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Molecular dynamic Simulationof Metal-Organic Framework
11
Presentation
Internship student : MTEC
Molecular dynamic Simulation
of Metal-Organic Framework
Mahidol University
Suniti Budhapongsiriporn (Po)
What is MD simulation
Molecular Dynamic Simulation
Classical molecular dynamics is a computer simulation method to study the equilibrium and transport properties of a classical many-body system by solving Newton's equations of motion for each component.
Type of Force field
1. UFF (Universal Force Field)
2. UFF4MOF
3. BTW-FF (Bristow Force Field)
4. DREIDING
5. DWES (IRMOF Force Field by
Dubbeldam, Walton, Ellis and Snurr)
6. OPLS-AA
Energy terms described in the Force field
Bonded interaction
Force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules.
The accuracy of the force field depends partly on the level of theory used for the intramolecular energies.
Force field
Non-bonded interaction
LAMMPS
Classical molecular dynamics (MD) simulation software
openMD
Software
MD simulation programs are often used in the study of materials and can help researchers gain insight about properties on an atomic or molecular level, be used to predict or verify experiments
DL_POLY
etc.
Macroscale
Mesoscale
Quantum Mechanics
Length and time scales
Simulation Scales
Molecular Dynamic
What is Metal-Organic Frameworks?
Metal–organic frameworks (MOFs) are a class of compounds consisting of metal ions or clusters coordinated to organic ligands
MOFs can be used for gas storage, purification and separation, as well catalysis and sensing applications.
MOFs
Activated carbon
Activated Aluminum
Adsorption
Zeolite
Adsorption is the adhesion of atoms, ions or molecules from a gas, liquid or dissolved solid to a surface.
This process creates a film of the adsorbate on the surface of the adsorbent.
Adsorption
Clay
Metal-Organic Frame work
Structure of MOF-5
(IRMOF-1)
Zn4O(BDC)3
MOF-5
Secondary building units (SBUs)
= [Zn O]
+6
4
Organic Ligand
= 1-4,benzodicarboxylate
= [O C−C H −CO ]
-2
2 6 4 2
Simulation Method
Materials Properties
of MOF-5
LAMMPS Molecular Dynamics Simulator
InternshipProject
Universal force field (UFF)
Open Visualization Tool (OVITO) Version 3.1.2
MOF-5 charge equilibration method
Condition of Thermal Expansion simulation
Temperature
80-500 Kelvin
Pressure
1 Bar
200 ps relaxation time
800 ps
simulation
Thermal Expansion
isothermal-isobaric
simulation
Linear thermal expansion coefficient of MOF-5
average 5 simulations
= -15.83 K
-1
Condition of Heat Capacity simulation
Temperature
80-500 Kelvin
Pressure
1 Bar
200 ps relaxation time
800 ps
simulation
Heat Capacity
isothermal-isobaric
simulation
Heat Capacity of MOF-5
average 5 simulations
= 174.38 J/kgK
Condition of Thermal Conductivity simulation
Temperature
300 Kelvin
Pressure
1 Bar
1200 ps relaxation time
1000 ps
simulation
Thermal Conductivity
Green-Kubo
equation
isothermal-isobaric
simulation
Thermal conductivity of MOF-5
average 5 simulations
= 0.177 W/mK
For the thermal conductivity, Green-Kubo expression is shown in following equation.
B
V = System volume
k = Boltzmann constant
T = System temperature
<Jx(0)Jx(t)> = Heat current autocorrelation
function (HCACF)
Summary
Jelle Wieme, et al., Thermal Engineering of Metal−Organic Frameworks for AdsorptionApplications: A Molecular Simulation Perspective. ACS Applied Materials & Interfaces, 2019. 11: p. 38697-38707.