scholarly journals Gas-Phase Infrared Spectrum of the Protonated Water Dimer: Molecular Dynamics Simulation and Accuracy of the Potential Energy Surface

ChemPhysChem ◽  
2005 ◽  
Vol 6 (9) ◽  
pp. 1706-1710 ◽  
Author(s):  
Joachim Sauer ◽  
Jens Döbler
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Infrared Spectrum ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Energy Surface ◽  
Water Dimer ◽  
Dynamics Simulation

Potential energy surface and molecular dynamics simulation of gold(I) in liquid nitromethane

2009 ◽  
Vol 147 (1-2) ◽  
pp. 64-70 ◽  
Author(s):  
Natcha Injan ◽  
Tünde Megyes ◽  
Tamas Radnai ◽  
Imre Bako ◽  
Szabolcz Balint ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Dynamics Simulation

Stilbene isomerization dynamics on multidimensional potential energy surface. Molecular dynamics simulation

1993 ◽  
Vol 215 (4) ◽  
pp. 306-314 ◽  
Author(s):  
Valentin D. Vachev ◽  
John H. Frederick ◽  
Boris A. Grishanin ◽  
Victor N. Zadkov ◽  
Nikolai I. Koroteev
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Dynamics Simulation

scholarly journals Using a monomer potential energy surface to perform approximate path integral molecular dynamics simulation of ab initio water at near-zero added cost

2019 ◽  
Vol 21 (1) ◽  
pp. 409-417 ◽  
Author(s):  
Daniel C. Elton ◽  
Michelle Fritz ◽  
Marivi Fernández-Serra
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Path Integral ◽  
Liquid Water ◽  
Density Functional ◽  
Energy Surface ◽  
Dynamics Simulation ◽  
Functional Theory

We present a new approximate method for doing path integral molecular dynamics simulation with density functional theory and show the utility of the method for liquid water.

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

2016 ◽  
Vol 195 ◽  
pp. 237-251 ◽  
Author(s):  
Rafał Szabla ◽  
Robert W. Góra ◽  
Mikołaj Janicki ◽  
Jiří Šponer
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Energy Surface ◽  
Water Molecules ◽  
Dynamics Simulations

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

2021 ◽  
Vol 23 (9) ◽  
pp. 5236-5243
Author(s):  
Ying Hu ◽  
Chao Xu ◽  
Linfeng Ye ◽  
Feng Long Gu ◽  
Chaoyuan Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Dynamics Simulation ◽  
Surface Hopping ◽  
Nonadiabatic Molecular Dynamics ◽  
Energy Surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation.

Dynamics and kinetics of the Si(1D) + H2/D2 reactions on a new global ab initio potential energy surface

2021 ◽  
Vol 23 (10) ◽  
pp. 6141-6153
Author(s):  
Jianwei Cao ◽  
Yanan Wu ◽  
Haitao Ma ◽  
Zhitao Shen ◽  
Wensheng Bian
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Quantum Dynamics ◽  
Energy Surface ◽  
Molecular Dynamics Calculations ◽  
Ring Polymer ◽  
Ring Polymer Molecular Dynamics ◽  
Kinetics Of

Quantum dynamics and ring polymer molecular dynamics calculations reveal interesting dynamical and kinetic behaviors of an endothermic complex-forming reaction.

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