scholarly journals Harnessing complexity in molecular self-assembly using computer simulations

2018 ◽  
Vol 20 (10) ◽  
pp. 6767-6776 ◽  
Author(s):  
Xiangze Zeng ◽  
Lizhe Zhu ◽  
Xiaoyan Zheng ◽  
Marco Cecchini ◽  
Xuhui Huang
Keyword(s):  
Computer Simulations ◽  
Self Assembly ◽  
Atomic Resolution ◽  
Computational Studies ◽  
Powerful Strategy

Computer simulations offer a powerful strategy to explore self-assembly with atomic resolution. Here, we review recent computational studies focusing on both thermodynamic and kinetic aspects.

Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

2020 ◽  
Vol 17 ◽  
Author(s):  
Ibrahim Yagiz Akbayrak ◽  
Sule Irem Caglayan ◽  
Zilan Ozcan ◽  
Vladimir N. Uversky ◽  
Orkid Coskuner-Weber
Keyword(s):  
Neurodegenerative Diseases ◽  
Computer Simulations ◽  
Conformational Changes ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Computational Studies ◽  
Accurate Data ◽  
Aggregation Propensity ◽  
Intrinsically Disordered ◽  
Future Developments

: Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations – including our own – revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.

Self-assembly of conformationally flexible molecules under 2D confinement: structural analysis from computer simulations

2018 ◽  
Vol 54 (63) ◽  
pp. 8749-8752 ◽  
Author(s):  
Damian Nieckarz ◽  
Paweł Szabelski
Keyword(s):  
Monte Carlo ◽  
Structural Analysis ◽  
Monte Carlo Simulations ◽  
Computer Simulations ◽  
Self Assembly ◽  
Flexible Molecules

Monte Carlo simulations reveal the role of surface conformers in self-assembly on crystalline supports.

Computational studies of shape rectification in directed self-assembly

2014 ◽  
Author(s):  
Tatsuhiro Iwama ◽  
Nabil Laachi ◽  
Kris T. Delaney ◽  
Bongkeun Kim ◽  
Glenn H. Fredrickson
Keyword(s):  
Self Assembly ◽  
Computational Studies

Spectroscopic and computational studies on self-assembly complexes of bis(pyrrol-2- ylmethyleneamine) ligands linked by alkyl spacers with Cu(II)

2007 ◽  
Vol 38 (5) ◽  
pp. 483-495 ◽  
Author(s):  
Wei Li ◽  
Yibo Wang ◽  
Lanying Yang ◽  
Adriana Szeghalmi ◽  
Yong Ye ◽  
...  
Keyword(s):  
Self Assembly ◽  
Computational Studies

scholarly journals Self Assembly of Disordered Folded Multiphase Proteins by Computer Simulations

2016 ◽  
Vol 110 (3) ◽  
pp. 323a
Author(s):  
Eduardo R. Cruz-Chu ◽  
Konstantinos Gkagkas ◽  
Frauke Graeter
Keyword(s):  
Computer Simulations ◽  
Self Assembly

Self-assembly of colloidal micelles in microfluidic channels

Soft Matter ◽  
2017 ◽  
Vol 13 (1) ◽  
pp. 222-229 ◽  
Author(s):  
Arash Nikoubashman
Keyword(s):  
Computer Simulations ◽  
Poiseuille Flow ◽  
Self Assembly ◽  
The Self ◽  
Microfluidic Channels ◽  
Distinct Cluster ◽  
Channel Center

The self-assembly of amphiphilic Janus colloids in microfluidic channels under Poiseuille flow is studied using computer simulations. The aggregates grow in the weakly sheared channel center, whereas a distinct cluster breakup occurs in strongly sheared channel regions.

Synthesis, Characterization, Self-Assembly, Gelation, Morphology and Computational Studies of Alkynylgold(III) Complexes of 2,6-Bis(benzimidazol-2′-yl)pyridine Derivatives

2014 ◽  
Vol 20 (32) ◽  
pp. 9930-9939 ◽  
Author(s):  
King-Chin Yim ◽  
Elizabeth Suk-Hang Lam ◽  
Keith Man-Chung Wong ◽  
Vonika Ka-Man Au ◽  
Chi-Chiu Ko ◽  
...  
Keyword(s):  
Self Assembly ◽  
Computational Studies ◽  
Pyridine Derivatives

scholarly journals Pt(II)-Coordinated Tricomponent Supramolecular Assemblies of Tetrapyridyl Porphyrin and Dicarboxylate Ligands: Are They 2D Bow Ties or 3D Prisms?

2021 ◽  
Author(s):  
Paola Benavides ◽  
Monica A. Gordillo ◽  
Ashok Yadav ◽  
M. Andrey Joaqui-Joaqui ◽  
Sourav Saha
Keyword(s):  
Self Assembly ◽  
Nmr Spectra ◽  
Structural Complexity ◽  
2D Nmr ◽  
Coordination Complexes ◽  
The Self ◽  
Computational Studies ◽  
X Ray ◽  
Supramolecular Coordination ◽  
Bow Tie

Thermodynamically favored heteroleptic coordination of one aza- and another oxo-coordinating ligand with Pt(II) ions yield tricomponent supramolecular coordination complexes (SCCs) that have much greater structural complexity and functional diversity than the traditional bicomponent SCCs containing only one of the ligands. Herein, we demonstrate that heteroleptic coordination of tetrapyridyl porphyrins (M¢TPP, M¢ = Zn or H2) and various dicarboxylate ligands (XDC) having different lengths and rigidity with cis- (Et3P)2PtII corners actually yields bow tie (⋈)-shaped tricomponent [{cis-(Et3P)2Pt}4(M¢TPP)(XDC)2] 4+ complexes featuring a M¢TPP core and two parallel XDC linkers held together by four heteroligated PtII(N,O) corners. Although previous reports have claimed that the self-assembly of these three components produced tetragonal prisms having two cofacial M¢TPP planes connected by four XDC linkers via eight PtII(N,O) corners, our extensive 1 H, 31P, and 2D NMR, ESI-MS, X-ray crystallographic, and computational studies unequivocally demonstrated that in reality, no such prism was formed because instead of connecting two cofacial M¢TPP ligands, the XDC linkers actually bridged two adjacent pyridyl termini of an M¢TPP ligand via shared PtII(N,O) corners, forming bow tie complexes. In addition to direct crystallographic evidence, the NMR spectra of these complexes revealed that the M¢TPP ligands contained two distinct pyrrole protons (4 each)—those located inside the triangles were shielded by and coupled to adjacent XDC linkers, whereas the exposed ones were not—an unmistakable sign of their bow tie structures. Thus, this work not only unveiled novel bow tie-shaped coordination complexes, but also accurately defined the actual structures and compositions of M¢TPP-based tricomponent SCCs.

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