Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer

Journal Article · Thu Mar 10 00:00:00 EST 2016 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

DOI:https://doi.org/10.1021/acs.jpcb.5b12277· OSTI ID:1254562

Daily, Michael D.; Baer, Marcel D.; Mundy, Christopher J.

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical forcefield (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through sidechain-sidechain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described. MDD was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. Research was funded by the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. MDB acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Material & Engineering. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1254562
• Report Number(s): PNNL-SA-115083; KC0301050; KC0203010
• Journal Information: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Vol. 120, Issue 9; ISSN 1520-6106
• Publisher: American Chemical Society
• Country of Publication: United States
• Language: English