Total synthesis of ent-pavettamine

• Memory Zimuwandeyi,
• Manuel A. Fernandes,
• Amanda L. Rousseau and
• Moira L. Bode

Beilstein J. Org. Chem. 2021, 17, 1440–1446, doi:10.3762/bjoc.17.99

• close to the OTBS center. At this point, it was crucial to conclusively characterize the unexpected product 9. Fortuitously, we were able to obtain crystals for this compound after several recrystallization attempts. The crystal structure for 9 (Figure 2) very surprisingly showed the OTBS group on the

• pavettamine, in order to obtain the enantiomer. The final deprotection step proved particularly efficient, with two protecting groups being removed simultaneously to unveil the desired target. Structure of pavettamine 1 and its enantiomer 2. Crystal structure of compound 9. Single crystal X-ray structure of

• %; f) 95% TFA, 2.5% H2O, 2.5% triisopropylamine, rt, overnight, quantitative yield. Supporting Information Detailed experimental methods and NMR spectra for all compounds prepared and crystal structure data for compounds 4 and 9 is available as supporting information. Supporting Information File 178

Analogs of the carotane antibiotic fulvoferruginin from submerged cultures of a Thai Marasmius sp.

• Birthe Sandargo,
• Leon Kaysan,
• Rémy B. Teponno,
• Christian Richter,
• Benjarong Thongbai,
• Frank Surup and
• Marc Stadler

Beilstein J. Org. Chem. 2021, 17, 1385–1391, doi:10.3762/bjoc.17.97

• of potential pharmaceutical interest. Klein et al. obtained a crystal structure of fulvoferruginin (1) [8], as did Huneck et al. for hercynolactone [9], verifying their relative configuration. Huo et al. have further confirmed the absolute configuration of compound 1 by utilizing the CD exciton

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

• the crystallographic structural characteristics of 13 mesox-halo-substituted porphyrins. Data obtained from the CSD crystal structure database accompanied by data obtained from our group are discussed [25]. Furthermore, any general structural motif that appears consistent among the mesox-halo

• further exploration of the ground state geometries and concurrently frontier molecular orbitals (FMOs) and sigma-holes have been displayed. Results and Discussion Crystal structure analyses 5-Halo-substituted porphyrins First, considering the 5-halo-10,20-diphenylporphyrins (Figure 1); in this series, we

• the tolyl group breaks the high-ordered packing previously observed. The chlorine atom does not appear to have any substantial interactions present in the crystal structure. The structure of compound 5 only differs from the structure of compound 1 by the addition of a phenyl moiety. In this structure

Synthesis of functionalized imidazo[4,5-e]thiazolo[3,2-b]triazines by condensation of imidazo[4,5-e]triazinethiones with DMAD or DEAD and rearrangement to imidazo[4,5-e]thiazolo[2,3-c]triazines

• Alexei N. Izmest’ev,
• Dmitry B. Vinogradov,
• Natalya G. Kolotyrkina,
• Angelina N. Kravchenko and
• Galina A. Gazieva

Beilstein J. Org. Chem. 2021, 17, 1141–1148, doi:10.3762/bjoc.17.87

• further transformations in basic media, are continuing. Biologically active compounds having thiazolidin-4-one and thiazolo-1,2,4-triazine units. 1H NMR spectra of compounds 4h and 5h in DMSO-d6 in the region of 3.5–8.8 ppm. X-ray crystal structure of compound 5i. Regioselectivity of the cyclization of 3

• conditionsa. Supporting Information Supporting Information File 167: Experimental and analytical data. Supporting Information File 168: CIF file for compound 5i. Acknowledgements Crystal structure determination was performed in the Department of Structural Studies of the N. D. Zelinsky Institute of Organic

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

• nuclease-resistant probes for studying RNA–protein interactions [70]. To better elucidate the structural features of 3'-NP DNA responsible for this enhanced selective binding and stability, the Egli group determined the crystal structure of the fully modified 3'-NP DNA duplex with the sequence 5'-d

• necessary protecting groups are present on the nucleobase and sugar moieties [76][77]. Unlike the phosphodiester linkage of natural DNA, the AM1 modification is an example of a non-ionic backbone. The crystal structure of a 13-mer RNA duplex with a single central AM1 modification revealed that this

• increase in silencing activity for AM1-modified siRNAs with amide linkages at specific sites [75]. Structural insight into this observation was obtained using the crystal structure of the complex between Bacillus halodurans RNase H and the r(GAC ACC UGA UAM1UC) - d(GAA TCA GGT GTC) hybrid duplex [73

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

• /EtOAc 10:1 to 1:1) to give keto lactam 13. Selected alkaloids containing the pyrrolidone motif. X-ray crystal structure of the major (2R,4S)-alkoxyamine hydrochloride derived from 9j. Displacement ellipsoids at 30% probability level and a disordered CHCl3 solvent molecule is not shown for clarity. X-ray

• crystal structure of the minor cis-diastereomers of the keto lactam 13j (left) and the hydroxy lactam 12k (right). Displacement ellipsoids are drawn at the 30% probability level. A) Classical γ-lactam synthesis by atom transfer radical cyclizations; B) previously developed tandem epoxide opening/Brook

Synthesis, structural characterization, and optical properties of benzo[f]naphtho[2,3-b]phosphoindoles

• Mio Matsumura,
• Takahiro Teramoto,
• Masato Kawakubo,
• Masatoshi Kawahata,
• Yuki Murata,
• Kentaro Yamaguchi,
• Masanobu Uchiyama and
• Shuji Yasuike

Beilstein J. Org. Chem. 2021, 17, 671–677, doi:10.3762/bjoc.17.56

• isomers, in which the position of the fused benzene rings is different; of these, three are shown in Figure 1. The synthesis, crystal structure, and dynamic behavior of benzo[e]naphtho[2,1-b]phosphindole (A) with the C2 symmetry axis on the binaphthyl skeleton have been reported [9][10][11]. Synthetic

• of the phosphorus atom. X-ray crystal analysis showed that the parent trivalent phosphole has a considerably planar benzonaphthophosphoindole skeleton in its crystal structure. 1H and 13C NMR observations revealed that all the phospholes obtained in this study had a highly symmetric structure in

• functional π-electron materials for organic electronics applications is under progress, and the results will be reported in due time. Benzonaphthophosphindoles. Crystal structure of 2: different views. a) Absorption spectra and b) normalized fluorescence spectra for selected compounds in CHCl3. The spatial

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

• and 424.3 Da for 65Cu followed the same fragmentation pattern for both ions. The proposal of the fragmentation pathway, based on the X-ray crystal structure of the Cu(II) complex with 7 (L3) (Figure 4, vide infra), is shown in Scheme 3. The MS/MS fragmentation analysis of the [(L3)Cu(II)Cl]+ complex 8

• unit. Their geometry was fully optimized in vacuum using the DFT method with the crystal structure coordinates as the input geometry (optimized at the CAM-B3LYP/6–311++G(d,p)/LanL2DZ(Cu) level of theory). However, due to the convergence failure during the geometry optimization of the dimer of molecules

• angles equal to 27.61 and 28.71°, respectively, and moreover, the methyl groups of the methoxy substituents are directed opposite and towards to the pyridin-2-yl substituents, respectively. The crystal structure of complex 17 is stabilized with a 3D intermolecular hydrogen bond network (Figure S1a

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

• crystal structure of the protein (all residues were in the trans-amide conformation). The structure showed the R-Flp and S-Mep residues adopting exo- and endo-pucker conformations, respectively. This arrangement created a tight packing between the R-Flp and S-Mep side-chains, as shown in Figure 12B. The

• -Flp. The protein containing R-Flp exhibited a slightly lowered stability compared to the parent enzyme. The crystal structure depicts R-Flp at 32 different positions (Figure 12C), including two proline residues forming cis-amide bonds (positions 300 and 579) and two oligoproline stretches (positions

• 300–302 and 368–369). A defined pucker could be observed clearly in 28 out of 32 residues; 26 residues out of this set were in the exo-pucker conformation. In contrast, the crystal structure of the wild-type protein showed 18 residues adopting single pucker conformations, and only 7 from this set were

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• their complexation. In salt 9, the bromide ions are held in the crystal structure by hydrogen bonds N15–H15···Br1b [D···A = 3.2774(17) Å, D–H···A = 142°; symmetry code: (b) –x + y + 1/3, −x + 2/3, z + 2/3] and N25–H25···Br2 (D···A = 3.2654(17) Å, D–H···A = 144°). There are also intramolecular hydrogen

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

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

Exploring the possibility of using fluorine-involved non-conjugated electron-withdrawing groups for thermally activated delayed fluorescence emitters by TD-DFT calculation

• Dongyang Chen and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2021, 17, 210–223, doi:10.3762/bjoc.17.21

• emitters possessing a diphenyltriazine as the acceptor and different regiochemistry of the carbazole donors; the ΔESTs increased to 0.10 eV for 2,4-2CzTRZ and 0.29 eV for 3,4-2CzTRZ. The single crystal structure of 2,6-2CzTRZ revealed a highly twisted structure with large torsions (81.0o and 76.3o) between

Synthesis of tetrafluorinated piperidines from nitrones via a visible-light-promoted annelation reaction

• Vyacheslav I. Supranovich,
• Igor A. Dmitriev and
• Alexander D. Dilman

Beilstein J. Org. Chem. 2020, 16, 3104–3108, doi:10.3762/bjoc.16.260

• experimental details, compound characterization, X-ray data, and copies of NMR spectra. Supporting Information File 507: Crystallographic information file for compound 3f. Supporting Information File 508: Crystallographic information file for compound 3h. Acknowledgements The crystal structure determination

Naphthalonitriles featuring efficient emission in solution and in the solid state

• Sidharth Thulaseedharan Nair Sailaja,
• Iván Maisuls,
• Jutta Kösters,
• Alexander Hepp,
• Andreas Faust,
• Jens Voskuhl and
• Cristian A. Strassert

Beilstein J. Org. Chem. 2020, 16, 2960–2970, doi:10.3762/bjoc.16.246

• -electron donating capability. Interestingly, upon aggregation in water-containing media, H, Me and t-Bu show a slight red-shift of the emission and a blue-shift is observed for OMe, SMe and NMe2. The crystal structure of Me allowed a detailed discussion of the structure–property relationship. Clearly, N

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

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• are related to the possibility of controlling the crystal structure properties of the final product in nanomaterials syntheses [5]. For this reason, theoretical scientific research is currently directed towards the understanding of the physical phenomena involved in sonocrystallization mechanisms [6

• angle of 64.5°. The intermolecular distances are situated in the range 2.3–2.6 Å disclosing the lack of intermolecular interactions in the crystal structure. Scanning electron microscopy (SEM) analysis Besides process intensification leading to a shorter reaction time, another advantage of the

• diethyl ether. After evaporation of the organic solvent the solid product was collected and purified by recrystallization from a suitable solvent. Crystal structure of 2-phenothiazinyl-2-(p-tolylamino)acetonitrile 2a. a) ORTEP plot and b) crystallographic cell unit. SEM images recorded at 200× for the raw

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• of the material was confirmed by powder diffraction data and compared to simulated powder diffraction data from the single crystal diffraction experiment. The reaction conditions, mass spectrometry, and NMR data are given in Table 1 and Table 3. Crystal structure of 2a, with the thermal ellipsoids

• drawn at 30% probability. Crystal structure of 7a, with the thermal ellipsoids drawn at 30% probability. Top: 19F NMR spectra of 3a acquired over a sample temperature range of 223–373 K. Left: Fitted plot of integrated intensity vs interpulse delay time from the experiment inverting the minor rotamer of

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

• Yuvixza Lizarme-Salas,
• Alexandra Daryl Ariawan,
• Ranjala Ratnayake,
• Hendrik Luesch,
• Angela Finch and
• Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

• populated in solution. A similar situation occurs for piperine itself; an indirect evidence for this comes from the crystal structure of 1 (Figure 1), where there is a second molecule in the unit cell (not shown) that has the alternative ring pucker [14]. The next-higher energy calculated structure of 2

• twisted to a lesser degree in that case (8° away from planarity). It is interesting that in the crystal structure of piperine itself (1, Figure 1) [14], the amide bond is also twisted by 15° away from planarity. In this case the distortion might be attributable to a H···H clash (1.99 Å). Structure 2f

• for this work; the crystal structure is shown [14]. In this work, a hypothetical analog 2 was designed to mimic parent compound 1. The predicted low-energy rotamers of 2 about the F–C–C–F and F–C–C=O bonds are shown; rotamers I and IV give the best mimicry of 1. Conformational analysis of 2 by DFT and

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• synthesized in moderate yields of 24% and 26%, respectively, over three steps from the same two building blocks, the ditosylate 5 and the monobutyl-protected NDI precursor 7 (Scheme 1). The connectivity and conformation of exTTFC7 was observed in the crystal structure obtained from crystals generated through

• slow evaporation of a CH2Cl2/CH3CN solution. The structure of the exTTF unit does not exhibit any significant changes upon incorporation into the crown ether [48]. No intermolecular stacking between the exTTF units was observed in the crystal structure of exTTFC7 (Figure 2a and section 2 in Supporting

• the experiment. The folded structure observed in the crystal structure hints towards a possible “side-on” complex, where the ammonium axle is not threading through the ring of the macrocycle, yet still forms hydrogen bonds to the crown ether [24][25] (see spectroelectrochemical measurements below

Synthesis of novel fluorinated building blocks via halofluorination and related reactions

• Attila Márió Remete,
• Tamás T. Novák,
• Melinda Nonn,
• Matti Haukka,
• Ferenc Fülöp and
• Loránd Kiss

Beilstein J. Org. Chem. 2020, 16, 2562–2575, doi:10.3762/bjoc.16.208

• fine-tuning the reaction conditions of other halofluorination and fluoroselenation reactions are currently being studied in our research group. Crystal structure of (rac)-11b. Crystal structure of the product (rac)-15a. Crystal structure of the product (rac)-15b. Proposed outcome of the

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• S6 in Supporting Information File 1). Movahedin et al. hypothesized that the glycan modulates the conformation of the peptide portion of the Tn-antigen and does not bind directly, noting that in the crystal structure GalNAc is positioned 4 Å away from the side chain of Tyr100, and indicating that any

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

• the number of methyl groups [29][49]. On the protein surface, both ligands showed a clear preference for the sterically most accessible dimethyl-lysine residue K34Me2 which is located in a solvent-accessible loop. Binding of cucurbit[7]uril to this residue was confirmed by the co-crystal structure of

• isomerase hPin1 (original data) is shown as an example in Figure 3. On the regulatory N-domain of of the AAA+ ATPase p97 (p97-N), tweezers were found to bind only 6 patches even though this protein domain contains 30 Lys and Arg residues (26 of these are observable in the p97 crystal structure, pdb # 3CF3

Chan–Evans–Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

• Viktor M. Tkachuk,
• Oleh O. Lukianov,
• Mykhailo V. Vovk,
• Isabelle Gillaizeau and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2020, 16, 2304–2313, doi:10.3762/bjoc.16.191

• analogous enamides [57], the facile [2 + 2] photocycloaddition process likely occurred due to favorable orientation of the interacting molecules and close contacts between alkene carbon atoms in the crystal structure. Consequently, the synthesis of product 5c was performed in darkness. N1-Styryl-substituted

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• this software a user uploads a glycan binding protein complexed to a carbohydrate fragment in PDB format. This need not be a co-crystal structure, and can be a modeled structure as well. The application then finds glycans that contain this fragment which are present on the CFG microarray data and