Evidence map›Paper›PMID 30428551›Full record

ArticleMolecules (Basel, Switzerland)2018

Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard⁻Jones Parameters for Water and to Study Solvation of TiO₂ Nanoparticles.

Asmus Ougaard Dohn, Daniele Selli, Gianluca Fazio, Lorenzo Ferraro, Jens Jørgen Mortensen, Bartolomeo Civalleri, Cristiana Di Valentin

Abstract read
In one paragraph

Article in Molecules (Basel, Switzerland), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Review
  3. Dopamine-Decorated TiOJournal of chemical theory and computation · 2020
    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

7 authors.

Asmus Ougaard DohnFaculty of Physical Sciences and Science Institute, University of Iceland, 107 Reykjavík, Iceland. asod@hi.is.ORCID 0000-0002-5172-7168
Daniele SelliDipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy. daniele.selli@unimib.it.
Gianluca FazioDipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy. g.fazio3@campus.unimib.it.
Lorenzo FerraroDipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy. lorenzo.ferraro@unimib.it.
Jens Jørgen MortensenCAMD, Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. jjmo@dtu.dk.
Bartolomeo CivalleriDipartimento di Chimica, Università di Torino and NIS Centre of Excellence, Via P. Giuria 7, I-10129 Torino, Italy. bartolomeo.civalleri@unito.it.ORCID 0000-0003-3198-3161
Cristiana Di ValentinDipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy. cristiana.divalentin@unimib.it.ORCID 0000-0003-4163-8062

Funding

European Research Council 647020Icelandic Research Fund 174244-051
6 · The paper itself

Abstract

Metal oxide nanoparticles (NPs) are regarded as good candidates for many technological applications, where their functional environment is often an aqueous solution. The correct description of metal oxide electronic structure is still a challenge for local and semilocal density functionals, whereas hybrid functional methods provide an improved description, and local atomic function-based codes such as CRYSTAL17 outperform plane wave codes when it comes to hybrid functional calculations. However, the computational cost of hybrids are still prohibitive for systems of real sizes, in a real environment. Therefore, we here present and critically assess the accuracy of our electrostatic embedding quantum mechanical/molecular mechanical (QM/MM) coupling between CRYSTAL17 and AMBER16, and demonstrate some of its capabilities via the case study of TiO₂ NPs in water. First, we produced new Lennard⁻Jones (LJ) parameters that improve the accuracy of water⁻water interactions in the B3LYP/TIP3P coupling. We found that optimizing LJ parameters based on water tri- to deca-mer clusters provides a less overstructured QM/MM liquid water description than when fitting LJ parameters only based on the water dimer. Then, we applied our QM/MM coupling methodology to describe the interaction of a 1 nm wide multilayer of water surrounding a spherical TiO₂ nanoparticle (NP). Optimizing the QM/MM water⁻water parameters was found to have little to no effect on the local NP properties, which provide insights into the range of influence that can be attributed to the LJ term in the QM/MM coupling. The effect of adding additional water in an MM fashion on the geometry optimized nanoparticle structure is small, but more evident effects are seen in its electronic properties. We also show that there is good transferability of existing QM/MM LJ parameters for organic molecules⁻water interactions to our QM/MM implementation, even though these parameters were obtained with a different QM code and QM/MM implementation, but with the same functional.

Indexed as

Quantum TheoryMetal NanoparticlesModels, MolecularSolventsTitaniumWaterSolventsTitaniumtitanium dioxideWaterforce field parametersgeometry optimizationmolecular dynamicsmultiscalenanoparticlesQM/MMtitanium dioxidewater

Identifiers

PMID30428551
PMCPMC6278561

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.