Molecular shape overview

In the rest of this book we will be examining in more detail ligands, metal-ligand assembly and the consequences. These include molecular shape, stability, properties and how we can measure and interpret these. Further, we will look at metal complexes in place -in nature and in commerce, and speculate on the future. Overall, the intent is to give as broad and deep an overview as is both reasonable and proper in an introductory text. Pray continue. 

The notion of molecular shape is ubiquitous and pervasive in the vocabulary and the work of all chemists. As computational chemists, we would like to provide a hard, quantitative expression of this property, especially one that will allow us to compare molecules. However, shape cannot be compared in the same way that many other molecular properties are studied. There is no unique classical or quantum mechanical property that relates to the shape of a molecule or molecular assembly. It is up to us to build descriptors of molecular shape in each case. This chapter provides an overview of ideas and methodologies aimed at quantifying this property in several cases of interest. 

Several other techniques for 2D surface matching and relative comparison have been proposed. A detailed discussion is beyond the goal of this chapter on basic molecular shape descriptors. An overview of different alternatives can be gathered by comparing the work in Refs. 2, 155, 240, and 241. 

ABSTRACT. The amount of published work on molecular shape-selective catalysis with zeolites is vast. In this paper, a brief overview of the general principles involved in molecular shape-selectivity is provided. The recently proposed distinction between primary and secondary shape-selectivity is discussed. Whereas primary shape-selectivity is the result of the interaction of a reactant with a micropore system, secondary shape-selectivity is caused by mutual interactions of reactant molecules in micropores. The potential of diffusion/reaction kinetic analysis and molecular graphics for rationalizing molecular shape-selectivity is illustrated, and an alternative explanation for the cage and window effect in cracking and hydrocracking is proposed. Pore mouth catalysis is a speculative mechanism advanced for some systems (a combination of a specific zeolite and a reactant), which exhibit peculiar selectivities and for which the intracrystalline diffusion rates of reactants are very low. 

In order to have a better overview of this important work, all, 5-diketonato complexes will be discussed together, irrespeetive of classifications based on molecular shape and mesomorphism. This is done as classical taxonomy does not work too well with these materials and also because it serves to illustrate the limitations of such taxonomy indeed, it might be argued that some of the more interesting stmcture/property relationships exist at the limits of classification. 

One can describe a molecule in many ways and the same applies to bioisosteres. Molecular descriptor methods are covered in the third part by the application of different representations. A number of computational approaches to bioisosteric replacement are covered in chapters on physicochemical properties, molecular topology, molecular shape, and the use of protein structure information. Each chapter covers many common methods and overviews of when best to apply these methods, and where they have been successfully applied. 

In this chapter, we provided a general overview of nonlinear chromatography. In nonlinear chromatography, the shape of the nonlinear isotherms and the molecular interactions leading to a... 

We now turn from the use of quantum mechanics and its description of the atom to an elementary description of molecules. Although most of the discussion of bonding in this book uses the molecular orbital approach to chemical bonding, simpler methods that provide approximate pictures of the overall shapes and polarities of molecules are also very useful. This chapter provides an overview of Lewis dot structures, valence shell electron pair repulsion (VSEPR), and related topics. The molecular orbital descriptions of some of the same molecules are presented in Chapter 5 and later chapters, but the ideas of this chapter provide a starting point for that more modem treatment. General chemistry texts include discussions of most of these topics this chapter provides a review for those who have not used them recently. 

The determination of molecular sizes and weights for humic substances is a task complicated by the nature of these materials. A brief overview of the methods most commonly used to determine molecular sizes and weights of humic substances has been presented in this chapter. Many of the methods discussed are powerful techniques that can yield information about the molecular size, shape, and weight of humic substances. No single method alone, however, is sufficient to provide a complete understanding of these molecular characteristics. Meaningful and accurate conclusions can only be made by using the data provided by different methods of analysis. 

A short overview of the quantum chemical and statistical physical methods of modelling the solvent effects in condensed disordered media is presented. In particular, the methods for the calculation of the electrostatic, dispersion and cavity formation contributions to the solvation energy of electroneutral solutes are considered. The calculated solvation free energies, proceeding from different geometrical shapes for the solute cavity are compared with the experimental data. The self-consistent reaction field theory has been used for a correct prediction of the tautomeric equilibrium constant of acetylacetone in different dielectric media,. Finally, solvent effects on the molecular geometry and charge distribution in condensed media are discussed. 

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