Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.

Anders S Christensen, Casper Steinmann, Dmitri G Fedorov, Jan H Jensen

Open access · goldAbstract read

In one paragraph

Article in PloS one, 2014. 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

1.5field-weighted citation impact, top 17% of its field

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, 12 citations in OpenAlex.

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

4 authors at 3 institutions in 2 countries.

Anders S ChristensenDepartment of Chemistry, University of Copenhagen, Copenhagen, Denmark.

Casper SteinmannDepartment of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark.

Dmitri G FedorovNanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.

Jan H JensenDepartment of Chemistry, University of Copenhagen, Copenhagen, Denmark.

University of Copenhagen · DKNational Institute of Advanced Industrial Science and Technology · JPUniversity of Southern Denmark · DK

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.

Indexed as

Models, MolecularProtein MultimerizationProteinsProtein Structure, QuaternaryProtein Structure, TertiaryQuantum TheoryThermodynamicsProteins

Identifiers

PMID24558430

DOI10.1371/journal.pone.0088800

PMCPMC3928295

OpenAlexW2059119853

What OpenQuestion holds

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LicenceCC BY

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Registered trials

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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.