Symbolic representation structure elements

Electron dot formulas are useful for deducing the structures of organic molecules, but it is more convenient to use simpler representations—structural or graphic formulas—in which a line is used to denote a shared pair of electrons. Because each pair of electrons shared between two atoms is equivalent to a total bond order of 1, each shared pair can be represented by a line between the symbols of the elements. Unshared electrons on the atoms are usually not shown in this kind of representation. The resulting representations of molecules are called graphic formulas or structural formulas. The structural formulas for the compounds (a) to (e) described in Example 21.1 may be written as follows ... 

From this description, however, alternative (and/or complementary) presentations of the structure and different symbolic representations can be deduced. These are often differently defined for specific groups of compounds and may be useful to obtain a clearer view of the atomic assembly and/or to make an easier comparison between different compounds. In other words it must be underlined that there is no ideal way of describing all structure types. The most appropriate way of description depends on the structure itself but also on a number of points we are interested in emphasizing (comparison with other structural types, comparison with other compounds of the same element, etc.). These points will be discussed in a few subsequent sections after the presentation of the conventional description. 

Figure 23 The overall structure of the (GlyProPro)io foldon (PDB accession number 1 NAY). The symmetry axis and symmetry elements are shown by a line and symbolic representations, respectively. The backbones of different chains are shown in red, blue, and green. The figure was generated using the UCSF Chimera package. ...

Protein topology cartoons (TOPS) are two-dimensional schematic representations of protein structures as a sequence of secondary structure elements in space and direction (Flores et al, 1994 Sternberg and Thornton, 1977). The TOPS of trypsin domains as exemplified in Figure 4.9 have the following symbolisms ... 

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). 

Lewis structure a symbolic representation of the arrangement of the valence electrons of an element (2.2)... 

The Lewis theory readily allows the graphic representation of molecular structures. Since, in general, only the valence electrons are involved in bonds, electrons of inner shells need not be depicted. The symbol of the element represents the atom without its outermost shell of electrons this part of the atom is known as the kernel. The electrons are shown as dots about the symbols, those electrons that are shared as bonds being placed between the appropriate symbols, the others around the symbol of the atom to which they belong. Electrons that are paired are placed close to each other. Thus the... 

The valence electrons in the outermost energy level of an atom are responsible for the electron activity that occurs to form chemical bonds. The Lewis structure of an atom is a representation that shows the valence electrons for that atom. American chemist Gilbert N. Lewis (1875-1946) proposed using the symbol for the element and dots for electrons. The number of dots placed around the symbol equals the number of s and p electrons in the outermost energy level of the atom. Paired dots represent paired electrons unpaired dots represent unpaired electrons. For example, H" is the Lewis symbol for a hydrogen atom, Is B is the Lewis symbol for a boron atom, with valence electrons 2s 2p In the case of boron, the symbol B represents the boron nucleus and the Is electrons the dots represent only the 2s 2p electrons. 

To show the outermost electrons of an atom, we commonly use a representation called a Lewis structure, after the American chemist Gilbert N. Lewis (1875-1946), who devised this notation. A Lewis structure shows the symbol of the element, surrounded by a number of dots equal to the number of electrons in the outer shell of an atom of that element. In Lewis structures, the atomic symbol represents the nucleus and all filled inner shells. Table 1.3 shows Lewis structures for the first 18 elements of the Periodic Table. As you study the entries in the table, note that, with the exception of helium, the number of valence electrons of the element corresponds to the group number of the element in the Periodic Table for example, oxygen, with six valence electrons, is in Group 6A. 

A simplified way to represent the valence-shell electrons of atoms was invented by G. N. Lewis. In these representations, called electron-dot formulas or Lewis structures, the symbol for an element represents the nucleus and all electrons around the nucleus except those in the valence shell. Valence-shell electrons are shown as dots around the symbol. Thus, rubidium is represented as Rb-. 

Note that a vacancy is denoted by the symbol V. In view of the possibility of confusion with the representation of vanadium, which has the same symbol, the lUPAC advocates that, where structure elements are involved, the symbol for vanadium is replaced by Va . 

Expression (3) means that if a molecule contains group A, then the set of frequencies u , lUj, will occur in the spectrum. Indeed, the expression (3) is a symbolic representation of the fact that the vibrations are characteristic for the Ai group. According to expression (3), the presence of the frequencies in, in,. ..inj, is a necessary condition for the molecule to contain the structural group A,. Expression (4), equivalent to expression (3). shows that the sufficient condition for the absence of a structural element in the molecule under investigation is that the spectrum should not contain at least one of the characteristic frequencies of this group. 

Valence electrons When elements combine chemically, only the electrons in the highest principal energy level of each atom are involved. Therefore, these outermost electrons, called valence electrons, determine most of the chemical properties of an element. Later in your chemistry course, you will study the way in which elements form chemical bonds. Because bonding involves an atom s valence electrons, it is useful to be able to sketch a representation of an element s valence electrons. The American chemist G. N. Lewis devised the electron-dot structure to show an atom s valence electrons by writing dots around the symbol of the element. 

A methyl group may be shown in a structural representation as CH3 or Me, and similar pseudo-elemental symbols are used for ethyl, propyl and butyl side chains. It is cortrmon to represent a phenyl group as either Ph or as a hexagon with a circle irtscribed within it. This circle is meant to represent electron density that lies above and beneath the main plane of the molecule. However, when faced with... 

FIGURE 60 Formulas of organic substances. The molecular formula of an organic substance conveys information about the nature of the component elements (expressed by symbols) and the number of atoms of each element that make up a molecule of the substance if greater than one, the number of atoms of each element is indicated by a subscript. The structural formula provides a two-dimensional representation of the arrangement of the atoms in the molecule, showing how they are attached to one another and the type of bonds involved. 

A single unstable compound of known composition is placed in the main first volume and is located on the basis of its empirical molecular formula expressed in the Hill system used by Chemical Abstracts (C and H if present, then all other element symbols alphabetically). The use of this indexing basis permits a compound to be located if its structure can be drawn, irrespective of whether a valid name is known for it. A representation of the structure of each compound is given on the third bold title line while the name of the compound appears as the first bold title line. References to the information source are given, followed by a statement of the observed hazard, with any relevant explanation. Cross-reference to similar compounds, often in a group entry, completes the entry. See Trifluoroacetyl nitrite p. 244. 

Understanding chemistry requires above all a knowledge of the language used. The preceding section introduced one of the basic shorthand systems used in chemistry the use of a symbol, usually one or two letters, to denote the elements. Symbols can be used in text as synonyms for the element, in discussion of nuclear structure as representation of a single atom of the element, or in equations as a fixed measure (such as the mole - see Section 2.3... 

These orbital pictures tend to get a little confusing, in that we really need to put in the elemental symbol to distinguish it from carbon, and we usually wish to show the lone pair electrons. We accordingly use a compromise representation that employs the cleaner line drawings for part of the structure and shows the all-important orbital with its lone pair of electrons. These are duly shown for ammonia and water. 

NE OF THE CENTRAL THEMES of this book is to show how the development of the concept of neutral salt in the eighteenth century made possible the creation of a compositional nomenclature by L.-B. Guyton de Morveau in 1782, which when adapted to the new chemistry of Lavoisier led to the creation of a definition of simple body the material element. The second major theme then describes how this new chemistry led to the final development of modern chemical composition in its atomic structure introduced by John Dalton. His atomic theory contained the symbolic operators that furnished the most convenient representation of the material composition of bodies that had become available by the end of the eighteenth century. The idea of an individual atomic weight unique to each element depended most immediately upon the concept of simple body, introduced by the authors of the M thode de nomenclature chimique in 1787. The new nomenclature was itself based on the principle that a name of a body ought to correspond to its composition. 

Before looking at molecules, we need to review the structure of atoms. Most of the mass of an atom is concentrated in the nucleus. The nucleus consists of protons, which are positively charged, and neutrons, which are neutral. To counterbalance the charge on the nucleus due to the positive protons, the atom has an equal number of negative electrons in shells or orbitals around the nucleus. Because the electrons in the outermost electron shell (the valence electrons) control how the atom bonds, atoms are often represented by their respective atomic symbol surrounded by dots representing the outer-shell electrons. Such representations for some of the elements of interest to us are shown in Figure 1.1. The number of electrons in the valence shell of an atom is the same as the group number of that atom in the periodic table. 

DENDRAL suite is similar to a connection table. Each structure receives an atom list. The first line contains an identifier (Cl), the element symbol (C), and a sequential number (1). Following is a list of nonhydrogen bond partners represented by their atom numbers (2, 3, 7), the number of multiple bonds (1) attached to the atom, and the number of hydrogen atoms (0). (b) The matrix representation of residues in the PREDICTOR system of the DENDRAL. The example show a phenyl residue including in the first line an identifier, the element symbol, and a sequential number, similar to the example in Figure 6.1a. The list of nonhydrogen bond partners represented by their atom numbers (2, x, 7), indicates two known partners and one unknown the number of hydrogen atoms is indicated as unknown (-). 

Lewis structure A representation of a molecule that consists of the elemental symbol for each atom in the molecule, lines to show covalent bonds, and pairs of dots to indicate lone pairs. 

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