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Polarizable Density Embedding for Large Biomolecular Systems

preprint
revised on 21.07.2020 and posted on 22.07.2020 by Peter Reinholdt, Frederik Kamper Jørgensen, Jacob Kongsted, Jógvan Magnus Haugaard Olsen
We present an efficient and robust fragment-based quantum–classical embedding model capable of accurately capturing effects from complex environments such as proteins and nucleic acids. This is realized by combining the molecular fractionation with conjugate caps (MFCC) procedure with the polarizable density embedding (PDE) model at the level of Fock matrix construction. The Fock matrix of the core region is constructed using the local molecular basis of the individual fragments rather than the supermolecular basis of the entire system. Thereby, we avoid complications associated with the application of the fragmentation procedure on environment quantities used in the PDE model, such as electronic densities and molecular-orbital energies. Moreover, the computational cost associated with solving self-consistent field (SCF) equations of the core region remains unchanged from that of purely classical polarized embedding models. We analyze the performance of the resulting model in terms of the reproduction of the electrostatic potential of an insulin monomer protein and further in the context of solving problems related to electron spill-out. Finally, we showcase the model for the calculation of one- and two-photon properties of the Nile Red molecule in protein environments. Based on our analyses, we find that the combination of the MFCC approach with the PDE model is an efficient, yet accurate approach for calculating molecular properties of molecules embedded in structured biomolecular environments.

Funding

Hylleraas Center

The Research Council of Norway

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Rational design of optical probes for sensing in cellular membranes

Danish Agency for Science and Higher Education

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Training network for COmputational Spectroscopy In Natural sciences and Engineering

European Commission

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History

Email Address of Submitting Author

jmho@chem.au.dk

Institution

Aarhus University

Country

Denmark

ORCID For Submitting Author

0000-0001-7487-944X

Declaration of Conflict of Interest

No conflict of interest

Licence

Exports