Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

A fast charge-Dependent atom-pairwise dispersion correction for DFTB3

(2015) Riccardo Petraglia et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Nonstatistical Dynamics in the Thermal C2–C6/Diels–Alder Cyclization of Enyne-Allenes: Effect of Topology

(2015) Debabrata Samanta et al.   JOURNAL OF ORGANIC CHEMISTRY

Origins of Stereoselectivity in Intramolecular Aldol Reactions Catalyzed by Cinchona Amines

(2015) Yu-hong Lam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Thermodynamic Evaluation of Aromatic CH/π Interactions and Rotational Entropy in a Molecular Rotor

(2015) Salvador Pérez-Estrada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Dynamics of the Diels–Alder Reactions of Tetrazines with Alkenes and N2 Extrusions from Adducts

(2015) Lisa Törk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Case Study of the Mechanism of Alcohol-Mediated Morita Baylis–Hillman Reactions. The Importance of Experimental Observations

(2015) R. Erik Plata et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Organic Chemistry: Bridging Theory and Experiment in Establishing the Mechanisms of Chemical Reactions

(2015) Gui-Juan Cheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Competition Between Concerted and Stepwise Dynamics in the Triplet Di-π-Methane Rearrangement

(2014) Gonzalo Jiménez-Osés et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Tunneling Assists the 1,2-Hydrogen Shift in N-Heterocyclic Carbenes

(2014) Sharmistha Karmakar et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Dynamic Effects Dictate the Mechanism and Selectivity of Dehydration-Rearrangement Reactions of Protonated Alcohols [Me2(R)CCH(OH2)Me]+(R=Me, Et,iPr) in the Gas Phase

(2014) Miguel A. F. de Souza  et al.   CHEMISTRY-A EUROPEAN JOURNAL

How important is self-consistency for the dDsC density dependent dispersion correction?

(2014) Éric Brémond et al.   JOURNAL OF CHEMICAL PHYSICS

Vibrational Entropy of a Protein: Large Differences between Distinct Conformations

(2014) Martin Goethe et al.   Journal of Chemical Theory and Computation

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

(2014) Michael Gaus et al.   Journal of Chemical Theory and Computation

Concerted or Stepwise: How Much Do Free-Energy Landscapes Tell Us about the Mechanisms of Elimination Reactions?

(2014) Fernanda Duarte et al.   JOURNAL OF ORGANIC CHEMISTRY

Nonstatistical Dynamics in the Thermal Garratt–Braverman/[1,5]-H Shift of One Ene–diallene: An Experimental and Computational Study

(2014) Debabrata Samanta et al.   JOURNAL OF ORGANIC CHEMISTRY

Challenges in Predicting ΔrxnG in Solution: The Mechanism of Ether-Catalyzed Hydroboration of Alkenes

(2014) Daniel J. S. Sandbeck et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Fast and Highly Chemoselective Alkynylation of Thiols with Hypervalent Iodine Reagents Enabled through a Low Energy Barrier Concerted Mechanism

(2014) Reto Frei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enhanced sampling of chemical and biochemical reactions with metadynamics

(2014) Shaohui Zheng et al.   MOLECULAR SIMULATION

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

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

X-ray imaging of chemically active valence electrons during a pericyclic reaction

(2014) Timm Bredtmann et al.   Nature Communications

Energy Disposition in Reactive Intermediates

(2013) Barry K. Carpenter   CHEMICAL REVIEWS

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

(2013) Michele Ceriotti et al.   COMPUTER PHYSICS COMMUNICATIONS

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

(2013) Cameron Abrams et al.   Entropy

Electron–Nuclear Motion in the Cope Rearrangement of Semibullvalene: Ever Synchronous?

(2013) Timm Bredtmann et al.   Journal of Chemical Theory and Computation

Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length

(2013) Mariana Rossi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient Parallel Implementations of QM/MM-REMD (Quantum Mechanical/Molecular Mechanics-Replica-Exchange MD) and Umbrella Sampling: Isomerization of H2O2 in Aqueous Solution

(2013) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Mechanistic Rationale for the 9-Amino(9-deoxy)epi Cinchona Alkaloids Catalyzed Asymmetric Reactions via Iminium Ion Activation of Enones

(2013) Antonio Moran et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simulation of the (H2O)8 cluster with the SCC-DFTB electronic structure method

(2012) Tae Hoon Choi   CHEMICAL PHYSICS LETTERS

Parametrization and Benchmark of DFTB3 for Organic Molecules

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

Structure–Correlation Principles Connecting Ground State Properties and Reaction Barrier Heights for the Cope Rearrangement of Semibullvalenes

(2012) Daniel F. Jana et al.   JOURNAL OF ORGANIC CHEMISTRY

DFT and Experimental Exploration of the Mechanism of InCl3-Catalyzed Type II Cycloisomerization of 1,6-Enynes: Identifying InCl2+ as the Catalytic Species and Answering Why Nonconjugated Dienes Are Generated

(2012) Lian-Gang Zhuo et al.   JOURNAL OF ORGANIC CHEMISTRY

How a Quantum Chemical Topology Analysis Enables Prediction of Electron Density Transfers in Chemical Reactions. The Degenerated Cope Rearrangement of Semibullvalene

(2012) Patricio González-Navarrete et al.   Journal of Physical Chemistry Letters

Tunnelling control of chemical reactions – the organic chemist's perspective

(2012) David Ley et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Dynamics, transition states, and timing of bond formation in Diels-Alder reactions

(2012) K. Black et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electronic Bond-to-Bond Fluxes in Pericyclic Reactions: Synchronous or Asynchronous?

(2011) Timm Bredtmann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Experimental Realization of a Neutral Homoaromatic Carbocycle

(2011) Peter R. Griffiths et al.   CHEMISTRY-A EUROPEAN JOURNAL

A Density Dependent Dispersion Correction

(2011) Stephan N. Steinmann et al.   CHIMIA

A generalized-gradient approximation exchange hole model for dispersion coefficients

(2011) Stephan N. Steinmann et al.   JOURNAL OF CHEMICAL PHYSICS

Comprehensive Benchmarking of a Density-Dependent Dispersion Correction

(2011) Stephan N. Steinmann et al.   Journal of Chemical Theory and Computation

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

(2011) Denis Bucher et al.   Journal of Chemical Theory and Computation

Electronic Quantum Fluxes during Pericyclic Reactions Exemplified for the Cope Rearrangement of Semibullvalene

(2011) Dirk Andrae et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theoretical study on the Cope rearrangement mechanisms and the homoaromaticity of semibullvalene, barbaralane, and 1,5-methanosemibullvalene

(2011) Yuka Ichikawa et al.   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

Conformational Study of 9-Dehydro-9-Trifluoromethyl Cinchona Alkaloids via19F NMR Spectroscopy: Emergence of Trifluoromethyl Moiety as a Conformational Stabilizer and a Probe

(2011) G. K. Surya Prakash et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Do we fully understand what controls chemical selectivity?

(2011) Julia Rehbein et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Racemization as a stereochemical measure of dynamics and robustness in shape-shifting organic molecules

(2011) M. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The inefficiency of re-weighted sampling and the curse of system size in high-order path integration

(2011) M. Ceriotti et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Methylhydroxycarbene: Tunneling Control of a Chemical Reaction

(2011) P. R. Schreiner et al.   SCIENCE

Molpro: a general-purpose quantum chemistry program package

(2011) Hans-Joachim Werner et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

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

Interplay between Theory and Experiment: Computational Organometallic and Transition Metal Chemistry

(2010) Zhenyang Lin   ACCOUNTS OF CHEMICAL RESEARCH

Exchange Often and Properly in Replica Exchange Molecular Dynamics

(2010) Daniel J. Sindhikara et al.   Journal of Chemical Theory and Computation

A System-Dependent Density-Based Dispersion Correction

(2010) Stephan N. Steinmann et al.   Journal of Chemical Theory and Computation

Homoaromaticity in aza- and phosphasemibullvalenes. A computational study

(2010) Daniel R. Greve   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

Entropy effects in hydrocarbon conversion reactions: free-energy integrations and transition-path sampling

(2010) T Bucko et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Challenges in protein-folding simulations

(2010) Peter L. Freddolino et al.   Nature Physics

Calculations Predict That Carbon Tunneling Allows the Degenerate Cope Rearrangement of Semibullvalene to Occur Rapidly at Cryogenic Temperatures

(2010) Xue Zhang et al.   ORGANIC LETTERS

Dynamics of 1,3-Dipolar Cycloaddition Reactions of Diazonium Betaines to Acetylene and Ethylene: Bending Vibrations Facilitate Reaction

(2009) Lai Xu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born−Oppenheimer ab Initio QM/MM Molecular Dynamics Study

(2009) Ruibo Wu et al.   Journal of Chemical Theory and Computation

An Improved Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Set of Parameters for Simulation of Bulk and Molecular Systems Involving Titanium

(2009) Grygoriy Dolgonos et al.   Journal of Chemical Theory and Computation

The role of water in silicate oligomerization reaction

(2009) Thuat T. Trinh et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Density Functionals with Broad Applicability in Chemistry

(2008) Yan Zhao et al.   ACCOUNTS OF CHEMICAL RESEARCH

Primary-Amine-Catalyzed Enantioselective Intramolecular Aldolizations

(2008) Jian Zhou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Bifurcations on Potential Energy Surfaces of Organic Reactions

(2008) Daniel H. Ess et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Thermal Rearrangements of 2-Ethynylbiphenyl: A DFT Study of Competing Reaction Mechanisms

(2008) Iain D. Mackie et al.   JOURNAL OF ORGANIC CHEMISTRY

On the Nature of the Intermediates and the Role of Chloride Ions in Pd-Catalyzed Allylic Alkylations: Added Insight from Density Functional Theory†

(2008) Peter Fristrup et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Ruthenium-Catalyzed Azide−Alkyne Cycloaddition: Scope and Mechanism

(2008) Brant C. Boren et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Capture of hydroxymethylene and its fast disappearance through tunnelling

(2008) Peter R. Schreiner et al.   NATURE