Stationary Points on the PES of N-Methoxy Peptides and Their Boron Isosteres:  An Ab Initio Study

The conformational space of N-methoxy-N-methylacetamide [CH3-CO-N(OCH3)CH3, NMA-NOM] and its boron isostere [CH3-CO-B(OCH3)CH3, BMA-BOM] has been studied at the HF, B3LYP, and MP2 levels of theory with the 6-31+G* basis set. The minima, saddle points, and rotation barriers on the PES of these molecules have been located, and the energy barriers estimated. The omega rotation barrier is relatively lower in the boron isostere than in NMA-NOM. The difference in the rotation barrier has been attributed to second-order orbital interactions, like negative hyperconjugation, as revealed by NBO calculations. As an extension, N-acetyl-N'-methoxy-N'-methylamide of alanine (Ala-NOM) and its boron isostere (B-Ala-BOM) have been adopted as model peptides to study the conformational preferences about the φ and ψ torsion angles. The study reveals a strong preference for conformations of type-V beta turn and left-handed α-helix for Ala-NOM. B-Ala-BOM, on the other hand, favors conformations of type-Va beta turn, mirror image of Poly-L-Pro II helix, and structures with positive φ and extended ψ. The replacement of nitrogen by boron changes the electronic and conformational properties of the peptide, extends greater flexibility around the omega angle, induces a strong preference for positive phi values, and shifts the site of nucleophilic attack from the carbonyl group to boron.