Construction of pillar[4]arene[1]quinone–1,10-dibromodecane pseudorotaxanes in solution and in the solid state

• Xinru Sheng,
• Errui Li and
• Feihe Huang

Beilstein J. Org. Chem. 2020, 16, 2954–2959, doi:10.3762/bjoc.16.245

• crystallography revealed that two host molecules complex one guest molecule, forming a [3]pseudorotaxane in the solid state (Figure 1). In the crystal structure, the alkyl chain of the guest is threaded through the cavities of two host molecules, which is stabilized by multiple CH∙∙∙π interactions and hydrogen

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

• complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it

• the validation of 3D glycoprotein structures. Keywords: electron cryomicroscopy; glycoinformatics; glycomics; Privateer; X-ray crystallography; Introduction Glycosylation-related processes are prevalent in life. The attachment of carbohydrates to macromolecules extends the capabilities of cells to

• glycoproteins Several experimental techniques can be used to obtain 3D structures of glycoproteins: X-ray crystallography (MX, which stands for macromolecular crystallography), nuclear magnetic resonance spectroscopy (NMR) and electron cryomicroscopy (cryo-EM). As of publication date, the overwhelming majority

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

• negatively charged patches, depending on the functional groups present. X-ray crystallography is a useful tool to obtain structural information about the binding modes of supramolecular ligands on proteins (reviewed in [76]). However, the crystallization of proteins with supramolecular ligands can be very

• they have been used to serve as scaffolds for the assembly of protein arrays and crystallization aids [23][24][25][26][27][28]. In addition, a terbiumIII complex termed crystallophore has been developed as a crystallographic nucleation and phasing tool for protein crystallography that can also easily

• phosphonato-calix[n]arenes of different ring sizes (n = 4, 6 or 8) to Cyt c [20][23][24][26][27][28] and the antifungal protein PAF [25] as model proteins. These studies combined 15N-HSQC titrations with X-ray crystallography, isothermal titration calorimetry (ITC) and size exclusion with light scattering

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

• areas of chemical and biochemical fragmentations followed by analysis using mass spectroscopy, nuclear magnetic resonance, crystallography and computational modelling. There have been some initiatives by independent research groups worldwide, that pushed the development of visual tools to improve some

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

• two days to afford the required complex whose structure was confirmed by X-ray crystallography (Scheme 37). 3 Synthesis of heterosumanene derivatives Doping the backbone of buckybowls such as sumanene and corannulene with heteroatoms (N, P, O, S, Si, and Te) is a promising tactic to modulate the

• the hexabromination using Br2 and iron powder in PhNO2. The brominated derivative 157 was then converted to the hexathiolated trithiasumanenes 158a–c by substitution reaction (Scheme 41). The structures of these functionalized heterosumanenes were confirmed by spectroscopy as well as crystallography

Access to highly substituted oxazoles by the reaction of α-azidochalcone with potassium thiocyanate

• Mysore Bhyrappa Harisha,
• Pandi Dhanalakshmi,
• Rajendran Suresh,
• Raju Ranjith Kumar and
• Shanmugam Muthusubramanian

Beilstein J. Org. Chem. 2020, 16, 2108–2118, doi:10.3762/bjoc.16.178

• in 3d proceeded smoothly with acetyl chloride in the presence of sodium hydride to afford 5 in good yield. The structure of the product and the site of acetylation was confirmed by X-ray crystallography of a single crystal of 5 [71] (Figure 3). The methylated and benzylated derivatives 6 and 7 were

Synthesis of 3(2)-phosphonylated thiazolo[3,2-a]oxopyrimidines

• Ksenia I. Kaskevich,
• Anastasia A. Babushkina,
• Vladislav V. Gurzhiy,
• Dmitrij M. Egorov,
• Nataly I. Svintsitskaya and
• Albina V. Dogadina

Beilstein J. Org. Chem. 2020, 16, 1947–1954, doi:10.3762/bjoc.16.161

• Ksenia I. Kaskevich Anastasia A. Babushkina Vladislav V. Gurzhiy Dmitrij M. Egorov Nataly I. Svintsitskaya Albina V. Dogadina Department of Organic Chemistry, St. Petersburg State Institute of Technology, Moskovskii pr. 26, St. Petersburg, 190013, Russia Department of Crystallography, Institute of

One-pot and metal-free synthesis of 3-arylated-4-nitrophenols via polyfunctionalized cyclohexanones from β-nitrostyrenes

• Haruyasu Asahara,
• Minami Hiraishi and
• Nagatoshi Nishiwaki

Beilstein J. Org. Chem. 2020, 16, 1830–1836, doi:10.3762/bjoc.16.150

• afforded trace amounts of 3a and 4a, both of which were obtained as a mixture of diastereomeric isomers (Table 1, entry 1). The stereochemistry of the major product 4a was determined to be trans,trans (all-equatorial) by X-ray crystallography (Figure 1). Among the solvents tested, less polar solvents, such

• afford nitrophenol 5b, which eluted with hexane/ethyl acetate 8:2 (41.7 mg, 0.17 mmol, 34%) as yellow solid. When the other nitroalkenes 1c–f were used, the reaction was conducted in the same way. X-ray crystallography of the major isomer of 4a. The thermal ellipsoids indicate 50% probability. Resonance

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

• developed by reacting 5-amino-1,2,3,4-tetrazole with aromatic aldehydes and cyanamide in pyridine under controlled microwave heating with high yields. X-ray crystallography confirmed the structure of the obtained products. Keywords: microwave irradiation; N2-(tetrazol-5-yl)-6-aryl/heteroaryl-1,3,5-triazine

• -2,4-diamines; one-pot synthesis; X-ray crystallography; Introduction The family of triazines is of considerable interest in fields related to organic and medicinal chemistry. 2,4-Diaminotriazines are privileged scaffolds exhibiting diverse biological activities such as antibacterial [1], anti-HSV-1

Distinctive reactivity of N-benzylidene-[1,1'-biphenyl]-2-amines under photoredox conditions

• Shrikant D. Tambe,
• Kwan Hong Min,
• Naeem Iqbal and
• Eun Jin Cho

Beilstein J. Org. Chem. 2020, 16, 1335–1342, doi:10.3762/bjoc.16.114

• product 3a was unambiguously confirmed using X-ray crystallography [57]. To further extend the diversity of the reactivity of the imines in this process, we also attempted the use of a reducing agent in the reaction of 1a. Pleasingly, the reaction of 1a with 2 equivalents of the Hantzsch ester in CH3CN

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

• Carlos H. Escalante,
• Eder I. Martínez-Mora,
• Carlos Espinoza-Hicks,
• Alejandro A. Camacho-Dávila,
• Fernando R. Ramos-Morales,
• Francisco Delgado and
• Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

• diffraction crystallography of both endo 9m and exo 10m adducts (Figure 2) [43]. In addition, the thermal cycloadditions of 2-vinylpyrroles 8a–j and maleimides 7b,c took place satisfactorily to deliver the expected adducts 9e–p/10e–p, also with high endo diastereoselectivity and good yields (Table 2, entries

• natural pyrrolizine- and isoindole-containing alkaloids. Structures of 9m (a) and 10m (b) as determined by single-crystal X-ray diffraction crystallography (ellipsoids at the 30% probability level). M06-2X/6-31+G(d,p) Optimized geometry for each of the SCs (a and d), TSs (b and e) and ADs (c and f) of the

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

• emitting diodes (LEDs) were purchased from Topbright. X-ray crystallography Single crystals of 2c and 4a of suitable quality for X-ray diffraction measurements were grown by slow diffusion of n-pentane into CH2Cl2 solutions of the crude product at –18 °C for several weeks. One selected single crystal was

Copper catalysis with redox-active ligands

• Agnideep Das,
• Yufeng Ren,
• Cheriehan Hessin and
• Marine Desage-El Murr

Beilstein J. Org. Chem. 2020, 16, 858–870, doi:10.3762/bjoc.16.77

• Chaudhuri on GAO mimics [11][12][13], Safaei and Storr have reported Cu(II) complexes bearing a non-innocent amidophenolate type benzoxazole ligand which was fully characterized by X-ray crystallography and other spectroscopic techniques (Scheme 1) [14]. These complexes were found to perform the aerobic

One-pot synthesis of dicyclopenta-fused peropyrene via a fourfold alkyne annulation

• Ji Ma,
• Yubin Fu,
• Junzhi Liu and
• Xinliang Feng

Beilstein J. Org. Chem. 2020, 16, 791–797, doi:10.3762/bjoc.16.72

• twofold [3 + 2] cyclopentannulation and subsequent twofold [4 + 2] benzannulation. The structure of 1 is unambiguously confirmed by X-ray crystallography; 1 adopted a twisted geometry due to the steric hindrance of the phenyl rings and the hydrogen substituents at the bay regions. Notably, compound 1

• 1 were obtained by slow evaporation from a carbon disulfide solution, allowing us to disclose the molecular structure by X-ray crystallography (Figure 2a). As shown in Figure 2a, the crystal structure of 1 clearly displayed a nonplanar conformation, resulting from steric repulsion between the phenyl

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

• combination of 20 mol % of tetrabutylammonium bromide (TBAB) and NaOH (20 mol %) yielded the desired product, 2,2,2-trifluoro-1-(1H-indol-3-yl)ethan-1-ol (3a) in 93% yield (Table 1, entry 4). The product 3a was isolated by filtration and confirmed by NMR and X-ray crystallography analysis (CCDC-1973322, see

Synthesis of six-membered silacycles by borane-catalyzed double sila-Friedel–Crafts reaction

• Yafang Dong,
• Masahiko Sakai,
• Kazuto Fuji,
• Kohei Sekine and
• Yoichiro Kuninobu

Beilstein J. Org. Chem. 2020, 16, 409–414, doi:10.3762/bjoc.16.39

• reaction between 1a with 2a proceeded to give phenoxasilin 3a in 60% yield (Table 1, entry 1). The structure of phenoxasilin 3a was confirmed using single-crystal X-ray crystallography (see Supporting Information File 1 for details) [42]. Upon increasing the reaction temperature to 140 °C, the yield of 3a

Six-fold C–H borylation of hexa-peri-hexabenzocoronene

• Mai Nagase,
• Kenta Kato,
• Akiko Yagi,
• Yasutomo Segawa and
• Kenichiro Itami

Beilstein J. Org. Chem. 2020, 16, 391–397, doi:10.3762/bjoc.16.37

• -catalyzed six-fold C–H borylation of HBC was successfully achieved by screening solvents. The crystal structure of hexaborylated HBC was confirmed via X-ray crystallography. Optoelectronic properties of the thus-obtained hexaborylated HBC were analyzed with the support of density functional theory

• calculations. The spectra revealed a bathochromic shift of absorption bands compared with unsubstituted HBC under the effect of the σ-donation of boryl groups. Keywords: C–H borylation; hexa-peri-hexabenzocoronene; iridium catalyst; X-ray crystallography; Introduction Polycyclic aromatic hydrocarbons (PAHs

• hexaborylated HBC 1. The structure of thus-obtained 1 was confirmed by X-ray crystallography, and the electronic effects of the boryl groups were investigated through optoelectronic measurements and density functional theory (DFT) calculations. Results and Discussion We have examined the conditions for C–H

Synthesis and circularly polarized luminescence properties of BINOL-derived bisbenzofuro[2,3-b:3’,2’-e]pyridines (BBZFPys)

• Ryo Takishima,
• Yuji Nishii,
• Tomoaki Hinoue,
• Yoshitane Imai and
• Masahiro Miura

Beilstein J. Org. Chem. 2020, 16, 325–336, doi:10.3762/bjoc.16.32

• Information File 290: Summary of X-ray crystallography data, copy of NMR spectra, and copy of HPLC charts. Funding This work was supported by JSPS KAKENHI Grant No. JP 19K15586 (Grant-in-Aid for Young Scientists) to Y.N. and JP 17H06092 (Grant-in-Aid for Specially Promoted Research) to M.M.

SnCl₄-catalyzed solvent-free acetolysis of 2,7-anhydrosialic acid derivatives

• Kesatebrhan Haile Asressu and
• Cheng-Chung Wang

Beilstein J. Org. Chem. 2019, 15, 2990–2999, doi:10.3762/bjoc.15.295

• crystallography, compounds 2 and 3 were acetylated with Ac2O in the presence of a catalytic amount of 4-(dimethylamino)pyridine (DMAP) in pyridine to give 5 [6] and 6 in 75 and 77% yield, respectively (Scheme 1), and the compatibility of acetyl protecting groups with the Lewis acids during acetolysis reactions

• editing and proofreading of the manuscript. We also thank Dr. Su-Ching Lin, Ms. Yi-Ping Huang, and Ms. Mei-Man Chen for their help with NMR experiments, Dr. Yuh-Sheng Wen for the X-ray crystallography experiment, and Ms. Ping-Yu Lin for conducting mass spectrometry experiments. Funding This work was

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

• Sara Tejera,
• Giada Caniglia,
• Rosa L. Dorta,
• Andrea Favero,
• Javier González-Platas and
• Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

• 12 led to single crystals suitable for X-ray crystallography. Its analysis (Figure 3) not only confirmed the structure, but in addition showed a well-organized crystal packing (Figure 4) where the alternate disposition of the molecules displayed a parallelism between the p-bromophenyl groups as well

A chiral self-sorting photoresponsive coordination cage based on overcrowded alkenes

• Constantin Stuckhardt,
• Diederik Roke,
• Wojciech Danowski,
• Edwin Otten,
• Sander J. Wezenberg and
• Ben L. Feringa

Beilstein J. Org. Chem. 2019, 15, 2767–2773, doi:10.3762/bjoc.15.268

• corresponding stable isomer. Supporting Information Supporting Information File 538: Experimental procedures, compound characterization, CD spectroscopy, binding studies, NMR studies of the photochemical and thermal isomerizations, X-ray crystallography, computational details and Cartesian coordinates of DFT

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• , 0.012 and 0.087 for 4pzMe-Cl2, 4pzMe-OMe2 and 4pzMe-Pyr2, respectively; see Figure 6 for 4pzH-F2 and 4pzH-Cl2). To experimentally compare the conformations of the E-isomers, we were able to characterize 4pzMe-F2, 4pzMe-Cl2 and 4pzH-F2 by X-ray crystallography (Figure 7). In agreement with the

• characterization and X-ray crystallography data. Supporting Information File 536: CIF files for 4pzMe-F2, 4pzMe-OMe2, 4pzMe-OMe2_diethylether and 4pzH-F2. Acknowledgements J.C. acknowledges the Generalitat Valenciana for the postdoctoral APOSTD/2017/081 fellowship. R.S.L.G would like to thank the Faculty of

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• C22H35O5+ [M – H2O + H]+, 379.2479; found, 379.2473. Crystallography Crystals suitable for single crystal X-ray diffraction analysis were obtained for 1, 4 and 9, providing confirmation of the spectroscopic structural elucidation. Indirect confirmation of the structures of 2 and 3 was obtained following

Photochromic diarylethene ligands featuring 2-(imidazol-2-yl)pyridine coordination site and their iron(II) complexes

• Andrey G. Lvov,
• Max Mörtel,
• Anton V. Yadykov,
• Frank W. Heinemann,
• Valerii Z. Shirinian and
• Marat M. Khusniyarov

Beilstein J. Org. Chem. 2019, 15, 2428–2437, doi:10.3762/bjoc.15.235

• . Unexpectedly, dinuclear and tetranuclear iron(II) complexes were obtained, which were thoroughly characterized by X-ray crystallography, magnetic measurements, and Mössbauer spectroscopy. The formation of multinuclear complexes is facilitated by two coordination sites of the diarylethene, acting as a bridging

• condensation [33] of 3-(hydroxyimino)pentane-2,4-dione, aniline, and 2-pyridinecarboxaldehyde (Scheme 1). The structure of 1 was confirmed by X-ray crystallography [34]. The ketone 1 was subsequently used for the synthesis of desired photochromic ligands with cyclopentenone (3), cyclopentene (4), and

• successfully applied for the synthesis of a new family of photochromic ligands. The structures of the synthesized diarylethene-based ligands 3, 4, 6, and 7 were confirmed by 1H and 13C NMR spectroscopy and mass spectrometry. The molecular structure of 6 was additionally confirmed by X-ray crystallography. In

Effect of ring size on photoisomerization properties of stiff stilbene macrocycles

• Sandra Olsson,
• Óscar Benito Pérez,
• Magnus Blom and
• Adolf Gogoll

Beilstein J. Org. Chem. 2019, 15, 2408–2418, doi:10.3762/bjoc.15.233

• of the macrocyclic stiff stilbene diethers, a conformational analysis was undertaken (Figure 6). According to X-ray crystallography, in compound (E)-7 (Scheme 4) the aromatic rings of the two indane units are in the same plane (dihedral angle 180°), whereas in (Z)-7 this angle is 9.1° [21]. In the