Synthesis of novel derivatives of 5-hydroxymethylcytosine and 5-formylcytosine as tools for epigenetics

• Anna Chentsova,
• Era Kapourani and
• Athanassios Giannis

Beilstein J. Org. Chem. 2014, 10, 7–11, doi:10.3762/bjoc.10.2

• the aldehyde group (1,2-addition) were not observed. The formation of compounds 8a–d can be explained assuming a Michael-type reaction of aldehyde 5 with organometallic reagents, subsequent isomerisation of the double bond followed by removal of one TCBoc group during the reaction and work-up as shown

Elucidation of the regio- and chemoselectivity of enzymatic allylic oxidations with Pleurotus sapidus – conversion of selected spirocyclic terpenoids and computational analysis

• Verena Weidmann,
• Mathias Schaffrath,
• Holger Zorn,
• Julia Rehbein and
• Wolfgang Maison

Beilstein J. Org. Chem. 2013, 9, 2233–2241, doi:10.3762/bjoc.9.262

• the literature protocol using m-chloroperbenzoic acid. The major epoxide 4a was obtained in good yield and a diastereoselectivity of 11:1. Isomerisation of epoxide 4a to allyl alcohol 22 was reported with aluminium triisopropoxide at 140 °C [46]. However, in our hands this procedure gave only complex

Synthesis of enones, pyrazolines and pyrrolines with gem-difluoroalkyl side chains

• Assaad Nasr El Dine,
• Ali Khalaf,
• Danielle Grée,
• Olivier Tasseau,
• Fares Fares,
• Nada Jaber,
• Philippe Lesot,
• Ali Hachem and
• René Grée

Beilstein J. Org. Chem. 2013, 9, 1943–1948, doi:10.3762/bjoc.9.230

• -mediated isomerisation affords enones in fair yields with a gem-difluoroalkyl chain. These derivatives were used to prepare pyrazolines and pyrrolines with the desired gem-difluoroalkyl side chain by cyclocondensations in good yields and with excellent stereoselectivity. A one-pot process was also

• ][21][22]. The goal of the present work is to demonstrate that selected propargylic derivatives [23][24][25] can be employed for the preparation of enones with a gem-difluoroalkyl chain by using an isomerisation process (Scheme 1). These intermediates can be employed for the preparation of

• base-mediated isomerisation process for an alkyne activated by an ester group was reported by Nineham and Raphael in 1949 [26]. Later, extension to other electrophilic alkynes was demonstrated by Sonye and Koide [27]. Recently, it has been established by Yamazaki’s group that propargylic alcohols

Ring opening of 2-aza-3-borabicyclo[2.2.0]hex-5-ene, the Dewar form of 1,2-dihydro-1,2-azaborine: stepwise versus concerted mechanisms

• Holger F. Bettinger and
• Otto Hauler

Beilstein J. Org. Chem. 2013, 9, 761–766, doi:10.3762/bjoc.9.86

• isomerisation reaction, 22 kcal mol−1, should be high enough for an experimental observation in solution. However, in solution the dimerisation of 3 is computed to have a very low barrier (3 kcal mol−1), and thus 3 is expected to be a short-lived reactive intermediate. Keywords: ab initio; azaborine; BN

• isomerisation reaction (Scheme 1) [2][3][4][5][6]. The relatively high barrier (ΔH‡ = 25.1 ± 2 kcal mol–1) [7][8] is due to the fact that the formation of benzene from 1 would require a disrotatory ring opening that is orbital-symmetry-forbidden according to the Woodward–Hoffmann rules [9][10][11]. The allowed

• conrotatory electrocyclic opening of one of the cyclobutene moieties of 1, on the other hand, would result in a highly strained cis,cis,trans-cyclohexa-1,3,5-triene (trans-benzene) isomer [10][11]. Computational investigations of the isomerisation have been performed to reveal mechanistic details [12][13][14

Photoionisation of the tropyl radical

• Kathrin H. Fischer,
• Patrick Hemberger,
• Andras Bodi and
• Ingo Fischer

Beilstein J. Org. Chem. 2013, 9, 681–688, doi:10.3762/bjoc.9.77

• an isomerisation in the pyrolysis. Benzyl is by about 70 kJ mol−1 more stable than tropyl [12][37][38], but a high activation barrier can be assumed for the isomerisation reaction in the pyrolysis source. Although we cannot exclude that the signal in the m/z = 91 mass channel might have some

Alkyne hydroarylation with Au N-heterocyclic carbene catalysts

• Cristina Tubaro,
• Marco Baron,
• Andrea Biffis and
• Marino Basato

Beilstein J. Org. Chem. 2013, 9, 246–253, doi:10.3762/bjoc.9.29

• catalysis, such as, e.g., products of double-bond isomerisation or deriving from insertion of more than one alkyne molecule into the same arene C–H bond, were however never detected with Au catalysts. Only in the case of p-xylene was the reaction again fully selective, albeit sluggish. Variations of the

Synthesis and testing of the first azobenzene mannobioside as photoswitchable ligand for the bacterial lectin FimH

• Vijayanand Chandrasekaran,
• Katharina Kolbe,
• Femke Beiroth and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2013, 9, 223–233, doi:10.3762/bjoc.9.26

• control of carbohydrate-specific bacterial adhesion, it has become our goal to synthesise azobenzene mannosides as photoswitchable inhibitors of type 1 fimbriae-mediated adhesion of E. coli. An azobenzene mannobioside 2 was prepared and its photochromic properties were investigated. The E→Z isomerisation

• ) in order to make a photoswitchable FimH antagonist available. Photoirradiation of azobenzene glycosides at ~365 nm effects E→Z isomerisation of the N=N double bond, and thermal relaxation or irradiation at ~450 nm leads to Z→E back isomerisation [13][14]. In the case that the E→Z isomerisation

• other hand, showed good solubility in polar organic solvents as well as in pure water. Thus, it was amenable to biological testing in aqueous buffer. E→Z photoisomerisation of azobenzene mannoside 6 was studied in DMSO, while isomerisation of azobenzene mannobioside 2 was performed in water

The Amadori rearrangement as glycoconjugation method: Synthesis of non-natural C-glycosyl type glycoconjugates

• Katharina Gallas,
• Gerit Pototschnig,
• Florian Adanitsch,
• Arnold E. Stütz and
• Tanja M. Wrodnigg

Beilstein J. Org. Chem. 2012, 8, 1619–1629, doi:10.3762/bjoc.8.185

• synthetic use, several steps during the introduction of the amine and the subsequent isomerisation to the ketose are reversible, and furthermore, the product itself can enter the Maillard reaction cascade [9][10] pathway. Consequently, a range of side and degradation products can be formed. In general, the

• rearrangement are known in the literature [11][12][13][14][15][16][17][18][19][20]. However, this reaction accomplishes the introduction of various amines onto the position C-1 of aldoses and at the same time the isomerisation to the corresponding 1-aminodeoxyketose without the requirement for protecting-group

Organocatalytic C–H activation reactions

• Subhas Chandra Pan

Beilstein J. Org. Chem. 2012, 8, 1374–1384, doi:10.3762/bjoc.8.159

• generate iminium ion 6. Finally, ring closure and proton loss provides the formation of the product 3. Redox alkylation In 2009, Tunge and co-workers demonstrated the synthesis of N-alkyl-pyrroles by redox isomerisation from the reaction of 3-pyrroline and aldehydes or ketones (Scheme 6) [17]. A series of

Recent advances towards azobenzene-based light-driven real-time information-transmitting materials

• Jaume García-Amorós and
• Dolores Velasco

Beilstein J. Org. Chem. 2012, 8, 1003–1017, doi:10.3762/bjoc.8.113

• -chromophore and the thermal cis-to-trans isomerisation, the kinetics and mechanism are also discussed as a key point for reaching azoderivatives endowed with fast thermal back-isomerisation kinetics. Keywords: kinetics; light-controlled materials; molecular switches; photochromic switches; push–pull

• azophenols; thermal isomerisation; Introduction Nowadays, there is an ever growing interest in molecular switching materials because of the very rapid development of modern technology. This tendency arises from the great applicability of such systems as active data elaboration, storage and communication

• applications are certainly azobenzenes. Azobenzene, a photochromic T-type system, exhibits a reversible isomerisation process between its trans and cis isomers of different stability. In this process, the photoreaction simply causes the rearrangement of the electronic and nuclear structure of the molecule

Algicidal lactones from the marine Roseobacter clade bacterium Ruegeria pomeroyi

• Ramona Riclea,
• Julia Gleitzmann,
• Hilke Bruns,
• Corina Junker,
• Barbara Schulz and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2012, 8, 941–950, doi:10.3762/bjoc.8.106

• ) that upon catalytic hydrogenation yielded cis-2-methylpentan-4-olide (7) as a single diastereomer, as reported previously [28]. Under prolonged treatment with KOt-Bu in t-BuOH under reflux, partial isomerisation to trans-2-methylpentan-4-olide (8) was achieved. Longer reaction times did not result in

• higher yields of the trans isomer, but instead in loss of material due to decomposition, and therefore the isomerisation was stopped after one day. By using the same approach starting from 12 and pent-1-en-3-ol (14) pure cis-2-methylhexan-4-olide (9) was obtained by esterification to pent-1-en-3-yl

• methacrylate (16), ring-closing metathesis to 2-methylhex-2-en-4-olide (17), and catalytic hydrogenation. The isomerisation of 9 with KOt-Bu in t-BuOH again provided a mixture of 9 and its diastereomer trans-2-methylhexan-4-olide (10). Comparison of GC retention times and mass spectra of the synthetic material

Intramolecular carbenoid ylide forming reactions of 2-diazo-3-keto-4-phthalimidocarboxylic esters derived from methionine and cysteine

• Marc Enßle,
• Stefan Buck,
• Roland Werz and
• Gerhard Maas

Beilstein J. Org. Chem. 2012, 8, 433–440, doi:10.3762/bjoc.8.49

• ][6][7][8] illustrate the wide range of applications. As far as sulfonium ylides are concerned, thermally induced isomerisation, that is the 1,2-shift of a substituent (Stevens rearrangement) and [2,3]-sigmatropic rearrangement of allylsulfonium ylides [9][10][11], and the use as C1 building blocks in

Liquid-crystalline nanoparticles: Hybrid design and mesophase structures

• Gareth L. Nealon,
• Romain Greget,
• Cristina Dominguez,
• Zsuzsanna T. Nagy,
• Daniel Guillon,
• Jean-Louis Gallani and
• Bertrand Donnio

Beilstein J. Org. Chem. 2012, 8, 349–370, doi:10.3762/bjoc.8.39

• magnetisation, and which the authors attributed to a change in the electric polarisation at the surface induced by the cis–trans isomerisation of the azo moiety upon irradiation, although no indication was given as to whether the hybrids displayed any mesophase behaviour. Nanoparticles coated with rodlike proto

Meta-metallation of N,N-dimethylaniline: Contrasting direct sodium-mediated zincation with indirect sodiation-dialkylzinc co-complexation

• David R. Armstrong,
• Liam Balloch,
• Eva Hevia,
• Alan R. Kennedy,
• Robert E. Mulvey,
• Charles T. O'Hara and
• Stuart D. Robertson

Beilstein J. Org. Chem. 2011, 7, 1234–1248, doi:10.3762/bjoc.7.144

• -) metallation was favoured by direct sodium-mediated zincation. Keywords: alkali metal; crystal structure; isomerisation; metallation; zincation; Introduction While the metallation reaction remains an essential tool for constructing substituted aromatic compounds [1][2], the quest for new improved reagents

• experimental evidence for a two-step mechanism in deprotonative metallations with TMP-zincates but additionally pose the question; “is the unique meta-metallation of N,N-dimethylaniline a consequence of TMP induced isomerisation?” This study attempts to answer this important question. Herein we investigate in

• the secondary amine facilitates rearrangement of some ortho-zincated aryl molecules to meta- and para-isomers (in a 4.3:2.6:1 ratio, resulting from the amination reaction of TMP(H) with one t-Bu group) [28]. The smaller degree of isomerisation in the N,N-dimethylaniline system can be rationalised at

Intramolecular hydroamination of alkynic sulfonamides catalyzed by a gold–triethynylphosphine complex: Construction of azepine frameworks by 7-exo-dig cyclization

• Hideto Ito,
• Tomoya Harada,
• Hirohisa Ohmiya and
• Masaya Sawamura

Beilstein J. Org. Chem. 2011, 7, 951–959, doi:10.3762/bjoc.7.106

• unstable at room temperature even in the absence of the gold-catalyst. According to these results, the formation of exomethylene compound 6 and subsequent alkene isomerisation should not be a major pathway to 5. Instead, a possible reaction pathway from 4a to 5a is illustrated in Figure 4. First, the

• that the reaction of the N-tosylbenzamide 4n afforded exceptionally the exomethylene isomer 6n. One conceivable reason is that the alkene isomerisation was prevented due to a ring strain in the seven-membered ring of 5n, of which six out of seven atoms are sp2-hybridized. Conclusion We demonstrated

Application of the diastereoselective photodeconjugation of α,β-unsaturated esters to the synthesis of gymnastatin H

• Ludovic Raffier and
• Olivier Piva

Beilstein J. Org. Chem. 2011, 7, 151–155, doi:10.3762/bjoc.7.21

• configuration of the C-6 centre of the target molecule was controlled. Keywords: amide; diastereoselective protonation; dienol; isomerisation; Wittig reaction; Introduction The photodeconjugation of α,β-unsaturated esters 1 – which bear at least one hydrogen atom on γ-position – allows a straightforward

• from a [1,5]-sigmatropic rearrangement). It was shown that the efficiency of the isomerisation process is highly dependent on the nature of the solvent and on the presence of various additives (e.g., amines) which could catalyse the reketonisation of the transient dienol [4] (Scheme 1). Despite the

• potential interest in β,γ-unsaturated acid derivatives, until recently only a few applications of this photochemical transformation in total synthesis appeared in the literature. However, the scope of the photochemical isomerisation has been greatly enhanced thanks to the development of diastereo- and

Stereoselectivity of supported alkene metathesis catalysts: a goal and a tool to characterize active sites

• Christophe Copéret

Beilstein J. Org. Chem. 2011, 7, 13–21, doi:10.3762/bjoc.7.3

• )-alkene products (AlkR1R1 and AlkR2R2), two are degenerate leaving the reactant untouched (Z-AlkR1R2 → Z-AlkR1R2), and two yield the alkene reactant with the opposite stereochemistry (Z-AlkR1R2 → E-AlkR1R2); the latter corresponding to an isomerisation. As the products AlkR1R1 and AlkR2R2 build up in the

• reaction mixture, they will undergo the same processes, including isomerisation, until the overall thermodynamic equilibrium is reached, typically leading to the formation of the E-products for di-substituted alkenes, in particular when one of the substituent is an electron withdrawing group. Any kinetic

• information will be obtained only at low conversions, where isomerisation is minimal. This can be performed by looking at the (E/Z) ratio of products at low conversions, but the best approach is to study the evolution of the (E/Z) ratio of the reactant (E/Z)t-reactant vs products (E/Z)t-product as a function

The cross-metathesis of methyl oleate with cis-2-butene-1,4-diyl diacetate and the influence of protecting groups

• Arno Behr and
• Jessica Pérez Gomes

Beilstein J. Org. Chem. 2011, 7, 1–8, doi:10.3762/bjoc.7.1

• observed between the benzylidene catalyst [Ru]-1 and its indenylidene counterpart [Ru]-3. The self-metathesis of methyl oleate (1) mentioned above could not be suppressed. Other side-reactions were not observed. No double-bound isomerisation took place. Promising results were obtained with catalysts

About the activity and selectivity of less well-known metathesis catalysts during ADMET polymerizations

• Hatice Mutlu,
• Lucas Montero de Espinosa,
• Oĝuz Türünç and
• Michael A. R. Meier

Beilstein J. Org. Chem. 2010, 6, 1149–1158, doi:10.3762/bjoc.6.131

• isomerization. As a result, the corresponding transesterified polymer yields a mixture of diesters with different chain lengths, since double bond isomerisation and olefin metathesis occur concurrently. The molecular weight of the isomerized diesters thus varies by multiples of 14 g/mol (one methylene group

Light-induced olefin metathesis

• Yuval Vidavsky and
• N. Gabriel Lemcoff

Beilstein J. Org. Chem. 2010, 6, 1106–1119, doi:10.3762/bjoc.6.127

• early beginnings of light induced olefin metathesis by the use of ill defined tungsten complexes, up to the most recent developments in light induced ruthenium based isomerisation and activation. Review Early tungsten catalysed photometathesis The first examples for photoinitiated metathesis were

Redox-active tetrathiafulvalene and dithiolene compounds derived from allylic 1,4-diol rearrangement products of disubstituted 1,3-dithiole derivatives

• Filipe Vilela,
• Peter J. Skabara,
• Christopher R. Mason,
• Thomas D. J. Westgate,
• Asun Luquin,
• Simon J. Coles and
• Michael B. Hursthouse

Beilstein J. Org. Chem. 2010, 6, 1002–1014, doi:10.3762/bjoc.6.113

• rotation and therefore isomerisation. It can be anticipated that the two isomers will not differ significantly in their electrochemical properties (see below). Compound 3 was trans-chalcogenated by mercury(II)acetate in a mixture of acetic acid and CH2Cl2 to give the oxo derivative 26 in 89% yield

The C–F bond as a conformational tool in organic and biological chemistry

• Luke Hunter

Beilstein J. Org. Chem. 2010, 6, No. 38, doi:10.3762/bjoc.6.38

• (41), the electronegative fluorine atom exerts an inductive “pull” which lowers the C(O)–N bond order [46]. This reduces the energy barrier to cis/trans isomerisation, allowing the peptide strand to pre-organise into the required all-trans conformation and thereby facilitating triple helix formation

Synthesis of phosphonate and phostone analogues of ribose-1-phosphates

• Pitak Nasomjai,
• David O'Hagan and
• Alexandra M. Z. Slawin

Beilstein J. Org. Chem. 2009, 5, No. 37, doi:10.3762/bjoc.5.37

• ). This phosphate intermediate becomes the substrate for a ring opening isomerisation reaction converting 5-fluoro-5-deoxyribose-1-phosphate (5) to 5-fluoro-5-deoxyribulose-1-phosphate (6). Further processing to fluoroacetaldehyde (7) and then conversion to fluoroacetate (1) and 4-fluorothreonine (2

• both 5′-FDA and adenosine, and thus the presence or absence of fluorine at the C-5′-position is not a requisite for catalysis. The next enzymatic step involves a ring opening isomerisation of the ribose-1-phosphate 5. In this paper we report the synthesis of phosphonate analogues 8 and 9 of ribose-1

Mitomycins syntheses: a recent update

• Jean-Christophe Andrez

Beilstein J. Org. Chem. 2009, 5, No. 33, doi:10.3762/bjoc.5.33

Convenient methods for preparing π-conjugated linkers as building blocks for modular chemistry

• Jiří Kulhánek,
• Filip Bureš and
• Miroslav Ludwig

Beilstein J. Org. Chem. 2009, 5, No. 11, doi:10.3762/bjoc.5.11

• pure (E)-stilbenes [38]. However, compared to N,N-dimethylaminostilbene, the isomerization of 4-bromo-4′-methoxystilbene required twelve times the prolonged reaction time (4 vs. 48 h) while the isomerisation of unsubstituted 4-bromostilbene did not take a place at all. Hence, 5a had to be prepared by