Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• the DFT calculation realized by the PWscf code of Quantum ESPRESSO [30][31][32], the DFT-D3 correlation [33] together with PBEsol functional [34] for the exchange-correlation functional described van der Waals interaction between graphene and pyrene fragment in PASE. Ultrasoft pseudopotentials [35

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

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

• is driven by van der Waals interactions, and no new electronic states are created by electronic perturbations between the host and the guest, except for a few examples using special fullerenes as guest molecules, i.e. [11]CPP⊃La@C82 [39], and [10]CPP⊃Li+@C60 [40], and [10]CPP⊃(C59N)2 [41], or

• + and [10]CPP is 0.365 nm, which is very close to the sum of the van der Waals radii of an sp2 carbon (0.340 nm) [44]. This mode of interaction is similar to that observed in the complex formed from [10]CPP and C70 [24]. In contrast, complex 2 has a less ordered interaction compared to 1; while each

• line (Figure 5c), significantly stabilizing the complex formation. These results confirm the importance of van der Waals interactions for the formation of [10]CPP⊃[5]CPP2+. Mulliken population analysis indicates 10 to ≈15% electron transfer from the host [10]CPP to the guest [5]CPP2+ in complexes 1, 2

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• + C60 to assess the effect ionization produced by the electron beam has in the process. Before the reaction takes place, a stabilizing van der Waals complex between the two C60 molecules was formed (Figure 2), with an interdimer distance around 3 Å (slightly larger for the neutral profile). For dimer 1

• inside the CNT was analyzed. In contrast to the gas phase reaction, we now only found the initial van der Waals complex and a single transition state TS for both the neutral and the radical cation profiles (Figure 3). The van der Waals complex shows an interdimer C···C distance of 2.86 Å, slightly

• differences, which corroborates the validity of our periodic approximation to study the dimerization of the radical cation inside the CNT (see below). The rate-determining transition state for the radical cation and for the neutral dimer is the same (TS2) as well as the lowest-energy intermediate (van der

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

• –180° [39][49][50], and with halogen bond lengths that are typically less than or equal to the sum of the atomic Van der Waals radii of the engaged atoms [33]. The strength of a subsequent halogen bond is influenced by the magnitudes of the positive electrostatic potential (VS,max) of the donor and the

• ). The authors’ explanation for the improved reactivity of o-anisyl derivative 39 was based on its improved solubility in dichloromethane. The contact distances were both within the Van der Waals radii criteria for confirming non-covalent interactions [33], which likely contributed to the ylide’s

A new oxidatively stable ligand for the chiral functionalization of amino acids in Ni(II)–Schiff base complexes

• Alena V. Dmitrieva,
• Oleg A. Levitskiy,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2023, 19, 566–574, doi:10.3762/bjoc.19.41

• are presented in different colors: the hydrogen bonding are labeled in blue color of the reduced density gradient isosurface; green color corresponds to the dispersion interactions (van der Waals interactions, the π-stacking); red color represents steric clashes. The interplay of these through-space

• protons. Low-gradient isosurfaces with low densities (blue color of the isosurface corresponds to the hydrogen bonding; the dispersion interactions (van der Waals interactions, the π-stacking) are marked in green color; red color indicates steric clashes) obtained for the ʟ- (left image) and ᴅ-alanine

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• symmetrical sandwich configuration as optimal for the largest exciton splitting, while other reports suggested a favored orientation with one aromatic moiety displaced (ca 1.4 Å) from the other to minimize van der Waals repulsion [30]. Redistribution of charges at acidic pH (protonated phenanthridine nitrogen

Computational studies of Brønsted acid-catalyzed transannular cycloadditions of cycloalkenone hydrazones

• Manuel Pedrón,
• Jana Sendra,
• Irene Ginés,
• Tomás Tejero,
• Jose L. Vicario and
• Pedro Merino

Beilstein J. Org. Chem. 2023, 19, 477–486, doi:10.3762/bjoc.19.37

• cyclohexanes. The resulting system is given in square brackets. In parentheses the integration over the volumes of −λ2·ρ2 representing the total integration data corresponding to the weak noncovalent van der Waals interactions (represented in green). Higher forces like H-bonds are indicated as blue discs. In

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• other related molecules. Based on the collected data, the porphyrin complex 160 was found to show J-type aggregation in both polar and nonpolar solvents. In polar solvents, aggregation was induced by van der Waals interactions between H-cardanol moieties, while π–π stacking interactions between

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• /MM optimized complexes 28:dGMII (top) and 31:dGMII (bottom) [22]. N-2-naphthylmethyl group (grey) and (R)-1-hydroxyethyl group (green) of 28 and the hydroxymethyl group (green) of 31 are visualized by van der Waals spheres to highlight the unfavorable interaction (marked with a black arrow) between

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

• of 14-3-3ζ with GCP and lysine ligands, we proceeded as follows. The GCP and lysine ligand geometries were calculated in OpenBabel v2.3.2 [30] starting from a SMILES string of each ligand. The van der Waals radii of ligand atoms were added automatically by OpenBabel. The 14-3-3ζ structure (PDB 4IHL

• , [20]) was refined with MODELLER [31] as described in reference [26]. Charges, van der Waals radii and missing hydrogen atoms were added by PDB2PQR v2.0.0 [27][28] at pH 6.5 with the Amber force field option (values are provided as a table in Supporting Information File 2 and in Supporting Information

• generate a pre-calculated Hamiltonian for a grid-based description of the electrostatic and van der Waals interactions. We have also tried a grid resolution of 0.8 Å which would have allowed more efficient calculations. However, the 0.8 Å resolution was not fine enough to accurately capture essential

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• by accounting for molecular repulsion and attraction caused by van-der-Waals forces, hydrogen bonding, and Coulomb forces. The ePC-SAFT parameters of the nucleotides were fitted in previous works to experimental osmotic pressures of pseudo-binary mixtures of nucleotide and water [29][33]. As

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• aromatic walls that offer van-der-Waals and π–π stacking interactions in order to compensate for the absence of a strong electrostatic interaction. These non-covalent/ionic interactions play an important role in encapsulating aromatic organic molecules, especially in aqueous medium. Along this rationale

Host–guest interaction and properties of cucurbit[8]uril with chloramphenicol

• Lin Zhang,
• Jun Zheng,
• Guangyan Luo,
• Xiaoyue Li,
• Yunqian Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 2832–2839, doi:10.3762/bjoc.17.194

• and carbon atoms and the cavity has a certain degree of hydrophobicity that can form a stable host–guest inclusion complex with a guest molecule via non-bonding interactions, such as hydrogen bonds, van der Waals forces and ionic dipoles [21][22][23][24][25][26][27][28]. It has been proved that

Targeting active site residues and structural anchoring positions in terpene synthases

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 2441–2449, doi:10.3762/bjoc.17.161

• ). SmTS1 has a low amino acid sequence identity to other characterised TPSs, with the diterpene synthase (DTS) for cattleyene from Streptomyces cattleya as one of the closest relatives, which shows only 29% sequence identity [17]. We have recently shown that the sum of the calculated van der Waals volumina

Constrained thermoresponsive polymers – new insights into fundamentals and applications

• Patricia Flemming,
• Alexander S. Münch,
• Andreas Fery and
• Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

• –temperature graphs for polymer brushes. With regard to the interactions between the chains, a distinction is made between so-called classical polymer brushes, in which only van der Waals interactions dominate between the chains, nonclassical neutral brushes, in which additional specific interactions occur

• detail. According to the type of supramolecular interactions governing the thermoresponsive behavior UCST type polymers can be classified into two categories. Although various molecular forces such as van der Waals interactions and hydrophobic effects contribute to the thermoresponsiveness of polymers

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• –C triplets than J when binding to dsRNA, which was suggested to be a combined effect of improved van der Waals contacts, base stacking, hydrogen bonding, and reduced dehydration energy [98]. Replacement of three Js with Ls increased the binding affinity of a PNA 8-mer ≈4-fold [98]. In addition, the

Co-crystallization of an organic solid and a tetraaryladamantane at room temperature

• Fabian Rami,
• Jan Nowak,
• Felix Krupp,
• Wolfgang Frey and
• Clemens Richert

Beilstein J. Org. Chem. 2021, 17, 1476–1480, doi:10.3762/bjoc.17.103

• have thus far evaded crystallization by themselves. Structure of TDA and TEO, the crystallization hosts used for co-crystallization. Details of the X-ray crystal structures obtained, shown as ORTEP plots at 50% probability, with van der Waals radii of the phenol molecules set to 60%. a) Asymmetric unit

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• ‘guests’ within the crystal lattice, through hydrogen-bonding and van der Waals forces. Thereafter, research over the crystal engineering of porphyrins has focused on the noncovalent interactions, such as hydrogen bonds and halogen bonds, or metal coordination interactions [2][3][4][5][6][7][8][9][10][11

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• show no hydrogen bonds in their crystal structures and only van der Waals interactions take place between the molecules. The bistetrazolium salt 9 (bromide salt of mesoionic compound 10) crystallizes in the trigonal space group , with 18 formula units in the unit cell. The asymmetric unit includes one

Annulation of a 1,3-dithiole ring to a sterically hindered o-quinone core. Novel ditopic redox-active ligands

• Sergey V. Norkov,
• Anton V. Cherkasov,
• Andrey S. Shavyrin,
• Maxim V. Arsenyev,
• Viacheslav A. Kuropatov and
• Vladimir K. Cherkasov

Beilstein J. Org. Chem. 2021, 17, 273–282, doi:10.3762/bjoc.17.26

• intramolecular contacts with the sulfur atoms. The S(1)–O(2) distance (Figure S4 in Supporting Information File 1) is 2.560(2) Å, it is less than the sum of the van der Waals radii. A very similar geometry was previously observed in the case of the acetylacetonate unit attached to a 1,3-dithiole ring [31]. o

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• photocatalytic reaction with a rate acceleration facilitated by supramolecular host–guest interactions and hybrid materials are typically assisted by noncovalent forces, including Coulomb and van der Waals forces, hydrogen bonding, and π–π interactions. For potential supramolecular photocatalysts, they should

• the outside possesses the polyhydroxy structure. This unique asymmetric barrel-shaped cavity allows them to combine with various guests. The driving forces for the formation of cyclodextrin-based supramolecular complexes are hydrophobic and van der Waals interactions between the cavity and 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

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• -aminobutyric acid associate with membrane-bound protein receptors and trigger changes in receptor shape and activity with subsequent signaling across the membrane. Noncovalent H-bonding and van der Waals interactions are the basis for the selective molecular recognition between a G-coupled protein receptor and