1
|
Yilmazer S, Schwaller D, Mésini PJ. Beyond Sol-Gel: Molecular Gels with Different Transitions. Gels 2023; 9:gels9040273. [PMID: 37102885 PMCID: PMC10137434 DOI: 10.3390/gels9040273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
The existence of sol–gel transitions is one of the most manifest properties of molecular gels. These transitions reflect their nature since they correspond to the association or dissociation of low weight molecules through non-covalent interactions to form the network constitutive of the gel. Most described molecular gels undergo only one gel-to-sol transition upon heating, and the reverse sol-to-gel transition upon cooling. It has been long observed that different conditions of formation could lead to gels with different morphologies, and that gels can undergo a transition from gel to crystals. However, more recent publications report molecular gels which exhibit additional transitions, for instance gel-to-gel transitions. This review surveys the molecular gels for which, in addition to sol–gel transitions, transitions of different nature have been reported: gel-to-gel transitions, gel-to-crystal transition, liquid–liquid phase separations, eutectic transformations, and synereses.
Collapse
|
2
|
Batra R, Loeffler TD, Chan H, Srinivasan S, Cui H, Korendovych IV, Nanda V, Palmer LC, Solomon LA, Fry HC, Sankaranarayanan SKRS. Machine learning overcomes human bias in the discovery of self-assembling peptides. Nat Chem 2022; 14:1427-1435. [PMID: 36316409 PMCID: PMC9844539 DOI: 10.1038/s41557-022-01055-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/01/2022] [Indexed: 12/23/2022]
Abstract
Peptide materials have a wide array of functions, from tissue engineering and surface coatings to catalysis and sensing. Tuning the sequence of amino acids that comprise the peptide modulates peptide functionality, but a small increase in sequence length leads to a dramatic increase in the number of peptide candidates. Traditionally, peptide design is guided by human expertise and intuition and typically yields fewer than ten peptides per study, but these approaches are not easily scalable and are susceptible to human bias. Here we introduce a machine learning workflow-AI-expert-that combines Monte Carlo tree search and random forest with molecular dynamics simulations to develop a fully autonomous computational search engine to discover peptide sequences with high potential for self-assembly. We demonstrate the efficacy of the AI-expert to efficiently search large spaces of tripeptides and pentapeptides. The predictability of AI-expert performs on par or better than our human experts and suggests several non-intuitive sequences with high self-assembly propensity, outlining its potential to overcome human bias and accelerate peptide discovery.
Collapse
Affiliation(s)
- Rohit Batra
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Troy D Loeffler
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, USA
| | - Henry Chan
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, USA
| | - Srilok Srinivasan
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Liam C Palmer
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Lee A Solomon
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA, USA
| | - H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA.
| | - Subramanian K R S Sankaranarayanan
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA.
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, USA.
| |
Collapse
|
3
|
Misra R, Tang Y, Chen Y, Chakraborty P, Netti F, Vijayakanth T, Shimon LJW, Wei G, Adler-Abramovich L. Exploiting Minimalistic Backbone Engineered γ-Phenylalanine for the Formation of Supramolecular Co-Polymer. Macromol Rapid Commun 2022; 43:e2200223. [PMID: 35920234 DOI: 10.1002/marc.202200223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/07/2022] [Indexed: 11/09/2022]
Abstract
Ordered supramolecular hydrogels assembled by modified aromatic amino acids often exhibit low mechanical rigidity. Aiming to stabilize the hydrogel and understand the impact of conformational freedom and hydrophobicity on the self-assembly process, we designed two building blocks based on 9-fluorenyl-methoxycarbonyl-phenylalanine (Fmoc-Phe) gelator which contain two extra methylene units in the backbone, generating Fmoc-γPhe and Fmoc-(3-hydroxy)-γPhe. Fmoc-γPhe spontaneously assembled in aqueous media forming a hydrogel with exceptional mechanical and thermal stability. Moreover, Fmoc-(3-hydroxy)-γPhe, with an extra backbone hydroxyl group decreasing its hydrophobicity while maintaining some molecular flexibility, self-assembled into a transient fibrillar hydrogel, that later formed microcrystalline aggregates through phase transition. Molecular dynamics simulations and single crystal X-ray analyses revealed the mechanism underlying the two residues' distinct self-assembly behaviors. Finally, we demonstrated Fmoc-γPhe and Fmoc-(3-OH)-γPhe co-assembly to form a supramolecular hydrogel with notable mechanical properties. We believe that the understanding of the structure-assembly relationship will enable the design of new functional amino acid-based hydrogels. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, the Center for Nanoscience and Nanotechnology, the Center for the Physics and Chemistry of Living Systems, Tel-Aviv University, Tel-Aviv, 69978, Israel.,Dept. of Med. Chem, NIPER Mohali, S.A.S. Nagar (Mohali), 160062, India
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai, 200433, P. R. China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai, 200433, P. R. China
| | - Priyadarshi Chakraborty
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, the Center for Nanoscience and Nanotechnology, the Center for the Physics and Chemistry of Living Systems, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Francesca Netti
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, the Center for Nanoscience and Nanotechnology, the Center for the Physics and Chemistry of Living Systems, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Thangavel Vijayakanth
- The Shmunis School of Biomedicine and Cancer Research George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai, 200433, P. R. China
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, the Center for Nanoscience and Nanotechnology, the Center for the Physics and Chemistry of Living Systems, Tel-Aviv University, Tel-Aviv, 69978, Israel
| |
Collapse
|
4
|
Nakayama S, Kojima T, Kaburagi M, Kikuchi T, Asakura K, Banno T. Chemotaxis of Oil Droplets and Their Phase Transition to Aggregates with Membrane Structures in Surfactant Solution Containing Metal Salts. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sepia Nakayama
- Department of Applied Chemistry Faculty of Science and Technology Keio University 3-14-1 Hiyoshi, Kohoku-ku Yokohama 223-8522 Japan
| | - Tomoya Kojima
- Department of Applied Chemistry Faculty of Science and Technology Keio University 3-14-1 Hiyoshi, Kohoku-ku Yokohama 223-8522 Japan
| | - Mari Kaburagi
- Department of Applied Chemistry Faculty of Science and Technology Keio University 3-14-1 Hiyoshi, Kohoku-ku Yokohama 223-8522 Japan
| | - Takanori Kikuchi
- Department of Applied Chemistry Faculty of Science and Technology Keio University 3-14-1 Hiyoshi, Kohoku-ku Yokohama 223-8522 Japan
| | - Kouichi Asakura
- Department of Applied Chemistry Faculty of Science and Technology Keio University 3-14-1 Hiyoshi, Kohoku-ku Yokohama 223-8522 Japan
| | - Taisuke Banno
- Department of Applied Chemistry Faculty of Science and Technology Keio University 3-14-1 Hiyoshi, Kohoku-ku Yokohama 223-8522 Japan
| |
Collapse
|
5
|
Gayen K, Nandi N, Das KS, Hermida-Merino D, Hamley IW, Banerjee A. The aging effect on the enhancement of thermal stability, mechanical stiffness and fluorescence properties of histidine-appended naphthalenediimide based two-component hydrogels. SOFT MATTER 2020; 16:10106-10114. [PMID: 32716462 DOI: 10.1039/d0sm00468e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A histidine attached naphthalenediimide (NDI)-containing amphiphilic molecule (NDIP) self-assembles into nanotubes in aqueous solution at pH 6.6 as revealed by high-resolution transmission electron microscopy studies. This histidine-appended NDI forms a two-component hydrogel in the presence of tartaric acid at a molar ratio of 1 : 2. A morphological transformation was observed from a nanotube structure in the non-gel aggregated state of histidine appended NDI to interconnected cross-linked nanofibers of the two-component hydrogel in the presence of tartaric acid. Interestingly, the gel exhibits an unusual behavior upon aging compared to the fresh gel. It is found that the thermal stability and gel stiffness increase very significantly upon aging. Another important feature noted is that the very weak fluorescence of the fresh gel is transformed into bright greenish fluorescence upon aging. These results suggest that intermolecular interactions among the gelator molecules and tartaric acid in the gel phase slowly increase with time to form a mechanically very stiff and thermally robust gel.
Collapse
Affiliation(s)
- Kousik Gayen
- School of Biological Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India.
| | | | | | | | | | | |
Collapse
|
6
|
Chakraborty P, Tang Y, Guterman T, Arnon ZA, Yao Y, Wei G, Gazit E. Co‐Assembly between Fmoc Diphenylalanine and Diphenylalanine within a 3D Fibrous Viscous Network Confers Atypical Curvature and Branching. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Priyadarshi Chakraborty
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Yiming Tang
- Department of Physics State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) Fudan University Shanghai 200433 People's Republic of China
| | - Tom Guterman
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Zohar A. Arnon
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Yifei Yao
- Department of Physics State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) Fudan University Shanghai 200433 People's Republic of China
| | - Guanghong Wei
- Department of Physics State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) Fudan University Shanghai 200433 People's Republic of China
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering Tel Aviv University Tel Aviv 6997801 Israel
| |
Collapse
|
7
|
Chakraborty P, Tang Y, Guterman T, Arnon ZA, Yao Y, Wei G, Gazit E. Co‐Assembly between Fmoc Diphenylalanine and Diphenylalanine within a 3D Fibrous Viscous Network Confers Atypical Curvature and Branching. Angew Chem Int Ed Engl 2020; 59:23731-23739. [DOI: 10.1002/anie.202009488] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Priyadarshi Chakraborty
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Yiming Tang
- Department of Physics State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) Fudan University Shanghai 200433 People's Republic of China
| | - Tom Guterman
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Zohar A. Arnon
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Yifei Yao
- Department of Physics State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) Fudan University Shanghai 200433 People's Republic of China
| | - Guanghong Wei
- Department of Physics State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) Fudan University Shanghai 200433 People's Republic of China
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering Tel Aviv University Tel Aviv 6997801 Israel
| |
Collapse
|