SCF-MO study of the polyhydration of N,N'-dimethylmalonamide

Extended form of a retro-inverso peptide stabilized by beta-sheet unidirectional H-bonds: Crystallographic and NMR evidence

The crystallographic investigation of the retro-inverso peptide Bz-S-gAla-R-mAla-NHPh reveals an extended backbone conformation where the NH groups of the gem-diamino alkyl moiety and the CO groups of the malonyl residue face side by side. This extended conformation, presenting all carbonyls on opposite sides of the NH groups, is stabilized by interstrand H-bonds running in a single direction of the parallel beta-sheets that characterize the crystal packing. These sheets differ from the beta-sheets formed by native amino acids only. (1)H-NMR nuclear Overhauser effect spectroscopy (NOESY) experiments suggest that a conformation similar to that found in the crystal also prevails in dimethylsulfoxide solution. Previous potential energy calculations of gem-diamino alkyl (g) and malonyl (m) Ala residues predicted that extended forms were less stable than the helical ones because of strong electrostatic repulsions between the parallel polar groups. Similar arguments were invoked to give more weight to helical forms of the retro-peptide units in the proposal of packing models of some nylons in their crystalline polar regions. The present findings show that both g and m Ala residues can experience the extended conformation in the beta-sheet aggregation. The energy increase occurring in one strand, due to the parallel orientation of consecutive peptide dipoles, is more than compensated by favorable cooperative interactions among head-to-tail aligned peptide dipoles of facing strands, resulting in the formation of two C==O...H==N H-bonds per residue.

Incorporation of diacids into the polyglycine II structure: model studies

Aliphatic diacids are often incorporated into polypeptide structures in order to obtain model compounds for hormones, protein turns, etc. They are also fundamental components of many commercial polyamides. On the other hand glycine, the simplest amino acid, shows unique conformational features. In order to better understand the structure of such compounds, we have synthetized and determined the molecular structure of three models represented by the general formula CH3-CH2-CH2-NH-CO-CH2-NH-CO-(CH2)n-2-CO-NH-CH2-CO-NH-CH2-CH2-CH3, with n = 3, 4, or 6. Conformational differences have been found in the dicarboxylic moiety, whereas glycine always has the polyglycine II conformation. The -CO-(CH2)n-2-CO-segment adopts a folded conformation: SS, TGT, and SGTGS for n = 3, 4, and 6, respectively. Molecular packing is always pseudohexagonal and a network of hydrogen bonds oriented in three directions at 120 degrees is formed. The results are of interest in order to provide information about polyamides in which glycine residues are incorporated. Our results confirm the tendency of glycine residues to adopt the polyglycine II conformation in its copolymers with aliphatic compounds.

Conformational study of alanine and alpha-aminoisobutyric psi [NHCO]-retroamide peptide analogues

The minimum-energy conformations of N,N'-dimethyl-2-methylmalondiamide (2mMA) and N,N'-dimethyl-2-dimethylmalondiamide (2dmMA) have been computed using the AM1 method. The results show that molecules tend to form an intramolecular six-membered ring hydrogen-bond system. The same trend is observed in crystals of malonamide derivatives substituted in the central carbon atom. The results are also compared with previous molecular-mechanics calculations. The conformational trends of 2mMA and 2dmMA are very similar to those showed by N,N'-dimethylmalondiamide. Details of the computed conformational energy maps for 2mMA and 2dmMA compounds are given.