Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• possesses a −log(Kd) value of 8.36 suggesting that it too would be on a par with panobinostat (8.47). Our previous study showed that the hydroxamate tail of TOI1, TOI2, and TOI4 formed a bidentate interaction with the Zn2+ ion at the base of the HDAC8 receptor, which is consistent with the crystal structure

• Biotek Synergy HTX multimodal plate reader after incubation for 30 minutes. Preparation of the HDAC8 receptor for docking The HDAC8 crystal structure (protein database pdb: 1W22) [32] was utilized as the docking receptor for all compounds. This receptor is crystalized as a dimer thus only the A chain was

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

• subjected to X-ray crystallographic analysis. Orange single crystals were formed by the diffusion of pentane vapor to a 1,1,1-trichloroethane solution of 1 synthesized by the C–H borylation method. The crystal structure confirmed that the C–H borylation proceeded regioselectively at the least hindered 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

• stacking distance of around 3.45 Å. It is noteworthy that both 4b and 4c pile up while minimizing the steric repulsion between the tert-butyl groups which occupy “staggered” orientations in their crystal structures (Figure 5c and 5d). Unfortunately, the crystal structure of 4a was not determined after

Absolute configurations of talaromycones A and B, α-diversonolic ester, and aspergillusone B from endophytic Talaromyces sp. ECN211

• Ken-ichi Nakashima,
• Junko Tomida,
• Takao Hirai,
• Yoshiaki Kawamura and
• Makoto Inoue

Beilstein J. Org. Chem. 2020, 16, 290–296, doi:10.3762/bjoc.16.28

• . Supporting Information File 266: Crystal structure information files for 1, 3, and 5. Acknowledgements The authors thank the Rigaku Corporation for the single-crystal X-ray structural analysis of talaromycone A. The authors are also grateful to Dr. Hiromi Ota at the Division of Instrumental Analysis for the

Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors

• Man-Man Wang,
• Hao Huang,
• Lei Shu,
• Jian-Min Liu,
• Jian-Qiu Zhang,
• Yi-Le Yan and
• Da-Yong Zhang

Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25

• /methanol to afford a colorless transparent crystal. It crystallized in the monoclinic space group: P–1 (2), cell: a = 5.191(5) Å, b = 12.133(12) Å, c = 13.576(14) Å, α = 80.141(13)°, β = 81.978(12)°, γ = 79.496(12)°, temperature: 296 K. X-ray crystal structure of compound I18 and III4 are shown in Figure 3

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• , nitrogen, fluorine) and have been observed to govern the conformational structure of some molecules as well as the alignment of the molecules within a crystal structure [27][28][29]. Moreover, HBs have been reported to play a vital role in a ligand–receptor interaction that determines the biological

• crystal structure and solution-state NMR data of the coumarin 6 were studied to examine any C–F···H–C hydrogen bond interactions. DFT calculations were performed to determine the preferred conformations of the structure that might exhibit a C–F···H–C hydrogen bond. Results and Discussion Synthesis of 2

• the distances F–H5 and F–H3 fall inside the limit of ≈2.55 Å, although not simultaneously. For a fixed geometry like that of the crystal structure, this would suggest that through-space F–H coupling would be observed between F and H5 but not between F and H3, as in Figure 1, where there is an obvious

The reaction of arylmethyl isocyanides and arylmethylamines with xanthate esters: a facile and unexpected synthesis of carbamothioates

• Narasimhamurthy Rajeev,
• Toreshettahally R. Swaroop,
• Ahmad I. Alrawashdeh,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Seegehalli M. Anil,
• Kuppalli R. Kiran,
• Chandra,
• Paris E. Georghiou,
• Kanchugarakoppal S. Rangappa and
• Maralinganadoddi P. Sadashiva

Beilstein J. Org. Chem. 2020, 16, 159–167, doi:10.3762/bjoc.16.18

• favor of 4cB. The resulting calculated equilibrium constant of 2.042, corresponding to a 67.1/32.9 ratio of the rotamers (4cB/4cA), was in good agreement with the experimentally by 1H NMR (CDCl3) observed ratio of 65/35. Significantly, the single crystal of 4c, which afforded the crystal structure shown

• of the final products were detected in the NMR spectra, and a representative DFT computational analysis conducted with 4c (this compound also yielded a crystal structure) was in agreement with the ratio of the two rotamers that were observed in the corresponding NMR spectra. A mechanism was proposed

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• been reviewed elsewhere [3][10][11][12][13][14][15][16][17]. The first crystal structure of a monoterpene cyclase [18] was reported in 2002. Subsequently, the first crystal structures of a sesquiterpene [19][20] and a triterpene [21] cyclase were published in 1997. Less than a decade ago, the first

• crystal structure of a diterpene cyclase was reported by Christianson and co-workers [22]. These structures, in conjunction with extensive biochemical work [10][13][14][23], have contributed to the understanding of mechanistic details of terpene cyclases and facilitated rational enzyme design [24

• relevant, i.e., that have a ligand bound in a reactive configuration and have a fully closed active site. Recently, a crystal structure of the CotB2 enzyme that met these criteria was published [42]. In the current work, we describe the crucial role of the amino acids in the active site on the reaction

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

• characterize the formation of the 2,7-anhydro skeleton, triols 2 and 3 were treated with 2,2-dimethoxypropane in the presence of a catalytic amount of camphorsulfonic acid (CSA) in acetonitrile to afford compound 4 in 63% and azide acceptor 4a in quantitative yield (Scheme 1). The crystal structure of 4

Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis

• David C. B. Siebert,
• Roman Sommer,
• Domen Pogorevc,
• Michael Hoffmann,
• Silke C. Wenzel,
• Rolf Müller and
• Alexander Titz

Beilstein J. Org. Chem. 2019, 15, 2922–2929, doi:10.3762/bjoc.15.286

• , encoded by the gene fusA1) as their target [11][12]. The co-crystal structure of argyrin B (2) and P. aeruginosa EF-G1 provides structural information of the complex at atomic resolution as basis for further structure-based optimization [11]. Jones and colleagues analyzed possible resistance mechanisms to

• ’-methoxy group to halogens or other substituents in different positions led to a loss of antibacterial activity, whereas the 5’-methoxytryptophan regioisomer largely retained activity against P. aeruginosa PAO1. Inspection of the crystal structure of argyrin in complex with the bacterial elongation factor

• possibility resides in the dehydroalanine-sarcosine motif and modification seems possible as deduced from the crystal structure [11] of argyrin with elongation factor G1. Despite the successful implementation of total syntheses of argyrin derivatives, a more rapid access towards diversity in the argyrins and

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• -en-7-ol (23, Figure 7a) synthase, for which the active-site residues responsible for cationic intermediate stabilization were identified through analysis of the crystal structure [122] and structural modeling [123]. Mutations of the identified residues were shown to alter product profiles and yielded

Preparation of anthracene-based tetraperimidine hexafluorophosphate and selective recognition of chromium(III) ions

• Qing-Xiang Liu,
• Feng Yang,
• Zhi-Xiang Zhao,
• Shao-Cong Yu and
• Yue Ding

Beilstein J. Org. Chem. 2019, 15, 2847–2855, doi:10.3762/bjoc.15.278

• signal corresponding to the NCHN motif in perimidine was present at δ = 8.69 ppm [42]. Structure elucidation of compound 3 As can be seen in the crystal structure of 3 in Figure 1, the cationic moiety of the complex contained two (N-ethylperimidinyl–C2H4)2NCH2– arms attached to the 9- and 10-positions of

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• % (Table 2). Consequently, our newly optimized conditions allowed the synthesis of products 5h–j in moderate to good yields (Table 2). The structure of 5c was independently confirmed by X-ray crystal structure analysis. Figure 2 shows the planar benzofuroindol core structure with an orthogonally oriented

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

• crystal of Pd2(stable E-1)4 formed from a racemic mixture of ligand E-1 suitable for X-ray structure determination was grown by vapor diffusion of a 1:1 mixture of benzene and diethyl ether into a solution of the cage in a 1:1 mixture of acetonitrile and chloroform. The crystal structure shows cage

• (stable Z-1)4 (top) and E-1 and cage complex Pd2(stable E-1)4 (bottom). HRMS spectra of cage complex Pd2(stable Z-1)4 (top) and cage complex Pd2(stable E-1)4 (bottom); Insets: comparison of simulated and measured isotopic patterns of Pd2L4(NO3)3+ ions. Crystal structure of cage complex Pd2(stable E-1)4

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

• crystal structure). We attribute this to a packing effect in the solid state. To the best of our knowledge, an E-isomer azo photoswitch with this type of solid state packing is unprecedented and may open new possibilities in solid state photoswitchable materials applications. The benzene ring in 4pzH-F2

Emission solvatochromic, solid-state and aggregation-induced emissive α-pyrones and emission-tuneable 1H-pyridines by Michael addition–cyclocondensation sequences

• Natascha Breuer,
• Irina Gruber,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2019, 15, 2684–2703, doi:10.3762/bjoc.15.262

• -dimethylaminophenyl substituent furnishes α-pyrone 6g (Table 4, entry 13). For synthesizing 1H-pyridine derivatives 8 with an electron-donating group we employed the isolated dimer 7 and were able to isolate 1H-pyridines 8 in 52 and 34% yield (Scheme 10). Crystal structure of 1H-pyridine 5a The structure of 1H

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

• absolute structures, however their anomalous dispersion statistics indicate that the assignments are very likely to be correct. The crystal structure of 1 has four crystallographically-independent molecules, while the structures of 2b and 3b have two crystallographically-independent molecules, and the

• File 565: Details of cultivation media, fractionation schemes, NMR spectra and tabulated 2D NMR data for all compounds, detailed X-ray crystallographic details and CCDC deposition numbers, bioassay procedures and genomic data. Supporting Information File 566: Crystal structure information files for

1,5-Phosphonium betaines from N-triflylpropiolamides, triphenylphosphane, and active methylene compounds

• Vito A. Fiore,
• Chiara Freisler and
• Gerhard Maas

Beilstein J. Org. Chem. 2019, 15, 2603–2611, doi:10.3762/bjoc.15.253

• broad O–H absorption bands in their IR spectra (≈3400–3500 cm−1) and the presence of hydrogen-bonded water molecules in the crystal structure of E-3e (vide infra) indicate. The formation of betaines 3 includes the elimination of the N-phenyltriflamide anion, which is known as an excellent leaving group

• Information Supporting Information File 640: Experimental procedures, characterization data, NMR spectra (1H, 13C, 31P, 19F) and IR spectra for the synthesized compounds, and data for the X-ray crystal structure determinations.

Formation of alkyne-bridged ferrocenophanes using ring-closing alkyne metathesis on 1,1’-diacetylenic ferrocenes

• Celine Bittner,
• Dirk Bockfeld and
• Matthias Tamm

Beilstein J. Org. Chem. 2019, 15, 2534–2543, doi:10.3762/bjoc.15.246

• characterisation, crystallographic data. Acknowledgements The authors wish to thank Dr. Holger Ott from Bruker AXS Inc., Karlsruhe, for the crystal structure determination of compound 4.

Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• similar affinity towards the Me4N+ cation as 2. Also, all our attempts to obtain a solid-state single crystal structure of 1 with a cationic guest were unsuccessful. It is possible that the observation of such complexes requires special conditions present in the ESI source. To obtain more detailed

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

• ). Apparently, this product is the result of destruction of bis(pyrazolyl)borate moieties of complex 8 by methanol. Species 9 crystallizes as red, block-shaped crystals in the triclinic P−1 space group with one molecule in the unit cell. The crystal structure reveals two pairs of differently substituted iron

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

• macrocyclic diethers 1a–d, all Z-isomers have a dihedral angle of 12–14°, roughly similar to the one in the crystal structure of (Z)-7. The deviation of this angle from 0° is due to steric interaction between two aromatic protons in position 4 (Figure 9). In the E-isomers, an increasing distortion of the

Reversible switching of arylazopyrazole within a metal–organic cage

• Anton I. Hanopolskyi,
• Soumen De,
• Michał J. Białek,
• Yael Diskin-Posner,
• Liat Avram,
• Moran Feller and
• Rafal Klajn

Beilstein J. Org. Chem. 2019, 15, 2398–2407, doi:10.3762/bjoc.15.232

• , Supporting Information File 1). Front view (a) and side view (b) of the X-ray crystal structure of (E-1)22 (major conformations of 1 and 2; see also Supporting Information File 1, Figures S15 and S16). The horizontal plane (pink) denotes the positions of eight equatorial imidazole groups; four axial

In water multicomponent synthesis of low-molecular-mass 4,7-dihydrotetrazolo[1,5-a]pyrimidines

• Irina G. Tkachenko,
• Sergey A. Komykhov,
• Vladimir I. Musatov,
• Svitlana V. Shishkina,
• Viktoriya V. Dyakonenko,
• Vladimir N. Shvets,
• Mikhail V. Diachkov,
• Valentyn A. Chebanov and
• Sergey M. Desenko

Beilstein J. Org. Chem. 2019, 15, 2390–2397, doi:10.3762/bjoc.15.231

• . Crystal data: The crystal structure of compound 9a was measured on an Xcalibur-3 diffractometer (graphite monochromated Mo Kα radiation, CCD detector, ω-scanning). The structure was solved by the direct method using the SHELXTL package [34][35]. Full-matrix least-squares refinement against F2 in

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• mutagenesis have exciting applications for the sustainable production of high value bioactive substances. Keywords: biotechnology; CotB2; crystal structure; cyclooctatin; diterpene; reaction mechanism; terpene synthase; Introduction Terpenes represent one of the most diverse groups of natural biomolecules

• subsequent cyclization unlikely. Crystal structure of CotB2wt·Mg2+3·F-Dola resembles the closed, active conformation The structure of CotB2wt·Mg2+3·F-Dola has been obtained by co-crystallization of CotB2wt and FGGDP (PDB-ID 6GGI; [37]), representing the closed, active conformation. Fluorinated substrates

• -crystallized with AHD, a compound that mimics the diphosphate group of GGDP and acts as a suicide inhibitor. The crystal structure of CotB2wt·Mg2+3·AHD (PDB-ID 6GGJ; [37]) confirmed the active site architecture as observed in the structure of CotB2wt·Mg2+3·F-Dola and more importantly, that the folding of the C