Evidence map›Paper›PMID 38557841›Full record

ArticleThe Journal of chemical physics2024

Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations.

Jorge Nochebuena, Shubin Liu, G Andrés Cisneros

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. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Jorge NochebuenaDepartment of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA.ORCID 0000-0003-0707-1066
Shubin LiuResearch Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.ORCID 0000-0001-9331-0427
G Andrés CisnerosDepartment of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA.ORCID 0000-0001-6629-3430

Funding

Theory and Simulation of DNA Repair Enzymes; Mechanism, Structure and FunctionR01GM108583 · NIGMS · WAYNE STATE UNIVERSITY · PI CISNEROS, GERARDO ANDRES · 2014 to 2022
$2.9M
Computational Simulations of DNA Transaction Enzymes - Application and DevelopmentR35GM151951 · NIGMS · UNIVERSITY OF TEXAS DALLAS · PI Gerardo Andres Cisneros · 2024 to 2026
$1.2M
NIGMS NIH HHS R01 GM108583NIGMS NIH HHS R35 GM151951
6 · The paper itself

Abstract

QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise. We showed that despite those limitations, polarizable and non-polarizable force fields can reproduce relative cooperativity achieved using density functional theory due to error compensation mechanisms. In this contribution, we assess the performance of QM/MM methods in reproducing these phenomena. Our study highlights the significance of the QM region size and force field choice in QM/MM calculations, emphasizing the importance of parameter validation to obtain accurate interaction energy predictions.

Identifiers

PMID38557841
PMCPMC13074183

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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.