Molecular Simulations of Pore Diffusion in Zeolites

1998 ◽  
Vol 527 ◽  
Author(s):  
P.I. Pohl ◽  
D.K. Fisler ◽  
T.M. Nenoff
Keyword(s):  
Molecular Dynamics ◽  
Energy Surface ◽  
Diffusion Rate ◽  
Pore Diffusion ◽  
High Permeability ◽  
Ionic Size ◽  
Gas Molecules ◽  
Dynamics Simulations ◽  
High Degree

ABSTRACTA combination of molecular dynamics and energy barrier mapping has been used to study diffusion of xylene gas molecules in silica zeolites. Rigid ion models were created for silicalite phases and the energy barriers to xylene permeation by pore diffusion were mapped using constrained steps and energy minimization. Zeolite ZSM-5 proved to exhibit the desirable properties of a high degree of selectivity while retaining a high permeability to p-xylene. The model zeolite was then minimized with various cation dopants using a shell model to mimic ionic polarization, and changes in cell size and energy surface were examined. Long term molecular dynamics simulations showed an increased diffusion rate for the structures doped with cations of larger ionic size.

scholarly journals Permeabilities of CO2, H2S and CH4 through Choline-Based Ionic Liquids: Atomistic-Scale Simulations

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 2014 ◽  
Author(s):  
Abdukarem Amhamed ◽  
Mert Atilhan ◽  
Golibjon Berdiyorov
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Diffusion Rate ◽  
The Other ◽  
Permeability Coefficients ◽  
Gas Molecules ◽  
Dynamics Simulations ◽  
And Diffusion

Molecular dynamics simulations are used to study the transport of CO 2 , H 2 S and CH 4 molecules across environmentally friendly choline-benzoate and choline-lactate ionic liquids (ILs). The permeability coefficients of the considered molecules are calculated using the free energy and diffusion rate profiles. Both systems show the largest resistance to CH 4 , whereas more than 5 orders of magnitude larger permeability coefficients are obtained for the other two gas molecules. The CO 2 /CH 4 and H 2 S/CH 4 selectivity was estimated to be more than 10 4 and 10 5 , respectively. These results indicate the great potential of the considered ILs for greenhouse gas control.

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>

scholarly journals A [1 + 2] cycloaddition instead of usual [2 + 3] cycloaddition between the B12N12 cluster and methyl azide: Potential energy surface calculations and Born–Oppenheimer molecular dynamics simulations

2020 ◽  
Vol 45 ◽  
pp. 146867831990058
Author(s):  
Parvaneh Pakravan ◽  
Seyyed Amir Siadati
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Energy Surface ◽  
Cycloaddition Reaction ◽  
Reliable Data ◽  
Reaction Channel ◽  
Dynamics Simulations

We have examined here the possibility of functionalization of the B12N12 cluster by methyl azide by means of a [2 + 3] cycloaddition reaction in analogy with the spontaneous functionalization of C20 fullerene using the same reaction. To achieve more reliable data, all possible interactions at different positions and orientations were considered by reaction channel study and potential energy surface calculations. Also, Born–Oppenheimer molecular dynamics simulations were used to find probable species which could emerge during the reactions.

Investigation of the Dynamic Behavior of Railway Ballast Using Molecular Dynamics Simulations

2001 ◽  
Author(s):  
Holger Kruse ◽  
Karl Popp
Keyword(s):  
Molecular Dynamics ◽  
Initial Conditions ◽  
Contact Forces ◽  
Contact Network ◽  
Railway Ballast ◽  
Particle Layer ◽  
Dynamics Simulations ◽  
Long Term Behavior ◽  
Overlap Area

Abstract The molecular dynamics method (MD method) is a powerful tool for the investigation of granular materials like the railway ballast. The characteristics of this method are explained in detail. In contrast to a continuum description, each single stone of the ballast is taken into account. Since the ballast settlement is strongly influenced by the shape of the stones, in the two-dimensional model polygonal particles are used. These particles are surrounded by fixed boundary walls. At the top of the ballast particle layer, a single sleeper is positioned which is loaded by forces occurring at the real track. The contact forces are calculated from the overlap area of the particle geometries. The paper includes information about the sensitivity of the model behavior on initial conditions and contact law parameters. Furthermore, the contact network, the quasi-static stiffness of the ballast layer and its long-term behavior are addressed. Particular emphasis is put on the description of current difficulties and challenges in applying the MD method.

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.

Study on the Effect of Different Factors of Displacement Cascades in Alpha-Fe by Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Pandong Lin ◽  
Junfeng Nie ◽  
Meidan Liu
Keyword(s):  
Molecular Dynamics ◽  
Tensile Strain ◽  
Vacancy Concentration ◽  
Irradiation Damage ◽  
Effect Of Temperature ◽  
Displacement Cascade ◽  
Rpv Steel ◽  
Dynamics Simulations ◽  
Dynamics Method

Abstract As the key component of RPV steel, α-Fe is under neutron irradiation during its long-term service, and lattice atoms of α-Fe are knocked by neutrons, which leads to irradiation damage. In this paper, molecular dynamics method is conducted to investigate the effect of temperature, vacancy concentration and tensile strain on irradiation-induced damage by displacement cascade simulations in α-Fe. The simulations are performed with primary knock-on atom energies ranging from 0.1 to 5 keV, temperature ranging from 100 to 500K, vacancy concentration ranging from 0% to 1% and applied tensile strain ranging from 0 to 5%. The time evolution of defects produced during displacement cascade can be obtained where the surviving number of Frenkel pairs increases rapidly at first, then decrease and comes to stability finally. The influence of these factors on defect production can be concluded as following: The increase of PKA energy, vacancy concentration and applied tensile strain can lead to the increase of defect numbers. In contrast, the increase of temperature decreases the defect numbers. Vacancies and interstitials cluster size distributions are varied in different case. The results are meaningful to describe some microcosmic mechanisms of RPV steels in nuclear system.

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>

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