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

CF₃SO₂X (X = Na, Cl) as reagents for trifluoromethylation, trifluoromethylsulfenyl-, -sulfinyl- and -sulfonylation. Part 1: Use of CF₃SO₂Na

• Hélène Guyon,
• Hélène Chachignon and
• Dominique Cahard

Beilstein J. Org. Chem. 2017, 13, 2764–2799, doi:10.3762/bjoc.13.272

• contain it. The CF3 group has a large van der Waals volume somewhere between those of the iPr and the t-Bu groups [9]. Its electronegativity is comparable to that of oxygen (4.0 versus 3.5 on the Pauling scale) and its hydrophobicity is large (0 for H, 0.51 for Me, and 1.07 for CF3) [10]. In this respect

Spatial effects in polymer chemistry

• Helmut Ritter

Beilstein J. Org. Chem. 2017, 13, 2015–2016, doi:10.3762/bjoc.13.198

• play a crucial role for the chain growth and chemical conversion of polymers in many cases. Among the spatial effects are H-bonds, van der Waals interactions, ionic forces, dipolar interactions, self-ordering effects and steric influences. Through IR-spectroscopic studies we have recently found that

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

• the CD macrocycle’s dimensions. The host–guest interactions established in the cavity are of van der Waals type, whereas between parts of the guest extending out of the cavity and the host’s hydroxy groups are H-bonding interactions and/or of electrostatic nature. CDs have been studied and used for

Aggregation behaviour of a single-chain, phenylene-modified bolalipid and its miscibility with classical phospholipids

• Simon Drescher,
• Vasil M. Garamus,
• Christopher J. Garvey,
• Annette Meister and
• Alfred Blume

Beilstein J. Org. Chem. 2017, 13, 995–1007, doi:10.3762/bjoc.13.99

• DSC heating scan are about 5 K higher compared to Tm-values of the lipid analogue PC-C17pPhC17-PC with a slightly shorter alkyl chain (two methylene units) [35]. The increase in Tm is caused by the elongation of the alkyl chain, which leads to an increase in van-der-Waals contacts of neighbouring bola

• . However, due to the very long alkyl chains, the remaining van-der-Waals contacts are sufficient for the formation of fibrous aggregates above the first transition [26][40]. This seems to be also the case for PC-C18pPhC18-PC. SANS In order to ensure the results obtained with TEM and IR, SANS measurements

• above the first transition via van-der-Waals interactions. The mixing of PC-C18pPhC18-PC with bilayer-forming phosphatidylcholines (DMPC, DPPC, or DSPC) leads in most cases to the formation of small elongated micelles, bilayer fragments, or disk-like aggregates. However, an increased thermal stability

Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

• Franca Castiglione,
• Fabio Ganazzoli,
• Luciana Malpezzi,
• Andrea Mele,
• Walter Panzeri and
• Giuseppina Raffaini

Beilstein J. Org. Chem. 2017, 13, 714–719, doi:10.3762/bjoc.13.70

• integrated using the Verlet algorithm with a time step of 1 fs at a temperature of 300 K, controlled through the Berendsen thermostat. Equilibration of the resulting adducts was monitored through the time change of the total energy and of its components (including also the van der Waals components) and of

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• interaction between the positively charged amino group in DOX and the negatively charged groups on the CD surface can take place. Also van der Waals and π–π stacking interactions were attributed as contributing factors to the DOX loading and DOX incorporation into the hollow CD cavity. Drug release at acidic

• intermediates; while glucose mostly interacts with the amine dopants through intramolecular forces such as van der Waals’ forces and hydrogen bonds. The latter weaker interactions cause the intermediates to break down into small fragments during the heating process resulting in smaller CDs. In the case of N

A new class of organogelators based on triphenylmethyl derivatives of primary alcohols: hydrophobic interactions alone can mediate gelation

• Wangkhem P. Singh and
• Rajkumar S. Singh

Beilstein J. Org. Chem. 2017, 13, 138–149, doi:10.3762/bjoc.13.17

• -stacking, donor–acceptor interaction, electrostatic, metal coordination, hydrophobic forces or van der Waals’ interactions [4][5][6]. We know a great deal about the aggregation behaviour of gelator molecules from many studies conducted during the past several years. However, rational design and accurate

The synthesis of α-aryl-α-aminophosphonates and α-aryl-α-aminophosphine oxides by the microwave-assisted Pudovik reaction

• Erika Bálint,
• Ádám Tajti,
• Anna Ádám,
• István Csontos,
• Konstantin Karaghiosoff,
• Mátyás Czugler,
• Péter Ábrányi-Balogh and
• György Keglevich

Beilstein J. Org. Chem. 2017, 13, 76–86, doi:10.3762/bjoc.13.10

• compound 5d, where all H···H contacts appear around or longer than the respective sums of van der Waals radii, and the only short attractive contact is in the H-bridge promoted dimer. Theoretical study on the addition of the >P(O)H species to N-benzylideneamines The calculations were carried out by the

Supramolecular frameworks based on [60]fullerene hexakisadducts

• Andreas Kraft,
• Johannes Stangl,
• Ana-Maria Krause,
• Klaus Müller-Buschbaum and
• Florian Beuerle

Beilstein J. Org. Chem. 2017, 13, 1–9, doi:10.3762/bjoc.13.1

• (left part of Figure 4). Interestingly, this packing motif results in the interpenetration of two independent hydrogen bonding networks (indicated in purple and cyan in Figure 5). Therefore, the individual layers are densely packed exhibiting linear columns of fullerenes in van-der-Waals distance