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Special Issue "Protecting Group in Organic Synthesis"

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

Deadline for manuscript submissions: closed (30 April 2011)

Special Issue Editors

Guest Editor
Prof. Dr. Jyoti Chattopadhyaya

Department of Cell and Molecular Biology, Bioorganic Chemistry, Uppsala University, Biomedical Center Husargatan 3, Box 581 SE-751 23 Uppsala, Sweden
Interests: synthesis; physico-chemistry; 1H; 13C; 15N; 31P-NMR spectroscopy of carbohydrates; nucleosides; nucleoside analogues; phosphorylation methods; nucleotides; nucleotide analogues; oligo-DNA; oligo-RNA; lariat- and branched-RNA; RNA catalysis; ribozyme; antisense; RNAi; siRNA; conformationally constrained nucleosides; tethers; protecting group chemistry; hydroxyl; amino; internucleosidyl phosphate; heterocyclic antibacterial compounds against multiresistant strains
Guest Editor
Dr. Andras Földesi

Department of Cell and Molecular Biology, Bioorganic Chemistry, Uppsala University, Biomedical Center, Husargatan 3, Box 581 SE-751 23; Uppsala Sweden

Special Issue Information

Dear Colleagues,

Protecting groups play an instrumental role in the synthesis of complex organic molecules. This special issue is to cover the newest developments in the field reporting on new hydroxyl, amino, carbonyl, carboxyl and phosphate protecting groups or new ways of application of existing ones useful in the synthesis of biomolecules (such as carbohydrates, peptides and oligonucleotides) or other pharmacologically or industrially relevant compounds in solution or on solid phase.

Prof. Dr. Jyoti Chattopadhyaya
Dr. Andras Földesi
Guest Editors

Keywords

  • protecting group
  • temporary-permanent
  • functional groups: amino, hydroxyl, carbonyl, carboxyl, phosphate
  • introduction
  • removal
  • orthogonality
  • compatibility
  • mechanistic, rate consequences

Published Papers (7 papers)

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Research

Jump to: Review

Open AccessArticle Computational and Spectral Investigation of 5,12-Dihydro-5,12-ethanonaphthacene-13-carbaldehyde
Molecules 2011, 16(8), 6741-6746; doi:10.3390/molecules16086741
Received: 15 May 2011 / Revised: 2 August 2011 / Accepted: 2 August 2011 / Published: 9 August 2011
Cited by 1 | PDF Full-text (379 KB)
Abstract
A conformational search of 5,12-dihydro-5,12-ethanonaphthacene-13-carbaldehyde predicted the presence of twelve conformations. The geometry of the twelve conformations established at the B3LYP/6-31G* level showed only six unique ones. Vibrational frequencies were calculated at the B3LYP/6-31G* level. The calculated vibrational frequencies enabled us to [...] Read more.
A conformational search of 5,12-dihydro-5,12-ethanonaphthacene-13-carbaldehyde predicted the presence of twelve conformations. The geometry of the twelve conformations established at the B3LYP/6-31G* level showed only six unique ones. Vibrational frequencies were calculated at the B3LYP/6-31G* level. The calculated vibrational frequencies enabled us to interpret the appearance of two bands corresponding to the C=O stretching mode of 5,12-dihydro-5,12-ethanonaphthacene-13-carbaldehyde. The first band corresponded to the 5,12-dihydro-5,12-ethanonaphthacene-13-carbaldehyde structure where the aldehyde group O atom was above the benzene or naphthalene ring. The other band was due to the O atom of the aldehyde group pointing out of the benzene or naphthalene ring. Full article
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
Open AccessArticle Two-Carbon Homologation of Aldehydes and Ketones to α,β-Unsaturated Aldehydes
Molecules 2011, 16(6), 5062-5078; doi:10.3390/molecules16065062
Received: 28 April 2011 / Revised: 31 May 2011 / Accepted: 13 June 2011 / Published: 17 June 2011
Cited by 4 | PDF Full-text (206 KB)
Abstract
Phosphonate reagents were developed for the two-carbon homologation of aldehydes or ketones to unbranched- or methyl-branched α,β-unsaturated aldehydes. The phosphonate reagents, diethyl methylformyl-2-phosphonate dimethylhydrazone and diethyl ethylformyl-2-phosphonate dimethylhydrazone, contained a protected aldehyde group instead of the usual ester group. A homologation cycle [...] Read more.
Phosphonate reagents were developed for the two-carbon homologation of aldehydes or ketones to unbranched- or methyl-branched α,β-unsaturated aldehydes. The phosphonate reagents, diethyl methylformyl-2-phosphonate dimethylhydrazone and diethyl ethylformyl-2-phosphonate dimethylhydrazone, contained a protected aldehyde group instead of the usual ester group. A homologation cycle entailed condensation of the reagent with the starting aldehyde, followed by removal of the dimethylhydrazone protective group with a biphasic mixture of 1 M HCl and petroleum ether. This robust two-step process worked with a variety of aldehydes and ketones. Overall isolated yields of unsaturated aldehyde products ranged from 71% to 86% after the condensation and deprotection steps. Full article
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
Open AccessArticle Synthesis of Oligodeoxynucleotides Using Fully Protected Deoxynucleoside 3′-Phosphoramidite Building Blocks and Base Recognition of Oligodeoxynucleotides Incorporating N3-Cyano-Ethylthymine
Molecules 2010, 15(11), 7509-7531; doi:10.3390/molecules15117509
Received: 27 August 2010 / Revised: 8 October 2010 / Accepted: 14 October 2010 / Published: 27 October 2010
Cited by 1 | PDF Full-text (473 KB)
Abstract
Oligodeoxynucleotide (ODN) synthesis, which avoids the formation of side products, is of great importance to biochemistry-based technology development. One side reaction of ODN synthesis is the cyanoethylation of the nucleobases. We suppressed this reaction by synthesizing ODNs using fully protected deoxynucleoside 3′-phosphoramidite [...] Read more.
Oligodeoxynucleotide (ODN) synthesis, which avoids the formation of side products, is of great importance to biochemistry-based technology development. One side reaction of ODN synthesis is the cyanoethylation of the nucleobases. We suppressed this reaction by synthesizing ODNs using fully protected deoxynucleoside 3′-phosphoramidite building blocks, where the remaining reactive nucleobase residues were completely protected with acyl-, diacyl-, and acyl-oxyethylene-type groups. The detailed analysis of cyanoethylation at the nucleobase site showed that N3-protection of the thymine base efficiently suppressed the Michael addition of acrylonitrile. An ODN incorporating N3-cyanoethylthymine was synthesized using the phosphoramidite method, and primer extension reactions involving this ODN template were examined. As a result, the modified thymine produced has been proven to serve as a chain terminator. Full article
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
Open AccessArticle Synthesis and Application of a 2-[(4-Fluorophenyl)-sulfonyl]ethoxy Carbonyl(Fsec) Protected Glycosyl Donor in Carbohydrate Chemistry
Molecules 2010, 15(8), 5708-5720; doi:10.3390/molecules15085708
Received: 9 June 2010 / Revised: 10 August 2010 / Accepted: 18 August 2010 / Published: 19 August 2010
PDF Full-text (493 KB)
Abstract
The 2-[(4-fluorophenyl)sulfonyl]ethoxy carbonyl (Fsec) group for protection of hydroxyl groups has been designed, synthesized, and evaluated. Fsec-Cl was readily prepared in 91% yield over three steps and subsequently used to protect 4-fluorobenzyl alcohol in high yield. The Fsec group was cleaved from [...] Read more.
The 2-[(4-fluorophenyl)sulfonyl]ethoxy carbonyl (Fsec) group for protection of hydroxyl groups has been designed, synthesized, and evaluated. Fsec-Cl was readily prepared in 91% yield over three steps and subsequently used to protect 4-fluorobenzyl alcohol in high yield. The Fsec group was cleaved from the resulting model compound under mild basic conditions e.g., 20% piperidine in DMF and was stable under acidic conditions, e.g., neat acetic acid. The Fsec group was used to protect the unreactive 4-OH in a galactose building block that was later used in the synthesis of 6-aminohexyl galabioside. Full article
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
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Review

Jump to: Research

Open AccessReview Selenol Protecting Groups in Organic Chemistry: Special Emphasis on Selenocysteine Se-Protection in Solid Phase Peptide Synthesis
Molecules 2011, 16(4), 3232-3251; doi:10.3390/molecules16043232
Received: 1 March 2011 / Revised: 3 April 2011 / Accepted: 12 April 2011 / Published: 18 April 2011
Cited by 9 | PDF Full-text (308 KB)
Abstract
The appearance of selenium in organic synthesis is relatively rare, and thus examples in the literature pertaining to the masking of its considerable reactivity are similarly uncommon. Greene's Protecting Groups in Organic Synthesis, the standard reference for the state of the art [...] Read more.
The appearance of selenium in organic synthesis is relatively rare, and thus examples in the literature pertaining to the masking of its considerable reactivity are similarly uncommon. Greene's Protecting Groups in Organic Synthesis, the standard reference for the state of the art in this arena, offers no entries for selenium protective methodology, in stark comparison to its mention of the great variety of protecting groups germane to its chalcogen cousin sulfur. This scarcity of Se-protection methods makes it no less interesting and pertinent toward the construction of selenium-containing organic systems which do indeed require the iterative blocking and de-blocking of selenol functionalities. A selenium-containing system which is especially relevant is selenocysteine, as its use in Solid Phase Peptide Synthesis requires extensive protection of its selenol side chain. This review will attempt to summarize the current state of understanding with regard to selenium protection protocol in organic synthesis. Moreover, it will provide a special emphasis on selenocysteine side chain protection, comprising both the breadth of functionality used for this purpose as well as methods of deprotection. Full article
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
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Open AccessReview Protecting Groups in Carbohydrate Chemistry: Influence on Stereoselectivity of Glycosylations
Molecules 2010, 15(10), 7235-7265; doi:10.3390/molecules15107235
Received: 5 September 2010 / Accepted: 15 October 2010 / Published: 20 October 2010
Cited by 38 | PDF Full-text (1029 KB)
Abstract
Saccharides are polyhydroxy compounds, and their synthesis requires complex protecting group manipulations. Protecting groups are usually used to temporarily mask a functional group which may interfere with a certain reaction, but protecting groups in carbohydrate chemistry do more than protecting groups usually [...] Read more.
Saccharides are polyhydroxy compounds, and their synthesis requires complex protecting group manipulations. Protecting groups are usually used to temporarily mask a functional group which may interfere with a certain reaction, but protecting groups in carbohydrate chemistry do more than protecting groups usually do. Particularly, protecting groups can participate in reactions directly or indirectly, thus affecting the stereochemical outcomes, which is important for synthesis of oligosaccharides. Herein we present an overview of recent advances in protecting groups influencing stereoselectivity in glycosylation reactions, including participating protecting groups, and conformation-constraining protecting groups in general. Full article
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
Open AccessReview The 9-Phenyl-9-fluorenyl Group for Nitrogen Protection in Enantiospecific Synthesis
Molecules 2010, 15(9), 6512-6547; doi:10.3390/molecules15096512
Received: 12 August 2010 / Revised: 13 September 2010 / Accepted: 14 September 2010 / Published: 17 September 2010
Cited by 9 | PDF Full-text (1102 KB)
Abstract
One of the biggest challenges in asymmetric synthesis is to prevent racemization of enantiopure starting materials. However, at least some of the enantiopurity is lost in most of the existing reactions used in synthetic organic chemistry. This translates into unnecessary material losses. [...] Read more.
One of the biggest challenges in asymmetric synthesis is to prevent racemization of enantiopure starting materials. However, at least some of the enantiopurity is lost in most of the existing reactions used in synthetic organic chemistry. This translates into unnecessary material losses. Naturally enantiopure proteinogenic amino acids that can be transformed into many useful intermediates in drug syntheses, for example, are especially vulnerable to this. The phenylfluoren-9-yl (Pf) group, a relatively rarely used protecting group, has proven to be able to prevent racemization in α-amino compounds. This review article showcases the use of Pf-protected amino acid derivatives in enantiospecific synthesis. Full article
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
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