Ruthenium-based olefin metathesis catalysts with monodentate unsymmetrical NHC ligands

• Veronica Paradiso,
• Chiara Costabile and
• Fabia Grisi

Beilstein J. Org. Chem. 2018, 14, 3122–3149, doi:10.3762/bjoc.14.292

• and 25b this orientation was observed also in the solid state. Some metathesis reactions performed in this study with 24b and 25b in comparison to GII-SIMes and HGII-SIMes are summarized in Table 1. In the model RCM reaction of N,N-diallyl-p-toluenesulfonamide (26, Table 1, entry 1), catalysts 24a and

• , consistently, the same relative orientation between the indenylidene and mesityl unit. Complexes 41–43 were tested in various representative metathesis reactions of standard substrates and compared to the benchmark catalysts IndII-SIMes. Interestingly, all complexes showed a faster catalytic initiation than

• ruthenium complexes by physisorption rather than chemisorption, an unexpected molecular rearrangement of their ligand sphere, determining a cis orientation of the neutral ligands, was observed (113 and 114, Figure 20). The same unusual cis configuration was displayed by complex 115 (Figure 20) upon release

Thermophilic phosphoribosyltransferases Thermus thermophilus HB27 in nucleotide synthesis

• Ilja V. Fateev,
• Ekaterina V. Sinitsina,
• Aiguzel U. Bikanasova,
• Maria A. Kostromina,
• Elena S. Tuzova,
• Larisa V. Esipova,
• Tatiana I. Muravyova,
• Alexei L. Kayushin,
• Irina D. Konstantinova and
• Roman S. Esipov

Beilstein J. Org. Chem. 2018, 14, 3098–3105, doi:10.3762/bjoc.14.289

• equivalent to the concentration of 5-phosphoribosyl-α-1-pyrophosphate (1 mM), it can be assumed that the presence of magnesium ions promotes the proper spatial orientation of the substrate. The reaction also proceeds in the absence of magnesium ions in solution. A similar dependence is observed for TthAPRT

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• orientation and the six-membered ring in a twist-boat conformation (Figure 3b). Approximately 1 kJ/mol higher in energy was the second conformer where the furanose unit adopted a C3’-exo arrangement and the cyclohexene unit a half-chair conformation (Figure 3c). The C(5’) hydroxy group adopted in both

• , −sc). The angle β was found in the +ac or anti orientation, most likely due to either the boat or the twist-boat conformation of the cyclohexene ring. Furthermore, the angle γ was constrained to a +sc arrangement as also found in canonical A- or B-type helices. The torsion angle ε exhibited values in

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

• contribution of the N−H···O IHB to the stabilisation of the E-forms of 5a–7a appears to be small: in the 1H NMR spectra, the NHa signal is shifted to the low field by less than 1 ppm in comparison with Z-4a (Figure 1) [9]; in a DFT calculation, the mutual orientation of C=NH and the OMe groups is not optimal

Green synthesis of new chiral 1-(arylamino)imidazo[2,1-a]isoindole-2,5-diones from the corresponding α-amino acid arylhydrazides in aqueous medium

• Nadia Bouzayani,
• Jamil Kraїem,
• Sylvain Marque,
• Yakdhane Kacem,
• Abel Carlin-Sinclair,
• Jérôme Marrot and
• Béchir Ben Hassine

Beilstein J. Org. Chem. 2018, 14, 2923–2930, doi:10.3762/bjoc.14.271

• in a trans-orientation with H(4). In addition, various crystallization tests were carried out in order to confirm the absolute stereochemistry by X-ray diffraction. The chiral 3-(2-(methylthio)ethyl)-1-(phenylamino)-1H-imidazo[2,1-a]isoindole-2,5(3H,9bH)dione (5f) crystallized [44][45][46][47][48][49

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

• the case of the cation Bf, the signals of two isomers were found in the spectra in a ratio of 5 to 1. These isomers appear due to cis-, trans-orientation of t-Bu and ArS groups in the five-membered ring. To the best of our knowledge, this is one of the first examples of full NMR characterization of

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• database [82] was searched for structurally similar compounds leading to the identification of the meta-substituted tetrazole 33 (Figure 7), which was found to have a similar dissociation constant. Moreover, in order to predict the orientation of the fragments in the binding site, molecular docking of 33

Olefin metathesis catalysts embedded in β-barrel proteins: creating artificial metalloproteins for olefin metathesis

• Daniel F. Sauer,
• Johannes Schiffels,
• Takashi Hayashi,
• Ulrich Schwaneberg and
• Jun Okuda

Beilstein J. Org. Chem. 2018, 14, 2861–2871, doi:10.3762/bjoc.14.265

• formation of the E or the Z product is dependent on the orientation of the R groups in this step of the catalytic cycle (Scheme 1). In this short review, we focus on the status of embedding the GH-type catalyst into β-barrel proteins and show their application in various reactions using benchmark substrates

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• placing the cyclooctyne molecule in an upright orientation (molecular C2 axis aligned parallel to the z axis of the cell), with the triple bond aligned parallel to the y axis of the cell, the triple-bond centre located vertically above a lower surface atom (Sidown) at a height corresponding to a vertical

• minimum energy path for this system [8]. Potential energy surface scans were performed by displacing a cyclooctyne molecule in x and y direction while retaining the orientation (equivalent to the starting point of the adsorption energy profile) and a fixed distance Δz(Siup–Ctriple) above the surface. The

• with one adsorbate 1 and unit cell used in the PES scans (orientation of second adsorbate and scan path indicated) shown in Figure 5. Frozen PES scans of 1 along path indicated in Figure 4 (C2 axis parallel to z, C≡C parallel to y, Δz(Siup–Ctriple) = 5 Å) on (a) the clean and (b) the precovered surface

Domino ring-opening–ring-closing enyne metathesis vs enyne metathesis of norbornene derivatives with alkynyl side chains. Construction of condensed polycarbocycles

• Ritabrata Datta and
• Subrata Ghosh

Beilstein J. Org. Chem. 2018, 14, 2708–2714, doi:10.3762/bjoc.14.248

• characterization data see Supporting Information File 1). The stereochemical orientation of the secondary hydroxy group was determined through X-ray crystal structure of a compound derived from it in a subsequent step. The primary hydroxy group in the diol 6 was then selectively protected to provide the silyl

Synthesis of 3-aminocoumarin-N-benzylpyridinium conjugates with nanomolar inhibitory activity against acetylcholinesterase

• Nisachon Khunnawutmanotham,
• Cherdchai Laongthipparos,
• Patchreenart Saparpakorn,
• Nitirat Chimnoi and
• Supanna Techasakul

Beilstein J. Org. Chem. 2018, 14, 2545–2552, doi:10.3762/bjoc.14.231

• program [19] was used to investigate the orientation of the compounds in the rhAChE binding site. Compounds 4a, 9a, 9b, 9e, 9h, 9i, and 10a were selected as representatives for the docking study. The active site of human AChE, which is at the bottom of a deep and narrow gorge, consists of several major

• active site gorge. The PAS consists of Tyr72, Asp74, Tyr124, Trp286, and Tyr341 [23][24]. From the docking result, the docked orientation of donepezil showed a root-mean-square deviation (RMSD) of 0.474 Å when compared with the conformation in the crystal structure, thereby indicating its potential as a

• the CAS while the chromene rings were located at the PAS. Compounds 9a, 9b, 9e, 9h, and 9i revealed similar orientations in the binding pocket whereas the binding of compounds 4a and 10a was partially different. The orientation of the chromene ring of compound 4a was shifted away from the others

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

• )° and 168.6 (2)° (Figure 2). The triple bond shows a coplanar orientation to the pyrimidine ring with an inclination angle of 1.0 (4)°. The torsion angle χ [46] (−103.6° (2)) is high-anti [47]. This conformation results from restriction caused by the cyclic structure. Most nucleosides including dT (χ

Non-metal-templated approaches to bis(borane) derivatives of macrocyclic dibridgehead diphosphines via alkene metathesis

• Tobias Fiedler,
• Michał Barbasiewicz,
• Michael Stollenz and
• John A. Gladysz

Beilstein J. Org. Chem. 2018, 14, 2354–2365, doi:10.3762/bjoc.14.211

• result (as drawn in Scheme 7, the out,out isomer would be the kinetic product). When the first metathesis does not join the syn positions, as in VIII (front to rear), one phosphorus–boron bond must subsequently be rotated by 180° to create a syn orientation for the second metathesis. Of course, if the

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• host molecule cucurbit[8]uril (9), which is enlarged by an additional glycoluril unit in comparison to 7, provides sufficient space to accommodate two planar molecules with cofacial orientation [68]. When the water-soluble TTF derivative 10 gets oxidized to its radical cation 10●+, a 2:1 complex is

• diimide (NDI) unit and a divalent crown-ether wheel with a central TTF unit (Figure 17) [86]. The cofacial donor–acceptor complex whose formation is indicated by a deep green color is forced to stay in a cofacial orientation by mechanical bonding, even when the complex is redox-switched. UV–vis

• ][89]. An ordered array of molecules enables the possibility of concerted switching. The fixed orientation on a surface allows studying molecules with sophisticated techniques such as scanning tunneling microscopy. Furthermore, redox-switchable AMMs, containing for example TTF moieties, can be

Calix[6]arene-based atropoisomeric pseudo[2]rotaxanes

• Carmine Gaeta,
• Carmen Talotta and
• Placido Neri

Beilstein J. Org. Chem. 2018, 14, 2112–2124, doi:10.3762/bjoc.14.186

• bis(benzylalkylammonium) axle [19], where the stereoselective formation of the pseudo[3]rotaxane with endo-alkyl orientation VIII was observed [19]. Calixarene macrocycles [22] have found numerous applications in several areas of supramolecular chemistry, such as (bio)molecular recognition [23] and

• two respective proximal aromatic rings are oriented syn, as in the cone conformation. In contrast, a Δδ value of 0.3 or less is attributable to an anti-orientation between the phenol rings, as in alternate conformations. The de Mendoza’s “13C NMR single rule” [30][31], is focused on the 13C NMR

• chemical shift of the ArCH2Ar methylene C, which is 30–33 ppm for the syn-orientation of the proximal phenol rings and typically 36–39 ppm with anti-positioned phenol rings as in alternate conformations. As exemplified above, the calix[6]arene macrocycle has been widely used as wheel for the assembly of

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

• never been previously analysed by us in our earlier resorcinarene–PyNO H–G studies [39][40]. As shown in Figure 2, despite the BrC6 cavity’s flexible nature, the position of the methoxy substituent plays a crucial role for both guest orientation and the depth of the guest’s occupation of the cavity. For

• example, in 6@BrC6 (Figure 2d) and 7@BrC6 (Figure 2e), guests 6 and 7 have h = 3.23 Å and 3.50 Å, due to their steric demands. However, in complex 8@BrC6 (Figure 2f) the unhindered para-methoxy group facilitates 8 to sit deep inside the cavity at h = 2.82 Å. The guest’s parallel orientation to the host

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• direction to the other five, caused, probably, by the propeller orientation (Figure 1) of the three covalent junctions around the benzene core. In contrast, the energetic minimum of the ionic analogue 7b could be accessed in a gradual approach only. Thus, we had to start from a preliminary DFT calculation

• relationships found for model 10 to compounds with higher mass 8 and 9 (Figure 8) provided their energetic minima as to correspond to (i) a local propeller orientation of the G-1 branches around the s-triazin-2,4,6-triyl core (initial design, Figure 1) and (ii) a global vaulted form (“candelabrum” allure

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

• absence of their vicinal coupling in the 1D and 2D 1H NMR spectra. In congruence with the vicinal coupling constants J5/6 = J6/7 = 9.9 Hz suggesting the trans orientation of their protons, the model provided torsion angles of 161° and 178°, respectively. Similarly the vicinal coupling constants J13/14

• = 9.5 Hz and J14/15 = 8 Hz indicated the trans orientation of their protons in the macrolactone ring with torsion angles of 177° and 170°. Further, the distances between proton pairs showing NOE interactions in the ROESY spectra of 1/2 were analyzed (Table 2). These distances showed a very good relation

Recent advances in phosphorescent platinum complexes for organic light-emitting diodes

• Cristina Cebrián and
• Matteo Mauro

Beilstein J. Org. Chem. 2018, 14, 1459–1481, doi:10.3762/bjoc.14.124

• without and with outcoupling elements, respectively, via engineering of transition dipole moment orientation in the device active matrix. Owing to the enormous interest they are currently attracting, the scope of the present review article is to highlight the current trends and achievements in the field

• value as high as 38.8%, which approaches the maximum EQE estimated value of ca. 45%. This latter could be achieved in the case of a phosphor with 100% of PLQY with a fully parallel emitting dipole. The beneficial effect of the emitting dipole orientation on the light outcoupling efficiency was further

• crystallinity and molecular orientation are key parameters that can make great differences for the resulting thin-film optoelectronic performances. Apart from display applications, general lighting efficiency currently constitutes a main concern of our society and white-emitting OLEDs (WOLEDs) represent a

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• zwitterionic NAA-modified oligonucleotides with defined configuration at the 6'-position, i.e., with control over the spatial orientation of the positive charge [72][73]. Thus, the NAA-modification was placed in T–T ('TxT', with x representing the NAA-linkage) and A–T segments ('AxT') of the oligonucleotide

• investigated by CD spectroscopy. The following properties of TxT NAA-modified DNA oligonucleotides were reported [72]: (i) they formed reasonably stable duplexes with complementary counterstrands, in particular with native DNA; (ii) the influence of the spatial orientation of the positive charge, i.e., of the

Novel unit B cryptophycin analogues as payloads for targeted therapy

• Eduard Figueras,
• Adina Borbély,
• Mohamed Ismail,
• Marcel Frese and
• Norbert Sewald

Beilstein J. Org. Chem. 2018, 14, 1281–1286, doi:10.3762/bjoc.14.109

• magenta. Docking of 22 to the vinca domain of β-tubulin. Surface and backbone of β-tubulin are shown in blue, GDP in yellow. No hydrogen bond formation was detected. The orientation of the azidoethoxy-ethoxyethyl substituent prevents the inhibitor from the correct interaction with the protein. The epoxide

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

• several ways such as helical sense, pitch, groove width, base orientation and sugar pucker (Table 1). The major differences in the two generally encountered A- and B-forms of DNA is in the sugar pucker and their groove widths. In A-form DNA, the major groove is narrower but has a wide/shallow minor groove

• orientation and ≈12 Å groove width). However, in quadruplex fold-back structures, unusual loop connectivity gives rise to extremely wide grooves in addition to narrow and medium grooves [10] in which the width of wide grooves goes up to approximately 18 Å, far exceeding the groove widths found in B-DNA

• ). This has been attributed to strong self-association (dimerization) in an antiparallel, head-to-tail orientation in aqueous solution during complex formation with duplex DNA oligomers verified via NOE experiments [61]. They further reported several structurally diverse MGBs, derived from distamycin, in

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• = 13. In doing so, we focus on the importance of dispersion energy contributions to the interaction energy, including two-body and many-body dispersion effects. It will be shown that overall electron correlation effects have only a minor impact on the orientation of the water molecules in the various

• they possess different orientations of the hydrogen atoms. The first structure in Figure 5 corresponds to the equilibrium. As can be seen in the figure, the electrostatic interaction energy is strongly influenced by the orientation of the molecules and changes by almost +10 kcal/mol from the hydrogen

• clusters (in their equilibrium) could be approximated well by a pair-interaction model. Conclusion Different interaction energy contributions to the total interaction energy of water clusters have been analyzed in this work. It has been shown that the main orientation of the water clusters, characterised

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

• methyl group, which is perpendicular to the mean plane of the sterol’s ring system, and the inner H5 hydrogens of the 3rd and 4th glucopyranose of host A macrocycle. The C18 methyl group of the guest, which has the same orientation with that of C19, is located at the interface of the β-CD dimer and does

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• steric interactions between the C2'–OMe and the Ph group [81]. Because E3 is the favored conformer, an inside attack of the nucleophile (H−) results in an α orientation in the final product, which is evident from the the synthesis of 1 (OBn-substituted Pseudouridine, Figure 6D). Despite the greater