ArticleThe journal of physical chemistry. B2011
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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.
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.
Who cites it
17 citing papers in PubMed.
- Gold Nanocluster-Amino Acid Interactions: Assessment of DFTB with Dispersion Corrections.ACS omega · 2026Article
- Multi-proton dynamics near membrane-water interface.Nature communications · 2025Article
- Research of Water Molecules Cluster Structuring duringPlants (Basel, Switzerland) · 2022Article
- Using Machine Learning to Greatly Accelerate Path IntegralJournal of chemical theory and computation · 2022Article
- Morphological effect of side chain on HScientific reports · 2020Article
- Density-functional tight-binding: basic concepts and applications to molecules and clusters.Advances in physics: X · 2020Article
- Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.Chemical reviews · 2016Review
- Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis.Chemical science · 2015Article
- Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.The journal of physical chemistry. B · 2014Article
- Density functional tight binding: values of semi-empirical methods in an ab initio era.Physical chemistry chemical physics : PCCP · 2014Article
- A delocalized proton-binding site within a membrane protein.Biophysical journal · 2014Article
- Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions.Journal of chemical theory and computation · 2014Article
- Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel.Journal of chemical theory and computation · 2014Article
- Quantum mechanical force field for water with explicit electronic polarization.The Journal of chemical physics · 2013Article
- A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries.Chemical physics · 2012Article
- Insights into the mechanism of proton transport in cytochrome c oxidase.Journal of the American Chemical Society · 2012Article
- Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase.Biophysical journal · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The self-consistent charge density functional tight-binding (SCC-DFTB) method has been actively employed to study proton-transfer processes in biological systems. Recent studies in the literature employing SCC-DFTB reported that the method favors the Zundel form of the hydrated proton over the Eigen form, both in gas-phase water clusters and in bulk water, in disagreement with both higher-level calculations and experimental data. In this work, we explore the performance of SCC-DFTB for protonated gas-phase water clusters and bulk water (the latter both with and without an excess proton) with a modified O-H repulsive potential reported in our earlier work and with on-site third-order expansion of the DFT energy. Our results show that, with the proper set of published parameters, SCC-DFTB does correctly favor the Eigen form of the hydrated proton as compared to the Zundel form, both in gas-phase clusters and in the bulk; the amphiphilic character of the hydrated proton discussed in the literature has also been observed. The analyses do, however, bring forth remaining limitations in terms of the solvation structure around the hydrated proton as well as the structure of bulk water, which can guide future improvements of the method.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.