Evidence map›Paper›PMID 25691830›Full record

ArticleJournal of chemical theory and computation2015

Multipolar Ewald methods, 2: applications using a quantum mechanical force field.

Timothy J Giese, Maria T Panteva, Haoyuan Chen, Darrin M York

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery.Journal of chemical theory and computation · 2023
    Article
  5. Article
  6. Quantum mechanical force fields for condensed phase molecular simulations.Journal of physics. Condensed matter : an Institute of Physics journal · 2017
    Article
  7. Article
  8. Review
  9. Article
  10. Article
  11. 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.

Timothy J GieseCenter for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States
Maria T Panteva
Haoyuan Chen
Darrin M York

Funding

Multi-Scale Quantum Models for Ribozyme CatalysisR01GM062248 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Darrin M York · 2001 to 2026
$7.1M
NIGMS NIH HHS GM62248NIGMS NIH HHS R01 GM062248
6 · The paper itself

Abstract

A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework.

Indexed as

Quantum TheoryMolecular Dynamics SimulationNitrophenolsOrganophosphorus CompoundsSarcosineWaterdimethylglycineNitrophenolsnitrophenylphosphateOrganophosphorus CompoundsSarcosineWater

Identifiers

PMID25691830
PMCPMC4325604

What OpenQuestion holds

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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.