ArticleJournal of chemical theory and computation2015
Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.
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 25 papers.
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Who cites it
25 citing papers in PubMed, 49 citations in OpenAlex.
- Explainable QSAR models of 5-HT1A receptor ligands using conceptual DFT descriptors and no-code machine learning tools.Journal of computer-aided molecular design · 2026Article
- Evaluation of 3',4'-Di-Biomolecules · 2026Article
- Using Deep Graph Neural Networks Improves Physics-Based Hydration Free Energy Predictions Even for Molecules Outside of the Training Set Distribution.The journal of physical chemistry. B · 2025Article
- Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment.Journal of chemical theory and computation · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems.Journal of chemical information and modeling · 2023Article
- The role of loop dynamics in the prediction of ligand-protein binding enthalpy.Chemical science · 2023Article
- PERSISTENT PATH LAPLACIAN.Foundations of data science (Springfield, Mo.) · 2023Article
- Broad-Spectrum Extracellular Antiviral Properties of Cucurbit[ACS infectious diseases · 2022Article
- The Role of Packing, Dispersion, Electrostatics, and Solvation in High-Affinity Complexes of Cucurbit[n]urils with Uncharged Polar Guests.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails.Nature communications · 2021Article
- Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.Journal of chemical information and modeling · 2021Article
- SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.Journal of computer-aided molecular design · 2021Article
- Are 2D fingerprints still valuable for drug discovery?Physical chemistry chemical physics : PCCP · 2020Article
- Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.Journal of chemical theory and computation · 2019Article
- Generative network complex (GNC) for drug discovery.Communications in information and systems · 2019Article
- Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.The Journal of chemical physics · 2018Article
- Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.Journal of chemical theory and computation · 2018Article
- Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.Journal of chemical theory and computation · 2018Article
- High-Temperature Dynamic Behavior in Bulk Liquid Water: A Molecular Dynamics Simulation Study using the OPC and TIP4P-Ew Potentials.Frontiers of physics · 2018Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.
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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.