Representations of molecules

The representation of molecules by molecular surface properties was introduced in Section 2.10. Different properties such as the electrostatic potential, hydrogen bonding potential, or hydrophobicity potential can be mapped to this surface and seiwe for shape analysis [44] or the calculation of surface autocorrelation vectors (refer to Section 8.4.2). 

Computer Representations of Molecules, Chemical Databases and 2D Substructure Searching... 

In formulating a mathematical representation of molecules, it is necessary to define a reference system that is defined as having zero energy. This zero of energy is different from one approximation to the next. For ah initio or density functional theory (DFT) methods, which model all the electrons in a system, zero energy corresponds to having all nuclei and electrons at an infinite distance from one another. Most semiempirical methods use a valence energy that cor-... 

A simpler representation of molecules containing asymmetric carbon atoms is the Fischer projection, which is shown here for the same lactic acid configurations. A Fischer projection involves... 

An important approach to the graphic representation of molecules is the use of a connection table. A connection table is a data base that stores the available bond types and hybridizations for individual atoms. Using the chemical formula and the connection table, molecular stmctures may be generated through interactive graphics in a menu-driven environment (31—33) or by using a linear input of code words (34,35). The connection table approach may be carried to the next step, computer-aided molecular design (CAMD) (36). 

All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves. These are difficult to illustrate. Therefore we use different types of simplified representations, including space-filling models ball-and-stick models, where atoms are spheres and bonds are sticks and models that illustrate surface properties. The most detailed representation is the ball-and-stick model. However, a model of a protein structure where all atoms are displayed is confusing because of the sheer amount of information present (Figure 2.9a). 

Figure 3.6. Two-dimensional representation of molecules in a crystalline polymer according to the fringed micelle theory showing ordered regions (crystallites) embedded in an amorphous matrix.

The next most important aspect of a molecular compound is its shape. The pictorial representations of molecules that most accurately show their shapes are images based on computation or software that represents atoms by spheres of various sizes. An example is the space-filling model of an ethanol molecule shown in Fig. C.2a. The atoms are represented by colored spheres (they are not the actual colors of the atoms) that fit into one another. Another representation of the same molecule, called a ball-and-stick model, is shown in Fig. C.2b. Each ball represents the location of an atom, and the sticks represent the bonds. Although this kind of model does not represent the actual molecular shape as well as a space-filling model does, it shows bond lengths and angles more clearly. It is also easier to draw and interpret. 

Electron dot formulas are useful for deducing the structures of organic molecules, but it is more convenient to use simpler representations—structural or graphic formulas—in which a line is used to denote a shared pair of electrons. Because each pair of electrons shared between two atoms is equivalent to a total bond order of 1, each shared pair can be represented by a line between the symbols of the elements. Unshared electrons on the atoms are usually not shown in this kind of representation. The resulting representations of molecules are called graphic formulas or structural formulas. The structural formulas for the compounds (a) to (e) described in Example 21.1 may be written as follows ... 

Figure 2 Schematic representation of molecules examined in the text. The site of deprotonation is denoted by asterisks.

Before continuing with the discussion of how reactions are represented in EROS, it is more sensible to describe in outline some of the formal features associated with the representation of molecules. 

Another group has evaluated self-organizing maps [63] and shape/ pharmacophore models [64]. They developed a new method termed SQUIRREL to compare molecules in terms of both shape and pharmacophore points. Thus from a commercial library of 199,272 compounds, 1926 were selected based on self-organizing maps trained on peroxisome proliferator-activated receptor a (PPARa) "activity islands." The compounds were further evaluated with SQUIRREL and 7 out of 21 molecules selected were found to be active in PPARa. Furthermore, a new virtual screening technique (PhAST) was developed based on representation of molecules as text strings that describe their pharmacophores [65]. 

Lewis formulas are representations of molecules or ions which show... 

A molecule of methane contains just five atoms one of carbon and four of hydrogen. In chemical representations of molecules, each element is identified by a symbol. Carbon is represented by the symbol C hydrogen is represented by the symbol H. Thus, the molecular formula for methane is CH4. This representation, or model, tells us just one simple fact the methane molecule contains one carbon and four hydrogen atoms. ... 

XuE, L, Godden, J., and Bajorath, J. Database searching for compounds with similar biological activity using short binary bit string representations of molecules./. Chem. Inf. Comput. Sci. 1999, 39(5), 881-886. 

Chemoinformatics refers to the systems and scientific methods used to store, retrieve, and analyze the immense amount of molecular data that are generated in modern drug-discovery efforts. In general, these data fall into one of four categories structural, numerical, annotation/text, and graphical. However, it is fair to say that the molecular structure data are the most unique aspect that differentiate chemoinformatics from other database applications (1). Molecular structure refers to the 1-, 2-, or 3-D representations of molecules. Examples of numerical data include biological activity, p/C, log/5, or analytical results, to name a few. Annotation includes information such as experimental notes that are associated with a structure or data point. Finally, any structure... 

Recall the mutual exclusion rule stated in Section 6.7. The rule follows from the fact that the integral over all space of an odd ( ) function is zero. The functions x, y, and z belong to u representations of molecules with a center of symmetry, since inversion converts each to its negative. Hence one of the functions vjb and ib must belong to a g representation and one to a u representation if the integrand of (9.189) is not to be odd. Thus only g<->u IR transitions are allowed in molecules with a center of symmetry. In contrast, the functions (9.196) are all even (g), so that for centrosymmetric molecules only g<->g and u u Raman transitions are allowed. This proves the mutual exclusion rule. 

Furthermore, when modern tools for determining organic structures that involve actually measuring the distances between the atoms became available, these provided great convenience, but no great surprises. To be sure, a few structures turned out to be incorrect because they were based on faulty or inadequate experimental evidence. But, on the whole, the modern three-dimensional representations of molecules that accord with actual measurements of bond distances and angles are in no important respect different from the widely used three-dimensional ball-and-stick models of organic molecules, and these, in essentially their present form, date from at least as far back as E. Paterno, in 1869. 

Structural formulae are representations of molecules on paper. The MCAT may use any or all of the various formulae so you should be familiar with all of them. The most basic form of structural formula is tire Lewis dot structure. 

Almost simultaneous with the publication of Kossel s paper there appeared a rival electronic theory. The American chemist Lewis introduced the idea of the covalent electron-pair bond. Like Kossel, he was impressed by the apparent stability of the noble gas configuration. He was also impressed by the fact that, apart from many compounds of the transition elements, most compounds when rendered as molecules have even numbers of electrons, suggesting that electrons are usually found in pairs. Lewis devised the familiar representations of molecules and polyatomic ions (Lewis structures, or Lewis diagrams) in which electrons are shown as dots (or as noughts and crosses) to show how atoms can attain noble gas configurations by the sharing of electrons in pairs, as opposed to complete transfer as in Kossel s theory. It was soon apparent from the earliest X-ray studies that Kossel s theory was more appropriate... 

Although the concept of pharmacophores constituting a simple representation of molecules and chemical groups in certain order was introduced nearly a century ago [1], there has been increasing interest and focus on pharmacophores in recent years following the advances in computational chemistry research. The historical development of the pharmacophore concept has recently been reviewed [2],... 

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