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

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

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• energetically favourable non-covalent interactions, hydrogen bonds, and van der Waals interactions formed between the DNA/RNA and solvent, and between the compound 4 and solvent. The large positive entropy changes suggest solvent release upon binding, which makes a favourable contribution to the reaction Gibbs

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• TA spectra. The direct reaction between AQN and the substrate was not observed by TAS. The authors’ DFT calculations revealed reaction pathways that were thermodynamically and kinetically plausible. Initially, AQN and Selectfluor® (S0 in Scheme 16) form a van der Waals complex RC1, which is markedly

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

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• reaction of fluoroalkylidene-oxetanes was directed by the presence of the fluorine atom, enabling a two-step access to tetrasubstituted fluoroalkenes with excellent geometry control. Despite its small van der Waals radii electronic, rather than steric influences of the fluorine atom governed the ring

Models of necessity

• Timothy Clark and
• Martin G. Hicks

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

• classical mechanical model that punishes deviation from preferred bond lengths, angle and dihedrals, and considers non-bonded electrostatic and van der Waals contributions. Thus, there are potentials for bonds, angles between bonds, dihedrals and interactions between distant atoms combined with a point

• electrostatic potential on the van der Waals surface of the molecule, rather than the outdated and often misleading net atomic charges [95]. Simple additive models for polarizability already exist [96]. As quantitative models for intermolecular interaction energies can be built using these quantities [97

• . The nuclei are represented as spheres (whose size is vastly exaggerated) color coded according to their charge. The gray surface is approximately the 0.01 a.u. isodensity surface, which corresponds approximately to the van der Waals surface of the molecule. Jacobus van’t Hoff’s molecular models. The

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

• -stacking and Van der Waals interactions, rendering the material insoluble in most solvents [120][121]. g-C3N4 materials are typical organic semiconductors with band gaps of approximately 2–5 eV, usually showing a maximum absorbance at 420 nm, which yields its characteristic yellow colour [120]. Significant

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• and allows the establishment of an intramolecular contact between Cl1 and H7A. The non-bonding distance Cl1–H7A is 2.565(3) Å, which is much shorter than the sum of the van der Waals radii (2.95 Å) [51]. The same syn arrangement between the ortho-substituent and the benzylidene proton has also been

• shorter than the sum of the van der Waals radii (2.67 Å) [51]. This suggest a close interaction between these two atoms, as observed in the crystal structure of 2c (see above). The analysis of other internal bond distances and angles in the coordination sphere of the Pd atom shows that they are similar to

Ultrasonic-assisted unusual four-component synthesis of 7-azolylamino-4,5,6,7-tetrahydroazolo[1,5-a]pyrimidines

• Yana I. Sakhno,
• Maryna V. Murlykina,
• Oleksandr I. Zbruyev,
• Anton V. Kozyryev,
• Svetlana V. Shishkina,
• Dmytro Sysoiev,
• Vladimir I. Musatov,
• Sergey M. Desenko and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2020, 16, 281–289, doi:10.3762/bjoc.16.27

• endocyclic bond (the C4–N1–C3–C7 and N1–C3–C7–C12 torsion angles were −163.6(4)° and 19.7(7)°, respectively). Short intramolecular contacts appeared: the H1(N)···H12 distance was 2.10 Å and the van der Waals radii sum [37] was 2.34 Å, the H···N1 distance was 2.55 Å (and the van der Waals radii sum was 2.67 Å

• ), while the H1···C12 distance was 2.60 Å, with a van der Waals radii sum of 2.87 Å. The two vicinal substituents at the C1 atom had different orientations in relation to the partially saturated cycle: the ester substituent was in an axial position, while the other substituent was found in an equatorial

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• when the proton–fluorine closest approach distance is within the sum of the van der Waals radii of hydrogen and fluorine (c. 2.55 Å)...” [47]. During rotation of the fluorophenyl ring (Figure 6), the F–H distance (for both F–H5 and F–H3) varies between 2 and 5 Å, so for some part of the rotation, both

The use of isoxazoline and isoxazole scaffolding in the design of novel thiourea and amide liquid-crystalline compounds

• Itamar L. Gonçalves,
• Rafaela R. da Rosa,
• Vera L. Eifler-Lima and
• Aloir A. Merlo

Beilstein J. Org. Chem. 2020, 16, 175–184, doi:10.3762/bjoc.16.20

• ability to establish intra- and intermolecular hydrogen bonds [11]. In addition to π–π, dipole–dipole and van der Waals interactions, hydrogen bond interactions are involved in gel formation through self-aggregation of the small gelator molecules. In recent years, there has been increased interest in the

• , intensity, resolution and peaks of some phase transitions are lost. Considering that molecules self-organize upon cooling, first by hydrogen bonds followed by π-stacking and van der Waals forces, DSC scanning at 10 °C/min is too fast to allow the molecules to self-assemble in a perfect 3D matrix. Even with

Halogen-bonding-induced diverse aggregation of 4,5-diiodo-1,2,3-triazolium salts with different anions

• Xingyu Xu,
• Shiqing Huang,
• Zengyu Zhang,
• Lei Cao and
• Xiaoyu Yan

Beilstein J. Org. Chem. 2020, 16, 78–87, doi:10.3762/bjoc.16.10

• which are due to the XB. The C–I···I angles are 176.9(3)° and 176.2(3)° (Table 1). The I···I distance is short: the reduction ratio RXB [45], defined as the ratio of the actual distance over the sum of van der Waals radii, amounts to 0.81. The 2-Br crystal package has a similar package diagram. 2-Br

1,5-Phosphonium betaines from N-triflylpropiolamides, triphenylphosphane, and active methylene compounds

• Vito A. Fiore,
• Chiara Freisler and
• Gerhard Maas

Beilstein J. Org. Chem. 2019, 15, 2603–2611, doi:10.3762/bjoc.15.253

• properties of the substituent R (Scheme 7) [26][27][28]. In Z-3e, the intramolecular P···O distance is 2.691 Å, significantly longer than in compounds 8 (2.00–2.36 Å), but still much shorter than the sum of the van der Waals radii (3.32 Å). A distance similar to that in Z-3e has been reported for a betaine

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

• μe or μe − μg. The first value is the van der Waals radius ρ = (3V/4π)1/3, where the van der Waals volume V is the sum of atomic increments [64]. The second value was chosen arbitrarily as a typical value. In addition, both these values of ρ were not verified with respect to their applicability for

• der Waals radius ρ = 410 [51][52][55][57][58]. This fit yields μg = 7.81 D instead of 11.97 D (Table 2) and μe = 11.94 D instead of 18.30 D (Table 2). These values are close to μg = 8.2 D and μe = 14.4 D from reference [56], where both dipole moments were determined by similar analysis of absorption

• for NR is adapted for solvatochromy in our work, reliable values of the ground state and excited state dipole moments of NR can indeed be calculated. The crucial importance of the correct value for the Onsager radius is demonstrated by fitting data from Table 1 with Equation 2 and Equation 5 for a van

Reversible switching of arylazopyrazole within a metal–organic cage

• Anton I. Hanopolskyi,
• Soumen De,
• Michał J. Białek,
• Yael Diskin-Posner,
• Liat Avram,
• Moran Feller and
• Rafal Klajn

Beilstein J. Org. Chem. 2019, 15, 2398–2407, doi:10.3762/bjoc.15.232

• encapsulated two molecules of E-1 (in agreement with the NMR spectra), arranged in an antiparallel fashion (Figure 3). The binding of E-1 within 2 is driven by a combination of π–π stacking, van der Waals forces, and C–H···π interactions (vide infra); in addition, the encapsulation is likely facilitated by the

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

• to van der Waals contacts) All conformations possible at room temperature are considered To translate the atomic dimensions to a viewing process the van der Waals radii and the following scale has been applied: 1 pm 1 mm The hypothetical viewing distance for the mathematic calculation as well as for

• represent them spherically shaped (van der Waals spheres, stick model) or they convey the idea of gaps between the individual atoms and leave out their decrease of inner density (ball and stick model, wire model). Due to the limited validity of each individual model and the recognition of the