Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• Data Bank [16]. The main advantage that cryo-EM has compared to X-ray crystallography is that the former does not require crystals, thus making it easier or sometimes even possible at all to study flexible protein assemblies that do not crystallise. Albeit this, the main limitations of cryo-EM included

• subtilis 50S subunit-nascent chain-tRNA complex, EMD-4799, no available PDB [18]) were solved. Protein crystals can also be used in conjunction with cryo-EM, employing a technique known as microcrystal electron diffraction (MicroED). With this method, thin 3D crystal slices are used to obtain the protein

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• molecules of the synthesized α-(arylamino)acetonitrile derivatives in the aggregated crystalline state, single crystals suitable for X-ray analysis were obtained by crystallization from isopropanol. The crystallographic data for the structure 2a reported in this paper have been deposited at the Cambridge

•  2b). In Figure 3a, the magnification at 200× indicates sharp rod-like natured crystals of the amino-acetonitrile 2c obtained by the ultrasound-assisted reaction conditions in comparison with the crystallite aggregates obtained by the classical procedure (Figure 3b). Biological assay We chose the well

Synthesis of imidazo[1,5-a]pyridines via cyclocondensation of 2-(aminomethyl)pyridines with electrophilically activated nitroalkanes

• Dmitrii A. Aksenov,
• Nikolai A. Arutiunov,
• Vladimir V. Maliuga,
• Alexander V. Aksenov and
• Michael Rubin

Beilstein J. Org. Chem. 2020, 16, 2903–2910, doi:10.3762/bjoc.16.239

• colorless crystals of intermediate 2-((6-bromoquinolin-2-yl)methyl)isoindoline-1,3-dione. This material (3.05 g, 8.3 mmol) was suspended in ethanol, and hydrazine hydrate (50%, 1.0 g, 10 mmol) was added. The reaction mixture was refluxed for 5 h and then cooled down to 0 °C. The precipitated phthalyl

• mL). The combined organic extracts were concentrated, the residue dried in vacuum, and then purified by preparative column chromatography on silica gel, eluting with a mixture of petroleum ether and ethyl acetate. The titled compound was obtained as yellow solid (lit. [53] yellow crystals), yield 77

• bath preheated to 160 °C, and stirred for 2 h. Upon reaction completion, the aqueous work-up, isolation, and purification of the product was performed in the same way as described in the typical procedure 1. The titled compound was obtained as yellow solid (lit. [54] yellow crystals), yield 66% (96 mg

One-pot multicomponent green Hantzsch synthesis of 1,2-dihydropyridine derivatives with antiproliferative activity

• Giovanna Bosica,
• Kaylie Demanuele,
• José M. Padrón and
• Adrián Puerta

Beilstein J. Org. Chem. 2020, 16, 2862–2869, doi:10.3762/bjoc.16.235

• change from colorless to yellow, which darkened or brightened to orange or yellow and thickened with the occurrence of crystals on the sides of the flask. Once the spot or the peak corresponding to the benzaldehyde disappeared on the TLC plate or in the gas chromatogram, the time was taken as the

• reaction was finished. The reaction mixture, obtained as a viscous oil, was filtered through a sinter funnel to remove any catalyst and washed using acetone, which was then evaporated in a rotary evaporator. The resultant crystals were then recrystallized using hot ethanol. The products were then

Easy access to a carbohydrate-based template for stimuli-responsive surfactants

• Thomas Holmstrøm,
• Daniel Raydan and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2020, 16, 2788–2794, doi:10.3762/bjoc.16.229

• recrystallization, it was possible to isolate the β-anomer (5β) of the compound 5 as this anomer formed crystals in dichloromethane. Next, the diazide 5β was treated with different electrophiles (iodomethane, 1-bromopropane or 1-bromododecane) under basic conditions in DMF. By this synthesis, the three new methyl

A heterobimetallic tetrahedron from a linear platinum(II)-bis(acetylide) metalloligand

• Matthias Hardy,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2020, 16, 2701–2708, doi:10.3762/bjoc.16.220

• succeed to obtain single crystals of our metallosupramolecular assemblies that were suitable for single-crystal X-ray diffraction experiments. Therefore, we generated energy-minimized gas phase structures of 4, employing a force-field approach using the GFN2-xTB approach recently established to model

Synthesis and characterization of S,N-heterotetracenes

• Astrid Vogt,
• Florian Henne,
• Christoph Wetzel,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2020, 16, 2636–2644, doi:10.3762/bjoc.16.214

• quantitative yield [47]. Single crystals of intermediate thienopyrrole 25 were obtained by slow evaporation of a chloroform solution and an X-ray structure analysis was performed. Structural details and packing motifs of the molecule are described in Supporting Information File 1. Alkylation to N-propyl

Particle size effect in the mechanically assisted synthesis of β-cyclodextrin mesitylene sulfonate

• Stéphane Menuel,
• Sébastien Saitzek,
• Eric Monflier and
• Frédéric Hapiot

Beilstein J. Org. Chem. 2020, 16, 2598–2606, doi:10.3762/bjoc.16.211

• diffraction patterns recorded after various grinding times, and establish the extent of the amorphization of the reaction mixture during mechanochemical milling. The peaks corresponding to pure β-CD crystals decrease over time. Clearly, the polycrystalline β-CD powder becomes amorphous over time. The

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• synthesized in moderate yields of 24% and 26%, respectively, over three steps from the same two building blocks, the ditosylate 5 and the monobutyl-protected NDI precursor 7 (Scheme 1). The connectivity and conformation of exTTFC7 was observed in the crystal structure obtained from crystals generated through

• Information File 1). Slow diffusion of CH3CN into a concentrated solution of NDIC7 in CH2Cl2 yielded single crystals suitable for X-ray diffraction (Figure 2b). The macrocycle displays a folded conformation in the solid state due to the flexible linker, featuring an intramolecular NDI/naphthalene stacking

• with a typical π-stacking distance of 3.58 Å and a tilt angle of 5.8°. The free electron pair of the tertiary amine points towards the inside of the crown ether. In contrast, single crystals of NDIC8 (Figure 2c), obtained by slow evaporation of a concentrated dimethylformamide (DMF) solution, exhibit a

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• the slight shift of the peaks further indicates the successful complexation of TBTQ-(OG)6 and C60. Simulations of complex TBTQ-(OG)6 C60 in water. In spite of numerous attempts, we failed to obtain good-quality crystals to determine the binding conformation of complex TBTQ-(OG)6 C60 by X-ray

A new method for the synthesis of diamantane by hydroisomerization of binor-S on treatment with sulfuric acid

• Rishat I. Aminov and
• Ravil I. Khusnutdinov

Beilstein J. Org. Chem. 2020, 16, 2534–2539, doi:10.3762/bjoc.16.205

• 1:1 ethyl acetate/cyclohexane mixture. Colorless crystals; 68% yield; mp 104–106 °C; 1H NMR (400 MHz, CDCl3) δ 0.95–0.98 (m, 4H), 1.38 (s, 8H), 1.66–1.71 (m, 4H), 1.99–2.01 (m, 2H), 2.12–2.16 (m, 2H); 13С NMR (100 MHz, CDCl3) δ 33.42 (С6, С9, C13, C14), 35.63 (С1, С2, C7, C8), 37.82 (С5, С10), 38.27

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

• of glycoprotein structures have been solved using MX [24][25]. The biggest bottleneck in MX is the formation of crystals of the target macromolecule or complex. The quality of the crystal directly determines the resolution – a measure of the detail in the electron density map. Homogenous samples at

• high concentrations are required to produce well-diffracting crystals [26]. Samples containing glycoprotein molecules do not usually fulfill this criterion. More often than not, MX falls short at elucidating carbohydrate features in glycoproteins due to glycosylated proteins being inherently mobile and

• heterogeneous [22]. Moreover, oligosaccharides often significantly interfere with the formation of crystal contacts that allow the formation of well-diffracting crystals. Because of this, glycans are often truncated in MX samples to aid crystal formation [27]. In cryo-EM, samples of glycoproteins are vitrified

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• moderate binding affinities, the calixarenes are thought to explore the protein surface dynamically, ‘hopping’ from one basic residue to an adjacent one. In addition, different binding modes involving the same residue have been observed in the crystals and can further contribute to this phenomenon. While

• larger ordered structures makes especially the larger calixarenes potent “molecular glues” and crystallization aids [23][24][25][26][27][28]. The PAF protein for example did not yield diffracting crystals on its own, but good quality crystals were obtained in the presence of all calix[n]arenes [25]. The

Design and synthesis of a bis-macrocyclic host and guests as building blocks for small molecular knots

• Elizabeth A. Margolis,
• Rebecca J. Keyes,
• Stephen D. Lockey IV and
• Edward E. Fenlon

Beilstein J. Org. Chem. 2020, 16, 2314–2321, doi:10.3762/bjoc.16.192

• appeared to hinder the formation of crystals suitable for X-ray diffraction to prove the topology of the product. The second-generation TLC approach to trefoil knots is presented here. It involves the binding of an electron-poor guest (2 or 3) in an electron-rich host (1) to promote the threading step, an

• were formed (see Scheme S1 in Supporting Information File 1). Repeated attempts to grow X-ray crystals of the product failed. To test for topological chirality, a europium chiral shift reagent was added, but the 1H NMR spectrum was too noisy to discern any peak doubling. Additional experiments, such as

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• , after which the medium-containing MTT was discarded and formazan crystals were dissolved in 150 µL DMSO. The absorbance at 550 nm (with automatic discount of reference wavelength 630 nm) of the resulting solution was measured in a 96-well spectrophotometer microplate reader. The percentage of cell

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

• colorless crystals of 128. Along similar lines the crystals of 127 were achieved by following the same procedure. On the other hand, the groups of Amaya and Hirao have reported the synthesis of sumanenyl mono- and trihafnocene complexes 129 and 130, respectively, along with the catalytic activity of 129 for

Isolation and structure determination of a tetrameric sulfonyl dilithio methandiide in solution based on crystal structure analysis and ⁶Li/¹³C NMR spectroscopic data

• Jürgen Vollhardt,
• Hans Jörg Lindner and
• Hans-Joachim Gais

Beilstein J. Org. Chem. 2020, 16, 2057–2063, doi:10.3762/bjoc.16.172

• and sulfonyl-substituted dilithio methandiide 2a [14][15]. The use of n-BuLi, inadvertently containing Li2O, had yielded prismatic crystals of 2a. An X-ray crystal structure analysis had shown a Ci symmetric hexamer, (2a)6·Li2O·(THF)6, the dianionic C atoms of which are each coordinated by two Li

• mixture of THF and n-hexane with Li2O-free n-BuLi (1.88 equiv) in n-hexane at −90 °C followed by warming the solution to room temperature gave octahedral crystals of 2a. The use of two equivalents of the base led two a slower crystal growth. The X-ray crystal structure analysis showed a chiral C2

Controlling the stereochemistry in 2-oxo-aldehyde-derived Ugi adducts through the cinchona alkaloid-promoted electrophilic fluorination

• Yuqing Wang,
• Gaigai Wang,
• Anatoly A. Peshkov,
• Ruwei Yao,
• Muhammad Hasan,
• Manzoor Zaman,
• Chao Liu,
• Stepan Kashtanov,
• Olga P. Pereshivko and
• Vsevolod A. Peshkov

Beilstein J. Org. Chem. 2020, 16, 1963–1973, doi:10.3762/bjoc.16.163

• were able to obtain crystals suitable for the structure determination via X-ray crystallographic analysis. It was found that a part of the substance crystallized in a racemic form while the rest crystallized in an enantiopure form. By resolving both types of crystals [90], the configuration of the

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

• investigated with hydrobromic acid (HBr 33 wt % in AcOH, 2.3 equiv) in diethyl ether (Table 1, entry 4). This reaction proved faster and reached completion after 45 min at 20 °C, giving product 1d with an excellent yield of 94% and an E/Z selectivity of 89:11. The isomers could be separated and crystals of the

• following this two-step method, pure E-1c could be obtained while direct ring opening of 1 with BTSH and CSA resulted in a 25:75 mixture of E/Z-1c. A crystallographic analysis of crystals of Z-25 confirmed the nature and geometry of the obtained product (see Supporting Information File 2). Addition of

Synthesis and highly efficient light-induced rearrangements of diphenylmethylene(2-benzo[b]thienyl)fulgides and fulgimides

• Vladimir P. Rybalkin,
• Sofiya Yu. Zmeeva,
• Lidiya L. Popova,
• Valerii V. Tkachev,
• Andrey N. Utenyshev,
• Olga Yu. Karlutova,
• Alexander D. Dubonosov,
• Vladimir A. Bren,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2020, 16, 1820–1829, doi:10.3762/bjoc.16.149

• heterocyclic aldehydes or ketones with methylene succinates followed by subsequent hydrolysis and dehydration processes. Under exposure of solutions or crystals of thus prepared hetaryl(aryl)-substituted dihydrofuran-2,5-diones to UV light, those bearing an isopropylidene fragment attached to the furandione

• : The X-ray diffraction studies of crystals of 3Z, 3E and 9 were performed with a Bruker XSCANS device (λ(Мо Кα) = 0.71073 Å, \w scans). Bond lengths and valence angles of 3Z, 3E and 9 are presented in Tables S1–S3 (Supporting Information File 1). The main crystallographic data and characteristics are

Microwave-assisted efficient one-pot synthesis of N²-(tetrazol-5-yl)-6-aryl/heteroaryl-5,6-dihydro-1,3,5-triazine-2,4-diamines

• Moustafa Sherief Moustafa,
• Ramadan Ahmed Mekheimer,
• Saleh Mohammed Al-Mousawi,
• Mohamed Abd-Elmonem,
• Hesham El-Zorba,
• Afaf Mohamed Abdel Hameed,
• Tahany Mahmoud Mohamed and
• Kamal Usef Sadek

Beilstein J. Org. Chem. 2020, 16, 1706–1712, doi:10.3762/bjoc.16.142

• Labstation at 120 °C for 12 min. The solvent was removed under reduced pressure and the solid product was isolated by filtration and recrystallized from DMF. 6-(4-Chlorophenyl)-N2-(5H-tetrazol-5-yl)-5,6-dihydro-1,3,5-triazine-2,4-diamine (4a). Colorless crystals; mp 320–322 °C; yield 0.268 g, 92%; Rf 0.55 (1

• . calcd for C10H10ClN9: C, 41.17; H, 3.46; Cl, 12.15; N, 43.22; found: C, 41.22; H, 3.42; Cl, 12.11; N, 43.24; EIMS (m/z): 290.1 [M − 1]+. 6-(4-Methoxyphenyl)-N2-(5H-tetrazol-5-yl)-5,6-dihydro-1,3,5-triazine-2,4-diamine (4b). Colorless crystals; mp 306–308 °C; yield 0.255 g, 89%; 1H NMR (600 MHz, DMSO-d6

• ; N, 43.88; found: C, 45.89; H, 4.52; N, 43.90; EIMS (m/z): 286.1 [M − 1]+. 6-Phenyl-N2-(5H-tetrazol-5-yl)-5,6-dihydro-1,3,5-triazine-2,4-diamine (4c). Colorless crystals; mp 317–319 °C; yield 0.277 g, 93%; 1H NMR (600 MHz, DMSO-d6) δ 6.15 (s, 1H), 7.22 (s, 1H), 7.40–7.46 (m, 5H), 8.50 (br s, 1H

Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study

• Csilla Hargitai,
• Györgyi Koványi-Lax,
• Tamás Nagy,
• Péter Ábrányi-Balogh,
• András Dancsó,
• Gábor Tóth,
• Judit Halász,
• Angéla Pandur,
• Gyula Simig and
• Balázs Volk

Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136

• crystals from derivative 8a were unsuccessful. It has to be emphasized that theoretically, the formation of four dimer-like regioisomers could be expected from aldehydes 1a–d, each of them as the mixture of two diastereomeric racemates. Although HPLC–MS measurements indeed indicated the presence of

Azidophosphonium salt-directed chemoselective synthesis of (E)/(Z)-cinnamyl-1H-triazoles and regiospecific access to bromomethylcoumarins from Morita–Baylis–Hillman adducts

• Soundararajan Karthikeyan,
• Radha Krishnan Shobana,
• Kamarajapurathu Raju Subimol,
• J. Helen Ratna Monica and
• Ayyanoth Karthik Krishna Kumar

Beilstein J. Org. Chem. 2020, 16, 1579–1587, doi:10.3762/bjoc.16.130

• layer was washed with brine and dried over anhydrous MgSO4. The removal of the solvent in vacuo afforded the crude product, which was purified over silica gel (using hexane/EtOAc) to acquire 4a as colorless crystals. Proposed mechanism for the synthesis of 1,4-disubstituted triazoles. Proposed mechanism

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• structure of rotaxane 1a was determined by single crystal X-ray diffraction of crystals obtained by slow evaporation of a dichloromethane solution. The analysis of the X-ray solid-state structure of the rotaxane 1a showed a significant difference to Leigh’s rotaxane I [4]. Rotaxane I only presented two

• ; found, 501.20295. Crystal structure determination Single crystals of rotaxane 1a (C36H42FeN3O3) were obtained by slow evaporation of a dichloromethane solution. A suitable crystal was mounted on a cryoloop with paratone®-N oil on an AFC11 partial Chi goniometer. The data were collected at 120 K on

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

• observed that crystals of santonine would shatter when exposed to sunlight [28]. Credit for the pioneering of photochemistry is usually given to Ciamician, the “grandfather of photochemistry”, who reported many interesting transformations of chemical solutions when irradiated by sunlight [29][30]. His