Enhanced sampling of chemical and biochemical reactions with metadynamics

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

(2014) Harish Vashisth et al.   CHEMICAL REVIEWS

Car–Parrinello Molecular Dynamics + Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables

(2014) Shaohui Zheng et al.   Journal of Physical Chemistry C

A hybrid MC/MD reaction method with rare event-driving mechanism: Atomistic realization of 2-chlorobutane racemization process in DMF solution

(2013) Masataka Nagaoka et al.   CHEMICAL PHYSICS LETTERS

Formation of a Covalent Glycosyl-Enzyme Species in a Retaining Glycosyltransferase

(2013) Víctor Rojas-Cervellera et al.   CHEMISTRY-A EUROPEAN JOURNAL

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Sampling the energy landscape of Pt13 with metadynamics

(2013) Luca Pavan et al.   EUROPEAN PHYSICAL JOURNAL D

A boundary correction algorithm for metadynamics in multiple dimensions

(2013) Michael McGovern et al.   JOURNAL OF CHEMICAL PHYSICS

Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency

(2013) Baron Peters et al.   JOURNAL OF CHEMICAL PHYSICS

RNA/Peptide Binding Driven by Electrostatics—Insight from Bidirectional Pulling Simulations

(2013) Trang N. Do et al.   Journal of Chemical Theory and Computation

Demonstrating the Transferability and the Descriptive Power of Sketch-Map

(2013) Michele Ceriotti et al.   Journal of Chemical Theory and Computation

Effects of High Angular Momentum on the Unimolecular Dissociation of CD2CD2OH: Theory and Comparisons with Experiment

(2013) Benjamin G. McKown et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Free Energy Surface for Brønsted Acid-Catalyzed Glucose Ring-Opening in Aqueous Solution

(2013) Xianghong Qian   JOURNAL OF PHYSICAL CHEMISTRY B

Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene

(2013) Kenichi Koizumi et al.   Journal of Physical Chemistry Letters

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

Molecular Mechanism of Polyacrylate Helix Sense Switching across Its Free Energy Landscape

(2013) Adriana Pietropaolo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations

(2013) Matthew J. McGrath et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Free Energy and Electronic Properties of Water Adsorption on the SnO2(110) Surface

(2013) Gianluca Santarossa et al.   LANGMUIR

The Janus-faced role of external forces in mechanochemical disulfide bond cleavage

(2013) Przemyslaw Dopieralski et al.   Nature Chemistry

Chemical reactivity of aprotic electrolytes on a solid Li2O2 surface: screening solvents for Li–air batteries

(2013) Teodoro Laino et al.   NEW JOURNAL OF PHYSICS

Methanol synthesis on ZnO from molecular dynamics

(2013) Johannes Frenzel et al.   PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS

Density functional simulations of hexagonal Ge2Sb2Te5at high pressure

(2013) Sebastiano Caravati et al.   PHYSICAL REVIEW B

Water oxidation surface mechanisms replicated by a totally inorganic tetraruthenium-oxo molecular complex

(2013) S. Piccinin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The allosteric communication pathways in KIX domain of CBP

(2013) F. Palazzesi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Free-energy landscape of protein oligomerization from atomistic simulations

(2013) A. Barducci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Dynamics Kinetic Study on the Zeolite-Catalyzed Benzene Methylation in ZSM-5

(2013) Samuel L. C. Moors et al.   ACS Catalysis

The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach

(2012) Andrew J. Thompson et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biological Channeling of a Reactive Intermediate in the Bifunctional Enzyme DmpFG

(2012) Natalie E. Smith et al.   BIOPHYSICAL JOURNAL

The Nature of [PdCl2(C2H4)(H2O)] as an Active Species in the Wacker Process: New Insights from Ab Initio Molecular Dynamics Simulations

(2012) Gábor Kovács et al.   CHEMISTRY-A EUROPEAN JOURNAL

The Role of Pendant Amines in the Breaking and Forming of Molecular Hydrogen Catalyzed by Nickel Complexes

(2012) Simone Raugei et al.   CHEMISTRY-A EUROPEAN JOURNAL

Zinc Adsorption on Clays Inferred from Atomistic Simulations and EXAFS Spectroscopy

(2012) Sergey V. Churakov et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Staple Motifs, Initial Steps in the Formation of Thiolate-Protected Gold Nanoparticles: How Do They Form?

(2012) Víctor Rojas-Cervellera et al.   INORGANIC CHEMISTRY

Structure and Hydrolysis of the U(IV), U(V), and U(VI) Aqua Ions from Ab Initio Molecular Simulations

(2012) Raymond Atta-Fynn et al.   INORGANIC CHEMISTRY

Theoretical investigation of the proton transfer mechanism in guanine-cytosine and adenine-thymine base pairs

(2012) Shiyan Xiao et al.   JOURNAL OF CHEMICAL PHYSICS

Bridging Static and Dynamical Descriptions of Chemical Reactions: An ab Initio Study of CO2 Interacting with Water Molecules

(2012) Grégoire A. Gallet et al.   Journal of Chemical Theory and Computation

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

Metadynamics with Adaptive Gaussians

(2012) Davide Branduardi et al.   Journal of Chemical Theory and Computation

The Fate of a Zwitterion in Water from ab Initio Molecular Dynamics: Monoethanolamine (MEA)-CO2

(2012) Ciro A. Guido et al.   Journal of Chemical Theory and Computation

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

(2012) Michael Deighan et al.   Journal of Chemical Theory and Computation

Mechanisms of Propylene Glycol and Triacetin Pyrolysis

(2012) Teodoro Laino et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Theoretical Insight into Stereoselective Reaction Mechanisms of 2,4-Pentanediol-Tethered Ketene-Olefin [2 + 2] Cycloaddition

(2012) Katsumasa Kamiya et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Proton Transport Pathways in [NiFe]-Hydrogenase

(2012) Isaiah Sumner et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Glucose Isomerization to Fructose from ab Initio Molecular Dynamics Simulations

(2012) Xianghong Qian et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Collective Proton Dynamics at Highly Charged Interfaces Studied by Ab Initio Metadynamics

(2012) Swati Vartak et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of the Glycosylation Step Catalyzed by Human α-Galactosidase: A QM/MM Metadynamics Study

(2012) Xiao-Liang Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ab Initio Molecular Dynamics Study of the Dehydroxylation Reaction in a Smectite Model

(2012) D. Muñoz-Santiburcio et al.   Journal of Physical Chemistry C

Determination of the Surface Effects on Sarin Degradation

(2012) I-Feng W. Kuo et al.   Journal of Physical Chemistry C

The Elusive 5′-Deoxyadenosyl Radical in Coenzyme-B12-Mediated Reactions

(2012) Denis Bucher et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enhanced Thermal Decomposition of Nitromethane on Functionalized Graphene Sheets: Ab Initio Molecular Dynamics Simulations

(2012) Li-Min Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Proton Delivery and Removal in [Ni(PR2NR′2)2]2+ Hydrogen Production and Oxidation Catalysts

(2012) Molly O’Hagan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanistic Insights into the Hydrolysis of a Nucleoside Triphosphate Model in Neutral and Acidic Solution

(2012) Rachel Glaves et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ab Initio Dynamics of Cellulose Pyrolysis: Nascent Decomposition Pathways at 327 and 600 °C

(2012) Vishal Agarwal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural rearrangements and reaction intermediates in a di-Mn water oxidation catalyst

(2012) J. L. Vallés-Pardo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Hydroxyl radicals in ice: insights into local structure and dynamics

(2012) Edelsys Codorniu-Hernández et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

First-principles molecular dynamics simulations of condensed-phase V-type nerve agent reaction pathways and energy barriers

(2012) Richard H. Gee et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Microscopic mechanisms of initial oxidation of Si(100): Reaction pathways and free-energy barriers

(2012) Kenichi Koizumi et al.   PHYSICAL REVIEW B

Biapenem Inactivation by B2 Metallo β-Lactamases: Energy Landscape of the Post-Hydrolysis Reactions

(2012) Domenico L. Gatti   PLoS One

Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion

(2012) C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reaction Mechanisms of Water Splitting and H2 Evolution by a Ru(II)-Pincer Complex Identified with Ab Initio Metadynamics Simulations

(2012) Changru Ma et al.   ACS Catalysis

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Silver speciation in chloride-containing hydrothermal solutions from first principles molecular dynamics simulations

(2011) Xiandong Liu et al.   CHEMICAL GEOLOGY

Methanol synthesis on ZnO(0001¯). III. Free energy landscapes, reaction pathways, and mechanistic insights

(2011) Janos Kiss et al.   JOURNAL OF CHEMICAL PHYSICS

A chirality-based metrics for free-energy calculations in biomolecular systems

(2011) Adriana Pietropaolo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

LeuRS Synthetase: A First-Principles Investigation of the Water-Mediated Editing Reaction

(2011) Mauro Boero   JOURNAL OF PHYSICAL CHEMISTRY B

Mobility Mechanism of Hydroxyl Radicals in Aqueous Solution via Hydrogen Transfer

(2011) Edelsys Codorniu-Hernández et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate Rates of the Complex Mechanisms for Growth and Dissolution of Minerals Using a Combination of Rare-Event Theories

(2011) Andrew G. Stack et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Aggregation-Induced Chemical Reactions: Acid Dissociation in Growing Water Clusters

(2011) Harald Forbert et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Graph Theory MeetsAb InitioMolecular Dynamics: Atomic Structures and Transformations at the Nanoscale

(2011) Fabio Pietrucci et al.   PHYSICAL REVIEW LETTERS

Simplifying the representation of complex free-energy landscapes using sketch-map

(2011) Michele Ceriotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Targeting biomolecular flexibility with metadynamics

(2010) Vanessa Leone et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin

(2010) Ludovico Sutto et al.   Journal of Chemical Theory and Computation

Theoretical Validation of Chemical Kinetic Mechanisms: Combustion of Methanol

(2010) Rex T. Skodje et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A self-learning algorithm for biased molecular dynamics

(2010) Gareth A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

(2010) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Theoretical Analysis of the Possible Intermediates in the Formation of [W6O19]2–

(2009) Laia Vilà-Nadal et al.   EUROPEAN JOURNAL OF INORGANIC CHEMISTRY

Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model

(2009) Ilya Kaliman et al.   Journal of Chemical Theory and Computation

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics

(2009) M. Bonomi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Effects of Water on β-d-Xylose Condensation Reactions

(2009) Haitao Dong et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Conformational Free Energy Surface of α-N-Acetylneuraminic Acid: An Interplay Between Hydrogen Bonding and Solvation

(2009) Vojtěch Spiwok et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

(2009) Luis Petersen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions on Peptide Bond Formation and Peptide Hydrolysis

(2009) Eduard Schreiner et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations

(2009) Fabio Pietrucci et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Molecular Mechanism of the Catalase Reaction

(2009) Mercedes Alfonso-Prieto et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

First-principles simulations of hydrogen peroxide formation catalyzed by small neutral gold clusters

(2009) Katarzyna A. Kacprzak et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ab initiostudy of the diffusion and decomposition pathways ofSiHxspecies on Si(100)

(2009) Michele Ceriotti et al.   PHYSICAL REVIEW B

Nucleotide-dependent conformational states of actin

(2009) J. Pfaendtner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dipositively Charged Protonated a3and a2Ions: Generation by Fragmentation of [La(GGG)(CH3CN)2]3+

(2008) Tujin Shi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Insight into the Solvation and Isomerization of 3-Halo-1-azaallylic Anions from Ab Initio Metadynamics Calculations and NMR Experiments

(2008) Reinout Declerck et al.   CHEMISTRY-A EUROPEAN JOURNAL

DFT Research on the Dehydroxylation Reaction of Pyrophyllite 2. Characterization of Reactants, Intermediates, And Transition States along the Reaction Path

(2008) Esther Molina-Montes et al.   JOURNAL OF PHYSICAL CHEMISTRY A

DFT Research on the Dehydroxylation Reaction of Pyrophyllite 1. First-Principle Molecular Dynamics Simulations

(2008) Esther Molina-Montes et al.   JOURNAL OF PHYSICAL CHEMISTRY B

First-Principles Molecular Dynamics Study of the Heterogeneous Reduction of NO2 on Soot Surfaces

(2008) Antonio Rodríguez-Fortea et al.   Journal of Physical Chemistry C

Influence of Extreme Thermodynamic Conditions and Pyrite Surfaces on Peptide Synthesis in Aqueous Media

(2008) Eduard Schreiner et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Dynamics Prediction of the Mechanism of Ester Hydrolysis in Water

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

The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

(2008) Massimiliano Bonomi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

(2008) A. V. Vargiu et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

An Enzymatic Atavist Revealed in Dual Pathways for Water Activation

(2008) Donghong Min et al.   PLOS BIOLOGY

Predicting the Effect of a Point Mutation on a Protein Fold: The Villin and Advillin Headpieces and Their Pro62Ala Mutants

(2007) Stefano Piana et al.   JOURNAL OF MOLECULAR BIOLOGY