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Manuscript Preparation: MD Model of Chloride Doped PPy

Manuscript Preparation: MD Model of Chloride Doped PPy. John Fonner 2010.2.19. Model Parameters. Potential energy given as a sum of contributions: Bond stretch: Angle bend: Dihedral angle: Van der Waals: Electrostatic:. . . . Model Parameters. Bond Angles. Bond Lengths.

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Manuscript Preparation: MD Model of Chloride Doped PPy

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  1. Manuscript Preparation:MD Model of Chloride Doped PPy John Fonner 2010.2.19

  2. Model Parameters Potential energy given as a sum of contributions: • Bond stretch: • Angle bend: • Dihedral angle: • Van der Waals: • Electrostatic:   

  3. Model Parameters Bond Angles Bond Lengths Partial Charges Bond Angles Bond Lengths Partial Charges Undoped PPy Chloride Doped PPy 0.141 0.154 -0.215 125.9 -0.195 125.8 107.4 0.994 1.028 107.5 N 107.5 0.107 N 1.457 107.4 0.269 1.366 110.1 1.413 110.3 1.353 121.3 N 124.1 N -0.386 124.4 1.364 -0.486 N N 124.9 1.420 1.422 0.320 1.072 1.366 0.363 1.070 Total charge:0.000 Total charge:0.333

  4. Model Parameters H NA CW CS HA

  5. Torsion Energy Profile Undoped PPy Chloride Doped PPy

  6. Minimum Energy Structure Comparison Undoped PPy RMSD = 0.145Å Doped PPyCl RMSD = 0.043Å QM = gray MM = color

  7. Density Values • Two Problems: • Experimentally “reported” density values are usually ~1.45 g/cm3 • Cascales, et al. report in silico density values between 1.33 and 1.47 using a primitive MD model

  8. Thermal Annealing Method

  9. Potential Scaling Method

  10. Doped PPy Matrix Formation • “Gas phase” simulations do not properly sample PPy-dopant interactions • Start with final undoped PPy structures • Randomly add Cl- and slowly turn on interactions • Mutate PPy from undoped to doped electrostatics Mutate PPy→PPyCl Add Cl-

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

  12. Electrostatic Scaling of

  13. Radial Distribution Function

  14. Radial Distribution Function

  15. Powder X-Ray Diffraction

  16. West, et al. 1990

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