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Development of a Molecular Mechanics Model for Chloride-Doped Polypyrrole

Development of a Molecular Mechanics Model for Chloride-Doped Polypyrrole. John M. Fonner 1 , Christine E. Schmidt 1, 2 , Pengyu Ren 1 1 Department of Biomedical Engineering, University of Texas at Austin, TX 2 Department of Chemical Engineering, University of Texas at Austin, TX.

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Development of a Molecular Mechanics Model for Chloride-Doped Polypyrrole

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  1. Development of a Molecular Mechanics Model for Chloride-Doped Polypyrrole John M. Fonner1, Christine E. Schmidt1, 2, Pengyu Ren1 1Department of Biomedical Engineering, University of Texas at Austin, TX 2Department of Chemical Engineering, University of Texas at Austin, TX

  2. Polypyrrole (PPy) Background • Organic Conducting Polymer • Anion doping greatly increases conductivity • Easily synthesized chemically and electrochemically • “Biocompatible” • Difficult to Characterize • Amorphous • Insoluble • Very sensitive to synthesis conditions • Incomplete Understanding of Nano-scale Properties

  3. PPy as a Neural Implant • Chemical, Topographical, and Electrical Properties • Neural probes (Cui, 2001) • Nerve guidance channels (Schmidt, 1997) • Non-bonded surface modification using the T59 peptide • Modify surface chemistry while maintaining bulk conductivity • Selective binding • From biocompatibleto bioactive Sanghvi, 2005

  4. Specific Aims

  5. Molecular Mechanics Parameters • Optimized Potential for Liquid Simulations (OPLS) force field (Jorgensen, 1988) • All Atom (AA) model (Hydrogens are treated separately) • Bond stretch: • Angle bend: • Torsion angle: • Partial charges:

  6. 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

  7. 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

  8. 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

  9. 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

  10. TorsionEnergyTerm–UndopedPPy • Rotate • Minimize • Measure Energy (MP2/6-31++G**) *CIS configuration defined as zero degrees

  11. TorsionEnergyTerm–UndopedPPy

  12. TorsionEnergyTerm–UndopedPPy

  13. TorsionEnergyTerm–UndopedPPy MM QM

  14. Torsional Energy of Doped PPy

  15. Matrix Formation – UndopedPPy • Simulated Annealing • Bond Length Constrained • Movie shows the firstnanosecond • Particle Mesh Ewald • Starting Temp.: 300K • Ending Temp.: 1200K • Polymer strands clump within ~150ps

  16. Summary and Conclusion • UndopedPPy has a flexible backbone with energy minima at ~±30 degrees • Doped PPy has a high torsional energy barrier that will trap the polymer at zero or 180 degree torsion angles • High intramolecular attraction of undopedPPy causes rapid aggregation in gas-phase MD simulations • Future Work: • Refine MM “building blocks” for doped PPy • Explore potential smoothing or Monte Carlo methods for PPy film creation

  17. Acknowledgements • Dr. PengyuRen • Computational Biomolecular Engineering Lab • Dr. Christine Schmidt • Molecular Tissue Engineering Lab • Funding Resources • National Institutes of Health (R01 EB004529) • American Chemical Society (PRF 45792-G6 )

  18. Backup Slides

  19. Why Computational Modeling? • Useful for studying: • Small things (sub-angstrom – nanometers) • Fast things (sub-femtosecond – nanoseconds) • Why not? • Computational power • Expense (time and $) • Accuracy of techniques

  20. A Note on Energy • ΔG = ΔH - TΔS = Gibbs Free Energy • H = Enthalpy = E + PV • S = Entropy • E = Internal Energy • Includes: • Vibrational energy • Rotational energy • Chemical bonding energy • Nonbonding energy • Boltzmann Distribution

  21. 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

  22. 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

  23. Polypyrrole (PPy) Background …that can promote cell growth through electrical stimulation… • Easily synthesized conducting polymer… Sanghvi, et al. 2005 Schmidt, et al. 1997 …and present chemical cues to cells via T59 affinity binding.

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