Connection Tables CTs

A major disadvantage of a matrix representation for a molecular graph is that the number of entries increases with the square of the number of atoms in the molecule. What is needed is a representation of a molecular graph where the number of entries increases only as a linear function of the number of atoms in the molecule. Such a representation can be obtained by listing, in tabular form only the atoms and the bonds of a molecular structure. In this case, the indices of the row and column of a matrix entry can be used for identifying an entry. In essence, one has to distinguish each atom and each bond in a molecule. This is achieved by a list of the atoms and a list of the bonds giving the coimections between the atoms. Such a representation is called a connection table (CT). 

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

Compounds are stored as connection tables (CT) in structure and reaction databases, e.g., Beilstein, Cmelin, CAS Registry, and CASREACT. 

The Chemical Abstracts Service has institutionalized the use of graphic representations for identification of and retrieval of information about chemical compounds through their Graphical Data Stmcture (GDS) and connection table (CT). Two information packages. Messenger and STN Express, are the basis for this on-line retrieval system (42). 

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

Connectivity matrix and connection table. The most frequently used forms for representing chemical structures in the computer are the connectivity matrix (CM) and the connection table (CT). In the CM, the diagonal element cii is a chemical symbol of the i-th atoms, while the off-diagonal elements cjj represent bond orders... 

Fig. 4.2 The connectivity matrix (CM) (left) and the connection table (CT) (right) of the 3-amino cyclohexanone (middle).

All these formats are based on a connection table (CT from this comes the name CTFile formats) for description of a molecular structure and differ in their capabilities and purpose. Table 5.2 gives an overview of the most commonly found CTFile formats. 

The structures of the Beilstein compounds are stored in connection tables (CT s) to allow a very flexible structure and substructure search. Since most commercially available structure/substructure handling programs such as MACCS (MDL) or DARC (Telesystemes/Questel) work on the basis of CT s, the Beilstein Registry Connection Table (BRCT) can be easily adapted for in-house systems. 

CT block To represent chemical structure information in computer readable forms, many methods have been proposed (9-14). According to our general policy mentioned in the previous section we prefer a topological representation of structures in the form of a connection table (CT) rather than a linear notation. We... 

Acetyl peroxynitrate (18) and perfluoroacetyl peroxynitrate (19), two important atmospheric oxidation products of hydrocarbons (formation of 18) or chlorofluorocarbon replacements, such as CF3CH3 (formation of 19), preferentially adopt a gauche conformation (C—O—O—N = 84.7° for 18 and 85.8° for 19 electron diffraction). The two peroxides are characterized by comparatively short 0—0 bonds on one side and long 0°—N connectivities (Table 5) on the other. The observed O —N distances may be explained on the basis of an no ct od-n orbital overlap. This type of interaction lowers the 0°—N bond order and could explain the low bond dissociation energies of this connectivity in peroxides 18 and 19 (118 4 klmol for both compounds). It should be noted that this interpretation does not reflect a possible r-type interaction between a lone pair at 0° and virtual orbitals of the nitro group and therefore requires future investigation. 

It can be seen that a number of information in CM is redundant (each bond is listed twice) and that a large portion of matrix is empty (elements are equal to zero). This indicates the structure can be represented more economically with a table of constant width w. Such representation requires only wN instead of N variables. In the i-th row of the new representation w data associated with i-th atom (chemical symbol of the element, sequential numbers and bond types to its neighbors) are stored. Such representation is called the connection table of a chemical structure or CT (Fig. 4.2). 

CT-Generator. This part contains the main module for the generation of connection tables and virtual (device-independent) graphic coordinates. 

BEGIN CT Indicate beginning of connection table input block. 

The section of a GEMINI specification which specifies the actual connection table information must be delimited by begin—ct and end ct. This dehmits the repetitive structure specification block in formats which allow multiple connection tables in one file. 

CAS = Chemical Abstracts Service CSD = Cambridge Stmctural Database CT = connection table DBMS = database management system MDL = Molecular Design Ltd. RN = registration number, RTECS=Registry of Toxic Effects... 

CAS = Chemical Abstracts Service CT = connection table GFDB = Gmelin Factual Database ICSD = Inorganic Crystal Structure Database MF = molecular formula NIST = US National Institute of Standards and Technology STN = Scientific and Technological Network. 

CAS = Chemical Abstracts Service CT = connection table IDC = Internationale Dokumentationsgesellschaft fiir Chemie (International Documentation Society for Chemistry) 1ST = inorganic structure table ROSDAL = representation of structure description arranged linearly SDF = strucmre distribution file. 

BRCT = Beilstein Registry Connection Table BRN = Beilstein Registry Number CAS = Chemical Abstracts Service CNOC = Commission on the Nomenclature of Organic Chemistry CT = connection table ICRS = Index Chemicus Registry System ISI = Institute for Scientific Information RN = CAS Registry Number SCN = Structure Code Number SSSR = smallest set of smallest rings WLN = Wiswesser Line-formula Notation. 

Both tables, the atom and the bond lists, are linked through the atom indices. An alternative coimection table in the form of a redundant CT is shown in Figure 2-21. There, the first two columns give the index of an atom and the corresponding element symbol. The bond list is integrated into a tabular form in which the atoms are defined. Thus, the bond list extends the table behind the first two columns of the atom list. An atom can be bonded to several other atoms the atom with index 1 is connected to the atoms 2, 4, 5, and 6. These can also be written on one line. Then, a given row contains a focused atom in the atom list, followed by the indices of all the atoms to which this atom is bonded. Additionally, the bond orders are inserted directly following the atom in-... 

I,// 2 =//f = maximum resistance of the connecting leads from the CT terminals to the relay terminals. For calculating this, for an estimated length and size, refer to cable data in Table 13.15... 

In table 5.2, we list the maximal numbers of possible cycle states CotI Ct for OT and T rules, respectively, the total number of possible distinct state transition topologies (including trees), fd iGc), and the number of equivalence classes Q, for small N in T 2. The number of possible state transition topologies is evidently much smaller than the number of distinct connected topologies (= , [cvet79]). Note that the sets Cot and Ct are the same for even-N, while for odd-N, Cot is the same as Cot for N — 1) (since... 

Table 5.2 Number of topologically distinct connected graphs ) ), number of cyclic equivalence classes Q, maximal numbers of possible cycle sets Cot and Ct for OT and T rules, respectively, and the maximal number of possible distinct topologies of the state transition graph, calculated for graphs with size fV=5,6,..., 12 in T 2. ...

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