Development and Application of a Nonbonded Cu $^{2+}$ Model That Includes the Jahn–Teller Effect

Metal ions are both ubiquitous to and crucial in biology. In classical simulations, they are typically described as simple van der Waals spheres, making it difficult to provide reliable force field descriptions for them. An alternative is given by nonbonded dummy models, in which the central metal atom is surrounded by dummy particles that each carry a partial charge. While such dummy models already exist for other metal ions, none is available yet for Cu2+ because of the challenge to reproduce the Jahn–Teller distortion. This challenge is addressed in the current study, where, for the first time, a dummy model including a Jahn–Teller effect is developed for Cu2+. We successfully validate its usefulness by studying metal binding in two biological systems: the amyloid-β peptide and the mixed-metal enzyme superoxide dismutase. We believe that our parameters will be of significant value for the computational study of Cu2+-dependent biological systems using classical models