Molecular graphics description

Fig. 1.14. Graphic description of combination of two I5 orbitals to give two molecular orbitals for H2 (A) and HHe+ (B).

Molecular graphics (Henkel and Clarke, 1985) refers to a technique for the visualization and manipulation of molecules on a graphical display device. The technique provides an exciting opportunity to augment the traditional description of chemical structures by allowing the manipulation and observation in real time and in three dimensions, of both molecular structures and many of their calculated properties. Recent advances in this area allow visualization of even intimate mechanisms of chemical reactions by graphical representation of the distribution and redistribution of electron density in atoms and molecules along the reaction pathway. 

Graphic description of combination of two Is orbitals to give two molecular orbitals... 

As computational chemistry tools have developed over the last decade or so, molecular graphics and visualization have played a prominent role in expressing complex three-and higher-dimensional properties of molecules, such as, e.g., wavefunctions. Just as structured languages such as HTML and its incorporation of URL descriptors were used to achieve structure and context for text-based documents, so there came a realization that a three-dimensional object description language was needed to express the context in more complex 3D scenes, or worlds as they became known. 

Boyd, D.B., Introduction and foreword to the Special issue commemorating the 25th anniversary of molecular connectivity as a structure description system editorial, J. Mol. Graphics Modelling, 20, 1-3, 2001. 

Because of the graphic nature of most molecular representations, the formats used to store such information are mostly oriented toward description of this graph. While this fact is more pronounced in some formats and less obvious in others, a graph is always hidden inside the format. 

Leicester, S.E., Finney, J.L. and Bywater, R.P. (1988). Description of Molecular Surface Shape Using Fourier Descriptors. J.Mol.Graphics, 6,104-108. 

This is thus a chemically oriented, not too advanced book, written in an easy-going style. Without loss of correctness, the physical insight is maximized and abundant graphical illustrations are used. A large number rf figures (127) and many diagrams help to make the book less dense and more instructive. The relationships between the more formally based qnantum-mechanical formalisms and the traditional chemical descriptions of atomic and molecular structure are established and discussed in a critical manner. 

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