Substructure indicators

Table A.l. Table of average bond lengths in organic compounds (T in column Substructure indicates that restrictions on -factor and reported e.s.d. s were removed to obtain these average values. The numbers in column Note refer to the entries in Thble A.4)...

Temperature-dependent NMR, COSY, and NOESY experiments of the constrained Leu(5)-enkephalin amide analogue 16 containing a ferrocene substructure indicate an intramolecular hydrogen bond between Fc(l)CO and Fc(4)NH, creating a yS-turn structure [72]. The rotational barrier... 

For the classification of larger data sets, more general group-contribution models have been derived on the basis of substructure indicators, which may... 

Similar relationships have also been derived with other descriptors that are generally collinear with log for non-polar non-specific toxicants for example, water solubility (Konemann, 1981b Zaroogian et al., 1985), topological indices (Basak and Magnuson, 1983 Koch, 1983 Sabljic, 1983), or with substructure indicators (Hall, Maynard and Kier, 1989), which may be applied if the log P of the test compounds cannot be estimated, and also to cross-check the predictions obtained, especially when there is reasonable doubt about the correctness of the respective log P values. 

Nendza, M. Muller, M. 2007. Discriminating toxicant classes by mode of action 3. Substructure indicators. SAR and QSAR in Environmental Research, Vol. 18, No 1-2,... 

Besides specifications on atoms, bonds, branches, and ring closure, SLN additionally provides information on attributes of atoms and bonds, such as charge or stereochemistry. These are also indicated in square [ ] or angle < > brackets behind the entity e.g., trans-butane CH3CH=[s=t]CHCH3). Furthermore, macro atoms allow the shorthand specification of groups of atoms such as amino adds, e.g., Ala, Protein2, etc. A detailed description of these specifications and also specifications for 2D substructure queries or combinatorial libraries can be found in the literature [26]. 

Figure 2-65. This fingerprint was received by hashing, whereas only one part of all the substructures is specified in the illustration. The asterisk indicates the address of a collision in the bit string, generated by the algorithm.

A substructure search algorithm is usually the first step in the implementation of other important topological procedures for the analysis of chemical structures such as identification of equivalent atoms, determination of maximal common substructure, ring detection, calculation of topological indices, etc. 

Figure 10.3-38. An Indication of other speclRcatlon elements for a substructure query, For both the atom specifications and the bond specifications a vast list of attributes can be set (aromatic/ not aromatic, member of ring with n atoms, substituted, etc.).

Figure 10.3-54. Derivation of a reaction substructure search query. The a" for atom 1 and 8 indicates that these atoms have to be aromatic in the found reactions.

Database searches can be used to find a reference to a known compound with a matching substructure. This is a particularly good technique if a portion of the molecule has an unusual structure. It may indicate a synthesis route or simply identify a likely starting material. 

The force fields available are MM2, MM3, AMBER, OPLSA, AMBER94, and MMFF. The asterisk ( ) indicates force fields that use a modification of the original description in the literature. There is support for user-defined metal atoms, but not many metals are predefined. MM2 has atom types for describing transition structures. The user can designate a substructure for energy computation. 

As indicated in Chapter 11, the base pairing in DNA is very specific the purine adenine pairs with the pyrimidine thymine the purine guanine pairs with the pyrimidine cytosine. Further, the A T pair and G C pair have virtually identical dimensions (Figure 12.10). Watson and Crick realized that units of such similarity could serve as spatially invariant substructures to build a polymer whose exterior dimensions would be uniform along its length, regardless of the sequence of bases. 

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