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

abstract

• 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.

authors

• Brothers, Ed

published proceedings

• JOURNAL OF PHYSICAL CHEMISTRY B

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

publisher

• American Chemical Society (ACS)  Publisher

published in

• The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter  Journal

keywords

• 34 Chemical Sciences
• 3407 Theoretical And Computational Chemistry

Digital Object Identifier (DOI)

• 10.1021/jp012637q

start page

• 2779

end page

• 2785

volume

• 106

issue

• 10

URL

• http://dx.doi.org/10.1021/jp012637q