Atom list

There are many ways of presenting a connection table. One is first to label each atom of a molecule arbitrarily and to arrange them in an atom list (Figure 2-20). Then the bond information is stored in a second table with indices of the atoms that are connected by a bond. Additionally, the bond order of the corresponding coimection is stored as an integer code (1 = single bond, 2 = double bond, etc.) in the third column. 

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-... 

In order to allow any multiple chlorination of the biphenyl skeleton, the user may define an atom list (eonsisting of hydrogen and chlorine atoms) and substitute all H-atoms by this list. One may click on the drop-down selection box behind the element icons, select the options Generics. .set the user-defined atom to A1 and quit by the OK button. As a result this atom selection is active for the subsequent drawing steps. After this atom list is drawn ten times as the ten substituents, its composition has to be defined by clicking the A, icon on the left-hand side of the structure editor and by selecting H and Cl in the periodic table (Figure 5-16). 

Figure 5-16. Structure editor of the CrossFire ComiTiander V6, showing the definition ofan atom list (consisting of hydrogen and chlorine atoms) for polychlorinated biphenyls.

An alternative to retrieval by means of an atom list is a structure search performed by means of a user-defined generic group which contains only chlorine... 

Substructure searches provide another method of searching for available starting materials. They arc used primarily for planning the synthesis of combinatorial libraries. After the target compound has been dissected into a set of suitable precursors, substructure searches can provide for each of them a series of representatives of a certain class of compounds, Siibsti ucturc searches enable the user to specify attributes such as open sites or atom lists at certain positions of the structure. Figure 10.3-38 shows the possible specification elements for the query in a substructure search. 

Note that the strict foiiriat of the ethylene output file was not followed in adding new atoms. Be careful of your connected atom list to the right of the input file it is a rich source of potential errors. Use your graph to keep the numbering straight. 

Up to this point, we have used a numerical input file to stress the fact that computers work on numbers, not diagrams, MM3 and TINKER work from numerical input files that are similar but not identical. Both can be adapted to wo rk u n de r th e c om m an d o f a g ra p h i c al w se r i n terface, G UI (p ro n o u n c ed g oo ey , Before going into more detail concerning MM, we shall solve a geometry optimization using the GUT of PCMODEL (Serena Sortware). The input is constructed by using a mouse to point and click on each atom of the connected atom list or skeleton of the molecule. This yields Fig. 4-6 (top). 

Table 7.1 Ground configurations and ground states of atoms, listed in increasing order of atomic number Z, and their first ionization energies, E...

Note that the inner carbon atoms are the first two atoms listed for each compound. The predicted NMR shielding values will appear in the output in the same order as the atoms are listed in the molecule specification section. 

The center numbers for the atoms of interest. Gaussian s numbering scheme assigns each atom the number corresponding to its input line within the molecule specification section, where the charge and multiplicity line is line 0. Thus, the first atom listed is center number 1, and so on. 

Histamine, whose release in the body triggers nasal secretions and constricted airways, has three nitrogen atoms. List them in order of increasing basicity, and explain your ordering. 

To place this argument in perspective assume that both trans and cis adducts were equally likely. Then stereoselectivity would not be observed. All of the adducts to base atoms listed in Table XII for trans addition correspond to the sterically forbidden possibilities for cis addition and vice versa. Therefore, l(+) and i(-) isomers would bind equally well to N2(g). This does not occur. Rather the favored Sjj2 reaction over the Sjjl reaction weights trans addition heavily. Therefore, in our interpretation of experimental yields, the smaller yield of i(-) with N2(G) is predicted to be a cis addition product. The argument can be extended to demonstrate that trans l(-)-N6(A) and 06(G) and cis l(+)-N6(A) and 06(G) adducts should be expected. 

Note The values in this table represent average values for the dissociation of bonds between the pairs of atoms listed. The true values may vary for different molecules. 

To facilitate discussion of these somewhat more complicated fullerenes with one or more atoms inside the cage, a special symbolism and nomenclature was introduced [66]. Thereby the symbol is used to indicate the atoms in the interior of the fullerene. All atoms listed to the left of the symbol are located inside the cage and all atoms to the right are a part of the cage structure, which includes heterofullerenes, e.g. C59B. A Cgg-caged metal species is then written as M Cgg, expanded as metal at Cgg . The corresponding lUPAC nomenclature is different from the conventional M C representation. lUPAC recommend that M C be called [rt]fuUerene-incar-lanthanum and should be written iMC [4]. 

Atomic mass The mass of an element s atoms listed in the periodic table as an average value based on the relative abundance of the elements isotopes. 

The atoms listed in this section may combine with many metals to form binary compounds (compounds made up of two elements) that are saltlike in nature, but are not derived from acids. For purposes of naming, it is convenient to assign negative charges to these atoms. Except in the names of the oxides, the suffixes -ous and -ic are not used with metals forming compounds in this group. The names of all these compounds end in -ide. Only the metal oxides of this... 

Central atoms in noncaged polynuclear structures are numbered from one end along the path containing the greatest number of central atoms to the remote end. The number one terminal central atom is chosen first, by the priorities of the central atoms listed in Table 17, the highest priority... 

If you don t recognize which is the acid and which is the base, the base almost always has a lower (more negative) charge than the acid. Also, hydrogen is almost always the first atom listed in the formula of an acid. 

Write Lewis structures that obey the octet rule for each of the following. Except for HCN and H2CO, the first atom listed is. the central atom. For HCN and H2CO, carbon is the central atom. 

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