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Melissa Cederqvist Dr. Justin Houseknecht Dr. Douglas Dudis Chemistry & Computational Science Departments Wittenberg University, Springfield OH Wright Patterson Air Force Base, Dayton OH. Heat Transfer in Polymers Summer Research 2008. Outline. Introduction Methods Results Next step. - PowerPoint PPT Presentation
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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
Outline
Introduction
Methods
Results
Next step
http://www.wittenberg.eduhttp://www.wpafb.af.mil/
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
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
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>
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
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
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
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.
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
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
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
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
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
Geometry optimization: Result Monomer001
File: F:\Calculations\Monomer\Locked\RHF631Gd\Conformational search\Monomer001HFlocked.spartan
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
Geometry optimization: Result Dimer035
File: F:\Calculations\Dimer\Locked\RHF631Gd\dimer035HFlocked.spartan
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*
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
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
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/
LAMMPS
Simulate heating
Unit of EPON-862 DETDA
Enter
Exit
Exit
LAMMPS
Temperature vs. distance Insulator Conductor
r
T
Enter
Unit of EPON-862 DETDA
ExitExit
rr
Insulator
Conductor
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/
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
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
