A Full Additive QM/MM Scheme for the Computation of Molecular Crystals with Extension to Many-Body Expansions

Abstract

An additive quantum mechanics/molecular mechanics (QM/MM) model for the theoretical investigation of molecular crystals (AC-QM/MM) is presented. At the one-body level, a single molecule is chosen as the QM region. The MM region around it consists of a finite cluster of explicit MM atoms, represented by point charges and Lennard-Jones potentials, with additional background charges to mimic periodic electrostatics. Cluster charges are QM-derived and calculated self-consistently to ensure a polarizable embedding. We have also considered the extension to many-body QM corrections, calculating the interactions of a central molecule to neighbouring units in the crystal. Full gradient expressions have been derived, also including symmetry information. The scheme allows for the calculation of molecular properties as well as unconstrained optimisations of the molecular geometry and cell parameters with respect to the lattice energy. Benchmarking the approach with the X23 reference set confirms the convergence pattern of the many-body extension, although comparison to plane wave DFT reveals a systematic overestimation of cohesive energies by 6-16 kJ·mol<sup>−1</sup> . While the scheme primarily aims to provide an inexpensive and flexible way to model a molecule in a crystal environment, it can also be used to reach highly accurate cohesive energies by the straightforward application of wave function correlated approaches. Calculations with local coupled cluster with singles, doubles, and perturbative triples, albeit limited to numerical gradients, show an impressive agreement with experimental estimates for small molecular crystals.<br><br>

Trapping X‐ray Radiation Damage from Homolytic Se−C Bond Cleavage in BnSeSeBn Crystals (Bn=benzyl, CH2C6H5)

“…Therefore, an extended DFT optimization of the possible activated states was performed under the additive crystal QM/MM scheme (AC-QM/MM). [24] The latter allows with minimal added cost to optimise the structure of a defect (in this case a molecule found in an excited state) in the environment of an otherwise unperturbed crystal. Further details are available in the Supporting Information.…”

An Imbalance in the Force: The Need for Standardised Benchmarks for Molecular Simulation

“…The X23 database has been evaluated using FFs by Nyman et al 212 and by Teuteberg et al using combined quantum mechanics/molecular mechanics (QM/MM). 213 Bernardes & Joseph studied 18 drug-like aromatic compounds by performing experiments to evaluate the enthalpy of sublimation ∆H sub and then compared the results to FF simulations. Apart from the enthalphy of sublimation they also study the relative stability ∆ trs H of crystal polymorphs.…”

Off-the-shelf DFT-DISPersion methods: Are they now “on-trend” for organic molecular crystals?

“…Lattice energies can be calculated using classical, atomistic methods [14][15][16][17][18][19][20] , i.e. molecular mechanics based on force fields, quantum mechanical methods (see, for example the work of Yang et al 21 and the 2016 review and references within of Hoja, Reilly and Tkatchenko 22 ) and more rarely, hybrid quantum mechanics/molecular mechanics 23,24 . The choice of method depends on several factors, such as in-house expertise, computational resources and time allotted for the research, and not least the modelling aims.…”