A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• in plots of ΔH versus temperature from 283 to 313 K (Figure 5). The release of solvent molecules upon complex formation may account for the negative heat capacity change and similar heat capacity changes were also reported for the fullerenes recognition [40]. Meanwhile, the changes of ΔG for the

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

• of a mixture of 18 with DNA-APoly in thermal melting studies, as compared to the non-hybridized, single-stranded oligonucleotides [41]. This indicated a successful complex formation with ordered base stacking of the positively charged oligonucleotide analogue and its native DNA counterstrand. When

• -pairing fidelity of the pentameric thymidinyl DNmt. No increase in hyperchromicity was observed for combinations of DNmt-T5 with either DNA-GPoly, DNA-CPoly or DNA-TPoly, over a temperature range from 5 to 93 °C, thus ruling out complex formation with these fully mismatched native DNA counterstrands

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

• ). 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

• . designed novel polyamides, which were able to bind adjacent to the recognition sites of a broad-range of transcription factors TBP, Ets-1, LEF-1 and NF-κB [69], thereby inhibiting binding of these transcription factors to DNA and ternary complex formation [70]. Dervan et al. has further introduced a novel

•  10. Minor groove complex formation between DNA duplex and Hoechst 33258 is shown in Figure 7b [82]. X-ray crystallographic and NMR studies confirmed that Hoechst 33258 binds to the A·T-rich sequences in minor groove with the planar benzimidazole groups are oriented parallel to the direction of the

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• : specifically, solid solutions, cocrystals, polymorph transitions, carbon nanotube dissolution and inclusion complex formation. Keywords: DNA; green chemistry; mechanochemistry; nucleoside; nucleotide; Introduction Several definitions of mechanochemistry have been attempted since Ostwald included it as one of

• using mechanochemistry [94] and Rajamohan and co-workers described using a mortar and pestle to effect LAG of β-cyclodextrin with either inosine [95] or cytidine [96] in the presence of water. Weak complex formation was inferred by powder XRD for cytidine. Conclusion Access to reliable and reproducible

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 and the secondary rim protons of β-CD were indicated by NMR concluding to a probable 2:1 host/guest inclusion formation [26]; the formation of 1:1 stoichiometric complexes pointed out by phase solubility [25] or MD studies [29]; favorable inclusion complex formation with β-CD dimer was

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

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

• approach as it monitors changes of only one species involved in the complex formation and thus the interpretation of results is simple and straightforward. However, to design the polarization spectroscopy experiment accurately, it is essential that solutions of both the polynucleotide and the ligand are

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

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• consequent unfavourable effect on the complex formation entropy [43][50]. A further unfavourable contribution may also come from the increasingly difficult desolvation of the charged host. These combined effects cause the observed decrease of K values for the neutral guest 1. By contrast, for the anionic

Binding abilities of a chiral calix[4]resorcinarene: a polarimetric investigation on a complex case of study

• Marco Russo and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2698–2709, doi:10.3762/bjoc.13.268

• [41][42][43][44][45], this indicates the occurrence of severer and severer dynamic-conformational changes upon complex formation. Therefore, we can conclude that the overall bell-shaped trend for K1 values on passing from CAP−1 to CAP−4 is the outcome of a fine interplay between favourable

• complex formation. Interestingly, a fair upfield shift is observed also for the signals at 0.82 and 1.14 ppm (passing to 0.71 and 1.03 ppm, respectively) relevant to the propyl pendant groups linked at the 2, 8, 14 and 20 positions of the calixarene scaffold. Assuming for CAP the occurrence of an “all

• occurring in host–guest complex formation processes involving calixarenes in general. This can be particularly useful, even because CAP and structurally related ligands might find various interesting applications, due to their amphiphilic character, chirality and coordination ability towards metal cations

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• methods – FTIR–ATR and Raman were used for describing the way of PTX-CD interactions. The IR spectroscopy in the region characteristic for δ-HOH bending of water molecules attached to CDs (1600–1700 cm−1) is usually employed for tracking of the inclusion complex formation, however, Raman spectra of this

• identification of guest–host interactions is possible [17][18]. Any changes in the band position as well as increasing or decreasing of its intensity indicate complex formation. In that sense Raman spectroscopy emerges as an important technique for studying host–guest interactions, in particular for verifying if

• affinity toward PTX (Ka = 4 M−1). Findings from FTIR–ATR and Raman experiments demonstrate that the region of C=C bond vibrations of the guest is an excellent indicator of complex formation. The observed changes in this band (position and intensity), together with the information about possible appearance

Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• complexes with paraquats 8–10. Nevertheless, we have demonstrated qualitatively the complex formation of 6@8–6@10 by FAB–MS (Figures S43-S45, Supporting Information File 1). There are no hydrogen bonds between the protons of the terminal hydroxy groups and oxygen atoms in the complex of clip 2 with guest 8

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• p-tert-butylthiacalix[4]arene 4 is also of interest because this fragment contains a polar NH group able to interact with anionic substrates and a chromophore fragment necessary for the spectrophotometric detection of the complex formation. In this regard, the alkylation of monosubstituted

• hindrances to the complex formation. Review of literature data [62][63][64][65] indicate a good agreement between the results of calculations involving the complexes geometry determined by this method and experimental data. The PM3 method is used quite productively for molecular design and modeling of the

Influence of the milling parameters on the nucleophilic substitution reaction of activated β-cyclodextrins

• László Jicsinszky,
• Kata Tuza,
• Giancarlo Cravotto,
• Andrea Porcheddu,
• Francesco Delogu and
• Evelina Colacino

Beilstein J. Org. Chem. 2017, 13, 1893–1899, doi:10.3762/bjoc.13.184

• findings lend support to the idea that mechanical activation can induce chemical reactivity [29] and selectivity [30] which is different to that observed in solution, which can be further complicated by the inclusion complex formation property of cyclodextrins. How exactly the milling parameters influence

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

• crystals. The disagreement between solution and crystal structure in terms of complex formation and orientation/conformation of the guest indicates that the lattice forces and organization in the crystal prevail by far over the soft host–guest contacts established in solution and determines the final

Mechanochemical borylation of aryldiazonium salts; merging light and ball milling

• José G. Hernández

Beilstein J. Org. Chem. 2017, 13, 1463–1469, doi:10.3762/bjoc.13.144

• –solvent charge-transfer complex formation. Keywords: aryldiazonium salts; borylation; eosin Y; mechanochemistry; photocatalysis; Introduction The use of mechanical force to process materials or to induce chemical transformations is perhaps as old as the history of mankind itself [1]. Similarly, from

One-pot synthesis of block-copolyrotaxanes through controlled rotaxa-polymerization

• Jessica Hilschmann,
• Gerhard Wenz and
• Gergely Kali

Beilstein J. Org. Chem. 2017, 13, 1310–1315, doi:10.3762/bjoc.13.127

• hydrophobic interaction, as the driving force of complex formation, the threading of the CDs is only achievable in aqueous solution, but the hydrogen bonds between the hydroxy groups impede the water solubility of the products. Thus, the stoppering reaction is mostly limited to organic solutes, in which

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• it via noncovalent interactions. Figure 2 shows three different channels in a minimal replicating system. Building blocks A and B can react via the bimolecular reaction pathway, to form the template molecule T. In the second pathway – binary complex formation – A and B bind together reversibly to

Interactions between shape-persistent macromolecules as probed by AFM

• Johanna Blass,
• Jessica Brunke,
• Franziska Emmerich,
• Cédric Przybylski,
• Vasil M. Garamus,
• Artem Feoktystov,
• Roland Bennewitz,
• Gerhard Wenz and
• Marcel Albrecht

Beilstein J. Org. Chem. 2017, 13, 938–951, doi:10.3762/bjoc.13.95

• end groups were prepared starting from diacetylene-modified cyclodextrin monomers by a combined Glaser coupling/click chemistry approach. Structural perfection of the neutral CD polymers and inclusion complex formation with ditopic and monotopic guest molecules were proven by MALDI–TOF and UV–vis

Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

• Franca Castiglione,
• Fabio Ganazzoli,
• Luciana Malpezzi,
• Andrea Mele,
• Walter Panzeri and
• Giuseppina Raffaini

Beilstein J. Org. Chem. 2017, 13, 714–719, doi:10.3762/bjoc.13.70

• finally optimized up to an energy gradient lower than 4 × 10−3 kJ mol−1 Å−1. The simulation protocol closely followed the strategy proposed by some of us for modeling the inclusion complex formation without any a priori assumption about its possible geometry [17][18][19][20][21]. Thus, the optimized

• single bond. The lack of disorder in the C9–C10 segment suggests that complexation constrains 2 in a single conformation in the solid state. The MD simulations led to the formation of a 1:1 inclusion complex of β-CD with molecules 1 and 2 both in vacuo and in explicit water. In both cases, the complex

• formation was relatively fast, and allowed us to find the most stable geometry eventually achieved from the trial starting arrangements [17] mentioned in the Materials and Methods section. The most stable complex yielded inclusion of an aromatic ring in the β-CD, with the seven-membered ring, the side chain

Pd- and Cu-catalyzed approaches in the syntheses of new cholane aminoanthraquinone pincer-like ligands

• Nikolay V. Lukashev,
• Gennadii A. Grabovyi,
• Dmitry A. Erzunov,
• Alexey V. Kazantsev,
• Gennadij V. Latyshev,
• Alexei D. Averin and
• Irina P. Beletskaya.

Beilstein J. Org. Chem. 2017, 13, 564–570, doi:10.3762/bjoc.13.55

• determined for deoxycholic acid derived ligand 5d. Thus, there is no appreciable dependence between the value of the binding constants and the presence of an extra hydroxy group in the cholane fragment. To the best of our knowledge a complex formation of 1,8-diaminoanthraquinone derivatives with Al and Cr

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• in Figures S11 and S12 (Supporting Information File 1). The titration experiments of R2 with sodium salts of F− and AcO− ions revealed redshifts to 556 nm and 559 nm correspondingly with clear isosbestic points indicating complex formation. The titration profiles of R2 obtained by the addition of

• band at higher wavelength confirms the complex formation process. The HOMOs and LUMOs of R1–F− and R1–AcO− are represented in Figure 19 and Figure 20; the HOMOs and LUMOs of R2–F− and R2–AcO− are represented in Figure 21 and Figure 22. The decrease in the bond length value corresponding to the OH group

• in its original form. A significant hyperchromic effect is observed for the band at 477 nm when In 2 (F−) is in the ‘ON’ mode, i.e., during the R1–F− complex formation process. With the introduction of Hg2+ (In 3), the output attains the zero state (‘OFF’). In total, three input combinations lead to

Interactions between photoacidic 3-hydroxynaphtho[1,2-b]quinolizinium and cucurbit[7]uril: Influence on acidity in the ground and excited state

• Jonas Becher,
• Daria V. Berdnikova,
• Darinka Dzubiel,
• Heiko Ihmels and
• Phil M. Pithan

Beilstein J. Org. Chem. 2017, 13, 203–212, doi:10.3762/bjoc.13.23

• a complex formation, namely a hypochromic effect and red shift of the absorption as well as fluorescence quenching upon addition of the host (Figure 6 and Supporting Information File 1, Figure S3). Furthermore, the significant line broadening of the absorption bands occurs most likely due to

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

• Monica Ferro,
• Franca Castiglione,
• Nadia Pastori,
• Carlo Punta,
• Lucio Melone,
• Walter Panzeri,
• Barbara Rossi,
• Francesco Trotta and
• Andrea Mele

Beilstein J. Org. Chem. 2017, 13, 182–194, doi:10.3762/bjoc.13.21

• by exploiting the pores of the polymer network to encapsulate the guest molecules. However, it should be stressed that CD nanosponges similar to ours and prepared by using citric acid as cross-linker, showed a different behaviour towards ibuprofen: the authors provided evidence of inclusion complex

• formation as the main mechanism of absorption [33]. We may conclude that the type of monomer and the cross-linker agent both play a key role in driving the absorption towards inclusion complexes or segregation in the polymer pores, although a sufficient number of data is still missing to formulate a general