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Integrative Assembly of Heteroleptic Tetrahedra Controlled by Backbone Steric Bulk.

ABSTRACT: A bent fluorenone-based dipyridyl ligand L^A reacts with Pd^II cations to a solvent-dependent dynamic library of [Pd_nL_2n] assemblies, constituted by a [Pd₃L^A₆] ring and a [Pd₄L^A₈] tetrahedron as major components, and a [Pd₆L^A₁₂] octahedron as minor component. Introduction of backbone steric hindrance in ligand L^B allows exclusive formation of the [Pd₆L^B₁₂] octahedron. Combining equimolar amounts of both ligands results in integrative self-sorting to give an unprecedented [Pd₄L^A₄L^B₄] heteroleptic tetrahedron. Key to the non-statistical assembly outcome is exploiting the structural peculiarity of the [Pd₄L₈] tetrahedral topology, where the four lean ligands occupy two doubly bridged edges and the bulky ligands span the four remaining, singly bridged edges. Hence, the system finds a compromise between the entropic drive to form an assembly smaller than the octahedron and the enthalpic prohibition of pairing two bulky ligands on the same edge of the triangular ring. The emission of luminescent L^A is maintained in both homoleptic [Pd₃L^A₆] and heteroleptic [Pd₄L^A₄L^B₄].

SUBMITTER: Tessarolo J

PROVIDER: S-EPMC8154538 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Integrative Assembly of Heteroleptic Tetrahedra Controlled by Backbone Steric Bulk.

Tessarolo Jacopo J Lee Haeri H Sakuda Eri E Umakoshi Keisuke K Clever Guido H GH

Journal of the American Chemical Society 20210426 17

A bent fluorenone-based dipyridyl ligand LA reacts with PdII cations to a solvent-dependent dynamic library of [PdnL2n] assemblies, constituted by a [Pd3LA6] ring and a [Pd4LA8] tetrahedron as major components, and a [Pd6LA12] octahedron as minor component. Introduction of backbone steric hindrance in ligand LB allows exclusive fo ...[more]

PMID: 33900773

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Project description:Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (>or= 0.4 A overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations. Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%). For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is available from http://kinemage.biochem.duke.edu .

Dataset Information

Integrative Assembly of Heteroleptic Tetrahedra Controlled by Backbone Steric Bulk.

Publications

Integrative Assembly of Heteroleptic Tetrahedra Controlled by Backbone Steric Bulk.

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