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Stereoisomerism, crystal structures, and dynamics of belt-shaped cyclonaphthylenes.

ABSTRACT: The chemistry of a belt-shaped cyclic array of aromatic panels, a so-called "nanohoop," has increasingly attracted much interest, partly because it serves as a segmental model of single-wall carbon nanotubes with curved sp(2)-carbon networks. Although the unique molecular structure of nanohoops is expected to deepen our understanding in curved ?-systems, its structural chemistry is still in its infancy despite structural variants rapidly accumulated over the past several years. For instance, structural characteristics that endow the belt shapes with rigidity, an important structural feature relevant to carbon nanotubes, have not been clarified to date. We herein report the synthesis and structures of a series of belt-shaped cyclonaphthylenes. Random synthesis methods using three precursor units with different numbers of naphthylene panels allowed us to prepare 6 congeners consisting of 6 to 11 naphthylene panels, and relationships between the rigidity and the panel numbers, i.e., molecular structures, were investigated. Fundamental yet complicated stereoisomerism in the belt-shaped structures was disclosed by mathematical methods, and dynamics in the panel rotation was revealed by dynamic NMR studies with the aid of theoretical calculations.

SUBMITTER: Sun Z

PROVIDER: S-EPMC4961134 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Stereoisomerism, crystal structures, and dynamics of belt-shaped cyclonaphthylenes.

Sun Zhe Z Suenaga Takuya T Sarkar Parantap P Sato Sota S Kotani Motoko M Isobe Hiroyuki H

Proceedings of the National Academy of Sciences of the United States of America 20160629 29

The chemistry of a belt-shaped cyclic array of aromatic panels, a so-called "nanohoop," has increasingly attracted much interest, partly because it serves as a segmental model of single-wall carbon nanotubes with curved sp(2)-carbon networks. Although the unique molecular structure of nanohoops is expected to deepen our understanding in curved π-systems, its structural chemistry is still in its infancy despite structural variants rapidly accumulated over the past several years. For instance, str ...[more]

PMID: 27357686

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Project description:The function of proteins is influenced not only by the atomic structure but also by the detailed structure of the solvent surrounding it. Computational studies of protein structure also critically depend on the water structure around the protein. Herein we compare the water structure obtained from molecular dynamics (MD) simulations of galectin-3 in complex with two ligands to crystallographic water molecules observed in the corresponding crystal structures. We computed MD trajectories both in a water box, which mimics a protein in solution, and in a crystallographic unit cell, which mimics a protein in a crystal. The calculations were compared to crystal structures obtained at both cryogenic and room temperature. Two types of analyses of the MD simulations were performed. First, the positions of the crystallographic water molecules were compared to peaks in the MD density after alignment of the protein in each snapshot. The results of this analysis indicate that all simulations reproduce the crystallographic water structure rather poorly. However, if we define the crystallographic water sites based on their distances to nearby protein atoms and follow these sites throughout the simulations, the MD simulations reproduce the crystallographic water sites much better. This shows that the failure of MD simulations to reproduce the water structure around proteins in crystal structures observed both in this and previous studies is caused by the problem of identifying water sites for a flexible and dynamic protein (traditionally done by overlaying the structures). Our local clustering approach solves the problem and shows that the MD simulations reasonably reproduce the water structure observed in crystals. Furthermore, analysis of the crystal MD simulations indicates a few water molecules that are close to unmodeled electron density peaks in the crystal structures, suggesting that crystal MD could be used as a complementary tool for identifying and modelling water in protein crystallography.

Dataset Information

Stereoisomerism, crystal structures, and dynamics of belt-shaped cyclonaphthylenes.

Publications

Stereoisomerism, crystal structures, and dynamics of belt-shaped cyclonaphthylenes.

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