Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations

Abstract

We report a quantum mechanics/polarizable–molecular mechanics (QM/p–MM) potential based molecular dynamics (MD) technique where the core–shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car–Parrinello MD for the QM subsystem. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn–Sham (KS) orbitals describing the QM wavefunction. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In this respect, we also present here the Nosé–Hoover Chain thermostat implementation for the dynamical subsystems. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. A low point charge polarizable potential (p–MZHB) for pure siliceous systems is also reported here.

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

“…Very popular examples of this type are the Effective Fragment Potential (EFP) method 18 and the X-Pol strategy. 19 An alternative approach is to use MM but polarizable FFs [20][21][22][23] based either on Drude oscillators, [24][25][26][27][28][29] fluctuating charges [30][31][32][33][34] or induced point dipoles (IPD). 1,[35][36][37][38][39][40][41][42] We recall that within the latter framework, the MM subsystem is represented via a set of fixed point charges, and possibly higher order multipoles, and by endowing polarizable sites with atomic polarizabilities.…”

Exploring high‐dimensional free energy landscapes of chemical reactions

“…It was shown that US predicts a slightly different mechanism and a higher free energy barrier compared to TASS as a result of poor sampling of orthogonal coordinates by the former method. Sahoo and Nair used TASS to simulate proton exchange reaction between methane and acid sites within the H‐ZSM‐5 zeolite using DFT‐based QM/polarized‐MM simulations . Without invoking a controlled sampling of distance between CH 4 and the acid site in zeolite, the CH 4 molecule diffuses away from the acid sites.…”

A Many-Body, Fully Polarizable Approach to QM/MM Simulations

“…[11][12][13][14] A related approximation to the polarizable embedding was introduced with the LICHEM interface, which couples generic QM and MM software using a partially self-consistent polarization scheme, compromising some accuracy for a more generalized interface and grater computational efficiency. 15,16 By solving the QM equations and the MM polarization equations in a fully coupled fashion, some recent approaches adopt a more intimate coupling between the electron density in the QM region and the polarization in the MM region, with the latter being modeled by inducible point dipoles (IPD), [17][18][19][20][21][22][23][24][25] fluctuating charges, [26][27][28][29][30][31] Drude oscillators., [32][33][34][35][36][37] or using a response kernel. 38,39 In this contribution, we limit our discussion to IPD-based approaches, as this is the polarization model adopted by both the MB-pol [40][41][42] and AMOEBA 43,44 models used in this analysis.…”