Tosylhydrazine-promoted self-conjugate reduction–Michael/aldol reaction of 3-phenacylideneoxindoles towards dispirocyclopentanebisoxindole derivatives

• Sayan Pramanik and
• Chhanda Mukhopadhyay

Beilstein J. Org. Chem. 2022, 18, 469–478, doi:10.3762/bjoc.18.49

• synthesized compound was confirmed by an X-ray crystallography experiment on a Bruker SMART diffractometer. General procedure for the synthesis of compound 3: In a manner similar to [28], 3-phenacylideneoxindole (1 mmol), tosylhydrazine (0.5 mmol) and Et3N (1 equivalent) were added with 6 mL CH3CN in a dry 10

Site-selective reactions mediated by molecular containers

• Rui Wang and
• Yang Yu

Beilstein J. Org. Chem. 2022, 18, 309–324, doi:10.3762/bjoc.18.35

• and fixed orientation of the guests inside the cage A. One of the carbonyl groups of 10 was in close proximity to the methyl group of 11, which was determined by X-ray crystallography. The possible C-coupled 1,2-adduct and other coupling products were not detected. However, in the absence of host A, a

• alkenyl site, producing the final 1,2-reduction product cis-O-hydroxycinnamyl alcohol 19. As a comparison, in the absence of the β-cyclodextrin host, both the 1,2- and 1,4-reduction products were observed. X-ray crystallography determined the host–guest complex of the coumarin and β-cyclodextrin, which

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

• (15e, 15f, 15h). Sensitive functional groups like alkyl iodides were tolerated in the reaction, although product yields were slightly diminished. The relative stereo- and regiochemistry of the adducts was confirmed through NMR experiments and X-ray crystallography (15h) [67]. We next sought to

Ready access to 7,8-dihydroindolo[2,3-d][1]benzazepine-6(5H)-one scaffold and analogues via early-stage Fischer ring-closure reaction

• Irina Kuznetcova,
• Felix Bacher,
• Daniel Vegh,
• Hsiang-Yu Chuang and
• Vladimir B. Arion

Beilstein J. Org. Chem. 2022, 18, 143–151, doi:10.3762/bjoc.18.15

• , characterization data and 1H and 13C NMR spectra of compounds, NMR numbering schemes and X-ray crystallography data. Acknowledgements We also thank Mr. Alexander Roller and Ms. Natalie Gajic for collection of X-ray diffraction data. Funding Support from the Austrian Science Fund (FWF) (P31293-N37) and Slovak

Synthesis of new pyrazolo[1,2,3]triazines by cyclative cleavage of pyrazolyltriazenes

• Nicolai Wippert,
• Martin Nieger,
• Claudine Herlan,
• Nicole Jung and
• Stefan Bräse

Beilstein J. Org. Chem. 2021, 17, 2773–2780, doi:10.3762/bjoc.17.187

• able to exemplarily determine the molecular structure by X-ray crystallography, proving the regioisomer obtained in the alkylation reaction (Figure 2). While isomer 12 was used for the synthesis of pyrazolo[3,4-d][1,2,3]-3H-triazine derivatives of general structure 5, the isomer 13 was intended to

Asymmetric organocatalyzed synthesis of coumarin derivatives

• Natália M. Moreira,
• Lorena S. R. Martelli and
• Arlene G. Corrêa

Beilstein J. Org. Chem. 2021, 17, 1952–1980, doi:10.3762/bjoc.17.128

• substitution reaction between the coumarin and the activated MBH substrate, it is possible to obtain functionalized coumarins 41 (Scheme 13). Furthermore, the absolute configuration of the stereogenic center was determined by X-ray crystallography. The enantioselective synthesis of cyclopropa[c]coumarins 45

• compared to the one-pot procedure. The obtained products possess a (R)-configuration, determined by X-ray crystallography (Scheme 26). Sebesta and colleagues described an enantioselective Michael/hemiketalization addition of hydroxycoumarins 1 to enones 2 and ketoesters 86 using squaramide 85 [62]. The

• addition in the least hindered Re face, consequently resulting in products of (R)-configurations, which were determined via X-ray crystallography. A stereoselective [3 + 2] cycloaddition with indandione alkylidenes 103 and 3-homoacylcoumarin 70 as the 1,3-dipole precursor, to generate a series of coumarin

Development of N-F fluorinating agents and their fluorinations: Historical perspective

• Teruo Umemoto,
• Yuhao Yang and
• Gerald B. Hammond

Beilstein J. Org. Chem. 2021, 17, 1752–1813, doi:10.3762/bjoc.17.123

• . Deprotection followed by fluorination with FClO3 gave (R)- and (S)-28-3 in good yields. X-ray crystallography was used to determine the structure and confirm the absolute stereochemistry of (S)-28-3. The optically active reagents (R)- and (S)-28-3 were effective in the enantioselective fluorination of cyclic

• reported by Banks when quinuclidine was N-fluorinated with Selectfluor [62] (Scheme 67). Subsequently, in 2001, Shibata et al. presented full details of their studies including the definitive identification of N-fluorinated cinchona alkaloids by X-ray crystallography analysis and further applications [96

A recent overview on the synthesis of 1,4,5-trisubstituted 1,2,3-triazoles

• Pezhman Shiri,
• Ali Mohammad Amani and
• Thomas Mayer-Gall

Beilstein J. Org. Chem. 2021, 17, 1600–1628, doi:10.3762/bjoc.17.114

• one of the products was proved by NMR analysis and X-ray crystallography. A number of different substituents was introduced to the bromotriazole scaffold, where unsubstituted and electron-rich derivatives gave a good yield, while the presence of electron-withdrawing groups decreased the product yield

Breaking paracyclophane: the unexpected formation of non-symmetric disubstituted nitro[2.2]metaparacyclophanes

• Suraj Patel,
• Tyson N. Dais,
• Paul G. Plieger and
• Gareth J. Rowlands

Beilstein J. Org. Chem. 2021, 17, 1518–1526, doi:10.3762/bjoc.17.109

• mixture of starting material 6, the conjugate addition product 14, and a trace of the denitration product 15. The structure of both compounds was confirmed by single X-ray crystallography (Figure 4 and Figure 5). The addition of methanol is stereoselective with only a single diastereomer of 14 being

Co-crystallization of an organic solid and a tetraaryladamantane at room temperature

• Fabian Rami,
• Jan Nowak,
• Felix Krupp,
• Wolfgang Frey and
• Clemens Richert

Beilstein J. Org. Chem. 2021, 17, 1476–1480, doi:10.3762/bjoc.17.103

• evaporation or diffusion. The implications for generating other co-crystals of two solids are briefly discussed. Keywords: adamantanes; crystallization; organic solids; structure elucidation; X-ray crystallography; Introduction Obtaining a crystal suitable for X-ray crystallography can be a challenge for

• X-ray crystallography were collected after more than one week. Table 1 lists the details of the structures observed. In case of the TDA/phenol co-crystals (Figure 2a/c), the asymmetric unit is made up of one host and two guest molecules, so the overall stoichiometric ratio is 1:2 (TDA/phenol). One

• crystallography is typically attempted only after some pre-purification has been performed. This highlights what challenges have to be met when trying to co-crystallize two solids. The situation is different for solvents as the second component. Solvates are not uncommon [1]. However, obtaining a solvate is also

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• has been a topic of strong interest over the past decades. With this in mind we have characterized a series of direct meso-halogenated porphyrins using single crystal X-ray crystallography. This is accompanied by a detailed conformational analysis of all deposited meso-halogenated porphyrins in the

• Dimé et al. [58]. Crystallography Crystals were grown using techniques following the protocol developed by Hope [59]. Crystals were either grown by allowing the solvent to slowly evaporate over time or by a liquid:liquid diffusion process. The crystal was mounted on a MiTeGen MicroMount and single

Stereoselective synthesis and transformation of pinane-based 2-amino-1,3-diols

• Ákos Bajtel,
• Mounir Raji,
• Matti Haukka,
• Ferenc Fülöp and
• Zsolt Szakonyi

Beilstein J. Org. Chem. 2021, 17, 983–990, doi:10.3762/bjoc.17.80

• 9 ring system (Scheme 1). The absolute configuration of compound 9 was determined by 2D NMR spectroscopic techniques. Clear NOE signals were observed between the H-7a and Me-10 as well as the Ha-9 and Me-10 protons. Beside NOESY experiments, the structure was also elucidated by X-ray crystallography

• exclusively [41]. The configuration of oxazolidine 17 was determined by 2D NMR spectroscopic techniques. Clear NOE signals were observed between the H-7a and Me-10 as well as the Ha-9 and Me-10 protons. In addition to NOESY experiments, the structure was also elucidated by X-ray crystallography (Figure 3

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified

• oligonucleotides that have been explored for gene silencing. Keywords: antisense; chemically modified oligonucleotides; crystallography; siRNA; structure; Introduction The natural nucleic acids sugar-phosphate backbone comes in two flavors, 2'-deoxyribose in DNA and ribose in RNA. However, this relative

α,γ-Dioxygenated amides via tandem Brook rearrangement/radical oxygenation reactions and their application to syntheses of γ-lactams

• Mikhail K. Klychnikov,
• Radek Pohl,
• Ivana Císařová and
• Ullrich Jahn

Beilstein J. Org. Chem. 2021, 17, 688–704, doi:10.3762/bjoc.17.58

• oxide ((R)-7b) provided the product (2S,4R)-9i in a much better 8:1 anti/syn coupling diastereoselectivity (Table 2, entry 10). The configuration of the major anti-diastereomer of alkoxyamine 9j was determined by X-ray crystallography after desilylation and hydrochloride formation (see Supporting

• -ray crystallography (Figure 3, vide infra). Similarly, the minor cis-diastereomer of hydroxy lactam 12k crystallized and its configuration was confirmed. The configuration of the other lactams was assigned by analogy, by base-mediated equilibration and oxidation experiments (vide infra). The α

• for 12m. However, the coupling diastereoselectivity with TEMPO (3) amounted to 4:1 for the trans diastereomers 12nA,B and exclusive for the cis isomer 12nC. The relative configuration of diastereomer 12nA was unequivocally established by X-ray crystallography of the hydrochloride adduct of the keto

Amino- and polyaminophthalazin-1(2H)-ones: synthesis, coordination properties, and biological activity

• Zbigniew Malinowski,
• Emilia Fornal,
• Agata Sumara,
• Renata Kontek,
• Karol Bukowski,
• Beata Pasternak,
• Dariusz Sroczyński,
• Joachim Kusz,
• Magdalena Małecka and
• Monika Nowak

Beilstein J. Org. Chem. 2021, 17, 558–568, doi:10.3762/bjoc.17.50

• compound moiety. Based on the results of X-ray structural analysis of the Cu(II) complex with 7, it can be assumed, that also in the case of ligand 5i (L2) the nitrogen atoms of the pyridin-2-yl and azomethin moiety participate in the coordination with Cu(II) ions. Crystallography of complex 17 The copper

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

• Kenji Morokuma,
• Shuntaro Tsukamoto,
• Kyosuke Mori,
• Kei Miyako,
• Ryuichi Sakai,
• Raku Irie and
• Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

• analysis by NMR, conformational calculation, and X-ray crystallography. A mice in vivo assay showed that (2R)-MC-27, with a six-membered oxacycle, is neuroactive, whereas the (2S)-counterpart is inactive. It was also found that TKM-38, with an eight-membered azacycle, is neuronally inactive, showing that

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• the fact that alanine mimics the secondary structure preferences of most proteinogenic amino acids, allowing the relative importance of each side chain for the biological function to be determined [23]. Classical X-ray crystallography also employs the polyalanine model for backbone chain tracing to

CF₃-substituted carbocations: underexploited intermediates with great potential in modern synthetic chemistry

• Anthony J. Fernandes,
• Armen Panossian,
• Bastien Michelet,
• Agnès Martin-Mingot,
• Frédéric R. Leroux and
• Sébastien Thibaudeau

Beilstein J. Org. Chem. 2021, 17, 343–378, doi:10.3762/bjoc.17.32

• analysis of the structures of 56f, 13f, and 21f by X-ray diffraction crystallography revealed similar bond angle distortions [64][65]. A considerable delocalization of the positive charge in the aryl ring was therefore suggested (Scheme 15): in the dominant resonance form 25f’, 48f’, or 14f’, the α

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• their functional architecture. Such an approach typically includes the use of a variety of high-resolution proteomic tools, cryo-electron microscopy and X-ray crystallography to achieve full molecular characterization at the atomic level. However, macromolecules such as DNA/RNA and proteins are not

Annulation of a 1,3-dithiole ring to a sterically hindered o-quinone core. Novel ditopic redox-active ligands

• Sergey V. Norkov,
• Anton V. Cherkasov,
• Andrey S. Shavyrin,
• Maxim V. Arsenyev,
• Viacheslav A. Kuropatov and
• Vladimir K. Cherkasov

Beilstein J. Org. Chem. 2021, 17, 273–282, doi:10.3762/bjoc.17.26

• electrode (2 mm diameter), platinum wire counter electrode and Ag/AgCl/KCl reference electrode. X-ray crystallography The X-ray data for 6a–d and 7–9 were collected on Rigaku OD Xcalibur (6b–d, 7, 9) and Bruker D8 Quest (6a, 8) diffractometers (Mo Kα radiation, ω-scans technique, λ = 0.71073 Å) using APEX3

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

• methods. These methods are summarised in Figure 1. Atomic resolution methods focus on the structure determination of protein complexes and elucidating the PPIs at a near-atomic resolution. Such methods include X-ray crystallography [12], nuclear magnetic resonance (NMR) [13], and cryogenic electron

• microscopy (cryo-EM) [14]. Traditionally, X-ray crystallography was the preferred method to solve the protein structure and determine protein–protein interfaces. However, protein crystallography has the limitation that some protein assemblies have a low diffraction quality and are difficult to crystallise

• 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

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