ChemDyME: Kinetically Steered, Automated Mechanism Generation through Combined Molecular Dynamics and Master Equation Calculations

The Exploration of Chemical Reaction Networks

(2020) Jan P. Unsleber et al.   Annual Review of Physical Chemistry

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

(2020) B. Hourahine et al.   JOURNAL OF CHEMICAL PHYSICS

NWChem: Past, present, and future

(2020) E. Aprà et al.   JOURNAL OF CHEMICAL PHYSICS

Low-temperature oxidation of diethyl ether: Reactions of hot radicals across coupled potential energy surfaces

(2020) Aaron D. Danilack et al.   PROCEEDINGS OF THE COMBUSTION INSTITUTE

GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions

(2019) Christoph Bannwarth et al.   Journal of Chemical Theory and Computation

Highly Oxygenated Organic Molecules (HOM) from Gas-Phase Autoxidation Involving Peroxy Radicals: A Key Contributor to Atmospheric Aerosol

(2019) Federico Bianchi et al.   CHEMICAL REVIEWS

Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations

(2019) Stefan Grimme   Journal of Chemical Theory and Computation

KinBot: Automated stationary point search on potential energy surfaces

(2019) Ruben Van de Vijver et al.   COMPUTER PHYSICS COMMUNICATIONS

The impact of roaming radicals on the combustion properties of transportation fuels

(2018) Richard H. West et al.   COMBUSTION AND FLAME

Minimum Energy Paths and Transition States by Curve Optimization

(2018) Alain C. Vaucher et al.   Journal of Chemical Theory and Computation

A Simple “Boxed Molecular Kinetics” Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation

(2018) Robin Shannon et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamics on the Double Morse Potential: A Paradigm for Roaming Reactions with no Saddle Points

(2018) Barry K. Carpenter et al.   REGULAR & CHAOTIC DYNAMICS

Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space

(2018) Robin J. Shannon et al.   Journal of Chemical Theory and Computation

tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics

(2018) Aurelio Rodríguez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Exploration of Reaction Pathways and Chemical Transformation Networks

(2018) Gregor N. Simm et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Automatic Generation of Microkinetic Mechanisms for Heterogeneous Catalysis

(2017) C. Franklin Goldsmith et al.   Journal of Physical Chemistry C

The atomic simulation environment—a Python library for working with atoms

(2017) Ask Hjorth Larsen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis

(2017) J. A. Varela et al.   Chemical Science

Methods for exploring reaction space in molecular systems

(2017) Amanda L. Dewyer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

(2016) Connie W. Gao et al.   COMPUTER PHYSICS COMMUNICATIONS

Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics

(2016) Mike O'Connor et al.   FARADAY DISCUSSIONS

Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics

(2016) Jonathan J. Booth et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics

(2016) Mike O'Connor et al.   FARADAY DISCUSSIONS

Effects of Chemical Complexity on the Autoxidation Mechanisms of Endocyclic Alkene Ozonolysis Products: From Methylcyclohexenes toward Understanding α-Pinene

(2015) Matti P. Rissanen et al.   JOURNAL OF PHYSICAL CHEMISTRY A

An automated transition state search using classical trajectories initialized at multiple minima

(2015) Emilio Martínez-Núñez   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Adventures on the C 3 H 5 O potential energy surface: OH + propyne, OH + allene and related reactions

(2015) Judit Zádor et al.   PROCEEDINGS OF THE COMBUSTION INSTITUTE

Effect of non-thermal product energy distributions on ketohydroperoxide decomposition kinetics

(2015) C. Franklin Goldsmith et al.   PROCEEDINGS OF THE COMBUSTION INSTITUTE

General master equation formulation of a reversible dissociation/association reaction

(2014) Nicholas J.B. Green et al.   CHEMICAL PHYSICS LETTERS

Consecutive Chemical Activation Steps in the OH-Initiated Atmospheric Degradation of Isoprene: An Analysis with Coupled Master Equations

(2014) Mark Pfeifle et al.   INTERNATIONAL JOURNAL OF CHEMICAL KINETICS

An automated method to find transition states using chemical dynamics simulations

(2014) Emilio Martínez-Núñez   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Discovering chemistry with an ab initio nanoreactor

(2014) Lee-Ping Wang et al.   Nature Chemistry

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

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

The reactions of Criegee intermediates with alkenes, ozone, and carbonyl oxides

(2014) L. Vereecken et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Reliable Transition State Searches Integrated with the Growing String Method

(2013) Paul Zimmerman   Journal of Chemical Theory and Computation

Reformulation and Solution of the Master Equation for Multiple-Well Chemical Reactions

(2013) Yuri Georgievskii et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Autoxidation of Organic Compounds in the Atmosphere

(2013) John D. Crounse et al.   Journal of Physical Chemistry Letters

Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods

(2013) Satoshi Maeda et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

(2012) Dmitrii V. Shalashilin et al.   JOURNAL OF CHEMICAL PHYSICS

MESMER: An Open-Source Master Equation Solver for Multi-Energy Well Reactions

(2012) David R. Glowacki et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Interception of Excited Vibrational Quantum States by O2 in Atmospheric Association Reactions

(2012) D. R. Glowacki et al.   SCIENCE

Roaming Radicals

(2011) Joel M. Bowman et al.   Annual Review of Physical Chemistry

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

(2011) David R. Glowacki et al.   Journal of Chemical Theory and Computation

Toward Predicting Full Catalytic Cycle Using Automatic Reaction Path Search Method: A Case Study on HCo(CO)3-Catalyzed Hydroformylation

(2011) Satoshi Maeda et al.   Journal of Chemical Theory and Computation

Theoretical Study of Isomerization and Dissociation Transition States of C3H5O Radical Isomers: Ab Initio Characterization of the Critical Points and Statistical Transition-State Theory Modeling of the Dynamics

(2011) Benjamin FitzPatrick   JOURNAL OF PHYSICAL CHEMISTRY A

Roaming Radical Reactions

(2011) Nuradhika Herath et al.   Journal of Physical Chemistry Letters

Kinetics of elementary reactions in low-temperature autoignition chemistry

(2010) Judit Zádor et al.   PROGRESS IN ENERGY AND COMBUSTION SCIENCE

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Markovian milestoning with Voronoi tessellations

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems

(2009) David R. Glowacki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evolution of Organic Aerosols in the Atmosphere

(2009) J. L. Jimenez et al.   SCIENCE

Atmospheric organic particulate matter: From smoke to secondary organic aerosol

(2008) Neil M. Donahue et al.   ATMOSPHERIC ENVIRONMENT

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

(2008) Noel M O'Boyle et al.   Chemistry Central Journal

Kinetic activation-relaxation technique: An off-lattice self-learning kinetic Monte Carlo algorithm

(2008) Fedwa El-Mellouhi et al.   PHYSICAL REVIEW B

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