• Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials 

      Marefat Khah, Alireza; Reinholdt, Peter; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob; Hattig, Christof (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-02-07)
      QM/MM calculations of electronic excitations with diffuse basis sets often have large errors due to spill-out of electrons from the quantum subsystem. The Pauli repulsion of the electrons by the environment has to be included to avoid this. We propose transferable atomic all-electron pseudopotentials that can readily be combined with most MM force fields to avoid electron spill-out. QM/MM excitation ...
    • Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments 

      Reinholdt, Peter; Kjellgren, Erik Rosendahl; Steinmann, Casper; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-12-19)
      The fragment-based polarizable embedding (PE) model combined with an appropriate electronic structure method constitutes a highly efficient and accurate multiscale approach for computing spectroscopic properties of a central moiety including effects from its molecular environment through an embedding potential. There is, however, a comparatively high computational overhead associated with the ...
    • CPPE: An Open-Source C++ and Python Library for Polarizable Embedding 

      Scheurer, Maximilian; Reinholdt, Peter; Kjellgren, Erik Rosendahl; Olsen, Jógvan Magnus Haugaard; Dreuw, Andreas; Kongsted, Jacob (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-10-03)
      We present a modular open-source library for polarizable embedding (PE) named CPPE. The library is implemented in C++, and it additionally provides a Python interface for rapid prototyping and experimentation in a high-level scripting language. Our library integrates seamlessly with existing quantum chemical program packages through an intuitive and minimal interface. Until now, CPPE has been ...
    • Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems 

      Olsen, Jógvan Magnus Haugaard; Reine, Simen Sommerfelt; Vahtras, Olav; Kjellgren, Erik; Reinholdt, Peter; Dundas, Karen O.H; Li, Xin; Cukras, Janusz; Ringholm, Magnus; Hedegård, Erik Donovan; Di Remigio, Roberto; List, Nanna H.; Faber, Rasmus; Tenorio, Bruno Nunes Cabral; Bast, Radovan; Pedersen, Thomas Bondo; Rinkevicius, Zilvinas; Sauer, Stephan P. A.; Mikkelsen, Kurt V.; Kongsted, Jacob; Coriani, Sonia; Ruud, Kenneth; Helgaker, Trygve; Jensen, Hans Jørgen Aa.; Norman, Patrick (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-06-05)
      The <i>Dalton Project</i> provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to ...
    • Polarizable Density Embedding for Large Biomolecular Systems 

      Reinholdt, Peter; Jørgensen, Frederik Kamper; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-09-29)
      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 PDE contributions to the ...
    • Response properties of embedded molecules through the polarizable embedding model 

      Steinmann, Casper; Reinholdt, Peter; Nørby, Morten Steen; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-04)
      The polarizable embedding (PE) model is a fragment‐based quantum‐classical approach aimed at accurate inclusion of environment effects in quantum‐mechanical response property calculations. The aim of this tutorial review is to give insight into the practical use of the PE model. Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to ...