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Reactive Intermediates in Organic Chemistry
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Reactive Intermediates in Organic Chemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: closed (31 August 2020) | Viewed by 22526

Special Issue Editor

Prof. Dr. Edward Lee-Ruff

E-Mail Website
Guest Editor
Chemistry, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
Interests: photochemistry; nucleosides; strained compounds; small rings; physical organic chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are delighted to announce that we have launched a new Special Issue on the topic, "Reactive Intermediates". We are trying to approach potential contributors in the field of strained molecules, transient species relevant to mechanistic studies, computational studies of high energy intermediates, aromaticity and antiaromaticity. It is anticipated that this Special Issue will contain at least ten contributions entailing current research or reviews. We welcome any contributions on these topics and look forward to receiving them.

Kind regards,

Prof. emer Edward Lee-Ruff
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Carbon-centered radicals
  • Carbocations
  • Strain in molecules
  • Photochemistry
  • Short-lived transients and mechanistic studies

Published Papers (6 papers)

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Research

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15 pages, 1862 KiB  
Article
Photophysical Properties of Donor-Acceptor Stenhouse Adducts and Their Inclusion Complexes with Cyclodextrins and Cucurbit[7]uril
by Liam Payne, Jason D. Josephson, R. Scott Murphy and Brian D. Wagner
Molecules 2020, 25(21), 4928; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25214928 - 24 Oct 2020
Cited by 12 | Viewed by 3593
Abstract
Donor-acceptor Stenhouse adducts (DASAs) are a novel class of solvatochromic photoswitches with increasing importance in photochemistry. Known for their reversibility between open triene and closed cyclized states, these push-pull molecules are applicable in a suite of light-controlled applications. Recent works have sought to [...] Read more.
Donor-acceptor Stenhouse adducts (DASAs) are a novel class of solvatochromic photoswitches with increasing importance in photochemistry. Known for their reversibility between open triene and closed cyclized states, these push-pull molecules are applicable in a suite of light-controlled applications. Recent works have sought to understand the DASA photoswitching mechanism and reactive state, as DASAs are vulnerable to irreversible “dark switching” in polar protic solvents. Despite the utility of fluorescence spectroscopy for providing information regarding the electronic structure of organic compounds and gaining mechanistic insight, there have been few studies of DASA fluorescence. Herein, we characterize various photophysical properties of two common DASAs based on Meldrum’s acid and dimethylbarbituric acid by fluorescence spectroscopy. This approach is applied in tandem with complexation by cyclodextrins and cucurbiturils to reveal the zwitterionic charge separation of these photoswitches in aqueous solution and the protective nature of supramolecular complexation against degradative dark switching. DASA-M, for example, was found to form a weak host-guest inclusion complex with (2-hydroxypropyl)-γ-cyclodextrin, with a binding constant K = 60 M−1, but a very strong inclusion complex with cucurbit[7]uril, with K = 27,000 M−1. This complexation within the host cavity was found to increase the half-life of both DASAs in aqueous solution, indicating the significant and potentially useful stabilization of these DASAs by host encapsulation. Full article
(This article belongs to the Special Issue Reactive Intermediates in Organic Chemistry)
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17 pages, 2853 KiB  
Article
Predicted Reversal in N-Methylazepine/N-Methyl-7-azanorcaradiene Equilibrium upon Formation of Their N-Oxides
by René Fournier, Alexa R. Green, Arthur Greenberg, Edward Lee-Ruff, Joel F. Liebman and Anita Rágyanszki
Molecules 2020, 25(20), 4767; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25204767 - 16 Oct 2020
Cited by 3 | Viewed by 2066
Abstract
Density functional calculations and up to five different basis sets have been applied to the exploration of the structural, enthalpy and free energy changes upon conversion of the azepine to the corresponding N-oxide. Although it is well known that azepines are typically [...] Read more.
Density functional calculations and up to five different basis sets have been applied to the exploration of the structural, enthalpy and free energy changes upon conversion of the azepine to the corresponding N-oxide. Although it is well known that azepines are typically much more stable than their 7-azanorcaradiene valence isomers, the stabilities are reversed for the corresponding N-oxides. Structural, thermochemical as well as nucleus-independent chemical shift (NICS) criteria are employed to probe the potential aromaticity, antiaromaticity and nonaromaticity of N-methylazepine, its 7-azanorcaradiene valence isomer. For the sake of comparison, analogous studies are performed on N-methylpyrrole and its N-oxide. Full article
(This article belongs to the Special Issue Reactive Intermediates in Organic Chemistry)
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12 pages, 3579 KiB  
Article
Cytochrome P450 Can Epoxidize an Oxepin to a Reactive 2,3-Epoxyoxepin Intermediate: Potential Insights into Metabolic Ring-Opening of Benzene
by Holly M. Weaver-Guevara, Ryan W. Fitzgerald, Noah A. Cote and Arthur Greenberg
Molecules 2020, 25(19), 4542; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25194542 - 03 Oct 2020
Cited by 6 | Viewed by 2822
Abstract
Dimethyldioxirane epoxidizes 4,5-benzoxepin to form the reactive 2,3-epoxyoxepin intermediate followed by very rapid ring-opening to an o-xylylene that immediately isomerizes to the stable product 1H-2-benzopyran-1-carboxaldehyde. The present study demonstrates that separate incubations of 4,5-benzoxepin with three cytochrome P450 isoforms (2E1, [...] Read more.
Dimethyldioxirane epoxidizes 4,5-benzoxepin to form the reactive 2,3-epoxyoxepin intermediate followed by very rapid ring-opening to an o-xylylene that immediately isomerizes to the stable product 1H-2-benzopyran-1-carboxaldehyde. The present study demonstrates that separate incubations of 4,5-benzoxepin with three cytochrome P450 isoforms (2E1, 1A2, and 3A4) as well as pooled human liver microsomes (pHLM) also produce 1H-2-benzopyran-1-carboxaldehyde as the major product, likely via the 2,3-epoxyoxepin. The reaction of 4,5-benzoxepin with cerium (IV) ammonium nitrate (CAN) yields a dimeric oxidized molecule that is also a lesser product of the P450 oxidation of 4,5-benzoxepin. The observation that P450 enzymes epoxidize 4,5-benzoxepin suggests that the 2,3-epoxidation of oxepin is a major pathway for the ring-opening metabolism of benzene to muconaldehyde. Full article
(This article belongs to the Special Issue Reactive Intermediates in Organic Chemistry)
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17 pages, 2280 KiB  
Article
Computational Study of Selected Amine and Lactam N-Oxides Including Comparisons of N-O Bond Dissociation Enthalpies with Those of Pyridine N-Oxides
by Arthur Greenberg, Alexa R. Green and Joel F. Liebman
Molecules 2020, 25(16), 3703; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25163703 - 14 Aug 2020
Cited by 7 | Viewed by 2557
Abstract
A computational study of the structures and energetics of amine N-oxides, including pyridine N-oxides, trimethylamine N-oxide, bridgehead bicyclic amine N-oxides, and lactam N-oxides, allowed comparisons with published experimental data. Most of the computations employed the B3LYP/6-31G* and M06/6-311G+(d,p) models and comparisons were also [...] Read more.
A computational study of the structures and energetics of amine N-oxides, including pyridine N-oxides, trimethylamine N-oxide, bridgehead bicyclic amine N-oxides, and lactam N-oxides, allowed comparisons with published experimental data. Most of the computations employed the B3LYP/6-31G* and M06/6-311G+(d,p) models and comparisons were also made between the results of the HF 6-31G*, B3LYP/6-31G**, B3PW91/6-31G*, B3PW91/6-31G**, and the B3PW91/6-311G+(d,p) models. The range of calculated N-O bond dissociation energies (BDE) (actually enthalpies) was about 40 kcal/mol. Of particular interest was the BDE difference between pyridine N-oxide (PNO) and trimethylamine N-oxide (TMAO). Published thermochemical and computational (HF 6-31G*) data suggest that the BDE of PNO was only about 2 kcal/mol greater than that of TMAO. The higher IR frequency for N-O stretch in PNO and its shorter N-O bond length suggest a greater difference in BDE values, predicted at 10–14 kcal/mol in the present work. Determination of the enthalpy of sublimation of TMAO, or at least the enthalpy of fusion and estimation of the enthalpy of vaporization might solve this dichotomy. The “extra” resonance stabilization in pyridine N-oxide relative to pyridine was consistent with the 10–14 kcal/mol increase in BDE, relative to TMAO, and was about half the “extra” stabilization in phenoxide, relative to phenol or benzene. Comparison of pyridine N-oxide with its acyclic model nitrone (“Dewar-Breslow model”) indicated aromaticity slightly less than that of pyridine. Full article
(This article belongs to the Special Issue Reactive Intermediates in Organic Chemistry)

Review

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25 pages, 6712 KiB  
Review
Superelectrophiles: Recent Advances
by Douglas A. Klumpp and Maksim V. Anokhin
Molecules 2020, 25(14), 3281; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25143281 - 19 Jul 2020
Cited by 13 | Viewed by 3818
Abstract
Superelectrophiles are reactive species that often carry multiple positive charges. They have been useful in numerous synthetic methods and they often exhibit highly unusual reactivities. Recent advances in superelectrophile chemistry are discussed in this review. Full article
(This article belongs to the Special Issue Reactive Intermediates in Organic Chemistry)
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27 pages, 8503 KiB  
Review
Recent Advances in Chemical Biology Using Benzophenones and Diazirines as Radical Precursors
by Muhammad Murtaza Hassan and Olasunkanmi O. Olaoye
Molecules 2020, 25(10), 2285; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25102285 - 13 May 2020
Cited by 27 | Viewed by 6703
Abstract
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein–protein, protein–nucleic acid, protein–ligand (drug, probe), and protein–co-factor interactions, [...] Read more.
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein–protein, protein–nucleic acid, protein–ligand (drug, probe), and protein–co-factor interactions, among others. This technique, often referred to as photoaffinity labelling, uses radical precursors that react almost instantaneously to yield spatial and temporal information about the nature of the interaction and the interacting partner(s). This review focuses on the recent advances in chemical biology in the use of benzophenones and diazirines, two of the most commonly known light-activatable radical precursors, with a focus on the last three years, and is intended to provide a solid understanding of their chemical and biological principles and their applications. Full article
(This article belongs to the Special Issue Reactive Intermediates in Organic Chemistry)
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