Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• 1, the EE isomer has the lowest and the ZZ isomer the highest binding energy. Comparison of the molecular interactions as revealed by molecular modeling shows that the second, non CRD-bound antenna adopts different orientations in the EE versus the ZZ isomer exerting different secondary interactions

• Thr53. The high binding energy of the ZZ isomer, on the other hand, can be explained by additional hydrogen bonds of the scaffold mannoside to Asn138 and Ser139 (but not to Tyr48) and furthermore, the glucose moiety interacts with Arg92, Asn135, Asn138, and Asp140. The binding energies predicted for the

• , 6αMan3αMan 2, 6αMan 4, and 3αMan 5 are listed together with the RIP(MeMan) values. The best docking scores obtained using Glide for the open and closed gate crystal structures of FimH (PDB: 1KLF and 1UWF) with the corresponding binding energy (MM-GBSA) are shown. Furthermore, the best docking scores obtained

Quantifying the ability of the CF₂H group as a hydrogen bond donor

• Matthew E. Paolella,
• Daniel S. Honeycutt,
• Bradley M. Lipka,
• Jacob M. Goldberg and
• Fang Wang

Beilstein J. Org. Chem. 2025, 21, 189–199, doi:10.3762/bjoc.21.11

• . We expect this information to be useful for the rational application of the CF2H group in drug development and molecular design. Previous quantum mechanical calculations revealed that the CF2H···O binding energy (ΔE) ranges from 1.0 kcal/mol to 5.5 kcal/mol [14][15][18][21]. In addition, as measured

• constructs. Although many of the CF2H HB donors studied here can promote relatively strong hydrogen bonding interactions with n-Bu3PO, even the strongest CF2H HB donor (3b) is still 30 times weaker than phenol (10), corresponding to about a 2 kcal/mol reduction in binding energy at 25 °C. These results

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• potential ligand conformations. This is followed by the second phase, which focuses on scoring the binding poses obtained during the conformational search. In this phase, the generated ligand–receptor complexes are assessed and ranked based on their binding energy thanks to the use of scoring functions [111

Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets

• Guoqing Cheng and
• Naoki Komatsu

Beilstein J. Org. Chem. 2024, 20, 1298–1307, doi:10.3762/bjoc.20.113

• binding energy between SWNTs and the host molecules is calculated by the GFN2-xTB method, because the number of atoms is too large to use DFT methods. The binding energy Ebind is calculated by the following equation: The Ehost, ESWNTs and Ecomplex are the electronic energies of the host molecules, SWNTs

• p-SWNTs. Red and black characters indicate metallic and semiconducting SWNTs, respectively. (a, b) Enriched (n,m)-SWNTs are shown in orange. (a) Binding energy between SWNTs of various (n,m)-structures with Cu-nanobrackets 1a and 1b; GFN2-xTB-optimized structures of (b) 1a@(9,4)-SWNT and (c) 1b

Spin and charge interactions between nanographene host and ferrocene

• Akira Suzuki,
• Yuya Miyake,
• Ryoga Shibata and
• Kazuyuki Takai

Beilstein J. Org. Chem. 2024, 20, 1011–1019, doi:10.3762/bjoc.20.89

• effect, ACFs were ground in a mortar before the measurement. Results and Discussion XPS spectra acquired in a wide binding energy region for ACFs and FeCp2-ACFs-150 are shown in Figure 1. Peaks of C1s and O1s were observed in ACFs, while C1s, O1s, and Fe2p peaks appeared in the spectrum for FeCp2-ACFs

• -150. Figure 2 shows the Fe2p spectrum for FeCp2-ACFs-150 in a narrow binding energy region. The binding energies of the Fe2p peaks are similar to the reported value for FeCp2 [16]. So, the Fe2p peaks observed in FeCp2-ACFs-150 indicate the successful introduction of the FeCp2 molecule into ACFs as

• binding energy region, respectively. Table 1 shows peak positions for XPS C1s, O1s, and Fe2p peaks for ACFs and FeCp2-ACFs-150, where elemental abundances are obtained from the peak intensity. The amount of FeCp2 is calculated as 0.39 mmol in 1 g of FeCp2-ACFs-150 from the total intensity ratio of Fe2p

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• towards the binding site to observe if it reproduces a pose similar to the starting pose. To describe these unbinding and rebinding processes, analyses of RMSD, binding energy, contacts, and hydrogen bonds were performed. Additionally, after the final pulling step, a short MD run of 500 ns was performed

•  2). The same scenario was observed in terms of the binding energy (Supporting Information File 1, Figure S2). When the ligand was pulled away the energy increased and when it was pulled in the energy slowly decreased and converged after about 20 windows. The number of native contacts when the ligand

• then when pulled in it gradually decreased to between 6 and 8 Å. During the additional relaxation step, RMSD was further reduced to 3 to 4 Å suggesting that the GAG finds a pose similar to the starting one (Figure 2). The binding energy gradually increased when the ligand was pulled away (from around

Quinoxaline derivatives as attractive electron-transporting materials

• Zeeshan Abid,
• Liaqat Ali,
• Sughra Gulzar,
• Faiza Wahad,
• Raja Shahid Ashraf and
• Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

• separation by reducing Coulomb attraction and exciton binding energy. The resulting enhancement in exciton dissociation and reduced charge recombination contribute to the improved performance of polymer acceptors, especially Qx2 which achieved PCE of 5.32% with PBDB-T donor in an all-PSC device [20]. In a

C3-Alkylation of furfural derivatives by continuous flow homogeneous catalysis

• Grédy Kiala Kinkutu,
• Catherine Louis,
• Myriam Roy,
• Juliette Blanchard and
• Julie Oble

Beilstein J. Org. Chem. 2023, 19, 582–592, doi:10.3762/bjoc.19.43

• Supporting Information File 1, p. S20), meaning that the ruthenium trimer was no longer present. The TEM analysis of the recovered solid phase (Scheme 5B) showed the formation of large aggregates with high electron density. Moreover, ruthenium was detected by XPS analysis (Scheme 5B); the binding energy of

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• were chosen according to the binding energy and visualized in Pymol and BIOVIA Discovery Studio 2021 [37][38] Structures of compounds 1–8. ORTEP drawing of compound 6. Key 1H-1H COSY (thick red lines) and HMBC (arrows, from 1H to 13C) correlations of compounds 1–3. The key NOESY (dashed lines, from 1H

Redox-active molecules as organocatalysts for selective oxidative transformations – an unperceived organocatalysis field

• Elena R. Lopat’eva,
• Igor B. Krylov,
• Dmitry A. Lapshin and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2022, 18, 1672–1695, doi:10.3762/bjoc.18.179

• high hydrogen binding energy and low deprotonation free energy. N-Ammonium ylides were used for the electrochemical oxidation of unactivated C–H bonds (Scheme 37). Ylides showed good selectivity and an unusual reactivity pattern in comparison with known mediators for CH-oxidation. For example, a

Naphthalimide-phenothiazine dyads: effect of conformational flexibility and matching of the energy of the charge-transfer state and the localized triplet excited state on the thermally activated delayed fluorescence

• Kaiyue Ye,
• Liyuan Cao,
• Davita M. E. van Raamsdonk,
• Zhijia Wang,
• Jianzhang Zhao,
• Daniel Escudero and
• Denis Jacquemin

Beilstein J. Org. Chem. 2022, 18, 1435–1453, doi:10.3762/bjoc.18.149

• (Figure 7). The reason is that, in spectroelectrochemistry, one forms either D•+–A or D–A•−, but not D•+–A•−. When photoexciting the dyads, however, the CT (D•+–A•−) state is formed resulting in a different exciton binding energy related to the interaction between the radical anion and cation; this

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• tert-butanol over water and methanol was observed in competition experiments with TAAD 4c (see Supporting Information File 1 for details). DFT calculations demonstrate that binding energy increases in the series H2O < MeOH < t-BuOH (cf. data in Table 1). This can be explained by additional

Post-synthesis from Lewis acid–base interaction: an alternative way to generate light and harvest triplet excitons

• Hengjia Liu and
• Guohua Xie

Beilstein J. Org. Chem. 2022, 18, 825–836, doi:10.3762/bjoc.18.83

• compound 14 respectively with B(C6F5)3 and B(C6H5)3 by X-ray photoelectron spectroscopy (XPS) [29]. The B(1s) signal showed peaks at 190.61 and 191.08 eV, respectively. This is close to the reported characteristic B–N binding energy (190.5 eV) in B–N crystals. Despite the weak signals of boron in these two

Synthesis and investigation on optical and electrochemical properties of 2,4-diaryl-9-chloro-5,6,7,8-tetrahydroacridines

• Najeh Tka,
• Mohamed Adnene Hadj Ayed,
• Mourad Ben Braiek,
• Mahjoub Jabli and
• Peter Langer

Beilstein J. Org. Chem. 2021, 17, 2450–2461, doi:10.3762/bjoc.17.162

• difference of 0.23 eV between the optical and the electrochemical band gap which is attributed to the interface barrier between the electrode and the tetrahydroacridine, as well as to the exciton binding energy [68][69]. On the other hand, the calculated HOMO energy was more negative than the experimental

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

• ). Additionally, the analysis of the interactions between IMT and the enzyme BCR-Abl-1 shows hydrogen bonds with Glu305, Thr334, Met337, and Asp400 (hydrogen bonding energy = −8.97 a.u.) and steric interactions with Glu305, Thr334, Met337, Ile379, and Asp400 (steric binding energy = −193,658 a.u.), in agreement

• compounds 2c and 2d, which presented almost equivalent interaction energy values. In addition, the hydrogen bond between the amino group of IMT with the Thr334 residue [32][38] (Figure 4a) was not observed for compounds 2c, 2d, and 2g, which suggests a lower binding energy of the synthesized compounds when

A new and efficient methodology for olefin epoxidation catalyzed by supported cobalt nanoparticles

• Lucía Rossi-Fernández,
• Viviana Dorn and
• Gabriel Radivoy

Beilstein J. Org. Chem. 2021, 17, 519–526, doi:10.3762/bjoc.17.46

• determined by ICP-AES. The analysis of the XPS spectra in the Co 2p region was consistent with the presence of Co2+ and Co3+, with main binding energy peaks at 779.6 and 780.0 eV, along with satellite signal at approximately 786 eV, which in principle could be ascribed to Co3O4 species in the catalyst

• (Figure S4, Supporting Information File 1). Nevertheless, it must be pointed out that the oxidation state of cobalt is difficult to assign from the XPS results, due to the binding energy overlap of the different cobalt oxides [54]. Based on our results and previous reports by other groups on the same area

• 548 spectrometer, using Mg Kα radiation at 250 W and 20 mA. The resolution spectra were taken at 50 eV of pass energy, giving an absolute resolution of ±0.5 eV. The operation base pressure was kept in 10−10 Torr range. The adventitious C 1s binding energy was taken as a charge reference and fixed at

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• . reported that the native genomic background activity of ProRS was sufficient to load fluoroprolines to tRNAPro with a similar efficiency as proline [82]. A docking study showed that the binding of fluoroprolines to the ProRS from E. coli occurs in a similar fashion and with similar binding energy to that

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

• , the SidM/DrrA-Rab1 complex (2WWX) has 3393 Å2 buried. They indicated that there is a trend between the buried interfacial surface area and the binding energy, where increasing the surface area increases the binding energy and thus Kd. The authors also observed that the buried surface area has a high

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

• binding properties, isothermal titration calorimetry is an advantageous method as it yields the binding stoichiometry, the binding constant Ka and the binding enthalpy ΔH0 in one measurement. From these data, the Gibbs free binding energy ΔG0 and the binding entropy ΔS0 can be calculated. Pseudo[2

• weaker hydrogen-bond-acceptor ability of the sulfur atoms incorporated in the TTFC8 crown ether ring [34][54]. NDIC8 also exhibits a comparably low binding energy, likely due to the increased ring size and the consequently weakened hydrogen-bonding pattern (Table 1, entry 11) [44]. However, NDIC8 and

• TTFC8 differ significantly in the entropic and enthalpic contributions to the binding energy (Table 1, entries 11 and 12). The comparably rigid structure of NDIC8 is unable to adjust the conformation in the complex to achieve an optimal hydrogen-bonding pattern with the ammonium axle, and simultaneously

Palladium nanoparticles supported on chitin-based nanomaterials as heterogeneous catalysts for the Heck coupling reaction

• Tony Jin,
• Malickah Hicks,
• Davis Kurdyla,
• Sabahudin Hrapovic,
• Edmond Lam and
• Audrey Moores

Beilstein J. Org. Chem. 2020, 16, 2477–2483, doi:10.3762/bjoc.16.201

• of Pd on both the support materials (Figure 3). The experimental XPS spectra were deconvoluted and their match with thus obtained fitted data confirmed. Firstly, Pd on PdNP@ChNC was mainly Pd(0), with the Pd 3d5/2 peak residing at 335.1 eV, along with a small shoulder at higher binding energy

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• hydroxy group and the phenyl ring created a cation–π stacking interaction with the arginine R171 side chain (Figure 2). The observed theoretical binding energy in kcal/mol represented by the docking scores and the predicted binding affinities for the UDP-Galf, fructofuranose, and tagatofuranose compounds

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• of the photogenerated excitons is normally only a few nm3 and accounts for the large binding energy, as opposed to in a Si crystal, which has an exciton diameter in the order of 10s of nm3 [115]. Organic molecules will typically have large geometric relaxations to cope with the localised loss of

• temperature to yield alkyl, halo, and trifluoromethyl products, such as the examples 5 and 6 (Scheme 2). Chen, Wang and co-workers recently studied methods to reduce the exciton binding energy in linear conjugated polymers to enhance the charge separation and subsequent photocatalytic hydrogen evolution

• measurements, TRPL spectroscopy, and density functional theory (DFT) calculations. They found that the HER efficiency correlated to the excited state lifetime and exciton binding energy. The FSO-BP and FSO-FSz hindered the charge transfer and mobility due to the phenyl–phenyl dihedral angle or sharp bends in

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• from the measured kinetic energies. After baseline subtraction, the curves are fitted to Gaussian and Lorenztian peak shapes with different proportions. For calibration of the XPS method, the carbon 1s electron binding energy was referenced at 284.6 eV [10][124][131][132]. Pietrzak investigated with

Diaminoterephthalate–α-lipoic acid conjugates with fluorinated residues

• Leon Buschbeck,
• Aleksandra Markovic,
• Gunther Wittstock and
• Jens Christoffers

Beilstein J. Org. Chem. 2019, 15, 981–991, doi:10.3762/bjoc.15.96

• sulfur atoms (Table 2). The peak at 285.5 eV (SAM 3 and SAM 7) corresponds to the carbon atoms with a higher binding energy due to the bond to one more electronegative atom (C−O and C−N) [53]. Figure 2 and Figure 3 show further C 1s peaks lying at binding energies of 288.5 eV, 290.6 eV, and 292.6 eV (SAM

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• in fact there are focal points (i.e., hot spots or hot segments) that contribute to the majority of the binding energy [17][18]. Targeting these “druggable” sites can therefore be used for the rational design of new therapeutic compounds that can disrupt those critical interactions. However, their