophenyl)-5H-1,2,3-dithiazole-5-thione, C8H4INS3
  44. Crystal structure of bis{μ2-(4-acetyl-phenoxy)acetato-κ2 O:O′}-bis{μ2-(4-acetyl-phenoxy)acetato-κ3 O,O′:O)- bis{(4-acetyl-phenoxy)acetato-κ2 O,O′}-bis(phenanthrolin-κ2 N,N′)didysprosium(III) tetrahydrate, C84H78N4O28Dy2
  45. Crystal structure of Eu2Pd3.37(1)Zn13.63(1)
  46. Crystal structure of 2-methoxy-4-(methoxy-carbonyl)phenyl 2-chloro-4-fluorobenzoate, C16H12ClFO5
  47. Crystal structure of catena-poly[bis(μ2-dicyanamide-κ2 N:N′)-bis(4-vinylpyridine-κN)-copper(II)], C18H14CuN8
  48. The crystal structure of iguratimod-dimethylformamide (1/1), C17H14N2O6S·C3H7NO
  49. Synthesis and crystal structure of 1-((3R,10S,13S,17S)-10,13-dimethyl-3-(m-tolylamino)hexadecahydro-1H-cyclopenta[α]phenanthren-17-yl)ethan-1-one, C28H41NO
  50. The crystal structure of diaqua-bis(4-bromo-2-formylphenoxy)zinc(II), C14H12Br2O6Zn
  51. The crystal structure of tetra(1-ethylimidazole-κ 1 N)-[μ 4-imidazole-4,5-dicarboxylato-κ 4 O, N, O′, N′]-trioxido-divanadium, C25H33N10O7V2
  52. The crystal structure of (E)-N′-(1-(4-fluorophenyl)propylidene)-2-hydroxybenzohydrazide, C16H15FN2O2
Heruntergeladen am 14.10.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2023-0037/html
Button zum nach oben scrollen