ArticleJournal of chemical theory and computation2014
Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Quantum chemical investigation of the effect of alkali metal ions on the dynamic structure of water in aqueous solutions.RSC advances · 2022Article
- Using Machine Learning to Greatly Accelerate Path IntegralJournal of chemical theory and computation · 2022Article
- Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.Journal of the American Chemical Society · 2022Article
- Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.The journal of physical chemistry. B · 2020Article
- Density-Functional Tight-Binding Study of Carbonaceous Species Diffusion on the (100)-γ-AlACS omega · 2020Article
- Quantum Phonon Transport in Nanomaterials: Combining Atomistic with Non-Equilibrium Green's Function Techniques.Entropy (Basel, Switzerland) · 2019Review
- Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.Journal of computational chemistry · 2017Article
- Water Multilayers on TiOJournal of chemical theory and computation · 2017Article
- Acid activation mechanism of the influenza A M2 proton channel.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins.Journal of chemical theory and computation · 2016Article
- Hydrated Excess Protons Can Create Their Own Water Wires.The journal of physical chemistry. B · 2015Article
- 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
- Multiscale Reactive Molecular Dynamics for Absolute pJournal of chemical theory and computation · 2014Article
- A delocalized proton-binding site within a membrane protein.Biophysical journal · 2014Article
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3 authors.
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Abstract
The self-consistent charge density functional tight binding (SCC-DFTB) method has been increasingly applied to study proton transport (PT) in biological environments. However, recent studies revealing some significant limitations of SCC-DFTB for proton and hydroxide solvation and transport in bulk aqueous systems call into question its accuracy for simulating PT in biological systems. The current work benchmarks the SCC-DFTB/MM method against more accurate DFT/MM by simulating PT in a synthetic leucine-serine channel (LS2), which emulates the structure and function of biomolecular proton channels. It is observed that SCC-DFTB/MM produces over-coordinated and less structured pore water, an over-coordinated excess proton, weak hydrogen bonds around the excess proton charge defect and qualitatively different PT dynamics. Similar issues are demonstrated for PT in a carbon nanotube, indicating that the inaccuracies found for SCC-DFTB are not due to the point charge based QM/MM electrostatic coupling scheme, but rather to the approximations of the semiempirical method itself. The results presented in this work highlight the limitations of the present form of the SCC-DFTB/MM approach for simulating PT processes in biological protein or channel-like environments, while providing benchmark results that may lead to an improvement of the underlying method.
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