Molecular mechanics models overview

In this section, a group of related approaches is discussed in which the continuum dielectric description of the microscopic environment is replaced by a more detailed model in which the atomic details of the structure and the dynamics of the microscopic environment are taken into account. These models will be referred to here as coupled DFT/Molecular Mechanics (DFT/MM). For a general overview of coupled ab initio/Molecular Mechanics methods, see the recent reviews by Aquist and Warshel186 and by Gao187. 

A few words about the basics of molecular mechanics (19,20) may provide the elements of understanding for what follows. This is not meant to be comprehensive, but rather a simple overview, to remind the reader of a few cmcial points. For a comprehensive overview of molecular modeling, the reader is referred to the excellent text by Leach (21). The interactions between atoms are divided into bonded and nonbonded classes. Nonbonded forces between atoms are based on an attractive interaction that has a firm theoretical basis and varies as the inverse of the 6th power of... 

See also Molecular modeling overview of. 919-920 plianiiaaiplioie concept in. 944 predictive ADMB in. >44- >45 quantum mechanics methods in. 923. 935-939... 

We have four goals for this chapter 1) present an overview of the steps commonly employed to study organometallic catalysis, 2) show how the principles underlying molecular mechanics methods are applied to three specific examples (stereoselectivity in asymmetric hydrogenation, olefin polymerization, and host/guest interactions in zeolites), 3) briefly illustrate the practical applications of molecular modeling to catalysts used in industry, and 4) present a limited survey of the literature to illustrate how different workers have applied molecular mechanics to the study of properties of catalysts of importance to organometallic chemists. 

Models used in the zeolite science can be divided into two categories (i) models that do not explicitly consider any electron in the system (molecular mechanics, interactions described with interatomic potential functions) and (ii) models that explicitly consider part of the electrons in the system (either at semiempirical level or at ab initio level). This text should serve as an introductory overview of quantum chemical approaches (excluding semiempirical methods) and models available for zeolite modeling. It is impossible to review the quantum chemical calculations in zeolite science on pages available here. Only qualitative description of methods will be given, avoiding mathematical equations. More details can be found, e. g., in Refs. [1-5]. 

This review will present an overview of current molecular mechanics techniques and discuss some of their limitations. We will then look at knowledge-based protein prediction strategies and examine the incorporation of such empirical rules into refinement methodologies for model protein systems. More comprehensive reviews of molecular dynamics simulations, knowledge-based protein modeling, and protein folding simulations are available. - " ... 

This extremely cursory overview suffices to show that there are several molecular and atomistic level interactions that are involved in any single corrosion event and that there is a large number of possible mechanisms that still require a rigorous theoretical treatment. In the following section, we introduce a number of molecular-level modeling techniques that have been, or could be, applied to the further detailed study of these mechanisms for materials presently used in industry and materials yet to be discovered and/or applied. 

The aim of this chapter is to provide an overview of the theories and methodologies governing MM of crystal structure and surfaces, growth morphology, and the effects of impurities and additives on crystallization. Different computational methods are used in these modelings, including ab initio or molecular orbital calculations, semiempirical methods, molecular mechanics, molecular dynamics, and Monte Carlo (MC) simulation. The reader is recommended to some excellent reference textbooks on the principles of MM and simulation (Hinchliffe 2003 Leach 2001 Myerson 1999). 

A molecule s electronic distribution is perhaps the most fundamental property that must be reproduced by an electronic structure method. An overview of how to compute molecular electrostatic potentials and their influence on chemical reactivity has been presented by Politzer and Murray. Without an accurate electronic structure, no other property is likely to be accurately described by a quantum mechanical model. It is sometimes unclear just how to determine the accuracy of a theoretical method, but one way is to compare calculated and experimental dipole moments. From good electronic distributions, one can extract atom-centered point charges for use in molecular mechanical applications. 

In this chapter an overview of conceptually different fracture theories is presented which have in common that they do not make explicite reference to the characteristic properties of the molecular chains, their configurational and super-molecular order and their thermal and mechanical interaction. This will be seen to apply to the classical failure criteria and general continuum mechanical models. Rate process fracture theories take into consideration the viscoelastic behavior of polymeric materials but do not derive their fracture criteria from detailed morphological analysis. These basic theories are invaluable, however, to elucidate statistical, non-morphological, or continuum mechanical aspects of the fracture process. 

In this paper, an overview of the origin of second-order nonlinear optical processes in molecular and thin film materials is presented. The tutorial begins with a discussion of the basic physical description of second-order nonlinear optical processes. Simple models are used to describe molecular responses and propagation characteristics of polarization and field components. A brief discussion of quantum mechanical approaches is followed by a discussion of the 2-level model and some structure property relationships are illustrated. The relationships between microscopic and macroscopic nonlinearities in crystals, polymers, and molecular assemblies are discussed. Finally, several of the more common experimental methods for determining nonlinear optical coefficients are reviewed. 

Different scales presented in Figure 3-1 are related to different approximation levels. For an overview of conventional molecular modelling methods, (see e.g.1-3). Bridging the above mentioned disparate time scales for the description of biologically relevant collective motions requires hierarchical, multi-scale approaches. In practice, to describe real complex (bio)molecular or material systems and processes various models have to be coupled to each other. Selected coupling mechanisms will be briefly reviewed. 

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