Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• dispersion interactions would be insufficient to explain a 20-fold increase in affinity. It is unlikely that this hydrogen bond explains a 20-fold increase in affinity yet note that the mobility of the glycan moiety allows the hydrogen-bond interaction to occur. The hydrogen-bonding preferences and

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• -solvent can induce unfolding of the protein, which is reflected by a collapse of signal dispersion in the HSQC spectrum, resulting in most amide signals moving into the random coil region between ≈7.5–8.5 ppm (in the 1H dimension). We found that a maximum of ≈5% of DMSO-d6 seems to be a good rule of thumb

• dispersion and more favorable relaxation properties compared to CH2 groups, so they are mostly used to observe the interactions of a protein with its binding partners. Especially methyl groups bound to a hetero atom like sulfur (in methionine) or nitrogen (e.g., in methylated lysine) have unique chemical

• only is signal overlap reduced compared to the 1H,13C-HSQC because less signals appear in the spectrum, but also the observed signal dispersion is superior due to a larger dispersion in the 15N dimension. The H2(C)N spectra have proven to be very sensitive to tweezer and calixarene binding. Similar to

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• spectra of pyrene could be used to estimate the polarity of the environment of the dye in an empirical way. The ratio of the two bands in an environment of unknown polarity can be compared with the values of this ratio in solvents of known polarity. The spectrum of pyrene dissolved in a water dispersion

• min at 59 kHz. The dispersion was filtered over a 0.2 µm nylon membrane recovering both solid and solution. This protocol was repeated and then the solid was washed over the filter with ethanol (2 × 30 mL) and dried under vacuum to obtain 250 mg of Dex-1a as orange solid. FTIR data are shown in Figure

• was recovered, dissolved in DMSO (6.6 mL) and the product precipitated from cold ethanol (50 mL) and filtered over a 0.2 µm nylon membrane. The powder was recovered and dispersed (6.8 mg/mL) in ethanol and sonicated for 5 min at 59 kHz. The dispersion was filtered over a 0.2 µm nylon membrane

Natural dolomitic limestone-catalyzed synthesis of benzimidazoles, dihydropyrimidinones, and highly substituted pyridines under ultrasound irradiation

• Kumar Godugu,
• Venkata Divya Sri Yadala,
• Mohammad Khaja Mohinuddin Pinjari,
• Trivikram Reddy Gundala,
• Lakshmi Reddy Sanapareddy and
• Chinna Gangi Reddy Nallagondu

Beilstein J. Org. Chem. 2020, 16, 1881–1900, doi:10.3762/bjoc.16.156

• positions might be due to the presence of trace metal contents and impurities. The morphology of the NDL catalyst was analyzed by scanning electron microscopy (Figure 5). The SEM images revealed that the morphology of the NDL catalyst consists of irregular shapes and sizes with a random dispersion. Further

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• cellulose were also investigated. An optimum amount of 0.2 g of 4 wt % Ru/C led to 56% of isosorbide whereas 0.4 g of 2% Ru/C led to a lower isosorbide yield (24%) despite the same amount of Ru atoms on these catalysts. The metal dispersion of these two catalysts was almost identical but the particle size

Models of necessity

• Timothy Clark and
• Martin G. Hicks

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

• . Descriptions of directional non-covalent interactions, for instance, are necessary for any applications involving crystal engineering. These can be treated adequately using anisotropic electrostatics [102] and dispersion [103]. It is, however, important to limit these extensions to models that are as

Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study

• Csilla Hargitai,
• Györgyi Koványi-Lax,
• Tamás Nagy,
• Péter Ábrányi-Balogh,
• András Dancsó,
• Gábor Tóth,
• Judit Halász,
• Angéla Pandur,
• Gyula Simig and
• Balázs Volk

Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136

• ) spectrometer equipped with a Prodigy cryo-probehead. The pulse programs were taken from the Bruker software library (TopSpin 3.5) and full 1H and 13C assignments were achieved with widely accepted strategies [34][35]. 1H NMR assignments were accomplished using general knowledge of chemical shift dispersion

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

• -potential, which explained the stability of the dispersion. As shown in Figure 5, all CD nanosponges exhibited a negative ζ-potential and this was in line with previous literature [2][9][30]. The negative charge seemed to be related to the amount of crosslinker: the larger the amount, the more negative the

• dispersion, followed by heating at 85 °C in an oil bath for 4 h. The final product was washed with an excess of water and then extracted with acetone using PSE to remove the unreacted dyes. FTIR analysis of βNS-CDI 1:4, before and after treatment for 4 h in H2O at 40 °C, synthesized with and without solvent

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

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

• Carlos H. Escalante,
• Eder I. Martínez-Mora,
• Carlos Espinoza-Hicks,
• Alejandro A. Camacho-Dávila,
• Fernando R. Ramos-Morales,
• Francisco Delgado and
• Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

• endo selectivity in the Diels–Alder cycloadditions. Since experimental and theoretical results have demonstrated that the nature of the C–H···π interaction mainly depends on the dispersion interactions [64][67][77], these are probably not only at the origin of the endo stereoselectivity of the present

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

• /O elemental analysis, EDX, XPS, XRD and TGA. Keywords: activated carbon; catalysis; characterization techniques; metal supported on carbon catalysts; preparation methods; Introduction Support materials for metal catalysts allow the dispersion and stabilization of small metal particles on a surface

• the aqueous metal solution during the impregnation process and results in a better platinum dispersion. Nevertheless, less acidic and more thermally stable surface groups avoid the sintering of the metal particles by enhanced metal–carbon interaction [109]. Figueiredo et al. observed different types

• the precursor and supporting material and its pore systems shows the greatest influence on the dispersion of the metal on the support and thereby limits the metal loading [134]. Various factors play also a role in the distribution of the metal precursor on the support: type of metal compound, solvent

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

• in an aqueous medium under aerobic conditions at 70 °C (Scheme 20). In another example, GO was effectively modified with CuO nanoparticles through a facile pathway that can be seen below [83]. In the next step, GO was sonicated in isopropyl alcohol for 0.5 h to produce a black dispersion. After

• , copper acetate monohydrate was added to the GO to afford a brown dispersion that was stirred at 83 °C for 0.5 h. After the addition of water, the reaction mixture was stirred at 83 °C for 0.5 h and then cooled to ambient temperature. The solid product CuO–GO was centrifuged, washed with ethanol, and

Formal preparation of regioregular and alternating thiophene–thiophene copolymers bearing different substituents

• Atsunori Mori,
• Keisuke Fujita,
• Chihiro Kubota,
• Toyoko Suzuki,
• Kentaro Okano,
• Takuya Matsumoto,
• Takashi Nishino and
• Masaki Horie

Beilstein J. Org. Chem. 2020, 16, 317–324, doi:10.3762/bjoc.16.31

• RINT-2000(CuKα) device. Concerning the solvent of the nickel- and palladium-catalyzed reactions, THF (anhydrous grade) was purchased from Kanto Chemical Co. Ltd. and passed through alumina and copper columns (Nikko Hansen & Co. Ltd.) or distilled from a sodium dispersion in mineral oil/benzophenone

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• that maximized intramolecular dispersion interactions [45][46]. In the active site model of E, the carbocation at C6 had a greater distance from the pyrophosphate group than C2 in cation D (6.03 Å vs 5.03 Å) and likely contributed to a slight destabilizing effect in the active site model. This was in

Starazo triple switches – synthesis of unsymmetrical 1,3,5-tris(arylazo)benzenes

• Andreas H. Heindl and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2020, 16, 22–31, doi:10.3762/bjoc.16.4

• substitution prolongs the thermal stability up to years [4], while electron-donating groups attached to the different phenyl rings decrease the thermal half-lives below the time scale of seconds. Even subtle interactions, such as London dispersion in alkyl-substituted ABs, can have a significant influence on

Why do thioureas and squaramides slow down the Ireland–Claisen rearrangement?

• Dominika Krištofíková,
• Juraj Filo,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2019, 15, 2948–2957, doi:10.3762/bjoc.15.290

• quantum-chemical calculations employing long-range corrected hybrid density ωB97X-D functional [42]. This dispersion-corrected functional displays very balanced overall performances and has demonstrated excellent treatment of noncovalent interactions [43], which are very important in our studied system

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

• Sara Tejera,
• Giada Caniglia,
• Rosa L. Dorta,
• Andrea Favero,
• Javier González-Platas and
• Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

• diffraction; Introduction Structures self-assembled by noncovalent interactions give rise to supramolecular architectures with specific physical and/or chemical properties. Gels are colloid systems in which the dispersed phase has combined with the dispersion medium to yield a semisolid material. Gels from

Carbazole-functionalized hyper-cross-linked polymers for CO₂ uptake based on Friedel–Crafts polymerization on 9-phenylcarbazole

• Dandan Fang,
• Xiaodong Li,
• Meishuai Zou,
• Xiaoyan Guo and
• Aijuan Zhang

Beilstein J. Org. Chem. 2019, 15, 2856–2863, doi:10.3762/bjoc.15.279

• , 0.152 g) were dispersed in DCE (18 mL) and then anhydrous FeCl3 (4 mmol, 0.64 g) was added to the dispersion; the mixture was allowed to react at room temperature for 5 h, then at 80 °C for 19 h with vigorous stirring. Then the mixture was cooled to room temperature and quenched by using 20 mL of CH3OH

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• calculations of the noncovalent index (NCI) surfaces indicate that dispersion forces exist between pyrrolidine groups and the heteroaromatic ring (green surfaces in Figure 3). The inclusion of one pyrrolidine (4pzH-Pyr1) promotes weak but stabilizing noncovalent interactions between the ortho group and the

• ). The analysis of the NCI surfaces indicates that inclusion of F atoms in the ortho-position promotes stabilizing dispersion interactions with the pyrazole ring, provoking a tilting of the heteroring from 92° in 4pzH to 118° in 4pzH-F1 and to 121° in 4pzH-F2 (Figure 4). Stabilizing F···pyrazole

• ring in both 4pzH-X and 4pzMe-X families (Figure S7, Supporting Information File 1). These favorable dispersion and electrostatic interactions stabilize the Z-isomer ground state compared to the corresponding transition state, which in part explains the increase in energy barriers and in turn half

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• absolute structures, however their anomalous dispersion statistics indicate that the assignments are very likely to be correct. The crystal structure of 1 has four crystallographically-independent molecules, while the structures of 2b and 3b have two crystallographically-independent molecules, and the

Probing of local polarity in poly(methyl methacrylate) with the charge transfer transition in Nile red

• Aydan Yadigarli,
• Qimeng Song,
• Sergey I. Druzhinin and
• Holger Schönherr

Beilstein J. Org. Chem. 2019, 15, 2552–2562, doi:10.3762/bjoc.15.248

• and fluorescence spectra of NR. Thus, the large dispersion of reported NR dipole moments [44][47][48][51][52][53][54][55][56][62][63] is mainly caused by insufficient precision of the value for the cavity radius of NR. Polymer polarity probed with NR The fluorescence spectra of NR in low and high

Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• ) without (PBE0/def2-TZVP) and with (PBE0-D3/def2-TZVP) dispersion correction because in the gas phase dispersion plays an important role in the formation of supramolecular complexes [24][25][26][27][28][29][30]. Conformational analysis was first performed for both tautomers of the monomer to ensure that

• dispersion correction (hydrogen bond lengths are listed in Table S2, Supporting Information File 1). This is expected, because the standard hybrid functionals are able to describe strong hydrogen bonds such as NH···O and OH···O in a reasonable manner [31][32]. Due to the encapsulated guest molecule, the [12

• different geometries, [12 + Me4Nexo1]+ and [12 + Me4Nexo2]+ (Figure S7, Supporting Information File 1). In [12 + Me4Nexo1]+, the Me4N+ cation interacts with the lower rim isobutyl groups only when the dispersion interaction is included in calculations, whereas at the PBE0/def2-TZVP level [12 + Me4Nexo1]+ is

Fluorinated azobenzenes as supramolecular halogen-bonding building blocks

• Esther Nieland,
• Oliver Weingart and
• Bernd M. Schmidt

Beilstein J. Org. Chem. 2019, 15, 2013–2019, doi:10.3762/bjoc.15.197

• dispersion correction, using the Gaussian 16 program package (see Supporting Information File 1). The azobenzenes were embedded in a continuum using the polarizable continuum model (PCM) for the solvent MeCN. The DGZVP all electron basis was used for iodine. Vertical excitation energies for the π→π* and n→π

• help of quantum mechanical calculations involving a combination of low-cost implicit solvation models and hybrid density functionals when including dispersion corrections. Electrostatic potential map at different isodensity values (B3LYP/ def2/TZVP/DGZVP optimized geometries) with a) ρ = 0.0001, and b

• ) ρ = 0.001. For visualization, the MoleCoolQt software was used [47]. Top: Vertical electronic absorption spectra of a) A2 and b) A3, calculated using TD-B3LYP/def2-TZVP level of theory with Grimme D3 dispersion corrections and implicit MeCN solvent. Pink line: Z-isomer, purple line: E-isomer. Bottom

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

• this and several related points more quantitatively, various features of the K/Cs/[allyl]− system were modeled with DFT calculations, using the B3PW91 hybrid functional [27][28] with Grimme’s -D3 dispersion corrections (GD3BJ) [29]. A calculation on the simple model systems [K(C3H5)] and [Cs(C3H5

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

• Manuel Pedrón,
• Laura Legnani,
• Maria-Assunta Chiacchio,
• Pierluigi Caramella,
• Tomás Tejero and
• Pedro Merino

Beilstein J. Org. Chem. 2019, 15, 1552–1562, doi:10.3762/bjoc.15.158

• ]. Computations were done using the B3LYP functional [48][49] in conjunction with Grimme’s dispersion correction [50][51] (henceforth referred to as B3LYP-d3bj). The standard basis set Def2SVP was employed [52][53]. For the purpose of comparison optimizations at gas phase and considering solvent effects (both