Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration

• Yipeng Yin,
• Reed Arneson,
• Alexander Apostle,
• Adikari M. D. N. Eriyagama,
• Komal Chillar,
• Emma Burke,
• Martina Jahfetson,
• Yinan Yuan and
• Shiyue Fang

Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146

• compared with the authentic dsODNs using agarose gel electrophoresis (steps 3 and 3', Figure 1). As shown in Figure 2A,B, the synthesized and authentic samples have similar migration distances. The identity of the ODNs was then determined by Sanger sequencing. The PCR products were cloned into the pCR

• and reverse primers (step 6). The PCR products were analyzed with agarose gel electrophoresis (step 5', Figure 1, and Figure 3). Based on migration distances, in the case of 399 bp sequence, 20 out of 32 colonies likely contained the expected 399 bp fragment. Three colonies were submitted for Sanger

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• essential in the cell biology [15][16]. In addition, GAGs also facilitate cell migration, act as shock-absorbers in joints and as a sieve in extracellular matrices and are important in maintaining the compressibility of the cartilage. The participation of GAGs in physiological, pathological, and therapeutic

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

• Alessandro L. Alves,
• Simone V. Bernardino,
• Carlos H. Stadtlober,
• Edivandro Girotto,
• Giliandro Farias,
• Rodney M. do Nascimento,
• Sergio F. Curcio,
• Thiago Cazati,
• Marta E. R. Dotto,
• Juliana Eccher,
• Leonardo N. Furini,
• Hugo Gallardo,
• Harald Bock and
• Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

• ), organic light-emitting diodes (OLEDs) and sensors [1][2]. Columnar liquid crystals are attractive due to their solution processability and their self-organization in highly anisotropic supramolecular architectures, which favors the mainly one-dimensional migration of charge carriers with an anisotropy of

• charge transport behavior. DFT calculations assisted the interpretation of electron and hole migration mechanism using the frontier orbital energies and the conjugation within the π-system. Results and Discussion The syntheses of 1 and 2 were previously published in [25] and [26], respectively. 1 is a

N-Sulfenylsuccinimide/phthalimide: an alternative sulfenylating reagent in organic transformations

• Fatemeh Doraghi,
• Seyedeh Pegah Aledavoud,
• Mehdi Ghanbarlou,
• Bagher Larijani and
• Mohammad Mahdavi

Beilstein J. Org. Chem. 2023, 19, 1471–1502, doi:10.3762/bjoc.19.106

• efficient Lewis acid catalyst (Scheme 10) [50]. In the procedure, oxidative cleavage of one S–N bond and 1,2-sulfur migration afforded π-conjugated 6-substituted 2,3-diarylbenzo[b]thiophenes 16. A plausible mechanism is shown in Scheme 11. The coordination of AlCl3 with the phthalimide/succinimide unit of 1

• , which underwent a ring expansion and 1,2-sulfur migration and subsequent deprotonation/aromatization to deliver product 16. Another work in the use of AlCl3 for cyclization of N‑arylpropynamides 17 with N‑sulfanylsuccinimides 1 was described by Gao and Zhou et al. (Scheme 12) [51]. Annulation in the

• , CF3CO2SR, which was produced in the previous step, as a sulfenylating reagent, reacted with I to form the 3,3-bis-sulfide indolenium III. The migration of a sulfide group to the C2-site of indole, generated 2,3-disubstituted indole V. Protonation of V resulted in indolenium intermediate VI. Finally

Application of N-heterocyclic carbene–Cu(I) complexes as catalysts in organic synthesis: a review

• Nosheen Beig,
• Varsha Goyal and
• Raj K. Bansal

Beilstein J. Org. Chem. 2023, 19, 1408–1442, doi:10.3762/bjoc.19.102

• isomerization-induced alkenylation of electron-rich heteroarenes 187 and 188 utilizing allyl halides as reactants. The same catalyst system was found to effectively promote double-bond migration of the initially formed allylarenes resulting in vinylarene products. This method has been successfully used to

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• ) The second scheme is shorter (Figure 4D) and starts with the acylation of 4.16 to produce 4.17. Then, the debenzylation of the primary alcohol produced 4.18. Interestingly, the migration of the acetyl group from sn-2 to sn-3 position was not observed. Finally, the installation of the phosphocholine

• whereas heating it in 75% acetic acid solution produced the deprotected compound but migration of the acyl group from the sn-2 to the sn-3 position lead to an inseparable mixture of regioisomers. A selective desilylation of 12.5 was finally achieved with BF3·Et2O producing 12.6 without migration of the

• constitutive Ca2+ entry thus influencing breast cancer cell migration [106]. 1.4 Analogues of PAF with modification at the sn-3 position Finally, a series of PAF’s analogues were reported by changing the structure of the phosphocholine polar head group. Ohno et al. replaced the trimethylammonium moiety by

The unique reactivity of 5,6-unsubstituted 1,4-dihydropyridine in the Huisgen 1,4-diploar cycloaddition and formal [2 + 2] cycloaddition

• Xiu-Yu Chen,
• Hui Zheng,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2023, 19, 982–990, doi:10.3762/bjoc.19.73

• acetylenedicarboxylate to give the adduct C. Then, the direct coupling of the positive charge and the negative charge affords the 2-azabicyclo[4.2.0]octa-3,7-diene 5. On the other hand, a carbenium ion D can be formed by migration of a hydrogen atom in intermediate C, which in turn converts into a fused bicyclic

A new oxidatively stable ligand for the chiral functionalization of amino acids in Ni(II)–Schiff base complexes

• Alena V. Dmitrieva,
• Oleg A. Levitskiy,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2023, 19, 566–574, doi:10.3762/bjoc.19.41

• to rt in [40]) allowed obtaining the targeted compound; however, acylation was accompanied with the migration of the t-Bu group yielding 2-benzoyl-4-tert-butylaniline and the corresponding 5-butylated isomer in a 10:1 ratio. Our attempts to separate the isomers were unsuccessful. However, as it will

Transition-metal-catalyzed domino reactions of strained bicyclic alkenes

• Austin Pounder,
• Eric Neufeld,
• Peter Myler and
• William Tam

Beilstein J. Org. Chem. 2023, 19, 487–540, doi:10.3762/bjoc.19.38

• ) [49]. In contrast to the 1,2-difunctionalization of bicyclic alkenes via arylzinc reagents reported by Nakamura under Fe catalysis (Scheme 13) [48], this reaction is considered to undergo a 1,4-Co migration ultimately generating 1,4-difunctionalization species. Mechanistically, the reaction likely

• would afford the [2 + 2] adduct. Hydroruthenation of the allene produces 103 which can either undergo reductive elimination to afford the cyclopropanated bicyclic alkene or undergo a [2 + 2] cycloreversion to generate the Ru–carbene 104. The Ru–carbene 104 can rearrange to 100 through a 1,3-migration of

• previously been a challenging transformation due to the propensity of these systems to produce non-cyclized hydroarylation products due to an unproductive rhodium 1,4-migration on heteroaromatic moieties. The use of benzothiophene, benzofurans, and benzopyrrole boronate esters in this investigation prevented

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• assignments and even error propagation, and shows the importance of structure elucidation by classical methods, i.e., isolation and compound characterisation by NMR spectroscopy and determination of optical rotation. Compound 51 can be generated biosynthetically from I3a through 1,2-methyl migration to I3b

1,4-Dithianes: attractive C2-building blocks for the synthesis of complex molecular architectures

• Bram Ryckaert,
• Ellen Demeyere,
• Frederick Degroote,
• Hilde Janssens and
• Johan M. Winne

Beilstein J. Org. Chem. 2023, 19, 115–132, doi:10.3762/bjoc.19.12

• pioneered by Parham and co-workers to be the most suited (Scheme 4, 12 → 2) [28][29][30]. Parham described a ring expansion of 1,3-dithiolanes derived from α-halocarbonyls into the 1,4-dithianes which then dehydrohalogenate to afford dihydrodithiins. The ring expansion involves a 1,2-sulfur migration of a β

• the relative stereochemistry (Scheme 17) [108][109]. 6 Synthetic equivalents of vinyl carbenes in (2 + 1) cycloadditions: Au(I)-catalyzed generation of 1,4-dithiane-fused vinylcarbene species In 2007, Wang and co-workers reported a gold-catalyzed Parham-type 1,2-sulfur migration to generate in situ a

• during our (formal) total synthesis of (±)-cephalotaxine (130, Scheme 20b) [112]. Here, the desired desulfurization of a 1,4-dithiane could not be achieved without concomitant migration of an alkene double bond (viz 127 → 128), making the final steps to complete the synthesis quite cumbersome, as at best

Combining the best of both worlds: radical-based divergent total synthesis

• Kyriaki Gennaiou,
• Antonios Kelesidis,
• Maria Kourgiantaki and
• Alexandros L. Zografos

Beilstein J. Org. Chem. 2023, 19, 1–26, doi:10.3762/bjoc.19.1

• a semipinacol rearrangement leading to 95, followed by subsequent cyclization to natural products guignardone A (96) and C (97). This process involved 1,2-allyl migration and C–O bond formation through a semipinacol rearrangement and a cyclodehydration cascade reaction (Scheme 8). Following the same

Total synthesis of grayanane natural products

• Nicolas Fay,
• Rémi Blieck,
• Cyrille Kouklovsky and
• Aurélien de la Torre

Beilstein J. Org. Chem. 2022, 18, 1707–1719, doi:10.3762/bjoc.18.181

• cyclization based on a bridgehead tertiary carbocation intermediate forging the B ring; iii) redox manipulations and a 1,2-migration as final steps. The synthesis started from (S)-ketone 44 which was prepared via asymmetric CBS reduction of diketone 26 (Scheme 7). Firstly, this (S)-ketone 44 was transformed

Redox-active molecules as organocatalysts for selective oxidative transformations – an unperceived organocatalysis field

• Elena R. Lopat’eva,
• Igor B. Krylov,
• Dmitry A. Lapshin and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2022, 18, 1672–1695, doi:10.3762/bjoc.18.179

• chiral copper complex. An extraordinary example of an asymmetric difluorination of alkenes with the migration of aryl or methyl groups was shown using a chiral aryl iodide catalyst [149][150] (Scheme 35). Depending on the nature of the migrating group, two mechanisms are possible that determine the

• -organocatalyzed vinylarene diamination. Iodoarene-organocatalyzed asymmetric CH-hydroxylation of benzylic substrates. Iodoarene-organocatalyzed asymmetric difluorination of alkenes with migration of aryl or methyl groups. Examples of 1,2-diiodo-4,5-dimethoxybenzene-catalyzed electrochemical oxidative

Preparation of β-cyclodextrin-based dimers with selectively methylated rims and their use for solubilization of tetracene

• Konstantin Lebedinskiy,
• Volodymyr Lobaz and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2022, 18, 1596–1606, doi:10.3762/bjoc.18.170

• selectively methylated rims The important part of this work was proving the structure of the synthesized compounds because we worked with non-symmetrical CDs; moreover, we used protection–deprotection methods for partial methylation, so we could expect a cleavage or even migration of protective groups

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• enormous number of interactions with other proteins. Currently, more than 200 interacting proteins are known. 14-3-3 proteins play a significant role in cell signaling [2][3] and they were found to be essential in processes such as differentiation, apoptosis, or migration [4]. 14-3-3 proteins also play a

Modular synthesis of 2-furyl carbinols from 3-benzyldimethylsilylfurfural platforms relying on oxygen-assisted C–Si bond functionalization

• Sebastien Curpanen,
• Per Reichert,
• Gabriele Lupidi,
• Giovanni Poli,
• Julie Oble and
• Alejandro Perez-Luna

Beilstein J. Org. Chem. 2022, 18, 1256–1263, doi:10.3762/bjoc.18.131

• alkoxides We first contemplated the possibility to promote C3–Si bond functionalization through intramolecular activation by alkoxides [15]. It was reported that lithium alkoxides A undergo 1,4-silyl migration (Brook rearrangement) to generate C2-lithiated furans C, which in turn can react in the presence

• from E, and thus affording the C3-lithiated furan derivative G upon 1,4-silyl migration as well as the electrophilic substitution product H in the presence of an appropriate electrophile (Scheme 3, bottom). However, treatment of aldehyde 1b with n-BuLi, followed by addition of benzaldehyde in THF/DMPU

• [25], afforded only the addition product 3b without any detectable formation of product 9, expected from 1,4-silyl migration/electrophilic substitution of 8 (Scheme 4, top). Conversely, treatment of alcohol 3a with t-BuOCu in the presence of allyl chloride, according to conditions developed by Takeda

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• biocatalytic dimerization reactions [20]. Contrary to flavone dimers and oligomers being abundant in nature, only limited dimeric compounds have been reported for isoflavones. Isoflavones bear a characteristic 3-phenylchroman skeleton, which is formed by the B-ring migration from the flavonoid scaffold

Inductive heating and flow chemistry – a perfect synergy of emerging enabling technologies

• Conrad Kuhwald,
• Sibel Türkhan and
• Andreas Kirschning

Beilstein J. Org. Chem. 2022, 18, 688–706, doi:10.3762/bjoc.18.70

• , yielding a reduced arylation product 77 [86][87]. Mechanistically, either diazo or carbene intermediates can be proposed, as Barluenga has outlined, and migration of the aryl group leads to an alkylboronic acid, which is hydrolyzed by protodeboronation, yielding the arylation product 77. A two-step flow

Unusual highly diastereoselective Rh(II)-catalyzed dimerization of 3-diazo-2-arylidenesuccinimides provides access to a new dibenzazulene scaffold

• Anastasia Vepreva,
• Alexander S. Bunev,
• Andrey Yu. Kudinov,
• Grigory Kantin,
• Mikhail Krasavin and
• Dmitry Dar’in

Beilstein J. Org. Chem. 2022, 18, 533–538, doi:10.3762/bjoc.18.55

• hydrogen shift. Indene C can either convert into the final indene 3a via a slow 1,3-migration of the hydrogen atom, or is intercepted by carbene A with the formation of cyclopropane D. The relative rates of these competing processes likely determine the composition of the final product mixture. The

• intermediate D into cycloheptadiene E is an example of a relatively rare reaction of the cyclopropane-ring expansion through a 1,5-C‒C bond migration [15][16][17]. This concerted process is followed by yet another 1,5-migration of the hydrogen atom, leading to the final dimer 2a. The formation of a single

Menadione: a platform and a target to valuable compounds synthesis

• Acácio S. de Souza,
• Ruan Carlos B. Ribeiro,
• Dora C. S. Costa,
• Fernanda P. Pauli,
• David R. Pinho,
• Matheus G. de Moraes,
• Fernando de C. da Silva,
• Luana da S. M. Forezi and
• Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 381–419, doi:10.3762/bjoc.18.43

• )ruthenium(II) dichloride as catalyst. Then, a BF3·OEt2-catalzyed migration of the methyl group to the C-2 position and removal of the tert-butoxy group in a 1,1,1,3,3,3-hexafluoroisopropanol (HFIP)/toluene mixture afforded 2-methyl-1,4-benzoquinone (29). Finally, a Diels–Alder reaction was performed with

Iridium-catalyzed hydroacylation reactions of C1-substituted oxabenzonorbornadienes with salicylaldehyde: an experimental and computational study

• Angel Ho,
• Austin Pounder,
• Krish Valluru,
• Leanne D. Chen and
• William Tam

Beilstein J. Org. Chem. 2022, 18, 251–261, doi:10.3762/bjoc.18.30

• explanation towards the sole production of the experimentally observed anti-acylated product 15. Although Weller and co-workers have elegantly demonstrated hydride migration, rather than the alternative carbometalation, occurs during rhodium-catalyzed intermolecular alkyne hydroacylation [78], no such

• experiment has been carried out under iridium catalysis. As such, we set out to explore the possibility acyl migration is favored over hydride migration in iridium-catalyzed hydroacylation reactions (Figure 2). Beginning with the two exo-η2-coordinated intermediates IN1a and IN1b, two possible transition

• states for the acyl migration, which exhibit a distorted Ir–C–C’–C’’ four-membered ring geometry, can be located. Directly comparing the hydrometalation process (Figure 1) to the carbometalation process, we see that acyl migration is unfavored, exhibiting activation energies of 19.2 (1bTS2d) to 20.7

Trichloroacetic acid fueled practical amine purifications

• Aleena Thomas,
• Baptiste Gasch,
• Enzo Olivieri and
• Adrien Quintard

Beilstein J. Org. Chem. 2022, 18, 225–231, doi:10.3762/bjoc.18.26

• 1). Presence of TCA in the 1H NMR spectra is easily monitored through a broad peak around 9 ppm and also through the upfield migration of the other peaks of the amine ammonium salt. Heating the amine salt precipitate neat at 100 °C also provided partial decarboxylation (Table 1, entry 2). In sharp

The enzyme mechanism of patchoulol synthase

• Houchao Xu,
• Bernd Goldfuss,
• Gregor Schnakenburg and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 13–24, doi:10.3762/bjoc.18.2

• migration from C to D in Scheme 1A), and a Wagner–Meerwein rearrangement to G. The final steps are identical to those in Akhila’s mechanism (Scheme 2A). This work also reported on a labelling experiment with (2-2H)FPP that was enzymatically converted with PTS with incorporation of deuterium at C2 of 3

• Information File 1). Notably, not only the double deuterium uptake into 3 from D2O, but also the loss of deuterium from (6-2H)FPP contradicts the mechanisms of Scheme 1 and Scheme 3 that both propose a migration of hydrogen from C6 to C3, either through a 1,4- or a 1,3-hydride shift. An additional experiment