Evidence map›Paper›PMID 39132799›Full record

ArticleThe Journal of chemical physics2024

A new method to calculate broadband dielectric spectra of solvents from molecular dynamics simulations demonstrated with polarizable force fields.

Rebecca A Bone, Moses K J Chung, Jay W Ponder, Demian Riccardi, Chris Muzny, Ravishankar Sundararaman, Kathleen Schwarz

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

7 authors.

Rebecca A BoneTheiss Research, P.O. Box 127, La Jolla, California 92038, USA.ORCID 0000-0003-4743-8475
Moses K J ChungDepartment of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA.ORCID 0000-0002-9516-1477
Jay W PonderDepartment of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA.ORCID 0000-0001-5450-9230
Demian RiccardiMaterial Measurement Laboratory, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA.ORCID 0000-0001-8095-7803
Chris MuznyMaterial Measurement Laboratory, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA.ORCID 0000-0003-1153-983X
Ravishankar SundararamanDepartment of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th St., Troy, New York 12180, USA.ORCID 0000-0002-0625-4592
Kathleen SchwarzMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, Maryland 20899, USA.ORCID 0000-0002-1539-4511

Funding

NATIONAL RESEARCH SERVICE AWARD-MEDICAL SCIENTISTT32GM007200 · NIGMS · WASHINGTON UNIVERSITY · PI YOKOYAMA, WAYNE M. · 1985 to 2024
$59.8M
DEVELOPMENT OF A NEXT-GENERATION NUCLEIC ACID FORCE FIELDR01GM106137 · NIGMS · WASHINGTON UNIVERSITY · PI JAY PONDER, Pengyu Ren · 2013 to 2026
$3.5M
Specificity and Selectivity in Protein-Ion BindingR01GM114237 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI PONDER, JAY, REN, PENGYU · 2015 to 2023
$2.6M
NIGMS NIH HHS R01 GM106137NIGMS NIH HHS R01 GM114237NIGMS NIH HHS T32 GM007200
6 · The paper itself

Abstract

Simulating the dielectric spectra of solvents requires the nuanced definition of inter- and intra-molecular forces. Non-polarizable force fields, while thoroughly benchmarked for dielectric applications, do not capture all the spectral features of solvents, such as water. Conversely, polarizable force fields have been largely untested in the context of dielectric spectroscopy but include charge and dipole fluctuations that contribute to intermolecular interactions. We benchmark non-polarizable force fields and the polarizable force fields AMOEBA03 and HIPPO for liquid water and find that the polarizable force fields can capture all the experimentally observed spectral features with varying degrees of accuracy. However, the non-polarizable force fields miss at least one peak. To diagnose this deficiency, we decompose the liquid water spectra from polarizable force fields at multiple temperatures into static and induced dipole contributions and find that the peak originates from induced dipole contributions. Broadening our inquiry to other solvents parameterized with the AMOEBA09 force field, we demonstrate good agreement between the experimental and simulated dielectric spectra of methanol and formamide. To produce these spectra, we develop a new computational approach to calculate the dielectric spectrum via the fluctuation dissipation theorem. This method minimizes the error in both the low and high frequency portions of the spectrum, improving the overall accuracy of the simulated spectrum and broadening the computed frequency range.

Identifiers

PMID39132799
PMCPMC11324330

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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.