國立虎尾科技大學 |

Unraveling Foldamer Secondary Structure : = A Computational Investigation of New Folding Oligomers.

Record Type:	Language materials, manuscript : Monograph/item
Title/Author:	Unraveling Foldamer Secondary Structure :/
Reminder of title:	A Computational Investigation of New Folding Oligomers.
Author:	Fobe, Theodore L.
Description:	1 online resource (212 pages)
Notes:	Source: Dissertations Abstracts International, Volume: 85-06, Section: B.
Contained By:	Dissertations Abstracts International85-06B.
Subject:	Computational chemistry. -
Online resource:	click for full text (PQDT)
ISBN:	9798381164138

Unraveling Foldamer Secondary Structure : = A Computational Investigation of New Folding Oligomers.
Fobe, Theodore L.

Unraveling Foldamer Secondary Structure :A Computational Investigation of New Folding Oligomers. - 1 online resource (212 pages)

Source: Dissertations Abstracts International, Volume: 85-06, Section: B.

Thesis (Ph.D.)--University of Colorado at Boulder, 2023.

Includes bibliographical references

Biology achieves an astounding range of functions from proteins and nucleic acids. In the pursuit of imitating the functional macromolecules seen in nature, researchers synthesized a new class of polymer materials called foldamers. Foldamers are linear polymers that readily fold into a distinct folded state in solution. The incorporation of different chemistries into the foldamer backbone allows researchers to create new folded secondary structures not observed in nature. Because of foldamers' ability to self-assemble into well-defined nano-scale structures, they are a promising candidate for use in molecular signaling, anti-viral and anti-fungal agents, biomimetic therapeutics, molecular sensors, and catalysis.In this thesis, I explore and develop various computational methods to study foldamer molecules. In chapter 1, I present a thorough review of existing computational methods to study foldamer molecules. Since foldamers are similar to other well-studied biopolymers, such as proteins and nucleic acids, there is a large amount of overlap in computational methods used to study biopolymers and foldamers. In chapter 2, I apply a top-down modeling approach to study foldamers with a series of simple coarse-grained (CG) models. In these CG models, we explore the effects of several monomer characteristics effect on the secondary structure these CG models adopt. The effect of monomer characteristics on foldamer secondary structure in these generic models generalizes to all foldamer chemistries and can be used to select chemistry in new atomistic foldamers. In chapter 3, I use molecular simulations to identify secondary structure in a novel para-ortho-para-terphenyl foldamer chemistry. I find that partial helical motifs are stabilized, however, these motifs are unable to to form in series. In chapter 4, I continue the investigation of terphenyl foldamer chemistry and develop an enhanced sampling workflow that can identify secondary structures in a set of different terphenyl foldamer chemistry. Here, I use molecular simulations of short terphenyl oligomers to identify secondary structures in terphenyl molecules. Reconstructing the identified secondary structures in longer oligomers shows that longer oligomers are able to stabilize these secondary structure motifs.The collection of work presented here exemplifies the usefulness of computational methods for studying new foldamer systems. In a field of study that has primarily been dominated by experimental synthesis and characterization over the past 20 years, computational methods offer an alternative approach to not only identify and characterize existing foldamer chemistries but also help guide the discovery of new foldamers.

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2024

Mode of access: World Wide Web

ISBN: 9798381164138Subjects--Topical Terms:

1190332
Computational chemistry.
Subjects--Index Terms:

Enhanced samplingIndex Terms--Genre/Form:

554714
Electronic books.

Unraveling Foldamer Secondary Structure : = A Computational Investigation of New Folding Oligomers.
LDR:04184ntm a22004217 4500 001 1147112
005 20240909062218.5
006 m o d
007 cr bn ---uuuuu
008 250605s2023 xx obm 000 0 eng d
020 $a 9798381164138
035 $a (MiAaPQ)AAI30813300
035 $a AAI30813300
040 $a MiAaPQ $b eng $c MiAaPQ $d NTU
100 1 $a Fobe, Theodore L. $3 1472760
245 1 0 $a Unraveling Foldamer Secondary Structure : $b A Computational Investigation of New Folding Oligomers.
264 0 $c 2023
300 $a 1 online resource (212 pages)
336 $a text $b txt $2 rdacontent
337 $a computer $b c $2 rdamedia
338 $a online resource $b cr $2 rdacarrier
500 $a Source: Dissertations Abstracts International, Volume: 85-06, Section: B.
500 $a Advisor: Shirts, Michael R.
502 $a Thesis (Ph.D.)--University of Colorado at Boulder, 2023.
504 $a Includes bibliographical references
520 $a Biology achieves an astounding range of functions from proteins and nucleic acids. In the pursuit of imitating the functional macromolecules seen in nature, researchers synthesized a new class of polymer materials called foldamers. Foldamers are linear polymers that readily fold into a distinct folded state in solution. The incorporation of different chemistries into the foldamer backbone allows researchers to create new folded secondary structures not observed in nature. Because of foldamers' ability to self-assemble into well-defined nano-scale structures, they are a promising candidate for use in molecular signaling, anti-viral and anti-fungal agents, biomimetic therapeutics, molecular sensors, and catalysis.In this thesis, I explore and develop various computational methods to study foldamer molecules. In chapter 1, I present a thorough review of existing computational methods to study foldamer molecules. Since foldamers are similar to other well-studied biopolymers, such as proteins and nucleic acids, there is a large amount of overlap in computational methods used to study biopolymers and foldamers. In chapter 2, I apply a top-down modeling approach to study foldamers with a series of simple coarse-grained (CG) models. In these CG models, we explore the effects of several monomer characteristics effect on the secondary structure these CG models adopt. The effect of monomer characteristics on foldamer secondary structure in these generic models generalizes to all foldamer chemistries and can be used to select chemistry in new atomistic foldamers. In chapter 3, I use molecular simulations to identify secondary structure in a novel para-ortho-para-terphenyl foldamer chemistry. I find that partial helical motifs are stabilized, however, these motifs are unable to to form in series. In chapter 4, I continue the investigation of terphenyl foldamer chemistry and develop an enhanced sampling workflow that can identify secondary structures in a set of different terphenyl foldamer chemistry. Here, I use molecular simulations of short terphenyl oligomers to identify secondary structures in terphenyl molecules. Reconstructing the identified secondary structures in longer oligomers shows that longer oligomers are able to stabilize these secondary structure motifs.The collection of work presented here exemplifies the usefulness of computational methods for studying new foldamer systems. In a field of study that has primarily been dominated by experimental synthesis and characterization over the past 20 years, computational methods offer an alternative approach to not only identify and characterize existing foldamer chemistries but also help guide the discovery of new foldamers.
533 $a Electronic reproduction. $b Ann Arbor, Mich. : $c ProQuest, $d 2024
538 $a Mode of access: World Wide Web
650 4 $a Computational chemistry. $3 1190332
650 4 $a Physical chemistry. $3 1148725
650 4 $a Biochemistry. $3 582831
650 4 $a Molecular chemistry. $3 1179636
653 $a Enhanced sampling
653 $a Foldamers
653 $a Molecular dynamics
653 $a Monte Carlo minimization
653 $a Nano-scale structures
653 $a Oligomers
655 7 $a Electronic books. $2 local $3 554714
690 $a 0219
690 $a 0431
690 $a 0487
690 $a 0494
710 2 $a ProQuest Information and Learning Co. $3 1178819
710 2 $a University of Colorado at Boulder. $b Chemical and Biological Engineering. $3 1241260
773 0 $t Dissertations Abstracts International $g 85-06B.
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=30813300 $z click for full text (PQDT)