Evidence map›Paper›PMID 32022044›Full record

ArticlePhysical chemistry chemical physics : PCCP2020

How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters?

Junbo Chen, Bun Chan, Yihan Shao, Junming Ho

Abstract read
In one paragraph

Article in Physical chemistry chemical physics : PCCP, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Article
  6. 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

4 authors.

Junbo ChenSchool of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia. junming.ho@unsw.edu.au.ORCID http://orcid.org/0000-0002-0714-6710
Bun ChanGraduate School of Engineering, Nagasaki University, Bunkyo-Machi 1-14, Nagasaki 852-8521, Japan. bun.chan@nagasaki-u.ac.jp.ORCID http://orcid.org/0000-0002-0082-5497
Yihan ShaoDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA.ORCID http://orcid.org/0000-0001-9337-341X
Junming HoSchool of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia. junming.ho@unsw.edu.au.ORCID http://orcid.org/0000-0001-9381-924X

Funding

Multiscale Modeling of Enzymatic Reactions and Firefly BioluminescenceR01GM135392 · NIGMS · UNIVERSITY OF OKLAHOMA · PI SHAO, YIHAN · 2019 to 2022
$1.0M
NIGMS NIH HHS R01 GM135392
6 · The paper itself

Abstract

In this paper, the performance of a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water. Three different charge states (neutral, proton transfer transition state and zwitterion) of glycine were solvated by 1 to 40 water molecules as sampled from molecular dynamics simulations. While some ab initio composite methods that employ insufficiently large basis sets incurred significant errors even for a cluster containing only 5 water molecules relative to the W1X-2 benchmark, the DLPNO-CCSD(T)/CBS and DSD-PBEP86 (triple zeta basis set) levels of theory predicted very accurate interaction energies. These levels of theory were used to benchmark the performance of 16 density functionals from different rungs of Jacob's Ladder. Of the Rung 4 functionals examined, the ωB97M-V and ωB97X-V functionals stood out for predicting absolute interaction energies in 40-water clusters with mean absolute deviations (MAD) ∼4 kJ mol-1. The B3LYP-D3(BJ) functional performed exceptionally well with a MAD ∼1.7 kJ mol-1 and is the overall best performing method. Calculations of relative interaction energies allow for cancellation of systematic errors, including basis set truncation and superposition errors, and the ωB97M-V and B3LYP-D3(BJ) double zeta basis set calculations yielded relative interaction energies that are within ∼3 kJ mol-1 of the benchmark. The ONIOM approximation provides another strategy for accelerating the calculation of accurate absolute interaction energies provided that the calculations have converged with respect to the size of the "high-level-layer".

Identifiers

PMID32022044
PMCPMC7394230

What OpenQuestion holds

Textmetadata
LicenceTDM
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.