Micelles of the chiral biocompatible surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl)dimethylammonium bromide (DMEB): molecular dynamics and fragmentation patterns in the gas phase

2017 ◽  
Vol 31 (13) ◽  
pp. 1158-1168
Author(s):  
David Bongiorno ◽  
Serena Indelicato ◽  
Leopoldo Ceraulo ◽  
Ugo Perricone ◽  
Valentina Calabrese ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Gas Phase ◽  
Fragmentation Patterns

scholarly journals Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

Open Physics ◽  
2014 ◽  
Vol 12 (2) ◽  
Author(s):  
Pablo López-Tarifa ◽  
Marie-Anne Hervé du Penhoat ◽  
Rodophe Vuilleumier ◽  
Marie-Pierre Gaigeot ◽  
Ursula Rothlisberger ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Time Dependent ◽  
Dynamics Simulation ◽  
Functional Theory ◽  
Fragmentation Patterns ◽  
Doubly Charged ◽  
Dependent Density

AbstractWe use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

Conformations of 2,4-Diphenylpentane:  A Quantum Chemistry and Gas-Phase Molecular Dynamics Simulation Study

1998 ◽  
Vol 102 (24) ◽  
pp. 4694-4702 ◽  
Author(s):  
Grant D. Smith ◽  
Chakravarthy Ayyagari ◽  
Richard L. Jaffe ◽  
Matthew Pekny ◽  
Aaron Bernarbo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Quantum Chemistry ◽  
Gas Phase ◽  
Simulation Study ◽  
Dynamics Simulation

scholarly journals Compaction of RNA Hairpins and Their Kissing Complexes in Native Electrospray Mass Spectrometry

2020 ◽  
Author(s):  
Joséphine Abi-Ghanem ◽  
Clémence Rabin ◽  
Massimiliano Porrini ◽  
Frédéric Rosu ◽  
Valerie Gabelica
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Gas Phase ◽  
Electrospray Mass Spectrometry ◽  
Initial Structure ◽  
Native Solution ◽  
Phase Structures ◽  
Rna Hairpins ◽  
Level Calculation ◽  
Structure In Solution

When electrosprayed from native solution conditions, RNA hairpins and kissing complexes acquire charge states at which they get significantly more compact in the gas phase than their initial structure in solution. Here we show the limits of using force field molecular dynamics to interpret the gas-phase structures of nucleic acid complexes in the gas phase, and we suggest that higher-level calculation levels should be used in the future.<br>

Characterizing gaseous peptide structure with action-EET and simulated annealing

2015 ◽  
Vol 17 (39) ◽  
pp. 25822-25827 ◽  
Author(s):  
Nathan G. Hendricks ◽  
Ryan R. Julian
Keyword(s):  
Molecular Dynamics ◽  
Energy Transfer ◽  
Simulated Annealing ◽  
Gas Phase ◽  
Peptide Structure

Distance-sensitive energy transfer and molecular dynamics are used to generate experimentally corroborated structures for peptides in the gas phase.

Gas-Phase Structure of the Histone Multimers Characterized by Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation

2013 ◽  
Vol 85 (8) ◽  
pp. 4165-4171 ◽  
Author(s):  
Kazumi Saikusa ◽  
Sotaro Fuchigami ◽  
Kyohei Takahashi ◽  
Yuuki Asano ◽  
Aritaka Nagadoi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Gas Phase ◽  
Ion Mobility ◽  
Phase Structure ◽  
Dynamics Simulation ◽  
Ion Mobility Mass Spectrometry ◽  
Gas Phase Structure

The cubyl cation rearrangements

2016 ◽  
Vol 52 (16) ◽  
pp. 3403-3405 ◽  
Author(s):  
Said Jalife ◽  
Sukanta Mondal ◽  
Jose Luis Cabellos ◽  
Gerardo Martinez-Guajardo ◽  
Maria A. Fernandez-Herrera ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Dynamics Simulations ◽  
High Level

Born–Oppenheimer molecular dynamics simulations and high-level ab initio computations predict that the cage-opening rearrangement of the cubyl cation to the 7H+-pentalenyl cation is feasible in the gas phase.

Sign in / Sign up

Export Citation Format

Share Document