Molecular descriptors unambiguity

Molecular descriptors can only be managed by computer software in an effective manner. Consequently, the calculation shall be computationally unambiguous and reasonably fast. The same algorithm shall result in the same descriptor as long as the molecule properties of interest do not change. 

Perhaps the most obvious way to characterise different chemical structures is to use experimental measurements of some characteristic properties, such as melting point, boiling point or refractive index for example. This approach has the advantage that these properties are unambiguously and easily defined and in many cases easily measured to any desired precision. Solubility is clearly an important factor in the biological activity of any compound, and indeed this was found to be one of the earliest successful molecular descriptors, where toxicity... 

The purpose of a molecular descriptor in quantitative structure-activity relationship (QSAR) applications is to provide a measure of a particular feature of the molecular structure of the compounds being studied. The goal is simply to measure the feature in question as accurately and unambiguously as possible. 

In QSAR modeling, the question of molecular representation is central. For the modeling, a molecule is represented as a multidimensional vector, i.e., a molecule is a point in multidimensional representational space. An ideal representation should be unique, uniform, reversible, and invariant on rotation and translation of molecules. Unique means that different structures give different representations, uniform means that the dimension of representation is the same for all structures, reversible means that the structure can be unambiguously reconstructed from the representation vector. Furthermore, invariant means that the representation is not sensitive if a molecule is rotated or translated. It is not expected that we would find a general representation that fulfills all requirements simultaneously [26]. Nowadays, thousands of descriptors and structural representations are in use [26-29]. We will give a short overview, and references about descriptors that often appear in QSAR studies related to mutagenicity of aromatic amines are presented in more detail. 

The rules we will present help one assign a simple and unambiguous stereotopicity descriptor - H, H, E, 3, D, D, or F - to each molecular face of an acyclic or monocyclic planar moiety. Paired homotopic (equivalent) faces are designated by the same descriptor H/H or H /H. For enantiotopic faces, the rules will help determine which face is E and which one is 3 for diastereotopic faces they will help tell which face is D, which one is F, which one is D and which one is F. The rules for each molecular system will be detailed below. 

A chemical substance which is to be recorded by machine processing in the CAS Chemical Registry System is described in terms of a set of topological characteristics. The structural data necessary include a molecular formula, the basic relationship of the atoms present, and other data to allow complete and unambiguous identification of the substance. Each substance registered is represented in the system by a unique record, with four components 1) the connection table topology, which is a detailed inventory of the atoms and bonds that comprise the basic structure of the substance and more recently the stereochemical information 2) an isotopic labeling component which identifies any labeled atoms in the structure 3) a derivative component, which indicates that the substance is a salt or a complex of the substance defined by the first two components of the record and 4) a text descriptor component,... 

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