MA'AT Analysis of Peptides: Conformational Equilibrium of Alanine Dipeptide in Aqueous Solution

The conformational properties of alanine dipeptide (1) have been widely investigated by molecular dynamics (MD) and quantum mechanics calculations. Nine idealized conformers have been identified (α_L, α_D, C₇^ax, β₂, C₅, α', C₇^eq, P_II, and α_R), distinguished by their preferred backbone torsion angles φ (C_car-N-C_α-C_car) and ψ (N-C_α-C_car-N). The relative energies of these conformers differ depending on the force fields or the level of theory used in the calculations. MA'AT analysis has been applied to give experiment-based probability distributions of φ and ψ in 1 in an aqueous solution for comparison to those obtained by aqueous MD. Using ¹³C- and ¹⁵N-labeled isotopomers of 1, 11 redundant NMR J-couplings that depend primarily on either φ or ψ were measured from 1D and 2D NMR spectra. Density functional theory calculations were conducted to obtain potential energy surface (PES) plots, and φ- and ψ-dependent J-couplings were calculated as a function of both angles. Parameterized J-coupling equations were used in conjunction with experimental J-values in MA'AT analysis to give a reproducible average unimodal model of φ (298.8° and 43.8°; mean and circular standard deviation) and a tentative bimodal model of ψ (mean values of 192° ± 32° and 318° ± 22° (mean ± STD); both states are approximately equally populated). The experimental J-couplings indicate highly favored trans configurations of both amide bonds in 1. These findings support an experiment-based conformational model of 1 in aqueous solution involving α_R ⇌ P_II exchange, which is qualitatively consistent with PES and MD data.