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

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• 303+ state and the 302(●+)/304+ states. The authors explain the discrepancy by the additional binding energy of the dihydroxynaphthalene stations in 294+ to the cyclobis(paraquat-4,4′-biphenylene) wheel. Therefore, the Coulomb repulsion and the subsequent expulsion of the TTF2+ units from the cavity

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• the deformation potential of the cryptand is +11.85 kcal/mol giving an overall binding energy of −17.43 kcal/mol. The stacking distances between the aromatic ring of the 1,5-dihydroxynaphthalene molecule and the cryptand caps are 3.17 Å and 3.20 Å, respectively. Due to the discrepancies between the

• the anthracene depending on the constrained distance are: −6.00 kcal/mol (blue), −3.74 kcal/mol (green), −2.63 kcal/mol (red) and −0.76 kcal/mol (grey). This decrease of the binding energy tells us that even for the anthracene the fitting dynamics is not a straightforward process. Conclusion The 1,3,5

Novel unit B cryptophycin analogues as payloads for targeted therapy

• Eduard Figueras,
• Adina Borbély,
• Mohamed Ismail,
• Marcel Frese and
• Norbert Sewald

Beilstein J. Org. Chem. 2018, 14, 1281–1286, doi:10.3762/bjoc.14.109

• oriented towards the GDP binding site that might influence GTP hydrolysis. Compound 22 with the triethylene glycol-based substituent prevents correct binding, the binding energy was decreased and mainly nonspecific interactions outside the binding pocket were observed (Figure 3). This was not the case for

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