The influence of base pair tautomerism on single point mutations in aqueous DNA

Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects

(2019) Bobo Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA

(2018) Susanta Das et al.   Journal of Chemical Theory and Computation

Mechanisms for guanine–cytosine tautomeric equilibrium in solution via steered molecular dynamic simulations

(2018) S. Tolosa et al.   JOURNAL OF MOLECULAR LIQUIDS

Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine–cytosine and adenine–thymine base pairs: a polarizable continuum model study

(2018) Eduardo E. Romero et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effects of Intense Electric Fields on the Double Proton Transfer in the Watson–Crick Guanine–Cytosine Base Pair

(2018) Alya A. Arabi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamic basis for dG•dT misincorporation via tautomerization and ionization

(2018) Isaac J. Kimsey et al.   NATURE

Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects

(2018) Holger Kruse et al.   Journal of Chemical Theory and Computation

Theoretical thermodynamic study of the adenine-thymine tautomeric equilibrium: Electronic structure calculations and steered molecular dynamic simulations

(2017) Santiago Tolosa et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model

(2017) Abir Ganguly et al.   Journal of Chemical Theory and Computation

Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA

(2017) Sven Roßbach et al.   Journal of Chemical Theory and Computation

Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals

(2017) Narbe Mardirossian et al.   MOLECULAR PHYSICS

Assessing the Current State of Amber Force Field Modifications for DNA

(2016) Rodrigo Galindo-Murillo et al.   Journal of Chemical Theory and Computation

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

(2016) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Long-timescale dynamics of the Drew–Dickerson dodecamer

(2016) Pablo D. Dans et al.   NUCLEIC ACIDS RESEARCH

On the calculation of equilibrium thermodynamic properties from molecular dynamics

(2016) Peter V. Coveney et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Optimizing link atom parameters for DNA QM/MM simulations

(2016) Manuel Hitzenberger et al.   THEORETICAL CHEMISTRY ACCOUNTS

Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes

(2015) Isaac J. Kimsey et al.   NATURE

Modelling proton tunnelling in the adenine–thymine base pair

(2015) A. D. Godbeer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the Importance of Proton Transfer Reactions in DNA

(2014) Denis Jacquemin et al.   ACCOUNTS OF CHEMICAL RESEARCH

Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field

(2014) Eliot Boulanger et al.   Journal of Chemical Theory and Computation

Electric field induced DNA damage: an open door for selective mutations

(2013) José Pedro Cerón-Carrasco et al.   CHEMICAL COMMUNICATIONS

Why the tautomerization of the G·C Watson–Crick base pairviathe DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis

(2013) Ol’ha O. Brovarets’ et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Can tautomerization of the A·T Watson–Crick base pairviadouble proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis

(2013) Ol’ha O. Brovarets et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Non-covalent interactions and thermochemistry using XDM-corrected hybrid and range-separated hybrid density functionals

(2013) A. Otero-de-la-Roza et al.   JOURNAL OF CHEMICAL PHYSICS

How DNA is damaged by external electric fields: selective mutation vs. random degradation

(2013) José Pedro Cerón-Carrasco et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

ChemShell-a modular software package for QM/MM simulations

(2013) Sebastian Metz et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

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

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

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

Monomeric adenine decay dynamics influenced by the DNA environment

(2012) You Lu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong et al.   NATURE

Electric-field induced mutation of DNA: a theoretical investigation of the GC base pair

(2012) José P. Cerón-Carrasco et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands

(2011) You Lu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Exploring the common molecular basis for the universal DNA mutation bias: Revival of Löwdin mutation model

(2011) Liang-Yu Fu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Combined effect of stacking and solvation on the spontaneous mutation in DNA

(2011) José P. Cerón-Carrasco et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis

(2011) W. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Density functional theory with London dispersion corrections

(2011) Stefan Grimme   Wiley Interdisciplinary Reviews-Computational Molecular Science

Theoretical Investigation of Hydrogen Atom Transfer in the Cytosine-Guanine Base Pair and Its Coupling with Electronic Rearrangement. Concerted vs Stepwise Mechanism

(2010) Giovanni Villani   JOURNAL OF PHYSICAL CHEMISTRY B

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Sequence-dependent proton-transfer reaction in stacked GC pair II: The origin of stabilities of proton-transfer products

(2009) Toru Matsui et al.   CHEMICAL PHYSICS LETTERS

A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the QM Region for Peptidic Systems†

(2009) Chris Vanessa Sumowski et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Intermolecular Proton Transfer in Microhydrated Guanine−Cytosine Base Pairs: a New Mechanism for Spontaneous Mutation in DNA

(2009) J. P. Cerón-Carrasco et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Effects of Hydration on the Proton Transfer Mechanism in the Adenine−Thymine Base Pair

(2009) J. P. Cerón-Carrasco et al.   JOURNAL OF PHYSICAL CHEMISTRY A

DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations†

(2009) Johannes Kästner et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Investigations on the migration behaviour of purines and pyrimidines in capillary electromigration techniques with UV detection and mass spectrometric detection

(2008) Manuela Haunschmidt et al.   JOURNAL OF CHROMATOGRAPHY A

Regulation of DNA repair throughout the cell cycle

(2008) Dana Branzei et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY