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

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• concepts to their own scaffolds of interest. Review 1 Alkanes The simplest organic scaffolds are the alkanes. In such molecules, C–C bond rotations often have low energy barriers, and they often deliver conformers that are similar in energy, and this means that many alkanes have considerable conformational

• this hyperconjugative stabilisation, and it is ≈1 kcal·mol−1 higher in energy. Thus, we now have a situation where the fluorinated structural motif is not a passive chameleon as was seen above for the 1,1-difluoro pattern, but rather it exerts its own conformational character [21]. The 1,2-difluoro

• offer interesting opportunities and challenges in terms of conformational control. For example, consider cyclododecane (35, Figure 5). This molecule has a global minimum energy conformation that features a square shape, but this conformation suffers from steric clashes between 1,4-pairs of hydrogen

Photochemically assisted synthesis of phenacenes fluorinated at the terminal benzene rings and their electronic spectra

• Yuuki Ishii,
• Minoru Yamaji,
• Fumito Tani,
• Kenta Goto,
• Yoshihiro Kubozono and
• Hideki Okamoto

Beilstein J. Org. Chem. 2025, 21, 670–679, doi:10.3762/bjoc.21.53

• aromatics [53]. Figure 5 shows the molecular orbitals (MOs) around the frontier MO levels and the eigenvalues. The shapes (symmetries) and the energy-level order of the MOs in the F8-phenacenes are the same as those of the corresponding parent phenacenes. It is characteristic that, upon the fluorination

• , the MO levels systematically lowered by 0.7–0.8 eV compared to the parent phenacenes, and that the energy gaps and the symmetry of the MOs are little affected by the fluorination. Accordingly, the electronic spectral behavior of the F8-phenacenes is essentially the same as that of the parent

• that, through the fluorination, one can tune the MO energy levels without changing the apparent electronic spectral features in solution, such as, electronic spectral shapes, wavelengths, and fluorescence quantum yields. Such fluorine-substitution effects on electronic spectra and MO levels were

Asymmetric synthesis of fluorinated derivatives of aromatic and γ-branched amino acids via a chiral Ni(II) complex

• Maurizio Iannuzzi,
• Thomas Hohmann,
• Michael Dyrks,
• Kilian Haoues,
• Katarzyna Salamon-Krokosz and
• Beate Koksch

Beilstein J. Org. Chem. 2025, 21, 659–669, doi:10.3762/bjoc.21.52

• (HREIMS) were measured on a MAT 711 (Varian MAT, Bremen, Germany). Electron energy for EI was set to 70 eV. Infrared spectra (IR) were measured on an ALPHA II (Bruker, Billerica, USA) spectrometer. Characteristic absorption bands are given in wave numbers (cm−1). Qualitative thin-layer chromatography (TLC

Recent advances in allylation of chiral secondary alkylcopper species

• Minjae Kim,
• Gwanggyun Kim,
• Doyoon Kim,
• Jun Hee Lee and
• Seung Hwan Cho

Beilstein J. Org. Chem. 2025, 21, 639–658, doi:10.3762/bjoc.21.51

• ligand L3 and the allylic electrophile 35. In contrast, a si-face attack leads to a higher-energy transition state due to significant steric repulsion. Enantioselective hydroallylation of vinyltrifluoromethyl compounds The direct functionalization of 1-trifluoromethylalkenes 38 through copper catalysis

• transition states: an open transition state TS7 facilitated by LiOt-Bu and a closed transition state TS6 without base assistance (Scheme 17a). The significant energy difference between these pathways (ΔΔG‡ = 4.3 kcal/mol) strongly favors the open transition state TS7 mechanism, attributed to reduced steric

• , computational density functional theory calculations were performed focusing on the oxidative addition transition states (S,R)-TS8 and (S,S)-TS9 (Scheme 19b). The theoretical analysis revealed a notable energy difference between these diastereomeric transition states, with (S,R)-TS8 being 4.11 kcal/mol lower in

Entry to 2-aminoprolines via electrochemical decarboxylative amidation of N‑acetylamino malonic acid monoesters

• Olesja Koleda,
• Janis Sadauskis,
• Darja Antonenko,
• Edvards Janis Treijs,
• Raivis Davis Steberis and
• Edgars Suna

Beilstein J. Org. Chem. 2025, 21, 630–638, doi:10.3762/bjoc.21.50

• observed by LC–MS when the electrolysis was performed in 5:1 MeCN/D2O (Scheme 2, reaction 2). The considerably higher O–H bond dissociation energy (119 kcal/mol) [12] as compared to that of the C–H bond in MeCN (86 kcal/mol) [13] renders the hydrogen atom abstraction from water by a carbon-centered radical

Photocatalyzed elaboration of antibody-based bioconjugates

• Marine Le Stum,
• Eugénie Romero and
• Gary A. Molander

Beilstein J. Org. Chem. 2025, 21, 616–629, doi:10.3762/bjoc.21.49

• the agency of low-energy visible light with specific functional groups on biomolecules. This allows precise control over the conjugation process, enabling targeted modifications without affecting non-reactive sites. Although previous reviews have discussed the more traditional synthetic methods

• catalysts, including photoredox catalysts, energy-transfer catalysts, and genetically encoded photocatalysts, highlighting their distinct features, mechanisms, applications, and prospects [41]. This thorough analysis showcased the promising advancements in the chemical modification of proteins. As this

• oxygen [42]. Through energy transfer (EnT) from the ruthenium-based photocatalyst to triplet oxygen, singlet oxygen is produced in a targeted manner, which oxidizes histidine to an endoperoxide, significantly increasing its reactivity toward nucleophiles (Figure 4A). This strategy employs a

Sequential two-step, one-pot microwave-assisted Urech synthesis of 5-monosubstituted hydantoins from L-amino acids in water

• Wei-Jin Chang,
• Sook Yee Liew,
• Thomas Kurz and
• Siow-Ping Tan

Beilstein J. Org. Chem. 2025, 21, 596–600, doi:10.3762/bjoc.21.46

• . Additionally, the reaction proceeds efficiently without the need for toxic or moisture-sensitive reagents, further making it suitable for large-scale applications. The shorter reaction time (less than 2 hours) also contributes to improve energy efficiency when compared to traditional methods. These factors

Deep-blue emitting 9,10-bis(perfluorobenzyl)anthracene

• Long K. San,
• Sebastian Balser,
• Brian J. Reeves,
• Tyler T. Clikeman,
• Yu-Sheng Chen,
• Steven H. Strauss and
• Olga V. Boltalina

Beilstein J. Org. Chem. 2025, 21, 515–525, doi:10.3762/bjoc.21.39

• Reineke for preliminary experiments on photoluminescence lifetimes. Part of the experimental work is based on doctoral theses of Dr. Long San [40] and Dr. Brian Reeves [41]. Funding We thank National Science Foundation (grant NSF/CHE-2153922 (O.V.B.), the Office of Basic Energy Sciences, and the Colorado

• State University Research Foundation for partial financial support. the Office of Basic Energy Sciences, and the Colorado State University Research Foundation for partial financial support. NSF’s ChemMatCARS Sector 15 is principally supported by the National Science Foundation under grant number NSF/CHE

• -1834750 and NSF/CHE-2335833. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science, and Office of Basic Energy Sciences under Contract DE-AC02-06CH11357.

Unprecedented visible light-initiated topochemical [2 + 2] cycloaddition in a functionalized bimane dye

• Metodej Dvoracek,
• Brendan Twamley,
• Mathias O. Senge and
• Mikhail A. Filatov

Beilstein J. Org. Chem. 2025, 21, 500–509, doi:10.3762/bjoc.21.37

• crystal lattice and are often reversible, requiring either high-energy light or heat for initiation [6][7][8]. Notably, topochemical polymerizations align with the principles of green chemistry, as they are solvent-free and do not involve toxic reagents [9]. The highly ordered and uniform nature of

Photomechanochemistry: harnessing mechanical forces to enhance photochemical reactions

• Francesco Mele,
• Ana M. Constantin,
• Andrea Porcheddu,
• Raimondo Maggi,
• Giovanni Maestri,
• Nicola Della Ca’ and
• Luca Capaldo

Beilstein J. Org. Chem. 2025, 21, 458–472, doi:10.3762/bjoc.21.33

• Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy 10.3762/bjoc.21.33 Abstract Photomechanochemistry, i.e., the merger of light energy and mechanical forces, is emerging as a new trend in organic synthesis, enabling unique reactivities of fleeting excited states under solvent

• rearrangements. Most organic molecules are colorless and, in fact, do not absorb visible light: highly energetic UV irradiation is typically needed. A milder approach is offered by photocatalytic approaches. Here, a photocatalyst is added to the reaction mixture to convert light energy into chemical potential to

• transform molecules. Intriguingly, photocatalysts typically absorb harmless visible light and can be chosen ad hoc to trigger the desired chemistry. Indeed, the photocatalyst–substrate interaction can occur via energy transfer [4][5][6][7][8], single-electron transfer [9][10][11][12], or hydrogen-atom

New tandem Ugi/intramolecular Diels–Alder reaction based on vinylfuran and 1,3-butadienylfuran derivatives

• Yuriy I. Horak,
• Roman Z. Lytvyn,
• Andrii R. Vakhula,
• Yuriy V. Homza,
• Nazariy T. Pokhodylo and
• Mykola D. Obushak

Beilstein J. Org. Chem. 2025, 21, 444–450, doi:10.3762/bjoc.21.31

• yields. The studied tandem Ugi and intramolecular Diels–Alder reactions allow high substituent variation in the named isoindoles. Keywords: 1,3-butadienylfuran; furo[2,3-f]isoindole; intramolecular Diels–Alder reaction; isoindole; one-pot; Ugi reaction; vinylfuran; Introduction Energy-saving and

Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• therefore can be subjected to automated and high-throughput crystallization studies and, with Szczypiński, Slater, Cooper and co-workers, we were able to isolate all five calculated lowest-energy conformers of cage 1 in the solid state (see crystal cavity heights marked under conformers in Figure 9A) [40

• free energy transition barrier can be framed in terms of contributions from polarization and organization by the catalyst/system. Typical catalysis modes using macrocycle cavities performing (non-specific) hydrophobic substrate binding. (A) Macrocycles that confine two reagents close together to alter

Unraveling aromaticity: the dual worlds of pyrazole, pyrazoline, and 3D carborane

• Zahra Noori,
• Miquel Solà,
• Clara Viñas,
• Francesc Teixidor and
• Jordi Poater

Beilstein J. Org. Chem. 2025, 21, 412–420, doi:10.3762/bjoc.21.29

• a Kohn–Sham molecular orbital analysis together with an energy decomposition analysis (Figure S1 in Supporting Information File 1). To form the broken bonds, both fragments have two unpaired electrons (at their triplet state). The interaction between both fragments amounts to −227.9 kcal mol−1

• -pyrazoline (13.0 kcal mol−1 higher in energy). Also in this case, the five-membered rings are clearly confirmed to be non-aromatic (Figure 4). Conclusion In this work, we have quantum chemically analyzed a series of o-carborane-fused pyrazoles that have been recently synthesized, and whose fusion was

• , the energy decomposition analysis has been performed at the ZORA-BLYP-D3(BJ)/TZ2P level of theory with AMS software [81][82][83][84]. Series o-carborane-fused pyrazoles under analysis. Bond lengths (in Å) of systems under analysis (top row) and reference systems (second and third rows) from the fusion

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

• ], cosmetics, and detergents. Carbohydrates are the most abundant and versatile renewable sources of energy on earth. However, extraction of naturally occurring complex glycans from natural sources is a laborious and cumbersome task. Moreover, the isolated samples provide a low-yield heterogenous mixture of

• pathway. The benchmark for the SN1 spectrum of the mechanistic continuum has been elaborately illustrated and supported by Codee et al. by mapping full ensemble of conformations that the glycosyl oxocarbenium ions can adopt by a complete conformational energy landscape (CEL) study in a quantitative manner

Synthesis, structure, ionochromic and cytotoxic properties of new 2-(indolin-2-yl)-1,3-tropolones

• Yurii A. Sayapin,
• Eugeny A. Gusakov,
• Inna O. Tupaeva,
• Alexander D. Dubonosov,
• Igor V. Dorogan,
• Valery V. Tkachev,
• Anna S. Goncharova,
• Gennady V. Shilov,
• Natalia S. Kuznetsova,
• Svetlana Y. Filippova,
• Tatyana A. Krasnikova,
• Yanis A. Boumber,
• Alexey Y. Maksimov,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2025, 21, 358–368, doi:10.3762/bjoc.21.26

• (Scheme 2). The structures of tautomeric forms of 7a, 7b, 8a, 8b and their energy characteristics were calculated by PBE0/6-311+G(d,p) method in the gas phase and polar solvent (DMSO) (Table 1, Figure 1 and Supporting Information File 3). According to the obtained data, the (NH) isomers of 7 and 8 are

• studied compounds. The difference in the energy characteristics of the (NH) and (OH) tautomeric forms of compounds 7a, 7b, 8a, and 8b in the polar solvent and the gas phase is small (2.0–3.8 kcal/mol), and probably the nature of the solvent can influence the shift of the equilibrium towards one of the

• energies with zero-point energy correction (Etot + ZPE, a.u.) and relative energies (ΔE, kcal/mol) of (NH) and (OH) isomers of compounds 7 and 8 calculated by the PBE0/6-311+G(d,p) method in the gas phase (gas) and DMSO solution (sol). Absorption and fluorescence spectral data of compounds 7a,b and 8a,b in

Synthesis of new condensed naphthoquinone, pyran and pyrimidine furancarboxylates

• Kirill A. Gomonov,
• Vasilii V. Pelipko,
• Igor A. Litvinov,
• Ilya A. Pilipenko,
• Anna M. Stepanova,
• Nikolai A. Lapatin,
• Ruslan I. Baichurin and
• Sergei V. Makarenko

Beilstein J. Org. Chem. 2025, 21, 340–347, doi:10.3762/bjoc.21.24

• furan-3-carboxylates 6c,d. It was shown that the increased number of conjugated bonds in their molecules leads to a decrease in the energy of the singlet–singlet π→π* transition and the possibility of exhibiting luminescence of the molecules under study. According to the luminescence excitation spectral

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• on forces and step size. The IEFPCM solvent model [33] was used to simulate the solvent effects of methanol and frequency calculations were used to determine the conformers as minima. Conformers 4.5 kcal/mol above the lowest energy conformer and double conformers were discarded. Time-dependent DFT

Red light excitation: illuminating photocatalysis in a new spectrum

• Lucas Fortier,
• Corentin Lefebvre and
• Norbert Hoffmann

Beilstein J. Org. Chem. 2025, 21, 296–326, doi:10.3762/bjoc.21.22

• become a powerful approach for achieving sustainable chemical transformations, combining high efficiency with energy-saving, mild conditions. By harnessing the deeper penetration and selectivity of red and near-infrared light, this method minimizes the side reactions typical of higher-energy sources

• driving chemical transformations under mild and efficient conditions. The use of red and near-infrared light enables deeper penetration into reaction media, reducing the high-energy side reactions commonly triggered by UV or blue light. These features make red-light photocatalysis particularly

• diverse catalyst types and applications. The first section is dedicated to metal-based photocatalysts. Complexes involving metals such as osmium and ruthenium, have dominated red-light photoredox catalysis because of their ability to absorb low-energy photons and sustain redox cycles via stable excited

Oxidation of [3]naphthylenes to cations and dications converts local paratropicity into global diatropicity

• Abel Cárdenas,
• Zexin Jin,
• Yong Ni,
• Jishan Wu,
• Yan Xia,
• Francisco Javier Ramírez and
• Juan Casado

Beilstein J. Org. Chem. 2025, 21, 277–285, doi:10.3762/bjoc.21.20

• attracted a growing interest in recent times, both from fundamental and technological reasons [9][10][11]. Antiaromaticity destabilizes the ground state of organic molecules by raising their highest energy occupied molecular orbitals, thus allowing for easy oxidation, doping, and electron-transfer reactions

• peaks, at 0.67 and 1.16 V, were clearly resolved for the linear oligomer 1. For the angular molecule 2, two partially overlapped one-electron peaks appeared at noticeably lower voltages, 0.28 and 0.44 V. This result reflects the higher energy lying HOMO (and easy of oxidation) and stronger overall

• is using energetic parameters unequivocally associated to individual bonds. This is the case of the vibrational force constants [22]. They are defined as the second derivative of the molecular energy, in the minimum energy molecular structure, with respect to the nuclear displacement coordinates

Synthesis and characterizations of highly luminescent 5-isopropoxybenzo[rst]pentaphene

• Islam S. Marae,
• Jingyun Tan,
• Rengo Yoshioka,
• Zakaria Ziadi,
• Eugene Khaskin,
• Serhii Vasylevskyi,
• Ryota Kabe,
• Xiushang Xu and
• Akimitsu Narita

Beilstein J. Org. Chem. 2025, 21, 270–276, doi:10.3762/bjoc.21.19

• -substituted derivatives [21][22]. In comparison to the absorption spectrum of BPP 2, this lowest-energy absorption band of BPP-OiPr 3 was red-shifted by ≈26 nm, which marked the inductive and resonance effects of the electron-donating isopropyloxy group with lone pairs of electrons, raising the HOMO level

• transitions as previously discussed for other BPP derivatives [21][22], the strikingly enhanced molar extinction coefficient observed for the lowest-energy band of BPP-dione 4 (ε = 17000 M−1 cm−1) indicates that the optical transition to the S1 state becomes allowed by this oxidation. BPP 2 and BPP-OiPr 3

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

• , various application examples of molecular photoswitches have been reported so far including volumetric 3D printing [12][13], photoresponsive semiconductors [14][15][16][17], photopharmacology [18][19], energy storage materials [20][21][22][23], data storage materials [24], super-resolution microscopy [25

• theory in combination with the 6-31G(d) basis set well reproduces the experimental value of the activation energy for the thermal back reaction of various diarylbenzenes, resulting in the accurate prediction of the half-lifte time [58][63]. Thus, the combination of experiments and theoretical

• 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

Heteroannulations of cyanoacetamide-based MCR scaffolds utilizing formamide

• Marios Zingiridis,
• Danae Papachristodoulou,
• Despoina Menegaki,
• Konstantinos G. Froudas and
• Constantinos G. Neochoritis

Beilstein J. Org. Chem. 2025, 21, 217–225, doi:10.3762/bjoc.21.13

• Goals (SDGs), wherein the 7th goal focuses on ensuring access to affordable, renewable and clean energy [1]. Moreover, the European Union has committed to ambitious environmental targets as part of the European Green Deal [2]. Advancements in C1 chemistry are pivotal to achieving this equilibrium. As

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

• , with other easily accessible parameters. We first calculated the Gibbs free energy of formation (ΔGcalc) of the HB complexes of HB donors with trimethylphosphine oxide (Me3PO), which models n-Bu3PO as a hydrogen bond acceptor, and compared these values with experimental data. We realized that such an

Recent advances in electrochemical copper catalysis for modern organic synthesis

• Yemin Kim and
• Won Jun Jang

Beilstein J. Org. Chem. 2025, 21, 155–178, doi:10.3762/bjoc.21.9

• remains a significant challenge owing to the high energy barrier required for oxidative addition and facile β-hydride elimination [12]. The development of radical approaches facilitated by transition-metal catalysis has provided a promising solution to overcome the limitations of conventional coupling