ArticleThe journal of physical chemistry. B2020
Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.
Article in The journal of physical chemistry. B, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Proton hopping and secondary gating reveal a universal transport mechanism in a minimal bacterial transporter EmrE.Biophysical journal · 2026Article
- Proton Transport on Graphamine: A Deep-Learning Potential Study.The journal of physical chemistry. C, Nanomaterials and interfaces · 2025Article
- Unveiling the intermediate hydrated proton in water through vibrational analysis on the 1750 cmNature communications · 2025Article
- In Silico Demonstration of Fast Anhydrous Proton Conduction on Graphanol.ACS applied materials & interfaces · 2023Article
- Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles.Journal of the American Chemical Society · 2023Article
- Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins.The journal of physical chemistry. B · 2022Article
- Improved Indicator Algorithms for Tracking a Hydrated Proton as A Local Structural Defect in Grotthuss Diffusion in Aqueous Solutions.Chemical physics letters · 2021Article
- Proton Traffic Jam: Effect of Nanoconfinement and Acid Concentration on Proton Hopping Mechanism.Angewandte Chemie (International ed. in English) · 2021Article
- Chemistrees: Data-Driven Identification of Reaction PathwaysJournal of chemical theory and computation · 2021Article
- Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface.Journal of chemical theory and computation · 2021Article
- Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
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2 authors.
Funding
Abstract
Proton transport in aqueous media is ubiquitously important in chemical and biological processes. Although ab initio molecular dynamics (AIMD) simulations have made great progress in characterizing proton transport, there has been a long-standing challenge in defining and tracking the excess proton, or more properly, the center of excess charge (CEC) created when a hydrogen nucleus distorts the electron distributions of water molecules in a delocalized and highly dynamic nature. Yet, defining (and biasing) such a CEC is essential when combining AIMD with enhanced sampling methods to calculate the relevant macroscopic properties via free-energy landscapes, which is the standard practice for most processes of interest. Several CEC formulas have been proposed and used, but none have yet been systematically tested or rigorously derived. In this paper, we show that the CEC can be used as a computational tool to disentangle IR features of the solvated excess proton from its surrounding solvent, and in turn, how correlating the features in the excess charge spectrum with the behavior of CEC in simulations enables a systematic evaluation of various CEC definitions. We present a new definition of CEC and show how it overcomes the limitations of those currently available both from a spectroscopic point of view and from a practical perspective of performance in enhanced sampling simulations.
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