Evidence map›Paper›PMID 21663351›Full record

ArticleThe Journal of chemical physics2011

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems.

Robert Send, Ville R I Kaila, Dage Sundholm

Open access · bronzeAbstract read
In one paragraph

Article in The Journal of chemical physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
2.6field-weighted citation impact, top 11% 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

12 citing papers in PubMed, 66 citations in OpenAlex.

  1. Modified chlorophyll pigment at ChlChemical science · 2025
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  2. Magnetically Induced Current-Density Susceptibility of Circum[The journal of physical chemistry. A · 2025
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  4. Quasiparticle Self-ConsistentJournal of chemical theory and computation · 2022
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  5. Article
  6. Review
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  8. Article
  9. Article
  10. Energetics and dynamics of a light-driven sodium-pumping rhodopsin.Proceedings of the National Academy of Sciences of the United States of America · 2017
    Article
  11. Article
  12. 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

3 authors at 3 institutions in 3 countries.

Robert SendInstitut für Physikalische Chemie, Karlsruher Institut für Technologie, Kaiserstrasse 12, 76131 Karlsruhe, Germany. Robert.Send@kit.edu
Ville R I Kaila
Dage Sundholm
Karlsruhe Institute of Technology · DENational Institutes of Health · USUniversity of Helsinki · FI

Funding

Intramural NIH HHS
6 · The paper itself

Abstract

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.

Indexed as

Molecular Dynamics SimulationBacterial ProteinsBenzyl CompoundsCluster AnalysisCoumaric AcidsEnergy TransferGreen Fluorescent ProteinsImidazolinesModels, ChemicalPhotoreceptors, MicrobialQuantum TheoryRetinaldehydeRhodopsinBacterial ProteinsBenzyl CompoundsCoumaric AcidsGreen Fluorescent ProteinsImidazolinesphotoactive yellow protein, BacteriaPhotoreceptors, Microbialp-hydroxybenzylideneimidazolinoneRetinaldehydeRhodopsin

Identifiers

PMID21663351
PMCPMC3133567
OpenAlexW1988332152

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.