Notation, molecular, examples

This sequence is one of the most ubiquituous in organic or organometallic chemistry and has already been discussed in preceding parts of this section. The chemical step may involve reactions (or a succession of chemical reactions) of high-order molecularities, not only first-order reactions as suggested by the notation. Classic examples are given by activated olefin electrohydrodimerization mechanisms ... 

We showed in Chapter 18 that the molecular diffusion term on the RHS of (18.1) can be neglected in atmospheric flows. In Chapter 18 we used index notation, for example, S(ujCi)/Sxj. Here we use both vector and index notation. The three wind velocity components can be denoted ( i, u2,u ),(uxi uy, u7), or (u,v,w) in Cartesian coordinates, and each of these notations has been used at various points in the book. 

It is clear from these examples that the usefulness of the molecular notation lies in its ability to differentiate between processes of common simplex notation for example, the three (l,l,2)j processes in Figure 8.12 are [1,1,2]j, [l,3]j and [4]j, respectively. The limitation of the molecular notation is seen in dissociative processes the three (l,l,2)j processes are uniformly described as... 

An alternative way to represent molecules is to use a linear notation. A linear notation uses alphanumeric characters to code the molecular structure. These have the advantage of being much more compact than the connection table and so can be particularly useful for transmif-ting information about large numbers of molecules. The most famous of the early line notations is the Wiswesser line notation [Wiswesser 1954] the-SMILES notation is a more recent example that is increasingly popular [Weininger 1988]. To construct the Wiswesser... 

Table 4.2 summarizes the molecular shapes that commonly occur. The VSEPR notation used for these shapes adopts the letter A to represent the central atom, the letter X to represent a bonding pair, and the letter E to represent a lone pair of electrons. For example, the VSEPR notation for NH3 is AX3E. This indicates that ammonia has three BPs around its central atom, and one LP. 

Number of electron groups Geometric arrangement of electron groups Type of electron pairs VSEPR notation Name of Molecular shape Example... 

A compact notation for the elemental composition of a species can be introduced that denotes the molecule s atomic composition coefficients. For element m in species k, call this coefficient Xmk Then, for example, the molecular weight of species k could be calculated as... 

Computer-Aided Property Estimation Computer-aided structure estimation requires the structure of the chemical compounds to be encoded in a computer-readable language. Computers most efficiently process linear strings of data, and hence linear notation systems were developed for chemical structure representation. Several such systems have been described in the literature. SMILES, the Simplified Molecular Input Line Entry System, by Weininger and collaborators [2-4], has found wide acceptance and is being used in the Toolkit. Here, only a brief summary of SMILES rules is given. A more detailed description, together with a tutorial and examples, is given in Appendix A. 

The Simplified Molecular Input Line Entry System (SMILES) is frequently used for computer-aided evaluation of molecular structures [1-3]. SMILES is widely accepted and computationally efficient because SMILES uses atomic symbols and a set of intuitive rules. Before presenting examples, the basic rules needed to enter molecular structures as SMILES notation are given. 

Table I taken in its entirety from an article by Kearns (16) summarizes the symmetry and state notations used for the polyacenes. It is an excellent example of the complex state of the vocabulary of the molecular spectroscopist.

In most interactions between two reactants, local shape complementarity of functional groups is of importance. A local shape complementarity of molecular electron densities represented by FIDCOs implies complementary curvatures for complementary values of the charge density threshold parameters a. For various curvature domains of a FIDCO, we shall use the notations originally proposed for complete molecues [2], For example, the symbol D2(b),i(a, Fj) stands for the i-th locally convex domain of a FIDCO G(a) of functional group Fj, where local convexity, denoted by subscript 2(b), is interpreted relative to a reference curvature b. For locally saddle type and locally concave domains relative to curvature b, the analogous subscripts 1(b) and 0(b) are used, respectively. 

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