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Interactions between tetrathiafulvalene units in dimeric structures - the influence of cyclic cores.

ABSTRACT: A selection of cyclic and acyclic acetylenic scaffolds bearing two tetrathiafulvalene (TTF) units was prepared by different metal-catalyzed coupling reactions. The bridge separating the two TTF units was systematically changed from linearly conjugated ethyne, butadiyne and tetraethynylethene (trans-substituted) units to a cross-conjugated tetraethynylethene unit, placed in either acyclic or cyclic arrangements. The cyclic structures correspond to so-called radiaannulenes having both endo- and exocyclic double bonds. Interactions between two redox-active TTF units in these molecules were investigated by cyclic voltammetry, UV-vis-NIR and EPR absorption spectroscopical methods of the electrochemically generated oxidized species. The electron-accepting properties of the acetylenic cores were also investigated electrochemically.

SUBMITTER: Jiang H

PROVIDER: S-EPMC4464444 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Interactions between tetrathiafulvalene units in dimeric structures - the influence of cyclic cores.

Jiang Huixin H Mazzanti Virginia V Parker Christian R CR Broman Søren Lindbæk SL Wallberg Jens Heide JH Lušpai Karol K Brincko Adam A Kjaergaard Henrik G HG Kadziola Anders A Rapta Peter P Hammerich Ole O Nielsen Mogens Brøndsted MB

Beilstein journal of organic chemistry 20150602

A selection of cyclic and acyclic acetylenic scaffolds bearing two tetrathiafulvalene (TTF) units was prepared by different metal-catalyzed coupling reactions. The bridge separating the two TTF units was systematically changed from linearly conjugated ethyne, butadiyne and tetraethynylethene (trans-substituted) units to a cross-conjugated tetraethynylethene unit, placed in either acyclic or cyclic arrangements. The cyclic structures correspond to so-called radiaannulenes having both endo- and ex ...[more]

PMID: 26124895

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Project description:We have designed an automated procedure to cut a protein into compact hydrophobic folding units. The hydrophobic units are large enough to contain tertiary non-local interactions, reflecting potential nucleation sites during protein folding. The quality of a hydrophobic folding unit is evaluated by four criteria. The first two correspond to visual characterization of a structural domain, namely, compactness and extent of isolation. We use the definition of Zehfus and Rose (Zehfus MH, Rose GD, 1986, Biochemistry 25:35-340) to calculate the compactness of a cut protein unit. The isolation of a unit is based on the solvent accessible surface area (ASA) originally buried in the interior and exposed to the solvent after cutting. The third quantity is the hydrophobicity, equivalent to the fraction of the buried non-polar ASA with respect to the total non-polar ASA. The last criterion in the evaluation of a folding unit is the number of segments it includes. To conform with the rationale of obtaining hydrophobic units, which may relate to early folding events, the hydrophobic interactions are implicitly and explicitly applied in their generation and assessment. We follow Holm and Sander (Holm L, Sander C, 1994, Proteins 19:256-268) to reduce the multiple cutting-point problem to a one-dimensional search for all reasonable trial cuts. However, as here we focus on the hydrophobic cores, the contact matrix used to obtain the first non-trivial eigenvector contains only hydrophobic contracts, rather than all, hydrophobic and hydrophilic, interactions. This dataset of hydrophobic folding units, derived from structurally dissimilar single chain monomers, is particularly useful for investigations of the mechanism of protein folding. For cases where there are kinetic data, the one or more hydrophobic folding units generated for a protein correlate with the two or with the three-state folding process observed. We carry out extensive amino acid sequence order independent structural comparisons to generate a structurally non-redundant set of hydrophobic folding units for fold recognition and for statistical purposes.

Dataset Information

Interactions between tetrathiafulvalene units in dimeric structures - the influence of cyclic cores.

Publications

Interactions between tetrathiafulvalene units in dimeric structures - the influence of cyclic cores.

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