Diazirine

Last updated
Diazirine
Diazirin - Diazirine.svg
3H-Diazirine-3D-balls.png
Identifiers
3D model (JSmol)
605387
ChEBI
ChemSpider
PubChem CID
  • InChI=1S/CH2N2/c1-2-3-1/h1H2
    Key: GKVDXUXIAHWQIK-UHFFFAOYSA-N
  • 3H:C1N=N1
Properties
CH2N2
Molar mass 42.041 g·mol−1
Related compounds
Related compounds
1H-Diazirine
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
A generic diazirine Diazirines.svg
A generic diazirine

In organic chemistry, diazirines are a class of organic molecules consisting of a carbon bound to two nitrogen atoms, which are double-bonded to each other, forming a cyclopropene-like ring, 3H-diazirine (>CN2). They are isomeric with diazocarbon groups (>C=N=N), and like them can serve as precursors for carbenes by loss of a molecule of dinitrogen. For example, irradiation of diazirines with ultraviolet light leads to carbene insertion into various C−H , N−H, and O−H bonds. [1] Hence, diazirines have grown in popularity as small, photo-reactive, crosslinking reagents. [2] They are often used in photoaffinity labeling studies to observe a variety of interactions, including ligand-receptor, ligand-enzyme, protein-protein, and protein-nucleic acid interactions. [3]

Contents

Synthesis

A number of methods exist in the literature for the preparation of diazirines, which begin from a variety of reagents. [4]

Synthesis from ketones

Generally, synthetic schemes that begin with ketones (>C=O) involve conversion of the ketone with the desired substituents to diaziridines (>CN2H2). These diaziridines are then subsequently oxidized to form the desired diazirines.

Diaziridines can be prepared from ketones by oximation, followed by tosylation (or mesylation), and then finally by treatment with ammonia (NH3). Generally, oximation reactions are performed by reacting the ketone with hydroxylammonium chloride (NH3OH−Cl+) under heat in the presence of a base such as pyridine. [5] [6] Subsequent tosylation or mesylation of the alpha-substituted oxygen with tosyl or mesyl chloride in the presence of base yields the tosyl or mesyl oxime. [7] The final treatment of the tosyl or mesyl oxime with ammonia produces the diaziridine. [1] [3] [7] [8]

Generic diaziridine synthesis by oximation, tosylation, and treatment with ammonia. Screen Shot 2015-12-01 at 12.35.12 PM .png
Generic diaziridine synthesis by oximation, tosylation, and treatment with ammonia.

Diaziridines can be also produced directly by the reaction of ketones with ammonia in the presence of an aminating agent such as a monochloramine or hydroxyl amine O-sulfonic acid. [9]

Diaziridines can be oxidized to diazirines by a number of methods. These include oxidation by chromium-based reagents such as the Jones oxidation, [10] oxidation by iodine and triethylamine, [5] oxidation by silver oxide, [11] oxidation by oxalyl chloride, [7] or even electrochemical oxidation on a platinum-titanium anode. [12]

Jones oxidation of a generic diaziridine to a diazirine. Screen Shot 2015-12-01 at 7.51.23 PM.png
Jones oxidation of a generic diaziridine to a diazirine.

Synthesis by Graham reaction

Diazirines can be alternatively formed in a one-pot process using the Graham reaction, starting from amidines. [13] This reaction yields a halogenated diazirine, whose halogen can be displaced by various nucleophilic reagents. [14]

Graham-reaction-2D-scheme.svg
The Graham reaction as a method of diazirine synthesis, where X = Cl or Br.
Diazirine Exchange screenshot.png
The diazirine exchange reaction using various anions and the counterion tetra-n-butylammonium.

Chemistry

Upon irradiation with UV light, diazirines form reactive carbene species. The carbene may exist in the singlet form, in which the two free electrons occupy the same orbital, or the triplet form, with two unpaired electrons in different orbitals.

Diazirines can be decomposed by using UV-light. Diazirines decomposition.svg
Diazirines can be decomposed by using UV-light.

Triplet vs singlet carbene products

The substituents on the diazirine affect which carbene species is generated upon irradiation and subsequent photolytic cleavage. Diazirine substituents that are electron donating in nature can donate electron density to the empty p-orbital of the carbene that will be formed, and hence can stabilize the singlet state. For example, phenyldiazirine produces phenylcarbene in the singlet carbene state [15] whereas 3-chloro-3-[(4-nitrophenyl)methyl]diazirine or trifluoromethylphenyldiazirine produce the respective triplet carbene products. [16] [17]

Electron donating substituents can also encourage photoisomerization to the linear diazo compound, [18] rather than the singlet carbene, and hence these compounds are unfavorable for use in biological assays. [19] On the other hand, trifluoroaryldiazirines in particular show favorable stability and photolytic qualities [19] and are most commonly used in biological applications. [1]

Three diazirines are shown above. Phenyldiazirine produces the singlet carbene whereas trifluoromethylphenyldiazirine and 3-chloro-3-[(4-nitrophenyl)methyl]diazirine produce triplet state carbenes. Screen Shot 2015-12-01 at 3.56.20 PM.png
Three diazirines are shown above. Phenyldiazirine produces the singlet carbene whereas trifluoromethylphenyldiazirine and 3-chloro-3-[(4-nitrophenyl)methyl]diazirine produce triplet state carbenes.

Carbenes produced from diazirines are quickly quenched by reaction with water molecules, [20] and hence yields for photoreactive crosslinking assays are often low. Yet, as this feature minimizes unspecific labeling, it is actually an advantage of using diazirines.

Use in photoreactive crosslinking

Diazirines are often used as photoreactive crosslinking reagents, as the reactive carbenes they form upon irradiation with UV light can insert into C-H, N-H, and O-H bonds. This results in proximity-dependent labeling of other species with the diazirine containing compound. However, studies have found that diazirines have some pH dependence in labeling preferences, favoring acidic residues such as glutamate. [21] Diazirine variants have been developed to reduce this bias. [22]

Diazirines are often preferred to other photoreactive crosslinking reagents due to their smaller size, longer irradiation wavelength, short period of irradiation required, and stability in the presence of various nucleophiles, and in both acidic and basic conditions. [23] Benzophenones, which form reactive triplet carbonyl species upon irradiation, often require long periods of irradiation which can result in non-specific labeling, and moreover are often inert to various polar solvents. [24] Aryl azides require a low wavelength of irradiation, which can damage the biological macromolecules under investigation.

Examples in receptor labeling studies

Diazirines are widely used in receptor labeling studies. This is because diazirine-containing analogs of various ligands can be synthesized and incubated with their respective receptors, and then subsequently exposed to light to produce reactive carbenes. The carbene will covalently bond to residues in the binding site of the receptor. The carbene compound may include a bioorthogonal tag or handle by which the protein of interest can be isolated. The protein can then be digested and sequenced by mass spectrometry in order to identify which residues the carbene containing ligand is bound to, and hence the identity of the binding site in the receptor.

Examples of diazirines used in receptor labeling studies include:

Brassinosteroid diazirine analog.jpg
Propofol.svg
M-Azipropofol.png
Propofol (left) and m-azipropofol, a diazirine analog of it

Examples in enzyme-substrate studies

In a manner analogous to receptor labeling, diazirine containing compounds that are analogs of natural substrates have also been used to identify binding pockets of enzymes. Examples include:

Examples in nucleic acid studies

Diazirines have been used in photoaffinity labeling experiments involving nucleic acids as well. Examples include:

1-s2.0-S0968089611005062-gr39.jpg

Diazirines have also been used to study protein lipid interactions, for example the interaction of various sphingolipids with proteins in vivo. [34]

Related Research Articles

Demethylation is the chemical process resulting in the removal of a methyl group (CH3) from a molecule. A common way of demethylation is the replacement of a methyl group by a hydrogen atom, resulting in a net loss of one carbon and two hydrogen atoms.

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

Benzophenone is a naturally occurring organic compound with the formula (C6H5)2CO, generally abbreviated Ph2CO. Benzophenone has been found in some fungi, fruits and plants, including grapes. It is a white solid with a low melting point and rose-like odor that is soluble in organic solvents. Benzophenone is the simplest diaromatic ketone. It is a widely used building block in organic chemistry, being the parent diarylketone.

<span class="mw-page-title-main">Enamine</span> Class of chemical compounds

An enamine is an unsaturated compound derived by the condensation of an aldehyde or ketone with a secondary amine. Enamines are versatile intermediates.

<span class="mw-page-title-main">Cross-link</span> Bonds linking one polymer chain to another

In chemistry and biology, a cross-link is a bond or a short sequence of bonds that links one polymer chain to another. These links may take the form of covalent bonds or ionic bonds and the polymers can be either synthetic polymers or natural polymers.

In organic chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The general formula is R−:C−R' or R=C: where the R represents substituents or hydrogen atoms.

A transition metal carbene complex is an organometallic compound featuring a divalent carbon ligand, itself also called a carbene. Carbene complexes have been synthesized from most transition metals and f-block metals, using many different synthetic routes such as nucleophilic addition and alpha-hydrogen abstraction. The term carbene ligand is a formalism since many are not directly derived from carbenes and most are much less reactive than lone carbenes. Described often as =CR2, carbene ligands are intermediate between alkyls (−CR3) and carbynes (≡CR). Many different carbene-based reagents such as Tebbe's reagent are used in synthesis. They also feature in catalytic reactions, especially alkene metathesis, and are of value in both industrial heterogeneous and in homogeneous catalysis for laboratory- and industrial-scale preparation of fine chemicals.

The Baeyer–Villiger oxidation is an organic reaction that forms an ester from a ketone or a lactone from a cyclic ketone, using peroxyacids or peroxides as the oxidant. The reaction is named after Adolf von Baeyer and Victor Villiger who first reported the reaction in 1899.

<span class="mw-page-title-main">Chromium hexacarbonyl</span> Chemical compound

Chromium hexacarbonyl is a chromium(0) organometallic compound with the formula Cr(CO)6. It is a homoleptic complex, which means that all the ligands are identical. It is a colorless crystalline air-stable solid, with a high vapor pressure.

Barrelene is a bicyclic organic compound with chemical formula C8H8 and systematic name bicyclo[2.2.2]octa-2,5,7-triene. First synthesized and described by Howard Zimmerman in 1960, the name derives from the resemblance to a barrel, with the staves being three ethylene units attached to two methine groups. It is the formal Diels–Alder adduct of benzene and acetylene. Due to its unusual molecular geometry, the compound is of considerable interest to theoretical chemists.

The Negishi coupling is a widely employed transition metal catalyzed cross-coupling reaction. The reaction couples organic halides or triflates with organozinc compounds, forming carbon-carbon bonds (C-C) in the process. A palladium (0) species is generally utilized as the catalyst, though nickel is sometimes used. A variety of nickel catalysts in either Ni0 or NiII oxidation state can be employed in Negishi cross couplings such as Ni(PPh3)4, Ni(acac)2, Ni(COD)2 etc.

<span class="mw-page-title-main">Crosslinking of DNA</span> Phenomenon in genetics

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<span class="mw-page-title-main">Carbonyl reduction</span> Organic reduction of any carbonyl group by a reducing agent

In organic chemistry, carbonyl reduction is the conversion of any carbonyl group, usually to an alcohol. It is a common transformation that is practiced in many ways. Ketones, aldehydes, carboxylic acids, esters, amides, and acid halides - some of the most pervasive functional groups, -comprise carbonyl compounds. Carboxylic acids, esters, and acid halides can be reduced to either aldehydes or a step further to primary alcohols, depending on the strength of the reducing agent. Aldehydes and ketones can be reduced respectively to primary and secondary alcohols. In deoxygenation, the alcohol group can be further reduced and removed altogether by replacement with H.

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David Markham Lemal is the Albert W. Smith Professor of Chemistry Emeritus and Research Professor of Chemistry at Dartmouth College. He received an A.B. degree (summa) from Amherst College in 1955 and a Ph.D. in chemistry from Harvard University in 1959. At Harvard he worked with R. B. Woodward on deoxy sugars and a synthesis of the alkaloid yohimbine.

Mark S. Cushman is an American chemist, whose primary research is in the area of medicinal chemistry. He completed his pre-pharmacy studies at Fresno State College (now California State University, Fresno) in 1965. He then attended the University of California San Francisco (as a University of California Regents Scholar), earning a Pharm.D. in 1969 and a Ph.D. in Medicinal Chemistry in 1973. Thereafter, he performed postdoctoral training in the laboratory of George Büchi, Ph.D., at the Massachusetts Institute of Technology (MIT). There, his research focused on the discovery and development of new synthetic methodologies, and the isolation and structural characterization of mycotoxins from Aspergillus niger. In 1975, he joined the Department of Medicinal Chemistry and Molecular Pharmacology (at the time, Department of Medicinal Chemistry and Pharmacognosy) at Purdue University. From 1983 to 1984, Prof. Cushman was a Senior Fulbright Scholar at Munich Technical University working in the laboratory of Professor Adelbert Bacher. His sabbatical work dealt with the design and synthesis of probes to elucidate key aspects of the biosynthesis of riboflavin (vitamin B2). Currently he holds the rank of Distinguished Professor Emeritus of Medicinal Chemistry at Purdue University. He has mentored 40 graduate students, 59 postdoctoral researchers, and 5 visiting scholars. He has published 348 papers and holds 41 patents. His work has ~17,000 citations with an h-index of 69. His most cited papers had 471, 403, and 299 citations as of August 2021. He has made seminal contributions to the fields of synthetic and medicinal chemistry including the development of new synthetic methodologies, the synthesis of natural products, and the preparation of antivirals, antibacterials, and anticancer agents, and mechanism probes to understand the function of over thirty macromolecular targets. One of his main scientific contributions is the development of the indenoisoquinolines, molecules that inhibit the action of toposiomerase I (Top1) and stabilize the G-quadruplex in the Myc promoter. Three indenoisoquinolines designed and synthesized by his research group at Purdue University [indotecan (LMP 400), indimitecan (LMP 776), and LMP 744] demonstrated potent anticancer activity in vivo and have completed phase I clinical trials at the National Institutes of Health.

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

A borylene is the boron analogue of a carbene. The general structure is R-B: with R an organic moiety and B a boron atom with two unshared electrons. Borylenes are of academic interest in organoboron chemistry. A singlet ground state is predominant with boron having two vacant sp2 orbitals and one doubly occupied one. With just one additional substituent the boron is more electron deficient than the carbon atom in a carbene. For this reason stable borylenes are more uncommon than stable carbenes. Some borylenes such as boron monofluoride (BF) and boron monohydride (BH) the parent compound also known simply as borylene, have been detected in microwave spectroscopy and may exist in stars. Other borylenes exist as reactive intermediates and can only be inferred by chemical trapping.

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

In organic chemistry, the Graham reaction is an oxidation reaction that converts an amidine into a diazirine using a hypohalite reagent. The halide of the hypohalite oxidant, or another similar anionic additive to the reaction, is retained as a substituent on the diazirine product. The reaction was first reported in 1965. Various reaction mechanisms have been proposed.

<span class="mw-page-title-main">Boraacenes</span> Boron containing acene compounds

Boraacenes are polycyclic aromatic hydrocarbons containing at least one boron atom. Structurally, they are related to acenes, linearly fused benzene rings. However, the boron atom is electron deficient and may act as a Lewis Acid when compared to carbon. This results in slightly less negative charge within the ring, smaller HOMO-LUMO gaps, as well as differences in redox chemistry when compared to their acene analogues. When incorporated into acenes, Boron maintains the planarity and aromaticity of carbon acenes, while adding an empty p-orbital, which can be utilized for the fine tuning of organic semiconductor band gaps. Due to this empty p orbital, however, it is also highly reactive when exposed to nucleophiles like water or normal atmosphere, as it will readily be attacked by oxygen, which must be addressed to maintain its stability.

<i>m</i>-Terphenyl Organic ligand

m-Terphenyls (also known as meta-terphenyls, meta-diphenylbenzenes, or meta-triphenyls) are organic molecules composed of two phenyl groups bonded to a benzene ring in the one and three positions. The simplest formula is C18H14, but many different substituents can be added to create a diverse class of molecules. Due to the extensive pi-conjugated system, the molecule it has a range of optical properties and because of its size, it is used to control the sterics in reactions with metals and main group elements. This is because of the disubstituted phenyl rings, which create a pocket for molecules and elements to bond without being connected to anything else. It is a popular choice in ligand, and the most chosen amongst the terphenyls because of its benefits in regards to sterics. Although many commercial methods exist to create m-terphenyl compounds, they can also be found naturally in plants such as mulberry trees.

Alkylidene ketenes are a class of organic compounds that are of the form R2C=C=C=O. They are a member of the family of heterocumulenes (R2C=(C)n=O), and are often considered an unsaturated homolog of ketenes (R2C=C=O). Sometimes referred to as methyleneketenes, these compounds are highly reactive and much more difficult to access than ketenes.

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