Organic molecules nucleophilic sites

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. 

NADH is a coenzyme, an organic molecule that can function only in the presence of an enzyme. The active site of the enzyme binds both the carbonyl substrate and NADH, keeping them in close proximity. NADH then donates H in much the same way as a metal hydride reagent that is, reduction consists of nucleophilic attack followed by protonation. 

In an organic molecule, the atoms of a covalent polar bond (i.e., a bond between lwo atoms of different electronegativity) may become the site of a chemical reaction in that either a nucleophilic species is attracted by the electron-deficient... 

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. 

In some instances, the reverse approach may be preferred, with functional amine groups on the sensor surface and activated carboxyhc groups. This strategy can be used when the molecule lacks appropriate reactive amines or other nucleophiles, or when the nucleophile is suspected to be close to the analyte binding site. The approach is particularly valuable when working with small organic molecules, as will be further described in Sect. 4.4. Amine groups can be introduced to the sensor surface in several ways. A convenient route involves the conversion of carboxylated surfaces via EDC/NHS activation and subsequent ethylene diamine reaction (Fig. 7). 

Organic chemists refer to Lewis acids as electrophiles because they are attracted to electron-rich sites on other molecules, and they refer to Lewis bases as nucleophiles because they are attracted to electron-deficient molecular sites. Ingold (1969) developed a classification of reaction mechanisms based on this idea and this classification is the foundation for modeling the mechanisms of organic reactions (Bruckner, 2002 Grossman, 1999). Casey (2001) and Casey and Swaddle (2003) adapted some of these principles to apply to the dissolution of oxides. The electron-rich, and therefore nucleophilic, sites on molecules are nicely visualized using the electron localization function (Gibbs et al, 2005). 

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. 

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