Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

Abstract

The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) have been used for the simulation of the For-Gly-NH₂ backbone. I propose two different methods for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID) which assumes scalar isotropic point polarizabilities and the polarization scheme by interacting induced dipoles (ID) which calculates tensor effective anisotropic point polarizabilities (method of Applequist). I present a comparative study of ECEPP2 and MM2 + polarization. I discuss molecular mechanics results including the total energy differences, partitional analyses of the total steric energies and torsion dihedral angles. The γ global and the α, β and Δ local minima are stabilized by intramolecular hydrogen bonds. Although ECEPP2-based calculations rather under or over-estimate the relative energy of some local minima, the ID polarization energy term represents a significant correction to the total relative energy.

Key Words:

• Polarization
• polarizability
• peptide models
• amino acids
• conformations
• stable
• molecular mechanics

ACS Classification Codes:

• Amino acids
• peptides and proteins
• biomolecules and their synthetic analogs
• physical organic chemistry
• general physical chemistry