A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• is larger than the distance (3.15 Å) determined for the triazine dimer [41]. As next step, the polycyclic aromatic hydrocarbons anthracene and pyrene were intercalated between the caps of the cryptand. The optimized geometry structures of these host–guest complexes were obtained using the same method

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

• aminoalkyl phosphoramidate-linked oligonucleotide 18. To study the hybridization properties of such cationic oligonucleotide analogues with native DNA and RNA, Letsinger and co-workers performed UV-monitored thermal denaturation experiments [40][41]. In the case of the modified deoxyadenosyl dimer 11

• ≈25 °C for the according hybridization with DNA was observed [40]. In addition, the cationic dimer 11 was shown to bind more tightly to native RNA and DNA strands in the presence of magnesium chloride [40]. For the cationic T-oligomer 18, Letsinger and co-workers reported a strongly reduced absorbance

• , thus weakening the attraction of the oppositely charged backbones [41]. In order to elucidate the stability of aminoethyl phosphoramidate-linked oligonucleotides to nuclease-catalysed degradation, Letsinger and co-workers described the incubation of such oligomers, the deoxyadenosyl dimer 11 and DNA

Are dispersion corrections accurate outside equilibrium? A case study on benzene

• Tim Gould,
• Erin R. Johnson and
• Sherif Abdulkader Tawfik

Beilstein J. Org. Chem. 2018, 14, 1181–1191, doi:10.3762/bjoc.14.99

• -energy curves of the benzene dimer to determine if they are capable of describing forces and energies outside equilibrium. We find the exchange-hole dipole moment (XDM) model describes most cases with the highest overall agreement with reference data for energies and forces, with many-body dispersion

• approaches in reproducing the energetics of the benzene dimer, an important model system, in different geometries. The coupled-cluster with singles, doubles and perturbative triples [CCSD(T)] benchmark set of Sinnokrot et al. [20] is used, with the aim of establishing which approximations can best reproduce

• ][35][36]. However, the most extreme deviations from the pairwise model do not affect the benzene dimer system. Note, the importance of higher-order (many-body) dispersion terms in “typical” systems has been the subject of some debate. It is critical to differentiate between non-additive many-body

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

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

• ; Introduction The description of the intermolecular interactions between water molecules is essential for an understanding of the structures and properties of water through the different stages of assemblies, from the dimer over the liquid phase to the bulk phase. Moreover, many chemical processes are

• high-level quantum chemistry results for the water dimer. Force fields belonging to this category are, e.g., the TTM3-F and TTM4-F models [6][7], the AMOEBA force field [8][9], the DPP2 model [10] and various force fields derived by Szalewicz and co-workers [11][12][13]. There also exist a number of

• essential to describe the structures of (H2O)2 and (H2O)3 in many different conformations [15]. A rather good correlation between the coupled-cluster energies and the force-field energies is found for the polarisable AMOEBA2003 [9][16] and TTM4-F [17] potentials both for the dimer and for the trimer. Both

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study

• Ahmet Altun,
• Frank Neese and
• Giovanni Bistoni

Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79

• the computational details, computed geometries and dissociation energies are compared with previously published experimental and computational data. In the following section, the decay of LED terms with the intermolecular distance between the monomers is discussed for the water dimer case, and results

• minimum (Conf1 of Figure 1) are compared with available experimental data and previously published computational predictions. For the water dimer in its global minimum, experiments estimate an r0(O···O) distance between 2.946 and 2.976 Å [67]. The CCSD(T)-based best estimate of re(O···O) reported in

• literature is 2.912 ± 0.005 Å [68]. The re(O···O) distance calculated in this work at the RI-MP2/aug-cc-pVTZ level (2.908 Å) is very close to the CCSD(T) prediction. The effect of excitations beyond CCSD(T) has been shown to be negligible by means of CCSDTQ calculations [69]. For the HF dimer, the re(F···F

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

• of cholesterol in β-CD. The inclusion complex crystallizes in the triclinic space group P1 forming head-to-head dimers which are stacked along the c-axis. One well-defined cholesterol molecule ‘axially’ encapsulated inside the β-CD dimer and 22 water molecules that stabilize the complexes in the

• host A and host B) arranged co-axially so that the secondary rim (head) of the one faces the secondary rim of the other forming a head-to-head dimer via intermolecular hydrogen bonds between their O3n-H hydroxy groups. A cholesterol molecule is found fully encapsulated inside the β-CD dimeric cavity

• 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

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

Investigating radical cation chain processes in the electrocatalytic Diels–Alder reaction

• Yasushi Imada,
• Yohei Okada and
• Kazuhiro Chiba

Beilstein J. Org. Chem. 2018, 14, 642–647, doi:10.3762/bjoc.14.51

• efficiency of 3167% (Table 2, entry 4). Under these conditions, the undesired dimerization of trans-anethole (1) took place to give the dimer 4. However, we found that the electrochemical radical cation Diels–Alder reaction was also possible from the dimer, whose photochemical version was reported by Yoon

• the electrocatalytic Diels–Alder reaction (1: 1 mM; 2: 2000 mM). GC–MS monitoring of the electrocatalytic Diels–Alder reaction (1: 2 M; 2: 6 M). Blue dots show the dimer 4. SET-triggered Diels–Alder reaction of trans-anethole (1) and isoprene (2). Undesired dimerization of trans-anethole (1

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

• neighboring monomers have reacted, and Figure 14b shows the binding mode of a GpppG dimer that was found to bind in a fashion described as structurally similar to the proposed intermediate shown on the left-hand side [53]. In the latter case, LNA residues were used in the template strand to facilitate

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• the modified ONs in addition to an increase in their nuclease resistance. Thus, two Japanese groups have proposed prodrug-type phosphotriester ONs responsive to GSH (Scheme 1) [13][14]. Ono presented a preliminary study on a model of a thymidine dimer with differently substituted benzyl groups at the

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• -protected monomer. Upon selective removal of either the 5'-O-DMTr group or the 3'-O-levulinoyl group, the dimer was extended in 5' or 3' direction [26]. All other reports describe strategies, where the dimers are extended unidirectional, either in 5'-direction [25][26][27][29][30] or 3'-direction [31][32

• -azidomethylbenzoyl)-protected nucelosides, followed by removal of the 5'-O-DMTr group and extension of the dimer to the trimer by coupling of another N-acyl-3'-O-(o-chlorophenylphosphate)nucleoside. The final removal of the 2-azidomethylbenzoyl group occurred by reduction of the azide with triphenylphosphine in

• group, the dimer was reacted with another N-acyl-5'-O-DMTr-protected nucleoside-3'-O-phosphoramidite to afford the trimer. The 3'-O-TBDMS group was selectively removed under mild conditions with trimethylamine/3HF (Figure 4B) with strict control of pH to leave the β-cyanoethyl groups at the

Recent developments in the asymmetric Reformatsky-type reaction

• Hélène Pellissier

Beilstein J. Org. Chem. 2018, 14, 325–344, doi:10.3762/bjoc.14.21

• nucleophilic addition of ethyl iodoacetate to the Si face of the cyclic imine 67 affording the final β-amino ester 68 and regenerating dimer M. In 2017, a related chiral ligand 69 employed at only 10–20 mol % of catalyst loading was reported by the same authors to be capable of catalyzing in combination with

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• ligand aggregates binding to polynucleotides (Figure 2). Many naturally occurring small molecules owe different biological activities due to aggregation, for instance, the close analogs netropsin (the single molecule in the DNA minor groove) and distamycin (the dimer in DNA minor groove) [13]. In

Photocatalytic formation of carbon–sulfur bonds

• Alexander Wimmer and
• Burkhard König

Beilstein J. Org. Chem. 2018, 14, 54–83, doi:10.3762/bjoc.14.4

From dipivaloylketene to tetraoxaadamantanes

• Gert Kollenz and
• Curt Wentrup

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

• unusual reaction steps: (i) the conversion of the dimer 3 of dipivaloylketene (2) to bisdioxines (2,6,9-trioxabicyclo[3.3.1]nona-3,7-dienes) 4, by the addition of nucleophiles, and (ii) the facile acid-catalyzed hydrolysis of 4 with concomitant transannular cyclization. Following this route a wide variety

• to −20 °C. However, it dimerizes at room temperature to afford an 88% yield of the thermally very stable dimer 3, which still carries a ketene function [16]. Compound 3 is formed through a [2 + 4] cycloaddition between one molecule of the α-oxoketene 2 and the carbonyl C=O bond of a second molecule

• . It is noteworthy that in the presence of DMSO a different dimer 7 is formed, again in high yield, originating from a [2 + 4] cycloaddition between a molecule of the α-oxoketene and the ketene C=O bond of the second molecule (Scheme 3) [17]. The treatment of the dimeric ketene 3 with nucleophiles

A Brønsted base-promoted diastereoselective dimerization of azlactones

• Danielle L. J. Pinheiro,
• Gabriel M. F. Batista,
• Pedro P. de Castro,
• Leonã S. Flores,
• Gustavo F. S. Andrade and
• Giovanni W. Amarante

Beilstein J. Org. Chem. 2017, 13, 2663–2670, doi:10.3762/bjoc.13.264

• dimer was assigned as being trans, by X-ray crystallographic analysis. The kinetic reaction profile was determined by using 1H NMR reaction monitoring and revealed a second order overall kinetic profile. Furthermore, by employing this methodology, a diastereoselective total synthesis of a functionalized

• azlactone dimer, which is a versatile heterocycle containing two stereogenic centers (Figure 1). Kobayashi and co-workers demonstrated the rich reactivity of azlactones conducting the dimerization reaction using strong bases as catalysts; however, higher temperatures and long reaction times were required

• diastereomer was assigned by X-ray analysis. Finally, one of the products was selectively reduced to provide a functionalized analogue of streptopyrrolidine, a marine natural product isolated from Streptomyces sp. As shown in Table 1, our studies started with the synthesis of dimer 2a using azlactone 1a in the

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

• heterochiral dimer in the crystal state. Intermolecular hydrogen bonds in the dimer are shown as dashed lines. Thermal ellipsoids are defined at 50% probability. Hydrogenation of compounds 4–6 and preparation of N1(3)-unsubstituted compounds 9–11d. Screening of the reaction conditions for organic base

What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• for the formation of a homodimer of A (Figure 8B) [40]. It is believed that this dimer enables transport of the lectin from the Golgi apparatus to cell membranes [73]. Due to a dislocated glutamate in the side chain of the homodimer (Figure 8B), the affinity for calcium binding and therefore also

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• observed in the molecular structures of the metallocene–nucleobase derivatives [24][29]. In addition, each molecule of 2 in the dimer is further involved in a Cl···O halogen bond with an adjacent molecule of chloroform (Figure 3). Further details of intermolecular interactions present in the crystal

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• concentrations of 100, 10, and 1 mM. 1H NMR spectra of 3-O-derivative 2b in D2O at concentrations of 100, 10, and 1 mM. Putative objects and interactions in naphthylallyl-γ-CD solution, depicted schematically for 6I-O-naphthylallyl-γ-CD (2c). (a) Cyclic supramolecular dimer based on inclusion complexation. (b

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• molecules (Figure 5b and Supporting Information File 1, section 7). Compound 5 may serve as a model for the crystal structure description. The molecules of 5 are linked by one C–H∙∙∙N hydrogen bond, so forming a dimer via eighteen-membered ring (e.g., see Figure 5c for 5) which can be described by graph-set

• gray. c) Capped-stick representation of 5, showing the dimer formed by C–H∙∙∙N hydrogen bond (orange stippled lines). Synthetic procedures for preparation of p-halogen-substituted and non-substituted phenyl-1,2,3-triazole 6-phenyl-2-(trifluoromethyl)quinolines. Reaction conditions and yields for the

One-pot syntheses of blue-luminescent 4-aryl-1H-benzo[f]isoindole-1,3(2H)-diones by T3P^® activation of 3-arylpropiolic acids

• Melanie Denißen,
• Alexander Kraus,
• Guido J. Reiss and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 2340–2351, doi:10.3762/bjoc.13.231

• 5 (left) and a centrosymmetric dimer formation by π–π interactions (right) (ellipsoids are drawn at the 40% probability level). The ORTEP-type plot of the asymmetric unit of the crystal structure 6 (top) and π-stacking interactions (bottom) (ellipsoids are drawn at the 40% probability level

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• phthalocyanine. Furthermore, it is known that iron phthalocyanines easily form a μ-oxo dimer [53] that is connected face-to-face via oxygen, but a spectroscopic investigation revealed that it is difficult to form when using TFEO-FePc. This remarkable stability of TFEO-FePc is due to the low energy of the highest

• compared with mononuclear phthalocyanines by chemically modifying each unit unsymmetrically caused by an electronic interaction between each unit [68]. In addition, since it is possible to separate charges in dimer-type phthalocyanines, they are expected to be applied to new electron or energy transfer

• systems [69] such as solar cell materials as well as photocatalysts for organic reactions. A phthalocyanine dimer in which TFEO-Pcs are directly linked by C–C bonds has been reported (Scheme 4) [70][71]. This homodimer was synthesized by a palladium-catalyzed homo-coupling reaction of two A3B type