ArticleJournal of chemical information and modeling2018
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.
Article in Journal of chemical information and modeling, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed.
- Long-Timescale Molecular Dynamics Reveal a Coordination-Biased Conformational Selection Mechanism for Sorcin Activation.bioRxiv : the preprint server for biology · 2026Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Getting the intermolecular forces correct: introducing the ASTA strategy for a water model.RSC advances · 2024Article
- Evaluating Polarizable Biomembrane Simulations against Experiments.Journal of chemical theory and computation · 2024Article
- Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field.Journal of chemical theory and computation · 2024Article
- Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.Journal of chemical theory and computation · 2023Article
- Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent.Journal of chemical theory and computation · 2023Article
- Capturing charge and size effects of ions at the graphene-electrolyte interface using polarizable force field simulations.Nanoscale advances · 2023Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Molecular Dynamics Investigation into pH Dependent Metal Binding of the Intrinsically Disordered Worm Jaw Protein, Nvjp-1.The journal of physical chemistry. B · 2022Article
- Does the inclusion of electronic polarisability lead to a better modelling of peptide aggregation?RSC advances · 2022Article
- Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.Journal of the American Chemical Society · 2022Article
- Recent progress in general force fields of small molecules.Current opinion in structural biology · 2022Review
- Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.Communications chemistry · 2022Review
- Methyl-Induced Polarization Destabilizes the Noncovalent Interactions of N-Methylated Lysines.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition.Journal of chemical information and modeling · 2021Article
- Uncovering Differences in Hydration Free Energies and Structures for Model Compound Mimics of Charged Side Chains of Amino Acids.The journal of physical chemistry. B · 2021Article
- Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.Journal of chemical theory and computation · 2021Article
- Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.Journal of molecular modeling · 2020Article
- Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.Journal of chemical theory and computation · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Development of accurate force field parameters for molecular ions in the context of a polarizable energy function based on the classical Drude oscillator is a crucial step toward an accurate polarizable model for modeling and simulations of biological macromolecules. Toward this goal we have undertaken a hierarchical approach in which force field parameter optimization is initially performed for small molecules for which experimental data exists that serve as building blocks of macromolecular systems. Small molecules representative of the ionic moieties of biological macromolecules include the cationic ammonium and methyl substituted ammonium derivatives, imidazolium, guanidinium and methylguanidinium, and the anionic acetate, phenolate, and alkanethiolates. In the present work, parameters for molecular ions in the context of the Drude polarizable force field are optimized and compared to results from the nonpolarizable additive CHARMM general force field (CGenFF). Electrostatic and Lennard-Jones parameters for the model compounds are developed in the context of the polarizable SWM4-NDP water model, with emphasis on assuring that the hydration free energies are consistent with previously reported parameters for atomic ions. The final parameters are shown to be in good agreement with the selected quantum mechanical (QM) and experimental target data. Analysis of the structure of water around the ions reveals substantial differences between the Drude and additive force fields indicating the important role of polarization in dictating the molecular details of aqueous solvation. The presented parameters represent the foundation for the charged functionalities in future generations of the Drude polarizable force field for biological macromolecules as well as for drug-like molecules.
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.