Evidence map›Paper›PMID 41190181›Full record

ArticleChemical science2025

Solvation strategies for free-energy calculations in a halogen-bonded complex: implicit, explicit, and machine learning approaches.

Jaroslav Vacek, Dávid Vrška, Debashree Manna, Rabindranath Lo, Pavel Hobza

Abstract read
In one paragraph

Article in Chemical science, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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.

Jaroslav VacekInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo náměstí 542/2 160 00 Prague Czech Republic debashree.manna@uochb.cas.cz rabindranath.lo@uochb.cas.cz pavel.hobza@uochb.cas.cz.ORCID https://orcid.org/0009-0008-7075-9668
Dávid VrškaInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo náměstí 542/2 160 00 Prague Czech Republic debashree.manna@uochb.cas.cz rabindranath.lo@uochb.cas.cz pavel.hobza@uochb.cas.cz.ORCID https://orcid.org/0000-0003-1632-6251
Debashree MannaInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo náměstí 542/2 160 00 Prague Czech Republic debashree.manna@uochb.cas.cz rabindranath.lo@uochb.cas.cz pavel.hobza@uochb.cas.cz.ORCID https://orcid.org/0000-0002-1080-8068
Rabindranath LoInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo náměstí 542/2 160 00 Prague Czech Republic debashree.manna@uochb.cas.cz rabindranath.lo@uochb.cas.cz pavel.hobza@uochb.cas.cz.ORCID https://orcid.org/0000-0002-4436-3618
Pavel HobzaInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo náměstí 542/2 160 00 Prague Czech Republic debashree.manna@uochb.cas.cz rabindranath.lo@uochb.cas.cz pavel.hobza@uochb.cas.cz.ORCID https://orcid.org/0000-0001-5292-6719

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In pursuit of an efficient solvation approach for the halogen bonded complex between molecular iodine and tetramethylthiourea that reliably reproduces experimental trends, we investigated a range of solvent models, from implicit representations to periodic metadynamics simulations alongside micro-solvation and ONIOM-based methods as robust alternatives. Implicit solvent models fail to describe halogen-bonded complexes in high-polar solvents but provide surprisingly accurate estimates of binding free energies in all low to moderately polar solvents. For accurate and reliable modeling, especially in polar media, explicit solvent representations are essential. Periodic metadynamics simulations typically provide enhanced accuracy in calculating free energy differences, particularly for systems with complex solvation behavior. However, they are computationally demanding and restricted to generalized gradient approximation functionals (GGA). To overcome this limitation and improve accuracy, we employed the machine learning perturbation theory technique, enabling the estimation of free energies at levels of theory beyond the GGA.

Identifiers

PMID41190181
PMCPMC12581015

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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.