Sodium parameters for AM1 and PM3 optimized using a modified genetic algorithm Academic Article uri icon


  • Sodium is very important as a counterion in biology. However, when used with the most common semiempirical Hamiltonians, such as AM1 or PM3, sodium is modeled as a point charge that can accept no electron density, called a "sparkle". To better model sodium, we derived two sets of sodium parameters, which treat sodium on the same footing as other atoms parametrized in semiempirical methods. One set is compatible with the AM1 parameter set, while the second is compatible with PM3. These parameters were derived using a modified genetic algorithm with a diverse set of 71 compounds. The average unsigned error for the heats of formation was 10.3 kcal/mol for AM1 and 10.5 kcal/mol for PM3.

published proceedings


author list (cited authors)

  • Brothers, E. N., & Merz, K. M.

citation count

  • 30

complete list of authors

  • Brothers, EN||Merz, KM

publication date

  • March 2002