Retrosynthetic analysis

Last updated

Retrosynthetic analysis is a technique for solving problems in the planning of organic syntheses. This is achieved by transforming a target molecule into simpler precursor structures regardless of any potential reactivity/interaction with reagents. Each precursor material is examined using the same method. This procedure is repeated until simple or commercially available structures are reached. These simpler/commercially available compounds can be used to form a synthesis of the target molecule. Retrosynthetic analysis was used as early as 1917 in Robinson's Tropinone total synthesis. [1] Important conceptual work on retrosynthetic analysis was published by George Vladutz in 1963. [2] [3] E.J. Corey formalized and popularized the concept from 1967 onwards in his article General methods for the construction of complex molecules and his book The Logic of Chemical Synthesis. [4] [5] [6] [7]

Contents

The power of retrosynthetic analysis becomes evident in the design of a synthesis. The goal of retrosynthetic analysis is a structural simplification. Often, a synthesis will have more than one possible synthetic route. Retrosynthesis is well suited for discovering different synthetic routes and comparing them in a logical and straightforward fashion. [8] A database may be consulted at each stage of the analysis, to determine whether a component already exists in the literature. In that case, no further exploration of that compound would be required. If that compound exists, it can be a jumping point for further steps developed to reach a synthesis.

Definitions

Disconnection
A retrosynthetic step involving the breaking of a bond to form two (or more) synthons.
Retron
A minimal molecular substructure that enables certain transformations.
Retrosynthetic tree
A directed acyclic graph of several (or all) possible retrosyntheses of a single target.
Synthon
A fragment of a compound that assists in the formation of a synthesis, derived from that target molecule. A synthon and the corresponding commercially available synthetic equivalent are shown below:
Synthon-example.gif
Target
The desired final compound.
Transform
The reverse of a synthetic reaction; the formation of starting materials from a single product.

Example

Shown below is a retrosynthetic analysis of phenylacetic acid:

Retrosynthetic analysis of phenylacetic acid.svg

In planning the synthesis, two synthons are identified. A nucleophilic "-COOH" group, and an electrophilic "PhCH2+" group. Both synthons do not exist as written; synthetic equivalents corresponding to the synthons are reacted to produce the desired product. In this case, the cyanide anion is the synthetic equivalent for the COOH synthon, while benzyl bromide is the synthetic equivalent for the benzyl synthon.

The synthesis of phenylacetic acid determined by retrosynthetic analysis is thus:

PhCH2Br + NaCN → PhCH2CN + NaBr
PhCH2CN + 2 H2O → PhCH2COOH + NH3
Synthesis of phenylacetic acid english.svg

In fact, phenylacetic acid has been synthesized from benzyl cyanide, [9] itself prepared by the analogous reaction of benzyl bromide with sodium cyanide. [10]

Strategies

Functional group strategies

Manipulation of functional groups can lead to significant reductions in molecular complexity.

Stereochemical strategies

Numerous chemical targets have distinct stereochemical demands. Stereochemical transformations (such as the Claisen rearrangement and Mitsunobu reaction) can remove or transfer the desired chirality thus simplifying the target.

Structure-goal strategies

Directing a synthesis toward a desirable intermediate can greatly narrow the focus of analysis. This allows bidirectional search techniques.

Transform-based strategies

The application of transformations to retrosynthetic analysis can lead to powerful reductions in molecular complexity. Unfortunately, powerful transform-based retrons are rarely present in complex molecules, and additional synthetic steps are often needed to establish their presence.

Topological strategies

The identification of one or more key bond disconnections may lead to the identification of key substructures or difficult to identify rearrangement transformations in order to identify the key structures.

See also

Related Research Articles

<span class="mw-page-title-main">Allenes</span> Any organic compound containing a C=C=C group

In organic chemistry, allenes are organic compounds in which one carbon atom has double bonds with each of its two adjacent carbon atoms. Allenes are classified as cumulated dienes. The parent compound of this class is propadiene, which is itself also called allene. A group of the structure R2C=C=CR− is called allenyl, while a substituent attached to an allene is referred to as an allenic substituent. In analogy to allylic and propargylic, a substituent attached to a saturated carbon α to an allene is referred to as an allenylic substituent. While allenes have two consecutive ('cumulated') double bonds, compounds with three or more cumulated double bonds are called cumulenes.

<span class="mw-page-title-main">Organic chemistry</span> Subdiscipline of chemistry, focusing on carbon compounds

Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms. Study of structure determines their structural formula. Study of properties includes physical and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical study.

Chemical synthesis is the artificial execution of chemical reactions to obtain one or several products. This occurs by physical and chemical manipulations usually involving one or more reactions. In modern laboratory uses, the process is reproducible and reliable.

<span class="mw-page-title-main">Elias James Corey</span> American chemist (born 1928)

Elias James Corey is an American organic chemist. In 1990, he won the Nobel Prize in Chemistry "for his development of the theory and methodology of organic synthesis", specifically retrosynthetic analysis.

In organic chemistry, a nitrile is any organic compound that has a −C≡N functional group. The name of the compound is composed of a base, which includes the carbon of the −C≡N, suffixed with "nitrile", so for example CH3CH2C≡N is called "propionitrile". The prefix cyano- is used interchangeably with the term nitrile in industrial literature. Nitriles are found in many useful compounds, including methyl cyanoacrylate, used in super glue, and nitrile rubber, a nitrile-containing polymer used in latex-free laboratory and medical gloves. Nitrile rubber is also widely used as automotive and other seals since it is resistant to fuels and oils. Organic compounds containing multiple nitrile groups are known as cyanocarbons.

Total synthesis, a specialized area within organic chemistry, focuses on constructing complex organic compounds, especially those found in nature, using laboratory methods. It often involves synthesizing natural products from basic, commercially available starting materials. Total synthesis targets can also be organometallic or inorganic. While total synthesis aims for complete construction from simple starting materials, modifying or partially synthesizing these compounds is known as semisynthesis.

<span class="mw-page-title-main">Medicinal chemistry</span> Scientific branch of chemistry

Medicinal or pharmaceutical chemistry is a scientific discipline at the intersection of chemistry and pharmacy involved with designing and developing pharmaceutical drugs. Medicinal chemistry involves the identification, synthesis and development of new chemical entities suitable for therapeutic use. It also includes the study of existing drugs, their biological properties, and their quantitative structure-activity relationships (QSAR).

Organic synthesis is a branch of chemical synthesis concerned with the construction of organic compounds. Organic compounds are molecules consisting of combinations of covalently-linked hydrogen, carbon, oxygen, and nitrogen atoms. Within the general subject of organic synthesis, there are many different types of synthetic routes that can be completed including total synthesis, stereoselective synthesis, automated synthesis, and many more. Additionally, in understanding organic synthesis it is necessary to be familiar with the methodology, techniques, and applications of the subject.

In retrosynthetic analysis, a synthon is a hypothetical unit within a target molecule that represents a potential starting reagent in the retroactive synthesis of that target molecule. The term was coined in 1967 by E. J. Corey. He noted in 1988 that the "word synthon has now come to be used to mean synthetic building block rather than retrosynthetic fragmentation structures". It was noted in 1998 that the phrase did not feature very prominently in Corey's 1981 book The Logic of Chemical Synthesis, as it was not included in the index. Because synthons are charged, when placed into a synthesis an uncharged form is found commercially instead of forming and using the potentially very unstable charged synthons.

<span class="mw-page-title-main">Macrocycle</span> Molecule with a large ring structure

Macrocycles are often described as molecules and ions containing a ring of twelve or more atoms. Classical examples include the crown ethers, calixarenes, porphyrins, and cyclodextrins. Macrocycles describe a large, mature area of chemistry.

<span class="mw-page-title-main">Chiral auxiliary</span> Stereogenic group placed on a molecule to encourage stereoselectivity in reactions

In stereochemistry, a chiral auxiliary is a stereogenic group or unit that is temporarily incorporated into an organic compound in order to control the stereochemical outcome of the synthesis. The chirality present in the auxiliary can bias the stereoselectivity of one or more subsequent reactions. The auxiliary can then be typically recovered for future use.

Benzyl chloride, or α-chlorotoluene, is an organic compound with the formula C6H5CH2Cl. This colorless liquid is a reactive organochlorine compound that is a widely used chemical building block.

In organic chemistry, umpolung or polarity inversion is the chemical modification of a functional group with the aim of the reversal of polarity of that group. This modification allows secondary reactions of this functional group that would otherwise not be possible. The concept was introduced by D. Seebach and E.J. Corey. Polarity analysis during retrosynthetic analysis tells a chemist when umpolung tactics are required to synthesize a target molecule.

<span class="mw-page-title-main">Ladderane</span>

In chemistry, a ladderane is an organic molecule containing two or more fused cyclobutane rings. The name arises from the resemblance of a series of fused cyclobutane rings to a ladder. Numerous synthetic approaches have been developed for the synthesis of ladderane compounds of various lengths. The mechanisms often involve [2 + 2] photocycloadditions, a useful reaction for creating strained 4-membered rings. Naturally occurring ladderanes have been identified as major components of the anammoxosome membrane of the anammox bacteria, phylum Planctomycetota.

<span class="mw-page-title-main">Benzyl cyanide</span> Chemical compound

Benzyl cyanide (abbreviated BnCN) is an organic compound with the chemical formula C6H5CH2CN. This colorless oily aromatic liquid is an important precursor to numerous compounds in organic chemistry. It is also an important pheromone in certain species.

In organic synthesis, cyanation is the attachment or substitution of a cyanide group on various substrates. Such transformations are high-value because they generate C-C bonds. Furthermore nitriles are versatile functional groups.

<span class="mw-page-title-main">Phil S. Baran</span> American organic chemist

Phil S. Baran is a synthetic organic chemist and Professor in the Department of Chemistry at the Scripps Research Institute. His work is focused on synthesizing complex natural products, the development of new reaction methodologies within synthetic organic electrochemistry, and the development of new reagents. He holds several patents and has authored nearly 300 research articles.

Biomimetic synthesis is an area of organic chemical synthesis that is specifically biologically inspired. The term encompasses both the testing of a "biogenetic hypothesis" through execution of a series of reactions designed to parallel the proposed biosynthesis, as well as programs of study where a synthetic reaction or reactions aimed at a desired synthetic goal are designed to mimic one or more known enzymic transformations of an established biosynthetic pathway. The earliest generally cited example of a biomimetic synthesis is Sir Robert Robinson's organic synthesis of the alkaloid tropinone.

<span class="mw-page-title-main">Rick L. Danheiser</span> American organic chemist

Rick L. Danheiser is an American organic chemist and is the Arthur C. Cope Professor of Chemistry at the Massachusetts Institute of Technology and chair of the MIT faculty. His research involves the invention of new methods for the synthesis of complex organic compounds. Danheiser is known for the Danheiser annulation and Danheiser benzannulation reactions.

References

  1. Robinson, R. (1917). "LXIII. A Synthesis of Tropinone". Journal of the Chemical Society, Transactions. 111: 762–768. doi:10.1039/CT9171100762.
  2. Ugi, Ivar; Bauer, Johannes; Bley, Klemens; Dengler, Alf; Dietz, Andreas; Fontain, Eric; Gruber, Bernhard; Herges, Rainer; Knauer, Michael; Reitsam, Klaus; Stein, Natalie (1993). "Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry". Angewandte Chemie International Edition in English. 32 (2): 201–227. doi:10.1002/anie.199302011.
  3. Vléduts, G.É. (1963). "Concerning one system of classification and codification of organic reactions". Information Storage and Retrieval. 1 (2–3): 117–146. doi:10.1016/0020-0271(63)90013-5.
  4. https://doi.org/10.1351/pac196714010019
  5. E. J. Corey, X-M. Cheng (1995). The Logic of Chemical Synthesis. New York: Wiley. ISBN   978-0-471-11594-6.
  6. E. J. Corey (1988). "Retrosynthetic Thinking – Essentials and Examples". Chem. Soc. Rev. 17: 111–133. doi:10.1039/CS9881700111.
  7. E. J. Corey (1991). "The Logic of Chemical Synthesis: Multistep Synthesis of Complex Carbogenic Molecules (Nobel Lecture)" (Reprint). Angewandte Chemie International Edition in English . 30 (5): 455–465. doi:10.1002/anie.199104553.
  8. James Law et.al:"Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation", Journal of Chemical Information and Modelling (ACS JCIM) Publication Date (Web): February 6, 2009; doi : 10.1021/ci800228y, http://pubs.acs.org/doi/abs/10.1021/ci800228y
  9. Wilhelm Wenner (1963). "Phenylacetamide". Organic Syntheses ; Collected Volumes, vol. 4, p. 760.
  10. Roger Adams; A. F. Thal (1941). "Benzyl Cyanide". Organic Syntheses {{cite journal}}: CS1 maint: multiple names: authors list (link); Collected Volumes, vol. 1, p. 107.