Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups

Abstract

We present a series of capping-potentials designed as link atoms to saturate dangling bonds at the quantum/classical interface within density functional theory-based hybrid QM/MM calculations. We aim at imitating the properties of different carbon-carbon bonds by means of monovalent analytic pseudopotentials. These effective potentials are optimized such that the perturbations of the quantum electronic density are minimized. This optimization is based on a stochastic scheme, which helps to avoid local minima trapping. For a series of common biomolecular groups, we find capping- potentials that outperform the more common hydrogen-capping in view of structural and spectroscopicproperties. To demonstrate the transferability to complex systems, we also benchmark our potentials with a hydrogen-bonded dimer, yielding systematic improvements in structural and spectroscopic parameters.