Quantum mechanical/molecular mechanics QM/MM methods

Friesner RA, Guallar V (2005) Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annu Rev Phys Chem 56 389 127... 

Riccardi D, Schaefer P, Yang Y, Yu HB, Ghosh N, Prat-resina X, Konig P, Li GH, Xu DG, Guo H, Elstner M, Cui Q (2006) Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B 110 6458-6469... 

The description of pure quantum mechanics (QM) methods presented in Section 3 has shown how in most cases they provide an accurate description of the electronic subtleties involved at the transition metal center of a catalytic process, but that they are unable to introduce the whole bulk of the catalyst substituents, which can be critical for selectivity issues. The description of pure molecular mechanics (MM) methods presented in subsection 4.1 has shown how these methods can easily introduce the steric bulk of the substituents, and accurately describe their steric interactions, but that they struggle badly when trying to describe properly the transition metal center and its immediate environment. The logical solution to this complementary limitations is to divide the chemical system in two regions, and to use a different description for each of them, QM for the metal and its environment, MM for the rest of the system. This is precisely the basic idea of hybrid quantum mechanics / molecular mechanics (QM/MM) methods. 

The isotope independent potential energy surface was evaluated using a mixed quantum mechanics/molecular mechanics (QM/MM) method. The system (N atoms) was partitioned into Nqm quantum mechanical atoms and Nmm classical mechanical atoms. Nqm consisted of the 15 atom substrate (phospho-D-glycerate)... 

From its inception, the combined Quantum Mechanics/Molecular Mechanics (QM/MM) method [1-3] has played an important roll in the explicit modeling of solvent [4], Whereas Molecular Mechanics (MM) methods on their own are generally only able to describe the effect of solvent on classical properties, QM/MM methods allow one to examine the effect of the solvent on solute properties that require a quantum mechanical (QM) description. In most cases, the solute, sometimes together with a few solvent molecules, is treated at the QM level of theory. The solvent molecules, except for those included in the QM region, are then treated with an MM force field. The resulting potential can be explored using Monte Carlo (MC) or Molecular Dynamics (MD) simulations. Besides the modeling of solvent, QM/MM methods have been particularly successful in the study of biochemical systems [5] and catalysis [6],... 

The ASEP/MD method, acronym for Averaged Solvent Electrostatic Potential from Molecular Dynamics, is a theoretical method addressed at the study of solvent effects that is half-way between continuum and quantum mechanics/molecular mechanics (QM/MM) methods. As in continuum or Langevin dipole methods, the solvent perturbation is introduced into the molecular Hamiltonian through a continuous distribution function, i.e. the method uses the mean field approximation (MFA). However, this distribution function is obtained from simulations, i.e., as in QM/MM methods, ASEP/MD combines quantum mechanics (QM) in the description of the solute with molecular dynamics (MD) calculations in the description of the solvent. 

Aguilar, Sanchez, Martin, Fdez. Galvan review the ASEP/MD method, acronym for Averaged Solvent Electrostatic Potential from Molecular Dynamics, showing how this method combines aspects of quantum mechanics/molecular mechanics (QM/MM) methods with aspects of continuum models. 

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods... 

In recent years, there have been many attempts to combine the best of both worlds. Continuum solvent models (reaction field and variations thereof) are very popular now in quantum chemistry but they do not solve all problems, since the environment is treated in a static mean-field approximation. The Car-Parrinello method has found its way into chemistry and it is probably the most rigorous of the methods presently feasible. However, its computational cost allows only the study of systems of a few dozen atoms for periods of a few dozen picoseconds. Semiempirical cluster calculations on chromophores in solvent structures obtained from classical Monte Carlo calculations are discussed in the contribution of Coutinho and Canuto in this volume. In the present article, we describe our attempts with so-called hybrid or quantum-mechanical/molecular-mechanical (QM/MM) methods. These concentrate on the part of the system which is of primary interest (the reactants or the electronically excited solute, say) and treat it by semiempirical quantum chemistry. The rest of the system (solvent, surface, outer part of enzyme) is described by a classical force field. With this, we hope to incorporate the essential influence of the in itself uninteresting environment on the dynamics of the primary system. The approach lacks the rigour of the Car-Parrinello scheme but it allows us to surround a primary system of up to a few dozen atoms by an environment of several ten thousand atoms and run the whole system for several hundred thousand time steps which is equivalent to several hundred picoseconds. 

Murphy RB, Philipp DM, Friesner RA. A Mixed quantum mechanics/molecular mechanics (QM/ MM) method for large-scale modeling of chemistry in protein environments. J Computational... 

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