The thermodynamics of phosphate versus phosphorothioate ester hydrolysis

Jamie Purcell1, Alvan C Hengge

  • 1Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.

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Phosphodiester Linkages

Overview
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
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Esters to Carboxylic Acids: Acid-Catalyzed Hydrolysis

Hydrolysis of esters under acidic conditions proceeds through a nucleophilic acyl substitution. In the presence of excess water, the reaction proceeds in a reversible manner, forming carboxylic acids and alcohols.
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Regioselective Formation of Enolates01:33

Regioselective Formation of Enolates

As depicted in the figure below, the unsymmetrical ketones can form two possible enolates: less substituted or more substituted enolates. Usually, the thermodynamic enolates are formed from the more substituted α-carbon atom, while the kinetic enolates are formed faster by deprotonation from the less substituted position. The thermodynamic enolates have lower energy, so they are more stable. But the energy required to form kinetic enolates is less.
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Esters to Carboxylic Acids: Saponification

Esters can be hydrolyzed to carboxylic acids under acidic or basic conditions. Base-promoted hydrolysis of esters is a nucleophilic acyl substitution reaction in which esters react with an aqueous base, followed by an acid to give carboxylic acids. This reaction is also known as saponification because it forms the basis for making soaps from fats.
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Phosphorylation

The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
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Amides to Carboxylic Acids: Hydrolysis01:28

Amides to Carboxylic Acids: Hydrolysis

Amides can undergo either acid-catalyzed hydrolysis or base-promoted hydrolysis through a typical nucleophilic acyl substitution. Each hydrolysis requires severe conditions.
Acid-catalyzed hydrolysis:
Hydrolysis of amides under acidic conditions yields carboxylic acids. Since the reaction occurs slowly, hydrolysis requires the conditions of heat.
The mechanism begins with the protonation of the carbonyl oxygen by the acid catalyst. The protonation makes the amide carbonyl carbon more...