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Heat Transfer in PolymersSummer Research 2008
Melissa CederqvistDr. Justin HouseknechtDr. Douglas DudisChemistry & Computational Science DepartmentsWittenberg University, Springfield OHWright Patterson Air Force Base, Dayton OH
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Outline
Introduction
Methods
Results
Next step
http://www.wittenberg.eduhttp://www.wpafb.af.mil/
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Heat Transfer in Polymers Heat dissipation
Materials and Manufacturing directorate Wright Patterson Air Force Base
Classical Molecular Dynamics simulations Changes in molecular motion ▪ EPON 862 & DETDA
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Crosslinked polymer EPON-862 & DETDA
O
OH
NH
O
OH
NH
EPON-862 DETDA
“Heat Transfer in Polymers” hand out from Dr. Justin Houseknecht, Wittenberg University
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Molecular Dynamics
A computer approach to statistical mechanics
Calculation of structure and properties for large systems
Motion
Nave, R. Georgia State University. June 9, 2008. <http://hyperphysics.phy-astr.gsu.edu/Hbase/thermo/heatra.html#c1>
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Purpose
Are classical molecular dynamics simulations useful for study of heat flow?
Heat Molecular motion Low frequency vibrations
Classical molecular dynamics uses molecular mechanics Parameterized for high frequency vibrations
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Name Use Energy Term
Harmonic Bond stretch
Harmonic Angle bend
Cosine Torsion
Leonard-Jones 6-12 van der Waals
Coulomb Electrostatic
Taylor Stretch-bend
Molecular Mechanics
Mathematical method to model the shape of molecules
Parameterized
Young, D. Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems. New York: John Wiley & Sons, Inc. 2001. p. 49-52p; p.60-62
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Ab initio
Based on interactions between nuclei and electrons No electron correlation
Not parameterized
Long time, no molecular dynamics
Analyze ability of molecular mechanics to calculate low frequency vibrations
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Adressing the problem
Calculate low frequency vibrations for a small portion of polymer Molecular mechanics (parameterized)▪ MMFF▪ DREIDING▪ UFF
Semi-empirical (parameterized)▪ AM1
Ab initio (not parameterized)▪ HF/6-31G*▪ HF/6-31+G*
Repeat molecular dynamics calculations with similar models
O
OH
NH
O
OH
NH
Cramer, Christopher J. Essentials of Computational Chemistry – Theories and Models. 2nd ed. West Sussex, England: John Wiley & Sons, Inc. 2006. p. 165-167.
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Geometry optimization Build unit of EPON-862 DETDA
Monomer at 20.2 Å Dimer at 39.0 Å
Optimize MMFF
Select five lowest energy conformations AM1 HF/6-31G* HF/6-31+G*
File: F:\Calculations\Monomer\Locked\MMFF\Conformational search\MCederqvistEPON-862 DETDA 1OPT9bconfirmsearch2-20.2.M001.spartan
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Geometry optimization
Similarity analysis Measure dihedral angle for atoms 1,2,3,4;
2,3,4,5 etc. in structureNH
O
OH
O NH
OH
1 2 34
5678910111213
14 15 16
1718
1920
From file: F:\Calculations\Monomer\Locked\RHF631+Gd\Monomer001HFlocked2.spartan
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Similarity analysis: Monomer
From file: F:\Analysis\Monomer\Monomersimilarity.xlsx
Structure Level of theory 12,13,14,15 13,14,15,16 14,15,16,17 15,16,17,18 16,17,18,19 17,18,19,20 STDMolecule001 MMFF 176.65 176.03 176.65 -166.78 -86.64 171.27 Molecule001 AM1 178.63 177.66 -172.94 -168.03 -82.35 -179.20Molecule001 HF/6-31G* -178.62 -179.52 -176.72 -177.22 -81.71 177.63 Molecule001 HF/6-31+G* -179.08 179.90 -176.54 -178.60 -81.68 177.63 ∆bond angle 4.73 4.45 6.63 11.82 4.96 3.17 4.94Molecule013 MMFF 173.74 176.05 178.66 -166.01 -84.33 172.47Molecule013 AM1 176.95 176.39 -174.05 -162.76 -85.01 -178.69 Molecule013 HF/6-31G* 177.01 -178.97 -177.73 -175.55 -82.75 178.06 ∆bond angle 3.27 4.98 7.29 12.79 2.26 8.84 7.56Molecule024 MMFF 173.03 176.32 179.62 -167.72 -85.74 172.98Molecule024 AM1 177.22 176.46 -174.03 -161.06 -85.45 -178.46 Molecule024 HF/6-31G* 177.14 -178.99 -177.74 -175.50 -82.67 178.21 ∆bond angle 4.19 4.69 6.35 14.44 3.07 8.56 7.79Molecule035 MMFF 173.20 176.81 177.97 -166.76 -83.56 170.95Molecule035 AM1 178.70 176.15 -173.44 -170.15 -82.95 -178.63 Molecule035 HF/6-31G* 177.93 -178.25 -176.59 -175.70 -81.22 177.52 ∆bond angle 5.50 5.60 8.59 8.94 2.34 10.42 8.51Molecule046 MMFF 174.07 175.78 178.15 -165.01 -84.37 172.67Molecule046 AM1 175.38 175.95 -173.82 -167.69 -76.06 178.96 Molecule046 HF/6-31G* 176.59 -179.27 -178.49 -175.26 -74.51 177.39 ∆bond angle 2.52 4.95 8.03 10.25 9.86 6.29 7.07
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Similarity analysis: Dimer
From file: F:\Analysis\Dimer\Dimersimilarity.xlsx
Structure Level of theory 12b,13b,14b,15b 13b,14b,15b,16b 14b,15b,16b,17b 15b,16b,17b,18b 16b,17b,18b,19b STDMolecule001 MMFF -170.86 -59.07 -175.12 -166.70 -83.92Molecule001 AM1 -176.35 -64.60 -175.98 -148.45 -78.90Molecule001 HF/6-31G* -175.82 -65.34 -175.05 -173.54 -81.92∆bond angle 5.49 6.27 0.93 25.09 5.02 10.04Molecule013 MMFF -172.66 -59.57 -176.06 -166.51 -85.39Molecule013 AM1 -175.41 -64.56 -175.85 -149.12 -79.52Molecule013 HF/6-31G* -175.81 -65.34 -175.07 -173.53 -81.84∆bond angle 3.15 5.77 0.99 24.41 5.87 10.27Molecule024 MMFF -170.73 -60.67 -178.27 -164.34 -81.01Molecule024 AM1 -177.58 -63.35 -171.68 -167.54 -72.90Molecule024 HF/6-31G* -175.49 -65.54 -175.98 -173.52 -74.08∆bond angle 6.85 4.87 6.59 9.18 8.11 9.74Molecule035 MMFF -165.94 -62.95 -175.18 -168.78 -87.55Molecule035 AM1 -171.59 -64.87 -175.67 -153.62 -82.46Molecule035 HF/6-31G* -172.38 -67.19 -175.31 -176.08 -82.60Molecule035 HF/6-31+G* - - - - -∆bond angle 6.44 4.24 0.49 22.46 5.09 9.38Molecule046 MMFF -171.85 -58.89 -175.58 -166.12 91.27Molecule046 AM1 -176.60 -65.12 -176.84 -143.72 106.85Molecule046 HF/6-31G* -177.71 -65.79 -174.13 -172.80 92.89∆bond angle 5.86 6.90 2.71 29.08 15.58 10.09
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Energy: Monomer
Conformations of EPON862 DETDA 1Opt9bconfirmsearch2 MMFF E(kJ/mol) MMFF Erel AM1 E(kJ/mol) AM1 Erel HF/6-31G* E (kJ/mol) G03 HF/6-31G* Erel
Molecule001 593.6 0.0 -570.9 0.0 -4259555.3 0.0
Molecule013 594.0 0.4 -570.7 0.2 -4259555.9 -0.7
Molecule024 595.1 1.5 -570.4 0.5 -4259557.2 -1.9
Molecule035 595.3 1.7 -570.3 0.6 -4259555.5 -0.3
Molecule046 598.3 4.7 -570.0 0.8 -4259551.8 3.4
File:F:\Analysis\Monomer \Energy.xlsx
Conformation chosenLowest energy
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Geometry optimization: Result Monomer001
File: F:\Calculations\Monomer\Locked\RHF631Gd\Conformational search\Monomer001HFlocked.spartan
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Energy: Dimer
File: F:\Analysis\Dimer\Energy.xlsx
Conformations of EPON 862 DETDA 2Opt2-39confirmsearch MMFF E(kJ/mol) MMFF Erel AM1 E (kJ/mol) AM1 Erel HF/6-31G* E (kJ/mol) G03 HF/6-31G* Erel
Molecule001 1233.1 0.0 -1097.8 0.0 -8371594.2 0.0
Molecule013 1234.8 1.7 -1097.5 0.3 -8371595.4 -1.2
Molecule024 1236.9 3.8 -1097.1 0.6 -8371590.4 3.8
Molecule035 1237.0 3.9 -1097.9 -0.1 -8371594.9 -0.7
Molecule046 1237.5 4.4 -1096.2 1.5 -8371588.0 6.2
Conformation chosenLowest energy
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Geometry optimization: Result Dimer035
File: F:\Calculations\Dimer\Locked\RHF631Gd\dimer035HFlocked.spartan
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Frequency analysis
Level of theory
Geometry 1
Geometry 2
MMFF MMFF HF/6-31+G*
SYBYL SYBYL HF/6-31+G*
AM1 AM1 HF/6-31+G*
HF/6-31G* HF/6-31G* HF/6-31+G*
HF/6-31+G* HF/6-31+G*
HF/6-31+G*
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Frequency analysis at HF/6-31+G*:A
%Std Level of theory//RHF/6-31G+*%MMFF//RHF/6-31+G* %SYBYL//RHF/6-31+G* %AM1//RHF/6-31+G* %RHF/6-31G*//RHF/6-31+G* %DREIDING//RHF/6-31+G* %UFF//RHF/6-31+G*
10 76 26 33 19 224 47 54 33 29 48
115 48 42 29 13 25108 57 43 1 28 3274 41 30 7 17 2754 25 25 9 5 2161 36 38 0 8 3367 33 32 1 20 4070 35 51 9 25 3858 21 30 5 9 2354 18 25 7 10 17
0 500 1000 1500 2000 2500 3000 3500 4000 45000
20406080
100120140
%MMFF//RHF/6-31+G*%SYBYL//RHF/6-31+G* %AM1//RHF/6-31+G* %RHF/6-31G*//RHF/6-31+G*%DREIDING//RHF/6-31+G*%UFF//RHF/6-31+G*
Monomer001 from RHF/6-31+G* geometry: Absolute Percent Error
Frequency (cm-1)
Perc
ent E
r-ro
r
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Frequency analysis at HF/6-31+G*:A
0 50 100 150 200 2500
20
40
60
80
100
120
140
%MMFF//RHF/6-31+G*%SYBYL//RHF/6-31+G* %AM1//RHF/6-31+G* %RHF/6-31G*//RHF/6-31+G*%DREIDING//RHF/6-31+G*%UFF//RHF/6-31+G*
Monomer001 from RHF/6-31+G* geometry: Absolute Percent Error
Frequency (cm-1)
Perc
ent E
rror
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LAMMPS Large-scale Atomic/Molecular Massively Parallel
Simulator
Sandia National Laboratories US Department of Energy laboratory
Classical Molecular Dynamics simulation
Model atomic, polymeric, biomolecular systems
Systems of a few to billions of particlesLAMMPS. Sandia Laboratories. May 21, 2008. June 23, 2008. http://lammps.sandia.gov/
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LAMMPS
Simulate heating
Unit of EPON-862 DETDA
Enter
Exit
Exit
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LAMMPS
Temperature vs. distance Insulator Conductor
r
T
Enter
Unit of EPON-862 DETDA
ExitExit
rr
Insulator
Conductor
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ReferencesCramer, Christopher J. Essentials of Computational Chemistry – Theories and Models. 2nd ed. West
Sussex, England: John Wiley & Sons, Inc. 2006. p. 165-167.
Houseknecht, Justin. PhD. “Heat Transfer in Polymers”. Wittenberg University. May 2008.
LAMMPS. Sandia Laboratories. May 21, 2008. June 23, 2008. http://lammps.sandia.gov/
Nave, R. Georgia State University. June 9, 2008. http://hyperphysics.phy-astr.gsu.edu/Hbase/thermo/heatra.html#c1
The College of St. Scholastica. June 16, 2008. http://faculty.css.edu/lmcgahey/web/CHM220/conform/diClEt.html
Young, D. Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems. New York: John Wiley & Sons, Inc. 2001. p. 19-21; 49-52p; 60-62; 78-82
Wittenberg University. June 23, 2008. http://www.wittenberg.edu/
Wright Patterson Air Force Base. June 23, 2008. http://www.wpafb.af.mil/
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Frequency analysis at HF/6-31+G*:NA
0 500 1000 1500 2000 2500 3000 3500 4000 4500
-75
-25
25
75
125
175
%MMFF//RHF/6-31+G*%SYBYL//RHF/6-31+G* %AM1//RHF/6-31+G* %RHF/6-31G*//RHF/6-31+G*%DREIDING//RHF/6-31+G*%UFF//RHF/6-31+G*
Monomer001 from RHF/6-31+G* geometry: Non Absolute Percent Error
Frequency (cm-1)
Perc
ent E
rror
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Frequency analysis at HF/6-31+G*:NA
0 50 100 150 200 250
-75
-25
25
75
125
175
%MMFF//RHF/6-31+G*%SYBYL//RHF/6-31+G* %AM1//RHF/6-31+G* %RHF/6-31G*//RHF/6-31+G*%DREIDING//RHF/6-31+G*%UFF//RHF/6-31+G*
Monomer001 from RHF/6-31+G* geometry: Non Absolute Percent Error
Frequency (cm-1)
Perc
ent E
rror