Interactions of cyclodextrins and their derivatives with toxic organophosphorus compounds

• Sophie Letort,
• Sébastien Balieu,
• William Erb,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2016, 12, 204–228, doi:10.3762/bjoc.12.23

• hydrophobic interactions, hydrogen bonding and van der Waals forces. In some cases, the formation of a stable inclusion complex results the guest’s hydrolysis reaction rate increase. Degradation/hydrolysis of pesticides The inclusion of organophosphorus pesticides into the CDs cavity could either promote or

Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

• Giuseppina Raffaini,
• Fabio Ganazzoli and
• Antonino Mazzaglia

Beilstein J. Org. Chem. 2016, 12, 73–80, doi:10.3762/bjoc.12.8

• last part of the MD run when no change was detected in the energy components (i.e., the intramolecular terms, the van der Waals component and the electrostatic one due to the dipolar interactions) showed that the first aggregate is more stable than the other one by about 1.32 ± 0.19 MJ, where the

Supramolecular polymer assembly in aqueous solution arising from cyclodextrin host–guest complexation

• Jie Wang,
• Zhiqiang Qiu,
• Yiming Wang,
• Li Li,
• Xuhong Guo,
• Duc-Truc Pham,
• Stephen F. Lincoln and
• Robert K. Prud’homme

Beilstein J. Org. Chem. 2016, 12, 50–72, doi:10.3762/bjoc.12.7

• Winnik et al. [63][64][65]. 2.2 Comparison of guests Cyclodextrin host–guest complexation of guest species in aqueous solutions is largely driven by van der Waals and hydrophobic interactions between the interior of the cyclodextrin annulus and the guest with dehydration of both substantially influencing

Determination of formation constants and structural characterization of cyclodextrin inclusion complexes with two phenolic isomers: carvacrol and thymol

• Miriana Kfoury,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2016, 12, 29–42, doi:10.3762/bjoc.12.5

• are inside the CD cavity [46]. This also indicated a shielding effect due to the interactions between guest and CD [47], particularly by van der Waals interactions [48]. These observations suggested that the whole guest molecule is involved in the binding process to CD with the aromatic cycle of both

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• Table 1. It seems that both flavanones interacted with cyclodextrins through van der Waals (vdW) force 2 to 5-fold stronger than electrostatic interaction. The ∆Evdw and ∆Eele of hesperetin/β-CD and hesperetin/DM-β-CD were −23.58 and −31.30 kcal·mol−1 and −9.95 and −5.90 kcal·mol−1, respectively (Table

Synthesis and photophysical characteristics of polyfluorene polyrotaxanes

• Aurica Farcas,
• Giulia Tregnago,
• Ana-Maria Resmerita,
• Pierre-Henri Aubert and
• Franco Cacialli

Beilstein J. Org. Chem. 2015, 11, 2677–2688, doi:10.3762/bjoc.11.288

• synthesis of 1·TM-βCD or 1·TM-γCD in polar protic solvents is driven by hydrophobic interactions in combination with electrostatic, van der Waals or π–π interactions. In comparison, in polar aprotic solvents such as DMF, THF relies mostly on host–guest specific interactions, such as dispersion or dipole

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• aggregation stage that may persist for quite a long time. The aggregation process led to an apparent equilibration, as suggested inter alia by the lack of change in the potential and van der Waals energy of the whole system in the last half of the MD run (see Figure 12). Of course much lengthier processes

• atoms of the hydroxyl groups at the secondary rim and in the P groups (red symbols) in cluster A plotted as a function of their distance r from the cluster c.o.m. The time change of the potential energy and of the van der Waals energy due to the dispersion and covolume interactions in the MD run of

Urethane tetrathiafulvalene derivatives: synthesis, self-assembly and electrochemical properties

• Xiang Sun,
• Guoqiao Lai,
• Zhifang Li,
• Yuwen Ma,
• Xiao Yuan,
• Yongjia Shen and
• Chengyun Wang

Beilstein J. Org. Chem. 2015, 11, 2343–2349, doi:10.3762/bjoc.11.255

• nanomaterials is generally accepted to be the self-assembly of supermolecules, which is constructed through weak noncovalent interactions such as π–π stacking, van der Waals interactions, charge transfer and H-bonding interactions [3][4][5][6]. Generally speaking, H-bonding interactions are the key

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• The gas phase energy, ΔEMM, is a summation of bonded and non-bonded (electrostatic and van der Waals (vdW)) energies obtained from molecular mechanics calculation. The ΔGsolv is solvation free energy. In general, there are several methods for ΔGsolv prediction. Some methods calculate the ΔGsolv using

• key factor controlling the formation of inclusion complexes; van der Waals interactions could be more important. The MM-PBSA result in Table S2, Supporting Information File 1, confirmed this assumption; the main contribution for α-MGS inclusion arises from van der Waals interactions (ΔEvdW) 7–8 fold

• > −5 kcal/mol in pure water and low ethanol concentrations to −8.69, −10.17 and −10.20 kcal/mol in 30, 60 and 100% v/v ethanol. By contrast, the van der Waals energy contribution (ΔEvdW) was reduced by ≈10–15 kcal/mol due to almost total displacement of the α-MGS xanthone ring from the β-CD cavity via

2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

• Yury A. Sayapin,
• Inna O. Tupaeva,
• Alexandra A. Kolodina,
• Eugeny A. Gusakov,
• Vitaly N. Komissarov,
• Igor V. Dorogan,
• Nadezhda I. Makarova,
• Anatoly V. Metelitsa,
• Valery V. Tkachev,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2015, 11, 2179–2188, doi:10.3762/bjoc.11.236

• along the C(2)–C(7) and C(3)–C(6) lines by 140–150°. As in the previously studied 2-hetaryl-1,3-tropolones [19][20][23] the O···N distances in 5g and 6e are about 0.5 Å shorter than the corresponding van der Waals contact. This geometric feature points to the very strong intramolecular N-H···O hydrogen

• strong intramolecular N–H···O hydrogen bond that closes up the cycle Н(1)–N(1)–С(8)–С(2)–С(3)–О(2). The N(1)···О(2) distance (2.514 Å) is 0.5 Å shorter than the corresponding van der Waals contact angle. The molecular structure of a representative 2-(2-ethoxycarbonyl-6-hydroxy-3,4,5-trichlorophenyl

Half-sandwich nickel(II) complexes bearing 1,3-di(cycloalkyl)imidazol-2-ylidene ligands

• Johnathon Yau,
• Kaarel E. Hunt,
• Laura McDougall,
• Alan R. Kennedy and
• David J. Nelson

Beilstein J. Org. Chem. 2015, 11, 2171–2178, doi:10.3762/bjoc.11.235

• the shortest Cl–H distance being ca. 2.9 Å, approximately the sum of van der Waals radii of the two atoms. Assessment of catalytic activity With these new complexes in hand, their activity in some model cross-coupling reactions was examined. Ritleng and Chetcuti have deployed [Ni(Cp)(X)(NHC

Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

• Zhan-Ting Li

Beilstein J. Org. Chem. 2015, 11, 2057–2071, doi:10.3762/bjoc.11.222

• bonding, but the stability decreases successively, which is consistent with the decrease of their electronegativity, but may also reflect the increase of the van der Waals radius. These weak intramolecular hydrogen bonds cannot compete with the strong intermolecular N–H···O=C hydrogen bonds of the amide

The simple production of nonsymmetric quaterpyridines through Kröhnke pyridine synthesis

• Isabelle Sasaki,
• Jean-Claude Daran and
• Gérard Commenges

Beilstein J. Org. Chem. 2015, 11, 1781–1785, doi:10.3762/bjoc.11.193

• -chair conformation. The packing is stabilised by van der Waals contacts and weak π–π interactions between symmetry related N2-C21-C22-C23-C24-C25 and N4-C41-C42-C43-C44-C45 pyridine rings (1+x, y, z) with a centroid-to-centroid distance of 3.761(2) Å, and an average interatomic distance between planes

Star-shaped tetrathiafulvalene oligomers towards the construction of conducting supramolecular assembly

• Masahiko Iyoda and
• Masashi Hasegawa

Beilstein J. Org. Chem. 2015, 11, 1596–1613, doi:10.3762/bjoc.11.175

• bonding, metal coordination, CT interaction, π···π stacking, van der Waals interaction, etc.) play an important role in the formation of the three-dimensional (3D) crystal structures [5]. For the construction of nanostructured objects, π···π, S···S, and other weak intermolecular interactions first

Thiazole-induced rigidification in substituted dithieno-tetrathiafulvalene: the effect of planarisation on charge transport properties

• Rupert G. D. Taylor,
• Joseph Cameron,
• Iain A. Wright,
• Neil Thomson,
• Olena Avramchenko,
• Alexander L. Kanibolotsky,
• Anto R. Inigo,
• Tell Tuttle and
• Peter J. Skabara

Beilstein J. Org. Chem. 2015, 11, 1148–1154, doi:10.3762/bjoc.11.129

• the influence of favourable S–N interactions contributes to a more planar structure. The S and N atoms are separated by a distance of 3.01 Å, 0.34 Å shorter than the sum of the van der Waals radii of the two atoms (3.35 Å). In the electrochemistry section of this paper we discussed how the S–N

New tris- and pentakis-fused donors containing extended tetrathiafulvalenes: New positive electrode materials for rechargeable batteries

• Shintaro Iwamoto,
• Yuu Inatomi,
• Daisuke Ogi,
• Satoshi Shibayama,
• Yukiko Murakami,
• Minami Kato,
• Kazuyuki Takahashi,
• Kazuyoshi Tanaka,
• Nobuhiko Hojo and
• Yohji Misaki

Beilstein J. Org. Chem. 2015, 11, 1136–1147, doi:10.3762/bjoc.11.128

• strong van der Waals force between the large π-electron frameworks of the thiophene-inserted pentakis-fused TTF. The energy densities for the first discharge process (1st energy densities) calculated by multiples of the initial discharge capacity and the average voltage are also summarized in Table 3

Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths

• Yuchun Ren,
• Bin Wang and
• Xiuqing Zhang

Beilstein J. Org. Chem. 2015, 11, 1089–1095, doi:10.3762/bjoc.11.122

• the aggregates change from flower-like, network and rod with different sizes. By using IR and XRD characterization, it is found that intermolecular H-bonding, the solvents and van der Waals interaction are the main contributions to the specific superstructure. Keywords: azobenzene; cholesterol

• ], etc. The driving force for the spontaneous formation of gel could be relatively non-covalent interactions such as π–π stacking [4][5][6][7], hydrogen bonding [7][8][9], dipole–dipole [10], and van der Waals interactions [11][12]. A series of cholesterol-based gelators were reported [13][14][15]. These

• new classes of organogelator architectures have been systematically studied because of their reversible gel process and unique directional self-association through weak van der Waals interactions [16][17]. Up to now, numerous attempts have been made to develop novel supramolecular architectures, which

Donor–acceptor type co-crystals of arylthio-substituted tetrathiafulvalenes and fullerenes

• Xiaofeng Lu,
• Jibin Sun,
• Shangxi Zhang,
• Longfei Ma,
• Lei Liu,
• Hui Qi,
• Yongliang Shao and
• Xiangfeng Shao

Beilstein J. Org. Chem. 2015, 11, 1043–1051, doi:10.3762/bjoc.11.117

• the different directions, which result in the 3D carrier transport pathway [38][39][40][41]. Structural comparison As has previously been reported, the van der Waals length of the C6S8 core in the Ar-S-TTF molecule is about 12.8 Å [61][63], which is larger than the van der Waals diameters of C60 (10 Å

• least one of the fullerene molecules. Moreover, the dimensionality of the packing motifs of fullerene molecules increases, resulting in a 2D network through multiple van der Waals forces. Upon further increase of the ratio of fullerene molecules in the co-crystal (e.g., 2·(C70)4·(PhCl)2), the packing

Tuning of tetrathiafulvalene properties: versatile synthesis of N-arylated monopyrrolotetrathiafulvalenes via Ullmann-type coupling reactions

• Vladimir A. Azov,
• Diana Janott,
• Dirk Schlüter and
• Matthias Zeller

Beilstein J. Org. Chem. 2015, 11, 860–868, doi:10.3762/bjoc.11.96

• directed weak hydrogen bonds as well as C–H···π and S···S interactions. Addition of new parallel layers, connected to the previous layers via dispersive interactions of the van der Waals type, can be assumed to be a much slower process, leading to plate like crystals that mimic the layered makeup at the

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• peptide atoms and both polymer and solvent atoms as the sum of van-der-Waals and electronic contributions (Table 2) While the interaction energies between peptides and solvents are, as expected, nearly identical for all three systems, the interaction of peptide atoms regarding polymer atoms amounts to

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

• Manuel Gensler,
• Christian Eidamshaus,
• Maurice Taszarek,
• Hans-Ulrich Reissig and
• Jürgen P. Rabe

Beilstein J. Org. Chem. 2015, 11, 817–827, doi:10.3762/bjoc.11.91

• UPy dimers (DDAA–AADD pairs) in hexadecane. The UPy dimers exhibit shorter rupture lengths of 0.20 nm compared to 0.29 nm, resulting in much higher rupture forces from 150 to 250 pN compared to 50–100 pN for UAT dimers. Another model system probing π–π-interactions associated with van-der-Waals forces

Anionic sigmatropic-electrocyclic-Chugaev cascades: accessing 12-aryl-5-(methylthiocarbonylthio)tetracenes and a related anthra[2,3-b]thiophene

• Laurence Burroughs,
• John Ritchie,
• Mkhethwa Ngwenya,
• Dilfaraz Khan,
• William Lewis and
• Simon Woodward

Beilstein J. Org. Chem. 2015, 11, 273–279, doi:10.3762/bjoc.11.31

• ]. This might also depopulate 5 limiting the final yield of 7. However, the following factors suggested to us the viability of Scheme 2: (i) traces of allenes have been observed when preparing xanthates from propargylic alcohols [17]; (ii) the relative van der Waals volumes of SOPh, Ph, CS2− and C(=S)SMe

Synthesis and characterization of pH responsive D-glucosamine based molecular gelators

• Navneet Goyal,
• Hari P. R. Mangunuru,
• Bargav Parikh,
• Sonu Shrestha and
• Guijun Wang

Beilstein J. Org. Chem. 2014, 10, 3111–3121, doi:10.3762/bjoc.10.328

• referred to as supramolecular gelators or molecular gelators. They can form reversible gels in organic solvents, aqueous mixtures, and water. The gelation process is completely driven by weak intermolecular forces such as hydrogen bonding, π–π stacking, hydrophobic forces, and van der Waals forces. The

Thermal and oxidative stability of the Ocimum basilicum L. essential oil/β-cyclodextrin supramolecular system

• Daniel I. Hădărugă,
• Nicoleta G. Hădărugă,
• Corina I. Costescu,
• Ioan David and
• Alexandra T. Gruia

Beilstein J. Org. Chem. 2014, 10, 2809–2820, doi:10.3762/bjoc.10.298

• relative encapsulation efficiency and the hydrophobicity (log P). These two variables include both structural characteristics (from E.E.) and transport/van der Waals interaction aspects (from log P). These parameters retain characteristics from one another. The PCA analysis allows extraction of the useful

Mono- and multilayers of molecular spoked carbazole wheels on graphite

• Stefan-S. Jester,
• A. Vikas Aggarwal,
• Daniel Kalle and
• Sigurd Höger

Beilstein J. Org. Chem. 2014, 10, 2783–2788, doi:10.3762/bjoc.10.295

• be ascribed to a mechanical interlocking together with a high van der Waals interaction due to the large molecule size. It is worth to note that these investigations may also give insight into the spoked wheel organization in the bulk material. Conclusion Precursor 1 and MSW 2 self-assemble at the OA