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Yadav Schmid S, Ma X, Hammons JA, Mergelsberg ST, Harris BS, Ferron T, Yang W, Zhou W, Zheng R, Zhang S, Legg BA, Van Buuren A, Baer MD, Chen CL, Tao J, De Yoreo JJ. Influence of Peptoid Sequence on the Mechanisms and Kinetics of 2D Assembly. ACS Nano 2024; 18:3497-3508. [PMID: 38215492 PMCID: PMC10832064 DOI: 10.1021/acsnano.3c10810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
Two-dimensional (2D) materials have attracted intense interest due to their potential for applications in fields ranging from chemical sensing to catalysis, energy storage, and biomedicine. Recently, peptoids, a class of biomimetic sequence-defined polymers, have been found to self-assemble into 2D crystalline sheets that exhibit unusual properties, such as high chemical stability and the ability to self-repair. The structure of a peptoid is close to that of a peptide except that the side chains are appended to the amide nitrogen rather than the α carbon. In this study, we investigated the effect of peptoid sequence on the mechanism and kinetics of 2D assembly on mica surfaces using in situ AFM and time-resolved X-ray scattering. We explored three distinct peptoid sequences that are amphiphilic in nature with hydrophobic and hydrophilic blocks and are known to self-assemble into 2D sheets. The results show that their assembly on mica starts with deposition of aggregates that spread to establish 2D islands, which then grow by attachment of peptoids, either monomers or unresolvable small oligomers, following well-known laws of crystal step advancement. Extraction of the solubility and kinetic coefficient from the dependence of the growth rate on peptoid concentration reveals striking differences between the sequences. The sequence with the slowest growth rate in bulk and with the highest solubility shows almost no detachment; i.e., once a growth unit attaches to the island edge, there is almost no probability of detaching. Furthermore, a peptoid sequence with a hydrophobic tail conjugated to the final carboxyl residue in the hydrophilic block has enhanced hydrophobic interactions and exhibits rapid assembly both in the bulk and on mica. These assembly outcomes suggest that, while the π-π interactions between adjacent hydrophobic blocks play a major role in peptoid assembly, sequence details, particularly the location of charged groups, as well as interaction with the underlying substrate can significantly alter the thermodynamic stability and assembly kinetics.
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Affiliation(s)
- Sakshi Yadav Schmid
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Xiang Ma
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Joshua A. Hammons
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Sebastian T. Mergelsberg
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Bradley S. Harris
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Thomas Ferron
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Wenchao Yang
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Wenhao Zhou
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Renyu Zheng
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Shuai Zhang
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Benjamin Adam Legg
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Anthony Van Buuren
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Marcel D. Baer
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Chun-Long Chen
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jinhui Tao
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - James J. De Yoreo
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
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Swanson HA, Lau KHA, Tuttle T. Minimal Peptoid Dynamics Inform Self-Assembly Propensity. J Phys Chem B 2023; 127:10601-10614. [PMID: 38038956 PMCID: PMC10726364 DOI: 10.1021/acs.jpcb.3c03725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Peptoids are structural isomers of natural peptides, with side chain attachment at the amide nitrogen, conferring this class of compounds with the ability to access both cis and trans ω torsions as well as an increased diversity of ψ/φ states with respect to peptides. Sampling within these dimensions is controlled through side chain selection, and an expansive set of viable peptoid residues exists. It has been shown recently that "minimal" di- and tripeptoids with aromatic side chains can self-assemble into highly ordered structures, with size and morphological definition varying as a function of sequence pattern (e.g., XFF and FXF, where X = a nonaromatic peptoid monomer). Aromatic groups, such as phenylalanine, are regularly used in the design of minimal peptide assemblers. In recognition of this, and to draw parallels between these compounds classes, we have developed a series of descriptors for intramolecular dynamics of aromatic side chains to discern whether these dynamics, in a preassembly condition, can be related to experimentally observed nanoscale assemblies. To do this, we have built on the atomistic peptoid force field reported by Weiser and Santiso (CGenFF-WS) through the rigorous fitting of partial charges and the collation of Charmm General Force Field (CGenFF) parameters relevant to these systems. Our study finds that the intramolecular dynamics of side chains, for a given sequence, is dependent on the specific combination of backbone ω torsions and that homogeneity of sampling across these states correlates well with the experimentally observed ability to assemble into nanomorphologies with long-range order. Sequence patterning is also shown to affect sampling, in a manner consistent for both tripeptoids and tripeptides. Additionally, sampling similarities between the nanofiber forming tripeptoid, Nf-Nke-Nf in the cc state, and the nanotube forming dipeptide FF, highlight a structural motif which may be relevant to the emergence of extended linear assemblies. To assess these properties, a variety of computational approaches have been employed.
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Affiliation(s)
- Hamish
W. A. Swanson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - King Hang Aaron Lau
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Tell Tuttle
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
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