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Challenges in Parameterization and Sampling for PPy: Data Analysis and Conformational Space Exploration

Explore challenges in parameterizing and sampling for PPy using data analysis and conformer energy calculation. Learn about adjusting torsion angles, improving sampling methods, and potentially adjusting charge parameters.

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Challenges in Parameterization and Sampling for PPy: Data Analysis and Conformational Space Exploration

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  1. Challenges in Parameterization and Sampling for PPy John Fonner Schmidt Lab Data Blitz 9.16.09

  2. Process Overview

  3. Parameterization H-N-H Conformer N-N-N Conformer Δenergy = 24.7kcal/mol N1 = -0.43298 N2 = -0.34026 N3 = -0.4101 Δenergy = 0.0 kcal/mol N1 = -0.26617 N2 = -0.19174 N3 = -0.28236 • Changes in charge distribution due to: • Polarization effects • “Many body problem” of partial charge assignment

  4. Torsion Energy Parameter Undoped PPy Doped PPy Energy (kcal/mol) Torsion Angle (degrees)

  5. Doped Torsion Energy Parameter

  6. 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: ~1.4g/ml • Water contact angle: 83.7° ± 6.6°

  7. Thermal Annealing Method

  8. Potential Scaling Method

  9. Biased Sampling

  10. Conclusions • Torsion parameter should be adjusted • Sampling methods can be improved • Charge parameters may need adjusting

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