Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups |
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Authors: | Ihrig Arvid Conrad Schiffmann Christoph Sebastiani Daniel |
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Affiliation: | Dahlem Center for Complex Quantum Systems, Physics Department, Freie Universita?t Berlin, Arnimallee 14, 14195 Berlin, Germany. |
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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. |
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