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Crystal structure of bis(methylammonium) hexadecaselenidopalladate(II), (CH3NH3)2PdSe16

  • Kang-Woo Kim ORCID logo EMAIL logo and Jong-Min Noh
Published/Copyright: April 4, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 3

Abstract

(CH3NH3)2PdSe16, tetragonal, P 4 ‾ b 2 (no. 117), a = 12.7821(4) Å, c = 7.1123(2) Å, V = 1162.02(8) Å3, Z = 2, R gt(F) = 0.0306, wR ref(F 2) = 0.0841, T = 223 K.

CCDC no.: 2341033

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: Black chunk
Size: 0.18 × 0.15 × 0.12 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 25.9 mm−1
Diffractometer, scan mode: PHOTON 100 CMOS, φ and ω
θ max, completeness: 28.3°, >99 %
N(hkl)measured, N(hkl)unique, R int: 40,693, 1457, 0.099
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 1377
N(param)refined: 54
Programs: Bruker [1], SHELX [2], WinGX/ORTEP [3], Diamond [4]
Table 2:

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

Atom x y z U iso*/U eq
Pd1 1.000000 1.000000 1.000000 0.0246 (2)
Se1 0.96361 (6) 0.81405 (6) 0.96910 (16) 0.0383 (2)
Se2 0.78848 (8) 0.79594 (7) 0.87366 (14) 0.0390 (2)
Se3 0.57833 (8) 0.80950 (8) 0.58501 (16) 0.0457 (3)
Se4 0.42052 (8) 0.81025 (7) 0.41248 (16) 0.0433 (3)
N1a 0.5309 (17) 0.9691 (17) 1.000000 0.156 (15)
H1Ab 0.586293 0.991373 1.067024 0.234*
H1Bb 0.550881 0.955961 0.881013 0.234*
H1Cb 0.505206 0.910286 1.051963 0.234*
C1a 0.5309 (17) 0.9691(17) 1.000000 0.156 (15)
H1Db 0.590771 0.993270 1.071608 0.234*
H1Eb 0.552140 0.954639 0.871705 0.234*
H1Fb 0.503341 0.905839 1.056687 0.234*
N2b 0.502 (4) 0.5567 (14) 0.489 (4) 0.060 (5)
H2Ab 0.438078 0.582056 0.459337 0.090*
H2Bb 0.548755 0.578798 0.403637 0.090*
H2Cb 0.520246 0.579637 0.603819 0.090*
C2b 0.502 (4) 0.5567 (14) 0.489 (4) 0.060 (5)
H2Db 0.433056 0.584030 0.457575 0.090*
H2Eb 0.552195 0.580523 0.396614 0.090*
H2Fb 0.521989 0.581412 0.612604 0.090*

  1. aOccupancy: 0.5, bOccupancy: 0.25.

1 Source of material

K2PdCl4 (0.020 g, 0.061 mmol), K2Se4 (0.096 g, 0.24 mmol) and CH3NH3Cl (0.008 g, 0.12 mmol) were charged to a Pyrex tube with diameter of 9 mm under an argon atmosphere and about 0.5 mL methanol was added as a solvent. While the solvent was being frozen, the Pyrex tube was evacuated under vacuum and sealed with the use of a flame. The sealed tube was placed in an oven and heated at 80 °C for 3 days, then cooled to room temperature. Black chunky crystals were isolated by filtration and washed with methanol and diethyl ether several times. Crystals of (CH3NH3)2PdSe16 were obtained in 11 % yield, based on the Pd metal used.

2 Experimental details

H atoms were positioned geometrically and treated as riding, with N–H = 0.90 Å and C–H = 0.97  Å; U iso(H) = 1.2U eq(N) and 1.5U eq(C). H atoms of NH3 and CH3 were positioned to be staggered with respect to the shortest other bond to the atom to which NH3 and CH3 is attached.

3 Comment

The structures of Pd polyselenide anions have proven to be highly sensitive to the size and shape of their counterions [5, 6]. As one of Pd polyselenide compounds, A2PdSe16 (A = Rb, Cs) is featured to possess a 2D layered Pd polyselenide anion, [Pd(Se4)2] n 2n− with encapsulated Se8 rings [7], [8], [9]. Smaller alkali metal ion such as K+ has been found to be inappropriate for the A2PdSe16 (A = Rb, Cs) compound, instead, to stabilize K4[Pd(Se4)2][Pd(Se6)2] with two independent interpenetrating 3D frameworks of [Pd(Se x )2] n 2n− (x = 4, 6), K6[Pd(Se5)4] with a discrete anion of [Pd(Se5)4]6−, and K2[Pd(Se5)2] with a 1D polymeric [Pd(Se5)2]2− anion [5, 10, 11]. Compared to the alkali metal cations, organic ammonium cations have the advantage of being removed with less damage to the chalcogenidometallate anion framework by thermal treatment at lower temperatures. Among organic ammonium cations, the smallest cation, CH3NH+ 3 is known to be in possession of a close ionic radius to those of Cs+ and Rb+. Successful replacement of Cs+ or Rb+ with CH3NH+ 3 has already been demonstrated for the preparation of organic–inorganic hybrid perovskite material such as CH3NH3PbI3 [12, 13].

(CH3NH3)2PdSe16 was prepared by the methanothermal reaction of K2PdCl4, K2Se4 and CH3NH3Cl in a molar ratio of 1:4:2. In the case of A2PdSe16 (A = Rb, Cs), the mixture of A2Se (A = Na, Cs) and elemental Se served as the source of Se4 2- ligands and Se8 rings, but K2Se4 was used instead for the preparation of (CH3NH3)2PdSe16.

The structure of (CH3NH3)2PdSe16 is isostructural to those of A2PdSe16 (A = Rb, Cs), as all three compounds are crystallized in the same space group P 4 ‾ b 2 . As with the A2PdSe16 (A = Rb, Cs) analogues, the structure of [PdSe16]2− in (CH3NH3)2PdSe16 consists of an array of Se8 rings and [Pd(Se4)2]2n− n layers running through the ab plane. The unit cell volume of (CH3NH3)2PdSe16 is 1162.02(8) Å3, which is considerably larger than that of A2PdSe16 (A = Rb, Cs) with values of 1112.9(2) and 1118.5(3) Å3, respectively. The increase in the unit cell volume of (CH3NH3)2PdSe16, compared to A2PdSe16 (A = Rb, Cs), is attributed not only to the increase in the c parameter but also to changes in both the a and c unit cell parameters. The Pd–Se bond length is 2.4319(8) Å and the Se–Se bond lengths are in the range of 2.350(2)–2.361(2) Å, which are similar values to those of the A2PdSe16 (A = Rb, Cs) analogues. Bond angles around Se atoms are in the range of 103.86(6)–107.73(4)°, noticeably greater than those values, 102.56(3)–106.3(3)° and 103.15(14)–105.90(12)° of A2PdSe16 (A = Rb, Cs). To accommodate a slightly larger cation, Se–Se chains in the [Pd(Se4)2]2n− n networks and Se8 rings were expanded by increasing the bond angles around Se atoms. In the structure of 2D [Pd(Se4)2]2n− n anion, there is a little distortion from the ideal square geometry around Pd, with Se1–Pd–Se1 angles of 90.468(6)° and 169.63(6)° for cis and trans Se atoms, respectively. A similar distortion around Pd was observed in the A2PdSe16 (A = Rb, Cs) analogues to a nearly identical extent. In the Rb2PdSe16, the distance between Rb(2) and Pd was found to be 3.464 Å, suggesting an interaction between the electron density of the Pd d 2 z orbital and the Rb+ s orbital. As CH3NH+ 3 cations are unable to participate in the interaction observed between Pd and heavy alkali metal cations, such interaction is not considered indispensable for the stabilization of the [Pd(Se4)2] n 2n− frameworks. There are two crystallographically independent CH3NH3 + cations in the structure of (CH3NH3)2PdSe16. Both CH3NH3 + cations occupy the sites where Rb+ and Cs+ cations are located in the A2PdSe16 (A = Rb, Cs) analogues. The C and N atoms of CH3NH3 + exhibit complete disorder and the midpoints of C–N bonds in CH3NH3 + cations are positioned at the sites where the centres of Rb+ and Cs+ cations are positioned. For the one CH3NH3 + cation, C1 and N1 atoms are simultaneously sitting at a site with coordinates (0.5 + x, 0.5 + y, 0.5 − z) near to the special position (0.5, 0.5, 0.5) with 4-fold symmetry, generating four symmetrically equivalent sites which are assigned for disordered C and N atoms with 25 % occupancy. For the other CH3NH3 + cation, C2 and N2 atoms are also simultaneously sitting at a site with coordinates (0.5 + x, 1.0 − y, 1.0), generating two symmetrically equivalent sites, which are assigned for disordered C and N atoms with 50 % occupancy.

Thermal stability and decomposition behaviour of (CH3NH3)2PdSe16 was examined by the TGA experiments. TGA results show that there are three decomposition steps upon heating to 900 °C under N2 flow. Based on the amount of weight loss during the periods of decomposition steps, CH3NH3 + cations were lost in the first step and seleniums were lost in the following two steps to leave PdSe as a final residue. The first decomposition step begins at about 150 °C and ends at about 200 °C. The other two steps occur between 300 and 420 °C and between 460 and 870 °C, respectively. While decomposition of both Rb2PdSe16 and Cs2PdSe16 analogues did not occur up to around 300 °C, (CH3NH3)2PdSe16 can lose its organic cation below 200 °C, and start its second decomposition at about 300 °C. When crystals of (CH3NH3)2PdSe16 were calcined at 250 °C under N2 flow for a day, the shape and morphology of the crystals remained intact, but numerous holes formed on the surface. The XRD pattern of the calcined crystals indicates a loss of crystallinity in (CH3NH3)2PdSe16 with no prominent crystalline peaks.

Corresponding author: Kang-Woo Kim, Department of Chemistry & Research Institute for Natural Sciences, Incheon National University, Incheon 22012, Korea, E-mail:

Acknowledgements

This work was supported by the Incheon National University Research Grant in 2023.

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

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

  3. Research funding: Incheon National University Research Grant in 2023.

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Received: 2024-02-12
Accepted: 2024-03-20
Published Online: 2024-04-04
Published in Print: 2024-06-25

© 2024 the author(s), published by De Gruyter, Berlin/Boston

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

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https://doi.org/10.1515/ncrs-2024-0064
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of tris((Z)-2-hydroxy-N-((E)-pyridin-2-ylmethylene)benzohydrazonato-k2O,N)europium(III), C39H30N9O6Eu
  4. Crystal structure of (E)-3-(benzylideneamino)-2-phenylthiazolidin-4-one, C16H14N2OS
  5. The crystal structure of (E)-4-fluoro-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H15FN2O
  6. Crystal structure of (6-chloropyridin-3-yl)methyl 2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  7. Crystal structure of methyl 3-methoxy-4-(2-methoxy-2-oxoethoxy)benzoate, C12H14O6
  8. The crystal structure of bis[(4-methoxyphenyl)(picolinoyl)amido-κ2 N:N′]copper(II), C26H22CuN4O4
  9. The crystal structure of poly[di(μ2-aqua)-diaqua-bis(3-aminopyridine-4-carboxylate-κ2 O: O′)-tetra(μ2-3-aminopyridine-4-carboxylate-κ2 O: O′)-dineodymium(III), [Nd2(C6H5N2O2)6(H2O)4] n
  10. The crystal structure of t-butyl 7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoate, C28H34FNO4
  11. Crystal structure of catena-poly[(benzylamine-κ1 N)-(sorbato-κ1 O)-(μ2-sorbato-κ2 O,O′)-copper(II), C19H23CuNO4
  12. Crystal structure of (4-(2-chlorophenyl)-1H-pyrrol-3-yl)(ferrocenyl) methanone, C21H16ClFeNO
  13. The crystal structure of N-[4-(4-bromophenyl)-1,3-thiazol-2-yl]-3-(2-methylphenyl)-2-sulfanylprop-2-enamide hydrate, C19H17BrN2O2S2
  14. The crystal structure of N′-{5-[2-(2,6-dimethylphenoxy) acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide hydrate
  15. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C26H24O3
  16. Crystal structure of naphthalen-1-ylmethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C25H22O3
  17. Crystal structure of poly[diaqua- (μ4-5-(1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ5N:O,O’:O’’:O’’’)calcium(II), C10H9CaN3O6
  18. Crystal structure of (E)-N′-(4-((E)-3-(dimethylamino)acryloyl)-3-hydroxyphenyl)-N, N-dimethylformimidamide, C14H19N3O2
  19. Crystal structure of (E)-3-(dimethylamino)-1-(2-hydroxy-4,6-dimethoxyphenyl)prop-2-en-1-one, C13H17NO4
  20. Crystal structure of (2-chloropyridin-3-yl)methyl-2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  21. The crystal structure of diethyl 4-(3,4-dimethylphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, C21H27NO4
  22. Crystal structure of (8R,9S,10R,13S,14S,17S)-17-hydroxy-10,13-dimethyl-17-((4-(2-phenylpropyl)phenyl)ethynyl)-1,2,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-3H-cyclopenta[a]phenanthren-3-one, C36H42O2
  23. Synthesis and crystal structure of 4-(4-cyclopropylnaphthalen-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, C15H13N3S
  24. Crystal structure of catena-poly[aqua-(2,6-di-(2-pyridyl)-pyridine-κ3 N,N′, N″)(μ2-1,4-naphthalene dicarboxylato-κ2 O,O′)nickel(II)], C27H19NiN3O5
  25. Crystal structure of 3-(diphenylphosphoryl)-3-hydroxy-1-phenylpropan-1-one, C21H19O3P
  26. The crystal structure of R,S-{N-[(2-oxidonaphthalen-1-yl)methylidene]phenylglycinato}divinylsilicon, C23H19NO3Si
  27. The crystal structure of 1,2,4-tris(bromomethyl)benzene, C9H9Br3
  28. Crystal structure of chlorido-[4-(pyridin-2-yl)benzaldehyde-κ2 N,C]-(diethylamine-κ1 N)platinum(II), C16H18ClN2OPt
  29. Crystal structure of 3-(methoxycarbonyl)-1-(4-methoxyphenyl)-2,3,4,9- tetrahydro-1H-pyrido[3,4-b]indol-2-ium chloride hydrate, C40H48Cl2N4O9
  30. The crystal structure of 1-(2-chlorobenzyl)-3-(3-chlorophenyl)urea, C14H12Cl2N2O
  31. Hydrothermal synthesis and crystal structure of aqua-tris(4-acetamidobenzoato-κ2 O,O′)-(1,10-phenanthroline-κ2 N,N′)terbium(III) hydrate C39H36N5O11Tb
  32. The crystal structure of zwitterionic 3-aminoisonicotinic acid, C6H6N2O2
  33. The crystal structure of bis{[monoaqua-μ2-4-[(pyridine-4-carbonyl)-amino]-phthalato-κ3 N:O,O′-(2,2′-bipyridine κ2 N,N′)copper(II)]}decahydrate, C48H56N8O22Cu2
  34. Crystal structure of poly[μ10-4,4′-methylene-bis(oxy)benzoatodipotassium], C15H10K2O6
  35. The crystal structure of catena-poly[[tetraaqua[(μ2-1,4-di(4-methyl-1-imidazolyl)benzene] cobalt(II)]bis(formate)], C16H24CoN4O8
  36. The crystal structure of (E)-2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine, C10H11ClN4O2
  37. The crystal structure of (E)-1-(((2-amino-4,5-dimethylphenyl)iminio)methyl)naphthalen-2-olate, C19H18N2O
  38. Crystal structure of N-(acridin-9-yl)-2-(4-methylpiperidin-1-yl) acetamide monohydrate, C21H25N3O2
  39. The crystal structure of dichlorido-bis(3-methyl-3-imidazolium-1-ylpropionato-κ2 O,O′)-zinc(II), C14H20Cl2N4O4Zn
  40. The crystal structure of 2,8-diethyl-1,3,7,9-tetramethyl-4λ4,5λ4-spiro[dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinine-5,2′-naphtho[1,8-de][1,3,2]dioxaborinine], C25H29BN2O2
  41. The crystal structure of 5-tert-butyl-2-(5-tert-butyl-3-iodo-benzofuran-2-yl)-3-iodobenzofuran, C24H24I2O2
  42. Synthesis and crystal structure of methyl 2-{[4-(4-cyclopropyl-1-naphthyl)-4H-1,2,4-triazole-3-yl]thio} acetate, C18H17N3O2S
  43. The crystal structure of n-propylammonium bis(2,3-dimethylbutane-2,3-diolato)borate-boric acid (1/1), [C3H10N][C12H24BO4]·B(OH)3
  44. Crystal structure of methyl 1-(2-bromophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C19H17BrN2O2
  45. Crystal structure of (4-bromobenzyl)triphenylphosphonium bromide ethanol solvate, C52H48Br4OP2
  46. The crystal structure of unsymmetrical BOPHY C26H27BN4
  47. The crystal structure of Tb3B5O11(OH)2
  48. The crystal structure of (Z)-4-ethyl-2-((4-ethyl-3,5-dimethyl-1H-pyrrol-2-yl)methylene)-3,5-dimethyl-2H-pyrrol-1-ium 2,2'-spirobi[naphtho[1,8-de][1,3,2]dioxaborinin]-2-uide, C37H37BN2O4
  49. Crystal structure of bis(methylammonium) hexadecaselenidopalladate(II), (CH3NH3)2PdSe16
  50. The crystal structure of (2-diphenylphosphanylphenyl) 2-[7-(dimethylamino)-2-oxochromen-4-yl]acetate, C31H26NO4P
  51. Crystal structure of (E)-6-(4-ethylpiperazin-1-yl)-2-(3-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C23H25FN2O
  52. The structure of RUB-56, (C6H16N)8 [Si32O64(OH)8]·32 H2O, a hydrous layer silicate (2D-zeolite) that contains microporous levyne-type silicate layers
  53. Crystal structure of 4-amino-3,5-dibromobenzonitrile, C7H4Br2N2
  54. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-acetoxybenzoate, C21H18O4
  55. Single-crystal structure determination of Tm3B12O19(OH)7
  56. Crystal structure determination of NdB3.6O7
  57. The crystal structure of NdB6O8(OH)5·H3BO3
  58. Crystal structure of 2-(5-ethylpyridin-2-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C23H25NO3
  59. Crystal structure of N-(1-(3,4-dimethoxyphenyl)-2-methylpropyl)aniline, C18H23NO2
  60. Crystal structure of Ba6Cd12Mn4SiF48
  61. Synthesis and crystal structure of 5-fluoro-1-methyl-2-oxo-3-(2-oxochroman-4-yl)indolin-3-yl acetate, C20H16FNO5
  62. The crystal structure of 6-methacryloylbenzo[d][1,3]dioxol-5-yl 4-nitrobenzenesulfonate, C17H13NO8S
  63. Crystal structure of ethyl 2-(3-benzyl-4-oxo-3,4-dihydrophthalazin-1-yl)- 2,2-difluoroacetate, C19H16F2N2O3
  64. The crystal structure of tetrakis(μ 2-(1H-benzimidazole-2-methoxo-κ2 N,O:O:O)-(n-butanol-κO)-chlorido)-tetranickel(II), C48H68Cl4N8O8Ni4
  65. Synthesis and crystal structure of trans-tetraaqua-bis((1-((7-hydroxy-3-(4-methoxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carbonyl)oxy-κO)zinc(II)hexahydrate, C46H64N2O28S2Zn
  66. The crystal structure of 1-(4-carboxybutyl)-3-methyl-1H-imidazol-3-ium hexafluoridophosphate, C9H15F6N2O2P
  67. Crystal structure of 1-(4-chlorophenyl)-4-(2-furoyl)-3-phenyl-1H-pyrazol-5-ol, C20H13ClN2O3
  68. Crystal structure of dimethyl (R)-2-(3-(1-phenylethyl)thioureido)-[1,1′-biphenyl]-4,4′-dicarboxylate, C25H24N2O4S
  69. The crystal structure of 1-(3-carboxypropyl)-1H-imidazole-3-oxide, C7H10N2O3
  70. Synthesis and crystal structure of dimethyl 4,4′-(propane-1,3-diylbis(oxy))dibenzoate, C19H20O6
  71. Crystal structure of methyl-1-(p-tolyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C20H20N2O2
  72. The crystal structure of 1-(1-adamantan-1-yl)ethyl-3-(3-methoxyphenyl)thiourea, C20H28N2OS
  73. The crystal structure of N,N′-carbonylbis(2,6-difluorobenzamide), C15H8F4N2O3
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