Date of Award

12-2025

Degree Type

Dissertation

Degree Name

Ph.D.

Degree Program

Chemistry

Department

Chemistry

Major Professor

Rick, Steven

Second Advisor

Trudell, Mark

Third Advisor

Summa, Chris

Fourth Advisor

Wiley, John

Abstract

Polypeptoids are N-substituted glycine polymers, which differ from peptides in the placement of the side chain being present on the amide nitrogen rather than the backbone Cα. While both peptoids and peptides are composed of linked amino acids, the structural changes resulting from the differing origin of the side chain leads to distinct backbone structure, as well as remove the chirality found in the peptide structure. These differences lead peptoids to have different physiochemical and biological properties, such as being resistant to proteolysis and diverse three-dimensional structures that are not observed in peptides. With the shifting of the side chain off the Cα, the hydrogen bonding patterns that facilitate the formation of α-helices and β-sheets in peptides are also changed. These differences encourage studies of the lesser-known N-substituted glycine polymers in various fields of research, including but not limited to biomedical research, drug development, nanotechnology, etc., where the differences can provide valuable properties desired in materials.

To facilitate the study of polypeptoids, Molecular Dynamics (MD) simulations are used to analyze the behavior of molecules over time. By numerically solving Newton’s equation of motions with defined initial conditions and interatomic potentials, MD simulations can provide insight into the behavior of molecular systems. Analysis from MD simulations can provide valuable information about the nature of the molecules being studied, such as the likelihood of micelle formation or tendency for the molecule to stabilize in cis/trans orientation. Due to the nature of the calculations for the simulations required for MD simulations, even with the help of supercomputer technology, the analysis can take a significant amount of time using the standard methods of MD simulations. In this study, MD simulation analysis using methods to help increase the speed of the simulations will be shown. In particular, the study will focus on the usage of Coarse-grained modeling force fields to reduce the number of interactions needed to be calculated during the simulation, and the usage of the recently developed Replica Exchange with Dynamical Scaling (REDS) method that reduces the number of replicas needed to model compared to the regular Replica Exchange method.

Rights

The University of New Orleans and its agents retain the non-exclusive license to archive and make accessible this dissertation or thesis in whole or in part in all forms of media, now or hereafter known. The author retains all other ownership rights to the copyright of the thesis or dissertation.

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