Chapter 1. QM/MM with Auxiliary DFT in deMon2k

Abstract

This chapter describes the theoretical background of the Quantum Mechanical/Molecular Mechanical (QM/MM) implementation in deMon2k within the framework of Auxiliary Density Functional Theory (ADFT). It aims to give the reader an overview of the current state-of-the-art of this QM/MM implementation and perspectives for its future development. To this end, we first derive the ADFT working equations for the QM and QM/MM energy and gradient expressions.Based on the joined QM/MM gradient expression, we present algorithms for QM/MM structure optimizations, transition state searches and molecular dynamics simulations. The use of auxiliary density perturbation theory (ADPT) in the framework of QM/MM is discussed on illustrative example implementations including analytic second-order ADFT energy derivatives, nuclear magnetic resonance chemical shift calculations and excited state calculations by time-dependent ADFT. The chapter closes with the description of a transformation program to generate deMon2k QM/MM inputs.

Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study

“…All calculations have been carried out with an in-house version of the deMon2k (version 6.1.6) implementing RT-TD-DFT within the Auxiliary DFT framework. , With this framework, the Coulomb contribution to the Kohn–Sham potential is calculated with the help of variationally fitted electron densities ρ̃. , The auxiliary fitted density is expressed as a linear combination over auxiliary functions k̅ ( ρ̃ = ∑ k̅ x k̅ k̅ ) , while, on the other hand the Kohn–Sham density is expressed as a linear combination of atomic orbitals, i.e., ρ = ∑ μ,ν P μν μν, where P is the density matrix, the element of which being defined as P μν = ∑ i occ c μi * c νi . The c , on one hand, and the μ and ν, on the other, are, respectively, the molecular orbital coefficients and the atomic orbital indexes.…”

“…The Journal of Physical Chemistry A All calculations have been carried out with an in-house version of the deMon2k 77 (version 6.1.6) implementing RT-TD-DFT within the Auxiliary DFT framework. 78,79 With this framework, the Coulomb contribution to the Kohn−Sham potential is calculated with the help of variationally fitted electron densities ρ. 80,81 The auxiliary fitted density is expressed as a linear combination over auxiliary functions k̅ x k ( )…”

Cartesian constraints in QM/MM optimizations

“…For the MM part of 100, 200, 300, 400, and 500 water molecules a simple point‐charge model 50 employing the OPLS‐AA force field 51 was used. The QM/MM optimizations are performed in the same way as for the QM only systems 31 …”

“…With the raise of quantum mechanical/molecular mechanical (QM/MM) calculations employing first‐principles QM approaches these two previously separated methodologies now join together in many quantum chemistry programs. In this respect, deMon2k 31 is no exception. By default, automatically generated delocalized internal coordinates are used for QM/MM local structure optimizations whereas Cartesian coordinates are used for QM/MM MD simulations.…”

Current status of deMon2k for the investigation of the early stages of matter irradiation by time-dependent DFT approaches

“…GROMACS [175]…) to deMon2k [176]. It is now straightforward to prepare input files for RT-TD-ADFT, BOMD, or Ehrenfest MD with QM/MM on complex biological structures (DNA/protein complexes, proteins embedded in a membrane, …).…”