Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• interaction with users, a graphical interface to the new functionality will be provided through the CCP4i2 [38] framework. This new version of the interface is at the testing stage at the time of publication. Comparison of the glycan features in electron density maps over a range of resolutions from selected

Palladium nanoparticles supported on chitin-based nanomaterials as heterogeneous catalysts for the Heck coupling reaction

• Tony Jin,
• Malickah Hicks,
• Davis Kurdyla,
• Sabahudin Hrapovic,
• Edmond Lam and
• Audrey Moores

Beilstein J. Org. Chem. 2020, 16, 2477–2483, doi:10.3762/bjoc.16.201

• DDA values of 5–10%, while the ChsNCs had DDA values between 80–95%. A full spectral assignment for all of the FTIR peaks can be found in our recent report [16]. This transformation of the acetamide functionality into an amine one had drastic effects on the physicochemical properties of the

• charged amino functionality, while ChNCs were less easily suspended. Zeta potential measurements of −24.6 mV for ChNCs and +36.8 mV for ChsNCs provided a rationale for these observations. With these differences between the two nanomaterials, we then explored how they behaved as catalyst supports for Pd

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• ://www.virtualglycome.org/DrawGlycan. The same web page gives access to a downloadable, standalone Graphical User Interface (GUI) version of this tool with additional functionality. It can be launched from different platforms including Windows, Mac or Linux. The program can be used to render glycans and glycopeptides using

Hierarchically assembled helicates as reaction platform – from stoichiometric Diels–Alder reactions to enamine catalysis

• David Van Craen,
• Jenny Begall,
• Johannes Großkurth,
• Leonard Himmel,
• Oliver Linnenberg,
• Elisabeth Isaak and
• Markus Albrecht

Beilstein J. Org. Chem. 2020, 16, 2338–2345, doi:10.3762/bjoc.16.195

• ]. Catechol ligands L-H2 with an ester functionality in the 3-position were prepared via conversion of the acid chloride of 2,3-dihydroxybenzoic acid to the corresponding esters. These ligands underwent a complexation with titanoyl(IV) bisacetylacetonate and lithium carbonate initially forming a mononuclear

Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 2212–2259, doi:10.3762/bjoc.16.186

• reaction followed by the reduction of the nitro functionality into the amine group and subsequently performing a Sandmeyer reaction as shown in Scheme 20 [14]. Additionally, they have reported the hydrogenation of sumanene to generate compound 89 having one benzene ring intact in the framework using Pd/C

• by condensing sumanenone 38 with the amino-system 133 in refluxing toluene. The synthesized compound 134 was then treated with Ag2O in THF to afford the corresponding quinonediimine 135 in respectable yield. Furthermore, the stepwise coordination of the imino functionality of compound 135 to the

• to the functional group transformation (molecular-surgery-type functionalization) by treating them with NaOH in EtOH/H2O (10:1) under reflux conditions to first convert esters functionality into the corresponding carboxylic acid derivatives. As displayed in Scheme 47, these acid derivatives were then

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• (Sciex) and HappyTools automated functionality. On close inspection, it was noted that peak integration under a Gaussian approximation would yield a high variation in the number of picked peaks per electropherogram (Figure 4A). The number of peaks picked using the automated approaches was on average 7

• the migration time at t in the electropherogram. For quantitation comparison, HappyTools Gaussian fitting and the Sciex 32Karat version 10.1 default peak area functionality was also calculated. A single bioreactor run with defined culture conditions for twelve days. (A to B) batch GU calculation using

A complementary approach to conjugated N-acyliminium formation through photoredox-catalyzed intermolecular radical addition to allenamides and allencarbamates

• Olusesan K. Koleoso,
• Matthew Turner,
• Felix Plasser and
• Marc C. Kimber

Beilstein J. Org. Chem. 2020, 16, 1983–1990, doi:10.3762/bjoc.16.165

• Scheme 4. Given our interest in the N,N’-aminal functionality [50], we also explored variation of the arylamine nucleophile. 2,4-Dimethylaniline, o-anisole, 2-trifluoromethoxyaniline and 3,5-ditrifluoromethylaniline were all effective in this transformation, giving their labile N,N’-allylaminal products

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• unsuccessful reduction of the corresponding ethyl ester (vide infra, 12). Then we turned our attention to the modified Julia reaction since the reduction of the ester functionality could be achieved at the sulfide stage [29], prior to its oxidation to give 6. Alcohol 6 was not stable in basic medium, as a

Three new O-isocrotonyl-3-hydroxybutyric acid congeners produced by a sea anemone-derived marine bacterium of the genus Vibrio

• Dandan Li,
• Enjuro Harunari,
• Tao Zhou,
• Naoya Oku and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1869–1874, doi:10.3762/bjoc.16.154

• showed HMBC correlations to the same carboxy carbon C1 (δC 165.6), revealing an intervening ester linkage. Finally, HMBC correlations from the methylene proton H22 and the oxymethine proton H3 to the other carboxy carbon C1 (δC 175.3) placed a carboxylic acid functionality on the methylene group, which

• chiral center and the carboxylic acid functionality [11]. Thus, the R-configuration was concluded for all four compounds 1–4. The compounds 1–4 are closely related to PHAs, the energy reserve substances for eubacteria and some species of archaea [12]. Both groups of compounds are composed of (R

Et₃N/DMSO-supported one-pot synthesis of highly fluorescent β-carboline-linked benzothiophenones via sulfur insertion and estimation of the photophysical properties

• Dharmender Singh,
• Vipin Kumar and
• Virender Singh

Beilstein J. Org. Chem. 2020, 16, 1740–1753, doi:10.3762/bjoc.16.146

• ] which were attributed to the presence of an electrophilic as well as a nucleophilic functionality in this natural product [1]. Encouraged by the applications of β-carboline and benzothiophene motifs in medicinal and materials chemistry, it was envisaged to construct a β-carboline-based novel molecular

Facile synthesis of 7-alkyl-1,2,3,4-tetrahydro-1,8-naphthyridines as arginine mimetics using a Horner–Wadsworth–Emmons-based approach

• Rhys A. Lippa,
• John A. Murphy and
• Tim N. Barrett

Beilstein J. Org. Chem. 2020, 16, 1617–1626, doi:10.3762/bjoc.16.134

• 13.8) [1] replicating the side-on salt-bridge binding interaction made between the guanidinium functionality of arginine and an aspartic acid residue in the protein. Consequently, this moiety has been used in various integrin inhibitors (Figure 1) [2][3][4][5][6][7][8]. Current routes to install

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

The McKenna reaction – avoiding side reactions in phosphonate deprotection

• Katarzyna Justyna,
• Joanna Małolepsza,
• Damian Kusy,
• Waldemar Maniukiewicz and
• Katarzyna M. Błażewska

Beilstein J. Org. Chem. 2020, 16, 1436–1446, doi:10.3762/bjoc.16.119

• from the reaction mixture by washing with aqueous sodium carbonate solution. The model compounds used for this study (in red: the functionality of the molecules vulnerable to side reactions). Schematic overview of the McKenna reaction including the decomposition of BTMS in protic solvents. The desired

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• -palladated complexes 4 with CO in methanol is a good option to promote the liberation of the organic cyclobutane, while retaining the functionalities already present (C–F, C–Cl, C–NO2, C–CF3 and –C(H)=C(H)– groups) and introducing a new functionality, i.e., the methoxycarbonyl group, selectively at the ortho

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• . Protons H-8 and H-9 showed three-bond couplings (J = 8.2 Hz), while H-9 showed a weak four-bond correlation with H-5 (J = 1.9 Hz). Relatively intense cross peaks from H-5 and H-9 to the deshielded carbon C-7 (δC 152.8) suggested the oxygen functionality at the meta-position to C-5 and C-9. Intense HMBC

Synthesis of novel multifunctional carbazole-based molecules and their thermal, electrochemical and optical properties

• Nuray Altinolcek,
• Ahmet Battal,
• Mustafa Tavasli,
• William J. Peveler,
• Holly A. Yu and
• Peter J. Skabara

Beilstein J. Org. Chem. 2020, 16, 1066–1074, doi:10.3762/bjoc.16.93

• transport properties with positive solvatochromism. Whilst 7a showed very low emission intensity, 7b showed very high emission intensity. It is noted that the conjugation in compound 7b encompasses the N atom of the carbazole ring and the formyl functionality (viz. the donor/acceptor units of the ICT

Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates

• Phil M. Pithan,
• Sören Steup and
• Heiko Ihmels

Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82

• upon the addition of Hg2+ may have been caused by the low propensity of these cations to coordinate to the imine functionality and/or the inability to be involved in the subsequent electron transfer. Conclusion The spirooxazine–quinolizinium conjugates 3a and 3b were synthesized by a base-catalyzed

Reaction of indoles with aromatic fluoromethyl ketones: an efficient synthesis of trifluoromethyl(indolyl)phenylmethanols using K₂CO₃/n-Bu₄PBr in water

• Thanigaimalai Pillaiyar,
• Masoud Sedaghati and
• Gregor Schnakenburg

Beilstein J. Org. Chem. 2020, 16, 778–790, doi:10.3762/bjoc.16.71

• product 3a by excluding A for the next catalytic cycle. Further, to prove this hypothesis the following control experiments were performed. The reaction of 1-methylindole (1l) with 2a failed to provide the product (Scheme 4). It suggests that the indole having a free NH-functionality is important to

Recent advances in Cu-catalyzed C(sp³)–Si and C(sp³)–B bond formation

• Balaram S. Takale,
• Ruchita R. Thakore,
• Elham Etemadi-Davan and
• Bruce H. Lipshutz

Beilstein J. Org. Chem. 2020, 16, 691–737, doi:10.3762/bjoc.16.67

• the Oestreich group in 2016 [27]. The reaction could be performed using CuCN as catalyst in the absence of a ligand. A wide variety of triflates 9, including some containing a remote tosylate, bromide, alkene, or alkyne functionality, afforded the desired alkylsilanes 10–16 in fair to good yields

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• Information File 1, Figure S7) and δ 6.57 and 7.63 ppm with a J value of 15 Hz for compound 18 (Supporting Information File 1, Figure S9) as inferred by 1H NMR analysis. The resulting Suzuki-coupled products 16 and 18, were subjected to benzylic oxidation expecting the olefin functionality would facilitate

Copper-catalyzed enantioselective conjugate reduction of α,β-unsaturated esters with chiral phenol–carbene ligands

• Shohei Mimura,
• Sho Mizushima,
• Yohei Shimizu and
• Masaya Sawamura

Beilstein J. Org. Chem. 2020, 16, 537–543, doi:10.3762/bjoc.16.50

• methoxy group (in L2), the enantioselectivity drastically dropped to −10% ee, while the yield remained 99% (Table 1, entry 2). Similarly, N,N'-dimesityl-NHC L3, which lacked an oxygen functionality in the N-aryl group, showed poor enantioselectivity (9% ee) with high yield (99% yield, Table 1, entry 3

Exploring the scope of DBU-promoted amidations of 7-methoxycarbonylpterin

• Anna R. Bockman and
• Jeffrey M. Pruet

Beilstein J. Org. Chem. 2020, 16, 509–514, doi:10.3762/bjoc.16.46

• activation of the methyl ester of 7-CMP (1), the use of an amine with an additional ester functionality can therefore pose a limitation in what this reaction may tolerate. Yields were diminished for this reaction, owing to a side reaction whereby the amine effectively polymerizes. However, the desired

• product was still accessible within a short reaction time, and easily purified [20]. This highlighted a limitation of the reaction, but nevertheless showed the reaction may be used in tethering additional reactive functionality to the pterin for future diversification. In an effort to better understand

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• in a given application which can be either a sensitizer, initiator, staining, activator or a filter material just to name a few possible examples. Unfortunately, literature often does not clearly distinguish between their functionality. Besides cyanines, there were made huge efforts to synthesize

• provides the living nature of the process as well as control over the control of functionality as confirmed by the spectroscopic analyses, and chain extension and block copolymerization experiments [138]. The same strategies were also performed in NIR region using NIR sensitizers comprising cationic

Architecture and synthesis of P,N-heterocyclic phosphine ligands

• Wisdom A. Munzeiwa,
• Bernard Omondi and
• Vincent O. Nyamori

Beilstein J. Org. Chem. 2020, 16, 362–383, doi:10.3762/bjoc.16.35

• sterically crowded biaryl ligands as they showed outstanding performances [8]. Phosphines with imidazole and imidazoline functional groups present some interesting features. The imidazolium functionality mimics active sites in biological molecules [83][84]. The ionic nature adds another dimension to the

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• presence of DNA. Based on our interest in the chemistry and biology of the oxime functionality [54][55][56][57], as well as in their DNA photolytic interaction upon UV irradiation [9][10][11][43] we have decided to investigate the behaviour of carefully designed O-carbamoyl derivatives of p-pyridine