Hydrogen-suppressed molecular graph

SMILES is based on the concept of hydrogen-suppressed molecular graphs (HSMG). The following example shows three representations of 1-butanol ... 

D structures of drugs were converted into hydrogen-suppressed molecular graphs, where nodes are labeled with atom types except hydrogens and edges are labeled with bond types. 

Labeled Hydrogen-Suppressed molecular Graph = H-depleted molecular graph molecular graph... 

Figure 2 Two hydrogen-suppressed molecular graphs with corresponding adjacency matrices and connectivity stacks.

Hydrogen suppressed molecular graph of adamantane defined by the list of vertices and the list of edges ... 

Figure 16. Some topologically chiral molecular graphs, (a) The Simmons-Paquette molecule.74 (b) Walba s 3-rung Mobius ladder molecule.75 (c) [4](l,l )[4](3,3 )[3](4 4 )-Ferrocenophan-16-one.76 (d) Triple-layered naphthalenophane.78 Unlabeled vertices represent carbon atoms, and hydrogen atoms are suppressed for clarity. Only one enantiomer of each molecule is shown.

Propane Molecular graph Hydrogen-suppressed graph... 

The approach used in chemical graph theory is to abstract from the molecular structure those elements that lead to structure variables in the form of numerical indexes. The set of atoms and connections is viewed as structure information but in a form not amenable directly to QSAR analysis. The first step is to adopt a form for the molecular skeleton as the basis for extraction of structure information. To represent the molecular skeleton, the hydrogen-suppressed graph is most commonly used hydrogen atoms are not explicitly considered hydrogen atoms are incorporated in skeletal groups which are the graph vertexes. 

Figure 1 The relationship between molecular formulas and the corresponding hydrogen-suppressed graphs.

The identifying characteristics of atoms include atomic number and number of electrons partitioned between valence electrons and core electrons. The immediate bonding environment of atoms in the molecular skeleton depends on the number and arrangement of the valence electrons and the number and type of bonds. In most graph theoretical methods, a hydrogen-suppressed skeleton is used to facilitate the counting and enumeration of skeletal features. 

With these considerations as a general background, let us summarize our approach. In the molecular connectivity approach, the molecule is represented by the hydrogen-suppressed graph. The key feature in the quantitation of the graph is the characterization of the atom in the molecular skeleton. The molecular connectivity method explicitly introduces the electronic character of atoms into the graphic representation of molecules. Atom identity is specified through the molecular connectivity delta values the simple delta, 6, and the valence delta,... 

One feature of most topological descriptors, including molecular connectivity indices, is the possibility of generating many different descriptors for the same molecule. The calculation of simple molecular coimectivity indices serves to illustrate this possibiHty. Figure 1 shows the hydrogen-suppressed graph for pentan-3-ol. 

Thus, there are four basic representation of the molecular structure which can be used as basis to build up the optimal descriptors (Fig. 12.3) (i) hydrogen suppressed graph (ii) hydrogen hlled graph (iii) GAO and (iv) SMILES. These representations also can be involved into hybrid version of the optimal descriptor where molecular features extracted from e.g. GAO and SMILES play the role of hybrid basis for a QSPR/QSAR predictions [27-32]. 

In the Daylight software the 2-D chemical structure of a molecule is represented by a SMILES (Simplified Molecular Input Line Entry System) string derived from the hydrogen-suppressed graph of the molecule . The MODSMI operations, the subject of this report, essentially involve ... 

To distinguish heteroatoms Kier and Hall considered a modification of the connectivity indices that formally alters the valence 5, of the atoms in a molecule. They viewed the i values as the difference between the number of valence electrons Z and the number of hydrogen atoms hi (which are usually suppressed in molecular graphs) ... 

Figure 23. The example of obtaining the values of the Wiener index for hypergraph and graph representations of the molecular structure with three-electron ligands hydrogens are suppressed in these representations...

Two graphs of molecular structure are shown in Figure 3. Consider the (1,4) bond in Figure 3a. The value of 1 for the terminal atom denotes a structure formed from a carbon atom and from three hydrogen atoms (suppressed in the skeleton structure). The structure of the atom with an adjacency of 4 makes a smaller contribution to the overall structure, since there are no hydrogen atoms attached. The structural contribution comes from the extension of the molecule in all directions around this atom. 

---