Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

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 QM/MM Methods To Obtain Ligand-Binding Free Energies

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

Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding

(2017) Daniele Loco et al.   Journal of Chemical Theory and Computation

The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein

(2017) Lina J. Nåbo et al.   Journal of Chemical Theory and Computation

Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA

(2017) Sven Roßbach 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

Systematic Quantum Mechanical Region Determination in QM/MM Simulation

(2017) Maria Karelina et al.   Journal of Chemical Theory and Computation

Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent

(2017) Joel M. Milanese et al.   Journal of Chemical Theory and Computation

Quantified electrostatic preorganization in enzymes using the geometry of the electron charge density

(2017) Amanda Morgenstern et al.   Chemical Science

Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α-Maltose

(2016) Mateusz Marianski et al.   Journal of Chemical Theory and Computation

Protein environmental effects on iron-sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres

(2016) Travis V. Harris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

(2016) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models

(2016) Makenzie R. Provorse et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase

(2016) Niladri Patra et al.   PLoS One

Convergence of Atomic Charges with the Size of the Enzymatic Environment

(2015) Danny E. P. Vanpoucke et al.   Journal of Chemical Information and Modeling

Polarizable QM/MM Multiconfiguration Self-Consistent Field Approach with State-Specific Corrections: Environment Effects on Cytosine Absorption Spectrum

(2015) Quansong Li et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Mediation of donor–acceptor distance in an enzymatic methyl transfer reaction

(2015) Jianyu Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization

(2015) Jeronimo Lameira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ribose-Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study

(2014) Keyarash Sadeghian et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Projected Hybrid Orbitals: A General QM/MM Method

(2014) Yingjie Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins

(2013) Sophie Sumner et al.   Journal of Chemical Theory and Computation

The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules

(2013) Christine M. Isborn et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theoretical Modeling of Large Molecular Systems. Advances in the Local Self Consistent Field Method for Mixed Quantum Mechanics/Molecular Mechanics Calculations

(2012) Antonio Monari et al.   ACCOUNTS OF CHEMICAL RESEARCH

Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase

(2012) Joost VandeVondele et al.   Journal of Chemical Theory and Computation

Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase

(2012) Rong-Zhen Liao et al.   Journal of Chemical Theory and Computation

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

(2012) LiHong Hu et al.   Journal of Chemical Theory and Computation

Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

(2012) Christine M. Isborn et al.   Journal of Chemical Theory and Computation

Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings

(2012) Denis Flaig et al.   Journal of Chemical Theory and Computation

Ligation of water to magnesium chelates of biological importance

(2012) Dorota Rutkowska-Zbik et al.   JOURNAL OF MOLECULAR MODELING

Ab Initio Quantum Chemistry for Protein Structures

(2012) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

\mathcal{O}(N) methods in electronic structure calculations

(2012) D R Bowler et al.   REPORTS ON PROGRESS IN PHYSICS

Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules

(2011) Stephen J. Fox et al.   JOURNAL OF CHEMICAL PHYSICS

Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods

(2011) Jan Řezáč et al.   Journal of Chemical Theory and Computation

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

(2011) Christine M. Isborn et al.   Journal of Chemical Theory and Computation

On the Convergence of QM/MM Energies

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

Dipole preserving and polarization consistent charges

(2011) Peng Zhang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

(2011) Katharina Meier et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics

(2011) Ivan S. Ufimtsev et al.   Journal of Physical Chemistry Letters

Enzymatic Methyl Transfer: Role of an Active Site Residue in Generating Active Site Compaction That Correlates with Catalytic Efficiency

(2011) Jianyu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm

(2010) Bo Wang et al.   Journal of Chemical Theory and Computation

Kohn−Sham Density Functional Theory Electronic Structure Calculations with Linearly Scaling Computational Time and Memory Usage

(2010) Elias Rudberg et al.   Journal of Chemical Theory and Computation

On the Role of Water in Peroxidase Catalysis: A Theoretical Investigation of HRP Compound I Formation

(2010) Pietro Vidossich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A long-range-corrected density functional that performs well for both ground-state properties and time-dependent density functional theory excitation energies, including charge-transfer excited states

(2009) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Robust Periodic Hartree−Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets

(2009) Manuel Guidon et al.   Journal of Chemical Theory and Computation

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Do Quantum Mechanical Energies Calculated for Small Models of Protein-Active Sites Converge?†

(2009) LiHong Hu et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Evaluating Boundary Dependent Errors in QM/MM Simulations

(2009) Iván Solt et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM simulations for methyl transfer in solution and catalysed by COMT: ensemble-averaging of kinetic isotope effects

(2008) Natalia Kanaan et al.   CHEMICAL COMMUNICATIONS

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

(2008) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase

(2008) K. Rutherford et al.   JOURNAL OF MOLECULAR BIOLOGY