Self-assembly of cyclo-diphenylalanine peptides in vacuum. Jeon, J. & Shell, M S. Journal of Physical Chemistry B, 118(24):6644–6652, June, 2014. Publisher: American Chemical Society
Self-assembly of cyclo-diphenylalanine peptides in vacuum [link]Paper  doi  abstract   bibtex   
The diphenylalanine (FF) peptide self-assembles into a variety of nanostructures, including hollow nanotubes that form in aqueous solution with an unusually high degree of hydrophilic surface area. In contrast, diphenylalanine can also be vapor-deposited in vacuum to produce rodlike assemblies that are extremely hydrophobic; in this process FF has been found to dehydrate and cyclize to cyclo-diphenylalanine (cyclo-FF). An earlier study used all-atom molecular dynamics (MD) simulations to understand the early stages of the self-assembly of linear-FF peptides in solution. Here, we examine the self-assembly of cyclo-FF peptides in vacuum and compare it to these previous results to understand the differences underlying the two cases. Using all-atom replica exchange MD simulations, we consider systems of 50 cyclo-FF peptides and examine free energies along various structural association coordinates. We find that cyclo-FF peptides form ladder-like structures connected by double hydrogen bonds, and that multiple such ladders linearly align in a cooperative manner to form larger-scale, elongated assemblies. Unlike linear-FFs which mainly assemble through the interplay between hydrophobic and hydrophilic interactions, the assembly of cyclo-FFs in vacuum is primarily driven by electrostatic interactions along the backbone that induce alignment at long-range, followed by van der Waals interactions between side chains that become important for close-range packing. While both solution and vacuum phase driving forces result in ladder-like structures, the clustering of ladders is opposite: linear-FF peptide ladders form assemblies with side-chains buried inward, while cyclo-FF ladders point outward.
@article{Jeon2014,
	title = {Self-assembly of cyclo-diphenylalanine peptides in vacuum},
	volume = {118},
	issn = {15205207},
	url = {http://dx.doi.org/10.1021/jp501503x},
	doi = {10.1021/jp501503x},
	abstract = {The diphenylalanine (FF) peptide self-assembles into a variety of nanostructures, including hollow nanotubes that form in aqueous solution with an unusually high degree of hydrophilic surface area. In contrast, diphenylalanine can also be vapor-deposited in vacuum to produce rodlike assemblies that are extremely hydrophobic; in this process FF has been found to dehydrate and cyclize to cyclo-diphenylalanine (cyclo-FF). An earlier study used all-atom molecular dynamics (MD) simulations to understand the early stages of the self-assembly of linear-FF peptides in solution. Here, we examine the self-assembly of cyclo-FF peptides in vacuum and compare it to these previous results to understand the differences underlying the two cases. Using all-atom replica exchange MD simulations, we consider systems of 50 cyclo-FF peptides and examine free energies along various structural association coordinates. We find that cyclo-FF peptides form ladder-like structures connected by double hydrogen bonds, and that multiple such ladders linearly align in a cooperative manner to form larger-scale, elongated assemblies. Unlike linear-FFs which mainly assemble through the interplay between hydrophobic and hydrophilic interactions, the assembly of cyclo-FFs in vacuum is primarily driven by electrostatic interactions along the backbone that induce alignment at long-range, followed by van der Waals interactions between side chains that become important for close-range packing. While both solution and vacuum phase driving forces result in ladder-like structures, the clustering of ladders is opposite: linear-FF peptide ladders form assemblies with side-chains buried inward, while cyclo-FF ladders point outward.},
	number = {24},
	journal = {Journal of Physical Chemistry B},
	author = {Jeon, Joohyun and Shell, M Scott},
	month = jun,
	year = {2014},
	pmid = {24877752},
	note = {Publisher: American Chemical Society},
	keywords = {Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Molecular Dynamics Simulation, Nanostructures, Nanostructures: chemistry, Peptides, Peptides: chemistry, Phenylalanine, Phenylalanine: analogs \& derivatives, Phenylalanine: chemistry, Static Electricity, Thermodynamics, Vacuum},
	pages = {6644--6652},
}

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