Journal of the American Chemical Society, Vol.121, No.34, 7885-7894, 1999
Critical role of anisotropy for the dimerization energies of two protein-protein recognition motifs: cis-N-methylacetamide versus a beta-sheet conformer of alanine dipeptide. A joint ab initio, density functional theory, and molecular mechanics investigation
The dimerization energies of formamide and cis-N-methylacetamide (cis-NMA) are compared with those of the Ala and Gly dipeptides in their canonical beta-sheet conformations using ab initio (SCF and MP2), density functional theory (DFT), and the SIBFA molecular mechanics procedure. Consistent with the gasphase ab initio and DFT results, the SIBFA procedure is able to account for the larger dimerization energies of formamide and cis-NMA than of the dipeptides. In contrast, the majority of "conventional" force fields produced an inversion of the relative dimerization energies, giving rise to a more favorable dimerization of the Ala dipeptide than of cis-NMA (Beachy, M. D.; et al. J. Am. Chem. Sac. 1997, 119, 5908). Energy decomposition analysis on the dimers of formamide and the Gly dipeptide shows the Coulombic energy contribution to be the most important term favoring the formamide dimer. The analysis based on the SIBFA procedure similarly;shows the multipolar energy term (E-MTP) to be the most important contributor to this difference. This is due to its monopole-dipole and monopole-quadrupole components. The issue of the transferability of the multipolar expansion is discussed in the context of simulations of oligopeptides.