A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes
出版年份 2018 全文链接
标题
A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes
作者
关键词
-
出版物
MOLECULES
Volume 23, Issue 10, Pages 2695
出版商
MDPI AG
发表日期
2018-10-19
DOI
10.3390/molecules23102695
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- 1-Butanol as a Solvent for Efficient Extraction of Polar Compounds from Aqueous Medium: Theoretical and Practical Aspects
- (2018) Gerhard König et al. JOURNAL OF PHYSICAL CHEMISTRY B
- How a Solvent Molecule Affects Competing Elimination and Substitution Dynamics. Insight into Mechanism Evolution with Increased Solvation
- (2018) Xu Liu et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- On the convergence of multi-scale free energy simulations
- (2018) Gerhard König et al. MOLECULAR SIMULATION
- Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
- (2018) Louis Lagardère et al. Chemical Science
- Mapping the Drude polarizable force field onto a multipole and induced dipole model
- (2017) Jing Huang et al. JOURNAL OF CHEMICAL PHYSICS
- Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model
- (2017) Abir Ganguly et al. Journal of Chemical Theory and Computation
- Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents
- (2017) Jin Zhang et al. Journal of Chemical Theory and Computation
- Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
- (2017) Yuezhi Mao et al. Journal of Chemical Theory and Computation
- Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs
- (2017) Matthew Harger et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models
- (2017) Samuel Genheden JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations
- (2016) Frank C. Pickard et al. BIOORGANIC & MEDICINAL CHEMISTRY
- An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
- (2016) Justin A. Lemkul et al. CHEMICAL REVIEWS
- Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
- (2016) Ulf Ryde et al. CHEMICAL REVIEWS
- TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
- (2016) Jacek Dziedzic et al. JOURNAL OF CHEMICAL PHYSICS
- Perspective: How good is DFT for water?
- (2016) Michael J. Gillan et al. JOURNAL OF CHEMICAL PHYSICS
- Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials
- (2016) Eric C. Dybeck et al. Journal of Chemical Theory and Computation
- Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters
- (2016) Pavlo O. Dral et al. Journal of Chemical Theory and Computation
- Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics
- (2016) Xiangyu Jia et al. Journal of Chemical Theory and Computation
- Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level
- (2016) Martin A. Olsson et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge
- (2016) Gerhard König et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections
- (2016) Frank C. Pickard et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model
- (2016) Sebastian Diaz-Rodriguez et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Advanced Potential Energy Surfaces for Molecular Simulation
- (2016) Alex Albaugh et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Why Is MP2-Water “Cooler” and “Denser” than DFT-Water?
- (2016) Soohaeng Yoo Willow et al. Journal of Physical Chemistry Letters
- Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations
- (2015) Gerhard König et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations
- (2015) Erich R. Kuechler et al. JOURNAL OF CHEMICAL PHYSICS
- Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method
- (2015) Gerhard König et al. Journal of Chemical Theory and Computation
- Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model
- (2015) Samuel Genheden et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- A “Stepping Stone” Approach for Obtaining Quantum Free Energies of Hydration
- (2015) Chris Sampson et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems
- (2015) Phillip S. Hudson et al. Journal of Physical Chemistry Letters
- Solubilities, Fugacities and All That in Solution Chemistry
- (2015) Emmerich Wilhelm JOURNAL OF SOLUTION CHEMISTRY
- Local structure analysis inab initioliquid water
- (2015) Biswajit Santra et al. MOLECULAR PHYSICS
- Computational Catalysis-Past, Present, and Future
- (2014) Walter Thiel ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water
- (2014) Robert A. DiStasio et al. JOURNAL OF CHEMICAL PHYSICS
- Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
- (2014) Gerhard König et al. Journal of Chemical Theory and Computation
- SAMPL4, a blind challenge for computational solvation free energies: the compounds considered
- (2014) J. Peter Guthrie JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4
- (2014) Gerhard König et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Blind prediction of solvation free energies from the SAMPL4 challenge
- (2014) David L. Mobley et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies
- (2014) Paulius Mikulskis et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation
- (2014) Christopher Cave-Ayland et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability
- (2013) Gerhard König et al. BIOPHYSICAL JOURNAL
- The new view of hydrophobic free energy
- (2013) Robert L. Baldwin FEBS LETTERS
- Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation
- (2013) Iakov Polyak et al. JOURNAL OF CHEMICAL PHYSICS
- Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields
- (2013) Bin Lin et al. JOURNAL OF CHEMICAL PHYSICS
- Free Energies of Binding from Large-Scale First-Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies
- (2013) Stephen J. Fox et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Properties of hydrophobic free energy found by gas-liquid transfer
- (2013) R. L. Baldwin PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics—Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections
- (2012) I-Chun Lin et al. Journal of Chemical Theory and Computation
- Generalized Born Solvation Model SM12
- (2012) Aleksandr V. Marenich et al. Journal of Chemical Theory and Computation
- Release of High-Energy Water as an Essential Driving Force for the High-Affinity Binding of Cucurbit[n]urils
- (2012) Frank Biedermann et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
- (2012) Jimmy Heimdal et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Gas-liquid transfer data used to analyze hydrophobic hydration and find the nature of the Kauzmann-Tanford hydrophobic factor
- (2012) R. L. Baldwin PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- On the Convergence Rates of Gauss and Clenshaw--Curtis Quadrature for Functions of Limited Regularity
- (2012) Shuhuang Xiang et al. SIAM JOURNAL ON NUMERICAL ANALYSIS
- Van der Waals effects inab initiowater at ambient and supercritical conditions
- (2011) Romain Jonchiere et al. JOURNAL OF CHEMICAL PHYSICS
- Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections
- (2011) Berhane Temelso et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Enhancing QM/MM Molecular Dynamics Sampling in Explicit Environments via an Orthogonal-Space-Random-Walk-Based Strategy
- (2011) Donghong Min et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks
- (2011) Nikolay V. Plotnikov et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations
- (2011) Frank R. Beierlein et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Use of a QM/MM-Based FEP Method to Evaluate the Anomalous Hydration Behavior of Simple Alkyl Amines and Amides: Application to the Design of FBPase Inhibitors for the Treatment of Type-2 Diabetes
- (2011) M. Rami Reddy et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Peptide Conformational Preferences in Osmolyte Solutions: Transfer Free Energies of Decaalanine
- (2011) Hironori Kokubo et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- QM/MM simulation of liquid water with an adaptive quantum region
- (2011) Noam Bernstein et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Communication: Thermodynamics of water modeled using ab initio simulations
- (2010) Valéry Weber et al. JOURNAL OF CHEMICAL PHYSICS
- Practically Efficient QM/MM Alchemical Free Energy Simulations: The Orthogonal Space Random Walk Strategy
- (2010) Donghong Min et al. Journal of Chemical Theory and Computation
- Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field
- (2010) Devleena Shivakumar et al. Journal of Chemical Theory and Computation
- Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration
- (2010) Stefan Bruckner et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules
- (2010) Gerhard König et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method
- (2010) Stefan Bruckner et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- The SAMPL2 blind prediction challenge: introduction and overview
- (2010) Matthew T. Geballe et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models
- (2010) Raphael F. Ribeiro et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
- (2010) Pavel V. Klimovich et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Accurate Predictions of Water Cluster Formation, (H2O)n=2−10
- (2010) Robert M. Shields et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Elucidating Solvent Contributions to Solution Reactions with Ab Initio QM/MM Methods†
- (2010) Hao Hu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Polarizable Water Molecules in Ligand−Macromolecule Recognition. Impact on the Relative Affinities of Competing Pyrrolopyrimidine Inhibitors for FAK Kinase
- (2010) Benoit de Courcy et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Water in Cavity−Ligand Recognition
- (2010) Riccardo Baron et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- QM/MM Methods for Biomolecular Systems
- (2009) Hans Martin Senn et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations
- (2009) David L. Mobley et al. Journal of Chemical Theory and Computation
- Unorthodox uses of Bennett's acceptance ratio method
- (2009) Gerhard König et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
- (2009) K. Vanommeslaeghe et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Molecular recognition of RNA: challenges for modelling interactions and plasticity
- (2009) Simone Fulle et al. JOURNAL OF MOLECULAR RECOGNITION
- A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview
- (2009) J. Peter Guthrie JOURNAL OF PHYSICAL CHEMISTRY B
- Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough
- (2009) Gerhard König et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies
- (2009) Aleksandr V. Marenich et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
- (2009) Aleksandr V. Marenich et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations
- (2009) Katherine E. Shaw et al. Journal of Physical Chemistry Letters
- Density Functionals with Broad Applicability in Chemistry
- (2008) Yan Zhao et al. ACCOUNTS OF CHEMICAL RESEARCH
- Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface
- (2008) Hao Hu et al. JOURNAL OF CHEMICAL PHYSICS
- Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach
- (2008) Xiancheng Zeng et al. JOURNAL OF CHEMICAL PHYSICS
- An efficient method for the calculation of quantum mechanics/molecular mechanics free energies
- (2008) Christopher J. Woods et al. JOURNAL OF CHEMICAL PHYSICS
- Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator
- (2008) Pedro E. M. Lopes et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry
- (2008) Anthony Nicholls et al. JOURNAL OF MEDICINAL CHEMISTRY
- Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field
- (2008) Edward Harder et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†
- (2008) Shina C. L. Kamerlin et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Is Gauss Quadrature Better than Clenshaw–Curtis?
- (2008) Lloyd N. Trefethen SIAM REVIEW
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started