The gyrobifastigium, not an uncommon shape in chemistry

Álvarez, Santiago

doi:10.1016/j.ccr.2017.03.012

Cited by 9 publications

(8 citation statements)

References 117 publications

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“…This is found as a coordination polyhedron of the Th site in the -ThSi 2 structure type, but has not been identified as such in the publications we are aware of. This elongated gyrobifastigium is distinct from the regular gyrobifastigium, which can be found in the same structure type (Alvarez, 2017), as depicted in Fig. 6.…”

Section: Shape Recognition and Classificationmentioning

confidence: 64%

Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures

Link,

Niewa

2023

J Appl Crystallogr

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Polynator is a Python program capable of identifying coordination polyhedra, molecules and other shapes in crystal structures and evaluating their distortions. Distortions are quantified by fitting the vertices of a model to a selected set of atoms. In contrast to earlier programs, models can be deformable, which allows them to represent a point group or a range of shapes such as the set of all trigonal prisms, rather than a specific, rigid shape such as the equilateral trigonal prism. The program comes with a graphical user interface and is freely available. This paper discusses its working principle and illustrates a number of applications.

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Section: Shape Recognition and Classificationmentioning

confidence: 64%

Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures

Link,

Niewa

2023

J Appl Crystallogr

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“…A competing geometrical arrangement for the {Pd 4 Y 4 } core and the predominant structural motif in many other tetrameric metal complexes is a distorted cube, cuboid, or square frustum . In this arrangement, the metal and chalcogen atoms alternate on the corners of a cuboid.…”

Section: Resultsmentioning

confidence: 99%

“…In [Pd 4 (L′ Se ) 4 ]• 4EtOH, the selenolato donors also contribute to the hydrogen bonding, whereas in [Pd 4 (L′ Te A competing geometrical arrangement for the {Pd 4 Y 4 } core and the predominant structural motif in many other tetrameric metal complexes is a distorted cube, cuboid, or square frustum. 70 In this arrangement, the metal and chalcogen atoms alternate on the corners of a cuboid. However, such arrangements are scarce for palladium and the gyrobifastigium dominates.…”

Section: ■ Introductionmentioning

confidence: 99%

Solvents and Ligands Matter: Structurally Variable Palladium and Nickel Clusters Assembled by Tridentate Selenium- and Tellurium-Containing Schiff Bases

2022

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Structurally variable organochalcogen clusters containing palladium(II) and nickel(II) ions were assembled starting from the salicylidene-substituted dichalcogenides (Y–C6H4–NCH–C6H4–OH)2 ({HLY}2, where Y = Se or Te), and palladium or nickel acetate. The tetrameric palladium clusters contain reduced chalcogenolato ligands {Y–C6H4–NCH–C6H4–O)}2– ({L′Y}2–, where Y = Se or Te), while the initially formed trimeric nickel clusters contain the intact, coordinated dichalcogenides. The palladium clusters have a general formula of [Pd4(L′Y)4] and represent the first examples of palladium complexes where both a gyrobifastigial and a pseudocubane arrangement of the central Pd4Y4 unit could be established with the same ligand, only depending on the solvents used for crystallization. Reduced density gradient (RDG) considerations based on density functional theory calculations suggest that the commonly referred to stabilizing chalcogen–palladium or palladium–palladium interactions for the two geometric arrangements are weak van der Waals contacts resulting from the contact of two nonbinding lone pairs. In the case of the pseudocubane arrangement, a repulsive steric effect, which is indicated by RDG analysis, is clearly supported by the cuplike distortions detected in the solid-state structure of the compound. In contrast to the reactions with palladium acetate, where the dichalcogenides were cleaved, during similar reactions with nickel acetate, the dichalcogenides remained intact and trimeric clusters of the composition [Ni-μ2-κ2-(Ni{κ5-LY}2)2-μ2-(OAc)2] (Y = Se, Te) were formed. Air oxidation and hydrolysis of [Ni-μ2-κ2-(Ni{κ5-LTe}2)2-μ2-(OAc)2] gave a rare example of a hexanuclear nickel cluster of the composition [Ni2-κ5-(Ni4-κ6-μ6-{(L′Te 2O3)(L′TeO2)2}2)-μ2-(H2O)2], which is composed of a well-defined framework consisting of tellurinic anhydride and tellurinate units, which proves the comparably higher oxidation sensitivity of the trinickel dichalcogenide complexes. Electron spray ionization mass spectrometry spectra of both the palladium and nickel clusters indicate that they show fluctional behavior with varying nuclearity in solution and can adopt multiple charge states especially because of the noninnocence of the chalcogen-based ligands. The complexes were fully characterized by spectroscopic methods, elemental analyses, and X-ray diffraction.

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“…The solid-state structure of 1 (Figure ) contains two pairs of Pd atoms, each pair held together by a combination of one metallophilic Pd···Pd contact (mean Pd–Pd 3.062 Å) and two secondary Cl→Sb interactions between the Cl and SbMe 2 Cl ligands on each Pd (mean Sb–Cl 2.947 Å). The two pairs are linked by a total of four Pd–Cl–Pd bridges (mean Pd–Cl 2.365 Å), forming a distorted gyrobifastigium Pd 4 Cl 4 core. Despite the pseudo- S 4 symmetry of the molecule (Figure , inset), each of the four PdCl 2 (SbMe 2 Cl) units is crystallographically independent.…”

Section: Results and Discussionmentioning

confidence: 99%

A Five-Membered PdSb_n Coordination Series

et al. 2018

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Five complexes of the general formula PdCl 2 (SbMe 2 Cl) n (n = 1-5) have been synthesised by combining [PdCl 2 (MeCN) 2 ] and SbMe 2 Cl in different molar ratios in toluene. Their solid-state structures have been determined by X-ray crystallography. The complexes display considerable structural diversity: [Pd 4 Cl 8 (SbMe 2 Cl) 4 ] (1, n = 1) is a chloride bridged tetramer, [Pd 2 Cl 4 (SbMe 2 Cl) 4 ] (2, n = 2) is a dimer, [PdCl(SbMe 2 Cl) 2 (SbMe 2 Cl 2)] (3, n = 3) is a supramolecular polymer, [Pd 2 (SbMe 2 Cl) 8 ]Cl 4 (4, n = 4) is a loosely associated dimer and [Pd(SbMe 2 Cl) 5 ]Cl 2 (5, n = 5) is a monomer with square pyramidal PdSb 5 coordination geometry. Each structure contains secondary interactions between coordinated Sb centres and chloride ligands or anions, resulting in five-coordinate Sb in all cases with a range of Sb•••Cl bond lengths. The electronic structures of these complexes have been investigated using DFT methods including NBO and Pipek-Mezey localised orbital methods in order to interrogate both the Sb-Pd and secondary Sb•••Cl bonding.

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The gyrobifastigium, not an uncommon shape in chemistry

Cited by 9 publications

References 117 publications

Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures

Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures

Solvents and Ligands Matter: Structurally Variable Palladium and Nickel Clusters Assembled by Tridentate Selenium- and Tellurium-Containing Schiff Bases

A Five-Membered PdSb_n Coordination Series

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The gyrobifastigium, not an uncommon shape in chemistry

Cited by 9 publications

References 117 publications

Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures

Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures

Solvents and Ligands Matter: Structurally Variable Palladium and Nickel Clusters Assembled by Tridentate Selenium- and Tellurium-Containing Schiff Bases

A Five-Membered PdSbn Coordination Series

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A Five-Membered PdSb_n Coordination Series