Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study

Barbora Profantová; Václav Profant; Vlastimil Zíma; Vladimír Kopecký; Lucie Bednárová; Christian Zentz; Vladimír Baumruk; Pierre-Yves Turpin; Josef Štěpánek

doi:10.1021/jp4099864

Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study

The Journal of Physical Chemistry B ◽

10.1021/jp4099864 ◽

2013 ◽

Vol 117 (50) ◽

pp. 16086-16095 ◽

Cited By ~ 5

Author(s):

Barbora Profantová ◽

Václav Profant ◽

Vlastimil Zíma ◽

Vladimír Kopecký ◽

Lucie Bednárová ◽

...

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Transcription Factor ◽

Optical Spectroscopy ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Functional Theory ◽

Theory Calculation ◽

Protonation Effect

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Computational insights into the sorption mechanism of polycyclic aromatic hydrocarbons by carbon nanotube through density functional theory calculation and molecular dynamics simulation

Computational Materials Science ◽

10.1016/j.commatsci.2020.109677 ◽

2020 ◽

Vol 179 ◽

pp. 109677 ◽

Cited By ~ 7

Author(s):

Baichun Hu ◽

Zisen Gao ◽

Hanxun Wang ◽

Jian Wang ◽

Maosheng Cheng

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Aromatic Hydrocarbons ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Dynamics Simulation ◽

Sorption Mechanism ◽

Functional Theory ◽

Polycyclic Aromatic ◽

Theory Calculation

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Prediction of Optical and Dielectric Properties of 4-Cyano-4-pentylbiphenyl Liquid Crystals by Molecular Dynamics Simulation, Coarse-Grained Dynamics Simulation, and Density Functional Theory Calculation

The Journal of Physical Chemistry C ◽

10.1021/acs.jpcc.5b12222 ◽

2016 ◽

Vol 120 (26) ◽

pp. 14277-14288 ◽

Cited By ~ 7

Author(s):

Shin-Pon Ju ◽

Sheng-Chieh Huang ◽

Ken-Huang Lin ◽

Hsing-Yin Chen ◽

Ting-Kai Shen

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Dielectric Properties ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Dynamics Simulation ◽

Coarse Grained ◽

Functional Theory ◽

Theory Calculation

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Understanding the structural, mechanical, thermal, and electronic properties of MgCa bulk metallic glasses by molecular dynamics simulation and density functional theory calculation

Computational Materials Science ◽

10.1016/j.commatsci.2018.08.007 ◽

2018 ◽

Vol 154 ◽

pp. 256-265 ◽

Cited By ~ 2

Author(s):

Shin-Pon Ju ◽

Cheng-Chia Yang

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Electronic Properties ◽

Metallic Glasses ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Dynamics Simulation ◽

Functional Theory ◽

Theory Calculation

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Doping Graphene with Ferroelectric β-PVDF Polymer Film: Density Functional Theory Calculation and Molecular Dynamics Simulation

Science of Advanced Materials ◽

10.1166/sam.2014.2221 ◽

2014 ◽

Vol 6 (11) ◽

pp. 2422-2427 ◽

Cited By ~ 2

Author(s):

Nodo Lee ◽

Jinhee Lee ◽

Taekhee Ryu ◽

Youngjune Kim ◽

Yves Lansac ◽

...

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Polymer Film ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Dynamics Simulation ◽

Functional Theory ◽

Film Density ◽

Theory Calculation

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Prediction of the variation of PGA strength during hydrolysis by a combination of empirical equation, density functional theory calculation, and molecular dynamics simulation

AIP Advances ◽

10.1063/1.4884195 ◽

2014 ◽

Vol 4 (7) ◽

pp. 077104 ◽

Cited By ~ 1

Author(s):

Chuan Chen ◽

Shin-Pon Ju ◽

Wei-Chun Huang ◽

Jenn-Sen Lin ◽

Chien-Chia Chen

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Density Functional ◽

Empirical Equation ◽

Density Functional Theory Calculation ◽

Dynamics Simulation ◽

Functional Theory ◽

Theory Calculation

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Effects of Strontium incorporation to Mg-Zn-Ca biodegradable bulk metallic glass investigated by molecular dynamics simulation and density functional theory calculation

Scientific Reports ◽

10.1038/s41598-020-58789-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Shih-Jye Sun ◽

Shin-Pon Ju ◽

Cheng-Chia Yang ◽

Kai-Chi Chang ◽

I-Jui Lee

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulation ◽

Metallic Glass ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Dynamics Simulation ◽

Functional Theory ◽

Strontium Incorporation ◽

Theory Calculation

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Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases

Journal of Chemical Theory and Computation ◽

10.1021/ct800342w ◽

2009 ◽

Vol 5 (4) ◽

pp. 1137-1145 ◽

Cited By ~ 40

Author(s):

Christopher H. Chang ◽

Kwiseon Kim

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Functional Theory ◽

Theory Calculation

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Corrosion-induced microstructure degradation of copper in sulfide-containing simulated anoxic groundwater studied by synchrotron high-energy X-ray diffraction and ab-initio density functional theory calculation

Corrosion Science ◽

10.1016/j.corsci.2021.109390 ◽

2021 ◽

Vol 184 ◽

pp. 109390

Author(s):

Fan Zhang ◽

Cem Örnek ◽

Min Liu ◽

Timo Müller ◽

Ulrich Lienert ◽

...

Keyword(s):

Density Functional Theory ◽

Ab Initio ◽

Density Functional ◽

Density Functional Theory Calculation ◽

High Energy ◽

X Ray Diffraction ◽

Functional Theory ◽

X Ray ◽

Theory Calculation

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Ordered boron phosphorus codoped graphene realizing widely tunable quasi Dirac-cone gap

Journal of Materials Chemistry C ◽

10.1039/d0tc04998k ◽

2021 ◽

Vol 9 (12) ◽

pp. 4316-4321

Author(s):

L.-B. Meng ◽

S. Ni ◽

Z. M. Zhang ◽

S. K. He ◽

W. M. Zhou

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Dirac Cone ◽

Functional Theory ◽

Theory Calculation

Density functional theory calculation predicts a novel ordered boron phosphorus codoped graphene realizing a widely tunable Dirac-cone gap.

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Excited state structural dynamics and Herzberg–Teller coupling of tetraphenylporphine explored via resonance Raman spectroscopy and density functional theory calculation

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy ◽

10.1016/j.saa.2009.10.054 ◽

2010 ◽

Vol 75 (5) ◽

pp. 1381-1387 ◽

Cited By ~ 6

Author(s):

Jun Xu ◽

Junmin Wan ◽

Yanying Zhao ◽

Miaoqiang Lv ◽

Xuming Zheng ◽

...

Keyword(s):

Density Functional Theory ◽

Raman Spectroscopy ◽

Excited State ◽

Structural Dynamics ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Resonance Raman Spectroscopy ◽

Resonance Raman ◽

Functional Theory ◽

Theory Calculation

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