Molecular Dynamics of Complex Gas-Phase Reactive Systems by Time-Dependent Groups†

2005 ◽  
Vol 109 (50) ◽  
pp. 11515-11520 ◽  
Author(s):  
Michael R. Salazar
Keyword(s):  
Molecular Dynamics ◽  
Gas Phase ◽  
Reactive Systems ◽  
Time Dependent

scholarly journals Photofragmentation of Gas-Phase Lanthanide Cyclopentadienyl Complexes: Experimental and Time-Dependent Excited-State Molecular Dynamics

2014 ◽  
Vol 33 (7) ◽  
pp. 1574-1586 ◽  
Author(s):  
Jiangchao Chen ◽  
Andrew M. Hochstatter ◽  
Dmitri Kilin ◽  
P. Stanley May ◽  
Qingguo Meng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Gas Phase ◽  
Time Dependent ◽  
Cyclopentadienyl Complexes

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>

Impact of vibronic coupling effects on light-driven charge transfer in pyrene-functionalized middle and large-sized Metalloid Gold Nanoclusters from Ehrenfest dynamics.

2021 ◽  
Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Gold Nanoclusters ◽  
Tight Binding ◽  
Time Dependent ◽  
Effective Strategy ◽  
Dynamics Simulations ◽  
Dependent Density

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...

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 A universal framework for featurization of atomistic systems

2021 ◽  
Author(s):  
Xiangyun Lei ◽  
Andrew Medford
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Force Fields ◽  
Reactive Systems ◽  
Quantum Molecular Dynamics ◽  
Learning Models ◽  
Fixed Dimension ◽  
Comparable Performance ◽  
Invaluable Tool ◽  
Dynamics Simulations

Abstract Molecular dynamics simulations are an invaluable tool in numerous scientific fields. However, the ubiquitous classical force fields cannot describe reactive systems, and quantum molecular dynamics are too computationally demanding to treat large systems or long timescales. Reactive force fields based on physics or machine learning can be used to bridge the gap in time and length scales, but these force fields require substantial effort to construct and are highly specific to a given chemical composition and application. A significant limitation of machine learning models is the use of element-specific features, leading to models that scale poorly with the number of elements. This work introduces the Gaussian multipole (GMP) featurization scheme that utilizes physically-relevant multipole expansions of the electron density around atoms to yield feature vectors that interpolate between element types and have a fixed dimension regardless of the number of elements present. We combine GMP with neural networks to directly compare it to the widely used Behler-Parinello symmetry functions for the MD17 dataset, revealing that it exhibits improved accuracy and computational efficiency. Further, we demonstrate that GMP-based models can achieve chemical accuracy for the QM9 dataset, and their accuracy remains reasonable even when extrapolating to new elements. Finally, we test GMP-based models for the Open Catalysis Project (OCP) dataset, revealing comparable performance to graph convolutional deep learning models. The results indicate that this featurization scheme fills a critical gap in the construction of efficient and transferable machine-learned force fields.

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>

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