Evidence map›Paper›PMID 23020318›Full record

ArticleThe Journal of chemical physics2012

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

Jaydeep P Bardhan, Pavel Jungwirth, Lee Makowski

Open access · bronzeAbstract read
In one paragraph

Article in The Journal of chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
2.6field-weighted citation impact, top 10% of its field
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

11 citing papers in PubMed, 49 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Accuracy limit of rigid 3-point water models.The Journal of chemical physics · 2016
    Article
  8. Article
  9. Article
  10. Introducing Charge Hydration Asymmetry into the Generalized Born Model.Journal of chemical theory and computation · 2014
    Article
  11. Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities.Journal of the mechanical behavior of materials · 2013
    Article
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

3 authors at 2 institutions in 2 countries.

Jaydeep P BardhanDepartment of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois 60612, USA.
Pavel Jungwirth
Lee Makowski
Northeastern University · USCzech Academy of Sciences, Institute of Organic Chemistry and Biochemistry · CZ

Funding

MADMAX: Precise Measurement of Conformational Changes in ProteinsR01GM085648 · NIGMS · UNIVERSITY OF CHICAGO · PI MAKOWSKI, LEE · 2008 to 2011
$1.2M
Understanding pH-Dependent Protein Behavior Using Advanced Continuum TheoryR21GM102642 · NIGMS · NORTHEASTERN UNIVERSITY · PI BARDHAN, JAYDEEP PORTER · 2012 to 2013
$376k
NIGMS NIH HHS GM085648NIGMS NIH HHS GM102642NIGMS NIH HHS R01 GM085648NIGMS NIH HHS R21 GM102642
6 · The paper itself

Abstract

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular "linear response" model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution).

Indexed as

Molecular Dynamics SimulationThermodynamicsIonsSolubilityIons

Identifiers

PMID23020318
PMCPMC3470608
OpenAlexW2081727601

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.