Structure and Shape of Molecules

Elaving developed ideas about Lewis structures and shapes of molecules, we are now in a position to explore some of the important properties of covalent bonds. These properties provide revealing evidence about molecular shapes. 

Describe the models that chemists use to describe the structure and shape of molecules and ions, and assess their value in terms of the information they communicate. 

To introduce the classical description of chemical bonding as a tool for describing and understanding the structures and shapes of molecules... 

You learned in Chapter 12 that atoms in molecular compounds and polyatomic ions are held together by covalent bonds. Lewis diagrams show, in two dimensions, how the atoms are connected. However, Lewis diagrams do not show how the atoms are arranged n three dimensions-the actual shape of the molecule. In this chapter you will learn how the distribution of atoms leads to the structure and shape of molecules. It begins with the Lewis diagram, and in case it has been a while since you studied Lewis diagrams, we will review them briefly. Important terms are printed in italics. 

Let s say that we want to determine the structure and shape of an enzyme or other biological molecule. The technique used is called X-ray ciystallography. 

From our considerations above, we can see just how important the interactions of various amino acid side-chains are to the structure and shape of proteins. These interactions tend to be located inside the protein molecule, stabilizing a particular conformation and generating the overall shape as in a globular protein. However, it is obvious that there are also going to be many amino acid side-chains located on the surface of a protein, and these in turn will be capable of interacting with other molecules. These interactions will be intermolecular, rather than the intramolecular interactions that contribute to protein structure. 

Drug Action and Shape of Molecules Some years ago two drug companies marketed a drug under the trade names Dexedrine and Benzedrine. The structure of the drug is shown below. 

The size and shape of molecules are as much a part of molecular structure as is the order in which the component atoms are bonded. Contrary to the impression you may get from structural formulas, complex molecules are not flat and formless, but have well-defined spatial arrangements that are determined by the lengths and directional character of their chemical bonds. It is not easy to visualize the possible arrangements of the bonds in space and it is very helpful to have some kind of mechanical model that reflects the molecular geometry, including at least an approximation to the relative lengths of the bonds. Ball-and-stick models such as the ones used by Patemo (Section 1-ID) fill this purpose admirably. 

This exercise will familiarise you with (he structures of some simple covalent compounds and the methods we have for representing the structure and shape of their molecules. 

The study of molecular interactions in liquid mixtures is of considerable importance in the elucidation of the structural properties of molecules. Interactions between molecules influence the structural arrangement and shape of molecules. Dielectric relaxation of polar molecules in non-polar solvents using microwave absorption has been widely employed to study molecular structures and molecular interactions in liquid mixtures [81]. Ever since Lagemann and Dunbar developed a US velocity approach for the qualitative determination of the degree of association in liquids [82], a number of scientists have used ultrasonic waves of low amplitude to investigate the nature of molecular interactions and the physico-chemical behaviour of pure liquids and binary, ternary and quaternary liquid mixtures, and found complex formation to occur if the observed values of excess parameters (e.g. excess adiabatic compressibility, intermolecular free length or volume) are negative. These parameters can be calculated from those for ultrasonic velocity (c) and density (p). Thus,... 

In the following sections we review the compositions of the main chemical classes and their biochemical functions. These functions are related to the structure and shape of the basic carbon skeleton of a molecule and the functional groups (see Box 2.1) attached to it. 

The amino acid cysteine is a thiol that has an important role to play in the structure and shape of many proteins. Two cysteine molecules can undergo oxidation to form cystine. The new bond formed is called a disulfide bond (—S—S—) bond. 

Wavefunction s Spartan Student Edition (6) is used extensively in this course for building molecules and visualizing molecular shape, polarity, intermolecular interactions, hydrogen bonding, solubility, protein and nucleic acid structure. Spartan exercises are used to investigate the connection between the structure and shape of water and its polarity, intermolecular interactions, and... 

Thus far we have considered methods for determining molecular weights, or overall sizes and shapes of molecules. There are also techniques for the measurement of bond lengths and bond angles, which provide much more detailed information about molecular structure. The most powerful and widely-used method is X-ray diffraction, which has provided a great deal of information about the detailed structures of proteins and other molecules of biological importance. Valuable information is also provided by use of X-ray absorption and the electron microscope. 

Some pioneering efforts relating Information Theory to electronic structure and properties of molecules can be already found in the seminal papers by Daudel in the framework of loge theory [6, 7], subsequently followed by Mezey [8] and reexamined later by Nalewajski [9], The studies of Mezey [10] and Avnir [11] on symmetry and chirality-related problems in molecules, and in other very diverse fields (e.g., image and texture analysis), are also examples of applications of informational measures on specific aspects of shape, disorder, and complexity. 

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