Computing pKa Shifts Using Traditional Molecular Dynamics: Example of Acid–Base Indicator Dyes in Organized Solutions

Vladimir S. Farafonov; Alexander V. Lebed; Nikolay O. Mchedlov-Petrossyan

doi:10.1021/acs.jctc.0c00231

Computing pKa Shifts Using Traditional Molecular Dynamics: Example of Acid–Base Indicator Dyes in Organized Solutions

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.0c00231 ◽

2020 ◽

Vol 16 (9) ◽

pp. 5852-5865

Author(s):

Vladimir S. Farafonov ◽

Alexander V. Lebed ◽

Nikolay O. Mchedlov-Petrossyan

Keyword(s):

Molecular Dynamics ◽

Acid Base ◽

Pka Shifts ◽

Indicator Dyes

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Structural and Molecular Dynamics Analysis of Plant Serotonin N ‐Acetyltransferase Reveal an Acid/Base‐Assisted Catalysis in Melatonin Biosynthesis

Angewandte Chemie ◽

10.1002/ange.202100992 ◽

2021 ◽

Author(s):

Lijing Liao ◽

Yuanze Zhou ◽

Youdong Xu ◽

Yuhao Zhang ◽

Xikai Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Dynamics Analysis ◽

Acid Base

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Molecular Dynamics Simulations of Proton Transport in Proton Exchange Membranes Based on Acid-Base Complexes

Molecular Interactions ◽

10.5772/36194 ◽

2012 ◽

Cited By ~ 2

Author(s):

Liuming Yan ◽

Liqing Xie

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Proton Transport ◽

Proton Exchange Membranes ◽

Proton Exchange ◽

Acid Base ◽

Dynamics Simulations

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Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20979 ◽

2006 ◽

Vol 64 (1) ◽

pp. 167-177 ◽

Cited By ~ 36

Author(s):

Emma Langella ◽

Roberto Improta ◽

Orlando Crescenzi ◽

Vincenzo Barone

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Prion Protein ◽

Acid Base ◽

Histidine Residues ◽

Conformational Properties ◽

Human Prion Protein ◽

Dynamics Simulations

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Interfacial electrostatic potential of polyions as probed by acid-base indicator dyes covalently attached to the main chain

Journal of Polymer Science Part A Polymer Chemistry ◽

10.1002/pola.1991.080290509 ◽

1991 ◽

Vol 29 (5) ◽

pp. 677-684 ◽

Cited By ~ 3

Author(s):

Yotaro Morishima ◽

Yuji Higuchi ◽

Mikiharu Kamachi

Keyword(s):

Electrostatic Potential ◽

Main Chain ◽

Acid Base ◽

Indicator Dyes

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Potential Energy and Free Energy Surfaces of All Ten Canonical and Methylated Nucleic Acid Base Pairs: Molecular Dynamics and Quantum Chemical ab Initio Studies

The Journal of Physical Chemistry B ◽

10.1021/jp0104886 ◽

2001 ◽

Vol 105 (24) ◽

pp. 5804-5817 ◽

Cited By ~ 59

Author(s):

Martin Kabeláč ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Nucleic Acid ◽

Potential Energy ◽

Ab Initio ◽

Quantum Chemical ◽

Acid Base ◽

Base Pairs ◽

Nucleic Acid Base ◽

Energy Surfaces

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Interfacial Electrical Properties of Nanodiamond Colloidal Species in Aqueous Medium as Examined by Acid-Base Indicator Dyes

Surface Engineering and Applied Electrochemistry ◽

10.3103/s1068375518010088 ◽

2018 ◽

Vol 54 (1) ◽

pp. 64-72 ◽

Cited By ~ 3

Author(s):

N. N. Kamneva ◽

V. V. Tkachenko ◽

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A. I. Marynin ◽

A. I. Ukrainets ◽

...

Keyword(s):

Electrical Properties ◽

Aqueous Medium ◽

Acid Base ◽

Indicator Dyes ◽

Colloidal Species

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Examining surfactant micelles via acid-base indicators: Revisiting the pioneering Hartley–Roe 1940 study by molecular dynamics modeling

Journal of Molecular Liquids ◽

10.1016/j.molliq.2018.05.076 ◽

2018 ◽

Vol 264 ◽

pp. 683-690 ◽

Cited By ~ 2

Author(s):

Nikolay O. Mchedlov-Petrossyan ◽

Vladimir S. Farafonov ◽

Alexander V. Lebed

Keyword(s):

Molecular Dynamics ◽

Dynamics Modeling ◽

Acid Base ◽

Surfactant Micelles ◽

Molecular Dynamics Modeling

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Molecular dynamics simulations of acid/base induced switching of a bistable rotaxane

Molecular Physics ◽

10.1080/00268976.2016.1258497 ◽

2016 ◽

Vol 115 (3) ◽

pp. 297-307 ◽

Cited By ~ 1

Author(s):

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Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Acid Base ◽

Dynamics Simulations ◽

Bistable Rotaxane

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pp. 8397-8405 ◽

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Benedito J. Costa Cabral ◽

Roberto Rivelino ◽

Kaline Coutinho ◽

Sylvio Canuto

Keyword(s):

Molecular Dynamics ◽

Absorption Spectrum ◽

Electronic Absorption Spectrum ◽

Lewis Acid ◽

Electronic Absorption ◽

Supercritical Co2 ◽

Acid Base

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Molecular dynamics study of an acid-base indicator dye in Triton X-100 non-ionic micelles

Voprosy Khimii i Khimicheskoi Tekhnologii ◽

10.32434/0321-4095-2019-128-1-97-103 ◽

2020 ◽

pp. 97-103 ◽

Cited By ~ 1

Author(s):

V.S. Farafonov ◽

◽

A.V. Lebed ◽

N.L. Khimenko ◽

N.O. Mchedlov-Petrossyan ◽

...

Keyword(s):

Molecular Dynamics ◽

Acid Base ◽

Ionic Micelles ◽

Triton X ◽

Indicator Dye

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