Weili Qian

A spectroscopically effective molecular mechanics model for the intermolecular interactions of the hydrogen-bonded N-methylacetamide dimer

Abstract An MP2/6-31+G ∗ calculation of the N -methylacetamide dimer shows that it has two minimum energy structures, both hydrogen bonded with peptide planes roughly perpendicular to each other. A complete molecular mechanics optimization of the dimer has been done, using a model for the intermolecular interactions consisting of charges, atomic dipoles, and van der Waals interactions and the methodology of our spectroscopically determined force field for the intramolecular interactions. The two structures are satisfactorily reproduced, as are their interaction energies, their dipole moments, and, from the point of view of our goal of a spectroscopically accurate force field, their six intermolecular normal mode frequencies.

Vibrational studies of the disulfied group in proteins part IV. SS and CS stretch frequencies of known peptide and protein disulfide bridges

Abstract We have used our previously derived ab initio disulfide and empirical polypeptide force field to calculate SS and CS stretch frequencies of disulfide bridges in a cyclic octapeptide and six proteins of known structure. Comparisons with Raman spectra show that the observed bands are very well reproduced by the normal mode calculations, thus validating the use of these force fields in studying detailed correlations between such spectra and disulfide bridge geometry.