Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• has been observed on at least two ThDP-dependent enzymes. Dihydrothiachromine diphosphate (TC) was observed in the X-ray structure of phosphoketolase from Bifidobacterium breve [46], and its hydroxyethyl derivative was identified in the structure of acetolactate synthase from Klebsiella pneumoniae

• whose crystals had been soaked with pyruvate [47]. In a very recent study, we used quantum chemical methodology to investigate the detailed reaction mechanism of benzoylformate decarboxylase (BFDC) [29]. A model of the active site was designed on the basis of the X-ray structure of BFDC in complex with

• in the absence of enzyme. Model C: active site including the crystallographic water In the X-ray structure of unliganded BFDC, there is a crystallographic water molecule that is displaced when a ligand is present [13][49]. In model C, that water molecule is included and is found to bind in the same

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• [43][44] followed by phosphitylation at the 3’-oxygen afforded the phosphoramidite 9. X-ray structure and molecular modeling of the 6’-diF-bc4,3 nucleoside To verify the relative configuration of nucleoside 6, crystals of this compound were subjected to X-ray diffraction analysis. The asymmetric unit

• complementary RNA strand less efficiently as compared to the natural DNA/RNA duplex. This is a promising finding which points to a possible application for both modifications in therapeutic gapmer oligonucleotides. Chemical structure of selected fluorine-modified nucleic acids. X-ray structure of nucleoside 6a

• National Science Foundation (grant-no: 200020_165778). We thank the group of Chemical Crystallography of the University of Bern (Prof. Dr. P. Macci) for the X-ray structure and the Swiss National Science Foundation (R’equip project 206021_128724) for co-funding of the single crystal X-ray diffractometer at

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• upon inserting an additional OMe group. Such a NHO bond is clearly visible in the X-ray structure of 6c (Figure 8). As a result, in solutions of 6c and 7c, NH2+ proton signals are observed separately up to 40 °C (for spectra in CD3CN see also Figures S20–S23 in Supporting Information File 1

Generation of 1,2-oxathiolium ions from (arysulfonyl)- and (arylsulfinyl)allenes in Brønsted acids. NMR and DFT study of these cations and their reactions

• Stanislav V. Lozovskiy,
• Alexander Yu. Ivanov,
• Olesya V. Khoroshilova and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2018, 14, 2897–2906, doi:10.3762/bjoc.14.268

• followed by acetylene–allene rearrangement was used to prepare (arylsulfinyl)allenes 1 according to the literature procedure [24][25]. The latter were in situ oxidized to (arylsulfonyl)allenes 2 (see X-ray structure of 2h in Figure 1). Allenes 1a,b were specially isolated to compare their reactivity with

• equivalent of TfOH to generate the corresponding cations Ba–h. Then, the reaction mixture was cooled down to −35 °C and quenched under very mild and low nucleophilic conditions with frozen aqueous HCl at −60 °C, that finally led quantitatively to butadienes 3a–h (see X-ray structure of 3e in Figure 1). Worth

• ). The exclusive formation of thiochromene 1,1-dioxides 5a–c was obtained by running the reaction of 2a,c,d with 1 equivalent of CF3SO3H at high temperature (reflux in ortho-dichlorobenzene at 144 °C) for 2 h (Scheme 5, see X-ray structure of 5c in Figure 1). It was found by H,H-NOESY and COSY

Synthesis of pyrrolidine-based hamamelitannin analogues as quorum sensing inhibitors in Staphylococcus aureus

• Jakob Bouton,
• Kristof Van Hecke,
• Reuven Rasooly and
• Serge Van Calenbergh

Beilstein J. Org. Chem. 2018, 14, 2822–2828, doi:10.3762/bjoc.14.260

• . Structures of hamamelitannin (1), lead compound 2 and target compounds 3. Molecular X-ray structure of 3a, showing thermal displacement ellipsoids at the 50% probability level. Positional disorder of the chlorophenyl ring and the water solvent molecule are not shown. Proposed strategy for the synthesis of

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• none of these compounds an X-ray structure in complex with PqsD has been reported although the apoenzyme as well as a substrate-bound form has been successfully crystallized [49]. Using these coordinates, employing in silico methods allowed proposing plausible binding poses for prototypic analogues of

Synthesis of aryl sulfides via radical–radical cross coupling of electron-rich arenes using visible light photoredox catalysis

• Amrita Das,
• Mitasree Maity,
• Simon Malcherek,
• Burkhard König and
• Julia Rehbein

Beilstein J. Org. Chem. 2018, 14, 2520–2528, doi:10.3762/bjoc.14.228

• the limit of the scope of the method. The substrate scope is shown in Scheme 3. The structures of compounds 3a, 3d, 3e and 3i in the solid state were determined by X-ray structure analysis (Figure 2). We performed various control experiments to support the proposed reaction mechanism, which is shown

Calixazulenes: azulene-based calixarene analogues – an overview and recent supramolecular complexation studies

• Paris E. Georghiou,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Hidetaka Nishimura,
• Jaehyun Lee,
• Atsushi Wakamiya and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2018, 14, 2488–2494, doi:10.3762/bjoc.14.225

• determinations were made on the possible major conformations, based upon those previously defined in reference [20]. Three distinct conformations (saddle, cone and 1,2-alternate) shown in Figure 2, were generated. Significantly, whereas for 3 which was based upon its X-ray structure, a partial cone conformer

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• reaction the use of the TBTA complex was essential for the cyclization of dC precursor 2 but not for dU precursor 7. Protection of precursor molecules is not required and only four steps are necessary to convert a nucleoside in a nucleoside macrocycle. The single crystal X-ray structure confirmed the click

• decrease. Next, a X-ray analysis was performed from the dU macrocycle 8, which was crystallized from methanolic solution containing traces of water. Colorless needles with a melting point of 260–265 °C (decomp.) were obtained. The solid state structure of the macrocycle is displayed in Figure 2. The X- ray

• structure of the macrocycle reflects the properties of the components with slight deviations. The glycosylic bond length (N1–C1’) of 8 is 1.459(3) Å and is in the range of 5-substituted 2’-deoxyuridines [45]. The alkynyl side chain (C5–C7–C8) and (C7–C8–C9) is slightly bend with bond angles of 172.1 (3

Hypervalent iodine compounds for anti-Markovnikov-type iodo-oxyimidation of vinylarenes

• Igor B. Krylov,
• Stanislav A. Paveliev,
• Mikhail A. Syroeshkin,
• Alexander A. Korlyukov,
• Pavel V. Dorovatovskii,
• Yan V. Zubavichus,
• Gennady I. Nikishin and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2018, 14, 2146–2155, doi:10.3762/bjoc.14.188

• Information File 214: X-ray structure analysis data for 3ca (CCDC-1845323). Acknowledgements This work was supported by the Russian Science Foundation (18-13-00027).

Evaluation of dispersion type metal···π arene interaction in arylbismuth compounds – an experimental and theoretical study

• Ana-Maria Preda,
• Małgorzata Krasowska,
• Lydia Wrobel,
• Philipp Kitschke,
• Phil C. Andrews,
• Jonathan G. MacLellan,
• Lutz Mertens,
• Marcus Korb,
• Tobias Rüffer,
• Heinrich Lang,
• Alexander A. Auer and
• Michael Mehring

Beilstein J. Org. Chem. 2018, 14, 2125–2145, doi:10.3762/bjoc.14.187

• dispersion energy donors in previous work. Keywords: arylbismuth compounds; DFT-D; dispersion type Bi···π arene interaction; DLPNO-CCSD(T); electronic structure calculations; polymorphism; single crystal X-ray structure; Introduction Although known for more than a century, the interest on metal···π arene

• interactions in the context of structure formation in R3Bi compounds (Bi···Bi contacts vary between 4.015 and 4.059 Å) [63]. (C6H4-OMe-4)3Bi (3) (C6H4-OMe-4)3Bi (3) crystallized from CHCl3 in the form of colorless cube-shaped or block-shaped crystals which were suitable for single crystal X-ray structure

Chiral bisoxazoline ligands designed to stabilize bimetallic complexes

• Deepankar Das,
• Rudrajit Mal,
• Nisha Mittal,
• Zhengbo Zhu,
• Thomas J. Emge and
• Daniel Seidel

Beilstein J. Org. Chem. 2018, 14, 2002–2011, doi:10.3762/bjoc.14.175

• ligand 25-H3 in 85% yield. Treatment of 25-H3 with nickel(II) acetate provided the binuclear complex 25·Ni2(OAc), the X-ray structure of which is shown in Figure 4. Each unit of the complex is comprised of two nickel(II) centers, each bound by three nitrogen atoms from the ligand skeleton and bridged by

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

• ) 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

• the iodine(V) products. X-ray structure of an independent crystal unit of IBS 6-K. Simplified representation of structure 6-K. Selected interatomic distances (Å): I(1)=O(1) 1.79; I(1)=O(2) 1.81; I(1)–O(3) 2.54; O(2)–I(2) 2.46; I(2)=O(7) 1.81; I(2)–O(6) 1.88; I(2)–O(8) 2.60; I(2)–O(16) 2.71; I(3)=O(11

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

• cavity is represented as ‘h’, defined as the measured distance from the centroid of the lower-rim host carbon atoms to the nearest endo guest non-hydrogen atom. In the X-ray structure of 3@BrC6 (Figure 2a), guest 3, oriented parallel to the host aromatic rings (h = 3.43 Å) is positioned in one corner of

• that in solution, the N–O group of guest 3 is pointing outward from the BrC6 cavity during endo complexation. In the X-ray structure of 3@BrC6, only the c-proton of 3 has C–H···π(host) short contacts with distances ranging between ca. 2.65 Å and 2.85 Å. This supports the maximum chemical shift change

Lanyamycin, a macrolide antibiotic from Sorangium cellulosum, strain Soce 481 (Myxobacteria)

• Lucky S. Mulwa,
• Rolf Jansen,
• Dimas F. Praditya,
• Kathrin I. Mohr,
• Patrick W. Okanya,
• Joachim Wink,
• Eike Steinmann and
• Marc Stadler

Beilstein J. Org. Chem. 2018, 14, 1554–1562, doi:10.3762/bjoc.14.132

• . Since the X-ray structure of bafilomycin A1 is available from CCDC it was used to calculate the 3D model of the lactone ring in 1/2 using HyperChem Prof. (version 8.0.10, Figure 4). Initially the X-ray structure was optimized with the mm+ method, which showed a good congruency of X-ray structure and mm

An unusual thionyl chloride-promoted C−C bond formation to obtain 4,4'-bipyrazolones

• Gernot A. Eller,
• Gytė Vilkauskaitė,
• Algirdas Šačkus,
• Vytas Martynaitis,
• Ashenafi Damtew Mamuye,
• Vittorio Pace and
• Wolfgang Holzer

Beilstein J. Org. Chem. 2018, 14, 1287–1292, doi:10.3762/bjoc.14.110

• prepared. Moreover, the structure of a representative 5,5'-dioxo-4,4'-bipyrazole-4,4'-dicarboxylate was confirmed by X-ray crystal structure analysis. Keywords: dimerization; NMR (1H; 13C; 15N); pyrazolones; thionyl chloride; X-ray structure analysis; Introduction Many biologically active substances

Stereoselective nucleophilic addition reactions to cyclic N-acyliminium ions using the indirect cation pool method: Elucidation of stereoselectivity by spectroscopic conformational analysis and DFT calculations

• Koichi Mitsudo,
• Junya Yamamoto,
• Tomoya Akagi,
• Atsuhiro Yamashita,
• Masahiro Haisa,
• Kazuki Yoshioka,
• Hiroki Mandai,
• Koji Ueoka,
• Christian Hempel,
• Jun-ichi Yoshida and
• Seiji Suga

Beilstein J. Org. Chem. 2018, 14, 1192–1202, doi:10.3762/bjoc.14.100

• –C6, and NMR spectra of all new compounds and C1–C6. Supporting Information File 156: X-ray structure analysis data for 1a (CCDC-1813600), 1b (CCDC-1813582), 1d (CCDC-1813594), 1e (CCDC-1813595), 1f (CCDC-1813596). These data can be obtained free of charge from The Cambridge Crystallographic Data

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

• . Supporting Information Supporting Information File 85: Experimental section. Supporting Information File 86: X-ray structure of 7a. Acknowledgements This work was supported by a research grant from the Russian Science Foundation (RSF-16-13-10081). A.S. is also thankful to JSPS Grant-in-Aid for Scientific

Oxidative cycloaddition of hydroxamic acids with dienes or guaiacols mediated by iodine(III) reagents

• Hisato Shimizu,
• Akira Yoshimura,
• Keiichi Noguchi,
• Victor N. Nemykin,
• Viktor V. Zhdankin and
• Akio Saito

Beilstein J. Org. Chem. 2018, 14, 531–536, doi:10.3762/bjoc.14.39

• Information File 19: Experimental section. Supporting Information File 20: X-ray structure of 3aa. Supporting Information File 21: X-ray structure of 4. Supporting Information File 22: X-ray structure of 6aa. Acknowledgements This work was partially supported by JSPS Grants-in-Aid for Scientific Research (C

Synthesis of fluoro-functionalized diaryl-λ³-iodonium salts and their cytotoxicity against human lymphoma U937 cells

• Prajwalita Das,
• Etsuko Tokunaga,
• Hidehiko Akiyama,
• Hiroki Doi,
• Norimichi Saito and
• Norio Shibata

Beilstein J. Org. Chem. 2018, 14, 364–372, doi:10.3762/bjoc.14.24

• SF5-diaryliodonium salts 3p, 4b, 5a and 6a were characterized spectroscopically. The single crystal X-ray structure of 3p was also analysed. The SF5-diaryliodonium salt 3p has a T-shaped geometry at the iodine centre, consistent with the general structure of diaryliodonium salts [33] (Figure 3

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

• )-diarylmethane 10 from diaryl ketone 11 and confirmation of configuration of (R)-13 by single crystal X-ray structure. Nucleophilic substitution reactions of racemic 7-[2H1]-benzyl bromide (4). Nucleophilic substitution reactions of 7-[2H1]-(R)-benzyl fluoride ((R)-1). Friedel–Crafts reactions of 7-[2H1]-(R

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

• -butylcalix[6]arene moiety in 37 (Figure 3), which is obtained from the bisdioxine diacid dichloride 12 and calixarene [42]. The wider upper rim is clearly seen in the X-ray structure and the compound demonstrates a pronounced ability to extract Cs+ ions from water into chloroform by forming endohedral

Electrophilic trifluoromethylselenolation of terminal alkynes with Se-(trifluoromethyl) 4-methylbenzenesulfonoselenoate

• Clément Ghiazza,
• Anis Tlili and
• Thierry Billard

Beilstein J. Org. Chem. 2017, 13, 2626–2630, doi:10.3762/bjoc.13.260

• . Further, a high regioselectivity is observed but, surprisingly, the anti-Markovnikov regioisomers were obtained. The stereochemistry and regiochemistry were confirmed thanks to the X-ray structure of compound 3a (Figure 1). From a mechanistic point of view, the reaction starts certainly with the

• reaction was stirred at 25 °C for 15–18 hours (conversion was checked by 19F NMR with PhOCF3 as internal standard). The crude residue was purified by chromatography to afford the desired products 3–5. Single-crystal X-ray structure of 3a. Electrophilic addition of 1a to alkynes. Yields shown are those of

Regioselective decarboxylative addition of malonic acid and its mono(thio)esters to 4-trifluoromethylpyrimidin-2(1H)-ones

• Sergii V. Melnykov,
• Andrii S. Pataman,
• Yurii V. Dmytriv,
• Svitlana V. Shishkina,
• Mykhailo V. Vovk and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2017, 13, 2617–2625, doi:10.3762/bjoc.13.259

• decarboxylative addition of malonic acid mono-4-methoxyphenyl thioester (1b) to 4-trifluoromethylpyrimidin-2(1H)-ones 2a–m. Supporting Information Supporting Information File 481: Experimental procedures, characterization data and X-ray structure determination for compound 11b. Supporting Information File 482

A concise flow synthesis of indole-3-carboxylic ester and its derivatisation to an auxin mimic

• Marcus Baumann,
• Ian R. Baxendale and
• Fabien Deplante

Beilstein J. Org. Chem. 2017, 13, 2549–2560, doi:10.3762/bjoc.13.251

• C11H7N3O2F3, 270.0490; found, 270.0497 (Δ = 2.6 ppm); melting range: decomposition >220 °C; X-ray crystal data: CCDC 1572809. Natural indole containing molecules 1–7 of biological importance and synthetic auxin analogue 8 required at scale and X-ray structure. X-ray structure of intermediate 11, and reductive