Symmetrical Tris(4,6-diamino-5-methylene-2-pyrimidones): New Building Blocks for Self-Assembly of Hollow Spherical Supramolecules Locked by Hydrogen Bonds

1996 ◽  
Vol 61 (10) ◽  
pp. 1464-1472 ◽  
Author(s):  
Daniel Alexander ◽  
Petr Holý ◽  
Pavel Fiedler ◽  
Zdeněk Havlas ◽  
Jiří Závada
Keyword(s):  
Molecular Modeling ◽  
Hydrogen Bonds ◽  
Gas Phase ◽  
Self Assembly ◽  
Building Blocks ◽  
The Self ◽  
Circumstantial Evidence ◽  
Self Assembling ◽  
Molecular Modeling Study ◽  
Modeling Study

Concise synthesis of the tris(pyrimidones) 1a,b is described. Molecular modeling study demonstrated that both the prepared models 1a,b are capable of self-assembling under formation of spherical dimers locked by 18 hydrogen bonds. Extreme insolubility in all common solvents precluded investigation of the self-assembly in solution. Circumstantial evidence in favor of the self-assembly has been provided in the solid and gas phase.

Molecular modeling study concerning the self-assembly capacity of some photosensitive amphiphilic polysiloxanes

2020 ◽  
Vol 300 ◽  
pp. 112298 ◽  
Author(s):  
Elena-Luiza Epure ◽  
Tudor Vasiliu ◽  
Nicolae Hurduc ◽  
Andrei Neamțu
Keyword(s):  
Molecular Modeling ◽  
Self Assembly ◽  
The Self ◽  
Molecular Modeling Study ◽  
Modeling Study

Understanding the properties of dithienylethenes functionalized for supramolecular self-assembly: a molecular modeling study

2020 ◽  
Vol 22 (13) ◽  
pp. 6942-6952 ◽  
Author(s):  
Laura Le Bras ◽  
Roxanne Berthin ◽  
Ismaïl Hamdi ◽  
Maroua Louati ◽  
Stéphane Aloïse ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Dft Calculations ◽  
Self Assembly ◽  
Supramolecular Assemblies ◽  
Molecular Modeling Study ◽  
Td Dft ◽  
Modeling Study

The behaviour of light-responsive supramolecular assemblies is rationalized with the help of molecular dynamics and TD-DFT calculations.

Thermodynamic insights into the self-assembly of capped nanoparticles using molecular dynamic simulations

2015 ◽  
Vol 17 (5) ◽  
pp. 3820-3831 ◽  
Author(s):  
André F. de Moura ◽  
Kalil Bernardino ◽  
Cleocir J. Dalmaschio ◽  
Edson R. Leite ◽  
Nicholas A. Kotov
Keyword(s):  
Molecular Modeling ◽  
Molecular Dynamic ◽  
Self Assembly ◽  
The Self ◽  
Molecular Dynamic Simulations ◽  
Research Issue ◽  
Dynamic Simulations ◽  
Self Assembling ◽  
Challenging Research

Although the molecular modeling of self-assembling processes stands as a challenging research issue, there have been a number of breakthroughs in recent years.

Study on the Interaction between a Self-Assembling Peptide and Paclitaxe

2013 ◽  
Vol 706-708 ◽  
pp. 284-291 ◽  
Author(s):  
Chen Hui ◽  
Zhi Hua Xing ◽  
Hong Chang Yu ◽  
Li Ping Ruan
Keyword(s):  
Molecular Modeling ◽  
Hydrogen Bonds ◽  
Fluorescence Spectroscopy ◽  
Thermodynamic Analysis ◽  
Fluorescence Intensity ◽  
Binding Constants ◽  
The Self ◽  
Remarkable Change ◽  
Binding Force ◽  
Self Assembling

In this work, the interaction between paclitaxel (PTX) and a designed peptide was investigated through AFM, CD and fluorescence spectroscopy. AFM images showed that the morphology of the self-assembling peptide with PTX addition had a remarkable change. Fluorescence data illustrated that PTX enhanced the fluorescence intensity of P1. The binding constants for the interaction between PTX and P1 in 25°Cand 35°Cwere 6.38×105 L/mol and 2.27×104 L/mol respectively. Moreover, thermodynamic analysis implied the main binding force between P1 and PTX was hydrogen bonds and vander Waals forces. CD results indicated that PTX caused an increase of unordered structure. Finally, a molecular modeling was proposed based on the research. The study will provide a reliable proof for designed peptide as a paclitaxel carrier for further research.

scholarly journals Interaction of a new antiviral and antitumor photosensitizer hypericin with human serum albumin: molecular modeling study

2002 ◽  
Vol 4 (2) ◽  
pp. 45-50 ◽  
Author(s):  
Jozef Hritz ◽  
Jozef Ulicny ◽  
Pavol Miskovsky
Keyword(s):  
Molecular Modeling ◽  
Human Serum Albumin ◽  
Hydrogen Bonds ◽  
Serum Albumin ◽  
Human Serum ◽  
Carbonyl Group ◽  
Structural Model ◽  
Hydroxyl Group ◽  
Molecular Modeling Study ◽  
Modeling Study

Molecular modeling has been employed to study the interaction of hypericin (Hyp) with human serum albumin (HSA). The structural model for Hyp/HSA complex is presented. Our results indicate that Hyp is bound in II A subdomain of HSA close to the tryptophan 214 (Trp214) (distance 5.12 Å between the centers of masses). In the presented model the carbonyl group of Hyp is hydrogen bonded to the Asn458. Another two candidates for hydrogen bonds have been identified between the bay-region hydroxyl group of Hyp and the carbonyl group of the Trp214 peptidic link and between the peri-region hydroxyl group of Hyp and Asn458 carbonyl group.

scholarly journals Peptide-Directed Supramolecular Self-Assembly of N-Substituted Perylene Imides

2021 ◽  
Author(s):  
◽  
Galen Eakins
Keyword(s):  
Organic Electronics ◽  
Self Assembly ◽  
Electronic Device ◽  
Functional Materials ◽  
Building Blocks ◽  
The Self ◽  
Structure Property ◽  
Hybrid Functional ◽  
Self Assembling ◽  
Natural Peptide

<p>Synthetic peptides offer enormous potential to encode the assembly of molecular electronic components, provided that the complex range of interactions is distilled into simple design rules. Herein is reported a spectroscopic investigation of aggregation in an extensive series of peptide-perylene imide conjugates designed to interrogate the effect of structural variations. Throughout the course of this study, the self-assembly and photophysical properties of the compounds are explored to better understand the behavior and application of these materials. Three principal avenues of inquiry are applied: (1) the evaluation of structure-property relationships from a thermodynamic perspective, (2) the examination of peptide chiral effects upon properties and self-assembly, and (3) an application of the understanding gained from rationally designed systems to effectively utilize naturally optimized peptides in bio-organic electronics.  By fitting different contributions to temperature-dependent optical absorption spectra, this study quantifies both the thermodynamics and the nature of aggregation for peptides with incrementally varying hydrophobicity, charge density, length, amphiphilic substitution with a hexyl chain, and stereocenter inversion. Coarse effects like hydrophobicity and hexyl substitution are seen to have the greatest impact on binding thermodynamics, which are evaluated separately as enthalpic and entropic contributions. Moreover, significant peptide packing effects are resolved via stereocenter inversion studies, particularly when examining the nature of aggregates formed and the coupling between π-electronic orbitals.  Peptide chirality overall is seen to influence the self-assembly of the perylene imide cores into chiral nanofibers, and peptide stereogenic positions, stereochemical configurations, amphiphilic substitution, and perylene core modification are evaluated with respect to chiral assembly. Stereocenters in peptide residue positions proximal to the perylene core (1-5 units) are seen to impart helical chirality to the perylene core, while stereocenters in more distal residue positions do not exert a chiral influence. Diastereomers involving stereocenter inversions within the proximal residues consequently manifest spectroscopically as pseudo-enantiomers. Increased side-chain steric demand in the proximal positions gives a similar chiral influence but exhibits diminished Cotton Effect intensity with additional longer wavelength features attributed to interchain excimers. Amphiphilic substitution of a peptide with an alkyl chain disrupts chiral self-assembly, while an amphiphilic structure achieved through the modification of the perylene imide core with a bisester moiety prompts strongly exciton-coupled, chiral, solvent-responsive self-assembly into long nanofilaments.  Informed by rationally designed sequences, and capitalizing upon the optimization seen in many natural systems, specific peptide sequences designed by inspection of protein-protein interfaces have been identified and used as tectons in hybrid functional materials. An 8-mer peptide derived from an interface of the peroxiredoxin family of self-assembling proteins is exploited to encode the assembly of perylene imide-based organic semiconductor building blocks. By augmenting the peptide with additional functionality to trigger aggregation and manipulate the directionality of peptide-semiconductor coupling, a series of hybrid materials based on the natural peptide interface is presented. Using spectroscopic probes, the mode of self-assembly and the electronic coupling between neighboring perylene units is shown to be strongly affected by the number of peptides attached, and by their backbone directionality. The disubstituted material with peptides extending in the N-C direction away from the perylene core exhibits strong coupling and long-range order, which are both attractive properties for electronic device applications. A bio-organic field-effect transistor is fabricated using this material, highlighting the possibilities of exploiting natural peptide tectons to encode self-assembly in other functional materials and devices.  These results advance the development of a quantitative framework for establishing structure-function relationships that will underpin the design of self-assembling peptide electronic materials. The results further advance a model for adapting natural peptide sequences resident in β-continuous interfaces as tectons for bio-organic electronics.</p>

scholarly journals Tuning the Hydrophobicity of a Hydrogel by Self-assembly of Polymer Cross-linkers

2019 ◽  
Author(s):  
Hee-Jin Kim ◽  
Sungwoo Cho ◽  
Seung Joo Oh ◽  
Sung Gyu Shin ◽  
Hee Wook Ryu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Fluorescence Analysis ◽  
Building Blocks ◽  
The Self ◽  
Cell Therapies ◽  
Self Assembling ◽  
Hydrophobically Modified ◽  
3D Matrix ◽  
Cellular Microenvironments ◽  
Irregular Arrangement

Hydrogels incorporated with hydrophobic motifs have received considerable attention to recapitulate the cellular microenvironments, specifically for the bio-mineralization of a 3D matrix. Introduction of hydrophobic motifs into a hydrogel often results in irregular arrangement of the motifs, and further phase separation of hydrophobic domains, but limited efforts have been made to resolve this challenge in the hydrophobically-modified hydrogel. Therefore, this study presents an advanced integrative strategy to incorporate hydrophobic domains regularly in a hydrogel by self-assembling of polymer cross-linkers, building blocks of a hydrogel. Self-assemblies between polymer cross-linkers were examined as micro-domains to incorporate hydrophobic motifs in a hydrogel. The self-assembled structures in a pre-gelled solution were confirmed with the fluorescence analysis and the hydrophobicity of a hydrogel could be tuned by incorporating the motifs in a controlled manner. Overall, the results of this study would greatly serve to tuning performance of a wide array of hydrophobically-modified hydrogels in drug delivery, cell therapies and tissue engineering.

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