User:Lazytitans03/Reaction intermediate

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In chemistry, a reaction intermediate or an intermediate is a molecular entity that is formed from the reactants (or preceding intermediates) but is consumed in further reactions in stepwise chemical reactions that contain multiple elementary steps. Intermediates are the reaction product of one elementary step, but do not appear in the chemical equation for an overall chemical reaction (Citation 2).

For example, consider this hypothetical stepwise reaction:

A + B → C + D

The reaction includes two elementary steps:

A + B → X

X → C + D

In this example, X is a reaction intermediate.

IUPAC definition

The IUPAC Gold Book delineates an "intermediate" as a compound that has a lifetime greater than a molecular vibration. The lifetime condition distinguishes true, chemically distinct intermediates from vibrational states or such transition states which, by definition have lifetime close to that of molecular vibration. (IUPAC Gold Book citation)

Kinetically, intermediates are often consumed quickly in a step-wise mechanism. The designation of "fast" or "slow" consumption speed is relative, and a reactive intermediate are sometimes separated from a reaction intermediate based on being relatively short-lived. Reactive intermediates are an unstable type of reaction intermediate, and are usually short-lived, high-energy, and seldom isolated. They do not remain in the product mixture due to their short lifetime, in contrast to other reaction intermediates.

Common intermediates

Carbocations

Cations, often carbocations, serve as intermediates in different types of reactions to synthesize new compounds. Due to the instability caused by charge separation, carbocations are unstable and short-lived. The stability of a carbocation largely depends on the degree of substitution and resonance.

Carbocation intermediates in alkene addition

Carbocations are formed in two major alkene addition reactions. In a HX addition reaction, the pi bond of an alkene acts as a nucleophile and bonds with the proton of an HX molecule, where the X is a halogen atom. This forms a carbocation intermediate, and the X bonds to the positive carbon that is available, as in the example reaction shown below.

CH₂CH₂ + HX → CH₂CH₃⁺ + X^-

CH₂CH₃⁺ + X^- →CH₂XCH₃

Similarly, in a H₂O addition reaction, the pi bond of an alkene acts as a nucleophile and bonds with the proton of a H₃O⁺ molecule. This forms a carbocation intermediate, and then, the oxygen atom of H₂O bonds with the positive carbon of the intermediate. The oxygen finally deprotonates to form a final alcohol product, as shown below.

CH₂CH₂ + H₃O⁺ → CH₂CH₃⁺ + H₂O

CH₂CH₃⁺ + H₂O → CH₂OH₂CH₃⁺

CH₂OH₂CH₃⁺ + H₂O → CH₂OHCH₃ +H₃O⁺

Carbocation intermediates in nucleophilic substitution

Nucleophilic substitution reactions occur when a nucleophilic molecule attacks a positive or partially positive electrophilic center by breaking and creating a new bond. S_N1 and S_N2 are two different mechanisms for nucleophilic substitution, and S_N1 involves a carbocation intermediate. In S_N1, A leaving group is broken off to create a carbocation reaction intermediate. Then, a nucleophile attacks and forms a new bond with the carbocation intermediate to form the final, substituted product, as shown in the reaction of 2-bromo-2-methylpropane to form 2-methyl-2-propanol.

(CH₃)₃CBr → (CH₃)₃C⁺

(CH₃)₃C⁺ + H₂O → (CH₃)₃OH₂⁺

(CH₃)₃OH₂⁺ → (CH₃)₃OH + H⁺

In this reaction, (CH₃)₃C⁺ is the formed carbocation intermediate to form the alcohol product.

Carbocation intermediates in β-elimination

β-elimination or elimination reactions occur through the loss of a substituent leaving group and loss of a proton to form a pi bond. E1 and E2 are two different mechanisms for elimination reactions, and E1 involves a carbocation intermediate. In E1, a leaving group detaches from a carbon to form a carbocation reaction intermediate. Then, a solvent removes a proton, but the electrons used to form the proton bond form a pi bond, as shown in the pictured reaction on the right.

Carbanions

A carbanion is a organic molecule where a carbon atom is not electron deficient but contain an overall negative charge (Citation 4). Carbanions are strong nucleophiles, which can be used to extend an alkene's carbon backbone in the synthesis reaction shown below.

C₂H₂ with NaNH₂ in NH₃ (l) → CHC^-

CHC^- + BrCH₂CH₃ → CHCCH₂CH₃

The alkyne carbanion, CHC^-, is a reaction intermediate in this reaction.

Radicals

Radicals are highly reactive and short-lived, as they have an unpaired electron which makes it extremely unstable. Radicals often react with hydrogens attached carbon molecules, effectively making the carbon a radical while stabilizing the former radical in a process called propagation. The formed product, a carbon radical, can react with non-radical molecule to continue propagation or react with another radical to form a new stable molecule such as a longer carbon chain or an alkyl halide.

The example below of methane chlorination shows a multi-step reaction involving radicals.

(original Diagram)

Applications

Biological intermediates

Reaction intermediates serve purposes in a variety of biological settings. An example of this is demonstrated with the enzyme reaction intermediate of metallo-β-lactamase, which bacteria can use to acquire resistance to commonly used antibiotics such as penicillin. Metallo-β-lactamase can catalyze β-lactams, a family of common antibiotics. Spectroscopy techniques have found that the reaction intermediate of metallo-β-lactamase uses zinc in the resistance pathway.

Another example of the importance of reaction intermediates is seen with AAA-ATPase p97, a protein that used in a variety of cellular metabolic processes. p97 is also linked to degenerative disease and cancer. In a study looking at reaction intermediates of the AAA-ATPase p97 function found an important ADP.P_i nucleotide intermediate is important in the p97 molecular operation.

An additional example of biologically relevant reaction intermediates can be found with the RCL enzymes, which catalyzes glycosidic bonds. When studied using methanolysis, it was found that the reaction required the formation of a reaction intermediate.

Chemical processing industry

In the chemical industry, the term intermediate may also refer to the (stable) product of a reaction that is itself valuable only as a precursor chemical for other industries. A common example is cumene which is made from benzene and propylene and used to make acetone and phenol in the cumene process. The cumene itself is of relatively little value in and of itself, and is typically only bought and sold by chemical companies.