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

Abstract Studies on periodic porosity and related properties and functions have been limited to insoluble solid-state materials. Self-assembly provides a straightforward and efficient strategy for the construction of soluble periodic porous supramolecular organic frameworks (SOFs) in water from rationally designed molecular building blocks. From rigid tri- and tetra-armed building blocks and cucurbitu[8]ril (CB[8]), a number of two-dimensional (2D) honeycomb, square and rhombic SOFs can be generated, which is driven by CB[8]-encapsulation-enhanced dimerization of two aromatic units on the periphery of the multi-armed molecules. By utilizing the same three-component host−guest motif as the driving force, three-dimensional (3D) diamondoid and cubic SOFs can be obtained from tetrahedral and [Ru(bipy)3]2+-derived octahedral monomers and CB[8]. All of the 2D and 3D periodic frameworks are soluble in water, and are able to maintain the periodicity as well as the pore sizes in the solid state. 3D SOFs are highly efficient homogeneous polycationic frameworks for reversible adsorption of anionic species including organic dyes, peptides, nucleic acids, drugs, dendrimers and Wells-Dawson-typed polyoxametallates (WD-POMs). WD-POM molecules adsorbed in the [Ru(bipy)3]2+-based SOF can catalyse the reduction of proton to H2 upon visible-light sensitization of [Ru(bipy)3]2+, which allows multiple electron transfer from [Ru(bipy)3]2+ to WD-POM. This review summarizes the design, formation and characterization of this new family of self-assembled frameworks, highlights their applications as homogeneous porous materials and finally outlines some future research directions.

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Nanoscale Self-Assembly Using Ion and Electron Beam Techniques: A Rapid Review

MRS Advances ◽

10.1557/adv.2020.349 ◽

2020 ◽

Vol 5 (64) ◽

pp. 3507-3520

Author(s):

Chunhui Dai ◽

Kriti Agarwal ◽

Jeong-Hyun Cho

Keyword(s):

Electron Beam ◽

Self Assembly ◽

Ion Beam ◽

Three Dimensional ◽

The Self ◽

Stress Generation ◽

Rapid Review ◽

High Yield ◽

3D Nanostructures ◽

Self Assembled

AbstractNanoscale self-assembly, as a technique to transform two-dimensional (2D) planar patterns into three-dimensional (3D) nanoscale architectures, has achieved tremendous success in the past decade. However, an assembly process at nanoscale is easily affected by small unavoidable variations in sample conditions and reaction environment, resulting in a low yield. Recently, in-situ monitored self-assembly based on ion and electron irradiation has stood out as a promising candidate to overcome this limitation. The usage of ion and electron beam allows stress generation and real-time observation simultaneously, which significantly enhances the controllability of self-assembly. This enables the realization of various complex 3D nanostructures with a high yield. The additional dimension of the self-assembled 3D nanostructures opens the possibility to explore novel properties that cannot be demonstrated in 2D planar patterns. Here, we present a rapid review on the recent achievements and challenges in nanoscale self-assembly using electron and ion beam techniques, followed by a discussion of the novel optical properties achieved in the self-assembled 3D nanostructures.

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Self-Assembly of Shape-Tunable Oblate Colloidal Particles into Orientationally Ordered Crystals, Glassy Crystals and Plastic Crystals

Soft Matter ◽

10.1039/d1sm00343g ◽

2021 ◽

Author(s):

Jiawei Lu ◽

Xiangyu Bu ◽

Xinghua Zhang ◽

Bing Liu

Keyword(s):

Crystal Structures ◽

Self Assembly ◽

Colloidal Particles ◽

Building Blocks ◽

Fundamental Question ◽

The Self ◽

Plastic Crystals ◽

Self Assembled ◽

Glassy Crystals ◽

The Relationship

The shapes of colloidal particles are crucial to the self-assembled superstructures. Understanding the relationship between the shapes of building blocks and the resulting crystal structures is an important fundamental question....

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Self-assembled three-dimensional hierarchical graphene hybrid hydrogels with ultrathin β-MnO2 nanobelts for high performance supercapacitors

Journal of Materials Chemistry A ◽

10.1039/c4ta04921g ◽

2015 ◽

Vol 3 (4) ◽

pp. 1540-1548 ◽

Cited By ~ 69

Author(s):

Sheng Zhu ◽

Hui Zhang ◽

Ping Chen ◽

Lin-Hui Nie ◽

Chuan-Hao Li ◽

...

Keyword(s):

Self Assembly ◽

High Performance ◽

Three Dimensional ◽

The Self ◽

Mass Loading ◽

Hybrid Hydrogel ◽

Precise Control ◽

Ultrafine Structure ◽

Hybrid Hydrogels ◽

Self Assembled

A facile protocol for the self-assembly of the rGO/β-MnO2 hybrid hydrogel with ultrafine structure and precise control of mass-loading for high performance supercapacitors is reported.

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Square-grid coordination networks of (5,10,15,20-tetra-4-pyridylporphyrinato)zinc(II) in its clathrate with two guest molecules of 1,2-dichlorobenzene: supramolecular isomerism of the porphyrin self-assembly

Acta Crystallographica Section C Crystal Structure Communications ◽

10.1107/s0108270109005691 ◽

2009 ◽

Vol 65 (3) ◽

pp. m139-m142 ◽

Cited By ~ 10

Author(s):

Rajesh Koner ◽

Israel Goldberg

Keyword(s):

Self Assembly ◽

Metal Ion ◽

Three Dimensional ◽

Two Dimensional ◽

Coordination Networks ◽

Guest Molecules ◽

Square Grid ◽

Supramolecular Isomerism ◽

Self Assembled ◽

Solvent Molecules

The title compound, (5,10,15,20-tetra-4-pyridylporphyrinato)zinc(II) 1,2-dichlorobenzene disolvate, [Zn(C40H24N8)]·2C6H4Cl2, contains a clathrate-type structure. It is composed of two-dimensional square-grid coordination networks of the self-assembled porphyrin moiety, which are stacked one on top of the other in a parallel manner. The interporphyrin cavities of the overlapping networks combine into channel voids accommodated by the dichlorobenzene solvent. Molecules of the porphyrin complex are located on crystallographic inversion centres. The observed two-dimensional assembly mode of the porphyrin units represents a supramolecular isomer of the unique three-dimensional coordination frameworks of the same porphyrin building block observed earlier. The significance of this study lies in the discovery of an additional supramolecular isomer of the rarely observed structures of metalloporphyrins self-assembled directly into extended coordination polymers without the use of external ligand or metal ion auxiliaries.

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Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

10.26434/chemrxiv.12186681.v1 ◽

2020 ◽

Cited By ~ 3

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 via the self-assembly of molecular building blocks (i.e., 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 CO2 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.

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Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

10.26434/chemrxiv.12186681 ◽

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 via the self-assembly of molecular building blocks (i.e., 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 CO2 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.

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Molecular Building Blocks in Low PH Silicon Sol-Gels: A Silicon-29 NMR Study

MRS Proceedings ◽

10.1557/proc-121-519 ◽

1988 ◽

Vol 121 ◽

Cited By ~ 3

Author(s):

Larry W. Kelts ◽

Nancy J. Armstrong

Keyword(s):

Sol Gel ◽

Building Blocks ◽

Low Ph ◽

Tetraethyl Orthosilicate ◽

Compact Ring ◽

Molar Ratios ◽

Molecular Building Blocks ◽

Nmr Study ◽

Ring Structures ◽

Silicon Sol

ABSTRACTHigh field Silicon-29 NMR is used to study the structural intermediates in tetramethyl and tetraethyl orthosilicate (TMOS and TEOS) low pH sol-gel reactions. Linear oligomers as well as ring components of various sizes are identified and their evolution in the sols is followed. Differences in the number of compact ring structures are related to differences in gel times. Reactions are followed for various silicon alkoxide:water:acid molar ratios.

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Self assembled nanocages from DNA–protoporphyrin hybrid molecules

RSC Advances ◽

10.1039/c5ra16851a ◽

2015 ◽

Vol 5 (108) ◽

pp. 89025-89029 ◽

Cited By ~ 3

Author(s):

Vandana Singh ◽

Mohan Monisha ◽

Roy Anindya ◽

Prolay Das

Keyword(s):

Functional Groups ◽

Protoporphyrin Ix ◽

Building Blocks ◽

Carboxyl Groups ◽

Dna Oligomers ◽

Organic Hybrid ◽

Molecular Building Blocks ◽

Modified Dna ◽

Hybrid Molecules ◽

Self Assembled

DNA–organic hybrid molecular building blocks are generated by covalent conjugation of the carboxyl groups of protoporphyrin IX with the amine functional groups of modified DNA oligomers.

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