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

Selectivity control towards CO versus H₂ for photo-driven CO₂ reduction with a novel Co(II) catalyst

• Lisa-Lou Gracia,
• Philip Henkel,
• Olaf Fuhr and
• Claudia Bizzarri

Beilstein J. Org. Chem. 2023, 19, 1766–1775, doi:10.3762/bjoc.19.129

• transition-metal-based complexes, the outcomes are generally two-electron reduction products, such as carbon monoxide (CO), formic acid (HCO2H), or formate (HCO2−). To mitigate the strong energetic requirements of the reaction shown in Equation 1, the reduction of CO2 occurs in the presence of protons, so

• ]. Among the most employed earth-abundant metal-based PS, Cu(I) complexes have the first place, not only in artificial photosynthesis, but also in a large variety of photo(redox)catalyses [12][13][14][15][16][17]. On the other hand, several complexes based on 3d transition metals, like manganese [18], iron

• ]. The use of bimetallic complexes has resulted in a favorable mechanism, increasing yields tremendously [36][37][38]. Targeting efficient completely earth-abundant metal-based systems, we have designed a novel Co(II) catalyst for the reduction of CO2 (complex 1 in Figure 1). The design aimed at a stable

Unprecedented synthesis of a 14-membered hexaazamacrocycle

• Anastasia A. Fesenko and
• Anatoly D. Shutalev

Beilstein J. Org. Chem. 2023, 19, 1728–1740, doi:10.3762/bjoc.19.126

• ., vitamin B12, chlorophyll, metalloproteins, cyclic peptides, etc). PAMs themselves and their metal complexes exhibit various useful properties [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31], particularly, they possess a wide range of biological activities and are used as contrast

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• cell membrane integrity [21]. In the context of cancer therapy development, metal complexes of N-acylhydrazones stand out. For example, Firmino et al. demonstrated that gallium(III) complexes of isoniazid-derived hydrazones exhibit strong cytotoxicity against HL-60 and HCT-116 cancer cell lines [22

• ]. The study also found that those coordination compounds were selective towards abnormal cells, exhibiting lower toxicity for healthy human hepatocytes. On the other hand, an important development in cancer research is the use of physiological metal ion complexes, which afford more biocompatibility and

• thus less side-effects in therapy [23]. In this sense, we have reported dicopper(II) complexes from different N-acylhydrazonic binucleating ligands with potent antiproliferative activity against a panel of cancer cell lines [24][25][26]. On the field of neurodegeneration, our research group was the

Decarboxylative 1,3-dipolar cycloaddition of amino acids for the synthesis of heterocyclic compounds

• Xiaofeng Zhang,
• Xiaoming Ma and
• Wei Zhang

Beilstein J. Org. Chem. 2023, 19, 1677–1693, doi:10.3762/bjoc.19.123

• aldehydes and α-amino esters (via dehydration) or α-amino acids (via decarboxylation) could be classified based on the substitution groups on the N atom to: 1) N-substituted (N–R type), 2) hydrogen containing (N–H type), and 3) metal complexes (N–M type) (Figure 1) [16][17]. These AMYs could also be

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• oligo(ethylene glycol) segment. These hybrid systems constitute a broad group of compounds, including crowned porphyrins, crownphyrins, and calixpyrrole-crown ether systems forming Pacman complexes with transition metals. Their unique nature accustoms them as excellent ligands and hosts capable of

• such as K+, NH4+, and Ba2+ required two crown ether cavities attached to the porphyrin to form the coordination complexes through the dimerisation of the macrocycle. The dimensions of the crown ether pocket determined the complex formation; for example, if there was a mismatch in the sizes of the

• [46]. The macrotetracycles and macropentacycles, apart from the apparent metal complexation within the porphyrin core, showed cationic guest binding upon adding different ammonium salts, forming 1:1 complexes. Later, in 1985, Camilleri and co-workers reported the synthesis of a capped porphyrin

Synthesis of 7-azabicyclo[4.3.1]decane ring systems from tricarbonyl(tropone)iron via intramolecular Heck reactions

• Aaron H. Shoemaker,
• Elizabeth A. Foker,
• Elena P. Uttaro,
• Sarah K. Beitel and
• Daniel R. Griffith

Beilstein J. Org. Chem. 2023, 19, 1615–1619, doi:10.3762/bjoc.19.118

• by Bennasar, which elevated the yield to 76% (Table 1, entry 7) [10]. It has been postulated [21] that phenoxide is capable of stabilizing one or more of the intermediate Pd complexes, which may account for the higher yield. Interestingly, applying these conditions to the vinyl bromide 7 resulted in

• cleanly according to TLC analysis, but the isolated yield of the intramolecular Heck product was low, perhaps due to instability of one of the intermediate palladium complexes and/or a slow olefin insertion step. Moreover, the product was obtained as an inseparable mixture of the allylic carbamate 18 and

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

• (OMRP) is also a commonly used polymerization method, which uses transition-metal complexes such as titanium and vanadium for coordination polymerization [69]. However, due to the high cost of these complexes and their post-processing, OMRP is not widely used. The chain termination reaction of OMRP is

• mechanism (cf. section 3.2) [86]. 2.3 Metal-free ring opening metathesis polymerization (MF-ROMP) ROMP is a powerful and broadly applicable technique for synthesizing polymers. Traditional ROMP systems are initiated by transition-metal complexes and Ru-based alkylidene complexes, which are also known as

Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration

• Ghenwa Nasr,
• Hélène Greige-Gerges,
• Sophie Fourmentin,
• Abdelhamid Elaissari and
• Nathalie Khreich

Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115

• fields, mainly in drug delivery where they are used as pharmaceutical excipients to increase the drug permeability through biological membranes improving drug bioavailability and efficacy [2][4][5]. Furthermore, the CDs peculiarities helped to develop a combined system in which CD–guest complexes are

• between HP-β-CD and DPPC rather than with CHOL which explains the obtained results. As for SBE-β-CD, it was reported that charged CDs could not interact with CHOL molecules and form inclusion complexes due to charge repulsion [26]. This could explain the results obtained for these two CDs. Hence, HP-β-CD

• ) was able to form two types of soluble complexes, with molar ratios of 1:1 and 1:2 (CHOL/DOM-β-CD). The latter (1:2 inclusion complex) occurred much more easily than that of the 1:1 complex showing a much higher equilibrium constant. At low CDs concentration, the formation of the 1:1 inclusion complex

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

• , these compounds are capable of forming complexes with small organic molecules. The current paper focuses on the synthesis of complexes between R[4]A and secondary aliphatic amines (sec-amines). Through NMR spectroscopy, it was observed that “in-out” complexes are formed depending on the solvent. It was

• also found that the stoichiometry of the formed complexes depends on the size of the amine molecule. The automated interaction sites screening (aISS) made it possible to generate molecular ensembles of complexes. The geometry of the ensembles was first optimized with the r2scan-3c functional and

• exchange and dispersion interactions in CHCl3 in relation to DMSO are the driving forces behind the placement of sec-amine molecules into the R[4]A cavity and the formation of “in” type complexes. Keywords: complexes; DFT calculations; hydrogen bond; resorcin[4]arene; supramolecular chemistry

Application of N-heterocyclic carbene–Cu(I) complexes as catalysts in organic synthesis: a review

• Nosheen Beig,
• Varsha Goyal and
• Raj K. Bansal

Beilstein J. Org. Chem. 2023, 19, 1408–1442, doi:10.3762/bjoc.19.102

• the metal to the π* orbital of the NHC. Over the last two decades, NHC–metal complexes have been extensively used as efficient catalysts in different types of organic reactions. Of these, NHC–Cu(I) complexes found prominence for various reasons, such as ease of preparation, possibility of structural

• diversity, low cost, and versatile applications. This article overviews applications of NHC–Cu(I) complexes as catalysts in organic synthesis over the last 12 years, which include hydrosilylation reactions, conjugate addition, [3 + 2] cycloaddition, A3 reaction, boration and hydroboration, N–H and C(sp2)–H

• carboxylation, C(sp2)–H alkenylation and allylation, C(sp2)–H arylation, C(sp2)–H amidation, and C(sp2)–H thiolation. Preceding the section of applications, a brief description of the structure of NHCs, nature of NHC–metal bond, and methods of preparation of NHC–Cu complexes is provided. Keywords: conjugate

Radical ligand transfer: a general strategy for radical functionalization

• David T. Nemoto Jr,
• Kang-Jie Bian,
• Shih-Chieh Kao and
• Julian G. West

Beilstein J. Org. Chem. 2023, 19, 1225–1233, doi:10.3762/bjoc.19.90

• paradigm by Groves and Kochi, many groups have adopted and characterized new ways of using RLT to form valuable carbon–heteroatom bonds from a diverse pool of simple starting materials. RLT has been especially present in modern catalysis, where complexes of earth abundant iron and manganese have been

Unravelling a trichloroacetic acid-catalyzed cascade access to benzo[f]chromeno[2,3-h]quinoxalinoporphyrins

• Chandra Sekhar Tekuri,
• Pargat Singh and
• Mahendra Nath

Beilstein J. Org. Chem. 2023, 19, 1216–1224, doi:10.3762/bjoc.19.89

• copper complexes of benzo[f]chromeno[2,3-h]quinoxalinoporphyrins 3–7 were converted to the corresponding free-base porphyrinoids 9–13 through a standard demetallation process using conc. H2SO4 in CHCl3 under cooling conditions (Scheme 1). On complexation with zinc by using Zn(OAc)2 in CHCl3/MeOH, free

Enabling artificial photosynthesis systems with molecular recycling: A review of photo- and electrochemical methods for regenerating organic sacrificial electron donors

• Grace A. Lowe

Beilstein J. Org. Chem. 2023, 19, 1198–1215, doi:10.3762/bjoc.19.88

• , inorganic Z-schemes have used cobalt complexes and polyoxometalates to shuttle electrons between water oxidation and carbon dioxide reduction photocatalysts [2][4]. However, the photocatalysts of these systems are usually first developed separately with sacrificial electron donors. Other methods for

• employ redox mediators can use compounds such as cobalt bipyridine complexes which undergo fast reversible electron transfer reactions [2][4][8]. Z-schemes require a steady state concentration of both oxidized and reduced redox mediator species to allow an efficient shuttling of electrons between

• predominantly earth-abundant materials. The recycling of NADH analogues has been carried out using precious metal complexes, such as [CpRh(bpy)(H2O)]2+ [47]. This rhodium complex was adhered to a photoelectrode in a photoelectrochemical cell which also contained a second photoelectrode functionalized with a set

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

• ][78][79][80][81][82]. Organocatalysis is also a common point of intersection for halogen- and hydrogen bonding, and this has been thoroughly explored using monovalent iodine catalysts [83][84][85]. 1.3 Halogen bonding in hypervalent iodine complexes Similar to monovalent iodine compounds, a diverse

• pyridine was in fact interacting with the LUMO+1 MO of I-7, corresponding to the σ* orbital oriented along the I–C bond axis [87]. Lüthi et al. quantified the symmetry-adapted perturbation theory (SAPT) interaction energies of halogen bonded acetonitrile complexes of HVI molecules [72], and Huber et al

• . used 1H NMR titrations and isothermal titration calorimetry (ITC) to experimentally determine interactions energies for I-9 complexes (e.g., I-9-lig, −6.3 kcal/mol), they also discovered that simultaneous binding to both σ-holes was possible [90]. Given these observations, it is unsurprising that HVI