Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• previously noted for water/DMSO mixtures [56]. The attachment of the BODIPY chromophore to the anchor groups thus reduces the binding constant by an additional factor of 10 for the aniline meso-group and by a factor of 1000 for the tetrafluoroaniline group in 4. We ascribe this to steric hindrance between

• model analytes (Figure 5). In order to determine the binding constants of the two analytes, the apparent binding constant of 2 at pH 3.1 was taken (Kapp = 6.7 × 105 M−1) and the displacement titrations were analysed with a competitive titration model [18][25]. This gave binding constants of 1.5 × 107 M

Synthesis of 9-arylalkynyl- and 9-aryl-substituted benzo[b]quinolizinium derivatives by Palladium-mediated cross-coupling reactions

• Siva Sankar Murthy Bandaru,
• Darinka Dzubiel,
• Heiko Ihmels,
• Mohebodin Karbasiyoun,
• Mohamed M. A. Mahmoud and
• Carola Schulzke

Beilstein J. Org. Chem. 2018, 14, 1871–1884, doi:10.3762/bjoc.14.161

• of 22AG to derivatives 2b and 2c could be used to deduce the binding constant Kb (Figure S2, Table 3). The addition of ct DNA to the derivative 2a led to quenching of the emission intensity (Figure 8A). In contrast, a light-up effect with a factor of 3 was observed upon the addition of ct DNA to

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

• the results are shown in Table 1. Generally, ZB4 shows weaker binding affinities to these guests than TA4 does with the same counterions. For example, ZB4 and cation 3+, with a binding constant of 5.4 × 104 M−1, was the best guest among the studied ones. However, the corresponding association constant

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

• of the binding equilibrium was called for. Bimolecular binding equilibria are usually described mathematically via the binding constant or dissociation constant. The latter is more intuitive, as it gives the concentration at which half of the binding partners are in the bound state and the other half

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

• over ligand), the application of the ECD method may be limited by available material and long times. This is particularly valid if the studied system and its binding constant are unknown and repetition/redesign of the experiment is necessary. Recently, Garbett, Ragazzon and Chaires [9] summarized a

• -polynucleotide; and iii) at least 10 µM binding constant (at common conditions, pH 5–8, I = 0.05–0.1, rt). b) Positive sign, non-linear relation of ICD intensity to ratio r[ligand]/[DNA] approaching saturation at about r = 0.2–0.3. This indicates either groove binding with a loose orientation of the ligand with

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

• outlines an important role assumed by π–π interactions. In fact, the small aromatic imidazolium cation 5 is appreciably included into CAP−2, although with a relatively small binding constant (K = 250 ± 20 M−1; ΔΘ = −14.6 ± 0.4 deg dm−1 M−1). It is interesting to notice that significant affinity towards CAP

• interaction, but do not allow a reliable estimation of the binding constant, whereas the benzylammonium cation 7 does not interact at all. By contrast, CAP−2 and CAP−3 include very well all the guests, forming in several cases the relevant 2:1 complexes. More in detail, the exclusive formation of the 1:1

• rotation of the pure host solution, ΔΘ is the differential molar optical rotation (i.e., the difference between the molar optical rotations of the complex and the free host, respectively), H0 and G0 are the concentrations of the host and guest mother solutions, respectively, K is the required binding

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

• binding constant and NA-γ-CD concentration (see Supporting Information, File 1). Number average and weight average degrees of polymerization (nn and nw) are given by standard relations derived for polycondensation [40] The values of nn and nw calculated from ITC results for 10 mM solutions of NA-γ-CD are

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

• polyrotaxane synthesis since it is highly water-soluble and provides a sufficiently high binding constant for isoprene [24][25]. Results and Discussion In a first trial, statistical RAFT copolymerization of isoprene complexed in RAMEB was performed with water-soluble bulky comonomers, namely N-[tris

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

• guest 10. Further information is provided in Supporting Information File 1. Incomplete complexation with cationic guest molecules is indicated by a significant lower binding constant of 670 M−1 for the second binding complexation step, which is strongly inhibited as a result of the electronic repulsion

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

• salts have not been investigated earlier. The ligands derived of 1,8-diaminoanthraquinone are convenient for the detection of the copper cation [45][46]: the tetradentate ligand N,N’-bis(β-dimethylaminoethyl)-1,8-diaminoanthraquinone [47] demonstrate a two orders of magnitude better binding constant

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

• for F− and AcO– ions allowing the real time analysis of these ions in aqueous media. The formation of the receptor–anion complexes has been supported by UV–vis titration studies and confirmed through binding constant calculations. The anion binding process follows a first order rate equation and the

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

• . Isosbestic points were only maintained during titration at pH 5. The analysis of the binding isotherms obtained from photometric titrations at pH 5 revealed a 1:1 stoichiometry of 2-CB[7] inclusion complex and a corresponding binding constant of Kb = 1.8 × 104 M−1 (Supporting Information File 1, Figure S5

• of the ligand at this pH. The analysis of the binding isotherm (pH 5) gave a binding constant Kb = 2 × 104 M−1 that is significantly lower than the ones observed for the benzo[b]quinolizinium derivatives 1b and 1c (≈ 108 M−1) [37], but comparable to the Kb value of the benzo[c]quinolizinium

• that can thread nicely into the binding site. Notably, the structurally resembling alkaloids berberine (8a) and palmatine (8b), that contain an angularly annelated quinolizinium unit, also bind to CB[7]. But whereas palmatine (8b) has essentially the same binding constant as 2 (Kb = 4.3 × 104 M−1, in

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• length of the fatty acid chain of the phospholipid, the cavity size, and the nature of the substituents at the CD [66]. In the literature, the binding constant between cholesterol and β-CD was estimated around 1.7 × 104 M−1 from a solubility method [67][68]. This value proves the good stability of the

• inclusion complex because of the driving force of complexation: hydrophobic interaction. Despite there is no information on the binding constant observed for the inclusion of cholesterol in γ-CD, the cavity internal diameter of the β-CD and its derivatives perfectly matches the size of the sterol molecules

• with α-, β-, HP-β-, and ME-β-CD. The estimated constants of free L-phenylalanine (Phe) increased in the order ME-β-CD ≈ HP-β-CD < α-CD < β-CD. Moreover, the results proved that the stability of oligopeptides containing Phe is higher than that of Phe itself. For instance, the binding constant of free

A self-assembled cyclodextrin nanocarrier for photoreactive squaraine

• Ulrike Kauscher and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2016, 12, 2535–2542, doi:10.3762/bjoc.12.248

• details) and the binding constant was determined to be Ka = 1.2 × 105 M−1. The high-affinity binding of AdSq is a clear indication that both adamantanes are involved in binding to the CDV and that the interaction is effectively divalent. In another set of experiments, giant unilamellar vesicles (GUVs) of

• 30 µM (since approximately 50% of the amphiphilic cyclodextrins reside at the interior surface of the CDV and AdSq is too large and too polar to pass the membrane), saturation is reached at a six-fold excess of host to guest, even though both are present in micromolar concentrations only. The binding

• constant of AdSq with the cyclodextrins in the CDV could be obtained by plotting the maximum fluorescence emission (at 676 nm) against the concentration of available cyclodextrin (Figure 3, bottom). The resulting Langmuir isotherm was fitted by linear regression (see Supporting Information File 1 for

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• that a 2:1 complex is formed. The straight slope and its saturation at a ratio of 0.5 indicate a high binding constant which cannot be determined from this set of data. To assess the terpyridine-metal complex formation, 1H NMR titration of 4a with HgCl2 has been performed. The addition of 0.25

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

• exceedingly stable capsular complexes (Figure 6). Regarding their stability, even at 5 μM, NMR showed complete encapsulation of estradiol; giving a minimum apparent binding constant for the empty capsule (the host is actually monomeric in the absence of guests) of 1 × 108 M−1. When the steroid was very large

Interactions between 4-thiothymidine and water-soluble cyclodextrins: Evidence for supramolecular structures in aqueous solutions

• Vito Rizzi,
• Sergio Matera,
• Paola Semeraro,
• Paola Fini and
• Pinalysa Cosma

Beilstein J. Org. Chem. 2016, 12, 549–563, doi:10.3762/bjoc.12.54

• powerful tools to clearly establish the presence of supramolecular structures involving S4TdR and CDs. Furthermore, assuming the formation of a 1:1 host–guest complex, in order to give details about the inclusion complexes the binding constant (K) and the stoichiometry of interaction, the Benesi–Hildebrand

Interactions of cyclodextrins and their derivatives with toxic organophosphorus compounds

• Sophie Letort,
• Sébastien Balieu,
• William Erb,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2016, 12, 204–228, doi:10.3762/bjoc.12.23

• binding constant values and the hydrophobicity of the pesticides, suggesting that steric effects are probably predominantly involved in complex formation. The inclusion of the apolar heterocyclic ring into the CD cavity is the most likely situation to occur. γ-CD has the largest secondary alcohols rim

• use this technique for routine analysis [48]. Finally the binding constant of the host-guest inclusion complex was reported at 690 ± 140 M−1. Pesticides bearing a non-aromatic group X-ray powder diffraction analysis and DSC validated the formation of a complex between (diethoxyphosphinoximino

• hydrolysis, than α- and β-CD could. β-CD:chloramidophos (9, Figure 3) complex was formed by a kneading method [51] and UV spectrophotometry analysis revealed a 1:1 stoichiometry and a binding constant of 203.0 M–1 for this complex. FTIR analysis revealed the disappearance of the absorbance band at 804 cm−1

Polydisperse methyl β-cyclodextrin–epichlorohydrin polymers: variable contact time ¹³C CP-MAS solid-state NMR characterization

• Isabelle Mallard,
• Davy Baudelet,
• Franca Castiglione,
• Monica Ferro,
• Walter Panzeri,
• Enzio Ragg and
• Andrea Mele

Beilstein J. Org. Chem. 2015, 11, 2785–2794, doi:10.3762/bjoc.11.299

• value of the binding constant between toluene and β-CD (Kf = 158 M−1) [33] and the high volatility of toluene leads to the conclusion that toluene is a good template for imprinting reactions. According to Ritter [34], the CD–toluene complex fosters mainly the formation of linear polymers instead of

Size-controlled and redox-responsive supramolecular nanoparticles

• Raquel Mejia-Ariza,
• Gavin A. Kronig and
• Jurriaan Huskens

Beilstein J. Org. Chem. 2015, 11, 2388–2399, doi:10.3762/bjoc.11.260

• results gave a binding constant (Ka) of 3 × 104 L mol−1. This is slightly lower than the interaction between native CD and Ad-TEG, for which a Ka value of 5 × 104 L mol−1 has been determined (see Figure 1b). It can therefore be concluded that the grafting of CD to PEI has a minor effect on the host–guest

• free CD, and to confirm the degree of functionalization, a calorimetric titration was performed with native CD, as shown in Figure 2. This titration confirmed that nearly 100% of Fc-PEG was formed. The Ka of Fc-PEG with native CD is 1.2 × 103 L mol−1, which is comparable to the binding constant of Fc

Glycoluril–tetrathiafulvalene molecular clips: on the influence of electronic and spatial properties for binding neutral accepting guests

• Yoann Cotelle,
• Marie Hardouin-Lerouge,
• Stéphanie Legoupy,
• Olivier Alévêque,
• Eric Levillain and
• Piétrick Hudhomme

Beilstein J. Org. Chem. 2015, 11, 1023–1036, doi:10.3762/bjoc.11.115

• :2 complex (F4-TCNQ)2@clip 3 (Figure 9 middle) with an average binding constant of Ka = (8 ± 5) × 108 M−1. Similar studies were carried out using molecular clip 4 and quantitative measurements were performed using UV–visible titration considering the changes in the spectra of F4-TCNQ at 860 nm upon

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• with peptide concentration. Isothermal titration calorimetry (ITC) was used to determine the thermodynamic parameters as well as the binding constant for the assembly of Au/MUA nanoparticles (Table 1). By fitting with a one set of binding site mode the binding stoichiometry N, the binding constant KB

• accordance with the observations made based on the UV–vis measurements. The shift in the absorption maximum obtained from UV–vis measurements for R2A2 is much smaller than that of VW05, but its binding constant of 18.2 . 105 M−1 is about 3.5-fold higher than that of VW05, although the amount of presented

• charges is reduced in R2A2. The stepwise increase in peptide length induced a dramatic decrease of the KB value. However, the KB of R2A3 is slightly higher compared to VW05. Only a further increase in peptide length lead to a significant decrease in the binding constant compared to VW05. Although gel

Fluoride-driven ‘turn on’ ESPT in the binding with a novel benzimidazole-based sensor

• Kai Liu,
• Xiaojun Zhao,
• Qingxiang Liu,
• Jianzhong Huo,
• Bolin Zhu and
• Shihua Diao

Beilstein J. Org. Chem. 2015, 11, 563–567, doi:10.3762/bjoc.11.61

• binding constant of BIP with F− was also determined by nonlinear regression based on spectrofluorometric titration. Good nonlinear curve fits (R = 0.9907) also indicated the formation of an 1:1 stoichiometric complex of BIP with F− (see Figure S2 in Supporting Information File 1). The association constant

Formation of nanoparticles by cooperative inclusion between (S)-camptothecin-modified dextrans and β-cyclodextrin polymers

• Thorbjørn Terndrup Nielsen,
• Catherine Amiel,
• Laurent Duroux,
• Kim Lambertsen Larsen,
• Lars Wagner Städe,
• Reinhard Wimmer and
• Véronique Wintgens

Beilstein J. Org. Chem. 2015, 11, 147–154, doi:10.3762/bjoc.11.14

• illustrates the influence of the cooperative inclusion as described by Breslow et. al in 1995 [18]. Formation of nanoparticles The influence of the backbone was not only reflected in the higher binding constant but also in the ability of the CPT-dextrans to form nanoparticles when associated with β-CD

• fitted with a theoretical titration curve using the instrument software, assuming a 1:1 complex. The enthalpy change, ΔH, the binding constant (K), and the stoichiometry (n), were the adjustable parameters. Fluorescence emission spectra were recorded on Varian Cary Eclipse fluorescence spectrophotometer

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• binding constant with telomeric quadruplex DNA, it has a lower affinity towards the ILPR quadruplex under the same conditions. In addition, thiazole orange (6) shows the least pronounced stabilization effect in the thermal denaturation experiment (Table 2). As cyanine dyes bind to quadruplex DNA by