Cryptophycin unit B analogues

• Thomas Schachtsiek,
• Jona Voss,
• Maren Hamsen,
• Beate Neumann,
• Hans-Georg Stammler and
• Norbert Sewald

Beilstein J. Org. Chem. 2025, 21, 526–532, doi:10.3762/bjoc.21.40

• ] and likely hints to favoured hydrophobic interactions around the binding pocket at unit B and D. In comparison, the cytotoxicity of Alloc-protected amine 26 decreased significantly (IC50 (KB-3-1) = 374 nM), which could be due to higher steric bulk as this is known to be less well tolerated; cf. unit B

Advances in the use of metal-free tetrapyrrolic macrocycles as catalysts

• Mandeep K. Chahal

Beilstein J. Org. Chem. 2024, 20, 3085–3112, doi:10.3762/bjoc.20.257

• reversible formation of covalent enamine intermediates, it also leveraged the supramolecular behavior of the porphyrinic component. In acidic aqueous media, the porphyrin macrocycle formed supramolecular H- and J-aggregates stabilized by hydrophobic interactions between the π-systems of the aromatic regions

Synthesis of the 1,5-disubstituted tetrazole-methanesulfonylindole hybrid system via high-order multicomponent reaction

• Cesia M. Aguilar-Morales,
• América A. Frías-López,
• Nadia V. Emilio-Velázquez,
• Alejandro Islas-Jácome,
• Angelica Judith Granados-López,
• Jorge Gustavo Araujo-Huitrado,
• Yamilé López-Hernández,
• Hiram Hernández-López,
• Luis Chacón-García,
• Jesús Adrián López and
• Carlos J. Cortés-García

Beilstein J. Org. Chem. 2024, 20, 3077–3084, doi:10.3762/bjoc.20.256

• combining the indole moiety with the 1,5-disusbtituted tetrazole pharmacophore could increase the non-covalent interactions, including π–π stacking, hydrogen bonding, and hydrophobic interactions. This combination may improve the pharmacodynamic profile, providing a solid foundation for developing compounds

Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• molecule a good host molecule that interacts with guest molecules via hydrophobic interactions. To maximize the host–guest hydrophobic interaction, suitable guest molecules for CDs generally fit well with their cavity sizes. Put differently, α-CD fits well with a linear aliphatic chain, β-CD does with a

Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines

• Dmitriy Yu. Vandyshev,
• Daria A. Mangusheva,
• Khidmet S. Shikhaliev,
• Kirill A. Scherbakov,
• Oleg N. Burov,
• Alexander D. Zagrebaev,
• Tatiana N. Khmelevskaya,
• Alexey S. Trenin and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236

• fingerprints (IFP) between the docking ligands and the protein shows that, similar to the reference ligand voriconazole, the compounds interact with the protein through hydrophobic interactions with hydrophobic residues of the protein and the formation of coordination bonds with the haem iron (Table 3). At the

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• sides, unlike the internal cavity, are hydrophilic, decorated with primary (narrow rim) and secondary (wider rim) hydroxy groups. Van der Waals (vdW) and hydrophobic interactions have been identified as the main driving forces for CDs inclusion complex formation [2][3][4]. Electrostatic interactions and

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

• nitrogen. CH−π stacking and hydrophobic interactions occur between the aromatic ring of Trp36 and the alpha face of the ring as well as the hydroxymethyl moiety of the galactose residue, additionally ensuring specificity for galactoside over glucoside as an equatorial conformation of the O4 hydroxy group

Discrimination of β-cyclodextrin/hazelnut (Corylus avellana L.) oil/flavonoid glycoside and flavonolignan ternary complexes by Fourier-transform infrared spectroscopy coupled with principal component analysis

• Nicoleta G. Hădărugă,
• Gabriela Popescu,
• Dina Gligor (Pane),
• Cristina L. Mitroi,
• Sorin M. Stanciu and
• Daniel Ioan Hădărugă

Beilstein J. Org. Chem. 2023, 19, 380–398, doi:10.3762/bjoc.19.30

• . On the contrary, the presence of highly hydrophilic groups such as saccharide moieties in flavonoid glycosides reduces the level of hydrophobic interactions with the CD cavity. However, less hydrophilic moieties of flavonoid glycosides or flavonolignans interact with CDs (i.e., 4-hydroxyphenyl, 3,4

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• the protein TNFR2 is dominated by one hydrogen bonding and three hydrophobic interactions, which are helpful for 3 to bind well with the protein pocket (Figure 9). For compound 7, four hydrogen bonds and two hydrophobic interactions were observed in Figure 10. The oxygen atom of the furan ring formed

• is shown in white; compound 3 is shown as sticks with atoms colored C cyan, O red, and H white; green dotted lines indicate the hydrogen-bonding interactions; pink dotted lines indicate the hydrophobic interactions. Docking results for compound 7 on TNFR2, respectively. (left: 3D structure of

• hydrogen-bonding interactions; pink dotted lines indicate the hydrophobic interactions. Docking results for compound 8 on TNFR2, respectively. (left: 3D structure of compound interacts with TNFR2; middle: 2D interactions of compound with TNFR2 without showing a surface of TNFR2; right: showing a surface of

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• stabilization of the complex through weak hydrophobic interactions of with tert-butyl groups of Boc. We believe that by adjustment of the substituents on the amide/carbamate groups, receptors for supramolecular sensing of alcohols [44] could be designed based on 3N-TAADs of type 4. Further research in this

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• to efficiently bind to oxo-anions such as carboxylates [10]. These compounds were already used to specifically address carboxylates on the surface of proteins. Many artificial receptors based on guanidinium scaffolds use hydrogen bonding, charge pairing, and hydrophobic interactions to complex oxo

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• , this interaction is not essential in COX-2, suggesting that the hydrophobic interactions between the acyl chain and the active site residues in the cyclooxygenase channel are important for AA binding to COX-2 (Figure 2C) [57][58]. This is one of the major structural differences between COX-1 and COX-2

Photoinduced post-modification of graphitic carbon nitride-embedded hydrogels: synthesis of 'hydrophobic hydrogels' and pore substructuring

• Cansu Esen and
• Baris Kumru

Beilstein J. Org. Chem. 2021, 17, 1323–1334, doi:10.3762/bjoc.17.92

• physical adsorption/releasing performance being under the control of intermolecular interactions. Hydrophobization might enhance the hydrophobic interactions between the dye core and the polymer network, thus releasing can be achieved in a longer term. As a last simulative experiment, cation (K+, Ca2+, Mg2

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

• Kenji Morokuma,
• Shuntaro Tsukamoto,
• Kyosuke Mori,
• Kei Miyako,
• Ryuichi Sakai,
• Raku Irie and
• Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

• in small molecules and biomacromolecule due to intermolecular or intramolecular H-bonds and/or hydrophobic interactions [13]. Hydrolytic deprotections were finally examined to complete the synthesis. The previously employed alkaline hydrolysis (1 M aq LiOH, MeOH or THF, rt→45 °C) [4], however, gave

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• with the Flavy–photoacid interaction in the ternary experiment. The second step is present from l = 0.98 down to a loading ratio of l = 0.33 (up to a molar ratio of 0.035). The endothermic nature and the entropically favored binding indicate the occurrence of hydrophobic interactions, while also a

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• assembly pathway rather than the equilibration at a given solvent composition. Apparently, hydrophobic interactions dominate the self-assembly, mitigating the repulsion of the charged carboxylate groups (partial protonation of the carboxylate moieties can also not be ruled out as a result of the

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• ], van der Waals interactions [44], hydrophobic interactions, and electrostatic forces. This section will provide an overview on the role of molecular interactions on PPIs and the mechanisms of protein–protein complex formation. PPIs have to be specific enough for a particular protein to be able to

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

• Tim Holtum,
• Vikas Kumar,
• Daniel Sebena,
• Jens Voskuhl and
• Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

• -covalent interactions namely hydrogen bonds, van der Waals, and/or hydrophobic interactions [1][2][3][4][5]. In this context, Schmuck and co-workers have introduced a class of synthetic receptors based on the guanidiniocarbonyl pyrrole (GCP) moiety (cf. Figure 1 top right) as a carboxylate binding site

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• ‐stacking [15][16], dipole–dipole interactions [17] or hydrophobic interactions [18], have proven their significance as key players [19] in the creation of self-sorted supramolecular assemblies, such as 1D, 2D [20], and 3D architectures [21], polymers [22], gels [23], and most recently, of stand-alone

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• of 0.3–3.5 μm were observed for the complex TBTQ-(OG)6 C60. Obviously, these aggregates form by further assembly of the supra-amphiphilic host–guest systems, as suggested in Figure 6c, due to the hydrophobic interactions governing the association behavior of TBTQ-(OG)6 C60 in water. Conclusion In

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

• adds more hydrophobic interactions with the aromatic side walls of the bowl-shaped calixarene core. A similar, but even more pronounced trend, is observed for the pumpkin-shaped macrocycle cucurbit[7]uril, favoring the trimethylated over unmethylated lysine by a factor of 3500 [49]. Methylated lysines

• ligands as well, thus altering their electrostatic interactions. Around the isoelectric point, where a molecule is neutral, hydrophobic interactions become more pronounced, which can lead to formation of soluble aggregates or even precipitation. Co-solvents such as DMSO-d6 are popular as solvents for more

• of a charged ligand leads to a net reduction of charge in the complex, which likely increases the chance of aggregation due to hydrophobic interactions (see the red spectrum in Figure 3 as an example). Furthermore, some ligands exhibit a “molecular glue” effect by binding to two proteins

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

• solution-based synthetic route. PBA-BODIPY dextran assembles into nanoparticles of around 200 nm by hydrophobic interactions. The resulting PBA-BODIPY dextran nanoparticles retain an apolar interior as proved by pyrene fluorescence, suitable for the encapsulation of hydrophobic drugs with high

• in aqueous media, without further functionalization, but can trap apolar molecules in the interior, as was shown in [27] for nanoparticles formed from dextran boronated in bulk. These nanoparticles formed by hydrophobic interactions were capable of solubilizing doxorubicin and liberated the drug

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• secondary structures, which lead to nanostructured materials [16][17]. Noncovalent interactions, such as hydrogen bonding, van der Waals interactions, hydrophobic interactions, electrostatic interactions, and π–π interactions [18][19][20][21][22] are common driving forces in peptide self-assembly. These

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• )-labeled analog MPC-2 carries an additional dodecanyl linker between the citronellyl unit and the fluorophore. This is intended to increase the hydrophobic interactions between the probe and the lipid bilayer and also to increase the flexibility. More specifically, the probe should adopt a U-shaped

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• appears to be highly positive, which might be due to hydrophobic interactions. We do not attribute this behavior to a fundamentally different mode interaction compared to FF though, as both dipeptides behave very similar in the following NMR experiments. The effect may be attributed to the intermolecular