Evidence map›Paper›PMID 39749917›Full record

ArticleJournal of computational chemistry2025

A Closer Look at the FeS Heme Bonds in Azotobacter vinelandii Bacterioferritin: QM/MM and Local Mode Analysis.

Marek Freindorf, Elfi Kraka

Abstract read
In one paragraph

Article in Journal of computational chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Local Vibrational Mode Analysis of Phonon Dispersion Relations in Crystals.Journal of chemical theory and computation · 2026
    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

2 authors.

Marek FreindorfChemistry Department, Southern Methodist University, Dallas, Texas, USA.
Elfi KrakaChemistry Department, Southern Methodist University, Dallas, Texas, USA.ORCID https://orcid.org/0000-0002-9658-5626

Funding

National Science Foundation CHE 2102461
6 · The paper itself

Abstract

Using the QM/MM methodology and a local mode analysis, we investigated a character and a strength of FeS bonds of heme groups in oxidized and reduced forms of Bacterioferritin from Azotobacter vinelandii. The strength of the FeS bonds was correlated with a bond length, an energy density at a bond critical point, and a charge difference of the F and S atoms. Changing the oxidation state from ferrous to ferric generally makes the FeS bonds weaker, longer, more covalent, and more polar. We also investigated the SFeS bond bending and found that the stronger FeS bond, generally makes the SFeS bond bending stiffer, which could play a key role in the balance between ferric and ferrous oxidation states and related biological activities.

Indexed as

Azotobacter vinelandiiBacterial ProteinsCytochrome b GroupFerritinsHemeModels, MolecularOxidation-ReductionQuantum TheoryBacterial ProteinsbacterioferritinCytochrome b GroupFerritinsHemebacterioferritinheme grouplocal mode analysisQM/MMvibrational spectroscopy

Identifiers

PMID39749917
PMCPMC11697534

What OpenQuestion holds

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LicenceCC BY-NC
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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.