Structure representation special problems

A number of special features of chemical structures, and certain types of structure, cause special problems, particularly for computer representation. Stereochemistry is one of the most important of these (see Stereochemistry Representation and Manipulation). 

The in-house systems REACCS, ISIS, and CrossFire handle aromaticity and tautomerism satisfactorily a user can enter structures as any chemist normally would without having to worry about the bond conventions used internally by the database system. This is not yet true for CASREACT and other reaction databases offered under STN Messenger. Here the user has to know the definition and use of normalized bonds, a special bond type defined to handle aromaticity and tautomerism in a formal way. This, unfortunately, corresponds only partially to these concepts ias used by chemists. CAS is working on Ais problem the SciFinder interface already offers a solution for exact structures, but not yet for substructures, falling into this category (see Structure Representation). 

Computer information systems for chemistry need to include representations of chemical structures, which show the way in which the atoms and bonds of a molecule are connected together. This is necessary if they are to compare Structures for identity (thus allowing a check on whether or not a particular compound is contained in a database), or to search for all compounds in a database containing a particular substructure, or group of atoms and bonds. Such representations may also allow display of conventional two-dimensional structure diagrams on computer screens, and the performance of a wide variety of other analyses on individual molecules or sets of molecules. Several different types of representation are used in computer systems, some of them adapted from structure representations developed before the computer age. This article describes the principal ones, and discusses some of the special problems that arise in the representation of chemical structures, and the feasibility of interconverting different representations. 

The problem of estimating crystal field parameters can be solved by considering the CFT/LFT as a special case of the effective Hamiltonian theory for one group of electrons of the whole A -electronic system in the presence of other groups of electrons. The standard CFT ignores all electrons outside the d-shell and takes into account only the symmetry of the external field and the electron-electron interaction inside the d-shell. The sequential deduction of the effective Hamiltonian for the d-shell, carried out in the work [133] is based on representation of the wave function of TMC as an antisymmetrized product of group functions of d-electrons and other (valence) electrons of a complex. This allows to express the CFT s (LFT s or AOM s) parameters through characteristics of electronic structure of the environment of the metal ion. Further we shall characterize the effective Hamiltonian of crystal field (EHCF) method and its numerical results. 

Special interest adheres to the group of cholinesterases (ChE), not only in view of their physiological role in conductive tissues, but also because their specific behavior towards substrates and inhibitors and their high efficiency towards cationic substrates permit exact kinetic measurements. In spite of an enormous amount of experimental work, the exact structure of the active surface of cholinesterases is still controversial [see the review of Whittaker (/)]. The following representation will discuss the results already achieved and point out the many problems in this field still awaiting solution. 

A special type of bond-type assignment problem concerns tautomerism. Some chemical databases provide specific tautomeric bond types, or analyse a query for either the keto or enol constructions and add the missing one (as an. OR. option) automatically. In the CSD, only the single tautomeric form identified by the crystal structure determination is encoded in the connectivity tables. The software has not yet been upgraded to accommodate searches for both forms, hence the onus is on the user to encode both representations if that is the desired goal of a query. 

To answer this problem, one must know the structures of the molecules in question and a couple of definitions. By definition, epimers are a pair of molecules that differ from each other only in their configuration at a single asymmetric center. Anomers are special epimers that differ only in their configuration at a carbonyl carbon hence, they are usually acetals or hemiacetals. An aldose-ketose pair is obvious. Inspection of Fischer representations of the molecular pairs leads to the conclusion that (a), (c), and (e) are aldose-ketose pairs (b) and (f) are epimers and (e) are anomers. 

In data structure terms, all these outputs are lists, but the last item is more. In ordinary terms, it is an organization chart. That is a special kind of data stmcture possessing hierarchy. As a data structure, the relationship possesses a hierarchical quality so it is not just a list but also a tree. Trees can be represented by a linear list data structure through the use of a special place marker that signifies change hierarchy level. In text representation, either a period or a parenthesis is used for that purpose. Whether a data structure is a list or is represented by a list is another of the unusual aspects of this field of knowledge. Nevertheless, these are just two aspects of the problem being dealt with, specifically ... 

A more complete view of the electronic structure can be obtained from quantum mechanics. All of this information is contained within the Brillouin zone, but this gives us a conceptual problem it is a complex three-dimensional shape that resides in reciprocal space. We can simplify any three-dimensional shape by cutting slices through it to create two-dimensional representations. In this way, a sphere becomes a circle and so on. We can do the same with the Brillouin zone. By slicing through certain pathways, called k vectors, which link k points (which are special positions in the three-dimensional Brillouin zone defined by the real-space crystal system) we generate the two-dimensional band structure diagrams. 

---