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

• modelling of glycoproteins and protein–carbohydrate complexes is pivotal in understanding the complex biochemical interactions that affect the physiological function of cells [1]. Any mechanistic analysis done with finely grained approaches such as QM/MM [2] relies heavily on the correctness of the starting

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• the 9-organoborane intermediate IM-16 probably through borane–olefin complexes. The suprafacial nature of the boron migration allowed the boron to be α-oriented in intermediate IM-16, which would give 10 with retention of the configuration after NaOH/H2O2 oxidation. The formation of a significant

Advancements in hydrochlorination of alkenes

• Daniel S. Müller

Beilstein J. Org. Chem. 2024, 20, 787–814, doi:10.3762/bjoc.20.72

• chloride metal halide complexes are −6 kJ mol−1 for SnCl4, −8 kJ mol−1 for BiCl3, −9 kJ mol−1 for ZnCl2, −15 kJ mol−1 for CdCl2, −16 kJ mol−1 for FeCl3, and −41 kJ mol−1 for AlCl3. d) Addition of chloride-containing salts (e.g., LiCl) accelerate the reaction. e) Traces of water can increase the rate of the

• forms a dissociated hydrogen chloride aggregate in the form of complexes 103 or 105. An X-ray structure of complex 105 was reported and the reaction 104 → 105 is described in the report by Snyder, though not stoichiometric balanced. These complexes seem to play a pivotal role in the hydrochlorination

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

• solubility [14][15]. As early examples of the latter approach in the 1990s, Wennerström and co-workers reported the study of supramolecular BiCAP complexation of C60 with γ-cyclodextrin (γ-CD) [16]. Shinkai and co-workers synthesized water-soluble calixarene derivatives to form water-soluble complexes with

• C60 [17][18]. By either chemical functionalization or complexation of the fullerene core, a number of biocompatible fullerene materials with interesting biological activities were recently prepared and reported [19][20][21][22][23][24]. We have reported water-soluble complexes of C60 with a nontoxic

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• accessible for the cell [2][3]. In addition to the siderophores forming the stable Fe(III) complexes described above, certain siderophores create Fe(III) complexes with the ability to release Fe(II) ions in a light-responsive manner within the extracellular environment. The released Fe(II) ions in the ocean

Evaluation of the enantioselectivity of new chiral ligands based on imidazolidin-4-one derivatives

• Jan Bartáček,
• Karel Chlumský,
• Jan Mrkvička,
• Lucie Paloušová,
• Miloš Sedlák and
• Pavel Drabina

Beilstein J. Org. Chem. 2024, 20, 684–691, doi:10.3762/bjoc.20.62

• based on derivatives of imidazolidin-4-one were synthesised and characterised. The catalytic activity and enantioselectivity of their corresponding copper(II) complexes were studied in asymmetric Henry reactions. It was found that the enantioselectivity of these catalysts is overall very high and

• ; Introduction The application of chiral metal complexes as enantioselective catalysts is among the fundamental strategies for preparing compounds in non-racemic forms [1][2][3][4]. These complexes typically comprise a chelating chiral ligand capable of coordinating with a metal ion; otherwise, a metal atom

• -(pyridin-2-yl)imidazolidin-4-one, differentiated by various substitutions at the imidazolidine ring [5][6][7]. Their copper(II) complexes were evaluated as efficient enantioselective catalysts, particularly in asymmetric Henry reactions (Scheme 1). Subsequent research has led to the development of various

A laterally-fused N-heterocyclic carbene framework from polysubstituted aminoimidazo[5,1-b]oxazol-6-ium salts

• Andrew D. Gillie,
• Matthew G. Wakeling,
• Bethan L. Greene,
• Louise Male and
• Paul W. Davies

Beilstein J. Org. Chem. 2024, 20, 621–627, doi:10.3762/bjoc.20.54

• provide scope to influence the reactivity profile of their resulting metal complexes through steric shielding, direct stabilising interactions with the metal, or by proximal effects to reactive species. Given the sensitivity of metal catalysis to even subtle steric and electronic changes in the ligand

• aminide 7 in good yield on a gram scale (Scheme 1b). With the novel 3-aminoimidazo[5,1-b]oxazol-6-ium salt in hand, we examined its use as an NHC precursor for the preparation of late transition metal complexes. Treating compound 9a with triethylamine and either dimethyl sulfide gold(I) chloride or copper

• (I) chloride in acetone led to the formation of the desired AImOxAuCl and AImOxCuCl metal chloride complexes 13 and 14, respectively (Scheme 2) [7]. The 1H NMR spectra of the resulting AImOx metal complexes show a loss of symmetry for the diisopropyl substituents, indicating restricted rotation about

Synthesis of photo- and ionochromic N-acylated 2-(aminomethylene)benzo[b]thiophene-3(2Н)-ones with a terminal phenanthroline group

• Vladimir P. Rybalkin,
• Sofiya Yu. Zmeeva,
• Lidiya L. Popova,
• Irina V. Dubonosova,
• Olga Yu. Karlutova,
• Oleg P. Demidov,
• Alexander D. Dubonosov and
• Vladimir A. Bren

Beilstein J. Org. Chem. 2024, 20, 552–560, doi:10.3762/bjoc.20.47

• were isolated preparatively and fully characterized by IR, 1H, and 13C NMR spectroscopy as well as HRMS and XRD methods. The reverse thermal reaction was catalyzed by protonic acids. N-Acylated compounds exclusively with Fe2+ formed nonfluorescent complexes with a contrast naked-eye effect: a color

• effect: a visually distinguishable color change of the solutions from yellow to dark orange (Figure 5). Other cations did not demonstrate a measurable effect (Figure 6). Complexes 2a–c with Fe2+ in acetonitrile and DMSO were nonfluorescent. According to spectrophotometric titration data and the isomolar

• series method, compounds 2a–c formed the 2:1 complexes 4a–c with Fe2+ (Scheme 3 and Figure 7). It was found that selective interaction of the resulting in situ complex 4a with AcO− led to restoration of the initial absorption and emission properties [31][32]. Other tetra-n-butylammonium salts (TBAX, X

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

• particularly evident for metal complexes, where the system's geometry can be finely tuned to modulate its response based on the selection of metal and ligand components. This aspect has been extensively explored by Schmittel and co-workers in a recent review [17]. Molecular tweezers have been developed in this

• et al. exploited the same scaffold to control the physical properties of materials. They incorporated planar terpyridine-alkyne Pt complexes as functional units and studied the intercalation of a Pt-complex guest in order to obtain Pt–Pt interactions in solution [23]. In the native state of 3, both

• arms with planar Pt complexes are parallel and the distance between them allows for the intercalation of another terpy-Pt complex. The guest intercalation coupled with the induction of short-range Pt–Pt interactions was followed by UV–vis absorption and emission spectroscopies with characteristic MMLCT

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

• solvent and anion effects add complexity to mechanistic interpretation, and the reluctance of alkylgold complexes to undergo protodeauration under similar conditions give us pause [28]. While computational studies support protodeauration, the significantly lower reactivity of alkenes compared to alkynes

• substrate is the most active. In 2012, Kojima and Mikami utilized bimetallic tropos BIPHEP [bis(phosphino)biphenyl]–digold complexes for enantioselective intramolecular hydroamination of N-alkenylureas [9], and they hypothesized that N-alkenylureas could be activated through bimetallic coordination not only

(E,Z)-1,1,1,4,4,4-Hexafluorobut-2-enes: hydrofluoroolefins halogenation/dehydrohalogenation cascade to reach new fluorinated allene

• Nataliia V. Kirij,
• Andrey A. Filatov,
• Yurii L. Yagupolskii,
• Sheng Peng and
• Lee Sprague

Beilstein J. Org. Chem. 2024, 20, 452–459, doi:10.3762/bjoc.20.40

• significantly. One of the new and budding directions in recent years is the stereoselective olefin metathesis processes based on catalysis by complexes of molybdenum, tungsten and ruthenium [3][4][5]. The first publications have recently appeared that molybdenum complexes can catalyze cross-metathesis of butene

• the corresponding =CF2 containing products [10]. In addition to complexes of aluminum and boron, several magnesium and lithium silyl reagents were prepared and proved to be good nucleophiles in reactions with (Z)-1,1,1,4,4,4-hexafluorobut-2-ene, as a result of which the corresponding

Enhanced host–guest interaction between [10]cycloparaphenylene ([10]CPP) and [5]CPP by cationic charges

• Eiichi Kayahara,
• Yoshiyuki Mizuhata and
• Shigeru Yamago

Beilstein J. Org. Chem. 2024, 20, 436–444, doi:10.3762/bjoc.20.38

• [23][24][25][26] and CH–π interactions [27][28][29][30], forming the corresponding host–guest complexes. In addition, the concave outer surface of the CPP also interacts with the convex surface of the CPP (Figure 1b) [31][32][33], resulting in the formation of the shortest possible double-layer CNTs

• up new possibilities for the fabrication of supramolecular structures based on the non-covalent interactions using carbon nanorings [37][38]. Despite the unique structure of the host–guest complexes, however, their electronic structures are not very attractive. This is because the complex formation

• that the complex formation occurs between neutral [10]CPP and [5]CPP2+ forming [10]CPP⊃[5]CPP2+ (Figure 1c, path A) [21]. The absence of signals in the ESR measurements at room temperature also suggests the formation of complexes with a closed-shell electronic structure. The same complex was formed

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

Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters

• Carlos R. Azpilcueta-Nicolas and
• Jean-Philip Lumb

Beilstein J. Org. Chem. 2024, 20, 346–378, doi:10.3762/bjoc.20.35

• electrochemical conditions and can be influenced by a number of factors, including the nature of the electron donor, the use of Brønsted and Lewis acids, and the possibility of forming charge-transfer complexes. Such versatility creates many opportunities to influence the reaction conditions, providing a number

• transfer complexes with a donor species 6 or via LUMO lowering activation with Brønsted and Lewis acids 7 (Scheme 2B), collectively offering a number of variables to influence their reactivity. Upon reduction, RAEs give rise to a radical anion 8 with a weakened N–O bond (BDE < 70 kcal/mol) [33]. While

• electronically excited substrate (*S) through an energy transfer (EnT) mechanism (path c). In addition to these mechanistic blueprints, the formation of charge-transfer complexes involving NHPI esters, as well as examples of photoinduced transition metal-catalyzed activation will be discussed. Depending on the

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

• modelling and solid-state X-ray analysis, provides a detailed description of the spatial arrangement of cyclodextrin host–guest complexes in solution. The chiral cavity of the cyclodextrin molecule creates an anisotropic environment for the guest molecule resulting in a splitting of its prochiral carbon

• crystallization of host–guest complexes and their crystallographic analysis. Keywords: anisotropy; 13C NMR; cyclodextrin; host–guest complexes; Introduction Complexation of organic and inorganic compounds with α-, β-, or γ-cyclodextrins and their derivatives [1] is an established tool used in medicine for drug

• calorimetry [13]. Single crystals for many host–guest complexes have been prepared, and their structure elucidated by X-ray crystallography [14][15]. Conformations of host–guest complexes in solution have been studied by 2D NMR experiments [11] (NOESY, ROESY) or proposed computationally [16][17] based on

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• both complexes, single crystals were mounted in a cryoloop after transfer in a cryoprotectant solution, composed of 30% PEG Smear Medium and 5 mM CdCl2, and flash-cooled in liquid nitrogen. Crystal diffraction was evaluated, and data were collected on the Proxima 1 and 2 beamlines at the synchrotron

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• for compounds containing a quinoline fragment in various fields of research. At the same time, quinoline bases are a popular platform for the molecular design of polycyclic systems with receptor properties; they easily form proton complexes with high stability and selectivity [5][6]. This, in turn

• complexes due to the presence of 5(8) substituents, emerging from the plane of the π-system (see the previous section), and 3) acidification of the hydrogen atoms of the CH2 groups, which can facilitate their subsequent elimination. The analysis of the 1Н NMR spectrum not only confirmed the structure of

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• and alkenes. The pioneering work by Bruce et al. in 1981 revealed that the cleavage of tetracyanoethylene (TCNE) under mild conditions via its reaction with metal acetylides yields metal complexes featuring the tetracyanobuta-1,3-diene (TCBD) structural motif [3]. Subsequently, numerous researchers

• generalizing the elucidated reaction mechanism to other [2 + 2] CA–RE reactions involving TCNE and TCNQ as electrophiles might be difficult. They emphasized the significance of considering a pre-equilibrium state of the charge-transfer complexes between the alkynes and alkenes and mentioned that the

• room-temperature solution (dichloromethane) and as a frozen matrix at 77 K [123]. This is in contrast with the typical homoleptic phenanthroline-based CuI complexes renowned for their emissions from a triplet metal-to-ligand charge transfer excited state. The absence of luminescence may be attributed

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• organic solvents (78–20% in MeCN). The quinolizinium derivatives bind to DNA by intercalation with binding constants of 6–11 × 104 M−1, as shown by photometric and fluorimetric titrations as well as by CD- and LD-spectroscopic analyses. These ligand–DNA complexes can also be established in situ upon

• [7], quinoxalines [8], naphthalimides [9], phenanthridines [10], cyanines [11], or indoles [12], as well as metal-organic complexes [13], and several others [1][2][4]. In this context, benzoquinolizinium derivatives and resembling polycyclic azoniahetarenes are an established class of DNA-binding

• turn oxidizes the DNA bases [46]. As a result, various classes of photosensitizers [47][48][49] have been established, for example, porphyrins [50], chlorins [51], phthalocyanines [52], porphycenes [53], metal-organic complexes [54][55][56], dye aggregates [57], as well as nano-drug carriers and metal

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions

• Matthias R. Steiner,
• Max Schmallegger,
• Larissa Donner,
• Johann A. Hlina,
• Christoph Marschner,
• Judith Baumgartner and
• Christian Slugovc

Beilstein J. Org. Chem. 2024, 20, 41–51, doi:10.3762/bjoc.20.6

• candidates as well. Ortho-hydroxy-substituted phosphines have been mainly used as chelating ligands for metal complexes until recently [16][17][18]. Further, ortho-hydroxy phosphines have been used for the synthesis of probes in metabolic labeling [19], as a photocatalyst in the defluoroalkylation of

Aldiminium and 1,2,3-triazolium dithiocarboxylate zwitterions derived from cyclic (alkyl)(amino) and mesoionic carbenes

• Nedra Touj,
• François Mazars,
• Guillermo Zaragoza and
• Lionel Delaude

Beilstein J. Org. Chem. 2023, 19, 1947–1956, doi:10.3762/bjoc.19.145

• of charges (Figure 1) [13][14][15][16]. Crabtree and co-workers first reported the abnormal binding of an imidazolium salt to an iridium hydride at the C4 carbon atom instead of C2 in 2001 [17][18]. Since then, many other metal complexes bearing imidazol-4-ylidene ligands (F) have been reported [7

• -dithiocarboxylate zwitterions (Figure 2) [30][31][32][33][34][35][36][37][38][39][40][41][42][43]. These 1,1-dithiolate inner salts strongly bind main group elements and transition metals through various coordination modes. Indeed, we and others have already reported the synthesis of diverse metallic complexes

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

• proteins. The structural and functional heterogeneities of GAGs as well as their ability to bind specific proteins are determined by the sugar composition of the GAG, the size of the GAG chains, and the degree and pattern of sulfation. A deep understanding of the interactions in protein–GAG complexes is

• complexity in decoding their sulfation pattern. Their charged nature necessitates the application of appropriate methods for electrostatics, ions, and solvent, particularly given their abundance in protein–GAG interfaces compared to complexes involving other classes of biomolecules. The periodicity can lead

• multipose character of GAG binding and the polarity of the binding poses of these periodic molecules. In the present work, all-atom MD simulations are conducted to study the dynamics of the protein–GAG complexes, and are complemented by free energy analysis. The free energy analysis of the protein–GAG

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

• dimer 37 decreased by 20%. This complementary decrease supported the formation of complex 41 with decreased electron deficiency. Control experiments with fullerene monomer 22 gave unchanged catalytic activity with intercalators 38 or 40, which suggested that complexes 42 and 43 do not form. The

• . This is not surprising because virtual complexes 52 and 48 are not expected to exist to an appreciable extent. With covalent modification, MWCNTs 53 with A/D53/23 = 7.3 outperformed the corresponding SWCNTs 49 with A/D49/23 = 2.0 clearly. This significant increase in activity was consistent with the

• injects the negative charge into the substrate right on top of the polarizable π surface of the tube. Inability of pristine MWCNTs 3 to open and cyclize epoxide 32 thus implied insufficient substrate binding to form substrate-catalyst complexes that can proceed to transition state XV (Figure 9A). To

Recent advancements in iodide/phosphine-mediated photoredox radical reactions

• Tinglan Liu,
• Yu Zhou,
• Junhong Tang and
• Chengming Wang

Beilstein J. Org. Chem. 2023, 19, 1785–1803, doi:10.3762/bjoc.19.131

• develop other alternative radical precursors, explore new different reaction types (rather than the decarboxylative process), and design novel EDA complexes for photoredox catalysis, in addition to the well-established methods mentioned earlier. Moreover, asymmetric versions of iodide/phosphine-mediated

Active-metal template clipping synthesis of novel [2]rotaxanes

• Cătălin C. Anghel,
• Teodor A. Cucuiet,
• Niculina D. Hădade and
• Ion Grosu

Beilstein J. Org. Chem. 2023, 19, 1776–1784, doi:10.3762/bjoc.19.130

• obtained by CuAAC in the presence of CuCl(SIMes)(4,7-diclorophenantroline) as catalyst, with very good yields. Next, we set to study the ability of compound 6 to form copper(I) complexes able to act as active-metal templates for [2]rotaxane synthesis. Therefore, complexation studies of 6 with CuCl(SIMes

• active-metal template and clipping methods to yield the target interlocked molecules via [1 + 1] or intramolecular macrocyclizations, realized through CuAAC reactions catalyzed by axle-copper(I) N-heterocyclic carbene complexes. The [2]rotaxane obtained by [1 + 1] clipping (R1) could be only observed by