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Molecular Mechanics of Polypyrrole

Molecular Mechanics of Polypyrrole. Research Update 3 .2.2009. Why Computational Modeling?. Useful for studying: Small things (sub-angstrom – nanometers) Fast things (sub- femtosecond – nanoseconds) Constantly improving Computational power Expense (time and $)

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Molecular Mechanics of Polypyrrole

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  1. Molecular Mechanics of Polypyrrole Research Update 3.2.2009

  2. Why Computational Modeling? • Useful for studying: • Small things (sub-angstrom – nanometers) • Fast things (sub-femtosecond – nanoseconds) • Constantly improving • Computational power • Expense (time and $) • Accuracy/efficiency of algorithms

  3. Moore’s Law

  4. Types of Molecular Models • Ab initio technique • Electrons are smallest modeled unit • Based on Schrödinger’s equations • System scaling is ~N4 • Single molecule (<100 atoms) structural minimization • Can be used for chemical reactions and electrical conduction • Requires parameterized force field • Atoms are smallest modeled unit • Based on Newtonian dynamics • Scaling is between Nlog(N) and N2 • Molecular Dynamics simulations up to ~100 nanoseconds for ~105 atoms • Can not model chemical reactions or electron conduction • Empirically parameterized force field • “United-atom” model with common chemical groups as smallest units • Based on Newtonian dynamics • Molecular Dynamics simulations for microseconds timescales or “very large” systems Quantum Mechanics Accuracy MolecularMechanics Coarse GrainModels System Size

  5. Molecular Mechanics (MM) Parameters Potential energy given as a sum of contributions: • Bond stretch: • Angle bend: • Dihedral angle: • Van der Waals: • Electrostatic:

  6. Molecular Mechanics Parameters Potential energy given as a sum of contributions: • Bond stretch:

  7. Molecular Mechanics Parameters Potential energy given as a sum of contributions: • Angle Bend:

  8. Molecular Mechanics Parameters Potential energy given as a sum of contributions: • Dihedral angle:

  9. Molecular Mechanics Parameters Potential energy given as a sum of contributions: • Electrostatic: + - +

  10. Molecular Mechanics Parameters Potential energy given as a sum of contributions: • Van der Waals: + - + -

  11. Molecular Mechanics (MM) Parameters Potential energy given as a sum of contributions: • Bond stretch: • Angle bend: • Dihedral angle: • Van der Waals: • Electrostatic:   

  12. Specific Aims

  13. Minimized Structure of PPy Crude starting structure Minimized structure using QM Partial charges for electrostatic parameter Bond lengths, angles

  14. Dihedral Angle Parameter • Constrain central dihedral angle • Minimize structure • Measure Energy (MP2/6-31++G**) *CIS configuration defined as zero degrees

  15. Dihedral Angle Parameter

  16. Dihedral Angle Parameter

  17. Dihedral Angle Parameter MM QM RMS: ~0.16 Å

  18. How do we build a PPy film in silico? • Chemical reactions not possible in MM • Electricity not possible in MM • Must “adequately” sample conformational space • Must match known bulk properties • Density: ~1.42g/ml • Water contact angle: 85° • Radial distribution function

  19. How do we build a PPy film in silico? • Start in gas phase • Use thermal annealing • Apply pressure to condense PPy Temperature Time Pressure Time

  20. Thermal Annealing to 1200K

  21. Sampling Conformational Space

  22. Potential Annealing vs. Thermal Annealing • In a canonical ensemble, Kinetic energy Ekinis related to T by the following equation: • Thus, thermal annealing essentially scales down potential energy Epot relative to Ekin

  23. VMD Videos • Electrostatics turned off • All interactions turned off

  24. Future Work • Build 5 or more undoped PPy films • Test density, water contact angle • Create in silico films of doped PPyClpolarons • Test density, water contact angle

  25. Thank You Questions? Comments? Suggestions? He’s almost here!

  26. Backup Slides

  27. Molecular Mechanics Parameters Potential energy given as a sum of contributions: • Bond stretch: • Angle bend: • Torsion angle: • Van der Waals: • Electrostatic:

  28. Quantum Mechanics - Charge • HF/6-31G* and CHELPG • Undoped and Chloride-doped PPy • Analyzed oligomers 3, 5, and 7 units in length • Charge spreading occurs, but over 80% of the charge is within the three central units • Experimental Doping ratios ~25-30% 0.2210 0.2217 0.5588 0.2170 0.2133 Net charge on each pyrrole unit 0.0685 0.4110 0.0726

  29. Minimized Structure - Undoped PPy 0.141 0.141 -0.215 -0.215 125.9 107.4 0.994 0.107 107.5 0.107 1.457 110.1 1.366 121.3 124.4 -0.386 1.364 1.422 0.320 1.072 Total charge:0.000

  30. Minimized Structure - Doped PPy 0.141 0.141 0.370 -0.201 -0.201 125.8 107.5 1.028 -0.479 0.400 107.4 0.400 1.413 110.3 1.353 124.1 0.107 0.300 -0.500 124.9 1.420 -0.100 -0.285 1.366 0.350 1.070 0.181 0.141 Total charge:0.530 Total charge:0.235

  31. Change in Partial Charges • PPy doped – PPyundoped 0.030 -0.114 0.293 0.293 0.014 0.014 0.000 0.000 Sum = 0.530

  32. Established Force Fields • Optimized Potential for Liquid Simulations (OPLS) force field (Jorgensen, 1988)

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