Wavy bond

Every chemistry rule method simply calls the executeRule() method by passing in the molfile and the name of the Cheshire script function that implements the rule. Take the wavy bond rule as an example. The following method removes wavy bonds in the molfile ... 

Figure 4-4. Reaction mechanism for the formation of 1,2,3- trithioethane phenylpropanoid monomers (4.25) from lignin (4.19). Ri is either an aryl group or a hydrogen atom. In H-residues both R3 and R5 are hydrogen atoms, in G-residues R3 is a methoxyl group and R5 is a hydrogen atom, and in S-residues both R3 and R5 are methoxyl groups. R4 is either a hydrogen atom or an alkyl group. The wavy bonds indicate that both the S- and R-stereo-isomers are present.

Bond information includes the bond order, that is, single, double, or triple bond, and bond style, such as simple straight-line bond, wedged bond, dashed bond, wavy bond, broken-line bond, bold bond, and so on. Bond information can also include some special bond types representing the aromatic bonds or bond stereochemistry, for example, wedged or dashed bond. Bond labels are also sometimes found in structures. Different types of bond information are illustrated in Figure 4.2. 

The wavy bond line means that the sterochemistry is unspecified. Cohen, T. Bhupathy, M. J. Am. Chem. Soc. 1983,105, 520-525. 

The side product of the reaction is most likely a mixture of bromoacetoxy compounds (unspecified stereochemistry is indicated by the wavy bond lines). Electrophilic additions in nucleophilic solvents often give a mixture of products because the nucleophile derived from the electrophilic reagent (e.g., Br ) and the solvent compete for the intermediate carbocation. 

At -50°C, 4-23 is the only product at 0°C, 4-23 is still the major product, but 4-24 and 4-25 are also produced. Note that, as the wavy bond lines indicate, both the exo and endo isomers of the 2-bromo compound 4-24 are produced. 

The radical addition of thiolacetic acid to )3-pinene gives unrearranged product. This result is evidence for the discrete existence of radical 5-9. That is, the rate of abstraction of a hydrogen atom from thiolacetic acid by 5-11 is faster than its rate of fragmentation. Note that the product is a mixture of stereoisomers, as indicated by the wavy bond lines. 

Wavy bond indicates that the stereochemistry is unspecified. 

Fructose is a reducing sugar because it undergoes two base-catalyzed keto-enol tautomerizations that result in conversion to an aldohexose. (The wavy bonds indicate unknown stereochemistry.)... 

Note In this chapter, the "wavy bond" symbol means the continuation of a polymer chain. 

Fig. 3. Schematic illustration of the Flory-Huggins lattice model for a polymer mixture. Lattice sites taken by (effective) monomers are indicated by full dots lattice sites taken by vacancies are denoted by empty circles. Chains of type A are indicated by thick bonds between the monomers, and B chains by wavy bonds. Nearest neighbor nonbonded interactions between monomers of the same kind (eAA or eBb) are shown as full straight lines and those between monomers of a different kind (eAB) by broken lines. Interactions between monomers and vacancies (or solvent molecules, respectively), eAV and ebv, could be introduced as well but will be assumed here to be zero throughout...

Figure 8.4 Process of solid-phase glycoside synthesis. In the process, X = linker which is later incorporated into the pol5mer matrix A = activating group for anomeric hydroxyl Y = temporary anomeric hydroxyl protecting group Tr = tiityl, and R = semipermanent protecting group for secondary hydroxyls. The wavy bond represents either a- or P-anomeric configuration...

In addition to the different bond orders, there are several other types of bonds to handle stereochemistry (bold, dotted and wavy bonds). Stereocenters are displayed by showing the respective atom in reverse video. For molecules with many stereocenters (e.g. sugar chemistry), the Fischer Projection Method can be used for entering stereocenters. (Figures 6,7)... 

The drawings of glucose and ribose show a number of stereogenic centres, with one centre undefined—an Off group shown with a wavy bond. This is because one centre in both sugars is a hemiacetal and therefore the molecule is in equilibrium with an open-chain hydroxy-aldehyde. For glucose, the open-chain form is this. 

Fig. 3 The general chemical structure of the major biomass components. The wavy bonds indicate further attachment in the biopolymer structure...

PROBLEM 14.16 Rewrite the partial polyurethane structure shown in eq. 14.30, but with one more monomer unit attached to each wavy bond. 

Note in passing that almost all transfers of protons to and from oxygen and nitrogen are fast, and they are almost never rate determining. The stereochemistry at the start, which has disappeared in the products (the wavy bond indicated unspecified stereochemistry), is deliberate— weTl look at the reasons for this in the next section, but for now, think about the shape of the carbocation intermediate and where it will be attacked. 

All of the reactions shown are fairly standard in type. The first is a Strecker synthesis the first formed product is the a-aminonitrile, which is then hydrolyzed to an amino acid. The second reaction is a standard oxime synthesis as the ketone is symmetric, there is no stereochemistry to worry about. In (c), an imine is formed the stereochemistry about the carbon-nitrogen double bond is determined by steric hindrance. Since the SM is racemic, two diastereoisomers will be formed, hence the wavy bond to the methyl group. In the final example, a hydrazine is prepared while it s not possible to be certain of the stereochemistry about the C=N double bond, it s logical to assume that the less sterically hindered isomer will predominate ... 

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