On-surface self-assembly of tetratopic molecular building blocks

2018 ◽  
Vol 20 (36) ◽  
pp. 23363-23377 ◽  
Author(s):  
Damian Nieckarz ◽  
Wojciech Rżysko ◽  
Paweł Szabelski
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Self Assembly ◽  
Building Blocks ◽  
Molecular Building Blocks

Monte Carlo simulations predict the surface-confined self-assembly of tetratopic building blocks into diverse 2D superstructures.

scholarly journals Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

2020 ◽  
Author(s):  
Zhenpeng Yao ◽  
Benjamin Sanchez-Lengeling ◽  
N. Scott Bobbitt ◽  
Benjamin J. Bucior ◽  
Sai Govind Hari Kumar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Metal Organic Framework ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Generative Models ◽  
Combinatorial Design ◽  
Surface Areas ◽  
Molecular Building Blocks ◽  
Metal Organic

Reticular frameworks are crystalline porous materials that form <i>via</i> the self-assembly of molecular building blocks (<i>i.e.</i>, nodes and linkers) in different topologies. Many of them have high internal surface areas and other desirable properties for gas storage, separation, and other applications. The notable variety of the possible building blocks and the diverse ways they can be assembled endow reticular frameworks with a near-infinite combinatorial design space, making reticular chemistry both promising and challenging for prospective materials design. Here, we propose an automated nanoporous materials discovery platform powered by a supramolecular variational autoencoder (SmVAE) for the generative design of reticular materials with desired functions. We demonstrate the automated design process with a class of metal-organic framework (MOF) structures and the goal of separating CO<sub>2</sub> from natural gas or flue gas. Our model exhibits high fidelity in capturing structural features and reconstructing MOF structures. We show that the autoencoder has a promising optimization capability when jointly trained with multiple top adsorbent candidates identified for superior gas separation. MOFs discovered here are strongly competitive against some of the best-performing MOFs/zeolites ever reported. This platform lays the groundwork for the design of reticular frameworks for desired applications.

scholarly journals Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

2020 ◽  
Author(s):  
Zhenpeng Yao ◽  
Benjamin Sanchez-Lengeling ◽  
N. Scott Bobbitt ◽  
Benjamin J. Bucior ◽  
Sai Govind Hari Kumar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Metal Organic Framework ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Generative Models ◽  
Combinatorial Design ◽  
Surface Areas ◽  
Molecular Building Blocks ◽  
Metal Organic

Reticular frameworks are crystalline porous materials that form <i>via</i> the self-assembly of molecular building blocks (<i>i.e.</i>, nodes and linkers) in different topologies. Many of them have high internal surface areas and other desirable properties for gas storage, separation, and other applications. The notable variety of the possible building blocks and the diverse ways they can be assembled endow reticular frameworks with a near-infinite combinatorial design space, making reticular chemistry both promising and challenging for prospective materials design. Here, we propose an automated nanoporous materials discovery platform powered by a supramolecular variational autoencoder (SmVAE) for the generative design of reticular materials with desired functions. We demonstrate the automated design process with a class of metal-organic framework (MOF) structures and the goal of separating CO<sub>2</sub> from natural gas or flue gas. Our model exhibits high fidelity in capturing structural features and reconstructing MOF structures. We show that the autoencoder has a promising optimization capability when jointly trained with multiple top adsorbent candidates identified for superior gas separation. MOFs discovered here are strongly competitive against some of the best-performing MOFs/zeolites ever reported. This platform lays the groundwork for the design of reticular frameworks for desired applications.

Self-assembly of AB diblock copolymer solutions confined in cylindrical nanopores

2017 ◽  
Vol 1 (3) ◽  
pp. 487-494 ◽  
Author(s):  
Yuping Sheng ◽  
Yutian Zhu ◽  
Wei Jiang ◽  
Zeyuan Dong
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Diblock Copolymer ◽  
Self Assembly ◽  
The Self

The self-assembly of AB diblock copolymer solutions confined in a cylindrical nanopore is investigated systematically via Monte Carlo simulations.

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.

scholarly journals Simulations of the 2D self-assembly of tripod-shaped building blocks

2020 ◽  
Vol 11 ◽  
pp. 884-890
Author(s):  
Łukasz Baran ◽  
Wojciech Rżysko ◽  
Edyta Słyk
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Diffraction Pattern ◽  
Triangular Lattice ◽  
Self Assembly ◽  
Building Blocks ◽  
Coarse Grained ◽  
Coarse Grained Model

We introduce a molecular dynamics (MD) coarse-grained model for the description of tripod building blocks. This model has been used by us already for linear, V-shape, and tetratopic molecules. We wanted to further extend its possibilities to trifunctional molecules to prove its versatility. For the chosen systems we have also compared the MD results with Monte Carlo results on a triangular lattice. We have shown that the constraints present in the latter method can enforce the formation of completely different structures, not reproducible with off-lattice simulations. In addition to that, we have characterized the obtained structures regarding various parameters such as theoretical diffraction pattern and average association number.

scholarly journals The Assembly of Porphyrin Systems in Well-Defined Nanostructures: An Update

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4307 ◽  
Author(s):  
Gabriele Magna ◽  
Donato Monti ◽  
Corrado Di Natale ◽  
Roberto Paolesse ◽  
Manuela Stefanelli
Keyword(s):  
Self Assembly ◽  
Energy Transport ◽  
Functional Materials ◽  
Building Blocks ◽  
Spatial Arrangement ◽  
Transport Processes ◽  
Internal Electric Field ◽  
Porphyrin Derivatives ◽  
Molecular Building Blocks ◽  
The Individual

The interest in assembling porphyrin derivatives is widespread and is accounted by the impressive impact of these suprastructures of controlled size and shapes in many applications from nanomedicine and sensors to photocatalysis and optoelectronics. The massive use of porphyrin dyes as molecular building blocks of functional materials at different length scales relies on the interdependent pair properties, consisting of their chemical stability/synthetic versatility and their quite unique physicochemical properties. Remarkably, the driven spatial arrangement of these platforms in well-defined suprastructures can synergically amplify the already excellent properties of the individual monomers, improving conjugation and enlarging the intensity of the absorption range of visible light, or forming an internal electric field exploitable in light-harvesting and charge-and energy-transport processes. The countless potentialities offered by these systems means that self-assembly concepts and tools are constantly explored, as confirmed by the significant number of published articles related to porphyrin assemblies in the 2015–2019 period, which is the focus of this review.

Self-Assembly of Proteins into Three-Dimensional Structures Using Bio-Conjugation

2014 ◽  
Vol 1663 ◽  
Author(s):  
Garima Thakur ◽  
Kovur Prashanthi ◽  
Thomas Thundat
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Gold Surface ◽  
Building Blocks ◽  
Growth Conditions ◽  
Base Layer ◽  
Chemical Structures ◽  
Molecular Building Blocks ◽  
Ring Structures ◽  
Self Assembled

ABSTRACTSelf–assembly of molecular building blocks provides an interesting route to produce well-defined chemical structures. Tailoring the functionalities on the building blocks and controlling the time of self-assembly could control the properties as well as the structure of the resultant patterns. Spontaneous self-assembly of biomolecules can generate bio-interfaces for myriad of potential applications. Here we report self-assembled patterning of human serum albumin (HSA) protein in to ring structures on a polyethylene glycol (PEG) modified gold surface. The structure of the self-assembled protein molecules and kinetics of structure formation entirely revolved around controlling the nucleation of the base layer. The formation of different sizes of ring patterns is attributed to growth conditions of the PEG islands for bio-conjugation. These assemblies might be beneficial in forming structurally ordered architectures of active proteins such as HSA or other globular proteins.

Large-Scale Monte Carlo Simulations for Aggregation, Self-Assembly, and Phase Equilibria

2008 ◽  
pp. 189-199
Author(s):  
Jake L. Rafferty ◽  
Ling Zhang ◽  
Nikolaj D. Zhuravlev ◽  
Kelly E. Anderson ◽  
Becky L. Eggimann ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Phase Equilibria ◽  
Monte Carlo Simulations ◽  
Self Assembly ◽  
Large Scale

Effect of backbone aspect ratio on the surface-confined self-assembly of tetratopic molecular building blocks

2019 ◽  
Vol 579 ◽  
pp. 123632 ◽  
Author(s):  
Damian Nieckarz ◽  
Wojciech Rżysko ◽  
Valery Lutsyk ◽  
Jakub Lisiecki ◽  
Paweł Szabelski
Keyword(s):  
Aspect Ratio ◽  
Self Assembly ◽  
Building Blocks ◽  
Molecular Building Blocks
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