Gas-Phase Chemical Dynamics Simulations on the Bifurcating Pathway of the Pimaradienyl Cation Rearrangement: Role of Enzymatic Steering in Abietic Acid Biosynthesis

2012 ◽  
Vol 8 (4) ◽  
pp. 1212-1222 ◽  
Author(s):  
Matthew R. Siebert ◽  
Paranjothy Manikandan ◽  
Rui Sun ◽  
Dean J. Tantillo ◽  
William L. Hase
Keyword(s):  
Gas Phase ◽  
Abietic Acid ◽  
Chemical Dynamics ◽  
Acid Biosynthesis ◽  
Dynamics Simulations ◽  
Phase Chemical

The Need for Enzymatic Steering in Abietic Acid Biosynthesis: Gas-Phase Chemical Dynamics Simulations of Carbocation Rearrangements on a Bifurcating Potential Energy Surface

2011 ◽  
Vol 133 (21) ◽  
pp. 8335-8343 ◽  
Author(s):  
Matthew R. Siebert ◽  
Jiaxu Zhang ◽  
Srirangam V. Addepalli ◽  
Dean J. Tantillo ◽  
William L. Hase
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Abietic Acid ◽  
Energy Surface ◽  
Chemical Dynamics ◽  
Acid Biosynthesis ◽  
Dynamics Simulations ◽  
Phase Chemical

Chemical Dynamics Simulations in the Gas Phase and on Complex Surfaces A Tribute to William Hase

2006 ◽  
Vol 110 (4) ◽  
pp. 1201-1202
Author(s):  
Mary T. Rodgers ◽  
Gang-yu Liu
Keyword(s):  
Gas Phase ◽  
Chemical Dynamics ◽  
Complex Surfaces ◽  
Dynamics Simulations

Gas phase fragmentation mechanisms of protonated testosterone as revealed by chemical dynamics simulations

2016 ◽  
Vol 407 ◽  
pp. 40-50 ◽  
Author(s):  
Giae Lee ◽  
Eunkyung Park ◽  
Heesun Chung ◽  
Yannick Jeanvoine ◽  
Kihyung Song ◽  
...  
Keyword(s):  
Gas Phase ◽  
Chemical Dynamics ◽  
Fragmentation Mechanisms ◽  
Dynamics Simulations ◽  
Gas Phase Fragmentation

THE GAS-PHASE CHEMICAL DYNAMICS ASSOCIATED WITH METEORS

2001 ◽  
pp. 268-348 ◽  
Author(s):  
Rainer A. Dressler ◽  
Edmond Murad
Keyword(s):  
Gas Phase ◽  
Chemical Dynamics ◽  
Phase Chemical

scholarly journals Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces

2019 ◽  
Vol 31 (1) ◽  
pp. 2-24 ◽  
Author(s):  
Ana Martin Somer ◽  
Veronica Macaluso ◽  
George L. Barnes ◽  
Li Yang ◽  
Subha Pratihar ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Collision Induced Dissociation ◽  
Chemical Dynamics ◽  
Organic Surfaces ◽  
Dynamics Simulations

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations

2012 ◽  
Vol 14 (33) ◽  
pp. 11724 ◽  
Author(s):  
Riccardo Spezia ◽  
Alvaro Cimas ◽  
Marie-Pierre Gaigeot ◽  
Jean-Yves Salpin ◽  
Kihyung Song ◽  
...  
Keyword(s):  
Gas Phase ◽  
Neutral Loss ◽  
Coulomb Explosion ◽  
Collision Induced Dissociation ◽  
Chemical Dynamics ◽  
Doubly Charged Ions ◽  
Dynamics Simulations ◽  
Doubly Charged ◽  
Charged Ions

scholarly journals Gas Phase Synthesis of Protonated Glycine by Chemical Dynamics Simulations

2018 ◽  
Vol 122 (3) ◽  
pp. 869-877 ◽  
Author(s):  
Yannick Jeanvoine ◽  
Antonio Largo ◽  
William L. Hase ◽  
Riccardo Spezia
Keyword(s):  
Gas Phase ◽  
Chemical Dynamics ◽  
Phase Synthesis ◽  
Gas Phase Synthesis ◽  
Dynamics Simulations

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

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