Evidence map›Paper›PMID 30830778›Full record

ArticleJournal of chemical theory and computation2019

Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields.

Vered Wineman-Fisher, Yasmine Al-Hamdani, Iqbal Addou, Alexandre Tkatchenko, Sameer Varma

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing 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

10 citing papers in PubMed.

  1. Article
  2. Polarizable AMOEBA Model for Simulating MgJournal of chemical information and modeling · 2024
    Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Transferable interactions of LiThe Journal of chemical physics · 2020
    Article
  10. 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

5 authors.

Vered Wineman-FisherDepartment of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States.ORCID http://orcid.org/0000-0002-5124-5900
Yasmine Al-HamdaniPhysics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Fïancerie , Luxembourg City , L-1511 , Luxembourg.
Iqbal AddouDepartment of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States.
Alexandre TkatchenkoPhysics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Fïancerie , Luxembourg City , L-1511 , Luxembourg.
Sameer VarmaDepartment of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States.

Funding

Accurate and Efficient Modeling of Biomolecular Ionic Interactions: Charge Redistribution, Polarization and DispersionR01GM118697 · NIGMS · UNIVERSITY OF SOUTH FLORIDA · PI VARMA, SAMEER · 2016 to 2019
$904k
NIGMS NIH HHS R01 GM118697
6 · The paper itself

Abstract

Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional groups, such as those present in biomolecules. However, several studies now demonstrate that this transferability assumption produces, in many different cases, large errors. Here we address this issue in a representative polarizable model and focus on transferability of cationic interactions from water to a series of alcohols. Both water and alcohols use hydroxyls for ion-coordination, and, therefore, this set of molecules constitutes the simplest possible case of transferability. We obtain gas phase reference data systematically from "gold-standard" quantum Monte Carlo and CCSD(T) methods, followed by benchmarked vdW-corrected DFT. We learn that the original polarizable model yields large gas phase water → alcohol transferability errors - the RMS and maximum errors are 2.3 and 5.1 kcal/mol, respectively. These errors are, nevertheless, systematic in that ion-alcohol interactions are overstabilized, and systematic errors typically imply that some essential physics is either missing or misrepresented. A comprehensive analysis shows that when both low- and high-field responses of ligand dipole polarization are described accurately, then transferability improves significantly - the RMS and maximum errors in the gas phase reduce, respectively, to 0.9 and 2.5 kcal/mol. Additionally, predictions of condensed phase transfer free energies also improve. Nevertheless, within the limits of the extrathermodynamic assumptions necessary to separate experimental estimates of salt dissolution into constituent cationic and anionic contributions, we note that the error in the condensed phase is systematic, which we attribute, at least, partially to the parametrization in long-range electrostatics. Overall, this work demonstrates a rational approach to boosting transferability of ionic interactions that will be applicable broadly to improving other polarizable and nonpolarizable models.

Identifiers

PMID30830778
PMCPMC6598712

What OpenQuestion holds

Textmetadata
LicenceTDM
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.