Binding of tryptophan and tryptophan-containing peptides in water by a glucose naphtho crown ether

• Gianpaolo Gallo and
• Bartosz Lewandowski

Beilstein J. Org. Chem. 2025, 21, 541–546, doi:10.3762/bjoc.21.42

• the host as well as Coulombic interactions between the crown ether and the ammonium could be involved. Furthermore, the ITC measurements revealed that the binding of 1 with both enantiomers of H-Trp-OH is predominantly entropy-driven suggesting that the hydrophobic effect plays an important role in

• extent. The receptor could instead potentially form H-bonds via its OH functionalities with the amide groups adjacent to the Trp residue in the peptide. The favourable negative entropy of the interaction between 1 and the tripeptides 2–7 suggests a significant contribution of the hydrophobic effect to

The effect of neighbouring group participation and possible long range remote group participation in O-glycosylation

• Rituparna Das and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2025, 21, 369–406, doi:10.3762/bjoc.21.27

• temperature or the activation entropy, hydrogen bonding, solvent [24], nature of the leaving groups and the promoter used [25]. The mechanism of glycosylation reactions has long been categorised mostly as dissociative SN1 reactions proceeding through stabilised oxocarbenium ions with the role of counterions

Effect of substitution position of aryl groups on the thermal back reactivity of aza-diarylethene photoswitches and prediction by density functional theory

• Misato Suganuma,
• Daichi Kitagawa,
• Shota Hamatani and
• Seiya Kobatake

Beilstein J. Org. Chem. 2025, 21, 242–252, doi:10.3762/bjoc.21.16

• compounds N3, N4, and I1–I4. The activation enthalpy (ΔH‡) and activation entropy (ΔS‡) in the thermal reaction were determined from the intercept and slope. Using these values, the experimental activation free energy (ΔG‡(exp)), the k value, and the half-life (t1/2) at 298 K were calculated and the results

Extension of the π-system of monoaryl-substituted norbornadienes with acetylene bridges: influence on the photochemical conversion and storage of light energy

• Robin Schulte,
• Dustin Schade,
• Thomas Paululat,
• Till J. B. Zähringer,
• Christoph Kerzig and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 3061–3068, doi:10.3762/bjoc.20.254

• . From these data, the rate constants of the cycloreversion reactions were generated according to first-order kinetics and used to calculate the enthalpy and entropy of activation with the Eyring equation (Table 1, cf. Supporting Information File 1, equation S5). The analyses revealed half-lives of the

Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• the deslipping-based conversion process [46]. Moreover, considering the similar activation entropy values, the faster deslipping of [3]rotaxane was mainly caused by its lower activation enthalpy than that of [2]rotaxane owing to the stabilization effect derived from the inclusion structure formation

Divergent role of PIDA and PIFA in the AlX₃ (X = Cl, Br) halogenation of 2-naphthol: a mechanistic study

• Kevin A. Juárez-Ornelas,
• Manuel Solís-Hernández,
• Pedro Navarro-Santos,
• J. Oscar C. Jiménez-Halla and
• César R. Solorio-Alvarado

Beilstein J. Org. Chem. 2024, 20, 1580–1589, doi:10.3762/bjoc.20.141

• ) must exhibit only positive harmonic frequencies, whereas each energy maximum (transition state) exhibited only one negative frequency. From these last calculations, zero-point energy, thermal, and entropy corrections were obtained, which were added to the electronic energy to express the calculated

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• due to stronger unfavorable entropy, they are in general of lower affinity. The validation of this proof-of-concept and the dissection of thermodynamics of binding will help for the further development of lectin ligands that can be controlled by light. Keywords: carbohydrates; glycosyl azobenzenes

• unfavorable entropy barrier, i.e. a more positive entropy contribution (−TΔS), varying from 10.3 to 18.5 kJ/mol for the Z-isomers, and from 8.8 to 13.1 kJ/mol for the E-isomers. As displayed in Figure 4, this enthalpy–entropy compensation results in a limited variation of ΔG and therefore in the observed

• agreement with a stronger enthalpy of interaction, while the entropy barrier could arise from a limitation of flexibility and/or blocking of water molecules at the new interface. Conclusion We have designed and synthesized in three to five steps O- and S-galactosyl azobenzenes targeting the Pseudomonas

Entry to new spiroheterocycles via tandem Rh(II)-catalyzed O–H insertion/base-promoted cyclization involving diazoarylidene succinimides

• Alexander Yanovich,
• Anastasia Vepreva,
• Ksenia Malkova,
• Grigory Kantin and
• Dmitry Dar’in

Beilstein J. Org. Chem. 2024, 20, 561–569, doi:10.3762/bjoc.20.48

• multiple bonds (10 and 12). However, in the case of shorter (from 2-bromoethanol) and longer (compound 24) chain intermediates, the cyclization is retarded due to the disadvantage of forming a strained four-membered ring in the former case and a significant loss of entropy during the formation of a seven

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• mechanism to a <1st-order dependence on catalyst, which could indicate a competing alcohol or H-bonding driven mechanism. In CD3OD, first-order-catalyst dependence is maintained. The entropy of activation reveals an organized transition state (−42.1 cal/mol·K) which would be consistent with the mechanism in

Anion–π catalysis on carbon allotropes

• M. Ángeles Gutiérrez López,
• Mei-Ling Tan,
• Giacomo Renno,
• Augustina Jozeliūnaitė,
• J. Jonathan Nué-Martinez,
• Javier Lopez-Andarias,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2023, 19, 1881–1894, doi:10.3762/bjoc.19.140

• (Figure 1C). Elongation of the tether in fullerenes 10 and 11 reduced product ratios to still significant A/D10/9 ~ A/D11/9 = 2.1. The origin of this decrease in anion–π catalysis is likely to include increasing entropy losses in pseudo-macrocyclic transition states. Normalized against the fullerene-free

• ammonium cation. Normalized against the fullerene-free control 18, an electron-withdrawing cyano group on the cyclopropane in 19 gave similarly poor A/D19/18 = 1.5. At constant tether length as short as possible, strong increases in anion–π catalysis were found by further minimizing entropy losses in

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• ) activation functions for each layer. Two dropout layers are interleaved after the first and second hidden layers with a dropout setting of 25% to avoid over-fitting issues. The training objective is a classification task between the 4 monomer categories with a cross-entropy loss function. To account for the

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

• -site binding model (Figure 7, Table 3). ITC experiments confirmed the binding of the ligand with human DPP III mutant E451A. The experiment resulted in positive peaks as a result of an endothermic reaction, which took place with an increase in entropy (Figure 7C, Table 3). This means that the binding

• -Py-1: endothermic reaction with an increase of entropy. The analogous guanidiniocarbonylpyrrole–pyrene conjugate showed a negative enthalpy change and an increase of entropy [17]. Conclusion Two novel phenanthridine–pyrene conjugates Phen-Py-1 and Phen-Py-2 were prepared by the condensation of

Computational studies of Brønsted acid-catalyzed transannular cycloadditions of cycloalkenone hydrazones

• Manuel Pedrón,
• Jana Sendra,
• Irene Ginés,
• Tomás Tejero,
• Jose L. Vicario and
• Pedro Merino

Beilstein J. Org. Chem. 2023, 19, 477–486, doi:10.3762/bjoc.19.37

• by the tethers, the entropy effects caused by them has also been studied. The analysis of the evolution of the electron localization function along the reaction revealed the highly concerted character of the reaction. Keywords: DFT; distortion model; hydrazones; transannular cycloadditions

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• temperature. But, if K′ is measured at different temperatures one can also calculate the standard transformed molar enthalpy of reaction ΔrH′° and then the standard transformed molar entropy of reaction ΔrS′°. Using ΔrH′° one may then calculate ΔrG′° and K′ at different temperatures. Additionally, a

• in the scientific literature. Thus, comparisons with previously measured values of K or K′ of the same or highly similar reactions should be made and reported. In thermodynamics, the measured quantities are frequently related to the Gibbs energy G, the enthalpy H, and the entropy S. The

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

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

• partially methylated CDs with the admixture of water in DMSO. All CDs interactions with tetracene were accompanied by sufficient entropy gain, which points to the desolvation of interacting molecules. The interaction of CD "monomers" 13 and 16 with tetracene is weakly endothermic and, therefore, understood

• as an entropy-driven process with the potential formation of a complex in 1:1 stoichiometry. All CD dimers interacted with tetracene exothermically. Since the overall amount of water in the system is one order lower than the amount of hydroxy groups in CDs, they preserve the capacity for hydrogen

• , USA), to the two independent binding sites model. From the fit, the stoichiometry (n), binding enthalpy change (ΔH, kJ·mol−1), affinity constant (Ka, M−1), binding free energy change (ΔG, kJ·mol−1), and binding entropy change (ΔS, J·mol–1·K−1) for the first binding site were calculated. The

A study of the DIBAL-promoted selective debenzylation of α-cyclodextrin protected with two different benzyl groups

• Naser-Abdul Yousefi,
• Morten L. Zimmermann and
• Mikael Bols

Beilstein J. Org. Chem. 2022, 18, 1553–1559, doi:10.3762/bjoc.18.165

• hydroxy groups pointing towards the sides [1]. This makes the ‘hole’ in the donut a lipophilic cavity that in water can form complexes with small hydrophobic molecules [2] driven by the entropy increase by expulsion of water [3]. Compound 1 has a wide range of applications where the complexation of

Mechanistic studies of the solvolysis of alkanesulfonyl and arenesulfonyl halides

• Malcolm J. D’Souza and
• Dennis N. Kevill

Beilstein J. Org. Chem. 2022, 18, 120–132, doi:10.3762/bjoc.18.13

• proceed in an alcoholysis reaction through a cyclic structure involving three molecules of the alcohol and the sulfur of the sulfonyl chloride present in the ring [52]. One would predict that such an extremely ordered pathway would have a very negative entropy of activation, but the required studies with

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

• solvation of the polymer chains (T > UCST). Compared to an entropy-driven LCST behavior of polymers, the enthalpy-driven UCST thermoresponse is based on spatially highly directed forces between polymer segments [51][52][54][55]. Understanding the molecular mechanism and thus precisely controlling the

• processes in general, and the mixing processes discussed here, has been thermodynamically formulated. Mathematically, this description results in the Gibbs energy of mixing ΔmG, which is linked to the enthalpy of mixing ∆mH and the entropy of mixing ∆mS via the following well-known connection: This means

• obtain for the entropy of mixing: Thus, the driving force of the mixing process is the increase in disorder due to the mixing of the particles of both species. ∆mG is therefore always negative for ideal mixtures of any composition with a minimum at a certain ratio A–B and is always smaller than the Gibbs

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• involving PNA usually follow the order PNA–PNA > PNA–RNA > PNA–DNA [20][21]. Hybridization of PNA with complementary nucleic acids is enthalpy driven, involving large favorable gains in enthalpy compensated by significant unfavorable entropy, as typically observed for nucleic acid complexes [22]. The

• (Figure 2B). An innovative design links the two ends together with an ethylene glycol linker (Figure 2C), which reduced the unfavorable loss of entropy by converting the binding event from a trimolecular to a bimolecular process [34][35][36]. The new bis-PNAs (Figure 2C) showed about two orders of

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

• + modifications led to the formation of duplexes with a thermal stability that was less dependent on the ionic strength than native DNA duplexes. The thermodynamic analysis of the melting curves revealed that it is the reduction in unfavourable entropy, despite the decrease in favourable enthalpy, which is

• deprived by an even higher entropy penalty leading to a loss in ΔG (ΔΔG298 = 33 kJ/mol), thus lowering the Tm value at 25 mM NaCl. For the unmodified RNA duplex (ON1/ON19), ΔΔH between 25 mM and 100 mM NaCl is 84 kJ/mol, and the corresponding entopic factor Δ(TΔS) is 84 kJ/mol. As a result, changes in

• was more favourable. According to Kuo et al. [37], an increase in the salt concentration stabilises the DNA duplex by reducing the entropy costs of duplex formation rather than by reducing the strand charge repulsion. This reduction of entropy costs for duplex formation is due to the endothermic

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

• interactions and secondary interactions such as π–π stacking [34][35][36][37][38][39][40]. The size and shape could be tuned through the free energy and the enthalpy/entropy interplay in the assembly process, which again are encoded in the molecular building block structure [31][37]. Supramolecular structures

• binding constants Kx, which are related to the free energy change ΔG and thus due to ΔG = ΔH − TΔS, also the entropy change ΔS is revealed. Table 5 summarizes the results from the full titration curve fitting. The values correlate to the binding of one monomer of the polymer to Flavy and/or photoacid. For

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• various main factors, such as the percentage of the host occupancy, the temperature, and the solvent but not on the entropy of the system. In continuation of their previous work, Inoue, Yang, et al. reported an alternative approach so that the chiral slipped 5,8:9',10'-cyclodimers 14 and 15 were

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

• methods are used to characterise the protein complex and to confirm the presence of certain interactions. Biophysical approaches are important to determine binding affinities, enthalpy changes, entropy changes, and the on- and off-rates of binding, amongst others. Examples include surface plasmon

• thermodynamic properties, including the binding constant Kb, the reaction stoichiometry (n), the observed molar calorimetric enthalpy ΔHobs, the entropy ΔS, the heat capacity of the binding ΔCp,obs, and the change in the Gibbs free energy ΔG. As a result, ITC is used to provide a complete thermodynamic

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• rotamers in hand, an Eyring plot was generated, and the enthalpy and entropy of activation were derived (Table 2). The structural identification of the major and minor rotamers was not attempted by NMR, but in silico investigations of 3a supported the intuitive notion that the rotamer of lower energy was

• , the enhanced imbalance in the population of the rotamers of 6a is notable and consistent with the amino moiety imposing a greater steric hindrance. The differences among the other compounds are more modest. The small entropy of activation is consistent with a simple rotation over a steric barrier

• tetrakis(trifluoromethyl)-1,3-dithietane (1) with compounds 2–7. Reaction products, conditions, yield, ratio of isomers, and melting points for the new materials. Enthalpy and entropy of activation for the rotameric interconversion of a subset of hexafluoroisopropyl azoles. NMR and MS data for the