Geometry Optimization, Energetics and Solvation Studies on 4-Membered and 5-Membered Cyclic and Disulfide-Bridged Peptides, using the Programs Quanta-3.3 and Charmm-22
by Momany, Frank A.; Rone, R.; Kunz, H.; Frey, Regina F.; Newton, Susan Quinlyn; Schäfer, Lothar
Force field parameters for peptides and proteins in the CHARMm 22 force field have been refined using the results of MP2/6-311G** calculations on N-formyl alanine amide (Frey et al., J. Am. Chem. Soc., 114 (1992) 5369) and other data (Remek et al., J. Mol. Struct. (Theochem), 235 (1991) 1). Significant changes in the peptide backbone torsional energy terms in CHARMm 22 were made in order to be consistent with the MP2 results relative to previously fitted HF results. To test the new force field parameters against experimental data, molecular mechanics calculations were carried out on small four- and five-membered cyclic and disulfide-bridged peptides. It was found that in general these molecules are in their calculated minimum energy conformation or a low energy conformation in the X-ray structure. The average deviation of the dihedral angles calculated for the seven energy minimized vacuum structures from the X-ray values is 10-degrees. The dihedral angle deviations of the minimized and dynamically averaged conformations are similar for studies which included explicit TIP3P solvent molecules. Upon solvation and minimization, internal vacuum energies increase by 4-7 kcal mol-1. In addition to calculated structural results, we report some of the force field parameters used for the calculations, energy decompositions, and harmonic vibrational free energies.
- Journal of Molecular Structure-Theochem
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- 2210-2728; 0166-1280