A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations

Abstract

We present a fully Hamiltonian and computationally efficient scheme to include the electrostatic effects due to the classical environment in a Car-Parrinello mixed quantum Mechanics/molecular mechanics ͑QM/MM͒ method. The polarization due to the MM atoms close to the quantum system is described by a Coulombic potential modified at short range. We show that the functional form of this potential has to be chosen carefully in order to obtain the correct interaction properties and to prevent an unphysical escape of the electronic density to the MM atoms ͑the so-called spill-out effect͒. The interaction between the QM system and the more distant MM atoms is modeled by a Hamiltonian term explicitly coupling the multipole moments of the quantum charge distribution with the classical point charges. Our approach remedies some of the well known deficiencies of current electrostatic coupling schemes in QM/MM methods, allowing molecular dynamics simulations of mixed systems within a fully consistent and energy conserving approach.

First principles view on chemical compound space: Gaining rigorous atomistic control of molecular properties

“…For this review, however, we will limit the discussion to the potential energy of interaction. Future work will deal with the inclusion of thermal and solvent effects for instance using ab initio molecular dynamics techniques [82] in conjunction with QM/MM [83] calculations. Moreover, even at the mere potential energy electronic structure level of theory, the accurate quantification and control of intercalated ellipticine derivatives is challenging: vdW forces dominate the binding.…”

“…Let us exemplify a DFTþvdW-based prediction of the binding energy of another mutant: ð21121Þ is predicted to bind to the DNA cluster in Figure 4 with E 21121 ¼ À38:5 kcal/mol. [83] For predicting the single point mutation (21121) …”

Quantitative Assessment of Electrostatic Embedding in Density Functional Theory Calculations of Biomolecular Systems

“…24,25 Indeed, at short distance, the validity of a point charge representation is questionable. In the context of this paper, as well as in a plane wave approach, 26 such a smearing is a convenient way of generating a charge density and a resulting Coulomb potential representable on a uniform mesh.…”

“…To address this problem in a molecular dynamics or geometry optimization context, the coordinates of some atoms at the QM frontier should be frozen so that these erroneous forces would not be active. 26 carrying out such a computation in an external Coulomb potential due to MM charges can potentially lead to the so-called electron spill-out effect. While one must be aware of this issue, the calculations reported in this paper using the parameters tabulated in Table 1 showed no measurable evidence of this phenomena.…”

A quantum-mechanics molecular-mechanics scheme for extended systems

“…In the context of molecular simulations, hybrid Quantum Mechanics-Molecular Mechanics (QM-MM) schemes consider the system as a sum of two parts: solute (QM fragment) and solvent (MM fragment) [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20]. The particles are assigned to one of these two groups according to their role: atoms directly involved in bonds breaking or forming, or in polarization or charge transfer effects, must be considered in the QM region, whereas those atoms not participating in these processes are included within the MM subsystem.…”