Cargando…

Solvent Organization and Rate Regulation of a Menshutkin Reaction by Oriented External Electric Fields are Revealed by Combined MD and QM/MM Calculations

[Image: see text] When and how do external electric fields (EEFs) lead to catalysis in the presence of a (polar or nonpolar) solvent? This is the question that is addressed here using a combination of molecular dynamics (MD) simulations, quantum mechanical/molecular mechanical calculations with EEF,...

Descripción completa

Detalles Bibliográficos
Autores principales:	Dutta Dubey, Kshatresh, Stuyver, Thijs, Kalita, Surajit, Shaik, Sason
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Chemical Society 2020
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304904/ https://www.ncbi.nlm.nih.gov/pubmed/32369357 http://dx.doi.org/10.1021/jacs.9b13029

Ejemplares similares

MD simulations and QM/MM calculations reveal the key mechanistic elements which are responsible for the efficient C–H amination reaction performed by a bioengineered P450 enzyme
por: Kalita, Surajit, et al.
Publicado: (2021)

MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450(BM3) alter the active site’s complexity and the chemoselectivity of oxidation without changing the active species
por: Dubey, Kshatresh Dutta, et al.
Publicado: (2017)

How Can Static and Oscillating Electric Fields Serve in Decomposing Alzheimer’s and Other Senile Plaques?
por: Kalita, Surajit, et al.
Publicado: (2023)

A porphyrin-based molecular cage guided by designed local-electric field is highly selective and efficient
por: Siddiqui, Shakir Ali, et al.
Publicado: (2023)

Developing C2-Aroyl Indoles as Novel Inhibitors of IDO1 and Understanding Their Mechanism of Inhibition via Mass Spectroscopy, QM/MM Calculations and Molecular Dynamics Simulation
por: Chauhan, Jyoti, et al.
Publicado: (2021)

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

Electro-Freezing of Supercooled Water Is Induced by Hydrated Al(3+) and Mg(2+) Ions: Experimental and Theoretical Studies
por: Fuhrman Javitt, Leah, et al.
Publicado: (2023)

The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study
por: Landi, Alessandro, et al.
Publicado: (2021)

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

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

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)

Unifying Conceptual Density Functional and Valence Bond Theory: The Hardness–Softness Conundrum Associated with Protonation Reactions and Uncovering Complementary Reactivity Modes
por: Stuyver, Thijs, et al.
Publicado: (2020)

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)

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

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)

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

Recent advances in QM/MM free energy calculations using reference potentials()
por: Duarte, Fernanda, et al.
Publicado: (2015)

Modulating the radical reactivity of phenyl radicals with the help of distonic charges: it is all about electrostatic catalysis
por: Mondal, Totan, et al.
Publicado: (2021)

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)

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems
por: Berraud-Pache, Romain, et al.
Publicado: (2018)

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes
por: Jin, Xinsheng, et al.
Publicado: (2018)

Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations
por: Voice, Angus T., et al.
Publicado: (2021)

How Do Local Reactivity Descriptors Shape the Potential Energy Surface Associated with Chemical Reactions? The Valence Bond Delocalization Perspective
por: Stuyver, Thijs, et al.
Publicado: (2020)

Correction to “How Do Local Reactivity Descriptors Shape the Potential Energy Surface Associated with Chemical Reactions? The Valence Bond Delocalization Perspective”
por: Stuyver, Thijs, et al.
Publicado: (2021)

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)

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

Structure–Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations
por: Schulz, Christine E., et al.
Publicado: (2021)

Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations
por: Korlyukov, Alexander A., et al.
Publicado: (2023)

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

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

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations
por: Fang, Dong, et al.
Publicado: (2014)

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)

Cannot write session to /tmp/vufind_sessions/sess_muc8dhi9ir97vg2j8js7b0fmi8