Molecular structures classification

Murzin A G, S E Brenner, T Hubbard and C Chothia 1995. SCOP A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247 536-540. 

In the last section we examined some of the categories into which polymers can be classified. Various aspects of molecular structure were used as the basis for classification in that section. Next we shall consider the chemical reactions that produce the molecules as a basis for classification. The objective of this discussion is simply to provide some orientation and to introduce some typical polymers. For this purpose a number of polymers may be classified as either addition or condensation polymers. Each of these classes of polymers are discussed in detail in Part II of this book, specifically Chaps. 5 and 6 for condensation and addition, respectively. Even though these categories are based on the reactions which produce the polymers, it should not be inferred that only two types of polymerization reactions exist. We have to start somewhere, and these two important categories are the usual place to begin. 

Structural classifications of oxides recognize discrete molecular species and structures which are polymeric in one or more dimensions leading to chains, layers, and ultimately, to three-dimensional networks. Some typical examples are in Table 14.14 structural details are given elsewhere under each individual element. The type of structure adopted in any particular case depends (obviously) not only on the... 

Bush K, Jacoby GA, Medeiros AA (1995) A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Che-mother 39 1211-1233... 

More than 50 proteins have been discovered in the cytosol of nonmuscle cells that bind to actin and affect the assembly and disassembly of actin filaments or the cross-linking of actin filaments with each other, with other filamentous components of the cytoskeleton, or with the plasma membrane. Collectively, these are known as actin-binding proteins (ABPs). Their mechanisms of actions are complex and are subject to regulation by specific binding affinities to actin and other molecules, cooperation or competition with other ABPs, local changes in the concentrations of ions in the cytosol, and physical forces (Way and Weeds, 1990). Classifications of ABPs have been proposed that are based on their site of binding to actin and on their molecular structure and function (Pollard and Cooper, 1986 Herrmann, 1989 Pollard et al., 1994). These include the following ... 

In the original kNN method, an unknown object (molecule) is classified according to the majority of the class memberships of its K nearest neighbors in the training set (Fig. 13.4). The nearness is measured by an appropriate distance metric (a molecular similarity measure as applied to the classification of molecular structures). It is implemented simply as follows ... 

Ihlenfeldt, W. D., Gasteiger,). Hash codes for the identification and classification of molecular structure elements. ]. Comput. Chem. 1994, 15, 793-813. 

ChemIDplus. Published by the U.S. National Library of Medicine, ChemIDplus [62] is a web-based search system, http //chem.sis.nlm.nih.gov/ chemidplus/, that provides free access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. ChemIDplus also provides structure searching and direct links to biomedical resources at NLM and on the Internet. The database contains over 349,000 chemical records, over 56,000 of which include chemical structures, and is searchable by name, synonym, CAS registry number, molecular formula, classification code, locator code, and structure. 

It should be noted that the above classification system of technetium cluster compounds is not the only possible one. In section 4 another classification is described, which is based on thermal stability and the mechanism of thermal decomposition. Section 2.2 is concerned with the classification based on methods of synthesizing cluster compounds. The classifications based on specific properties of clusters do not at all belittle the advantages of the basic structural classification they broaden the field of application of the latter, because for a better understanding and explanation of any chemical, physico-chemical and physical properties it is necessary to deal directly or indirectly with the molecular and/or electronic structures of the clusters. 

A structural classification of 8 is difficult due to the fact that an arrangement of metal atoms as in 8 is uncommon in the whole field of molecular metal clusters. For this reason, detailed understanding of the bonding properties in 8 requires quantum chemical calculations. Theoretical analysis seems to be especially applicable to learning more about the bond between the two tetrahedra, which appears at first to be an isolated metal-metal bond between two metal atoms in the formal oxidation state zero. 

It must be emphasized that the duodectet rule (4.6) initially has no structural connotation, but is based on composition only. Indeed, the compositional regularity expressed by (4.6) encompasses both molecular species (such as the metal alkyls) and extended lattices (such as the oxides and halides) and therefore appears to transcend important structural classifications. Nevertheless, we expect (following Lewis) that such a rule of 12 may be associated with specific electronic configurations, bond connectivities, and geometrical propensities (perhaps quite different from those of octet-rule-conforming main-group atoms) that provide a useful qualitative model of the chemical and structural properties of transition metals. 

From this information, general principles for the design of spherical molecular hosts have been developed. [11] These principles rely on the use of convex uniform polyhedra as models for spheroid design. To demonstrate the usefulness of this approach, structural classification of organic, inorganic, and biological hosts - frameworks which can be rationally compared on the basis of symmetry - has revealed an interplay between symmetry, structure, and function. [53]... 

K. Bush, G. A. Jacoby, A. A. Medeiros, A Functional Classification Scheme for /LLactamases and Its Correlation with Molecular Structure , Antimicrob. Agents Chemother. 1995, 39, 1211-1233. 

Hash codes for the identification and classification of molecular structure... 

Prediction of bioavailability from molecular structure is quite difficult, since bioavailability depends on absorption and first-pass clearance [141]. By applying fuzzy adaptive least squares , Yoshida and Topliss generated a QSAR model using logD at pH 7.4 and 6.5 as input for physicochemical properties and the presence/absence of certain functional groups as structural input. They achieved a classification of drugs into one of four bioavailability categories with an overall accuracy of 60% [142]. 

Naumann, T. and Matter, H. (2002) Structural classification of protein kinases using 3d molecular interaction field analysis of their ligand binding sites Target family landscapes../. Med. Chem. 45, 2366-2378. 

Chemical classifications of petroleums relate to the molecular structures of the molecules in the oil. Of course the smaller molecules, six carbon atoms and less, are predominately paraffins. So chemical classification is usually based on analysis of the petroleum after most of the light molecules are removed. 

Terms such as paraffinic, naphthenic, naphthenic-aromatic, and aromatic-asphaltic are used in the several classification methods which have been proposed. These terms obviously relate to the molecular structure of the chemical species most prominent in the crude oil mixture. However, such classification is made difficult because the large molecules usually consist of condensed aromatic and naphthenic rings with paraffinic side chains. The characteristic properties of the molecules depend on the proportions of these structures. 

Within each series of the Handbook the entries are ordered using the Beilstein System of Compound Classification this is a set of rules which enables each organic compound to be assigned a position within the Handbook solely on the basis of its molecular structure conversely, knowledge of the rules enables any compound from the c. 1 million compounds already described in the Handbook to be found rapidly, purely on the basis of its structure. A further advantage of the system is that many structurally related compounds are brought together within the same volume of the Handbook. 

Atwood, J. L., MacGillivray, L. R., Structural classification and general principles for the design of spherical molecular hosts , Angew. Chem. Lit. Ed. 1999, 38, 1018-1033. 

Figure 12.2. Model for molecular structures of black carbon (BC), elemental carbon (EC), and organic carbon (OC) and respective optical and thermochemical classification according to Poschl (2005).

We report an electron spin resonance (ESR) study on a C60 anion and a metal (M) encapsulated in fullerene (C ) (a metallofullerene M C ). The anisotropy components of the g-factor of Cg0 were determined accurately from the analysis of angular-dependent ESR spectra of single crystal Cg0 salt. The evaluation of the g-factor was performed according to the classification of symmetry of the C60 geometry. It was found out from the evaluation that the molecular structure of Cg0 should he distorted to lower symmetry, C2h or C,. The variety of ESR spectra of metallofullerenes of La C s was obtained in terms of a g-factor, a hyperfine coupling constant, and a line width. In the case of the isomer I of La C80 and the isomer II of La C84, an abnormally large line width was measured. The molecular structure with high symmetry would reflect on the specific spin dynamics. 

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