Cargando…

The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study

The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800–1000 ps to...

Descripción completa

Detalles Bibliográficos
Autores principales:	Landi, Alessandro, Capobianco, Amedeo, Peluso, Andrea
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2021
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8465834/ https://www.ncbi.nlm.nih.gov/pubmed/34576968 http://dx.doi.org/10.3390/molecules26185497

Ejemplares similares

Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations
por: Capobianco, Amedeo, et al.
Publicado: (2022)

Exploring the RING-Catalyzed Ubiquitin Transfer Mechanism by MD and QM/MM Calculations
por: Zhen, Yunmei, et al.
Publicado: (2014)

Solvent Organization and Rate Regulation of a Menshutkin Reaction by Oriented External Electric Fields are Revealed by Combined MD and QM/MM Calculations
por: Dutta Dubey, Kshatresh, et al.
Publicado: (2020)

Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study
por: Suenaga, Shunya, et al.
Publicado: (2023)

Targeted DNA oxidation and trajectory of radical DNA using DFT based QM/MM dynamics
por: Biswas, Pradip K, et al.
Publicado: (2019)

Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA
por: Landi, Alessandro, et al.
Publicado: (2020)

The Dynamics of Hole Transfer in DNA
por: Peluso, Andrea, et al.
Publicado: (2019)

Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations
por: Liu, Fei, et al.
Publicado: (2015)

The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study
por: Hitzenberger, Manuel, et al.
Publicado: (2017)

Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations
por: Reiter, Sebastian, et al.
Publicado: (2023)

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region
por: Jindal, Garima, et al.
Publicado: (2016)

Insights into the Interaction between Polyphenols and β-Lactoglobulin through Molecular Docking, MD Simulation, and QM/MM Approaches
por: Baruah, Indrani, et al.
Publicado: (2022)

On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis
por: Alvarado, Raúl, et al.
Publicado: (2022)

Review on the QM/MM Methodologies and Their Application to Metalloproteins
por: Tzeliou, Christina Eleftheria, et al.
Publicado: (2022)

QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase
por: Prejanò, Mario, et al.
Publicado: (2018)

Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods
por: Yildiz, Ibrahim, et al.
Publicado: (2018)

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
por: König, Gerhard, et al.
Publicado: (2014)

Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study
por: Romero-Téllez, Sonia, et al.
Publicado: (2019)

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase
por: Kulik, Heather J., et al.
Publicado: (2016)

Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis
por: Pérez-Barcia, Álvaro, et al.
Publicado: (2023)

QM/MM study of the reaction mechanism of sulfite oxidase
por: Caldararu, Octav, et al.
Publicado: (2018)

On the Difference Between Additive and Subtractive QM/MM Calculations
por: Cao, Lili, et al.
Publicado: (2018)

QM/MM Calculations with deMon2k
por: Salahub, Dennis R., et al.
Publicado: (2015)

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies
por: Elsässer, Brigitta, et al.
Publicado: (2021)

PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method
por: Chen, Cheng Giuseppe, et al.
Publicado: (2022)

Spin‐projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B−DNA by Singlet Oxygen
por: Saito, Toru, et al.
Publicado: (2021)

Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level
por: Li, Pengfei, et al.
Publicado: (2018)

A QM/MM Study on the Initiation Reaction of Firefly Bioluminescence—Enzymatic Oxidation of Luciferin
por: Yu, Mohan, et al.
Publicado: (2021)

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations
por: Pan, Xiaoliang, et al.
Publicado: (2018)

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions
por: Mulholland, Adrian J
Publicado: (2007)

QM/MM Molecular Dynamics Studies of Metal Binding Proteins
por: Vidossich, Pietro, et al.
Publicado: (2014)

Projected Hybrid Orbitals: A General QM/MM Method
por: Wang, Yingjie, et al.
Publicado: (2014)

Robotic QM/MM-driven maturation of antibody combining sites
por: Smirnov, Ivan V., et al.
Publicado: (2016)

NAMD goes quantum: An integrative suite for QM/MM simulations
por: Melo, Marcelo C. R., et al.
Publicado: (2018)

A QM/MM study of the nature of the entatic state in plastocyanin
por: Hurd, Catherine A., et al.
Publicado: (2016)

QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate
por: Boneta, Sergio, et al.
Publicado: (2021)

QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase
por: Grigorenko, Bella, et al.
Publicado: (2023)

The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin
por: Wang, Xianwei, et al.
Publicado: (2020)

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums
por: Ion, Bogdan F., et al.
Publicado: (2012)

Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations
por: Moriwaki, Yoshitaka, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_hc22tpqjis1paurvp601s4pfii