Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• mostly unstructured in solution, aptamers typically fold into their three-dimensional structure upon binding the respective target molecule [2]. Aptamers are normally identified by the in vitro selection from combinatorial libraries of nucleic acids [3]. In the past decades, interest in aptamers has

• triphosphate) [25]. The choice of this aptamer was expected to have various advantages. 1) Its three-dimensional structure has been reported [26], so the position for the incorporation of the metal-mediated base pair can be chosen in a meaningful way. 2) Its structure is based on a duplex rather than a

Dirhamnolipid ester – formation of reverse wormlike micelles in a binary (primerless) system

• David Liese,
• Hans Henning Wenk,
• Xin Lu,
• Jochen Kleinen and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2020, 16, 2820–2830, doi:10.3762/bjoc.16.232

• can be explained with an inhomogeneous breakup of the three-dimensional structure. In the beginning, the network collapses into big chunks, while the surrounding material is still rigid. A further increase in the temperature leads to a dominating viscous behavior until the whole sample becomes fluid

• caused by a slow formation of the three-dimensional network. The hysteresis gets smaller at low concentrations, indicating the approach of the critical gel-formation concentration. Deformation sweep To gather some more information about the viscoelastic material, a deformation sweep was performed. On the

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• monosaccharide minimal-energy conformation. While these features were recognised to address some long-standing needs in carbohydrate structure determination [39][40], significant challenges remain, particularly in the scenario where the glycan composition cannot be ascertained solely from the three-dimensional

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• aspects of glycan identification, quantification and visualisation, some of which will be further developed throughout this article. Biological molecules express their function throughout their three-dimensional structures. For this reason, structural biology places great emphasis on the three-dimensional

• glycoscience. The joint need to better perceive and manipulate the three-dimensional objects that make up molecular structures is leading to a rapid appropriation of techniques of Virtual Reality (VR) by the molecular biology community. Generic definitions describe VR as being immersion in an interactive

• constructing 3D models of glycans from a sequence using standard nomenclature accessible at http://www.glycosciences.de/modeling/sweet2/doc/index.php (Figure 9, top). This tool is available as a part of the glycosciences.de website, which also provides other options for analysing glycans in three-dimensional

One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway

• Esra Demir,
• Ozlem Sari,
• Yasin Çetinkaya,
• Ufuk Atmaca,
• Safiye Sağ Erdem and
• Murat Çelik

Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148

• energy of 16.2 kcal/mol with respect to the initial reactant complex RC1 (7f+CSI) (Figure 5). The overall process is exothermic by 56.2 kcal/mol. Three-dimensional (3D) views of all the optimized structures of path 2 are illustrated in Supporting Information File 1, Figure S2. As can be seen from the

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• chemists represent chemical structures as two-dimensional sketches made up of atoms and bonds, simplifying the complex three-dimensional molecules comprising nuclei and electrons of the quantum mechanical description, is the everyday language of chemistry. This language uses models, particularly of bonding

Mechanochemical green synthesis of hyper-crosslinked cyclodextrin polymers

• Alberto Rubin Pedrazzo,
• Fabrizio Caldera,
• Marco Zanetti,
• Silvia Lucia Appleton,
• Nilesh Kumar Dhakar and
• Francesco Trotta

Beilstein J. Org. Chem. 2020, 16, 1554–1563, doi:10.3762/bjoc.16.127

• . Polysaccharides and, among them, starch derivatives such as cyclodextrins (CD), have recently emerged as they are safe, of low cost and biodegradable. Cyclodextrin nanosponges (CD-NS) are crosslinked cyclodextrin polymers characterized by a nanosized three-dimensional network. The reactive hydroxy groups of CDs

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

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

• with a production of 1011–1012 tons per year, followed by lignin as second most abundant raw material [16]. Lignin is a three-dimensional phenolic polymer and is responsible for the cementation of cellulose fibres in plants [17]. Hemicelluloses, predominantly xylan, are non-cellulosic polysaccharides

The charge-assisted hydrogen-bonded organic framework (CAHOF) self-assembled from the conjugated acid of tetrakis(4-aminophenyl)methane and 2,6-naphthalenedisulfonate as a new class of recyclable Brønsted acid catalysts

• Svetlana A. Kuznetsova,
• Alexander S. Gak,
• Yulia V. Nelyubina,
• Vladimir A. Larionov,
• Han Li,
• Michael North,
• Vladimir P. Zhereb,
• Alexander F. Smol'yakov,
• Artem O. Dmitrienko,
• Michael G. Medvedev,
• Igor S. Gerasimov,
• Ashot S. Saghyan and
• Yuri N. Belokon

Beilstein J. Org. Chem. 2020, 16, 1124–1134, doi:10.3762/bjoc.16.99

• 2,6-naphthalenedisulfonate (NDS, 2 equivalents) and the tetrahydrochloride salt of tetrakis(4-aminophenyl)methane (TAPM, 1 equivalent) in water gave a novel three-dimensional charge-assisted hydrogen-bonded framework (CAHOF, F-1). The framework F-1 was characterized by X-ray diffraction, TGA

• Information File 1), so that the resulting three-dimensional network had no macro- or mesopores (Figure S1, Supporting Information File 1). The volume of the unit cell that was potentially accessible to a solvent was only 29.0 Å3, as calculated by PLATON [38]. The same crystal phase (F-1a) was present in F-1

• (4) Å3. The resulting structure designated as F-1 (F-1a’ phase, Figure 2) had two ammonium cations and four sulfonate dianions in the asymmetric part of the unit cell, with no traces of water molecules. Its three-dimensional network is built by charge-assisted hydrogen bonds between the ions (Table

Bipyrrole boomerangs via Pd-mediated tandem cyclization–oxygenation. Controlling reaction selectivity and electronic properties

• Liliia Moshniaha,
• Marika Żyła-Karwowska,
• Joanna Cybińska,
• Piotr J. Chmielewski,
• Ludovic Favereau and
• Marcin Stępień

Beilstein J. Org. Chem. 2020, 16, 895–903, doi:10.3762/bjoc.16.81

• spectrum is additionally complicated by the partially restricted rotation of the N,N-dimethylamide substituents in the NDA units. In conjunction with the helicity of the ring system, this restriction leads to effective diastereomerism. The three-dimensional structures of all boomerangs were modeled using

Diversity-oriented synthesis of 17-spirosteroids

• Benjamin Laroche,
• Thomas Bouvarel,
• Martin Louis-Sylvestre and
• Bastien Nay

Beilstein J. Org. Chem. 2020, 16, 880–887, doi:10.3762/bjoc.16.79

• their characteristic 3D geometry [68]. In particular, with 17-spirosteroids [69][70][71][72][73][74][75][76], the three dimensional complexity of the steroid CD-ring system is expected to be substantially affected. Results and Discussion The first goal of this work aimed at synthesizing spirocyclic

A systematic review on silica-, carbon-, and magnetic materials-supported copper species as efficient heterogeneous nanocatalysts in “click” reactions

• Pezhman Shiri and
• Jasem Aboonajmi

Beilstein J. Org. Chem. 2020, 16, 551–586, doi:10.3762/bjoc.16.52

• types of carbon nanomaterials, including a) zero-dimensional nanoparticles (NPs), b) one-dimensional nanotubes, c) two-dimensional graphene sheets, and d) three-dimensional mesoporous carbon have been reported in the literature [63]. In this regard, various functionalized carbon nanomaterials were

• , copper nanoparticles-decorated three-dimensional graphene (3D graphene/Cu nanocomposite 87) was reported as a catalyst to perform Huisgen 1,3‐dipolar cycloadditions. Therein, the GO material was mixed with EDA to produce a stable suspension that was transferred to a teflon‐lined autoclave. After heating

Synthesis and circularly polarized luminescence properties of BINOL-derived bisbenzofuro[2,3-b:3’,2’-e]pyridines (BBZFPys)

• Ryo Takishima,
• Yuji Nishii,
• Tomoaki Hinoue,
• Yoshitane Imai and
• Masahiro Miura

Beilstein J. Org. Chem. 2020, 16, 325–336, doi:10.3762/bjoc.16.32

• fluorophore unit in certain light-emitting functional materials (Scheme 1) [14]. Meanwhile, organic optoelectronic materials with circularly polarized luminescence (CPL) characteristics have attracted significant research interests in recent years [18][19][20][21] for their potential applications in three

• -dimensional displays [22], information storage systems [23], molecular photoswitches [24], etc. Among a series of chiral scaffolds for CPL emitting molecules, axially chiral 1,1’-bi-2-naphthol (BINOL) has been frequently adopted for the core structure owing to the availability of both enantiomers as well as

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• characterization of the newly-synthesized molecules gave evidence about structural and physicochemical properties with respect to a set of blockbuster drugs, and showed that such scaffolds are drug-like but more spherical and three-dimensional in character than the drugs. Keywords: chemical libraries

• generation of high-quality small molecule collections, taking advantage of the stereochemical diversity, and of their three-dimensional shape and structural bias to develop lead compounds, specifically in the field of protein–protein interactions [3][4][5][6]. Spiranic rings such as spiroketals are present

• shifting those compounds to a second cluster being positioned in the positive direction for both axes, together with drugs possessing large aromatic content, as benazepril and seroquel. The principal moments of inertia (PMI) analysis was also taken into account for the three-dimensional shape analysis of

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• restricted to the scale of a molecule and the directionality of its interactions with other molecules. Nevertheless, the three-dimensional structure of a molecule is decisive for its characteristic properties and hence its function in biological systems and materials [2]. In contrast, artistic concepts of

• Contextualization The understanding of space in chemistry is highly linked to the three-dimensional extensions of molecules and their directionality in chemical bonds, reactions, and processes. In this context, interactions, such as hydrogen-bonds [3], metal-coordination [4] or quadrupole interactions [5][6

Halide metathesis in overdrive: mechanochemical synthesis of a heterometallic group 1 allyl complex

• Ross F. Koby,
• Nicholas R. Rightmire,
• Nathan D. Schley,
• Timothy P. Hanusa and
• William W. Brennessel

Beilstein J. Org. Chem. 2019, 15, 1856–1863, doi:10.3762/bjoc.15.181

• -tri(tert-butyl)phenolate], for example, a Cs…CH3 contact of 3.596(5) Å contributes to its form as a 1D coordination polymer [33]. In the caesium salt of the gallium metallate [Cs(toluene)2{CN(GaMe3)2}], multiple Cs…CH3 interactions in the range from 3.54–3.64 Å help generate its three-dimensional

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• antifreeze activity, as well as to clarify the influence of hydrogen bonds on the preferred conformation of the molecule. Model AFGP analogues were investigated by NMR in order to elucidate the stereochemical influence of the amino acid configuration on the three-dimensional structure of the glycopeptides. A

• synthesis, the best yields were achieved for incorporation of natural amino acids into the peptide chain, where 1.2 equiv of glycosylated threonine were applied. NMR measurements were performed in order to elucidate the stereochemical influence of the amino acid configuration on the three-dimensional

Cyclobutane dication, (CH₂)₄²⁺: a model for a two-electron four-center (2e-4c) Woodward–Hoffmann frozen transition state

• G. K. Surya Prakash and
• Golam Rasul

Beilstein J. Org. Chem. 2019, 15, 1475–1479, doi:10.3762/bjoc.15.148

• . The various levels of calculations including MP2/6-31G* indicated that the structure vi was not a minimum [11]. The 1,3-dehydro-5,7-adamantanediyl dication (iii) [7] with 2e-4c bonding was generated and identified by 13C NMR spectroscopic and theoretical methods corresponding to a three dimensional

Photochemical generation of the 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) radical from caged nitroxides by near-infrared two-photon irradiation and its cytocidal effect on lung cancer cells

• Ayato Yamada,
• Manabu Abe,
• Yoshinobu Nishimura,
• Shoji Ishizaka,
• Masashi Namba,
• Taku Nakashima,
• Kiyofumi Shimoji and
• Noboru Hattori

Beilstein J. Org. Chem. 2019, 15, 863–873, doi:10.3762/bjoc.15.84

• issues can be solved by using the NIR-two-photon (TP) excitation technique [44], in which a molecule is electronically excited to the same state generated by one-photon (OP) excitation in the UV–vis region [45]. In addition to the advantages of TP excitation, three-dimensional control of the electronic

Application of olefin metathesis in the synthesis of functionalized polyhedral oligomeric silsesquioxanes (POSS) and POSS-containing polymeric materials

• Patrycja Żak and
• Cezary Pietraszuk

Beilstein J. Org. Chem. 2019, 15, 310–332, doi:10.3762/bjoc.15.28

• edges, chemically bonded with eight different or similar organic substituents so that it represents a truly hybrid architecture. The cubic silsesquioxane unit is characterized by a three-dimensional nanoscopic size structure with approximate Si–Si distance equal to 0.5 nm and an approximate R–R distance

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

• metallic nanotubes with easily polarizable electron densities, and they are less frequently found in three-dimensional metals [35][37][38]. Delocalized density fluctuations allow for the induction of large dipoles or higher multipoles that enhance weak molecular interaction: It is characteristic of

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• Streptomyces olivaceoviridis) [77][78]. This secreted protein was crystallized in 2010 by Patra et al., however, a three-dimensional structure has yet to be resolved [79]. Recently Nogueira et al. detected high titers of IgG antibodies against sMTL-13 in sera from TB patients, a response found to be diminished

Ring-opening metathesis of some strained bicyclic systems; stereocontrolled access to diolefinated saturated heterocycles with multiple stereogenic centers

• Zsanett Benke,
• Melinda Nonn,
• Márton Kardos,
• Santos Fustero and
• Loránd Kiss

Beilstein J. Org. Chem. 2018, 14, 2698–2707, doi:10.3762/bjoc.14.247

• of attention in synthetic organic chemistry, affording access to various highly functionalized, alkenylated molecular entities [1][2][3][4][5][6][7][8][9][10]. Highly functionalized three-dimensional organic scaffolds with multiple stereogenic centers as small molecular entities represent an

• multiple stereogenic centers thus synthesized can be considered interesting scaffolds for further transformations in view of the access of novel three-dimensional functionalized scaffolds through cross-metathesis (CM). An illustrative example is shown on Scheme 7. Divinylated γ-lactam (±)-19 selected as a

• stereogenic centers. The resulting diolefinated aminolactones, isoxazolines or lactam derivatives with multiple stereogenic centers might be considered to be interesting highly-functionalized three-dimensional compounds for further derivatizations. Extensions of the ROM of various bicyclic, conformationally

Impact of Pseudomonas aeruginosa quorum sensing signaling molecules on adhesion and inflammatory markers in endothelial cells

• Carmen Curutiu,
• Florin Iordache,
• Veronica Lazar,
• Aurelia Magdalena Pisoschi,
• Aneta Pop,
• Mariana Carmen Chifiriuc and
• Alina Maria Hoban

Beilstein J. Org. Chem. 2018, 14, 2580–2588, doi:10.3762/bjoc.14.235

• deficient strains differ in size and stability of the structure, being more flexible due to the production of QS-regulated extracellular DNA [8], which acts as a stabilizer of three-dimensional biofilm structure [8]. In patients with cystic fibrosis, the growth of bacteria in biofilm determines aggravation