Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• important facility, especially for novice users. To allow this to happen readily on PDB distribution sites, we present the Privateer database, a freely available, up-to-date collection of validation information for both the PDB and PDB-REDO [21] archives. Results and Discussion Format of the validation

(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• in exit vector analyses [25]. Here, the geometric relationship between the two substituents is measured and compared to those of the parent benzene. To compare physicochemical properties, the following indicators will generally be used: distribution coefficient (logD, desired range: 1–3 [26]) or

• their physicochemical properties were compared to those of the parent compounds (Figure 3) [26][33]. The reported distribution coefficients (logD) of enantiomeric 1,2-BCPs (+)-21 and (−)-21 are very similar to telmisartan, while the distribution coefficients of the lomitapide isosteres (+)-22 and (−)-22

• distribution coefficient (SF logD) and calculated partition coefficient (clogP). This analysis showed while the calculated partition coefficient was reduced by bioisosteric replacement of ortho-benzene the experimental distribution coefficient did not change significantly. However, while aqueous solubility

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• , the physiological function of its substrate NNG. This compound is one of the few known nitramine natural products and the only one produced by bacteria instead of fungi [22]. Its only known natural sources are strains of Streptomyces bacteria [23][24]. The abundance and distribution of these NNG

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• heterologous production of crocins in microorganisms to break the current bottleneck of a sustainable supply. It provides the basis for the further development of crocins in the food, cosmetic, and pharmaceutical industries. Review Chemical properties and distribution of crocins More than ten crocins have been

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• drugs by halting the growth of brain tumor cells and inhibiting the expression of inflammatory genes [7]. Since they can be administered orally, and they display satisfying distribution to the brain and plasma without leading to serious unwanted side effects, they have entered advanced stages of

Facile approach to N,O,S-heteropentacycles via condensation of sterically crowded 3H-phenoxazin-3-one with ortho-substituted anilines

• Eugeny Ivakhnenko,
• Vasily Malay,
• Pavel Knyazev,
• Nikita Merezhko,
• Nadezhda Makarova,
• Oleg Demidov,
• Gennady Borodkin,
• Andrey Starikov and
• Vladimir Minkin

Beilstein J. Org. Chem. 2024, 20, 336–345, doi:10.3762/bjoc.20.34

• highly basic amines (Scheme 1) [6]. The choice for one of the other two possible reaction pathways (nucleophilic additions to either the C(1) or C(2) center) critically depends on the electrophilicity. Figure 1 shows the distribution of electronic density in 6,8-di-tert-butyl-3H-phenoxazin-3-one (1

• formation [6]. In turn, without an acidic catalyst, it is driven by the distribution of the electron density (Figure 1), such that the nucleophilic attack occurs at the most electrophilic C(2) center. With this in mind, we presented a convenient procedure for the SNH reaction of aromatic amines with

• -311++G(d,p) level) and distribution of electronic density in 6,8-di-tert-butyl-3H-phenoxazin-3-one (1): Mulliken charges and molecular electrostatic potential (MEP, isovalue = 0.004). Molecular structure of 6,8-di-tert-butyl-2-(o-nitrophenylamino)-3H-phenoxazin-3-one (4f). a) Selected bond distances

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

• ten classical molecular dynamics (MD) simulations [16] (each lasting 100 ns, Figure 3). Then, we superimposed α-CD structures from different snapshots of each MD run. Further, the 3D densities, showing the spatial distribution of prochiral atoms of ligands (that rotate and wobble towards α-CD), were

• . The 3D densities show the spatial distribution of prochiral atoms within MD simulations. Studied host–guest complexes and splitting of guests’ prochiral carbons in their 13C NMR spectra. Molecular modelling of the host–guest complexes of compound 4 with α-CD, β-CD and γ-CD. X-ray analysis of the α-CD

Comparison of glycosyl donors: a supramer approach

• Anna V. Orlova,
• Nelly N. Malysheva,
• Maria V. Panova,
• Nikita M. Podvalnyy,
• Michael G. Medvedev and
• Leonid O. Kononov

Beilstein J. Org. Chem. 2024, 20, 181–192, doi:10.3762/bjoc.20.18

• measurement of the quartz standards (to monitor the instrument stability). Each measurement at a particular concentration was repeated 10 times, then averaged and plotted against concentration. The standard deviations were calculated by using the Student’s distribution (95% probability) and did not exceed 1

• % unless specified otherwise, see the error bars; the error bar is on the order of the symbol size if not visible). The standard deviations were calculated by using the Student’s distribution (95% probability). The grey boxes in the figure are drawn to guide the eye and designate different ranges of

Optimizing reaction conditions for the light-driven hydrogen evolution in a loop photoreactor

• Pengcheng Li,
• Daniel Kowalczyk,
• Johannes Liessem,
• Mohamed M. Elnagar,
• Dariusz Mitoraj,
• Radim Beranek and
• Dirk Ziegenbalg

Beilstein J. Org. Chem. 2024, 20, 74–91, doi:10.3762/bjoc.20.9

• microscopy (SEM) at different magnifications, as shown in Figure 1a–d. The images reveal a layered structure exhibiting a rough surface with agglomerated, irregular, and dense particles. Figure 2a–e shows the elemental mapping analysis of Pt-PCN conducted using SEM-EDX. A homogeneous distribution of Pt

• (Figure 2d) was found across the surfaces of the Pt-PCN, confirming their uniformity. To ensure that the homogeneous distribution of Pt on the surface of PCN is not random, multiple particles were analyzed using SEM-EDX (see Supporting Information File 1, Figure S1), which shows the uniform distribution

• photocatalyst is referred to as Pt-PCN. The surface morphology, chemical composition, and elemental distribution of the Pt-PCN were analyzed using a ZEISS LEO 1550 VP scanning electron microscope (SEM) equipped with energy dispersive spectroscopy (EDS) from Ametek, USA. The SEM was operated at an acceleration

Preparing a liquid crystalline dispersion of carbon nanotubes with high aspect ratio

• Keiko Kojima,
• Nodoka Kosugi,
• Hirokuni Jintoku,
• Kazufumi Kobashi and
• Toshiya Okazaki

Beilstein J. Org. Chem. 2024, 20, 52–58, doi:10.3762/bjoc.20.7

• , Figure S1e) [26]. The DWCNT powder was dispersed with a surfactant of sodium cholate (SC) in water by a two-step process [22][23] (see the Experimental section). The size distribution of the DWCNTs in the dispersion was estimated by DCS method (Figure 1a). The observed intense peak at approximately 9 nm

• -770 spectrometer. The film's thicknesses were measured using a laser confocal microscope (OLYMPUS, OLS-4500). (a) Size distribution of DWCNTs in dispersion by DCS measurements. (b) Optical microscopy image of the DWCNT dispersion. Scale bar is 100 µm. (a) Phase diagram of the DWCNT dispersion. The

Facile access to pyridinium-based bent aromatic amphiphiles: nonionic surface modification of nanocarbons in water

• Lorenzo Catti,
• Shinji Aoyama and
• Michito Yoshizawa

Beilstein J. Org. Chem. 2024, 20, 32–40, doi:10.3762/bjoc.20.5

• ; Figure S36 in Supporting Information File 1). The formation of spherical particles with narrow size distribution and an average diameter of ≈2 nm was confirmed by DLS and DOSY NMR measurements (Figure 3e and Figure S27 in Supporting Information File 1). Based on molecular modeling, these data suggested

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

• set categories (out of distribution, OOD), including disaccharides, a sulfated monosaccharide, and paracetamol. The outlying molecules represent potential "pollutions" in the analysis. This set of data is referred to as endogenous as it was measured on the same apparatus as the training set. For

• , which results in modulated peaks amplitudes. This was simulated as a linear variation of the signal amplitude across the spectral range. The variation was contained in a uniform distribution bounded by ±10%. Spectra can be recorded at increased speed for rapid analytical diagnostics, which traduces into

• constrains the weights posterior distribution to normal distributions instead of the more accurate Markov chain Monte-Carlo (MCMC) method for calculation efficiency. With this approach, a quantitative uncertainty of the model predictions can be achieved by inferring each spectrum category several times with

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

• Alessandro L. Alves,
• Simone V. Bernardino,
• Carlos H. Stadtlober,
• Edivandro Girotto,
• Giliandro Farias,
• Rodney M. do Nascimento,
• Sergio F. Curcio,
• Thiago Cazati,
• Marta E. R. Dotto,
• Juliana Eccher,
• Leonardo N. Furini,
• Hugo Gallardo,
• Harald Bock and
• Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

• considered. The parameters µ0 and γ implicitly include a monoenergetic trap distribution and can be obtained from fitting the SCLC regimes of the experimental J–V curves. The fits for each device are shown as red solid lines in Figure 6, and the values of µ0 and γ displayed in Table 3 were used to calculate

A deep-red fluorophore based on naphthothiadiazole as emitter with hybridized local and charge transfer and ambipolar transporting properties for electroluminescent devices

• Suangsiri Arunlimsawat,
• Patteera Funchien,
• Pongsakorn Chasing,
• Atthapon Saenubol,
• Taweesak Sudyoadsuk and
• Vinich Promarak

Beilstein J. Org. Chem. 2023, 19, 1664–1676, doi:10.3762/bjoc.19.122

• of the Nz moiety originating from its localized distribution of electrons and the high electronegativities of the N and S atoms, whereas its high HOMO level is attributed to the electron-donating property of the attached carbazoles and the π-conjugation of the carbazole–Nz–carbazole fragment. Such

Radical chemistry in polymer science: an overview and recent advances

• Zixiao Wang,
• Feichen Cui,
• Yang Sui and
• Jiajun Yan

Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116

• reaction mixture increases. This may lead to autoacceleration, also known as the Trommsdorff–Norrish effect, or even a violent explosive polymerization. At the same time, heat acquisition may cause a broad molecular weight distribution. Solution polymerization can effectively mitigate problems of bulk

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• reactive sites (aISS), for example, in the formation of supramolecular complexes [16]. The particularly fast GFN-xTB methods work well in geometry optimization, which is the most time-consuming step of the DFT calculation. There have also been developments in DFT methods concerning the energy distribution

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

• Moe Nakano,
• Rintaro Gemma and
• Hajime Sato

Beilstein J. Org. Chem. 2023, 19, 1503–1510, doi:10.3762/bjoc.19.107

• affected by hyperconjugation (C9–C10: 1.54 Å, C10–C11: 1.54 Å, C11–C1: 1.57 Å). We have also done a comparative analysis of the charge distribution in scenarios with and without cation–π interactions. In cases where the interaction is absent, the cationic character at C10 is pronounced. Conversely, in the

Cyclization of 1-aryl-4,4,4-trichlorobut-2-en-1-ones into 3-trichloromethylindan-1-ones in triflic acid

• Vladislav A. Sokolov,
• Andrei A. Golushko,
• Irina A. Boyarskaya and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2023, 19, 1460–1470, doi:10.3762/bjoc.19.105

• temperature. Then, we carried out DFT calculations of cations Aa–Da derived from protonation of compounds 1a and 2a. Thermodynamics of their formation, as Gibbs energies ΔG298 of the corresponding reactions, energies of HOMO/LUMO, electrophilicity indices ω [22][23], charge distribution, and contribution of

Functional characterisation of twelve terpene synthases from actinobacteria

• Anuj K. Chhalodia,
• Houchao Xu,
• Georges B. Tabekoueng,
• Binbin Gu,
• Kizerbo A. Taizoumbe,
• Lukas Lauterbach and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100

• were not taken as substrate. The newly identified enzyme was designated Streptomyces sp. Tü 2975 Sesterviolene Synthase (StSS). Conclusion Despite the accumulated knowledge on bacterial terpene synthases, the scattered distribution of sesqui-, di- and sesterterpene synthases in the phylogenetic tree of

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• distribution is heterogeneous with abundant amount (up to 50% of the phosphoethanolamine based lipids) in central nervous system (mainly as PE-plasmalogen), in skeletal muscle, heart, kidney and lungs [13]. At a cellular scale, the biosynthesis of ELs is initiated in peroxisome and maturation is completed in

Organic thermally activated delayed fluorescence material with strained benzoguanidine donor

• Alexander C. Brannan,
• Elvie F. P. Beaumont,
• Nguyen Le Phuoc,
• George F. S. Whitehead,
• Mikko Linnolahti and
• Alexander S. Romanov

Beilstein J. Org. Chem. 2023, 19, 1289–1298, doi:10.3762/bjoc.19.95

• , respectively [12]. These measurements correlate well with lower PLQY values for 4BGIPN compared with 4CzIPN, thus indicating that the use of a larger benzoguanidine donor ligand may open more nonradiative processes. This is reflected in the larger distribution in the torsion angles for 4BGIPN compared with

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

• halogen and its host, where polarization of the halogen’s electronic charge is directed towards the covalent bond [24]. This results in a phenomenon called polar flattening, resulting in a non-spherical distribution of electron density on the halogen’s surface, with a positive electrostatic potential

• ][36][37][38][39]. This anisotropic electron distribution manifests itself in many ways, such as the L-shaped packing observed with diatomic halogens resulting from the secondary bonding between the positive end of one halogen and the negative end of another [40]. σ-Holes can be assessed both

The effect of dark states on the intersystem crossing and thermally activated delayed fluorescence of naphthalimide-phenothiazine dyads

• Liyuan Cao,
• Xi Liu,
• Xue Zhang,
• Jianzhang Zhao,
• Fabiao Yu and
• Yan Wan

Beilstein J. Org. Chem. 2023, 19, 1028–1046, doi:10.3762/bjoc.19.79

• attributed to the electron-withdrawal or donating feature of the aryl substituent attached to the nitrogen atom of the NI moieties. Interestingly, although there is no distribution of LUMO on the aryl moiety, the LUMO energy of the dyads are varied by up to 0.12 eV. These subtle variations of the molecular

Eschenmoser coupling reactions starting from primary thioamides. When do they work and when not?

• Lukáš Marek,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2023, 19, 808–819, doi:10.3762/bjoc.19.61

• -dimethyl-1,4-dihydroisoquinoline-3(2H)-one, 4-bromoisoquinoline-1,3(2H,4H)-dione and two α-bromo(phenyl)acetamides were examined under various conditions (base, solvent, thiophile, temperature) and structure/medium features that influence product distribution (Eschenmoser coupling reaction, Hantzsch

• KHCO3 (Table 1, entry 11) the cyclization product 8a is dominant, but the ECR product 9a is also isolable from the reaction mixture in moderate yield. Unfortunately, the reaction carried out in such a heterogeneous system is not fully reproducible with respect to product distribution. The change of the

Synthesis of substituted 8H-benzo[h]pyrano[2,3-f]quinazolin-8-ones via photochemical 6π-electrocyclization of pyrimidines containing an allomaltol fragment

• Constantine V. Milyutin,
• Andrey N. Komogortsev,
• Boris V. Lichitsky,
• Mikhail E. Minyaev and
• Valeriya G. Melekhina

Beilstein J. Org. Chem. 2023, 19, 778–788, doi:10.3762/bjoc.19.58

• ]. After excitation the electron distribution significantly changes leading to substantial alterations in the chemical behavior of the starting compound. Thereby, UV-induced reactions are a useful addition to common thermal processes. In this regard, photochemical transformations have found wide