Effect of Acetonitrile-Water Composition on the Conformational Landscape of Alanine Dipeptide: A Molecular Dynamics Study

Understanding how solvent composition influences peptide conformations is crucial for insights into protein folding, stability, and solvation effects. In this study, we investigate the conformational preferences of alanine dipeptide in mixed acetonitrile (ACN) and water solutions using molecular dynamics simulations. Solvent boxes with 10% and 40% ACN were constructed using Packmol, and 1 ns simulation were performed with OpenMM. The resulting trajectories were analyzed using MDTraj to extract backbone dihedral angles (φ and ψ) and identify stable conformational basins. Results demonstrate that solvent composition significantly affects the population of conformers, with higher ACN content favoring extended or gauche structures. These findings provide a quantitative understanding of solvation effects on peptide flexibility, offering insights relevant for protein chemistry and solvent-dependent folding studies.