The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations

Survival of the most transferable at the top of Jacob’s ladder: Defining and testing the ωB97M(2) double hybrid density functional

(2018) Narbe Mardirossian et al.   JOURNAL OF CHEMICAL PHYSICS

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

(2018) Matthew P. Kroonblawd et al.   Journal of Chemical Theory and Computation

Revised M06 density functional for main-group and transition-metal chemistry

(2018) Ying Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

(2018) Hannes H. Loeffler et al.   Journal of Chemical Theory and Computation

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching

(2018) Phillip S. Hudson et al.   Journal of Chemical Theory and Computation

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

(2018) Pengfei Li et al.   Journal of Chemical Theory and Computation

Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies

(2017) Martin A. Olsson et al.   Journal of Chemical Theory and Computation

How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

(2017) Ulf Ryde   Journal of Chemical Theory and Computation

Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities

(2017) Fiona L. Kearns et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

(2017) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals

(2017) Narbe Mardirossian et al.   MOLECULAR PHYSICS

Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics

(2017) Ying Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesis and bioactivities of novel pyrazole oxime derivatives containing a 1,2,3-thiadiazole moiety

(2016) Hong Dai et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Novel 1,3,4-oxadiazole/oxime hybrids: Synthesis, docking studies and investigation of anti-inflammatory, ulcerogenic liability and analgesic activities

(2016) Heba S. Abd-Ellah et al.   BIOORGANIC CHEMISTRY

Discovery of Chromeno[4,3-c]pyrazol-4(2H)-one Containing Carbonyl or Oxime Derivatives as Potential, Selective Inhibitors PI3Kα

(2016) Liang Lu et al.   CHEMICAL & PHARMACEUTICAL BULLETIN

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

(2016) Ulf Ryde et al.   CHEMICAL REVIEWS

Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

(2016) Yuezhi Mao et al.   JOURNAL OF CHEMICAL PHYSICS

Blind test of density-functional-based methods on intermolecular interaction energies

(2016) DeCarlos E. Taylor et al.   JOURNAL OF CHEMICAL PHYSICS

ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation

(2016) Narbe Mardirossian et al.   JOURNAL OF CHEMICAL PHYSICS

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Convergence of single-step free energy perturbation

(2016) Stefan Boresch et al.   MOLECULAR PHYSICS

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

MN15: A Kohn–Sham global-hybrid exchange–correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions

(2016) Haoyu S. Yu et al.   Chemical Science

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

Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes

(2015) Phillip S. Hudson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Indirubin 3′-( O -oxiran-2-ylmethyl)oxime: A novel anticancer agent

(2015) Yoshimi Ichimaru et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching

(2015) Jicun Li et al.   JOURNAL OF CHEMICAL PHYSICS

Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm

(2015) Samuel Manzer et al.   JOURNAL OF CHEMICAL PHYSICS

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

(2015) Narbe Mardirossian et al.   JOURNAL OF CHEMICAL PHYSICS

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

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

(2014) Yuri Pevzner et al.   Journal of Chemical Information and Modeling

Achieving High-Accuracy Intermolecular Interactions by Combining Coulomb-Attenuated Second-Order Møller–Plesset Perturbation Theory with Coupled Kohn–Sham Dispersion

(2014) Yuanhang Huang et al.   Journal of Chemical Theory and Computation

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

Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations

(2014) Yan Zhou et al.   Journal of Chemical Theory and Computation

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

(2014) Samuel Genheden et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Separate Electronic Attenuation Allowing a Spin-Component-Scaled Second-Order Møller–Plesset Theory to Be Effective for Both Thermochemistry and Noncovalent Interactions

(2014) Matthew Goldey et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation

(2014) Christopher Cave-Ayland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB)

(2014) Jan Gerit Brandenburg et al.   Journal of Physical Chemistry Letters

Quest for a universal density functional: the accuracy of density functionals across a broad spectrum of databases in chemistry and physics

(2014) R. Peverati et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Density functional tight binding: values of semi-empirical methods in an ab initio era

(2014) Qiang Cui et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Advances in Binding Free Energies Calculations: QM/MM-Based Free Energy Perturbation Method for Drug Design

(2013) R.S. Rathore et al.   CURRENT PHARMACEUTICAL DESIGN

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

(2013) Christoph Dellago et al.   Entropy

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2012) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

(2012) Lee-Ping Wang et al.   Journal of Chemical Theory and Computation

The SAMPL3 blind prediction challenge: transfer energy overview

(2012) Matthew T. Geballe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Attenuating Away the Errors in Inter- and Intramolecular Interactions from Second-Order Møller–Plesset Calculations in the Small Aug-cc-pVDZ Basis Set

(2012) Matthew Goldey et al.   Journal of Physical Chemistry Letters

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

(2012) Jimmy Heimdal et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Synthesis, crystal structures and luminescent properties of two one-dimensional cadmium(II) coordination polymers generated from polydentate Schiff-base ligand

(2012) Yan Bai et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method

(2012) Eric R. Pinnick et al.   THEORETICAL CHEMISTRY ACCOUNTS

MSCALE: A General Utility for Multiscale Modeling

(2011) H. Lee Woodcock et al.   Journal of Chemical Theory and Computation

Approaching post-Hartree–Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method

(2011) Feng Wang et al.   MOLECULAR SIMULATION

Communication: Hybrid ensembles for improved force matching

(2010) Lee-Ping Wang et al.   JOURNAL OF CHEMICAL PHYSICS

The quest for the best nonpolarizable water model from the adaptive force matching method

(2010) Omololu Akin-Ojo 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

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

(2008) Omololu Akin-Ojo et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS