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Therefore, when they can be trapped and studied, these intermediates provide a glimpse at what the true transition state may look like. Enzymecatalyzed reactions go through intermediate states like this, mediated by the specific interactions of the protein and/or enzyme cofactors with the reactants and products of the chemical reaction being catalyzed. We shall have more to say about some of these intermediate species in Chapter 6. 3 ACID‒BASE CHEMISTRY In freshman chemistry we were introduced to the common Lewis definition of acids and bases: a L ewis acid is any substance that can act as an electron pair acceptor, and a L ewis base is any substance that can act as an electron pair donor.

This mechanism of providing a thermodynamic driving force for unfavorable reactions is quite common in biological catalysis. As we shall see in Chapter 3, many enzymes use nonprotein cofactors in the course of their catalytic reactions. In some cases these cofactors participate directly in the chemical transformations of the reactants (referred to as substrates by enzymologists) to products of the enzymatic reaction. In many other cases, however, the reactions of the cofactors are used to provide the thermodynamic driving force for catalysis.

The molecule would now have a different electronic configuration that would impart to the overall molecule more potential energy; that is, the molecule would be in an excited electronic state. Now, since in this excited state we have moved an electron from a bonding ( ) to an antibonding ( *) orbital, the overall molecule has acquired more antibonding character. As a consequence, the nuclei will occur at a longer equilibrium interatomic distance, relative to the ground state of the molecule. In other words, the potential energy minimum (also referred to as the zero-point energy) for the excited state occurs when the atoms are further apart from one another than they are for the potential energy minimum of the ground state.

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