Representations notation

A nomenclature or notation is called unambiguous if it produces only one structure. However, the structure could be expressed in this nomenclature or notation by more than one representation, all producing the same structure. Moreover, uniqueness" demands that the transformation results in only one - unique -structure or nomenclature, respectively, in both directions. 

In Sections 2,.3.1-2.3.4, only the four most popular line notations, Wiswesser (WLN), ROSDAL. SMILES, and Sybyl (SEN), arc discussed. Whereas WLN is now almost obsolete, SMILES is quite an important representation and is widely used (Figure 2-7). 

The ROSDAL (Representation of Organic Structures Description Arranged Linearly) syntax was developed by S. Welford, J. Barnard, and M.F. Lynch in 1985 for the Beilstein Institute. This line notation was intended to transmit structural information between the user and the Beilstein DIALOG system (Beilstein-Ohlme) during database retrieval queries and structure displays. This exchange of structure information by the ROSDAL ASCII character string is very fast. 

The ROSDAL syntax is characterized by a simple coding of a chemical structure using alphanumeric symbols which can easily be learned by a chemist [14]. In the linear structure representation, each atom of the structure is arbitrarily assigned a unique number, except for the hydrogen atoms. Carbon atoms are shown in the notation only by digits. The other types of atoms carry, in addition, their atomic symbol. In order to describe the bonds between atoms, bond symbols are inserted between the atom numbers. Branches are marked and separated from the other parts of the code by commas [15, 16] (Figure 2-9). The ROSDAL linear notation is rmambiguous but not unique. 

Figure 2-52. a) Two semipolar resonance structures are needed in a correct VB representation of the nitro group, b) Representation of a nitro group by a structure having a pentavalent nitrogen atom, c) The RAMSES notation of a nitro group needs no charged resonance structures. One jr-system contains four electrons on three atoms. 

RAMSES is usually generated from molecular structures in a VB representation. The details of the connection table (localized charges, lone pairs, and bond orders) are kept within the model and are accessible for further processes. Bond orders are stored with the n-systems, while the number of free electrons is stored with the atoms. Upon modification oF a molecule (e.g., in systems dealing with reactions), the VB representation has to be generated in an adapted Form from the RAMSES notation. 

Conversion in both directions needs heuristic information about conjugation. It would therefore be more sensible to input molecules directly into the RAMSES notation. Ultimately, we hope that the chemist s perception of bonding will abandon the connection table representation of a single VB structure and switch to one accounting for the problems addressed in this section in a manner such as that laid down in the RAMSES model. 

Chemical structures can be transformed into a language for computer representation via line notations such as ROSDAL, SMILES, Sybyl. 

The problem of perception complete structures is related to the problem of their representation, for which the basic requirements are to represent as much as possible the functionality of the structure, to be unique, and to allow the restoration of the structure. Various approaches have been devised to this end. They comprise the use of molecular formulas, molecular weights, trade and/or trivial names, various line notations, registry numbers, constitutional diagrams 2D representations), atom coordinates (2D or 3D representations), topological indices, hash codes, and others (see Chapter 2). 

Figure 6-1. Different forms of representation of a chemical graph a) labeled (numbered) graph b) adjacency matrix c) connectivity table, type I d) connectivity table, type II f) line notations g) structural index.

The operators F eorresponding to all physieally measurable quantities are Hermitian this means that their matrix representations obey (see Appendix C for a deseription of the bra I > and kef < notation used below) ... 

Shorthand Notation for Electrochemical Cells Although Figure 11.5 provides a useful picture of an electrochemical cell, it does not provide a convenient representation. A more useful representation is a shorthand, or schematic, notation that uses symbols to indicate the different phases present in the electrochemical cell, as well as the composition of each phase. A vertical slash ( ) indicates a phase boundary where a potential develops, and a comma (,) separates species in the same phase, or two phases where no potential develops. Shorthand cell notations begin with the anode and continue to the cathode. The electrochemical cell in Figure 11.5, for example, is described in shorthand notation as... 

When viscometric measurements of ECH homopolymer fractions were obtained in benzene, the nonperturbed dimensions and the steric hindrance parameter were calculated (24). Erom experimental data collected on polymer solubiUty in 39 solvents and intrinsic viscosity measurements in 19 solvents, Hansen (30) model parameters, 5 and 5 could be deterrnined (24). The notation 5 symbolizes the dispersion forces or nonpolar interactions 5 a representation of the sum of 8 (polar interactions) and 8 (hydrogen bonding interactions). The homopolymer is soluble in solvents that have solubility parameters 6 > 7.9, 6 > 5.5, and 0.2 < <5.0 (31). SolubiUty was also determined using a method (32) in which 8 represents the solubiUty parameter... 

Point group symmetry, notation and representations, and the group theoretical condition for when an integral is zero. 

We propose, then, that chemical bonds can form if valence electrons can be shared by two atoms using partially filled orbitals. We need a shorthand notation which aids in the use of this rule. Such a shorthand notation is called a representation of the bonding. 

The proof takes different forms in different representations. Here we assume that quantum states are column vectors (or spinors ) iji, with n elements, and that the scalar product has the form ft ip. If ip were a Schrodinger function, J ftipdr would take the place of this matrix product, and in Dirac s theory of the electron, it would be replaced by J fttpdr, iji being a four-component spinor. But the work goes through as below with only formal changes. Use of the bra-ket notation (Chapter 8) would cover all these cases, but it obscures some of the detail we wish to exhibit here. 

Fig. 2.3a, b. Graphical representation of a the stable thickness of a lamella as a function of temperature T b The temperature above which a lamella of a given thickness would be unstable. Other notation in the Figure is defined in the text... 

These representations offer the advantage that one need not argue which of the reagents carries OH or Cl into the transition state. Since that is usually not known, this notation sidesteps the issue. From the Brpnsted-Debye-Huckel equation, we recognize that the concentration of each transition state (and therefore the reaction rate) will vary with ionic strength in proportion to the values of K for the given equation. For the first term we have... 

In solution, most simple sugars and many of their derivatives occur as equilibrium mixtures of tautomers. The presence of a mixture of two anomers of the same ring size may be indicated in the name by the notation a,P-, e.g. a,P-D-gIucose. In formulae, the same situation can be expressed by separating the representation of the ligands at the anomeric centre from the a and P bonds [see examples (a) and (c)], or by use of a wavy line [(b) and (d)] (particularly if hydrogen atoms are omitted). 

The variants are distinguished by the locants of those ring atoms that lie outside a reference plane (defined below) and are listed for some examples in Table 1. The locants of ring atoms that lie on the side of the reference plane from which numbering appears clockwise (i.e. the upper side in the normal Haworth representation of furanoses and pyranoses) are written as superscripts and precede the letter those that lie on the other side are written as subscripts and follow the letter. Heteroatoms (e.g. O, S) are indicated by their subscript or superscript atomic symbols. Table 1 gives the notations and Chart III some examples. 

Related to the students eomprehension of ehemieal reaetions, two basie problems were pointed out by the teaehers (1) students are not interested in learning beeause they pereeive ehemieal reaetions as isolated faets that are not related to everyday life and (2) students gain a weak understanding of ehemieal reaetions as they primarily experienee them as notations at the symbolic type, whieh are not effieiently related to their representations and understanding in the submicro and macro types. 

Some tasks in the Test of Gained Knowledge required students to connect observations about the macro course of chemical reactions with their notations in the submicro and/or symbolic types of representation. The results indicate that most students were able to rearticulate the information about reactants and products of a chemical reaction from the textual description of chemical reaction into the form of word chemical equation (textual description of macros word equation of macro Task 8.2, f(o/ )=89.82% Task 9.1, f(o/ )=87.61%). This action corresponds to the first step in learning to write down chemical equation in the LON approach. It can easily be explained, because teachers described the learning process to be very efficient to this point, as is illustrated below ... 

Students ability to connect observations at the macroscopic level with their descriptions using the submicro and symbolic types of representation improved as a consequence of the LON teaching approach. Teachers attributed the improvement to the consistent use of all three types of representation and to the use of visible models as a tool for bridging the gap between macroscopic observations and symbolic notations of chemical equations. 

---