Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• X-ray crystallography, studies in solution add valuable information in molecular recognition studies as they take molecular dynamics as well as solvent effects into consideration. In the latter respect, photoaffinity labeling has evolved as a useful tool for studies under physiological conditions [1

Water-soluble SNS cationic palladium(II) complexes and their Suzuki–Miyaura cross-coupling reactions in aqueous medium

• Alphonse Fiebor,
• Richard Tia,
• Banothile C. E. Makhubela and
• Henok H. Kinfe

Beilstein J. Org. Chem. 2018, 14, 1859–1870, doi:10.3762/bjoc.14.160

• the formation of the corresponding pincer complexes 17c and 17d directly without formation of an isolable bidentate intermediate observed during the synthesis of complexes 17a and 17b. Furthermore, the successful synthesis of the pincer complexes was confirmed by X-ray crystallography and the

Preparation and X-ray structure of 2-iodoxybenzenesulfonic acid (IBS) – a powerful hypervalent iodine(V) oxidant

• Irina A. Mironova,
• Pavel S. Postnikov,
• Rosa Y. Yusubova,
• Akira Yoshimura,
• Thomas Wirth,
• Viktor V. Zhdankin,
• Victor N. Nemykin and
• Mekhman S. Yusubov

Beilstein J. Org. Chem. 2018, 14, 1854–1858, doi:10.3762/bjoc.14.159

• formation of a precipitate consisting of needle-shaped organic crystals and microcrystalline powder of inorganic salts was observed. The needle-shaped organic crystals were manually separated from the inorganic salts and analysed by NMR spectroscopy and X-ray crystallography. 1H and 13C NMR spectra of these

• ) was established by single-crystal X-ray crystallography (for crystallographic details, see Table S1 in Supporting Information File 1). The X-ray structure of an independent unit of IBS-K is shown in Figure 1, and the corresponding structural drawing with interatomic bond distances is presented in

First thia-Diels–Alder reactions of thiochalcones with 1,4-quinones

• Grzegorz Mlostoń,
• Katarzyna Urbaniak,
• Paweł Urbaniak,
• Anna Marko,
• Anthony Linden and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2018, 14, 1834–1839, doi:10.3762/bjoc.14.156

• X-ray crystallography (Figure 1). Remarkably, the presence of OH and Cl substituents in products 4i–l results in a bathochromic shift of UV–vis absorptions. The crystal structure of 4k is that of the regioisomer proposed on the basis of reactivity considerations. Since the space group is

Synthesis of spirocyclic scaffolds using hypervalent iodine reagents

• Fateh V. Singh,
• Priyanka B. Kole,
• Saeesh R. Mangaonkar and
• Samata E. Shetgaonkar

Beilstein J. Org. Chem. 2018, 14, 1778–1805, doi:10.3762/bjoc.14.152

• single crystal X-ray crystallography. Dong and co-workers [90] developed a novel way for the synthesis of five membered spiro pyrazolin-5-ones using amide and amine-containing precursors. Herein, five-membered azaheterocyclic derivatives were synthesized efficiently in presence of PIFA and with TFA as an

• groups. The structure of 75 was confirmed by single crystal X-ray crystallography. 3.2. Using hypervalent iodine reagents as catalysts In 2007, Kita and co-workers [98] investigated the first iodoarene-catalyzed spirocyclization of functionalized amides 76 to spirocyclic systems 77 by carbon–nitrogen

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

• Rakesh Puttreddy,
• Ngong Kodiah Beyeh,
• S. Maryamdokht Taimoory,
• Daniel Meister,
• John F. Trant and
• Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

• Discussion Solid-state X-ray crystallography Nine X-ray crystal structures were obtained from BrC6 in combination with twelve PyNO guest molecules. Several attempts to obtain single crystals of BrC6 by itself, 1+BrC6, 2+BrC6 and 9+BrC6 in methanol were unsuccessful. In the following discussions, for example

• crystallography and 1H NMR solution studies in three different hydrogen-bond-competitive solvents. In the solid state, BrC6 undergoes large cavity conformational changes to accommodate the N-oxide guests compared to our previously studied host systems, C-ethyl-2-bromoresorcinarene and C-propyl-2

• calculated energies of these bonds, E(x) (kcal/mol), proposed by Espinosa et al. [53][54]. Summary of endo/exo host–guest complexations studied in solution by 1H NMR in comparison to the solid state by single crystal X-ray crystallography. Supporting Information Supporting Information File 222: Experimental

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• IV and III, respectively, to achieve optimal binding [37]. This has been unambiguously confirmed by X-ray single crystallography (Figure 1b and 1c). Guest 10+ is a strong binder and its induction on the conformations of ZB4 was further analyzed. The guest exchange in solution of 10+@ZB4 is fast

• 14+@ZB4-III, 16+@ZB4-III, 18+@ZB4-III, and 21+@ZB4-III suitable for X-ray single crystallography, were obtained and their crystal structures are shown in Figure 3. The substituents of these four guests located at three representative positions in Figure 2. Therefore, a closer look at their crystal

• recognition of ZB4 using NMR, ITC titration and X-ray crystallography. Similar to TA4, ZB4 is able to host a wide range of organic cations. However, in contrast to TA4, ZB4 shows no large amplitude of conformational response to the electronic nature of substituents on the guests, and its binding affinities

One hundred years of benzotropone chemistry

• Arif Dastan,
• Haydar Kilic and
• Nurullah Saracoglu

Beilstein J. Org. Chem. 2018, 14, 1120–1180, doi:10.3762/bjoc.14.98

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• surface plasmon resonance, X-ray crystallography and molecular modeling [130]. These experiments revealed that these novel conjugates form 1:1 complexes

Preparation, structure, and reactivity of bicyclic benziodazole: a new hypervalent iodine heterocycle

• Akira Yoshimura,
• Michael T. Shea,
• Cody L. Makitalo,
• Melissa E. Jarvi,
• Gregory T. Rohde,
• Akio Saito,
• Mekhman S. Yusubov and
• Viktor V. Zhdankin

Beilstein J. Org. Chem. 2018, 14, 1016–1020, doi:10.3762/bjoc.14.87

• oxidation of 2-iodo-N,N’-diisopropylisophthalamide with m-chloroperoxybenzoic acid under mild conditions. Single crystal X-ray crystallography of this compound revealed a five-membered bis-heterocyclic structure with two covalent bonds between the iodine atom and the nitrogen atoms. This novel benziodazole

• and peptides [23][24][25]. Numerous examples of five-membered hypervalent iodine(III) heterocycles containing other than oxygen heteroatoms, such as sulfur [26], boron [27][28], phosphorous [29], or nitrogen [30][31][32], have been synthesized and characterized by X-ray crystallography. In particular

• refrigerator for several weeks. Solutions of 7a in CDCl3 or CD3CN did not show any decomposition even after storage for over one month at room temperature. The solid state structure of compound 7a was characterized by X-ray crystallography. A single crystal X-ray diffraction of 7a confirmed the bicyclic

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• characterization of the cholesterol/β-CD inclusion complex [22], its binding affinity [23][24][25], the inclusion mode of the complex [26] and its dynamic behavior through MD simulations [27][28][29] but its crystal structure is absent. In this work, the structure of CHL/β-CD is determined by X-ray crystallography

• dimers [24][25][33]. In this study, the determination by X-ray crystallography of the CHL inclusion in a head–head β-CD dimer conclusively resolves this ambiguity. The binding affinity calculations based on this model give high absolute ΔG values at both 300 K and 340 K temperatures (Table 2) indicating

• the slow cooling crystallization technique. More specific, 10.22 mg (0.026 mmoles) of CHL were added in a 2 mL equimolar aqueous solution of β-CD. The mixture was stirred at 70 °C for 4 h and gradually cooled to room temperature over a period of seven days. X-ray crystallography A prismatic colorless

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton

Enhanced quantum yields by sterically demanding aryl-substituted β-diketonate ancillary ligands

• Rebecca Pittkowski and
• Thomas Strassner

Beilstein J. Org. Chem. 2018, 14, 664–671, doi:10.3762/bjoc.14.54

• laboratory of the department using a Eurovektor Hekatech EA-3000 elemental analyzer. Melting points were measured on a Wagner and Munz Poly Therm A system and are not corrected. X-ray crystallography Crystallographic data for compound 3 were collected on Bruker D8 VENTURE Kappa Duo PHOTON200 by IμS micro

An air-stable bisboron complex: a practical bidentate Lewis acid catalyst

• Longcheng Hong,
• Sebastian Ahles,
• Andreas H. Heindl,
• Gastelle Tiétcha,
• Andrey Petrov,
• Zhenpin Lu,
• Christian Logemann and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 618–625, doi:10.3762/bjoc.14.48

• experimental procedures, copies of 1H and 13C NMR spectra, UV–vis spectra as well as the X-ray crystallography. Supporting Information File 32: CIF of bisborane complex B. Acknowledgements Funding by the BMEL (Federal Ministry of Food and Agriculture) within the project FOREST (22403116) and by the CMBlu AG

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• aminoimidazolides as monomers [52]; b) one of the structural arrangements found in a recent crystallography study that used oligophosphates as model compounds [53]. Proposed steps of enzyme-free primer extension with in situ activation, using the "general condensation buffer" containing EDC and 1-ethylimidazole as

5-Aminopyrazole as precursor in design and synthesis of fused pyrazoloazines

• Ranjana Aggarwal and
• Suresh Kumar

Beilstein J. Org. Chem. 2018, 14, 203–242, doi:10.3762/bjoc.14.15

• ] starting from 7-diethylaminocoumarin-3-aldehyde (26) and 5-aminopyrazole derivatives 16 (Scheme 4). The structure of the synthesized compounds was confirmed by X-ray crystallography, 1H and 13C NMR and HRMS studies. The relationships between the structures and chemical properties of these compounds were

Progress in copper-catalyzed trifluoromethylation

• Guan-bao Li,
• Chao Zhang,
• Chun Song and
• Yu-dao Ma

Beilstein J. Org. Chem. 2018, 14, 155–181, doi:10.3762/bjoc.14.11

• was characterized by X-ray crystallography. Aryl iodides, which contained nitrile, ketone, aldehyde, ester, methyl, phenyl groups, etc., were successfully reacted with this trifluoromethylation reagent to give the corresponding products in moderate to high yields. Also, a broad spectrum of heteroaryl

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• led to the development of a large number of techniques for such investigations. Among the most significant ones are NMR [1] and X-ray crystallography [2]. Both techniques offer a high structure resolution and NMR can also provide information on dynamics. However, there are occasions where NMR and X

• -ray crystallography suffer from drawbacks: the sample amount requirement and biomolecular size restriction for NMR and the difficulties in obtaining crystals and the obvious lack of solution dynamics for X-ray crystallography. An important method for biomolecular structure and dynamics investigations

• Å, respectively [25]. This is in contrast to previously reported values showing slight increases in helical twist and rise measured, for example, by sedimentation [77], gel electrophoresis [78][79], X-ray crystallography [74] and magnetic tweezers [75]. In our investigation we modeled the general

Stereochemical outcomes of C–F activation reactions of benzyl fluoride

• Neil S. Keddie,
• Pier Alexandre Champagne,
• Justine Desroches,
• Jean-François Paquin and
• David O'Hagan

Beilstein J. Org. Chem. 2018, 14, 106–113, doi:10.3762/bjoc.14.6

• stereochemistry of 12 was confirmed by X-ray crystallography of the 4-bromophenyl ester derivative 13. Alcohol 12 was activated as the tosyl ester at −20 °C, and then immediately displaced by LiAlD4 [17], inverting the stereocenter to afford the (S)-diarylmethane 10 isotopomer in 18% ee. 2H{1H} NMR in a PBLG

From dipivaloylketene to tetraoxaadamantanes

• Gert Kollenz and
• Curt Wentrup

Beilstein J. Org. Chem. 2018, 14, 1–10, doi:10.3762/bjoc.14.1

• and ethyl esters were determined by X-ray crystallography [19]. The X-ray structure of the Pt(II) chelate of tetramethyl 2,6,9-trioxabicyclo[3.3.1]nona-3,7-diene obtained from tris-acetylacetonato platinum(II) was determined previously [22][23], and the separation of the enantiomers of the free ligand

• was achieved by fractional crystallization [24]. Chirality of the bisdioxine dicarbaldehyde, 2,6,9-trioxabicyclo[3.3.l]nona-3,7-diene-4,8-dicarbaldehyde, obtained by extrusion of water from triformylmethane, has also been demonstrated [25], and X-ray crystallography confirmed the structure of this

• , urethanes and isocyanates point inward (Scheme 9). This observation was confirmed by X-ray crystallography as well as calculations at the B3LYP/6-31G** level [38][39]. The tert-butyl groups provide steric protection to the exo sides of the molecules, making the diisocyanate stable at ordinary temperatures

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols

• Katrina Tait,
• Alysia Horvath,
• Nicolas Blanchard and
• William Tam

Beilstein J. Org. Chem. 2017, 13, 2888–2894, doi:10.3762/bjoc.13.281

• reactions. The scope of the reaction was successfully expanded to include primary, secondary, and tertiary alcohol nucleophiles. Through X-ray crystallography, the stereochemistry of the product was determined which confirmed an SN2-like mechanism to form the ring-opened product. Keywords: acid catalysis

• most cases, the starting material was completely consumed, the yields of these ring-opening reactions were only moderate (26–61%). This may be due to the decomposition or polymerization of the cyclopropanated 3-aza-2-oxabicyclic alkene under the reaction conditions. Through X-ray crystallography [20

• of the reaction was successfully expanded to include primary, secondary, and tertiary alcohol nucleophiles. Through X-ray crystallography, the stereochemistry of the product was determined which confirmed an SN2-like mechanism to form the ring-opened product. Further investigation of the ring-opening

The photodecarboxylative addition of carboxylates to phthalimides as a key-step in the synthesis of biologically active 3-arylmethylene-2,3-dihydro-1H-isoindolin-1-ones

• Ommid Anamimoghadam,
• Saira Mumtaz,
• Anke Nietsch,
• Gaetano Saya,
• Cherie A. Motti,
• Jun Wang,
• Peter C. Junk,
• Ashfaq Mahmood Qureshi and
• Michael Oelgemöller

Beilstein J. Org. Chem. 2017, 13, 2833–2841, doi:10.3762/bjoc.13.275

• photoaddition products 3a and 3b were unambiguously confirmed by X-ray crystallography (Figure 2). In the solid state, molecules of both compounds undergo hydrogen bonding between the newly formed hydroxy group and the intact carbonyl group, resulting in a one-dimensional network (see Supporting Information

¹⁵N-Labelling and structure determination of adamantylated azolo-azines in solution

• Sergey L. Deev,
• Alexander S. Paramonov,
• Tatyana S. Shestakova,
• Igor A. Khalymbadzha,
• Oleg N. Chupakhin,
• Julia O. Subbotina,
• Oleg S. Eltsov,
• Pavel A. Slepukhin,
• Vladimir L. Rusinov,
• Alexander S. Arseniev and
• Zakhar O. Shenkarev

Beilstein J. Org. Chem. 2017, 13, 2535–2548, doi:10.3762/bjoc.13.250

• pure compounds, while the heterogeneity observed at 45 °C was connected to the presence of different rotameric states. To confirm the determined positions of the N-adamantane substitutions, compounds 15a and 15b were studied by X-ray crystallography. Suitable crystals of 15a and 15b were obtained by

Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity

• Tathagata Mukherjee,
• Soumik Biswas,
• Andreas Ehnbom,
• Subrata K. Ghosh,
• Ibrahim El-Zoghbi,
• Nattamai Bhuvanesh,
• Hassan S. Bazzi and
• John A. Gladysz

Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246

• spectra were recorded. The relative peak integrations gave the corresponding partition coefficients. Crystallography. A solution of 1,3,5-(Rf6)2C6H3I (ca. 0.05 g) in CHCl3/C6F6 (1.0 mL, 4:1 v/v) in an NMR tube was allowed to concentrate. After 2 d, colorless needles with well defined faces were obtained

Synthesis, effect of substituents on the regiochemistry and equilibrium studies of tetrazolo[1,5-a]pyrimidine/2-azidopyrimidines

• Elisandra Scapin,
• Paulo R. S. Salbego,
• Caroline R. Bender,
• Alexandre R. Meyer,
• Anderson B. Pagliari,
• Tainára Orlando,
• Geórgia C. Zimmer,
• Clarissa P. Frizzo,
• Helio G. Bonacorso,
• Nilo Zanatta and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 2396–2407, doi:10.3762/bjoc.13.237

• Information File 1. Similar to our study, Sirakanyan et al. [46] presented the synthesis and structure of condensed triazolo- and tetrazolopyrimidines, wherein, in DMSO-d6, tetrazolo-azidopyrimidines were in equilibrium. However, the structure confirmed by X-ray crystallography was the tetrazole form, which