Calculations of the phi-psi conformational contour maps for N-acetyl alanine N'-methyl amide and of the characteristic ratios of poly-L-alanine using various molecular mechanics forcefields.
We generated phi- psi conformational energy contour maps for the N-acetyl alanine N'-methyl amide using the molecular mechanics forcefields AMBER, AMBER3, BIO85, CFF91, CVFF, MM2, MM3, MM+, AND SYBYL. With MM2, MM3, and MM+ we used a dielectric constant of epsilon = 1.5, the default effective value for these forcefields. With the other forcefields we used epsilon = 1 and 4, except with SYBYL, which, in Spartan 3.1, has no electrostatic term. All forcefields yielded the C7eq conformation as a low-energy minimum or the global minimum. Most of the forcefields also yielded a minimum-energy conformation in the C5, alpha R, and alpha L regions of the phi-psi contour map. Fewer of the forcefields yielded a minimum in the C7ax region; however, adiabatic relaxation frequently lowered the relative energy of this region. Based on the appearance of the phi-psi maps, the following pairs of forcefields were broadly similar (but not identical) to each other but dissimilar to the other pairs: AMBER3 and AMBER, BIO85 and CHARMM, MM+ and MM2, SYBYL and ECEPP, and CFF91 and MM3. We used the data from the phi-psi contour maps to compute the characteristic ratio of poly-L-alanine. Most of the computed values deviated significantly from the experimental value. Only the computed characteristic ratio of CFF91 without adiabatic relaxation at epsilon = 4 and MM3 without adiabatic relaxation at epsilon = 1.5 agreed with the experimental value.
Lee
C H
CH
Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
Zimmerman
S S
SS
D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry; D003196:Computer Graphics; D003198:Computer Simulation; D008958:Models, Molecular; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D013314:Stress, Mechanical; D013816:Thermodynamics
D010455:Peptides; C024314:N-acetylalanyl-N-methylamide; C019529:polyalanine; D000409:Alanine