The influence of the cationic carbenes on the initiation kinetics of ruthenium-based metathesis catalysts; a DFT study

• Magdalena Jawiczuk,
• Angelika Janaszkiewicz and
• Bartosz Trzaskowski

Beilstein J. Org. Chem. 2018, 14, 2872–2880, doi:10.3762/bjoc.14.266

• interesting phenomenon, despite its very limited impact on their propensity to form transition metal complexes (Scheme 2) [50]. Many works have been devoted to the study of carbene dimerization and present evidence that mechanism of monomer–dimer equilibrium depends on the balance between the electronic and

• Gibbs free energy difference for the symmetric dimer A. In the case of carbene 3, the Gibbs free energy of dimerization could not be estimated due to instability of the monomer during geometry optimization. Thus, the results indicate higher stability of dimers for all examined NHC, which are in

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

• reflected in the Lewis structure is the tilting of the molecule upon adsorption leading to a chair-like conformer bending over the dimer rows on the surface [7]. Starting from this precovered surface (i.e., decorated with one adsorbate in the unit cell), we now investigate the adsorption of a second

• molecule of 1 on a neighbouring dimer leading to structure 3 (Figure 2). Although repulsive interactions might be expected for adsorption close to a rather large adsorbate, we find this mode to be the most stable adsorption mode for two molecules of 1 in the unit cell. Due to their conformational

• . This can be seen in the difference plot between the PES of the clean and precovered surface in Figure 5c. Only weak preference for the surface dimer adjacent to the already adsorbed molecule is found (less than 5 kJ·mol−1), which can be attributed to weak electrostatic attraction between the two

Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhimurium

• Matthew J. Styles and
• Helen E. Blackwell

Beilstein J. Org. Chem. 2018, 14, 2651–2664, doi:10.3762/bjoc.14.243

• [37]. Recently, two groups reported X-ray crystal structures of full-length EHEC SdiA as a homodimer in the presence of four naturally occurring AHLs (shown in Figure 1B) [21][22]. These studies reveal a structure for the SdiA dimer that incorporates LBD and DBD domains comparable to those of the

Synergistic approach to polycycles through Suzuki–Miyaura cross coupling and metathesis as key steps

• Sambasivarao Kotha,
• Milind Meshram and
• Chandravathi Chakkapalli

Beilstein J. Org. Chem. 2018, 14, 2468–2481, doi:10.3762/bjoc.14.223

• SM cross coupling followed by RCM as key steps [50]. To this end, dibromo compound 123 was subjected to diallylation by using allylboronate ester 12 to form the diallyl derivative 124 (73%). Treatment of compound 124 with G-I catalyst 1 gave unsaturated dimer 126 (30%) and monomer 125 (15

Efficient catalytic alkyne metathesis with a fluoroalkoxy-supported ditungsten(III) complex

• Henrike Ehrhorn,
• Janin Schlösser,
• Dirk Bockfeld and
• Matthias Tamm

Beilstein J. Org. Chem. 2018, 14, 2425–2434, doi:10.3762/bjoc.14.220

• ]. The desired hexakis(fluoroalkoxide) dimer [Mo2{OC(CF3)2Me}6] (Mo2F6) was first isolated by D. Rogers and his group by salt metathesis of [Mo2Cl6(dme)2] with 6 equiv of NaOC(CF3)2Me (Scheme 2) [73]. This reaction affords a red, sparingly soluble complex in moderate yield (28%). The bimetallic tungsten

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

• ) sulfate and ascorbic acid. TLC monitoring showed that the cyclization failed. Then, tris(benzyltriazoylmethyl)amine (TBTA) [40][41][42] was added as catalyst and macrocycle 4 was formed in 71% yield, which is extremely high for an intramolecular cyclization. The dimeric product 3 and the cyclic dimer 5

Dynamic light scattering studies of the effects of salts on the diffusivity of cationic and anionic cavitands

• Anthony Wishard and
• Bruce C. Gibb

Beilstein J. Org. Chem. 2018, 14, 2212–2219, doi:10.3762/bjoc.14.195

• − leads to an increase in the hydrodynamic diameter, with NaBr giving the largest increase to 2.6 nm. This corresponds to the formation of a dimer aggregate. Aggregation was even more extreme with the I− salts. All I− salts caused extensive aggregation of the host, and a determination of the maximum size

Selective formation of a zwitterion adduct and bicarbonate salt in the efficient CO₂ fixation by N-benzyl cyclic guanidine under dry and wet conditions

• Yoshiaki Yoshida,
• Naoto Aoyagi and
• Takeshi Endo

Beilstein J. Org. Chem. 2018, 14, 2204–2211, doi:10.3762/bjoc.14.194

• until 102 °C (i) and 173 °C (ii), respectively, and then the thermal decomposition of 2 has occurred completely around 270 °C (iii). This three-step behavior of weight loss suggested the dimer form of 2, which was constructed by the weak interaction between the anionic oxygen on the trapped CO2 and the

• active hydrogen on the nitrogen atom. Namely, one molecule of CO2 was released from the dimer of 2 in the first step, and then the intermediate complex was prepared from 1 and 2 due to the coordination between two anionic oxygens on the trapped CO2 and two active hydrogens on the guanidine moiety. Then

• , another CO2 molecule was released from the intermediate complex (2+1 dimer) and the dimer was decomposed into two molecules of 1 in the second step. The observed weight loss due to the released CO2 in each step agreed with the theoretical one (obs. (i) 10.3%, (ii) 10.6%, and (iii) 78.4%, theor. (i) 10.1

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

• strong absorption bands (≈450 and 800 nm), which yield an orange-brown solution. Initially, the low-energy band of 2●+ between 600–1000 nm was interpreted as a signature for an unusually stable TTF dimer [31]. However, later investigations showed that this band is an intrinsic SOMO-1→SOMO transition in

• so-called mixed-valence dimer (12) ●+. A mixed-valence dimer can be identified by splitting of the first TTF oxidation potential into two distinguishable waves. This change in redox behavior can be followed by electrochemical methods such as cyclic voltammetry. Another indication for a mixed-valence

• dimer interaction can be an emergent low-energy absorption band, usually in the NIR region. Both monomers show usually no absorption in this region. The radical-cation dimer (1●+)2 instead forms from two 1●+ radical cations and exhibits a very unusual binding situation. Whereas both monomers are

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

• the sum of the energies of all unrelaxed monomers (crystal structure geometry) included in the tetramer or dimer. Interaction energies of tetrameric, trimeric, and dimeric structures can yield information about the additivity of intermolecular interactions. Additionally, interaction energies of all Bi

• with this specific monomer are broken, which can involve contacts between neighboring molecules or long-range interactions. In tetramer 1a-1 the energy needed to remove one of the outer monomers (3 and 4) is almost equal to the interaction energy of one Bi···π arene dimer. This indicates that only one

• dimer breaks. To remove one of the inner monomers (2 or 1) an energy of 92 kJ mol−1 is required. This energy is very close to the sum of the interaction energies of two dimers. For example, Eremove of monomer 2 in tetramer 1a-1 is roughly the sum of the interaction energies of two Bi···π arene dimers

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• repetition rate of 64 Hz. For the spectrum of the PVE–MeOH dimer, 3 million FIDs were co-added. A resulting signal-to-noise ratio of about 500:1 to 600:1 for the stronger transitions of the dominant complex allowed us to determine the positions of the carbon atoms with respect to the center of mass of the

• are shown in Figure 3. Besides methanol monomer, methanol dimer and a signal clearly attributed to a larger cluster, only a single, reasonably narrow absorption at 3625 cm−1 is observed. It can be attributed to mixed dimers of MeOH with PVE and allows for a single rigorous conclusion, due to the

• linearity of the technique and the comparable IR absorption cross section of all predicted dimer conformations (cf. Table 1 and Table S1, Supporting Information File 1): the global minimum structure and any other, higher lying isomers which are initially formed and impeded from relaxation to the global

Drug targeting to decrease cardiotoxicity – determination of the cytotoxic effect of GnRH-based conjugates containing doxorubicin, daunorubicin and methotrexate on human cardiomyocytes and endothelial cells

• Livia Polgár,
• Eszter Lajkó,
• Pál Soós,
• Orsolya Láng,
• Marilena Manea,
• Béla Merkely,
• Gábor Mező and
• László Kőhidai

Beilstein J. Org. Chem. 2018, 14, 1583–1594, doi:10.3762/bjoc.14.136

• bifunctional daunorubicin-GnRH-III conjugates without spacer and modified in position 4 with Lys; (e) {GnRH-III(Dau=Aoa-C)}2 dimer and conjugates modified in position 4 with N-MeSer; (f) GFLG or YRRL spacer containing monomer and dimer conjugates (g) GnRH-III conjugates containing methotrexate and daunorubicin

• conjugates containing doxorubicin without spacer sequence; (c) with spacer sequence GFLG; (d) oxime bond-linked, mono- and bifunctional daunorubicin-GnRH-III conjugates without spacer and modified in position 4 with Lys; (e) {GnRH-III(Dau=Aoa-C)}2 dimer and conjugates modified in position 4 with N-MeSer; (f

• ) GFLG or YRRL spacer containing monomer and dimer conjugates; (g) GnRH-III conjugates containing methotrexate and daunorubicin. Comparative study of cytotoxic effects and cardiotoxicity elicited by GnRH-based antitumor compounds (1–15) and reference substances (AN-152, Dox, Dau, Mtx). IC50 values show

Steric “attraction”: not by dispersion alone

• Ganna Gryn’ova and
• Clémence Corminboeuf

Beilstein J. Org. Chem. 2018, 14, 1482–1490, doi:10.3762/bjoc.14.125

• not even a limit and stable diamondoid dimer with a central C–C bond as long as 1.71 Å has been achieved [7][8]. Bulky alkyl groups assist not only in achieving the longest C–C bonds, but also the shortest intermolecular H···H contacts [9], which are otherwise tackled by squeezing them inside the

• cages [10]. Intermolecular interactions in hydrocarbons are also subject to significant dispersion contribution. In the unsaturated systems, from benzene dimer to higher acenes and, ultimately, graphenes, dispersion is increasingly the key force behind the π–π stacking interactions [11]. Large and flat

• -tert-butylphenyl)methane dimer (the system mentioned above for its shortest intermolecular H···H contacts) comes from stabilizing electrostatics [9]. Similarly, the interaction energy difference between the all-meta-tert-butyl-hexaphenylethane and the bare hexaphenylethane features ≈14% electrostatic

Recent applications of chiral calixarenes in asymmetric catalysis

• Mustafa Durmaz,
• Erkan Halay and
• Selahattin Bozkurt

Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117

• reactions were compared to that of the model diphenylphosphino ferrocenes. When the allylpalladium chloride dimer was used as palladium precursor, good yields were obtained after 24 h. However, enantiomeric excesses for (S)-27 and (S)-28 (<5%) were lower than those obtained by using other phosphine-ether

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