Spatial arrangements of cyclodextrin host–guest complexes in solution studied by ¹³C NMR and molecular modelling

• Konstantin Lebedinskiy,
• Ivan Barvík,
• Zdeněk Tošner,
• Ivana Císařová,
• Jindřich Jindřich and
• Radim Hrdina

Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33

• delivery [2][3][4], in analytical and preparative chemistry for compound separation [5] and in materials science for small molecule detection [6][7]. Association (binding) constants between the host and guest molecules [8][9][10] are typically measured by 1H NMR titration [11][12] or isothermal titration

• calorimetry [13]. Single crystals for many host–guest complexes have been prepared, and their structure elucidated by X-ray crystallography [14][15]. Conformations of host–guest complexes in solution have been studied by 2D NMR experiments [11] (NOESY, ROESY) or proposed computationally [16][17] based on

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• . used 1H NMR titrations and isothermal titration calorimetry (ITC) to experimentally determine interactions energies for I-9 complexes (e.g., I-9-lig, −6.3 kcal/mol), they also discovered that simultaneous binding to both σ-holes was possible [90]. Given these observations, it is unsurprising that HVI

A fluorescent probe for detection of Hg²⁺ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene

• Xiaoqian Chen,
• Naqin Yang,
• Yue Ma,
• Xinan Yang and
• Peihua Ma

Beilstein J. Org. Chem. 2023, 19, 864–872, doi:10.3762/bjoc.19.63

• that a G and TMeQ[6] inclusion complex is formed with a 1:1 stoichiometry. Isothermal titration calorimetry (ITC) analysis The association constant and thermodynamic parameters of the host–guest interaction between G and TMeQ[6] can be obtained using ITC. At 25 °C, a neutral aqueous solution of TMeQ[6

• @TMeQ[6] aqueous solution at U = 520 V, slit = 5/5 and adding different equivalents of Hg2+ to G@TMeQ[6] aqueous solution at U = 500 V, slit = 5/5. Isothermal titration calorimetry (ITC) The neutral aqueous solution of TMeQ[6] (1.0 × 10–4 mol·L−1, 1.00 mL) was placed in a sample tank, and G solution

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• the complex. Every ΔTm value here reported was the average of at least two measurements. The error in ΔTm is ±0.5 °C. Isothermal titration calorimetry (ITC) experiments: A non-covalent interaction study of Phen-Py-1 with the human enzyme mutant DPP III E451A was performed on a MicroCal PEAQ-ITC

• at the liquid–air interface, testing solutions with a 2 mL volume were used. Fluorescence and CD spectra were recorded using appropriate 1 cm path quartz cuvettes; UV–vis spectra were recorded in 1 cm path quartz cuvettes or using an immersion probe with 5 cm light path length. Isothermal titration

• calorimetry (ITC) titrations were performed on a Malvern PEAQ-ITC microcalorimeter (MicroCal, Inc.,Northampton, MA, USA). MicroCal PEAQ-ITC analysis software, supplied by the manufacturer, was used for data analysis. Polynucleotides were purchased as noted: calf thymus (ct)-DNA, poly dAdT–poly dAdT, poly dGdC

Preparation of β-cyclodextrin-based dimers with selectively methylated rims and their use for solubilization of tetracene

• Konstantin Lebedinskiy,
• Volodymyr Lobaz and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2022, 18, 1596–1606, doi:10.3762/bjoc.18.170

• parameters is impossible. ITC (isothermal titration calorimetry) is a popular technique for evaluating supramolecular interaction with CDs [38], mainly in the aqueous medium. We performed the titrations of tetracene DMSO solution by the series of CDs used in the solubility experiments (Figure 7, Figure 8

Host–guest interaction and properties of cucurbit[8]uril with chloramphenicol

• Lin Zhang,
• Jun Zheng,
• Guangyan Luo,
• Xiaoyue Li,
• Yunqian Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 2832–2839, doi:10.3762/bjoc.17.194

• (CPE) was investigated using single-crystal X-ray diffraction spectroscopy, isothermal titration calorimetry (ITC) and UV–vis, NMR and IR spectroscopy. The effects of Q[8] on the stability, in vitro release performance and antibacterial activity of CPE were also studied. The results showed that CPE and

Constrained thermoresponsive polymers – new insights into fundamentals and applications

• Patricia Flemming,
• Alexander S. Münch,
• Andreas Fery and
• Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• , similar observations have been reported for DNA modified with methyl phosphotriester linkage (POMe) using isothermal titration calorimetry (ITC) measurements which provides ΔH values directly [37]. For the native DNA duplex (ON1/ON20), the more favourable ΔH at the low salt concentration (25 mM NaCl) was

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• particles, and information on the molecular structure was gained by UV–vis spectroscopy. Isothermal titration calorimetry (ITC) provided information on the thermodynamics and interaction forces in the supramolecular assembly formation. Keywords: electrostatic self-assembly; hydroxyflavylium

• spectroscopy, and isothermal titration calorimetry. Results and Discussion Characterization of the flavy building block In the first step the switchability and the photostability of pelargonidin chloride (Flavy) were investigated. The switching ability of Flavy is already well-known [79][80]. Here it was

• . Thermodynamic analysis of the assembly process For understanding the differences of the assemblies, isothermal titration calorimetry (ITC) was performed to elucidate the thermodynamics and to gain insight into the building block interactions in the assembly process. Basically, ITC measures the association heat

The fluorescence of a mercury probe based on osthol

• Guangyan Luo,
• Zhishu Zeng,
• Lin Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 22–27, doi:10.3762/bjoc.17.3

• mode between OST and Hg2+ is suggested as shown in Figure 7. Hg2+ and the oxygen atoms of the lactone ring and the methoxy group formed a stable complex, resulting in the enhanced fluorescence. Isothermal titration calorimetry analysis A Hg2+ solution (2 × 10−3 mol∙L−1, 25 μL) was added to the 1 × 10−4

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• resonance (SPR) spectroscopy [27][28], gel filtration [29], isothermal titration calorimetry (ITC) [30][31], fluorescence resonance energy transfer [32], and microscale thermophoresis [33]. In SPR spectroscopy, one of the protein molecules that make up the complex is first immobilised on a metal surface

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• described with regard to their potential to form redox-switchable rotaxanes. A combination of isothermal titration calorimetry and voltammetric techniques reveals correlations between the binding energies and redox-switching properties of the corresponding pseudorotaxanes with secondary ammonium ions. For

• corresponding free macrocycle. The detailed understanding of the thermodynamic and electrochemical properties of the tailor-made crown ethers lays the foundation for the construction of new types of molecular redox switches with emergent properties. Keywords: crown ether; isothermal titration calorimetry

• redox-active units were investigated with respect to the impact of the functionalization on the thermodynamic binding properties towards secondary ammonium axles using isothermal titration calorimetry (ITC). The electrochemical switching properties of the redox-active crown ethers were examined using

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• phosphonato-calix[n]arenes of different ring sizes (n = 4, 6 or 8) to Cyt c [20][23][24][26][27][28] and the antifungal protein PAF [25] as model proteins. These studies combined 15N-HSQC titrations with X-ray crystallography, isothermal titration calorimetry (ITC) and size exclusion with light scattering

• the lines and decreases the signal intensities even more. In addition, the stabilization of the 14-3-3 peptide interaction in the presence of the ligand was confirmed by biochemical assays such as isothermal titration calorimetry (ITC) and fluorescence anisotropy. On a quest for modulators of 14-3-3

• for measuring binding affinities, such as isothermal titration calorimetry (ITC) or fluorescence anisotropy/polarization, are only able to provide an averaged KD. Outlook In the last two decades, additional NMR methods have been developed to extend the size limits of NMR spectroscopy to very large

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• the free nucleic acid from Tm of the complex. Every ΔTm value reported herein was the average of at least two measurements. The error in ΔTm is ±0.5 °C. Isothermal titration calorimetry (ITC) experiments were performed on a MicroCal VP-ITC microcalorimeter (MicroCal, Inc., Northampton, MA, USA

• nevertheless obvious by systematic deviation from isoelliptic point and changes of ICD bands in opposite direction (Figures 2–4, and Figures S16–S20 in Supporting Information File 1). Hence, to characterise in more detail the thermodynamics of such multifaceted binding we performed isothermal titration

• calorimetry experiments (ITC), which allowed us to determine all thermodynamic components simultaneously in a single experiment (the equilibrium binding constant (Ka), reaction Gibbs free energy of binding (ΔrG), reaction enthalpy (ΔrH), reaction entropy (ΔrS), and the stoichiometry (n) of the complex formed

Host–guest interactions in nor-seco-cucurbit[10]uril: novel guest-dependent molecular recognition and stereoisomerism

• Xiaodong Zhang,
• Wei Wu,
• Zhu Tao and
• Xin-Long Ni

Beilstein J. Org. Chem. 2019, 15, 1705–1711, doi:10.3762/bjoc.15.166

• effect of the carbonyl-rimmed portal). Isothermal titration calorimetry results reveal a 2:1 G1/host-1 stoichiometry with a binding constant (Ka) of 1.32 × 105 M−1 (Table 1). These observations clearly indicate that host-1 recognizes and prefers to include the ADA moieties in both of the identical

• guest molecules is a classical hydrophobic effect; it has a favorable entropic component due to the delivery of surface-bound solvent molecules on the guest. Therefore, isothermal titration calorimetry could be employed to quantify the enthalpic and entropic contributions to the binding interactions

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• have found that squaraine affinities for tetralactam B are in the relative order of methanol < chloroform < water, reflecting the relatively large thermodynamic importance of the hydrophobic effect [60]. Interestingly, isothermal titration calorimetry studies revealed that the high squaraine binding in

New standards for collecting and fitting steady state kinetic data

• Kenneth A. Johnson

Beilstein J. Org. Chem. 2019, 15, 16–29, doi:10.3762/bjoc.15.2

• site titration to establish the concentration of active sites. One method is isothermal titration calorimetry relying on the heat change upon binding of a substrate analog. Because the method is relatively insensitive it requires high concentrations of protein (usually μM) so the stoichiometry is easy

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• thermodynamic profiles as measured via isothermal titration calorimetry (ITC) [55]. Despite its low molecular weight, 13 showed tight-binding kinetics and was able to reduce production of HHQ, as well as PQS. Furthermore, it was capable of attenuating biofilm production [54]. All the information gathered via

• . In order to block the thioesterase activity of the enzyme, a library of 500 fragments was screened via differential scanning fluorimetry (DSF) and the hit fragments 24–26 (Figure 11) were further validated using isothermal titration calorimetry (ITC) [66]. Binding to PqsE could be confirmed with KD

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

• via isothermal titration calorimetry [46]. When a downstream-binding strand was present, binding of the monomer was up to two orders of magnitude tighter than in its absence. Simulating primer extension With dissociation constants in hand, we were now in a position to determine rate constants for the

Carbohydrate inhibitors of cholera toxin

• Vajinder Kumar and
• W. Bruce Turnbull

Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34

• pocket. Both of these terminal sugar residues show hydrogen bonding interactions with the protein and associated water molecules. The GM1 oligosaccharide (GM1os) binds very tightly to CTB with a dissociation constant (Kd) of around 40 nM (measured by isothermal titration calorimetry, ITC), while simple

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

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

• were studied by a set of methods allowing characterization of supramolecular behavior at various levels – from binary complexation, over supramolecular oligomers to large assemblies; namely by isothermal titration calorimetry (ITC) [16], 1H nuclear magnetic resonance spectroscopy (1H NMR), dynamic

• preparation, we observed many sheet-like structures (Figure 6C), corresponding to the observations of Bonini et al [22]. Isothermal titration calorimetry (ITC) ITC experiments on NA-γ-CD cannot be carried out as classical titration experiments, i.e., by injecting the ligand solution into a solution of the

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• , chosen for this study (Figure 1). Results and Discussion Isothermal titration calorimetry (ITC) studies of substituted poly(acrylate) network formation In aqueous solution, the host β-CDen substituents of PAAβ-CDen complex the guest adamantyl substituents of PAAADen, PAAADhn and PAAADddn to form poly

• appear in the corresponding figure captions. Isothermal titration calorimetry (ITC) ITC measurements were made using a MicroCal VP isothermal titration calorimeter. In each titration, 10 mm3 aliquots of a 0.62 wt % PAAβ-CDen solution ([β-CDen] = 2.84 × 10−3 mol dm−3) were titrated into 1.46 cm3 of either

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

• connection of one CD moiety at each phenylene unit. Based on the stiffness of the polymer chain self-passivation of CD polymer modified surfaces is reduced to a minimum. Furthermore, the ethynyl end groups are easily functionalized by click chemistry. Isothermal titration calorimetry (ITC), fluorescence

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

• Vincent M. Rotello

Beilstein J. Org. Chem. 2016, 12, 1638–1646, doi:10.3762/bjoc.12.161

• the particle–protein binding process not denature the proteins, it actually stabilizes them [46]! This result stills surprises researchers who follow the dogma that proteins must denature at interfaces. One of the other observations we made using isothermal titration calorimetry is that nanoparticle