1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• interactions such as hydrogen bonding, π–π stacking, electrostatic interactions, van der Waals forces, hydrophobic/solvatophobic effects and coordination bonds [2][3]. Advances in supramolecules from molecular to macroscopic size with pre-structured or functionalized receptors and multivalent binding positions

Synthesis of benzo[d]imidazo[2,1-b]benzoselenoazoles: Cs₂CO₃-mediated cyclization of 1-(2-bromoaryl)benzimidazoles with selenium

• Mio Matsumura,
• Yuki Kitamura,
• Arisa Yamauchi,
• Yoshitaka Kanazawa,
• Yuki Murata,
• Tadashi Hyodo,
• Kentaro Yamaguchi and
• Shuji Yasuike

Beilstein J. Org. Chem. 2019, 15, 2029–2035, doi:10.3762/bjoc.15.199

• adjacent molecules being 3.333 (C8–C24) and 3.380 Å (C18–C13) (Figure 1b). Moreover, there were intermolecular interactions between Se(1) and N(3) atoms, and the Se(1)‒N(3) distance was 3.133 Å, which was 86% of the sum of the van der Waals radii (3.54 Å) of both elements (see Supporting Information File 1

Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• 3.136 Å (Cl−) or from 3.194 Å to 3.280 Å (Br−). The location of anion above the tetrazine centroid with the shorter distance than the sum of van der Waals radius indicated explicitly the typical noncovalent anion–π attraction. It is interesting to point out that in the host–guest complexes, all

Selenophene-containing heterotriacenes by a C–Se coupling/cyclization reaction

• Pierre-Olivier Schwartz,
• Sebastian Förtsch,
• Astrid Vogt,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2019, 15, 1379–1393, doi:10.3762/bjoc.15.138

• crystals continuously increased from DTT 1 to DSS 4 (190.8 Å3, 203.8 Å3, 206.3 Å3, and 216.2 Å3) mostly due to the larger van der Waals radii of the selenium versus sulfur atoms (190 vs 180 pm) [38]. Bond distances and angles showed the expected differences between selenophene and thiophene rings: C–Se

• Å with S and 3.028 Å with Se) in a face-to-edge orientation (Figure 3c, Table S4a in Supporting Information File 1) [40]. We found as well several non-bonding S–Se contacts (3.644 Å) with four neighboring molecules in all crystallographic axes, which are slightly shorter than the sum of the van der

• Waals radii (3.70 Å), implying a 3-dimensional electronic coupling between the molecules of DST 3 in the crystal (Figure 3c, Table S2 in Supporting Information File 1). A similar situation has also been observed for DTS 2 (Figure S5, Table S1, and Table S5 in Supporting Information File 1) and DSS 4

Formation of an unexpected 3,3-diphenyl-3H-indazole through a facile intramolecular [2 + 3] cycloaddition of the diazo intermediate

• Andrew T. King,
• Hugh G. Hiscocks,
• Lidia Matesic,
• Mohan Bhadbhade,
• Roger Bishop and
• Alison T. Ung

Beilstein J. Org. Chem. 2019, 15, 1347–1354, doi:10.3762/bjoc.15.134

• ) found here. Both distances are less than the van der Waals (VDW) separation of 2.40 Å [16]. The new cyclic example is slightly longer (2.48 Å), but well under the value of 2.80 Å (= VDW + 0.40) discussed by Dance [17]. All three distance values must be treated with caution since their H atoms are in

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• distortion of the pyranoside ring [1][2], which strongly modifies the chemical behaviour of the pyranoside substrate by influencing the spatial environment of the reaction center and changing stereoelectronic effects [3][4][5]. A rather complex case is observed for sulfate groups; in addition to van der

• Waals interactions their negative charges contribute to the electrostatic forces. The per-O-sulfation results in drastic conformational changes of pyranosides: β-glucopyranosides, β-xylopyranosides and β-glucuronides [6][7][8][9]. The furanosides are generally more conformationally flexible than

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

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• synclincal range and the 5’-hydroxy group in an axial arrangement. Additionally, the distance between the 5’-oxygen and the equatorial fluorine atom Fa of 2.80 Å (6a) and 2.73 Å (6b) correlated with the sum of their van der Waals radii (Table S1, Supporting Information File 1). Interestingly, the two

• arrangement and the 5’-hydroxy group a pseudoaxial orientation. Again, the spacing between the 5’-oxygen and the equatorial aligned fluorine atom Fa of 2.61 Å corresponded to the sum of their van der Waals radii. Interestingly, this distance was shorter in the minimal conformer of nucleoside 7 than in the

Dispersion interactions

• Peter R. Schreiner

Beilstein J. Org. Chem. 2018, 14, 3076–3077, doi:10.3762/bjoc.14.286

• Peter R. Schreiner Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany 10.3762/bjoc.14.286 Keywords: London dispersion; van-der-Waals potential; London dispersion (LD) [1][2][3], the attractive part of the van-der-Waals [4] (vdW) potential

• , enzyme catalysis, and much more. Hence, this thematic issue covers selected aspects of the role LD plays for structures and reactivity. Naturally, it addresses diverse topics for which LD is particularly apparent. Peter R. Schreiner Giessen, November 2018 Dispersion = attractive part of the van-der-Waals

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• limiting factor regarding the packing of molecules. Here we show that the attractive part of the van der Waals potential can be similarly decisive. For the semiconductor surface Si(001), an already covalently bonded molecule of cyclooctyne steers a second incoming molecule via dispersion interactions onto

• shown that dispersion effects are not only important for the thermodynamic stability of molecule–adsorbate complexes but they also crucially influence the adsorption path. While Pauli repulsion is often discussed as important effect for determining surface adsorption, the attractive part of the van der

• Waals potential can be of similar importance. For the system cyclooctyne on Si(001), attractive dispersion interactions lead to a preferred adsorption of a second molecule in the neighbourhood of a first adsorbate – an arrangement that is often excluded due to Pauli repulsion arguments. Experimental

Some mechanistic aspects regarding the Suzuki–Miyaura reaction between selected ortho-substituted phenylboronic acids and 3,4,5-tribromo-2,6-dimethylpyridine

• Piotr Pomarański,
• Piotr Roszkowski,
• Jan K. Maurin,
• Armand Budzianowski and
• Zbigniew Czarnocki

Beilstein J. Org. Chem. 2018, 14, 2384–2393, doi:10.3762/bjoc.14.214

• due to electronic reasons, but is strongly disfavoured by steric repulsion (bigger van der Waals radius of the bromine atom compared to the methyl group). This may be the reason for the first arylation to occur at the C-3(5) position in compound 4 and the second one preferably at the C-4 position

Evaluation of dispersion type metal···π arene interaction in arylbismuth compounds – an experimental and theoretical study

• Ana-Maria Preda,
• Małgorzata Krasowska,
• Lydia Wrobel,
• Philipp Kitschke,
• Phil C. Andrews,
• Jonathan G. MacLellan,
• Lutz Mertens,
• Marcus Korb,
• Tobias Rüffer,
• Heinrich Lang,
• Alexander A. Auer and
• Michael Mehring

Beilstein J. Org. Chem. 2018, 14, 2125–2145, doi:10.3762/bjoc.14.187

• the analysis of single crystal X-ray diffraction data and computational studies. First, the crystal structures of polymorphs of Ph3Bi (1) are described emphasizing on the description of London dispersion type bismuth···π arene interactions and other van der Waals interactions in the solid state and

• ···Cl and Bi···π arene interactions, resulting in an intermolecular pincer-type coordination at the bismuth atom. A detailed analysis of three polymorphs of Ph3Bi (1), which were chosen as model systems, at the DFT-D level of theory supported by DLPNO-CCSD(T) calculations reveals how van der Waals

• contacts are considerably shorter than the sum of the van der Waals radii of bismuth atoms (Bi···Bi contacts of 4.046 Å; ΣrvdW(Bi, Bi) 4.08–5.14 Å)) [60][61][62] and are in good agreement with the ones reported recently in a theoretical study by Jansen and co-workers who discussed dispersion type Bi···Bi

A self-assembled photoresponsive gel consisting of chiral nanofibers

• Lei Zou,
• Dan Han,
• Zhiyi Yuan,
• Dongdong Chang and
• Xiang Ma

Beilstein J. Org. Chem. 2018, 14, 1994–2001, doi:10.3762/bjoc.14.174

• by three-dimensional networks through self-assembly have drawn significant attention in the past decades. They are normally fabricated by means of noncovalent intermolecular interactions [3], such as π–π stacking, hydrogen bonding, van der Waals forces, hydrophobic, electrostatic, host–guest and

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

• Rakesh Puttreddy,
• Ngong Kodiah Beyeh,
• S. Maryamdokht Taimoory,
• Daniel Meister,
• John F. Trant and
• Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

• of Laplacians (2ρ(r)) at the BCPs were from 0.0134 to 0.0397 a.u. suggesting the existence of a weak “closed shell” [50][51][52] character for non-covalent interactions (such as ionic bonds, HBs, stacking type and van der Waals interactions) between 3 and BrC6 (Table 2). This is completely consistent

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

• Eric Detmar,
• Valentin Müller,
• Daniel Zell,
• Lutz Ackermann and
• Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

• – the attractive part of the van-der-Waals interaction – is known for more than 100 years [1][2]. The stabilizing nature of C–H···H–C interactions and their importance for organic transformations has only been fully realized within the last decades [3]. Among others, these interactions explain the

• agreement with the experimental findings: The calculated high barriers match the prolonged reaction times and high temperature required in the experimental studies and the reversible C–H metalation [30]. Influence of London dispersion In recent years, London dispersion, the attractive part of the van-der

• -Waals force, has been repeatedly identified as key to stabilizing organic structures and facilitating novel reactivities [3]. As the Cp* ligand is a C–H-rich molecule, we envisioned that dispersive interactions should be important for this transformation as well. As a consequence, we have analyzed this

Steric “attraction”: not by dispersion alone

• Ganna Gryn’ova and
• Clémence Corminboeuf

Beilstein J. Org. Chem. 2018, 14, 1482–1490, doi:10.3762/bjoc.14.125

• difference between the optimized and frozen dimers (i.e., ∆E = Etotal or component[optimized] – Etotal or component[frozen]) for the representative cores from classes (II) and (III), as well as the M06-2X/def2-SVP geometries of their optimized dimers (clipped van der Waals surfaces are shown in orange

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• van der Waals complexes near their equilibrium geometries [46]. The so-called basis set superposition error (BSSE) was not taken into account for the geometry optimization and intermolecular energy calculation, because this correction was included in the parametrization procedure of the XC functional

Are dispersion corrections accurate outside equilibrium? A case study on benzene

• Tim Gould,
• Erin R. Johnson and
• Sherif Abdulkader Tawfik

Beilstein J. Org. Chem. 2018, 14, 1181–1191, doi:10.3762/bjoc.14.99

• (MBD) and its fractionally ionic (FI) variant performing essentially as well. Popular approaches, such as Grimme-D and van der Waals density functional approximations (vdW-DFAs) underperform on our tests. The meta-GGA M06-L is surprisingly good for a method without explicit dispersion corrections. Some

• problems with SCAN+rVV10 are uncovered and briefly discussed. Keywords: benzene; DFT; dispersion; van der Waals; Introduction The past decade has seen an increasing awareness of the role played by van der Waals dispersion forces in chemistry and materials science [1][2][3][4][5][6]. It has consequently

• of dispersion correction models. Note, this is different to seamless approaches like MP2, RPA or other quantum chemistry methods which include dispersion forces automatically. Common van der Waals corrections can be broadly divided into three categories, as will be detailed below. Substantial effort

One hundred years of benzotropone chemistry

• Arif Dastan,
• Haydar Kilic and
• Nurullah Saracoglu

Beilstein J. Org. Chem. 2018, 14, 1120–1180, doi:10.3762/bjoc.14.98

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• interactions are also augmented by a series of electrostatic and van der Waals interactions including salt bridge formation with the phosphate backbone [1]. Although, the majority of proteins recognize DNA in the major groove due, in large part, to the potential and shape complementarity, several others also

• considered similar to a standard lock and key recognition [30]. Minor groove binding drugs (MGBs) are usually isohelical, crescent-shaped molecules, which are compatible with the shape of the minor groove. Binding of MGBs and proteins occurs primarily via H-bonds, electrostatics, van der Waals and

• activities were evaluated [102]. A molecular docking study has revealed that GRA interacts with ct-DNAs via hydrogen bonding interactions between the oxygen atoms of GRA and adenine bases of DNA and van der Waals interactions. Moreover, GRA significantly reduces the polymerization activity of DNA polymerase

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• ] force fields, which are based on a modeling of the water pair potential using an electrostatic contribution described by interacting point charges and a van der Waals interaction contribution using Lennard-Jones potentials. In more advanced ab initio water pair potentials the force field is fitted to

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study

• Ahmet Altun,
• Frank Neese and
• Giovanni Bistoni

Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79

• polarization effects compared with the dominating electrostatic interaction [15][16][18][19]. Herein, particular emphasis is given in discussing the role played by London dispersion, which constitutes the attractive part of the van der Waals potential and has long been considered a weak effect compared to the

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• numerous van der Waals and C–H···O interactions mainly between the guest and the inner dimeric host cavity. The observed host–guest interactions along with the extended hydrogen bond network between water molecules, hosts and guest are listed analytically in Supporting Information File 1, Table S1. In

• a very stable inclusion complex even at high temperatures. Van der Waals intermolecular forces are the predominant interactions sustaining the complex stability in aqueous solution (Table 2). Conclusion The crystal structure of CHL in β-CD reveals the formation of a 2:1 host:guest inclusion complex

• . CHL is found encapsulated axially in a head-to-head β-CD dimer (host A and host B), tightly bound via numerous van der Waals and C–H···O interactions to the inner dimeric host cavity. The hydroxy group and the isopropyl group of the guest protrude from the primary rim of the host A and host B

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

• Ido Azuri,
• Anna Hirsch,
• Anthony M. Reilly,
• Alexandre Tkatchenko,
• Shai Kendler,
• Oded Hod and
• Leeor Kronik

Beilstein J. Org. Chem. 2018, 14, 381–388, doi:10.3762/bjoc.14.26

• or without Tkatchenko–Scheffler–van der Waals (TS-vdW) interactions [28]. In this approach, the vdW energy is added as a pair-wise interaction and has only one semi-empirical parameter. This parameter determines the onset of the pair-wise interaction and is fitted, once and for all per a given

• interactions, lattice parameters are in general too large (owing to the lack of van der Waals attraction) and errors with respect to experiment are of the order of 5–10%. These observations are fully consistent with previous studies that have compared PBE and PBE+TS-vdW predictions for geometries [25][45

• , without TS-vdW interactions various vibrational modes are strongly shifted to much lower frequencies (consistent with the missing treatment of van der Waals interactions) and, furthermore, the overall spectral shape is different. Second, the calculation indicates that the experimental spectrum contains

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• ). All experiments were performed in triplicate. (a) Structures of isoleucine (1), leucine (2), and their fluorinated analogues 5,5,5-trifluoroisoleucine (3, TfIle) and 5,5,5,5’,5’,5’-hexafluoroleucine (4, HfLeu). The van der Waals volumes given in parentheses correspond to the side chains (starting at α