Hybrid polarizable simulations of a conventional hydrophobic polyelectrolyte. Toward a theoretical tool for green science innovation

Masella, Michel; Crudu, Alina; Léonforte, Fabien

doi:10.1063/5.0056508

Cited by 3 publications

(3 citation statements)

References 81 publications

(88 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These new ab initio -based modeling approach are of particular interest to theoretically investigate new chemical systems ahead of experiment. Moreover they may be also considered to complement data from popular simulation approaches (based on efficient pairwise force fields) to better assess the reliability of the conclusions that we may draw from molecular modeling simulations, in particular for polyelectrolyte solutions in which microscopic dynamical polarization effects can play a pivotal role or to be negligible depending on the local ionic structures (see the discussions in ref ( 39 )).…”

Section: Discussionmentioning

confidence: 99%

“…As compared to explicit all atom simulations that have been performed to investigate the properties of chitosan chains, ,− chitosan films and membranes (here we may also quote ab initio molecular dynamics simulations), and chitosan-decorated graphenes, as well as the chitin decrystallization process, the length of the chitosan chains that can be readily modeled using a coarse grained approach is at least 2 orders of magnitude larger. However, it is far from obvious to check whether a coarse grained approach is able to capture the strength and balance of microscopic phenomena modulating the properties of chitosan chains in complex environments, in particular microscopic polarization effects that are pivotal to understanding the properties in the aqueous phase from monatomic ions to polyelectrolytes. − …”

Section: Introductionmentioning

confidence: 99%

“…However, it is far from obvious to check whether a coarse grained approach is able to capture the strength and balance of microscopic phenomena modulating the properties of chitosan chains in complex environments, in particular microscopic polarization effects that are pivotal to understanding the properties in the aqueous phase from monatomic ions to polyelectrolytes. 35 − 39 …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Chitosan Polysaccharides from a Polarizable Multiscale Approach

Masella,

Léonforté

2023

ACS Omega

Self Cite

View full text Add to dashboard Cite

We report simulations of chitosan polysaccharides in the aqueous phase, at infinite dilute conditions and zero ionic strength. Those simulations are performed by means of a polarizable multiscale modeling scheme that relies on a polarizable all atom force field to model solutes and on a polarizable solvent coarse grained approach. Force field parameters are assigned only from quantum chemistry ab initio data. We simulate chitosan monomer units, dimers and 50-long chains. Regarding the 50-long chains we simulate three sets of ten randomly built chain replica at three different pH conditions (corresponding to different chain protonation states, the chain degree of deacetylation is 85%). Our simulations show the persistence length of 50-long chitosan chains at strong acidic conditions (pH <5) to be 24 ± 2 nm (at weak/negligible ionic strength conditions), and to be 1 order of magnitude shorter at usual pH conditions. Our simulation data support the most recent simulation and experimental studies devoted to chitosan polysaccharides in the aqueous phase.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Chitosan Polysaccharides from a Polarizable Multiscale Approach

Masella,

Léonforté

2023

ACS Omega

Self Cite

View full text Add to dashboard Cite

show abstract

Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors

Genovese

Dawson

Nakajima

et al. 2023

The Journal of Chemical Physics

View full text Add to dashboard Cite

We present a hybrid, multi-method, computational scheme for protein/ligand systems well suited to be used on modern and forthcoming massively parallel computing systems. The scheme relies on a multi-scale polarizable molecular modeling, approach to perform molecular dynamics simulations, and on an efficient Density Functional Theory (DFT) linear scaling method to post-process simulation snapshots. We use this scheme to investigate recent α-ketoamide inhibitors targeting the main protease of the SARS-CoV-2 virus. We assessed the reliability and the coherence of the hybrid scheme, in particular, by checking the ability of MM and DFT to reproduce results from high-end ab initio computations regarding such inhibitors. The DFT approach enables an a posteriori fragmentation of the system and an investigation into the strength of interaction among identified fragment pairs. We show the necessity of accounting for a large set of plausible protease/inhibitor conformations to generate reliable interaction data. Finally, we point out ways to further improve α-ketoamide inhibitors to more strongly interact with particular protease domains neighboring the active site.

show abstract

The multi-scale polarizable pseudo-particle solvent coarse-grained approach: From NaCl salt solutions to polyelectrolyte hydration

Masella,

Léonforté

2024

The Journal of Chemical Physics

View full text Add to dashboard Cite

We discuss key parameters that affect the reliability of hybrid simulations in the aqueous phase based on an efficient multi-scale coarse-grained polarizable pseudo-particle approach, denoted as pppl, to model the solvent water, whereas solutes are modeled using an all atom polarizable force field. Among those parameters, the extension of the solvent domain (SD) at the solute vicinity (domain in which each solvent particle corresponds to a single water molecule) and the magnitude of solute/solvent short range polarization damping effects are shown to be pivotal to model NaCl salty aqueous solutions and the hydration of charged systems, such as the hydrophobic polyelectrolyte polymer that we have recently investigated [Masella et al., J. Chem. Phys. 155, 114903 (2021)]. Strong short range damping is pivotal to simulate aqueous salt NaCl solutions at moderate concentration (up to 1.0M). The SD extension (as well as short range damping) has a weak effect on the polymer conformation; however, it plays a pivotal role in computing accurate polymer/solvent interaction energies. As the pppl approach is up to two orders of magnitude computationally more efficient than all atom polarizable force field methods, our results show it to be an efficient alternative route to investigate the equilibrium properties of complex charged molecular systems in extended chemical environments.

show abstract

Hybrid polarizable simulations of a conventional hydrophobic polyelectrolyte. Toward a theoretical tool for green science innovation

Cited by 3 publications

References 81 publications

Chitosan Polysaccharides from a Polarizable Multiscale Approach

Chitosan Polysaccharides from a Polarizable Multiscale Approach

Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors

The multi-scale polarizable pseudo-particle solvent coarse-grained approach: From NaCl salt solutions to polyelectrolyte hydration

Contact Info

Product

Resources

About