4.4 Article

Beyond Static Structures: Putting Forth REMD as a Tool to Solve Problems in Computational Organic Chemistry

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Enhanced sampling techniques in molecular dynamics simulations of biological systems

Rafael C. Bernardi et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)

Article Chemistry, Physical

A Fast Charge-Dependent Atom-Pairwise Dispersion Correction for DFTB3

Riccardo Petraglia et al.

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2015)

Article Chemistry, Organic

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

Debabrata Samanta et al.

JOURNAL OF ORGANIC CHEMISTRY (2015)

Article Chemistry, Multidisciplinary

Origins of Stereoselectivity in Intramolecular Aldol Reactions Catalyzed by Cinchona Amines

Yu-hong Lam et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Chemistry, Multidisciplinary

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

Salvador Perez-Estrada et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Chemistry, Multidisciplinary

Molecular Dynamics of the Diels-Alder Reactions of Tetrazines with Alkenes and N-2 Extrusions from Adducts

Lisa Toerk et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Chemistry, Multidisciplinary

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

R. Erik Plata et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Chemistry, Multidisciplinary

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

Gui-Juan Cheng et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Chemistry, Physical

Vibrational Entropy of a Protein: Large Differences between Distinct Conformations

Martin Goethe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Enhanced sampling of chemical and biochemical reactions with metadynamics

Shaohui Zheng et al.

MOLECULAR SIMULATION (2015)

Article Chemistry, Multidisciplinary

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

Gonzalo Jimenez-Oses et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

Article Chemistry, Multidisciplinary

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

Sharmistha Karmakar et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

Article Computer Science, Interdisciplinary Applications

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

Michele Ceriotti et al.

COMPUTER PHYSICS COMMUNICATIONS (2014)

Article Chemistry, Physical

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

Eric Bremond et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Physical

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

Michael Gaus et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

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

Daniel J. S. Sandbeck et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2014)

Article Chemistry, Physical

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

Qiang Cui et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)

Article Multidisciplinary Sciences

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

Timm Bredtmann et al.

NATURE COMMUNICATIONS (2014)

Review Chemistry, Multidisciplinary

Energy Disposition in Reactive Intermediates

Barry K. Carpenter

CHEMICAL REVIEWS (2013)

Article Chemistry, Physical

Parametrization and Benchmark of DFTB3 for Organic Molecules

Michael Gaus et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

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

Timm Bredtmann et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

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

Mariana Rossi et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Multidisciplinary

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

Antonio Moran et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Article Chemistry, Physical

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

Tae Hoon Choi

CHEMICAL PHYSICS LETTERS (2012)

Article Chemistry, Organic

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

David Ley et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2012)

Article Multidisciplinary Sciences

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

Kersey Black et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

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

Michele Ceriotti et al.

PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2012)

Review Chemistry, Multidisciplinary

Molpro: a general-purpose quantum chemistry program package

Hans-Joachim Werner et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)

Article Chemistry, Multidisciplinary

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

Timm Bredtmann et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2011)

Article Chemistry, Multidisciplinary

The Experimental Realization of a Neutral Homoaromatic Carbocycle

Peter R. Griffiths et al.

CHEMISTRY-A EUROPEAN JOURNAL (2011)

Article Chemistry, Multidisciplinary

A Density Dependent Dispersion Correction

Stephan N. Steinmann et al.

CHIMIA (2011)

Article Chemistry, Physical

A generalized-gradient approximation exchange hole model for dispersion coefficients

Stephan N. Steinmann et al.

JOURNAL OF CHEMICAL PHYSICS (2011)

Article Chemistry, Physical

Comprehensive Bench marking of a Density-Dependent Dispersion Correction

Stephan N. Steinmann et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Chemistry, Physical

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

Denis Bucher et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Chemistry, Physical

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

Dirk Andrae et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

Article Chemistry, Organic

Homoaromaticity in aza- and phosphasemibullvalenes. A computational study

Daniel R. Greve

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY (2011)

Article Chemistry, Physical

Do we fully understand what controls chemical selectivity?

Julia Rehbein et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)

Article Multidisciplinary Sciences

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

Maggie He et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Methylhydroxycarbene: Tunneling Control of a Chemical Reaction

Peter R. Schreiner et al.

SCIENCE (2011)

Review Chemistry, Multidisciplinary

Metadynamics

Alessandro Barducci et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)

Review Chemistry, Multidisciplinary

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

Zhenyang Lin

ACCOUNTS OF CHEMICAL RESEARCH (2010)

Article Chemistry, Physical

Exchange Often and Properly in Replica Exchange Molecular Dynamics

Daniel J. Sindhikara et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Physical

A System-Dependent Density-Based Dispersion Correction

Stephan N. Steinmann et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Physics, Condensed Matter

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

T. Bucko et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2010)

Review Physics, Multidisciplinary

Challenges in protein-folding simulations

Peter L. Freddolino et al.

NATURE PHYSICS (2010)

Article Chemistry, Organic

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

Iain D. Mackie et al.

JOURNAL OF ORGANIC CHEMISTRY (2009)

Article Chemistry, Physical

The role of water in silicate oligomerization reaction

Thuat T. Trinh et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2009)

Review Chemistry, Multidisciplinary

Density functionals with broad applicability in chemistry

Yan Zhao et al.

ACCOUNTS OF CHEMICAL RESEARCH (2008)

Article Chemistry, Multidisciplinary

Primary-amine-catalyzed enantioselective intramolecular aldolizations

Jian Zhou et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2008)

Review Chemistry, Multidisciplinary

Bifurcations on potential energy surfaces of organic reactions

Daniel H. Ess et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2008)

Article Chemistry, Multidisciplinary

Ruthenium-catalyzed azide-alkyne cycloaddition: Scope and mechanism

Brant C. Boren et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Article Multidisciplinary Sciences

Capture of hydroxymethylene and its fast disappearance through tunnelling

Peter R. Schreiner et al.

NATURE (2008)

Article Multidisciplinary Sciences

Chemical evolution: The mechanism of the formation of adenine under prebiotic conditions

Debjani Roy et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Physics, Multidisciplinary

Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics

Thomas D. Kuhne et al.

PHYSICAL REVIEW LETTERS (2007)

Article Chemistry, Multidisciplinary

Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics

Giovanni Bussi et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Physical

An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations

Teodoro Laino et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)

Article Chemistry, Physical

Crystal structure transformations in SiO2 from classical and ab initio metadynamics

Roman Martonak et al.

NATURE MATERIALS (2006)

Review Chemistry, Multidisciplinary

Molecular dynamics: Survey of methods for simulating the activity of proteins

Stewart A. Adcock et al.

CHEMICAL REVIEWS (2006)

Article Chemistry, Physical

Molecular dynamics simulation of liquid water: Hybrid density functionals

T Todorova et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Review Chemistry, Multidisciplinary

Metadynamics as a tool for exploring free energy landscapes of chemical reactions

B Ensing et al.

ACCOUNTS OF CHEMICAL RESEARCH (2006)

Article Chemistry, Physical

An efficient real space multigrid OM/MM electrostatic coupling

T Laino et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)

Article Chemistry, Multidisciplinary

Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics

I Ivanov et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Multidisciplinary

Copper(I)-catalyzed synthesis of azoles. DFT study predicts unprecedented reactivity and intermediates

F Himo et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Physical

Ab initio molecular dynamics simulation of the interaction between water and Ti in zeolitic systems

E Fois et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

Article Chemistry, Physical

Blue moon approach to rare events

G Ciccotti et al.

MOLECULAR SIMULATION (2004)

Article Chemistry, Physical

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

D Hamelberg et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Chemistry, Multidisciplinary

Neutral bishomoaromatic semibullvalenes

HS Wu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Physics, Multidisciplinary

Predicting crystal structures:: The Parrinello-Rahman method revisited -: art. no. 075503

R Martonák et al.

PHYSICAL REVIEW LETTERS (2003)

Article Chemistry, Multidisciplinary

Are 1,5-disubstituted semibullvalenes that have C2v equilibrium geometries necessarily bishomoaromatic?

EC Brown et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Multidisciplinary Sciences

Escaping free-energy minima

A Laio et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of biomolecules

M Karplus et al.

NATURE STRUCTURAL BIOLOGY (2002)

Article Chemistry, Physical

ReaxFF: A reactive force field for hydrocarbons

ACT van Duin et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2001)

Review Chemistry, Multidisciplinary

Chemistry with ADF

G te Velde et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2001)

Review Chemistry, Multidisciplinary

Homoaromaticity

RV Williams

CHEMICAL REVIEWS (2001)

Article Chemistry, Physical

Ab initio replica-exchange Monte Carlo method for cluster studies

Y Ishikawa et al.

CHEMICAL PHYSICS LETTERS (2001)