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Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent

https://doi.org/10.1021/jp0667442
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Performing Molecular Dynamics Simulations and Computing Hydration Free Energies on the B3LYP-D3(BJ) Potential Energy Surface with Adaptive Force Matching: A Benchmark Study with Seven Alcohols and One Amine
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Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations
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Comprehensive Framework for the Design of High-Performing and Sustainable Polyamides
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In SilicoStrategies for Modeling Stereoselective Metabolism of Pyrethroids
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Computing Relative Free Energies of Solvation Using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange
inferred← citeshttps://doi.org/10.1021/ct1006746openalex-snapshot
Efficient Solvation Free Energy Calculations of Amino Acid Analogs by Expanded Ensemble Molecular Simulation
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Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides
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Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
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Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
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Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field
inferred← citeshttps://doi.org/10.1021/ct300220popenalex-snapshot
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations
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3D-RISM-D ock : A New Fragment-Based Drug Design Protocol
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Hydration Free Energies of Multifunctional Nitroaromatic Compounds
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Physicochemical Properties of Hazardous Energetic Compounds from Molecular Simulation
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Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process
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Hirshfeld-E Partitioning: AIM Charges with an Improved Trade-off between Robustness and Accurate Electrostatics
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Calculating the Sensitivity and Robustness of Binding Free Energy Calculations to Force Field Parameters
inferred← citeshttps://doi.org/10.1021/ct4005068openalex-snapshot
Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions
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Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory
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Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites
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A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies
inferred← citeshttps://doi.org/10.1021/ct4011129openalex-snapshot
A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers
inferred← citeshttps://doi.org/10.1021/ct500016dopenalex-snapshot
Evaluation of CM5 Charges for Condensed-Phase Modeling
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Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies
inferred← citeshttps://doi.org/10.1021/ct500569bopenalex-snapshot
Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
inferred← citeshttps://doi.org/10.1021/ct5007828openalex-snapshot
KECSA-Movable Type Implicit Solvation Model (KMTISM)
inferred← citeshttps://doi.org/10.1021/ct500924fopenalex-snapshot
Solution Properties of Hemicellulose Polysaccharides with Four Common Carbohydrate Force Fields
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Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions
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Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method
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Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations
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Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS)
inferred← citeshttps://doi.org/10.1021/ct800445xopenalex-snapshot
Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model
inferred← citeshttps://doi.org/10.1021/ct900029dopenalex-snapshot
Integrated Continuum Dielectric Approaches To Treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation
inferred← citeshttps://doi.org/10.1021/ct900079topenalex-snapshot
Validating CHARMM Parameters and Exploring Charge Distribution Rules in Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1021/ct900214yopenalex-snapshot
1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies
inferred← citeshttps://doi.org/10.1021/ct9005773openalex-snapshot
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field
inferred← citeshttps://doi.org/10.1021/ct900587bopenalex-snapshot
Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field
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Effect of the Integration Method on the Accuracy and Computational Efficiency of Free Energy Calculations Using Thermodynamic Integration
inferred← citeshttps://doi.org/10.1021/ct900693qopenalex-snapshot
The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration
inferred← citeshttps://doi.org/10.1021/ie401295jopenalex-snapshot
Efficient Estimation of the Equilibrium Solution-Phase Fugacity of Soluble Nonelectrolyte Solids in Binary Solvents by Molecular Simulation
inferred← citeshttps://doi.org/10.1021/ja906399eopenalex-snapshot
Oil/Water Transfer Is Partly Driven by Molecular Shape, Not Just Size
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Predicting the Solubility of the Sparingly Soluble Solids 1,2,4,5-Tetramethylbenzene, Phenanthrene, and Fluorene in Various Organic Solvents by Molecular Simulation
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Temperature-Dependent Physicochemical Properties and Solvation Thermodynamics of Nitrotoluenes from Solvation Free Energies
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Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry
inferred← citeshttps://doi.org/10.1021/jo301119hopenalex-snapshot
Diastereomer Configurations from Joint Experimental–Computational Analysis
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The Effect of Solvation on Biomolecular Conformation: 2-Amino-1-phenylethanol
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Coupling of Complex Aromatic Ring Vibrations to Solvent through Hydrogen Bonds: Effect of Varied On-Ring and Off-Ring Hydrogen-Bonding Substitutions
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Prediction of Partition Coefficients by Multiscale Hybrid Atomic-Level/Coarse-Grain Simulations
inferred← citeshttps://doi.org/10.1021/jp0764384openalex-snapshot
Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules
inferred← citeshttps://doi.org/10.1021/jp076729copenalex-snapshot
Conformational Analysis of l -Prolines in Water
inferred← citeshttps://doi.org/10.1021/jp077179lopenalex-snapshot
Improving the Performance of the Coupled Reference Interaction Site Model−Hyper-netted Chain (RISM−HNC)/Simulation Method for Free Energy of Solvation
inferred← citeshttps://doi.org/10.1021/jp101597ropenalex-snapshot
Nonadditive Empirical Force Fields for Short-Chain Linear Alcohols: Methanol to Butanol. Hydration Free Energetics and Kirkwood−Buff Analysis Using Charge Equilibration Models
inferred← citeshttps://doi.org/10.1021/jp101909aopenalex-snapshot
Arginine-Assisted Solubilization System for Drug Substances: Solubility Experiment and Simulation
inferred← citeshttps://doi.org/10.1021/jp103050uopenalex-snapshot
New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of Their Accuracy and Precision
inferred← citeshttps://doi.org/10.1021/jp106282wopenalex-snapshot
Hydration Structure of the Quaternary Ammonium Cations
inferred← citeshttps://doi.org/10.1021/jp108173fopenalex-snapshot
Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule Hydration Free Energies in Explicit Solvent
inferred← citeshttps://doi.org/10.1021/jp200776topenalex-snapshot
Quantifying Water-Mediated Protein–Ligand Interactions in a Glutamate Receptor: A DFT Study
inferred← citeshttps://doi.org/10.1021/jp209041xopenalex-snapshot
Configurational Preferences of Arylamide α-Helix Mimetics via Alchemical Free Energy Calculations of Relative Binding Affinities
inferred← citeshttps://doi.org/10.1021/jp211083fopenalex-snapshot
Structures in Solutions from Joint Experimental-Computational Analysis: Applications to Cyclic Molecules and Studies of Noncovalent Interactions
inferred← citeshttps://doi.org/10.1021/jp2118373openalex-snapshot
Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies
inferred← citeshttps://doi.org/10.1021/jp305469popenalex-snapshot
The Effects of Chloride Binding on the Behavior of Cellulose-Derived Solutes in the Ionic Liquid 1-Butyl-3-methylimidazolium Chloride
inferred← citeshttps://doi.org/10.1021/jp404160yopenalex-snapshot
Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models
inferred← citeshttps://doi.org/10.1021/jp4111234openalex-snapshot
Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration
inferred← citeshttps://doi.org/10.1021/jp4115139openalex-snapshot
Field-SEA: A Model for Computing the Solvation Free Energies of Nonpolar, Polar, and Charged Solutes in Water
inferred← citeshttps://doi.org/10.1021/jp411529hopenalex-snapshot
A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration
inferred← citeshttps://doi.org/10.1021/jp411671aopenalex-snapshot
Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field
inferred← citeshttps://doi.org/10.1021/jp412195mopenalex-snapshot
Computation of Standard Binding Free Energies of Polar and Charged Ligands to the Glutamate Receptor GluA2
inferred← citeshttps://doi.org/10.1021/jp5024197openalex-snapshot
Solubility of Nonelectrolytes: A First-Principles Computational Approach
inferred← citeshttps://doi.org/10.1021/jp502475eopenalex-snapshot
Benchmarking Quantum Chemical Methods for the Calculation of Molecular Dipole Moments and Polarizabilities
inferred← citeshttps://doi.org/10.1021/jp505332popenalex-snapshot
Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/jp709958fopenalex-snapshot
Charge Asymmetries in Hydration of Polar Solutes
inferred← citeshttps://doi.org/10.1021/jp806838bopenalex-snapshot
Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/jp807701hopenalex-snapshot
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/jp809782zopenalex-snapshot
Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions
inferred← citeshttps://doi.org/10.1021/jp910674dopenalex-snapshot
Current Status of the AMOEBA Polarizable Force Field
inferred← citeshttps://doi.org/10.1021/jp911439qopenalex-snapshot
Computational Approach for Understanding the Interactions of UV-Degradable Dendrons with DNA and siRNA
inferred← citeshttps://doi.org/10.1021/jp911701hopenalex-snapshot
Accounting for Polarization Cost When Using Fixed Charge Force Fields. II. Method and Application for Computing Effect of Polarization Cost on Free Energy of Hydration
inferred← citeshttps://doi.org/10.1021/la201856popenalex-snapshot
Adsorption and Reduction of Glutathione Disulfide on α-Al2O3 Nanoparticles: Experiments and Modeling
inferred← citeshttps://doi.org/10.1021/ml100026aopenalex-snapshot
Computational Analysis of Protein Hotspots
inferred← citeshttps://doi.org/10.1021/mp8000606openalex-snapshot
Molecular Dynamics Simulations of Functional Group Effects on Solvation Thermodynamics of Model Solutes in Decane and Tricaprylin
inferred← citeshttps://doi.org/10.1038/s41524-024-01272-zopenalex-snapshot
Global ranking of the sensitivity of interaction potential contributions within classical molecular dynamics force fields
inferred← citeshttps://doi.org/10.1038/s42004-020-0291-4openalex-snapshot
Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)
inferred← citeshttps://doi.org/10.1039/b907383copenalex-snapshot
Entropic trends in aqueous solutions of the common functional groups
inferred← citeshttps://doi.org/10.1039/c1cp20110gopenalex-snapshot
Using molecular simulation to predict solute solvation and partition coefficients in solvents of different polarity
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