Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

• Bodee Nutho,
• Wasinee Khuntawee,
• Chompoonut Rungnim,
• Piamsook Pongsawasdi,
• Peter Wolschann,
• Alfred Karpfen,
• Nawee Kungwan and
• Thanyada Rungrotmongkol

Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296

• binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the

• of the two individual molecules upon complexation process was taken from the normal mode analysis. Therefore, Equation 2 can be rewritten as: where ΔEMM is the energy of molecular mechanics composed of bonded and non-bonded energies. The latter one contains the electrostatic (ΔEele) and van der Waals

• complexes (−9 to −11 kcal/mol), whilst slightly stronger van der Waals interactions (∆EvdW) by 1–2 kcal/mol were observed in the complexes II and III. As expected, the vdW force is the key interaction in forming the inclusion complex as seen by approximate 3-fold stronger interaction than electrostatic

Self-assembled monolayers of shape-persistent macrocycles on graphite: interior design and conformational polymorphism

• Joscha Vollmeyer,
• Friederike Eberhagen,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2014, 10, 2774–2782, doi:10.3762/bjoc.10.294

• carbon backbones axially rotated by 90°; Figure 1b) and a deq of 0.35 nm [9][10][11][12]. Shape-persistent macrocycles on HOPG form non-covalent 2D assemblies held together by the van der Waals interaction between the alkyl side chains even without the presence of any additional functional groups [13][14

• and the packing of the side chains that are adsorbed on the substrate. Reducing the symmetry of the hexagon, or reducing the numbers of side chains on some of the hexagon sides, should lead to an unequal van der Waals interaction strength along different directions, which would consequently allow also

• polymorph) and only slightly varying (dense polymorph) unit cell parameters for all three compounds are formed. This is a clear result of the driving force for the pattern formation, which is – at least for the porous polymorph – a combination of van der Waals interactions between the molecules and the

Synthesis and properties of novel star-shaped oligofluorene conjugated systems with BODIPY cores

• Clara Orofino-Pena,
• Diego Cortizo-Lacalle,
• Joseph Cameron,
• Muhammad T. Sajjad,
• Pavlos P. Manousiadis,
• Neil J. Findlay,
• Alexander L. Kanibolotsky,
• Dimali Amarasinghe,
• Peter J. Skabara,
• Tell Tuttle,
• Graham A. Turnbull and
• Ifor D. W. Samuel

Beilstein J. Org. Chem. 2014, 10, 2704–2714, doi:10.3762/bjoc.10.285

• methyl substituents at the 1,3,5,7-positions (Figure 4). The distance between the hydrogens of the fluorene and the fluorines of the BODIPY in Y-B1 are 2.20 Å and 2.23 Å. These distances are shorter than the sum of the van der Waals radii of H (1.20 Å) and F (1.47 Å), which is 2.67 Å. This implies that

• (2.42 Å and 2.44 Å) are also smaller than the sum of the van der Waals radii, also indicating the possibility of H–F interactions. The greater degree of planarity in Y-B1 leads to increased conjugation and therefore a lower HOMO–LUMO gap, which is predicted from the DFT calculations and is observed in

Molecular ordering at electrified interfaces: Template and potential effects

• Thanh Hai Phan and
• Klaus Wandelt

Beilstein J. Org. Chem. 2014, 10, 2243–2254, doi:10.3762/bjoc.10.233

• the former depend on the specific nature of the molecular building blocks, e.g., their shape, polarity, functional groups, etc., and may include all possible interactions from van der Waals forces to covalent bonds, the latter are described by the so-called “corrugation function”, i.e., the two

Scalable synthesis of 5,11-diethynylated indeno[1,2-b]fluorene-6,12-diones and exploration of their solid state packing

• Bradley D. Rose,
• Peter J. Santa Maria,
• Aaron G. Fix,
• Chris L. Vonnegut,
• Lev N. Zakharov,
• Sean R. Parkin and
• Michael M. Haley

Beilstein J. Org. Chem. 2014, 10, 2122–2130, doi:10.3762/bjoc.10.219

• utilized 3 – while the solid-state structure of 3 showed several sub-van der Waals contact distances, the n-type mobility of the OFET was very low (2 × 10−5 cm2 V−1 s−1) [14]. On the other hand, an OFET utilizing 4 (X = F) had measured electron mobilities of 0.17 cm2 V−1 s−1, and its X-ray crystal

Lateral ordering of PTCDA on the clean and the oxygen pre-covered Cu(100) surface investigated by scanning tunneling microscopy and low energy electron diffraction

• Stefan Gärtner,
• Benjamin Fiedler,
• Oliver Bauer,
• Antonela Marele and
• Moritz M. Sokolowski

Beilstein J. Org. Chem. 2014, 10, 2055–2064, doi:10.3762/bjoc.10.213

• ones. In order to determine the orientation of the two molecules within the unit cell the outer contours of the molecules given by the van der Waals spheres [13] were superimposed and fitted to the STM image. With an estimated uncertainty of about ±3° the long molecular axes are orientated 45° with

• preparation temperatures for highly ordered layers. However, the question whether the chemisorption is dissociative or not still needs to be answered. So far, all our structural findings stand against dissociative adsorption: (a) In STM images, like Figure 3(a), the van der Waals-radii of the PTCDA molecules

• ). 3 × 3 unit cells and the van der Waals radii [13] of the PTCDA molecules are indicated (black lines). (b) Hardsphere model for the (4√2 × 5√2)R45° structure of PTCDA on Cu(100). Carbon atoms: dark grey, oxygen atoms: red, and hydrogen atoms: white, copper atoms light grey. Further details see text

Theoretical study of the adsorption of benzene on coinage metals

• Werner Reckien,
• Melanie Eggers and
• Thomas Bredow

Beilstein J. Org. Chem. 2014, 10, 1775–1784, doi:10.3762/bjoc.10.185

• polarizability of the gold atoms. The adsorption distances are almost the same on these two surfaces due to the similar van der Waals radii of 172 pm for Ag [55] and 166 pm for Au [55]. Hence, the larger C6 coefficients of 317.2 a.u. for the gold atoms [56] (compared to 268.6 a.u. for the silver atoms [56

• smaller van der Waals radius of 140 pm [55]. From there the dispersion interaction to the copper surface is largest although Cu has the smallest C6 coefficients. PBE-D3, PBE-D3(BJ) and RPBE-D3 tend to slightly overestimate the adsorption energies in comparison to experiment, in particular for the Cu(111

Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

• Christian B. Winiger,
• Simon M. Langenegger,
• Oleg Khorev and
• Robert Häner

Beilstein J. Org. Chem. 2014, 10, 1589–1595, doi:10.3762/bjoc.10.164

• well as van der Waals, electrostatic and charge transfer interactions that can lead to a thermodynamically favourable association [8]. It is an important interaction in biological systems, drug receptor interactions, materials sciences, and supramolecular chemistry [8][9][10][11][12]. Such interactions

Biantennary oligoglycines and glyco-oligoglycines self-associating in aqueous medium

• Svetlana V. Tsygankova,
• Alexander A. Chinarev,
• Alexander B. Tuzikov,
• Nikolai Severin,
• Alexey A. Kalachev,
• Juergen P. Rabe,
• Alexandra S. Gambaryan and
• Nicolai V. Bovin

Beilstein J. Org. Chem. 2014, 10, 1372–1382, doi:10.3762/bjoc.10.140

• glycines. The more flexible core C10 should lead to a entropy driven destabilization. The opposite effect observed in reality is most probably caused by van der Waals interactions of hydrophobic fragments C10 closely situated in the PG II structure. The oligoethylene glycol core abolishes the formation of

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• the solute molecule forms a cavity within the dielectric continuum of permittivity ε that represents the solvent, and which neglects the cavitation and the solute–solvent dispersion term. For ε we chose 4.806 which is the value of chloroform. The distance of solvents to van der Waals radii of the atom

The influence of intraannular templates on the liquid crystallinity of shape-persistent macrocycles

• Joscha Vollmeyer,
• Ute Baumeister and
• Sigurd Höger

Beilstein J. Org. Chem. 2014, 10, 910–920, doi:10.3762/bjoc.10.89

• scanning calorimetry, optical microscopy and X-ray scattering. It can be assumed that the additional van der Waals interaction between the stretched intraannular alkyl chains stabilize the packing of the rings on top of each other. When the alkyl bridge is longer than the ring interior or when an

Molecular recognition of isomeric protonated amino acid esters monitored by ESI-mass spectrometry

• Andrea Liesenfeld and
• Arne Lützen

Beilstein J. Org. Chem. 2014, 10, 825–831, doi:10.3762/bjoc.10.78

• ][26] which causes a smaller van der Waals volume of the deuterated group [27][28][29][30][31][32]. In a first approximation, however, the dispersive interactions get stronger with an increasing size of the volume and consequently the contact area, and hence, the deuterated compounds ability to

Charge-transfer interaction mediated organogels from 18β-glycyrrhetinic acid appended pyrene

• Jun Hu,
• Jindan Wu,
• Qian Wang and
• Yong Ju

Beilstein J. Org. Chem. 2013, 9, 2877–2885, doi:10.3762/bjoc.9.324

• driving forces for the formation of such self-assembled fibrillar networks include hydrogen-bonding interaction, van der Waals force, π–π stacking, and donor–acceptor interaction [7][8][9][10]. Since LMWGs are often thermally reversible and the gelation can be triggered by pH or the addition of small

Synthesis of enantiomerically pure (2S,3S)-5,5,5-trifluoroisoleucine and (2R,3S)-5,5,5-trifluoro-allo-isoleucine

• Holger Erdbrink,
• Elisabeth K. Nyakatura,
• Susanne Huhmann,
• Ulla I. M. Gerling,
• Dieter Lentz,
• Beate Koksch and
• Constantin Czekelius

Beilstein J. Org. Chem. 2013, 9, 2009–2014, doi:10.3762/bjoc.9.236

• biological membrane or the kind of hydrophobic interactions, that would be present in hydrophobic cores of proteins and in ligand–receptor binding [27]. We extended these initial studies by 2-aminoheptanoic acid (Aha) as an amino acid with an unbranched aliphatic side chain. The van der Waals volumes of the

• packing arrangements within the hydrophobic core of coiled-coils [14][15], we believe that 5-F3Ile demonstrates a promising building block for fluorine modifications within this folding motif. Retention times of Fmoc amino acids plotted against the van der Waals volume of their side chains. Non-fluorinated

• der Waals volume versus their retention time from an RP-HPLC experiment, we previously investigated the relationship between size and hydrophobicity of various fluorinated and non-fluorinated amino acids [26]. In this experiment the non-polar phase of a reversed-phase column serves as a mimic of a

Synthesis and antibacterial activity of monocyclic 3-carboxamide tetramic acids

• Yong-Chul Jeong and
• Mark G. Moloney

Beilstein J. Org. Chem. 2013, 9, 1899–1906, doi:10.3762/bjoc.9.224

• ground state. MarvinSketch Version 5.3.8. (http://www.chemaxon.org) was used for the calculation of the van der Waals molecular surface area (MSA), the polar surface area (PSA), the calculated partition coefficient (c log P) under VG method, the calculated distribution coefficient at pH 7.4 [c log D (7.4

Self-assembly of 2,3-dihydroxycholestane steroids into supramolecular organogels as a soft template for the in-situ generation of silicate nanomaterials

• Valeria C. Edelsztein,
• Andrea S. Mac Cormack,
• Matías Ciarlantini and
• Pablo H. Di Chenna

Beilstein J. Org. Chem. 2013, 9, 1826–1836, doi:10.3762/bjoc.9.213

• , electrochemistry, light-harvesting materials and so on [1][2][3][4][5][6]. These small molecules self-assemble into regular supramolecular structures through non covalent interactions such as ion–ion, dipole–dipole, hydrogen bonding, π–π stacking, van der Waals, host–guest, and ion coordination, and in so doing

• organogelators [22]. The steroidal LMOGs usually have substituents attached to the 3β-OH of the cholestane A ring and synthetic variations at the steroidal skeleton are scarce. Cholesterol-based LMOGs build mesophases in which steroid–steroid stacking is controlled by van der Waals forces. These interactions

• energy for each dimer–dimer interface for the β-octamer A was 8.1 kcal/mol and for the β-octamer B 8.3 kcal/mol. This stabilization between the dimers arises from hydrogen bonding between the dimers with H–OH distances of about 2.8 Å, and van der Waals interactions between the hydrocarbonated skeletons

Electron self-exchange activation parameters of diethyl sulfide and tetrahydrothiophene

• Martin Goez and
• Martin Vogtherr

Beilstein J. Org. Chem. 2013, 9, 1448–1454, doi:10.3762/bjoc.9.164

• expectation because the restricted geometric freedom and more compact configuration of the aliphatic substituents leave the sulfur atom more accessible; furthermore, the obtained reaction distance is practically equal to twice the van-der-Waals radius of sulfur [50], so is also very plausible. Conclusion The

Space filling of β-cyclodextrin and β-cyclodextrin derivatives by volatile hydrophobic guests

• Sophie Fourmentin,
• Anca Ciobanu,
• David Landy and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1185–1191, doi:10.3762/bjoc.9.133

• mol−1 for p-tert-butylbenzoate [3]. The observed increase of complex stability with increasing size of the hydrophobic part of the guest can be explained by the increase of hydrophobic interactions as well as other nonpolar interactions, e.g., van der Waals and dispersive interactions [9]. The

Enhancement of efficiency in organic photovoltaic devices containing self-complementary hydrogen-bonding domains

• Rohan J. Kumar,
• Jegadesan Subbiah and
• Andrew B. Holmes

Beilstein J. Org. Chem. 2013, 9, 1102–1110, doi:10.3762/bjoc.9.122

• systems and dimerized nucleobases; however, in these cases an upfield change in chemical shift is generally observed, [5][30] in contrast to the downfield movement in chemical shift observed for the vinyl proton in compound 2. Non-specific van der Waals interactions are typically weaker than hydrogen

Ring opening of 2-aza-3-borabicyclo[2.2.0]hex-5-ene, the Dewar form of 1,2-dihydro-1,2-azaborine: stepwise versus concerted mechanisms

• Holger F. Bettinger and
• Otto Hauler

Beilstein J. Org. Chem. 2013, 9, 761–766, doi:10.3762/bjoc.9.86

• /def2-TZVP level of theory is only 3.4 kcal mol−1 with respect to infinitely separated monomers, and 5.6 kcal mol−1 with respect to the energy of a van-der-Waals complex of two monomers. Conclusion The following conclusions can be drawn from the computational investigation. 1. The “classical

Electron and hydrogen self-exchange of free radicals of sterically hindered tertiary aliphatic amines investigated by photo-CIDNP

• Martin Goez,
• Isabell Frisch and
• Ingo Sartorius

Beilstein J. Org. Chem. 2013, 9, 437–446, doi:10.3762/bjoc.9.46

• the latter. To get the molecular dimensions, we added the van-der-Waals radii of the respective outermost atoms along each semi-axis (N, 1.55 Å [51] for the shorter semi-axis of DABCO; H, 1.1 Å [52] for all other semi-axes) and averaged the three diameters. Identifying the shorter diameter with the

Spin state switching in iron coordination compounds

• Philipp Gütlich,
• Ana B. Gaspar and
• Yann Garcia

Beilstein J. Org. Chem. 2013, 9, 342–391, doi:10.3762/bjoc.9.39

• ][63]. One has also found that certain vibrational modes of lattice constituents, such as non-coordinating anions or solvent molecules, interconnecting the spin state changing metal complexes via hydrogen bonds, van der Waals or other interactions, can “feel” spin state changes at the metal centers and

A new family of four-ring bent-core nematic liquid crystals with highly polar transverse and end groups

• Kalpana Upadhyaya,
• Venkatesh Gude,
• Golam Mohiuddin and
• Rao V. S. Nandiraju

Beilstein J. Org. Chem. 2013, 9, 26–35, doi:10.3762/bjoc.9.4

• molecule and, hence, leads to an increase in the bending angle. An increase in bending angle may contribute to increased van der Waals interactions and dispersion forces and, hence, promote mesomorphism during the cooling cycle in these compounds. The absence of mesomorphism in 1e and 1f may be attributed

Theoretical study on β-cyclodextrin inclusion complexes with propiconazole and protonated propiconazole

• Adrian Fifere,
• Narcisa Marangoci,
• Stelian Maier,
• Adina Coroaba,
• Dan Maftei and
• Mariana Pinteala

Beilstein J. Org. Chem. 2012, 8, 2191–2201, doi:10.3762/bjoc.8.247

• compounds in aqueous solution. The driving forces leading to complexation are numerous, varying from van der Waals to hydrophobic and to dipole–dipole interactions [6][7]. Since CDs and their complexes are widely used in pharmaceutical sciences and synthesis, there is currently a great interest in the

• narrow rim into the β-cyclodextrin cavity. The β-CD/sulconazole is stabilized by van der Waals interactions and hydrogen bonds. In fact, the author explained the difference between the A and B orientations in the case of sulconazole by the occurrence of hydrogen bonds. In the present case, no hydrogen

A bisazobenzene crosslinker that isomerizes with visible light

• Subhas Samanta,
• Harris I. Qureshi and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2012, 8, 2184–2190, doi:10.3762/bjoc.8.246

• -isomers (force constant 16). Molecular dynamics runs were performed in vacuo, essentially as described previously [36], with a distance-dependent dielectric constant, and 1–4 scale factors of 0.833 for electrostatic and 0.5 for van der Waals interactions, a step size of 1 fs and 300 K as the simulation