Light-controllable dithienylethene-modified cyclic peptides: photoswitching the in vivo toxicity in zebrafish embryos

• Sergii Afonin,
• Oleg Babii,
• Aline Reuter,
• Volker Middel,
• Masanari Takamiya,
• Uwe Strähle,
• Igor V. Komarov and
• Anne S. Ulrich

Beilstein J. Org. Chem. 2020, 16, 39–49, doi:10.3762/bjoc.16.6

• -closed photoforms. The compound numbers are shown next to the data points. The in vitro data is from [30]. Values for the parent peptide 1 are marked black, and a white filling highlights the initial prototype 2. Color codes for the remaining peptides are the same as in Figure 3. Nomenclature, sequences

Synthetic terpenoids in the world of fragrances: Iso E Super^® is the showcase

• Alexey Stepanyuk and
• Andreas Kirschning

Beilstein J. Org. Chem. 2019, 15, 2590–2602, doi:10.3762/bjoc.15.252

• the amount of Iso E Super® (33) in a commercial perfume [25][26]. This trend culminated in Schön´s creation of Molecule 01 in the year 2005, a perfume that contains nothing else than Iso E Super® (33). Orb_ital from Nomenclature (75% Iso E Super®) followed in the year 2015. This fragrance collection

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• equivalent from one standpoint in a specific orientation. We termed such a group of such molecules perspective isomorphs. The general concept is outlined together with a nomenclature system. Furthermore, this concept has been visualized by artistic representations of molecules. The concept of perspective

• isomorphs and its discussions herein will extend current models and stimulate the discourse about the nature of atoms and molecules and especially their models. Keywords: art and science; nomenclature; perspective; representation in chemistry; structure; Introduction Up to now, epistemological concepts of

• , however, be placed into a different PI class, when viewed from a different angle. This way, they are perspective isomorphe with 4-fluorobiphenyl or benzoic acid. Nomenclature/coding of perspective isomorphs In order to make the concept of perspective isomorphs practicable and unmistakably understandable

An overview of the cycloaddition chemistry of fulvenes and emerging applications

• Ellen Swan,
• Kirsten Platts and
• Anton Blencowe

Beilstein J. Org. Chem. 2019, 15, 2113–2132, doi:10.3762/bjoc.15.209

• this review will lead to increased interest in these fields, and others yet to be investigated. General structure of fulvenes, named according to the number of carbon atoms in their ring. Whilst fulvenes have been numbered using several different systems, Chemical Abstracts nomenclature is used

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• ; TNF-α, tumor necrosis factor alpha; SCE, supercritical CO2 extraction; SL, sesquiterpene lactones. Comment on nomenclature This article uses semitrivial terpene nomenclature and hence the numbering of compounds atoms may differ from these obtained by using IUPAC names. The structure of the

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

• Tristan J. Keller,
• Joshua Bahr,
• Kristin Gratzfeld,
• Nina Schönfelder,
• Marcin A. Majewski,
• Marcin Stępień,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

• oriented relative to the HOPG main axis directions with γ(a,d1) = γ(b,d2) = (7 ± 2)°. The backbones are oriented with γ(c,d1) = (30 ± 4)° relative to the HOPG main axis direction d1. An additional nomenclature describes the orientation of the intermolecularly interdigitating OC16H33 (and OC10H21) side

New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita

• Frank Surup,
• Florian Hennicke,
• Nadine Sella,
• Maria Stroot,
• Steffen Bernecker,
• Sebastian Pfütze,
• Marc Stadler and
• Martin Rühl

Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98

• the leading peer-reviewed taxonomic journals, and the authors did not follow good scientific practice for typification when proposing these taxonomic changes. However, they subsequently published their entries in Index Fungorum, making them valid according to the current nomenclature rules, and the

Synthesis of a novel category of pseudo-peptides using an Ugi three-component reaction of levulinic acid as bifunctional substrate, amines, and amino acid-based isocyanides

• Maryam Khalesi,
• Azim Ziyaei Halimehjani and
• Jürgen Martens

Beilstein J. Org. Chem. 2019, 15, 852–857, doi:10.3762/bjoc.15.82

• . cIsolated yield of one of the diastereomers as pure stereoisomer after several recrystallization steps. ORTEP representation of compound (R*,S*)-4a with thermal ellipsoids at 50% probability. Opposite enantiomer is omitted for clarity. The atom numbering does not follow IUPAC nomenclature. Synthesis of

Carbonylonium ions: the onium ions of the carbonyl group

• Daniel Blanco-Ania and
• Floris P. J. T. Rutjes

Beilstein J. Org. Chem. 2018, 14, 2568–2571, doi:10.3762/bjoc.14.233

• Daniel Blanco-Ania Floris P. J. T. Rutjes Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands 10.3762/bjoc.14.233 Abstract The nomenclature of cations R1C(=O+R3)R2 (R1, R2, R3 = H or organyl) has been examined and shown to be in a state

• other fields of Organic Chemistry [24]. All these terms are ambiguous and none describes the actual structure of these intermediates. Some of these terms generated long ago when nomenclature was not as developed as it is today or were created without any sense of the etymology of the combined prefix and

• six valence electrons or a modification thereof. Discussion Oxacarbenium ions Firstly, “skeletal replacement” nomenclature (and also in Hantzsch–Widman nomenclature, but this kind of nomenclature is not applicable to the concerned intermediates) uses the “a” prefixes “oxa”, “aza”, “thia”… [25] for the

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• : the ether oxygen, the phenyl ring and the vinyl moiety. Since both the phenyl ring and the vinyl moiety interact with the solvent via a π cloud, preferred binding sites are indicated using the following nomenclature: P (phenyl) and E (ethenyl), respectively. The optimizations using B3LYP-D3(BJ)/def2

On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site

• Eirinaios I. Vrettos,
• Gábor Mező and
• Andreas G. Tzakos

Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80

• general, the ‘integrin’ nomenclature was first used in 1987 to describe a family of receptors, appearing as heterodimers of noncovalently associated α and β subunits, able to link the extracellular matrix (ECM) with the intracellular cytoskeleton to mediate cell adhesion, migration and proliferation [42

An alternative to hydrogenation processes. Electrocatalytic hydrogenation of benzophenone

• Cristina Mozo Mulero,
• Alfonso Sáez,
• Jesús Iniesta and
• Vicente Montiel

Beilstein J. Org. Chem. 2018, 14, 537–546, doi:10.3762/bjoc.14.40

• (nomenclature described in the experimental section) at different magnifications. The SEM image for the highest electrocatalytic loading discloses a brighter appearance compared to the lowest one since backscattering electrons from high atomic weight (e.g., palladium) are brighter than lower atomic weight (e.g

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• -carbon), and were calculated according to Zhao et al. [43]; (b) Names and amino acid sequences of the studied peptides; the substitution positions are marked as Xaa; Xaa = Leu, HfLeu, Ile or TfIle. Positions are named according to Schechter and Berger nomenclature [41]. Percentage of substrate remaining

Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

• José Enrique Barquera-Lozada and
• Gabriel Cuevas

Beilstein J. Org. Chem. 2017, 13, 1969–1976, doi:10.3762/bjoc.13.192

• coordinate of these four mechanisms. In the first proposed mechanism (path M, Figure 1) a conformational transformation of 1 must occur first. The most stable conformer has chair-boat conformation that according to Samek nomenclature is [15D5,1D14] (1a). This conformer is the one that is present in solution

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• mycolactone-producing bacteria should be reclassified as M. ulcerans [45]. Within this review, however, the originally proposed species names (M. marinum, M. ulcerans ecovar liflandii, M. pseudoshottsii, M. ulcerans subsp. shinshuense) will be used. It should also be noted at this point that the nomenclature

(Z)-Selective Takai olefination of salicylaldehydes

• Stephen M. Geddis,
• Caroline E. Hagerman,
• Warren R. J. D. Galloway,
• Hannah F. Sore,
• Jonathan M. Goodman and
• David R. Spring

Beilstein J. Org. Chem. 2017, 13, 323–328, doi:10.3762/bjoc.13.35

• of substituted salicylaldehydes. Ortho- and meta-nomenclature refers to the substituents’ relationship to the aldehyde moiety. Supporting Information Supporting Information File 36: Experimental procedures and analytical data. Acknowledgements The research leading to these results has received

Self-optimisation and model-based design of experiments for developing a C–H activation flow process

• Alexander Echtermeyer,
• Yehia Amar,
• Jacek Zakrzewski and
• Alexei Lapkin

Beilstein J. Org. Chem. 2017, 13, 150–163, doi:10.3762/bjoc.13.18

• successful predictions that met the target specifications.a Nomenclature. Supporting Information Supporting Information File 42: Details of experimental set-up and protocols, table of a priori data taken from our previous study, details of model development, MBDoE results, and LHS results. Acknowledgements

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934

• Veronika Ulrich,
• Clara Brieke and
• Max J. Cryle

Beilstein J. Org. Chem. 2016, 12, 2849–2864, doi:10.3762/bjoc.12.284

• arrows and the corresponding Oxy enzyme; (b) the structures of the glycopeptide antibiotics A47934, teicoplanin and vancomycin, with cross-links highlighted (blue) and standard ring nomenclature shown for A47934 (magenta). (a) Spectral analysis of StaF, showing the absorption spectra of ferric protein

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

Unconventional application of the Mitsunobu reaction: Selective flavonolignan dehydration yielding hydnocarpins

• Guozheng Huang,
• Simon Schramm,
• Jörg Heilmann,
• David Biedermann,
• Vladimír Křen and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 662–669, doi:10.3762/bjoc.12.66

• was first synthesized [14] and later isolated from various plant species (for reviews see [5][15]). In several references the nomenclature of hydnocarpins, assignment of their structures and/or enantiomeric purities are not used coherently or experimental and full structural evidence have not been

• (position 11 according to IUPAC nomenclature, but rarely used in the literature) without attacking other hydroxy groups, as reported by Wang et al. [9], and by our group [10]. Two different sequences of addition of reactants were applied, i.e., addition of solution of acid to the mixture of silibinin

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• serious Gram-positive infections, linezolid, was introduced in the markets in the year 2000. While also binding to the 50S subunit, it seems to unfold its inhibiting activity in a unique and early stage [13][14]. The nomenclature of the linezolid structure is shown in Figure 1 along with the pharmacophore

• suggestions, verifiable by the proposed ribosomal model. Two-dimensional structure and nomenclature of the oxazolidinone linezolid. The different rings are highlighted with capital letters A, B and C. The acetamidic substituent is denominated as C5 side chain. The pharmacophore portion is colored in blue

• paper. Superposition of all 43 minima of the ribosome–linezolid complex. Linezolid is shown in yellow and CCA-N-Phe in green. The nucleotide nomenclature is the same as the one reported in the crystal structure original paper [12]. Note the bent conformation of linezolid in its bioactive state and the

Recent highlights in biosynthesis research using stable isotopes

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2015, 11, 2493–2508, doi:10.3762/bjoc.11.271

• . It does not provide a comprehensive overview of all the work conducted, but tries to create a diversified picture of isotope usage in the study of selected interesting natural products. IUPAC nomenclature allows to distinguish isotopically substituted (every molecule in a sample is labeled at the

• designated position) and isotopically labeled compounds (a fraction of the molecules in a sample is labeled) by use of round or square brackets, respectively [14]. The assignments used in this article are based on the presentations in the original publications, even if the nomenclature in the original work

A new approach to ferrocene derived alkenes via copper-catalyzed olefination

• Vasily M. Muzalevskiy,
• Aleksei V. Shastin,
• Alexandra D. Demidovich,
• Namiq G. Shikhaliev,
• Abel M. Magerramov,
• Victor N. Khrustalev,
• Rustem D. Rakhimov,
• Sergey Z. Vatsadze and
• Valentine G. Nenajdenko

Beilstein J. Org. Chem. 2015, 11, 2072–2078, doi:10.3762/bjoc.11.223

• -isomer by systematic nomenclature, but trans-configuration of H and F) and 16.2 Hz (E-isomer). Acetylferrocene and 1,1’-diacetylferrocene were also involved successfully into this transformation (Scheme 4). Our preliminary study of the catalytic olefination of acetylferrocene by CF3CBr3 (alkene 8) and

Towards inhibitors of glycosyltransferases: A novel approach to the synthesis of 3-acetamido-3-deoxy-D-psicofuranose derivatives

• Maroš Bella,
• Miroslav Koóš and
• Chun-Hung Lin

Beilstein J. Org. Chem. 2015, 11, 1547–1552, doi:10.3762/bjoc.11.170

• ring (O5–C2–C3–C4-C5 according to the IUPAC hexofuranose nomenclature [29]) in 12 adopts the 2T1 conformation (C2TC1, twisted on C1–C2, C1-exo, C2-endo). For the five-membered 1,3-dioxolane ring (O2–C6–C1–O3–C7), the puckering parameters Q = 0.288(2) Å and Φ = 15.7(5)° and relevant torsion angles

Functionalized branched EDOT-terthiophene copolymer films by electropolymerization and post-polymerization “click”-reactions

• Miriam Goll,
• Adrian Ruff,
• Erna Muks,
• Felix Goerigk,
• Beatrice Omiecienski,
• Ines Ruff,
• Rafael C. González-Cano,
• Juan T. Lopez Navarrete,
• M. Carmen Ruiz Delgado and
• Sabine Ludwigs

Beilstein J. Org. Chem. 2015, 11, 335–347, doi:10.3762/bjoc.11.39

• the electropolymerization. The nomenclature of the copolymers is in accordance to our previous publication [24]: P(EDOT-co-3T)-1:1 means for example that a 1:1 mixture of 3T and EDOT is used during polymerization. Figure 1A summarizes representative cyclic voltammograms (CVs) of PEDOT, P3T, a PEDOT