Types of Fragments

In this section different types of fragments are classified with respect to their topology and the level of abstraction of molecular graphs. 

A tremendous number of various fragments are used in structure-property studies atoms, bonds, topological torsions , chains, cycles, atom- and bond-centered fragments, maximum common substructures, line notation (WLN and SMILES) fragments, atom pairs and topological multiplets, substituents and molecular frameworks, basic subgraphs, etc. Their detailed description is given below. 

Disconnected atoms represent the simplest type of fragments. They are used to assess a chemical or biological property P in the framework of an additive scheme based on atomic contributions  

Chemical bonds are another type of simple fragment. The first bond-based additive schemes, such as those of Zahn, Bernstein and Allen, appeared almost simultaneously with the atom-based ones and dealt, presumably, with predictions of some thermodynamic properties. 

MCASE) by Klopman NASAWIN by Baskin et al, BIBIGON by Kumskov, TRAIL and ISIDA by Solov ev and Varnek. Molecular pathways by Gakh and co-authors, and molecular walks by Riicker, represent chains of atoms. 

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This type of fragmentation is involved in the chain decomposition of alkyl hypochlor-... 

The numbers and types of fragments depend on the anthocyanin structure pattern. The aglycone (anthocyanidin) ordinarily is very stable and cannot be broken easily. In most cases, cleavage of the glycosidic groups will occur to generate small amounts of anthocyanidins in addition to the intact anthocyanin molecular ions. 

The type of interaction and its chemical influence are determined by phosphorus and boron coordination, by the type of the fragment separating them, and by molecular structure. Thus, it is reasonable to classify P,B-containing heterocycles according to the type of fragment separating phosphorus and boron. 

Perhaps of high interest to the hydrogenation chemist are the pertinent details of how gas-phase ions of organometallic catalysts are prepared. Of specific interest are the types of fragmentation events that can occur during the preparation of the gas phase ions, and what forms coordinatively unsaturated organometallic ions adopt in the gas phase. 

TABLE 6.2. Data for Calculation of Molecular Weights of Various Types of Fragment Ions... 

Before departing the topic of structural isomerism, we wish to point out that the key ideas presented here fit within a broad scheme of chemical reasoning. Thus, the combination of two different types of fragments, namely, two A and two B fragments to yield A2 plus B2 is less stable than the combination of the same fragments to yield 2 AB, the latter being superior because it involves a donor-acceptor pairing. 

Similarly, the combination of three different types of fragments, namely, A, B and two C fragments to yield AB plus C2 may be more or less stable than the combination of the same fragments to yield AC plus BC depending upon the donor-acceptor interrelationships. In all cases, however, the success of the approach is guaranteed only if matrix elements remain relatively constant. 

As pointed out, carbenium ions make up the largest portion of alkane mass spectra and dissociate further by alkene loss. This type of fragmentation is rather specific, nevertheless isomerizations of the carbenium ion can happen before. Generally, such processes will yield a more stable isomer, e.g., the tcrt-butyl ion instead of other [C4H9] isomers (Fig. 6.19). 

Note The McLafferty rearrangement and the RDA reaction have several features in common i) both belong to the rearrangement type of fragmentations, although the name conceals this fact in case of the latter, ii) both represent pathways for alkene loss from molecular ions, and iii) both are highly versatile in structure elucidation. 

Circular substructures of various sorts have been widely used for applications such as structure and substructure searching, constitutional symmetry, structure elucidation and the probabilistic modeling of bioactivity inter alia The work reported here demonstrates that this type of fragment is also very well suited to virtual screening using multiple reference structures. 

For many drug molecules this type of fragmentation dominates their mass spectra. 

More complex types of fragmentation involve rearrangement of the structure of a molecule prior to fragmentation and this is more likely to occur if the molecule has a ring in its structure. Figure 9.12 shows the El spectrum of cyclohexanol. 

Retro Diels-Alder fragmentation is another type of fragmentation which occurs in compounds with ring systems. 

A similar type of fragmentation dominates the spectrum of other local anaesthetics such as prilocaine and procaine and sympathomimetics such as ephedrine, salbutamol and terbutaline and P-adrenergic blockers such as propranolol and oxyprenolol. 

Cross-ring cleavage to form alkene and carbonyl fragments is the predominate type of fragmentation for oxetanes. The charge may reside on either fragment, as shown for oxetane (equation 1). 

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