title: 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 spectroscopic properties. 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.
authors.affiliation: Dahlem Center for Complex Quantum Systems, Physics Department, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
authors.forename: Arvid Conrad
authors.initials: AC
authors.lastname: Ihrig
authors.forename: Christoph
authors.initials: C
authors.lastname: Schiffmann
authors.forename: Daniel
authors.initials: D
authors.lastname: Sebastiani
mesh_terms: D000465:Algorithms; D020148:Butyric Acid / Q000737:chemistry; D002244:Carbon / Q000737:chemistry*; D019281:Dimerization; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D011522:Protons; D011789:Quantum Theory
chemical_list: D011522:Protons; D020148:Butyric Acid; D002244:Carbon