Molecules from Side Reactions

A topical collection in Molbank (ISSN 1422-8599). This collection belongs to the section "Organic Synthesis".

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Editor


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Collection Editor
Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
Interests: solid-phase synthesis; chemistry of nucleosides, nucleotides, and oligonucleotides; L-sugars; platinum complexes; heterocycles; bioorganic chemistry
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

Chemical reactions are powerful tools that allow researchers to obtain novel molecular scaffolds, materials, and drugs. By fine-tuning the conditions, it is possible to drive a reaction towards the obtainment of the desired target. In addition, it is a common experience that a reaction may also follow unexpected and unpredictable routes, yielding side products. These products are usually discarded and stored in the freezers of laboratories. The aim of this Topical Collection is to share research pertaining to side products with scientists all over the world. Considering the special nature of this Topical Collection, studies addressing low yields as well as a lack of biological activities will be welcome for publication. However, side products must be fully spectroscopically characterized in accordance with the rigorous Molbank criteria.

Dr. Stefano D’Errico
Collection Editor

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Keywords

  • organic synthesis
  • solid-phase synthesis
  • heterocycles
  • building blocks
  • intermediates
  • drugs
  • drug design
  • medicinal chemistry
  • chemical diversity
  • diversity-oriented synthesis
  • carbon-carbon bond formation
  • metal-mediated reactions
  • catalyzers

Related Special Issues

Published Papers (37 papers)

2024

Jump to: 2023, 2022, 2021, 2020, 2019

6 pages, 954 KiB  
Communication
Synthesis and Analytical Characterization of Cyclization Products of 3-Propargyloxy-5-benzyloxy-benzoic Acid Methyl Ester
by Matteo Mori, Giulia Cazzaniga, Donatella Nava and Elena Pini
Molbank 2024, 2024(2), M1806; https://doi.org/10.3390/M1806 - 16 Apr 2024
Viewed by 221
Abstract
In the context of our ongoing studies on chromane derivatives as inhibitors of the salicylate synthase from M. tuberculosis, we isolated a new, unexpected compound from the cyclization of 3-(propargyloxy)-5-benzyloxy-benzoic acid methyl ester. Its molecular structure was elucidated by means of 1D [...] Read more.
In the context of our ongoing studies on chromane derivatives as inhibitors of the salicylate synthase from M. tuberculosis, we isolated a new, unexpected compound from the cyclization of 3-(propargyloxy)-5-benzyloxy-benzoic acid methyl ester. Its molecular structure was elucidated by means of 1D and 2D NMR analyses, FT-IR, ESI-MS, and HRMS. Full article
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6 pages, 382 KiB  
Short Note
1,2-Dibenzoylthiosemicarbazide
by Burcă Ion, Badea Valentin, Todea Anamaria and Bercean Vasile-Nicolae
Molbank 2024, 2024(2), M1804; https://doi.org/10.3390/M1804 - 09 Apr 2024
Viewed by 247
Abstract
When 1-benzoylthiosemicarbazide (2) or thiosemicarbazide (1) were treated with benzoyl chloride in a basic medium, a mixture of two compounds was obtained: 1,2-dibenzoylthiosemicarbazide (3) and 1,4-dibenzoylthiosemicarbazide (4). To determine the structure of the novel compounds, [...] Read more.
When 1-benzoylthiosemicarbazide (2) or thiosemicarbazide (1) were treated with benzoyl chloride in a basic medium, a mixture of two compounds was obtained: 1,2-dibenzoylthiosemicarbazide (3) and 1,4-dibenzoylthiosemicarbazide (4). To determine the structure of the novel compounds, 2D NMR spectroscopy techniques such as 1H-13C and 1H-15N were employed. Full article
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Scheme 1

5 pages, 1296 KiB  
Short Note
2,3,5,6-Tetrafluoro-[N-(3-aminopropyl)-ε-caprolactam]-4-pyridine
by Chadron M. Friesen, Nathan J. Weeks and Scott T. Iacono
Molbank 2024, 2024(1), M1777; https://doi.org/10.3390/M1777 - 22 Feb 2024
Viewed by 759
Abstract
The title compound was synthesized at a near-quantitative yield using the nucleophilic aromatic substitution of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) with perfluoropyridine (PFP). The purity and structure were determined by NMR (1H, 13C, 19F), GC-EIMS, and single-crystal X-ray crystallography. Full article
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2023

Jump to: 2024, 2022, 2021, 2020, 2019

5 pages, 811 KiB  
Short Note
(1R/S,7aS/R)-1-Benzyl-1-[2,8-bis(trifluoromethyl)quinolin-4-yl]-hexahydro-oxazolo[3,4-a]pyridin-3-one
by Dawid J. Kucharski and Przemysław J. Boratyński
Molbank 2024, 2024(1), M1756; https://doi.org/10.3390/M1756 - 30 Dec 2023
Viewed by 1263
Abstract
An unexpected diastereoselective C-alkylation of a mefloquine derivative in up to 57% yield was the result of an attempted Williamson etherification of Boc-mefloquine. The domino reaction involved oxazolidinone ring closure, deprotonation, and stereoselective carbon–carbon bond formation. The structure was confirmed with 2D NMR [...] Read more.
An unexpected diastereoselective C-alkylation of a mefloquine derivative in up to 57% yield was the result of an attempted Williamson etherification of Boc-mefloquine. The domino reaction involved oxazolidinone ring closure, deprotonation, and stereoselective carbon–carbon bond formation. The structure was confirmed with 2D NMR experiments. Full article
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9 pages, 1120 KiB  
Short Note
4-(5-Benzyl-3-((4-fluorophenyl)sulfonyl)-5-methyl-4,5-dihydrofuran-2-yl)-2-nitrobenzamide
by Oscar Leonardo Avendaño Leon, Christophe Curti, Hussein El-Kashef, Youssef Kabri, Sébastien Redon and Patrice Vanelle
Molbank 2023, 2023(4), M1750; https://doi.org/10.3390/M1750 - 15 Dec 2023
Viewed by 1133
Abstract
As part of our ongoing attempt to broaden the applications of the amidoxime moiety as a potential source of new antileishmanial agents, this study focuses on the product 4-(5-Benzyl-3-((4-fluorophenyl)sulfonyl)-5-methyl-4,5-dihydrofuran-2-yl)-2-nitrobenzamide. This unexpected amide was obtained in an 85% yield as the major product with [...] Read more.
As part of our ongoing attempt to broaden the applications of the amidoxime moiety as a potential source of new antileishmanial agents, this study focuses on the product 4-(5-Benzyl-3-((4-fluorophenyl)sulfonyl)-5-methyl-4,5-dihydrofuran-2-yl)-2-nitrobenzamide. This unexpected amide was obtained in an 85% yield as the major product with a conventional amidoxime synthesis protocol (Ethanol/Na2CO3) involving the reaction of hydroxylamine and a nitrile group. The formation of this amide derivative instead of the expected amidoxime can be attributed to two complementary effects: the strong electron effect of the nitro group and the influence of ethanol, a polar protic solvent. Alternatively, the desired amidoxime derivative, 4-(5-benzyl-3-((4-fluorophenyl)sulfonyl)-5-methyl-4,5-dihydrofuran-2-yl)-N′-hydroxy-2-nitrobenzimidamide, was obtained in an 80% yield by an alternative protocol (DMSO/KOtBu). This original compound, featuring a nitro group in the ortho position to the amidoxime, will be further evaluated, both in the field of medicinal chemistry and in other relevant areas, highlighting an unusual method to access amidoximes from hindered substrates. Full article
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Scheme 1

5 pages, 513 KiB  
Editorial
Editorial: Special Issue “Molecules from Side Reactions II”
by Stefano D’Errico and Annalisa Guaragna
Molbank 2023, 2023(4), M1740; https://doi.org/10.3390/M1740 - 20 Oct 2023
Viewed by 897
Abstract
This Special Issue, “Molecules from Side Reactions II”, belongs to the section Organic Synthesis of the journal Molbank and was launched in 2021, after the first edition, “Molecules from Side Reactions” [...] Full article
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5 pages, 1260 KiB  
Short Note
2-(1-Methoxycarbonyl-2-phenyleth-1-yl)-1-benzylpyridin-1-ium Bromide
by Lorenzo Suigo, Valentina Straniero and Ermanno Valoti
Molbank 2023, 2023(4), M1738; https://doi.org/10.3390/M1738 - 16 Oct 2023
Viewed by 875
Abstract
In this work, we report the unexpected conversion of a pyridine derivative into the corresponding N-benzylated pyridinium salt due to the presence of unreacted benzyl bromide in the crude product. This transformation was observed at room temperature in a solvent-free environment and [...] Read more.
In this work, we report the unexpected conversion of a pyridine derivative into the corresponding N-benzylated pyridinium salt due to the presence of unreacted benzyl bromide in the crude product. This transformation was observed at room temperature in a solvent-free environment and without any stirring. These interesting data show how pyridinium salts can be formed in mild conditions, avoiding high temperatures that could promote the degradation of the desired product. Full article
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5 pages, 2375 KiB  
Short Note
2,8-Dibromo-6H,12H-6,12-epoxydibenzo[b,f][1,5]dioxocine
by R. Alan Aitken, David B. Cordes, An Jie Ler and Aidan P. McKay
Molbank 2023, 2023(3), M1729; https://doi.org/10.3390/M1729 - 19 Sep 2023
Viewed by 884
Abstract
The title dibromodisalicylaldehyde, obtained as a by-product in the m-chloroperoxybenzoic acid oxidation of 5-bromo-2-(methoxymethoxy)benzaldehyde, has been characterised by IR and NMR spectroscopy and X-ray diffraction. The structure features two independent molecules with a π–π stacking interaction between them. Full article
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Graphical abstract

7 pages, 609 KiB  
Short Note
4-(4-Ethoxyphenyl)-5-(4-methoxyphenyl)-2,4-dihydro-3H-1,2,4-triazol-3-one
by Ion Burcă, Valentin Badea, Calin Deleanu, Vasile-Nicolae Bercean and Francisc Péter
Molbank 2023, 2023(3), M1705; https://doi.org/10.3390/M1705 - 01 Aug 2023
Viewed by 874
Abstract
A new triazol-3-one resulted unexpectedly from the reduction reaction of a heterocyclic thioketone using sodium borohydride in pyridine containing a small amount of water. The structure of the new compound was characterised using FT-IR, 1D and 2D NMR, and HRMS spectroscopic methods. Full article
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Graphical abstract

9 pages, 1645 KiB  
Communication
Diethyl 2-((aryl(alkyl)amino)methylene)malonates: Unreported Mycelial Growth Inhibitors against Fusarium oxysporum
by Willy-Fernando Cely-Veloza, Diego Quiroga and Ericsson Coy-Barrera
Molbank 2023, 2023(2), M1630; https://doi.org/10.3390/M1630 - 23 Apr 2023
Viewed by 1094
Abstract
This paper presents the discovery and development of antifungal agents against Fusarium oxysporum (Fox), a devastating plant pathogen. Diethyl 2-((arylamino)methylene)malonates (DAMMs) were formed as side-products during the synthesis of polysubstituted-2-pyridones through a three-component domino reaction and seemed to have antifungal activity [...] Read more.
This paper presents the discovery and development of antifungal agents against Fusarium oxysporum (Fox), a devastating plant pathogen. Diethyl 2-((arylamino)methylene)malonates (DAMMs) were formed as side-products during the synthesis of polysubstituted-2-pyridones through a three-component domino reaction and seemed to have antifungal activity against Fox. DAMMs are typically employed as intermediates or precursors to produce further bioactive compounds, but they have never been examined as antifungals. To confirm this latter characteristic, we employed a single-step procedure (i.e., the first step of the Gould-Jacobs reaction) to prepare five DAMMs (74–96% yields) which were subsequently evaluated against Fox in terms of their abilities to inhibit mycelial growth. The antifungal outcome was promising (0.013 µM < IC50 < 35 µM), involving fungistatic or fungicide effects. This small group of active compounds showed differences in antifungal activity, constituting the basis of further studies to expand the DAMM chemical space and look for improved antifungal activity. Full article
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5 pages, 1305 KiB  
Communication
Manganese(II) Bromide Coordination toward the Target Product and By-Product of the Condensation Reaction between 2-Picolylamine and Acenaphthenequinone
by Vera V. Khrizanforova, Robert R. Fayzullin and Yulia H. Budnikova
Molbank 2023, 2023(1), M1606; https://doi.org/10.3390/M1606 - 22 Mar 2023
Cited by 1 | Viewed by 1075
Abstract
A heteroleptic binuclear manganese complex was obtained and characterized by single-crystal X-ray diffraction. Manganese ions coordinate with the target product and by-product of the condensation reaction between 2-picolylamine and acenaphthenequinone are characterized by different geometries in the resulting complex. Full article
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6 pages, 1093 KiB  
Short Note
(Z)-2′-((Adamantan-1-yl)thio)-1,1′-dimethyl-2′,3′-dihydro-[2,4′-biimidazolylidene]-4,5,5′(1H,1′H,3H)-trione
by Vladimir Burmistrov, Vladimir Mokhov, Robert R. Fayzullin and Gennady M. Butov
Molbank 2023, 2023(1), M1585; https://doi.org/10.3390/M1585 - 14 Feb 2023
Viewed by 1238
Abstract
The title compound, (Z)-2′-((adamantan-1-yl)thio)-1,1′-dimethyl-2′,3′-dihydro-[2,4′-biimidazolylidene]-4,5,5′(1H,1′H,3H)-trione, was found to be a by-product of the reaction of 1,3-dehydroadamantane with 3-methyl-2-thioxoimidazolidin-4-one and characterized via single-crystal X-ray diffraction. Full article
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9 pages, 1136 KiB  
Communication
Obtainment of Threo and Erythro Isomers of the 6-Fluoro-3-(2,3,6,7,8,9-hexahydronaphtho[2,3-b][1,4]dioxin-2-yl)-2,3-dihydrobenzo[b][1,4]dioxine-5-carboxamide
by Valentina Straniero, Lorenzo Suigo, Giulia Lodigiani and Ermanno Valoti
Molbank 2023, 2023(1), M1559; https://doi.org/10.3390/M1559 - 18 Jan 2023
Cited by 1 | Viewed by 1270
Abstract
2,6-difluorobenzamides have been deeply investigated as antibacterial drugs in the last few decades. Several 3-substituted-2,6-difluorobenzamides have proved their ability to interfere with the bacterial cell division cycle by inhibiting the protein FtsZ, the key player of the whole process. Recently, we developed a [...] Read more.
2,6-difluorobenzamides have been deeply investigated as antibacterial drugs in the last few decades. Several 3-substituted-2,6-difluorobenzamides have proved their ability to interfere with the bacterial cell division cycle by inhibiting the protein FtsZ, the key player of the whole process. Recently, we developed a novel family of 1,4-tetrahydronaphthodioxane benzamides, having an ethoxy linker, which reached sub-micromolar MICs towards Gram-positive Staphylococcus aureus and Bacillus subtilis. A further investigation of their mechanism of action should require the development of a fluorescent probe, and the consequent definition of a synthetic pathway for its obtainment. In the present work, we report the obtainment of an unexpected bicyclic side product, 6-fluoro-3-(2,3,6,7,8,9-hexahydronaphtho[2,3-b][1,4]dioxin-2-yl)-2,3-dihydrobenzo[b][1,4]dioxine-5-carboxamide, coming from the substitution of one aromatic fluorine by the in situ formed alkoxy group, in the final opening of an epoxide intermediate. This side product was similarly achieved, in good yields, by opening the ring of both erythro and threo epoxides, and the two compounds were fully characterized using HRMS, 1H-NMR, 13C-NMR, HPLC and DSC. Full article
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2022

Jump to: 2024, 2023, 2021, 2020, 2019

8 pages, 788 KiB  
Short Note
(3-Methylene-2,3-dihydronaphtho[2,3-b][1,4]dioxin-2-yl)methanol
by Lorenzo Suigo, Giulia Lodigiani, Valentina Straniero and Ermanno Valoti
Molbank 2022, 2022(4), M1521; https://doi.org/10.3390/M1521 - 06 Dec 2022
Cited by 1 | Viewed by 1421
Abstract
(3-Methylene-2,3-dihydronaphtho[2,3-b][1,4]dioxin-2-yl)methanol was unexpectedly achieved as the main reaction product while applying a standard Johnson–Corey–Chaykovsky procedure to the 2,3-dihydronaphtho[2,3-b][1,4]dioxine-2-carbaldehyde, aiming at obtaining the corresponding epoxide. The structure of the recovered compound was confirmed through NMR and HRMS, the melting point [...] Read more.
(3-Methylene-2,3-dihydronaphtho[2,3-b][1,4]dioxin-2-yl)methanol was unexpectedly achieved as the main reaction product while applying a standard Johnson–Corey–Chaykovsky procedure to the 2,3-dihydronaphtho[2,3-b][1,4]dioxine-2-carbaldehyde, aiming at obtaining the corresponding epoxide. The structure of the recovered compound was confirmed through NMR and HRMS, the melting point was measured by DSC, and the organic purity was assessed using HPLC. We hypothesized the possible mechanism for the obtainment of this side product, which should involve the opening of the dioxane ring soon after the nucleophilic attack of the ylide to the carbonyl function. The consequent transfer of the negative charge allows the achievement of the phenolate function. The tautomer further rearranges, forming the unstable oxirane, which opening is favored by the acidic phenolic function, thus closing into the more stable six-membered ring compound. We confirmed the hypothesized reaction mechanism by applying the same reaction conditions while starting from the corresponding methyl ketone. This undesired compound, easily and quantitatively obtained by standard Johnson–Corey–Chaykovsky conditions, could pave the way to a new methodology for the obtainment of 2,3-disubstituted 1,4-naphthodioxanes, further derivatizable. Full article
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5 pages, 523 KiB  
Short Note
19β,28-Epoxy-18α-olean-3β-ol-2-furoate from Allobetulin (19β,28-Epoxy-18α-olean-3β-ol)
by Fulgentius Nelson Lugemwa
Molbank 2022, 2022(4), M1499; https://doi.org/10.3390/M1499 - 18 Nov 2022
Viewed by 1050
Abstract
The E ring of betulin rearranges and forms a cyclic ether when treated with an acid. Treatment of betulin with iodine generated hydrogen iodide in situ, which went on to promote the rearrangement at C-19 and C-20, followed by cyclization to form allobetulin. [...] Read more.
The E ring of betulin rearranges and forms a cyclic ether when treated with an acid. Treatment of betulin with iodine generated hydrogen iodide in situ, which went on to promote the rearrangement at C-19 and C-20, followed by cyclization to form allobetulin. A reaction of allobetulin with 2-furoyl chloride yielded 19β,28-Epoxy-18α-olean-3β-ol-2-furoate. Full article
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Scheme 1

6 pages, 1364 KiB  
Short Note
Dichloro{4-(4-chlorophenoxy)phthalazin-1-yl} methylphosphonic dichloride
by Dyhia Amrane, Omar Khoumeri, Patrice Vanelle and Nicolas Primas
Molbank 2022, 2022(3), M1439; https://doi.org/10.3390/M1439 - 05 Sep 2022
Viewed by 1413
Abstract
As part of our ongoing scaffold-hopping work on an antiplasmodial 2-trichloromethylquinazoline scaffold, we aimed to explore the 1-trichloromethylphthalazine scaffold as a potential new antimalarial series. Using previously chlorination conditions described by our lab to obtain a trichloromethyl group from a methyl group, we [...] Read more.
As part of our ongoing scaffold-hopping work on an antiplasmodial 2-trichloromethylquinazoline scaffold, we aimed to explore the 1-trichloromethylphthalazine scaffold as a potential new antimalarial series. Using previously chlorination conditions described by our lab to obtain a trichloromethyl group from a methyl group, we did not obtain the target compound; instead, we obtained a dichloro methylphosphonic dichloride side product 3. The nature of this compound was then characterized by NMR, HRMS and X-ray crystallography. The same issue was previously reported by Kato et al., starting from the 2-methyl-3-nitropyridine. Finally, compound 3, although not cytotoxic, was not active against P. falciparum, the parasite responsible for human malaria. Full article
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7 pages, 673 KiB  
Short Note
O6-[(2″,3″-O-Isopropylidene-5″-O-tbutyldimethylsilyl)pentyl]-5′-O-tbutyldiphenylsilyl-2′,3′-O-isopropylideneinosine
by Maria Marzano, Monica Terracciano, Vincenzo Piccialli, Ahmed Mahal, Roberto Nilo and Stefano D’Errico
Molbank 2022, 2022(1), M1345; https://doi.org/10.3390/M1345 - 01 Mar 2022
Cited by 3 | Viewed by 2581
Abstract
Cyclic adenosine diphosphate ribose (cADPR) is a cyclic nucleotide involved in the Ca2+ homeostasis. In its structure, the northern ribose, bonded to adenosine through an N1 glycosidic bond, is connected to the southern ribose through a pyrophosphate bridge. Due to the chemical [...] Read more.
Cyclic adenosine diphosphate ribose (cADPR) is a cyclic nucleotide involved in the Ca2+ homeostasis. In its structure, the northern ribose, bonded to adenosine through an N1 glycosidic bond, is connected to the southern ribose through a pyrophosphate bridge. Due to the chemical instability at the N1 glycosidic bond, new bioactive cADPR derivatives have been synthesized. One of the most interesting analogues is the cyclic inosine diphosphate ribose (cIDPR), in which the hypoxanthine replaced adenosine. The efforts for synthesizing new linear and cyclic northern ribose modified cIDPR analogues led us to study in detail the inosine N1 alkylation reaction. In the last few years, we have produced new flexible cIDPR analogues, where the northern ribose has been replaced by alkyl chains. With the aim to obtain the closest flexible cIDPR analogue, we have attached to the inosine N1 position a 2″,3″-dihydroxypentyl chain, possessing the two OH groups in a ribose-like fashion. The inosine alkylation reaction afforded also the O6-alkylated regioisomer, which could be a useful intermediate for the construction of new kinds of cADPR mimics. Full article
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8 pages, 5776 KiB  
Short Note
3-Isobutyl-5,5,7-tris(3-methylbut-2-en-1-yl)-1-phenyl-1,7-dihydro-4H-indazole-4,6(5H)-dione
by José Edmilson Ribeiro do Nascimento, Daniela Hartwig, Raquel Guimarães Jacob and Márcio Santos Silva
Molbank 2022, 2022(1), M1330; https://doi.org/10.3390/M1330 - 01 Feb 2022
Viewed by 1723
Abstract
Here we describe the functionalization of lupulone natural compound in obtaining 3-isobutyl-5,5,7-tris(3-methylbut-2-en-1-yl)-1-phenyl-1,7-dihydro-4H-indazole-4,6(5H)-dione. The lupulone-H-indazole derivative was prepared with 75% yield through the reaction between lupulone and phenyl-hydrazine employing SiO2/ZnCl2 (30% m/m) [...] Read more.
Here we describe the functionalization of lupulone natural compound in obtaining 3-isobutyl-5,5,7-tris(3-methylbut-2-en-1-yl)-1-phenyl-1,7-dihydro-4H-indazole-4,6(5H)-dione. The lupulone-H-indazole derivative was prepared with 75% yield through the reaction between lupulone and phenyl-hydrazine employing SiO2/ZnCl2 (30% m/m) as a support solid in a solvent-free condition. Based on the possibilities of products, a complete NMR structural characterization of this lupulone-H-indazole was performed by 1H, 13C{1H}, COSY, HSQC and HMBC NMR experiments, showing an important contribution in producing the first results related to lupulone reactivity. Full article
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2021

Jump to: 2024, 2023, 2022, 2020, 2019

7 pages, 1899 KiB  
Short Note
Poly[3-methyl-1,3-oxazolidin-2-iminium[µ3-cyanido-tri-µ2-cyanido-κ9C:N-tricuprate(I)]]
by Leena N. Rachid and Peter W. R. Corfield
Molbank 2021, 2021(3), M1259; https://doi.org/10.3390/M1259 - 26 Jul 2021
Viewed by 1610
Abstract
The unexpected formation of an oxazole ring has occurred during synthesis of a copper(I) cyanide network polymer as part of our ongoing studies of the structural chemistry of these networks. Crystals of the title compound were formed during the synthesis of a previously [...] Read more.
The unexpected formation of an oxazole ring has occurred during synthesis of a copper(I) cyanide network polymer as part of our ongoing studies of the structural chemistry of these networks. Crystals of the title compound were formed during the synthesis of a previously reported CuCN network solid containing protonated N-methylethanolamine and have been characterized by single crystal X-ray structure analysis. The structure shows well-defined oxazole-2-iminium cations sitting in continuous channels along the short a-axis of the crystal in a new three-dimensional copper(I) cyanide polymeric network. Evidently, a reaction has occurred between the cyanide ion and the protonated N-methylethanolamine base. Full article
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5 pages, 1259 KiB  
Short Note
N,N-Bis(hexyl α-d-acetylmannosyl) Acrylamide
by Atsushi Miyagawa, Shinya Ohno and Hatsuo Yamamura
Molbank 2021, 2021(3), M1255; https://doi.org/10.3390/M1255 - 22 Jul 2021
Viewed by 1975
Abstract
Glycosyl monomers for the assembly of multivalent ligands are typically synthesized using carbohydrates with biological functions and polymerizable functional groups such as acrylamide or styrene introduced into the carbohydrate aglycon, and monomers polymerized using a radical initiator. Herein, we report the acryloylation of [...] Read more.
Glycosyl monomers for the assembly of multivalent ligands are typically synthesized using carbohydrates with biological functions and polymerizable functional groups such as acrylamide or styrene introduced into the carbohydrate aglycon, and monomers polymerized using a radical initiator. Herein, we report the acryloylation of 6-aminohexyl α-d-mannoside and its conversion into the glycosyl monomer bearing an acrylamide group. The general acryloylation procedure afforded the desired N-hexyl α-d-acetylmannosyl acrylamide monomer as well as an unexpected compound with a close Rf value. The compounds were separated and analyzed by nuclear magnetic resonance spectroscopy and mass spectrometry, which revealed the unknown compound to be the bivalent N,N-bis(hexyl α-d-acetylmannosyl) acrylamide monomer, which contains two hexyl mannose units and one acrylamide group. To the best of our knowledge, this side reaction has not previously been disclosed, and may be useful for the construction of multivalent sugar ligands. Full article
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5 pages, 989 KiB  
Short Note
N-{2-[(3-Oxo-1,3-dihydro-2-benzofuran-1-yl)acetyl]phenyl}acetamide
by Ricaurte Rodríguez, Omar León, Felipe Quiroga and Jonnathan Cifuentes
Molbank 2021, 2021(3), M1244; https://doi.org/10.3390/M1244 - 02 Jul 2021
Viewed by 1967
Abstract
With the aim of obtaining different derivatives belonging to the isoindolo[2,1-a]quinoline family, we have synthesized a novel N-{2-[(3-oxo-1,3-dihydro-2-benzofuran-1-yl)acetyl]phenyl}acetamide derivative by a Claisen–Smichdt-type condensation reaction in 75% yield. Full article
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5 pages, 301 KiB  
Communication
Unexpected Formation of 4-aryl-1-(Propane-2-ylidenehydrazono)-2,3-diazaspiro[5.5]undec-3-ene by the Reaction of Pyridazinethiones Derivatives with Hydrazine
by Csilla Sepsey Für, György Keglevich and Hedvig Bölcskei
Molbank 2021, 2021(3), M1243; https://doi.org/10.3390/M1243 - 02 Jul 2021
Viewed by 1871
Abstract
After making a new series of spiro[cycloalkane]pyridazinones with high Fsp3 character available, the new target was to synthesize derivatives comprising nitrogen-containing heterocycles, such as triazolo or tetrazolo rings. The corresponding thioxo derivatives (1a,b) seemed to be good starting [...] Read more.
After making a new series of spiro[cycloalkane]pyridazinones with high Fsp3 character available, the new target was to synthesize derivatives comprising nitrogen-containing heterocycles, such as triazolo or tetrazolo rings. The corresponding thioxo derivatives (1a,b) seemed to be good starting materials for the synthesis of tetrazolo derivatives. The reaction of the pyridazinethiones (1a,b) with hydrazine surprisingly resulted in Schiff bases (3a,b) deriving from the reaction of hydrazones (2a,b) with acetone. Full article
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Scheme 1

5 pages, 895 KiB  
Communication
Unexpected Metal-Free Dehydrogenation of a β-Ketoester to a Phenol Using a Recyclable Oxoammonium Salt
by Fabrizio Politano, William P. Brydon, Jyoti Nandi and Nicholas E. Leadbeater
Molbank 2021, 2021(1), M1180; https://doi.org/10.3390/M1180 - 13 Jan 2021
Cited by 6 | Viewed by 2878
Abstract
The conversion of ethyl 2-oxocyclohexanecarboxylate to ethyl salicylate using an oxoammonium salt is reported. The dehydrogenation reaction is operationally simple and compares favorably with previous literature examples for the same transformation and expands the scope of oxoammonium salts as reagents for oxidative functionalization [...] Read more.
The conversion of ethyl 2-oxocyclohexanecarboxylate to ethyl salicylate using an oxoammonium salt is reported. The dehydrogenation reaction is operationally simple and compares favorably with previous literature examples for the same transformation and expands the scope of oxoammonium salts as reagents for oxidative functionalization processes. Full article
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2020

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3 pages, 159 KiB  
Editorial
Editorial: Special Issue “Molecules from Side Reactions”
by Stefano D’Errico
Molbank 2020, 2020(4), M1172; https://doi.org/10.3390/M1172 - 30 Nov 2020
Viewed by 1643
Abstract
Organic synthesis is a powerful tool that allows researchers to express their scientific creativity [...] Full article
6 pages, 1458 KiB  
Short Note
Poly[1,3-Dimethyltetrahydropyrimidin-2(1H)-iminium [tri-µ2-cyanido-κ6C:N-dicuprate(I)]]
by Peter W. R. Corfield and Joseph R. Dayrit
Molbank 2020, 2020(4), M1170; https://doi.org/10.3390/M1170 - 24 Nov 2020
Cited by 2 | Viewed by 2235
Abstract
The title compound contains a guanidinium cation that was unexpectedly found during X-ray single crystal analysis of a copper(I) cyanide network expected to contain protonated N,N’-dimethyl-1,3-diaminopropane. The cation was presumably formed by reaction of the amine with cyanide ions in [...] Read more.
The title compound contains a guanidinium cation that was unexpectedly found during X-ray single crystal analysis of a copper(I) cyanide network expected to contain protonated N,N’-dimethyl-1,3-diaminopropane. The cation was presumably formed by reaction of the amine with cyanide ions in the aqueous sodium cyanide/copper cyanide mixtures used in the synthesis. The structure of the network solid features the guanidinium cation as a guest in an anionic two-dimensional polymeric framework with stoichiometry Cu2(CN)3. Confirmation of the structure was provided by analytical, thermal gravimetric and infrared data. Full article
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5 pages, 1170 KiB  
Short Note
4′-(N-(Propan-1,2-dienyl)pyrrol-2-yl)-2,2′:6′,2″-terpyridine
by Jérôme Husson and Laurent Guyard
Molbank 2020, 2020(2), M1142; https://doi.org/10.3390/M1142 - 10 Jun 2020
Cited by 5 | Viewed by 2370
Abstract
A new pyrrole-substituted terpyridine derivative that possesses an allene moiety was obtained as an “unexpected” sole product during an attempt to alkylate the N-atom of pyrrole with propargyl bromide in order to obtain an alkyne-functionalized terpyridine. Full article
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6 pages, 819 KiB  
Communication
Formation of an Isomeric Mixture of Dienynes Instead of a Diallene
by Susanne M. Petrova and Leiv K. Sydnes
Molbank 2020, 2020(2), M1133; https://doi.org/10.3390/M1133 - 11 May 2020
Cited by 1 | Viewed by 2158
Abstract
Attempts to convert 1,1,2,2,7,7,8,8-octaethoxyocta-3,5-diyne to a symmetric allene by reduction with lithium aluminum hydride failed. Instead reduction accompanied by isomerization occurred and afforded 1,1,2,7,8,8-hexaethoxyocta-2,6-dien-4-yne as a mixture of three isomers in 63% total isolated yield. Full article
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8 pages, 1272 KiB  
Communication
Unexpected Seven-Membered Ring Formation for Muraymycin-Type Nucleoside-Peptide Antibiotics
by Kristin Leyerer, Stefan Koppermann and Christian Ducho
Molbank 2020, 2020(2), M1122; https://doi.org/10.3390/M1122 - 26 Mar 2020
Cited by 1 | Viewed by 2267
Abstract
Naturally occurring nucleoside-peptide antibiotics such as muraymycins or caprazamycins are of major interest for the development of novel antibacterial agents. However, the synthesis of new analogues of these natural products for structure–activity relationship (SAR) studies is challenging. In our synthetic efforts towards a [...] Read more.
Naturally occurring nucleoside-peptide antibiotics such as muraymycins or caprazamycins are of major interest for the development of novel antibacterial agents. However, the synthesis of new analogues of these natural products for structure–activity relationship (SAR) studies is challenging. In our synthetic efforts towards a muraymycin-derived nucleoside building block suitable for attachment to a solid support, we came across an interesting side product. This compound resulted from an undesired Fmoc deprotection with subsequent cyclization, thus furnishing a remarkable caprazamycin-like seven-membered diazepanone ring. Full article
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9 pages, 927 KiB  
Communication
8-Fluoro-N-2-isobutyryl-2′-deoxyguanosine: Synthesis and Reactivity
by Andrei Solodinin, James Helmkay, Samuel Ollivier and Hongbin Yan
Molbank 2020, 2020(1), M1119; https://doi.org/10.3390/M1119 - 06 Mar 2020
Cited by 2 | Viewed by 2461
Abstract
3′,5′-O-Bis(tert-butyldimethylsilyl)-8-fluoro-N-2-isobutyryl-2′-deoxyguanosine was synthesized from 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-isobutyryl-2′-deoxyguanosine by the treatment with N-fluorobenzenesulfonimide. A similar fluorination reaction with 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-(N,N-dimethylformamidine)-2′-deoxyguanosine, however, failed to give [...] Read more.
3′,5′-O-Bis(tert-butyldimethylsilyl)-8-fluoro-N-2-isobutyryl-2′-deoxyguanosine was synthesized from 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-isobutyryl-2′-deoxyguanosine by the treatment with N-fluorobenzenesulfonimide. A similar fluorination reaction with 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-(N,N-dimethylformamidine)-2′-deoxyguanosine, however, failed to give the corresponding fluorinated product. It was found that 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine is labile under acidic conditions, but sufficiently stable in dichloroacetic acid used in solid phase synthesis. Incorporation of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis failed to give the desired products. Furthermore, treatment of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine with aqueous ammonium hydroxide did not give 8-fluoro-2′-deoxyguanosine, but led to the formation of a mixture consisting of 8-amino-N-2-isobutyryl-2′-deoxyguanosine and C8:5′-O-cyclo-2′-deoxyguanosine. Taken together, an alternative N-protecting group and possibly modified solid phase synthetic cycle conditions will be required for the incorporation of 8-fluoro-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis. Full article
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4 pages, 673 KiB  
Communication
Synthesis and Isolation of Diastereomeric Anomeric Sulfoxides from a d-Mannuronate Thioglycoside Building Block
by Eleni Dimitriou and Gavin J. Miller
Molbank 2020, 2020(1), M1111; https://doi.org/10.3390/M1111 - 18 Jan 2020
Cited by 1 | Viewed by 2136
Abstract
Methyl [S-phenyl 4-O-acetyl-2,3-di-O-benzyl-1-thio-α-d-mannopyranoside (R/S)S-oxide] uronate was synthesised from a thioglycoside mannosyl uronate donor in a 98% yield. By using one equivalent of meta-chloroperbenzoic acid (m-CPBA) as the sulphur oxidant, a smooth conversion to [...] Read more.
Methyl [S-phenyl 4-O-acetyl-2,3-di-O-benzyl-1-thio-α-d-mannopyranoside (R/S)S-oxide] uronate was synthesised from a thioglycoside mannosyl uronate donor in a 98% yield. By using one equivalent of meta-chloroperbenzoic acid (m-CPBA) as the sulphur oxidant, a smooth conversion to the diastereomeric sulfoxide products was achieved. The product was fully characterized by 1H, 13C and 2D NMR alongside MS analysis. Full article
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9 pages, 646 KiB  
Communication
Unexpected Formation of Oxetanes during the Synthesis of Dodeco-6,7-diuloses
by Marius Bayer, Cäcilia Maichle-Mössmer and Thomas Ziegler
Molbank 2020, 2020(1), M1108; https://doi.org/10.3390/M1108 - 14 Jan 2020
Cited by 2 | Viewed by 2848
Abstract
During the synthesis of symmetrical dodeco-6,7-diuloses that are potential candidates for inhibition of glycosidases, an unanticipated epoxide-oxetane rearrangement was observed. A bicyclic sugar consisting of a glycal moiety and an anomeric esterified furanose was oxidized under epoxidation conditions (mCPBA/KF). The isolation [...] Read more.
During the synthesis of symmetrical dodeco-6,7-diuloses that are potential candidates for inhibition of glycosidases, an unanticipated epoxide-oxetane rearrangement was observed. A bicyclic sugar consisting of a glycal moiety and an anomeric esterified furanose was oxidized under epoxidation conditions (mCPBA/KF). The isolation of the pure epoxide was not possible since a rapid reversible conversion accompanied by the migration of the ester group took place and resulted in the formation of an unusual oxetane-bridged disaccharide scaffold. X-ray diffractometric structure elucidation and the suggested mechanism of the rearrangement are provided. Full article
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5 pages, 372 KiB  
Short Note
N′-Acetyl-3-methyl-1,6-diphenyl-1H-pyrazolo[3,4-b]pyridine-4-carbohydrazide
by Júlio C. A. V. Soares and Luiza R. S. Dias
Molbank 2020, 2020(1), M1104; https://doi.org/10.3390/M1104 - 07 Jan 2020
Cited by 1 | Viewed by 2291
Abstract
Synthesis of N′-acetyl-3-methyl-1,6-diphenyl-1H-pyrazolo[3,4-b]pyridine-4-carbohydrazide from the phenyl acetates of 3-acetyl-5-(3-methyl-1,6-diphenyl-1H-pyrazolo[3,4-b]pyridine-4-yl)-2,3-dihydro-1,3,4-oxadiazol-2-yl in alkaline medium and its characterization by spectroscopic methods. Full article
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Scheme 1

2019

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6 pages, 2061 KiB  
Short Note
N-(2-Hydroxy-1,1-dimethylethyl)-3-methylbenzamide
by Hamad H. Al Mamari and Yousuf Al Lawati
Molbank 2020, 2020(1), M1099; https://doi.org/10.3390/M1099 - 19 Dec 2019
Cited by 5 | Viewed by 2594
Abstract
The title compound, N-(2-hydroxy-1,1-dimethylethyl)-3-methylbenzamide was synthesized by reacting 3-methylbenzoyl chloride or 3-methylbenzoic acid with 2-amino-2-methyl-1-propanol. In the present report, the synthesized target compound was fully characterized by various spectroscopic methods (1H NMR, 13C NMR, IR, GC-MS), its composition confirmed [...] Read more.
The title compound, N-(2-hydroxy-1,1-dimethylethyl)-3-methylbenzamide was synthesized by reacting 3-methylbenzoyl chloride or 3-methylbenzoic acid with 2-amino-2-methyl-1-propanol. In the present report, the synthesized target compound was fully characterized by various spectroscopic methods (1H NMR, 13C NMR, IR, GC-MS), its composition confirmed by elemental analysis, and its structure determined and confirmed by X-ray analysis. The importance of this compound lies in its possession of an N,O-bidentate directing group. Such a structural motif is potentially suitable for metal-catalyzed C–H bond functionalization reactions. Full article
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5 pages, 1069 KiB  
Short Note
5′-Chloro-5′-deoxy-2′,3′-O-isopropylidene-6-fluoro nebularine
by Andrea Patrizia Falanga, Maria Marzano, Monica Terracciano and Stefano D'Errico
Molbank 2019, 2019(4), M1097; https://doi.org/10.3390/M1097 - 13 Dec 2019
Cited by 1 | Viewed by 2378
Abstract
In this paper, we report on the synthesis and spectroscopic characterization of the novel nucleoside 5′-chloro-5′-deoxy-2′,3′-O-isopropylidene-6-fluoro nebularine, obtained as a side product during the second step of the synthesis of 5′-fluoro-5′-deoxy-5-aminoimidazole-4-carboxamide-β-d-riboside (5′-F-AICAR), a non-phosphorylable analogue of 5-aminoimidazole-4-carboxamide-β-d-riboside (AICAR). Full article
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8 pages, 973 KiB  
Communication
Access to d- and l-Psicose Derivatives via Hydroxy Methylation of Ribono Lactone
by Michael R. Imrich and Thomas Ziegler
Molbank 2019, 2019(4), M1096; https://doi.org/10.3390/M1096 - 10 Dec 2019
Cited by 1 | Viewed by 3090
Abstract
2,3,5-Tri-O-benzyl- and 2,3,5-tri-O-methyl-d-ribono-γ-lactone were converted with (methoxyethoxymethoxy)methyl and benzyloxy tributylstannane into the corresponding protected d-psicoses as mixtures of anomers in 31%–72% yield. Treatment of 2,3,5-tri-O-methyl-l-ribono-γ-lactone with benzyloxy tributylstannane afforded the corresponding l [...] Read more.
2,3,5-Tri-O-benzyl- and 2,3,5-tri-O-methyl-d-ribono-γ-lactone were converted with (methoxyethoxymethoxy)methyl and benzyloxy tributylstannane into the corresponding protected d-psicoses as mixtures of anomers in 31%–72% yield. Treatment of 2,3,5-tri-O-methyl-l-ribono-γ-lactone with benzyloxy tributylstannane afforded the corresponding l-psicose derivative as an anomeric mixture in 72% yield. Both methylated psicoses were further converted into 1,2-O-isopropylidene-3,4,6-tri-O-methyl-d- and l-psicofuranosides, the respective α- and β-anomers of which could be separated and characterized. Full article
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4 pages, 407 KiB  
Communication
Pyridine-Imidazlolium Salts: Oxidatively Cleavage of N-C Bond via Nitration
by Dumitrela Cucu (Diaconu) and Violeta Mangalagiu
Molbank 2019, 2019(4), M1095; https://doi.org/10.3390/M1095 - 23 Nov 2019
Cited by 3 | Viewed by 2173
Abstract
Azaheterocycles derivatives with pyridine-imidazole skeleton are compounds of great value for medicinal chemistry. We report herein the nitration of 1,1′-(pyridine-2,6-diylbis(methylene))bis{3-[2-(4-nitrophenyl)-2-oxoethyl]-1H-imidazol-3-ium} bromide using a typical mixture of nitric and sulphuric acid. The nitration occur with the oxidative cleavage of N–C bond between [...] Read more.
Azaheterocycles derivatives with pyridine-imidazole skeleton are compounds of great value for medicinal chemistry. We report herein the nitration of 1,1′-(pyridine-2,6-diylbis(methylene))bis{3-[2-(4-nitrophenyl)-2-oxoethyl]-1H-imidazol-3-ium} bromide using a typical mixture of nitric and sulphuric acid. The nitration occur with the oxidative cleavage of N–C bond between imidazolium ring and methylene group. Full article
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6 pages, 1522 KiB  
Short Note
(E)-4-(3-Phenylisoxazol-5-yl)but-3-en-2-one
by Nattawut Sawengngen, Alexandra A. Kolodina and Olga V. Serdyuk
Molbank 2019, 2019(3), M1081; https://doi.org/10.3390/M1081 - 18 Sep 2019
Cited by 4 | Viewed by 1946
Abstract
(E)-4-(3-Phenylisoxazol-5-yl)but-3-en-2-one was synthesized via the oxidative ring opening reaction of 2-(5-methylfuran-2-yl)-1-phenylethanone oxime, followed by the iodine mediated isomerization. Full article
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