Evidence map›Paper›PMID 39160094›Full record

ArticleJournal of chemical theory and computation2024

A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions.

Janak Prabhu, Matteo Frigerio, Emanuele Petretto, Pablo Campomanes, Stefan Salentinig, Stefano Vanni

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Janak PrabhuDepartment of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
Matteo FrigerioDepartment of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland.
Emanuele PetrettoDepartment of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
Pablo CampomanesDepartment of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
Stefan SalentinigDepartment of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland.ORCID 0000-0002-7541-2734
Stefano VanniDepartment of Biology, University of Fribourg, 1700 Fribourg, Switzerland.ORCID 0000-0003-2146-1140

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Aqueous ionic solutions are pivotal in various scientific domains due to their natural prevalence and vital roles in biological and chemical processes. Molecular dynamics has emerged as an effective methodology for studying the dynamic behavior of these systems. While all-atomistic models have made significant strides in accurately representing and simulating these ions, the challenge persists in achieving precise models for coarse-grained (CG) simulations. Our study introduces two optimized models for sodium and chloride ions within the nonpolarizable surface property fitting coarse-grained force field (SPICA-FF) framework. The two models represent solvated ions, such as the original FF model, and unsolvated or bare ions. The nonbonded Lennard-Jones interactions were reparameterized to faithfully reproduce bulk properties, including density and surface tension, in sodium chloride solutions at varying concentrations. Notably, these optimized models replicate experimental surface tensions at high ionic strengths, a property not well-captured by the ions of the original model in the SPICA-FF. The optimized unsolvated model also proved successful in reproducing experimental osmotic pressure. Additionally, the newly reparameterized ion models capture hydrophobic interactions within sodium chloride solutions and show qualitative agreement when modeling structural changes in phospholipid bilayers, aligning with experimental observations. For aqueous solutions, these optimized models promise a more precise representation of the ion behavior.

Identifiers

PMID39160094
PMCPMC11391577

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.