User:Gretashum/Condensation reaction

In organic chemistry, a condensation reaction is a type of chemical reaction in which two molecules are combined to form a single molecule, usually with the loss of a small molecule such as water or alcohol. If water is lost, the reaction is also known as a dehydration synthesis. However other molecules can also be lost, such as ammonia, ethanol, acetic acid and hydrogen sulfide. This class of reactions is a vital part of life as it is essential to the formation of peptide bonds between amino acids and to the biosynthesis of fatty acids. Since these reactions would also have been critical for the initial formation of prebiotic molecules, identifying environments in which these reactions can occur can provide a useful constraint when considering possible settings for the origin of life on Earth.

Overview of reaction stages and variations

The addition of the two molecules typically proceeds in a step-wise fashion to the addition product, usually in equilibrium, and with loss of a water molecule (hence the name condensation). The reaction may otherwise involve the functional groups of the molecule, and is a versatile class of reactions that can occur in acidic or basic conditions or in the presence of a catalyst.

Idealized scheme showing condensation of two amino acids to give a peptide bond.

Many variations of condensation reactions exist. Common examples include the aldol condensation and the Knoevenagel condensation, which both form water as a by-product, as well as the Claisen condensation and the Dieckman condensation (intramolecular Claisen condensation), which form alcohols as by-products.

Importance to biomolecules

Since the essential building blocks of life (nucleotides and amino acids) are assembled to form biopolymers (RNA, DNA, and proteins) using condensation reactions, these reactions are considered some of the most fundamental mechanisms of life on Earth, making up a large part of replication. Life exists in the balance between biopolymer synthesis and hydrolysis, which are, themselves governed by chemical thermodynamics and kinetics. Amino acids polymerize through peptide bonds and nucleic acids polymerize through ester bonds

Two mononucleotides (AMP + AMP) can be joined by ester bonds in the formation of dinucleotide (AMP–AMP) in the following way:

${\ce {AMP + AMP <=> AMP-AMP + H2O}}$

When compared in a pure solution, the hydrolysis reaction (here seen as right to left) proceeds much faster than the synthesis reaction, and the Gibbs free energy in the ester bond is positive. The addition of salt, such as MgCl₂ reduces the volume of water available to drive the reaction to the left, but MgCl₂ would take up water in its hydration shell, so the effective concentration would be adjusted.

Role in synthesis of prebiotic molecules

Condensation reactions would have played major roles in the synthesis of the first biotic molecules including early peptides and nucleic acids. In fact, condensation reactions would be required at multiple steps in RNA oligomerization, not just nucleotide polymerization, but also the condensation of nucleobases and pentose and in the phosphodiester bonds that build the sugar-phosphate backbone (aka nucleoside phosphorylation).

The role of wet-dry cycles

Reactions that lead to elongation of peptides and nucleic acids are endergonic, meaning that they require more energy to take place than they produce. Early life would not have been able to synthesize long polymers with the diminishing yield of repeated cycles except in an ideal wet-dry cycles, as in inland hot springs or evaporative lakes, in cases where the energy required to evaporate an aqueous solution of potential reactants from a cavity can be used to drive condensation reactions.

Plausible condensing agents for early life

Fortunately, both carbon–nitrogen- phosphorus- based condensing agents would likely have been available in prebiotic environments to facilitate the bonds formed in these reactions. These condensing agents include cyanamide, dicyandiamide, and urea. Cyanamide is likely to have been generated through the production of limestone in a prebiotic environment, and easily forms its dimer, dicyandiamide. Then, under mild conditions, in the presence of phosphate salt, can hydrolyze to urea. In addition to serving as a precursor for important biomolecules (purines, pyrimidines, and nucleotide precursors), it can serve as a condensing agent for various condensation reactions relevant to the Origin of Life, including dipeptides and nucleotides.

Condensed phosphates may also serve as condensing agents in prebiotic synthesis reactions.