@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 = {\#nosource, 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},
}

{"_id":"Jb9bZ8QGmpiQFbcja","bibbaseid":"jeon-shell-selfassemblyofcyclodiphenylalaninepeptidesinvacuum-2014","author_short":["Jeon, J.","Shell, M S."],"bibdata":{"bibtype":"article","type":"article","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":[{"propositions":[],"lastnames":["Jeon"],"firstnames":["Joohyun"],"suffixes":[]},{"propositions":[],"lastnames":["Shell"],"firstnames":["M","Scott"],"suffixes":[]}],"month":"June","year":"2014","pmid":"24877752","note":"Publisher: American Chemical Society","keywords":"#nosource, 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","bibtex":"@article{Jeon2014,\n\ttitle = {Self-assembly of cyclo-diphenylalanine peptides in vacuum},\n\tvolume = {118},\n\tissn = {15205207},\n\turl = {http://dx.doi.org/10.1021/jp501503x},\n\tdoi = {10.1021/jp501503x},\n\tabstract = {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.},\n\tnumber = {24},\n\tjournal = {Journal of Physical Chemistry B},\n\tauthor = {Jeon, Joohyun and Shell, M Scott},\n\tmonth = jun,\n\tyear = {2014},\n\tpmid = {24877752},\n\tnote = {Publisher: American Chemical Society},\n\tkeywords = {\\#nosource, 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},\n\tpages = {6644--6652},\n}\n\n\n\n","author_short":["Jeon, J.","Shell, M S."],"key":"Jeon2014","id":"Jeon2014","bibbaseid":"jeon-shell-selfassemblyofcyclodiphenylalaninepeptidesinvacuum-2014","role":"author","urls":{"Paper":"http://dx.doi.org/10.1021/jp501503x"},"keyword":["#nosource","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"],"metadata":{"authorlinks":{}},"html":""},"bibtype":"article","biburl":"https://bibbase.org/zotero/subhradip.paul","dataSources":["epdxi2MtNPwoQCL4d"],"keywords":["#nosource","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"],"search_terms":["self","assembly","cyclo","diphenylalanine","peptides","vacuum","jeon","shell"],"title":"Self-assembly of cyclo-diphenylalanine peptides in vacuum","year":2014}