Conformational Preferences in Small Peptide Models: The Relevance of cis/trans-Conformations.

The accurate description of cis/trans peptide structures is of fundamental relevance for the field of protein modeling and protein structure determination. A comprehensive conformational analysis of dipeptide model Ace-Gly-NMe (1) has been carried out by using a combination of theoretical calculations and experimental ((1) H and (13) C NMR and NOESY) spectroscopic measurements to assess the relevance of cis-peptide conformers. NMR measurements in dimethyl sulfoxide (DMSO) solution and calculations employing a continuum solvation model both point to the extended trans,trans conformer C5_tt as the global minimum. The cis-peptide structures C5_ct and C5_tc, with the N- or C-terminal amide group in cis-conformation, are observed separately and located 13.0±2 kJ mol(-1) higher in energy. This is in close agreement with the theoretical prediction of around 12 kJ mol(-1) in DMSO. The ability of common protein force fields to reproduce the energies of the cis-amide conformers C5_ct and C5_tc in 1 is limited, making these methods unsuitable for the description of cis-peptide structures in protein simulations.

The Proline Enamine Formation Pathway Revisited in Dimethyl Sulfoxide: Rate Constants Determined via NMR.

Enamine catalysis is a fundamental activation mode in organocatalysis and can be successfully combined with other catalytic methods, e.g., photocatalysis. Recently, the elusive enamine intermediates were detected, and their stabilization modes were revealed. However, the formation pathway of this central organocatalytic intermediate is still a matter of dispute, and several mechanisms involving iminium and/or oxazolidinone are proposed. Here, the first experimentally determined rate constants and rates of enamine formation are presented using 1D selective exchange spectroscopy (EXSY) buildup curves and initial rate approximation. The trends of the enamine formation rates from exo-oxazolidinones and endo-oxazolidinones upon variation of the proline and water concentrations as well as the nucelophilic/basic properties of additives are investigated together with isomerization rates of the oxazolidinones. These first kinetic data of enamine formations in combination with theoretical calculations reveal the deprotonation of iminium intermediates as the dominant pathway in dimethyl sulfoxide (DMSO). The dominant enamine formation pathway varies according to the experimental conditions, e.g., the presence and strength of basic additives. The enamine formation is zero-order in proline and oxazolidinones, which excludes the direct deprotonation of oxazolidinones via E2 mechanism. The nucleophilicity of the additives influences only the isomerization rates of the oxazolidinones and not the enamine formation rates, which excludes a nucleophile-assisted anti elimination of oxazolidinones as a major enamine formation pathway.