Description of Chemical Structures

In order to specify the structure of a chemical compound, we have to describe the spatial distribution of the atoms in an adequate manner. This can be done with the aid of chemical nomenclature, which is well developed, at least for small molecules. However, for solid-state structures, there exists no systematic nomenclature which allows us to specify structural facts. One manages with the specification of structure types in the following manner magnesium fluoride crystallizes in the rutile type , which expresses for MgF2 a distribution of Mg and F atoms corresponding to that of Ti and O atoms in rutile. Every structure type is designated by an arbitrarily chosen representative. How structural information can be expressed in formulas is treated in Section 2.1. 

Quantitative specifications are made with numeric values for interatomic distances and angles. The interatomic distance is defined as the distance between the nuclei of two atoms 

Graphic representations for a molecule of (UC15)2, all drawn to the same scale, 

Inorganic Structural Chemistry, Second Edition Ulrich Muller 2006 John Wiley Sons, Ltd. 

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Ivanduc, O., Balahan, A. T. The graph description of chemical structures. In Topological Indices and Related Descriptors in QSAR and QSPR, Devillers,). 

Kuchanov, S. Principles of Quantitive Description of Chemical Structure of Synthetic Polymers. Vol. 152,p. 157-202... 

After the description of chemical structure and control of meso-architecture and surface area, selected applications of such carbon materials as battery electrodes, supercapacitors, and in the design of controlled hybrid heterojunctions were presented. In the Li battery, coating or hybridization with hydrothermal carbon brought excellent capacities at simultaneous excellent stabilities and rate performances. This was exemplified by hybridization with Si, Sn02 (both anode materials) as well as LiFeP04 (a cathode material). In the design of supercapacitors, porous HTC carbons could easily reach the benchmark of optimized activated traditional carbons, with better stability and rate performance. 

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. 

With a few exceptions, we will focus our attention only on the semantic part of the description of chemical structures and disregard the presentational aspects of a chemical drawing. 

CML (Murray-Rust and Rzepa 1999,2003) is an XML-based format with basic characteristics very similar to those of CTFiles when it comes to description of chemical structures. There are two main published versions of CML CML 1 and CML 2. As the former one is already considered obsolete, we will describe only the properties of CML 2. 

Balaban, A.T, Mekenyan, O. and Bonchev, D. (1985a). Unique Description of Chemical Structures Based on Hierarchically Ordered Extended Connectivities (HOC Procedures). I. Algorithms for Finding Graph Orbits and Canonical Numbering of Atoms. J.Comput.Chem., 6, 538-551. 

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