Quantum mechanics methods simulations

Combined Quantum and Molecular Mechanical Simulations. A recentiy developed technique is one wherein a molecular dynamics simulation includes the treatment of some part of the system with a quantum mechanical technique. This approach, QM/MM, is similar to the coupled quantum and molecular mechanical methods introduced by Warshel and Karplus (45) and at the heart of the MMI, MMP2, and MM3 programs by AUinger (60). These latter programs use quantum mechanical methods to treat the TT-systems of the stmctures in question separately from the sigma framework. 

These apparent restrictions in size and length of simulation time of the fully quantum-mechanical methods or molecular-dynamics methods with continuous degrees of freedom in real space are the basic reason why the direct simulation of lattice models of the Ising type or of solid-on-solid type is still the most popular technique to simulate crystal growth processes. Consequently, a substantial part of this article will deal with scientific problems on those time and length scales which are simultaneously accessible by the experimental STM methods on one hand and by Monte Carlo lattice simulations on the other hand. Even these methods, however, are too microscopic to incorporate the boundary conditions from the laboratory set-up into the models in a reahstic way. Therefore one uses phenomenological models of the phase-field or sharp-interface type, and finally even finite-element methods, to treat the diffusion transport and hydrodynamic convections which control a reahstic crystal growth process from the melt on an industrial scale. 

All the macroscopic properties of polymers depend on a number of different factors prominent among them are the chemical structures as well as the arrangement of the macromolecules in a dense packing [1-6]. The relationships between the microscopic details and the macroscopic properties are the topics of interest here. In principle, computer simulation is a universal tool for deriving the macroscopic properties of materials from the microscopic input [7-14]. Starting from the chemical structure, quantum mechanical methods and spectroscopic information yield effective potentials that are used in Monte Carlo (MC) and molecular dynamics (MD) simulations in order to study the structure and dynamics of these materials on the relevant length scales and time scales, and to characterize the resulting thermal and mechanical proper-... 

Lu ZY, Zhang YK (2008) Interfacing ab initio quantum mechanical method with classical Drude os-illator polarizable model for molecular dynamics simulation of chemical reactions. J Chem Theory Comput 4(8) 1237-1248... 

From these early beginnings, computer studies have developed into sophisticated tools for the understanding of defects in solids. There are two principal methods used in routine investigations atomistic simulation and quantum mechanics. In simulation, the properties of a solid are calculated using theories such as classical electrostatics, which are applied to arrays of atoms. On the other hand, the calculation of the properties of a solid via quantum mechanics essentially involves solving the Schrodinger equation for the electrons in the material. 

Electron and charge transfer reactions play an important role in many chemical and biochemical processes. Dynamic solvation effects, among other factors, can largely contribute to determine the reaction rate of these processes and can be studied either by quantum mechanical or simulation methods. 

The previous two sections of this review deal with classical simulation methods. A description of the activation of adsorbates by acidic sites, together with any bond breaking or bond formation that may take place, is the realm of quantum mechanical (QM) simulations. These types of calculations are particularly well-suited to zeolite-adsorbate systems when the cluster approximation is used. The active acidic site in the zeolite is modeled by a molecular cluster, formed by cutting out a small portion of... 

With respect to the various spectroscopic methods not discussed so far there are four methodologically different concepts of molecular modeling (i) quantum-mechanical methods which result structural and electronic information (ii) MM-based structural modeling, followed by a single-point MO-based computation of the electronic properties (iii) spectra simulation with given electronic parameters in cases, where structural parameters (e.g., distances such as used in protein modeling, see above) are involved in the simulation (iv) structure property correlations. The latter approach will be discussed briefly at the end of this Section (redox potentials) and in Section 4. 

Whatever the choice of the quantum mechanical method, two representations are currently used to simulate semi-infinite surfaces slabs or clusters. Only the Cl method is restricted to cluster geometries. 

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