Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics I: Theory, Algorithm, and Performance

(2020) Hsin-Yu Ko et al.   Journal of Chemical Theory and Computation

Elucidating the Molecular Basis of Avibactam Mediated Inhibition of Class A β-Lactamases

(2020) Chandan Kumar Das et al.   CHEMISTRY-A EUROPEAN JOURNAL

Efficient computation of free energy surfaces of chemical reactions using ab initio molecular dynamics with hybrid functionals and plane waves

(2020) Sagarmoy Mandal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Faster exact exchange in periodic systems using single-precision arithmetic

(2020) John Vinson   JOURNAL OF CHEMICAL PHYSICS

Density Functional Theory for Molecule–Metal Surface Reactions: When Does the Generalized Gradient Approximation Get It Right, and What to Do If It Does Not

(2020) Nick Gerrits et al.   Journal of Physical Chemistry Letters

Integrating state of the art compute, communication, and autotuning strategies to multiply the performance of ab initio molecular dynamics on massively parallel multi-core supercomputers

(2020) Tobias Klöffel et al.   COMPUTER PHYSICS COMMUNICATIONS

β-Lactamases and β-Lactamase Inhibitors in the 21st Century

(2019) Catherine L. Tooke et al.   JOURNAL OF MOLECULAR BIOLOGY

From a week to less than a day: Speedup and scaling of coordinate-scaled exact exchange calculations in plane waves

(2019) Martin P. Bircher et al.   COMPUTER PHYSICS COMMUNICATIONS

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

(2019) Viacheslav Bolnykh et al.   Journal of Chemical Theory and Computation

Stable Surfaces That Bind Too Tightly: Can Range-Separated Hybrids or DFT+U Improve Paradoxical Descriptions of Surface Chemistry?

(2019) Qing Zhao et al.   Journal of Physical Chemistry Letters

Speeding-up ab initio molecular dynamics with hybrid functionals using adaptively compressed exchange operator based multiple timestepping

(2019) Sagarmoy Mandal et al.   JOURNAL OF CHEMICAL PHYSICS

On the hydrolysis mechanisms of amides and peptides

(2018) Allan L. L. East   INTERNATIONAL JOURNAL OF CHEMICAL KINETICS

Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods

(2018) Emre Sevgen et al.   Journal of Chemical Theory and Computation

A Versatile Multiple Time Step Scheme for Efficient ab Initio Molecular Dynamics Simulations

(2018) Elisa Liberatore et al.   Journal of Chemical Theory and Computation

Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study

(2018) Shalini Awasthi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploiting Coordinate Scaling Relations To Accelerate Exact Exchange Calculations

(2018) Martin P. Bircher et al.   Journal of Physical Chemistry Letters

Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers

(2018) Laura E Ratcliff et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer

(2018) Mohan Chen et al.   Nature Chemistry

Global increase and geographic convergence in antibiotic consumption between 2000 and 2015

(2018) Eili Y. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced sampling and free energy calculations with hybrid functionals and plane waves for chemical reactions

(2018) Sagarmoy Mandal et al.   JOURNAL OF CHEMICAL PHYSICS

Improving the Performance of Hybrid Functional-Based Molecular Dynamics Simulation through Screening of Hartree–Fock Exchange Forces

(2017) Guido Falk von Rudorff et al.   Journal of Chemical Theory and Computation

Adaptively Compressed Exchange Operator for Large-Scale Hybrid Density Functional Calculations with Applications to the Adsorption of Water on Silicene

(2017) Wei Hu et al.   Journal of Chemical Theory and Computation

Advanced capabilities for materials modelling with Quantum ESPRESSO

(2017) P Giannozzi et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Hydrolysis of cephalexin and meropenem by New Delhi metallo-β-lactamase: the substrate protonation mechanism is drug dependent

(2017) Chandan Kumar Das et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Adaptively Compressed Exchange Operator

(2016) Lin Lin   Journal of Chemical Theory and Computation

Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics

(2016) Shalini Awasthi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Deacylation Mechanism and Kinetics of Acyl–Enzyme Complex of Class C β-Lactamase and Cephalothin

(2016) Ravi Tripathi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural, Dynamical, and Electronic Properties of Liquid Water: A Hybrid Functional Study

(2016) Francesco Ambrosio et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Performance and Accuracy of Recursive Subspace Bisection for Hybrid DFT Calculations in Inhomogeneous Systems

(2015) William Dawson et al.   Journal of Chemical Theory and Computation

Multiple-Time Step Ab Initio Molecular Dynamics Based on Two-Electron Integral Screening

(2015) Shervin Fatehi et al.   Journal of Chemical Theory and Computation

Compressed Representation of Kohn–Sham Orbitals via Selected Columns of the Density Matrix

(2015) Anil Damle et al.   Journal of Chemical Theory and Computation

Density and Compressibility of Liquid Water and Ice from First-Principles Simulations with Hybrid Functionals

(2015) Alex P. Gaiduk et al.   Journal of Physical Chemistry Letters

A systematic study of chloride ion solvation in water using van der Waals inclusive hybrid density functional theory

(2015) Arindam Bankura et al.   MOLECULAR PHYSICS

Local structure analysis inab initioliquid water

(2015) Biswajit Santra et al.   MOLECULAR PHYSICS

Structural and electronic properties of aqueous NaCl solutions from ab initio molecular dynamics simulations with hybrid density functionals

(2014) Alex P. Gaiduk et al.   CHEMICAL PHYSICS LETTERS

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

Electronic Structure of Aqueous Sulfuric Acid from First-Principles Simulations with Hybrid Functionals

(2014) Quan Wan et al.   Journal of Physical Chemistry Letters

Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car–Parrinello calculations

(2013) Nicola Varini et al.   COMPUTER PHYSICS COMMUNICATIONS

Mechanism of Acyl–Enzyme Complex Formation from the Henry–Michaelis Complex of Class C β-Lactamases with β-Lactam Antibiotics

(2013) Ravi Tripathi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DFT and Proton Transfer Reactions: A Benchmark Study on Structure and Kinetics

(2012) Giuseppe Felice Mangiatordi et al.   Journal of Chemical Theory and Computation

Efficient Computation of Hartree–Fock Exchange Using Recursive Subspace Bisection

(2012) François Gygi et al.   Journal of Chemical Theory and Computation

Thermodynamic and Kinetic Stabilities of Active Site Protonation States of Class C β-Lactamase

(2012) Ravi Tripathi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Challenges for Density Functional Theory

(2011) Aron J. Cohen et al.   CHEMICAL REVIEWS

First Principles Simulations of the Infrared Spectrum of Liquid Water Using Hybrid Density Functionals

(2011) Cui Zhang et al.   Journal of Chemical Theory and Computation

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

(2011) Fangqiang Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accurate Band Gaps for Semiconductors from Density Functional Theory

(2011) Hai Xiao et al.   Journal of Physical Chemistry Letters

Theoretical study of the neutral hydrolysis of methyl formate via a concerted and stepwise water-assisted mechanism using free-energy curves and molecular dynamics simulation

(2011) S. Tolosa Arroyo et al.   STRUCTURAL CHEMISTRY

A scalable and accurate algorithm for the computation of Hartree–Fock exchange

(2010) Ivan Duchemin et al.   COMPUTER PHYSICS COMMUNICATIONS

Current Challenges in Antimicrobial Chemotherapy

(2010) Carine Bebrone et al.   DRUGS

Reversible Autocatalytic Hydrolysis of Alkyl Formate: Kinetic and Reactor Modeling

(2010) Olatunde Jogunola et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Density functional theory for transition metals and transition metal chemistry

(2009) Christopher J. Cramer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Order-Nimplementation of exact exchange in extended insulating systems

(2009) Xifan Wu et al.   PHYSICAL REVIEW B

Compact Representations of Kohn-Sham Invariant Subspaces

(2009) François Gygi   PHYSICAL REVIEW LETTERS

Hartree–Fock orbitals significantly improve the reaction barrier heights predicted by semilocal density functionals

(2008) Benjamin G. Janesko et al.   JOURNAL OF CHEMICAL PHYSICS

Ab initio molecular dynamics using hybrid density functionals

(2008) Manuel Guidon et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics Prediction of the Mechanism of Ester Hydrolysis in Water

(2008) Hakan Gunaydin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Screened hybrid density functionals for solid-state chemistry and physics

(2008) Benjamin G. Janesko et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Localization and Delocalization Errors in Density Functional Theory and Implications for Band-Gap Prediction

(2008) Paula Mori-Sánchez et al.   PHYSICAL REVIEW LETTERS

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Insights into Current Limitations of Density Functional Theory

(2008) A. J. Cohen et al.   SCIENCE