scholarly journals A class of organic cages featuring twin cavities

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhenyu Yang ◽  
Chunyang Yu ◽  
Junjie Ding ◽  
Lihua Chen ◽  
Huiyu Liu ◽  
...  

AbstractA variety of organic cages with different geometries have been developed during the last decade, most of them exhibiting a single cavity. In contrast, the number of organic cages featuring a pair of cavities remains scarce. These structures may pave the way towards novel porous materials with emergent properties and functions.We herein report on rational design of a three-dimensional hexaformyl precursor 1, which exhibits two types of conformers, i.e. Conformer-1 and -2, with different cleft positions and sizes. Aided by molecular dynamics simulations, we select two triamino conformation capturers (denoted CC). Small-sized CC-1 selectively capture Conformer-1 by matching its cleft size, while the large-sized CC-2 is able to match and capture both conformers. This strategy allows the formation of three compounds with twin cavities, which we coin diphane. The self-assembly of diphane units results in superstructures with tunable proton conductivity, which reaches up to 1.37×10-5 S cm-1.

Soft Matter ◽  
2016 ◽  
Vol 12 (7) ◽  
pp. 2066-2075 ◽  
Author(s):  
Arzu B. Yener ◽  
Sabine H. L. Klapp

Using molecular dynamics simulations we investigate the self-assembly behaviour of colloidal particles with laterally shifted dipoles.


Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...


Soft Matter ◽  
2018 ◽  
Vol 14 (23) ◽  
pp. 4762-4771 ◽  
Author(s):  
Denis Svechkarev ◽  
Alexander Kyrychenko ◽  
William M. Payne ◽  
Aaron M. Mohs

Side substituents on the hyaluronic acid backbone determine the morphology and hydration of the HA-derived nanoparticles hydrophobic domains.


2012 ◽  
Vol 1407 ◽  
Author(s):  
Andrew L. J. Pang ◽  
Viacheslav Sorkin ◽  
Yong-Wei Zhang

ABSTRACTWe studied the self-assembly mechanisms of Graphene Nanoribbon (GNR) with unsaturated edges and demonstrated the ability of GNR to self-assemble into novel stable structures. We proposed three mechanisms which dictate the self-assembly evolution of GNR with unsaturated edges. Using the Adaptive Intermolecular Reactive Empirical Bond-Order (AIREBO) potential, we performed molecular dynamics simulations on initially-planar GNRs with unsaturated edges. The simulation results showed that the self-assembly mechanisms and final conformations of the GNRs correlate well with the proposed GNR self-assembly mechanisms. Furthermore, the simulations also showed the ability of a narrow GNR to self-assemble into various nanostructures, such as tapered graphene nano-rings and graphene nanoscrolls with an embedded nanotube.


Soft Matter ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. 680-691 ◽  
Author(s):  
Anna Akinshina ◽  
Martin Walker ◽  
Mark R. Wilson ◽  
Gordon J. T. Tiddy ◽  
Andrew J. Masters ◽  
...  

Molecular dynamics simulations of non-ionic triphenylene-based chromonic liquid crystal molecules demonstrate self-assembly of the molecules into stacks and “quasi-isodesmic” aggregation behaviour.


2021 ◽  
Vol 22 (7) ◽  
pp. 3624
Author(s):  
Sutapa Dutta ◽  
Stefano Corni ◽  
Giorgia Brancolini

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.


2018 ◽  
Vol 20 (15) ◽  
pp. 10030-10037
Author(s):  
Xiangze Zeng ◽  
Zhan-Wei Li ◽  
Xiaoyan Zheng ◽  
Lizhe Zhu ◽  
Zhao-Yan Sun ◽  
...  

By constructing kinetic network models from extensive coarse-grained molecular dynamics simulations, we elucidated the formation mechanism of the dodecahedral cage and further improved the productivity of the dodecahedral cage through the rational design of the patch arrangement of patchy particles.


2015 ◽  
Vol 108 (2) ◽  
pp. 172a
Author(s):  
Valeria Marquez-Miranda ◽  
Iingrid Araya ◽  
Maria Belen Camarada ◽  
Lars Ratjen ◽  
Maria Carolina Otero ◽  
...  

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