Organic molecules electrophilic sites

In an extensive review on abiotic catalysis, Huang (2000) noted that the reactivity of hydrolyzable organic contaminants arises from the presence of electron-deficient (electrophilic) sites within the molecules. Figures 14.2 and 14.3 show the patterns of reactivity in two cases of nucleophihc substitution and monomolecular nucleophilic substitution. The Sj 2 mechanism (nucleophilic substitution) involves attack of the electrophilic sites by OH" or H O, generation of a higher coordination nnmber intermediate, subsequent elimination of the leaving group, and the formation of an hydrolysis product (Fig. 14.2). 

Similarly, relevant electrophiles (Lewis acids) including A-type metal cations (hard), bivalent transition metal ions (borderline), and B-type metal ions (soft) can be categorized (see Stumm and Morgan 1996). Note that in organic molecules, the atom where a nucleophile attacks (i.e., the electrophilic site) may possess harder (e.g., C=0, P=0) or softer (e.g., CH3-X) character. 

The concept of nucleophiles and electrophiles is one of the most important in organic chemistry. The reactions in this chapter, as well as most of the reactions that we will study in later chapters, involve a nucleophile bonding to an electrophile. If you can examine a molecule and identify whether it has a nucleophilic or an electrophilic site, not only will you know where that molecule is likely to react but you will also be able to identify what kind of partner is needed for a reaction because nucleophiles react with electrophiles. 

The nucleophilic or electrophilic sites within a neutral organic molecule can be determined by (i) the presence of lone pairs of electrons ... 

The amino acid side chains in the active site of enzymes catalyze proton transfers and nucleophilic substitutions. Other reactions require a group of nonprotein cofactors, that is, metal cations and the coenzymes. Metal ions are effective electrophiles, and they help orient the substrate within the active site. In addition, certain metal cations mediate redox reactions. Coenzymes are organic molecules that have a variety of functions in enzyme catalysis. 

TS-1 is an efficient and selective catalyst for the oxidation of various organic molecules with H O sulphur and nitrogen compounds, alcohols, olefins, aromatic and aliphatic C-H bonds [11, 92-93]. Selectivity is the result of the electrophilic properties of active oxidant species and of the shape selectivity. The latter arises from diffusion of reagents and products and from steric constraints in the transition state (restricted transition state shape selectivity). Molecules having a cross section larger than about 0.6 nm cannot difhise to TS-1 active sites and are not oxidised. This restricts TS-1 catalysis to almost linear molecules and mononuclear aromatic compounds, bearing small or no substituents. On the other hand, small molecules can be selectively oxidised in the presence of bulkier ones. 

Other prominent sites for electrophilic addition are non-bonding electron pairs as they are present in many heteroatom-containing organic molecules. One example has already been mentioned, namely the RS conjugation with the sulfur anion function in thiolate. As formulated in the back reaction of equilibrium (14) this yields the three-electron bonded disulfide radical anion, (RS SR)in which the unpaired thiyl electron couples with the free p-electron pair at the thiolate sulfur. In this context, a significant consequence emerges with respect to the overall redox properties of such a system. As has been stated already, the... 

The familiar chemistry of acids and bases provides a framework for understanding many of the most important reactions between organic molecules. Much of the chemistry we explore in the upcoming chapters expands on the concept that electrophiles and nucleophiles are mutually attractive species, analogous to acids and bases. By identifying polar sites in molecnles, we can develop the ability to nnderstand, and even to predict, what kinds of reactions these molecules will undergo. 

PES representation, students are asked to predict the reaction path. Locations, geometries, and energies of the two minima and of the transition state are also extracted from the PES graph (Figure 4). The AMI and PM3 results are compared with experimental and ab initio data. The last assignment is devoted to the molecular electrostatic potential (MEP) and HOMO of five organic molecules, which are calculated using AMI and displayed as 2D contours plots in HYPERCHEM. For each molecule, the more favorable sites for electrophilic attack are deduced from the position of the MEP minima and from the HOMO localization. Differences are discussed and results are con elated with gas phase proton affinity. 

Proposed mechanisms for polycondensations are essentially the same as those proposed in the organic chemistry of smaller molecules. Here, we will briefly consider several examples to illustrate this similarity between reaction mechanisms for small molecules and those forming polymers. For instance, the synthesis of polyamides (nylons) is envisioned as a simple Sn2 type Lewis acid-base reaction, with the Lewis base nucleophilic amine attacking the electron-poor, electrophilic carbonyl site followed by loss of a proton. 

The recent surge of interests in metal homoenolate chemistry has been stimulated by the recognition that the siloxycyclopropane route can afford novel reactive homoenolate species that are stable enough for isolation, purification, and characterization. The stability of such homoenolates crucially depends on the subtle balance of nucleophilic and electrophilic reactivity of the two reactive sites in the molecule. Naturally, homoenolates with metal-carbon bonds that are too stable do not serve as nucleophiles in organic synthesis. 

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