New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• complexed with 1,4-dioxane in 1970 [67]. The evidence of the actual bonding were found in these complexes as the O−Br distance in the crystal was about 2.71 Å (Scheme 12), which is 20% smaller than the sum of the van der Waals radii of oxygen and bromine (3.35 Å) while the angle between the O−Br and Br−Br

• one molecule of (S)-1,2-dibromohexafluoropropane. The Br−···Br distance (Scheme 13) is about 3.3 Å, which is approximately 20% shorter than the sum of the van der Waals radii. The angle between Br−···Br–C is about 175º. The strong Br−···Br–C halogen bonds are robust enough to drive the self-assembly

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• -based methods [90]. In Q-SiteFinder a van der Waals probe is used and the interaction energy between the probe and the protein is found in order to identify binding sites of the protein [91]. The SiteHound program is another energy-based method that uses two kinds of probes; a carbon probe and a

• mechanics. Electrostatic (coulombic) interactions and van der Waals interactions (Lennard-Jones potential) contribute to the interaction energy between a target–ligand complex. Two of the most widely used molecular mechanical force-fields are CHARMM [119] (Chemistry at HARvard Macromolecular Mechanics) and

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• solution, the complexation is enthalpically and entropically driven. In addition, complementary interactions (e.g., van der Waals forces, H-bonds, etc.) appear between the CD and the guest. The non-polar suitably-sized guest may be bound in numerous molar ratios (e.g., 1:1, 2:1, 1:2, etc.). In all cases

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• binding and activation at the catalytic sites of UP and TP. Whereas the substrate recognition of 4-thiouracil by the latter enzyme depends strongly on the electronic structure and/or the van der Waals radius of the substituent at C-4, UP is less sensitive to these differences, in particular, to

• -thiouracil, Supporting Information File 1, Tables S3 and S4) and to some extent by a distortion of architecture of the productive complex due to differences of the van der Waals radii of the substituents at the C-4 atom. In the case of 2-thiouracil, two tautomeric structures 8a and 8c are characterized by

Sydnone C-4 heteroarylation with an indolizine ring via Chichibabin indolizine synthesis

• Florin Albota,
• Mino R. Caira,
• Constantin Draghici,
• Florea Dumitrascu and
• Denisa E. Dumitrescu

Beilstein J. Org. Chem. 2016, 12, 2503–2510, doi:10.3762/bjoc.12.245

• charge located on the exocyclic oxygen atom. This robust supramolecular motif is characterized by an abnormally short C5···C5′ distance for the entries listed in the CSD, namely 3.088–3.338 Å. In the crystal of 9d, this distance is only 3.054(2) Å, i.e. 0.35 Å less than the sum of the van der Waals radii

Inhibition of peptide aggregation by means of enzymatic phosphorylation

• Kristin Folmert,
• Malgorzata Broncel,
• Hans v. Berlepsch,
• Christopher H. Ullrich,
• Mary-Ann Siegert and
• Beate Koksch

Beilstein J. Org. Chem. 2016, 12, 2462–2470, doi:10.3762/bjoc.12.240

• with increasing concentration of amyloid fibrils. The impact of phosphorylation must be considered with respect to three properties: steric bulk, charge and hydrophobicity. It was calculated that phosphorylation increases the van der Waals volume of the serine side chain by a factor of two [27] and it

On the mechanism of imine elimination from Fischer tungsten carbene complexes

• Philipp Veit,
• Christoph Förster and
• Katja Heinze

Beilstein J. Org. Chem. 2016, 12, 1322–1333, doi:10.3762/bjoc.12.125

• the 1,2-H shift in W(CO)5(Z-2) to give the imine complex W(CO)5(Z-3) amounts to ΔG‡ = 333 kJ mol−1 which is prohibitively large. For W(CO)5(E-2) → W(CO)5(E-3), this barrier is somewhat smaller (ΔG‡ = 284 kJ mol−1), yet this 1,2-H shift initially only leads to a van-der-Waals adduct of the imine E-3 [W

• ), the van-der-Waals adduct [W(CO)4…E-3] is the initial product implying the dissociation of the W–C(carbene) bond. The RDI for pathways 3a and 3b is W(CO)4(E-2). The RDTS’s are TS(W(CO)4(E-2) → [W(CO)4…E-3]) (ΔG‡total = 294 kJ mol−1, pathway 3a) and TS(W(CO)4(Z-2) → W(CO)4(Z-3)) (ΔG‡total = 274 kJ mol−1

Enantioselective carbenoid insertion into C(sp³)–H bonds

• J. V. Santiago and
• A. H. L. Machado

Beilstein J. Org. Chem. 2016, 12, 882–902, doi:10.3762/bjoc.12.87

• compound 32 to form the van der Waals complex 33 which undergoes through the transition state TS-34 to the product of the carbenoid insertion reaction 35, regenerating the dirhodium complex 27. In 2009, Davies and coworkers reported a DFT investigation of the relationship between the electronic

A convenient route to symmetrically and unsymmetrically substituted 3,5-diaryl-2,4,6-trimethylpyridines via Suzuki–Miyaura cross-coupling reaction

• Dariusz Błachut,
• Joanna Szawkało and
• Zbigniew Czarnocki

Beilstein J. Org. Chem. 2016, 12, 835–845, doi:10.3762/bjoc.12.82

• less susceptible to the cross-coupling reaction. If the steric repulsion of the pyridine methyl group, at least in part, corresponds to its van der Waals radii, the degree of steric repulsion of the selected ortho-substituents in arylboronic acids can be listed in the following order: I > Br > Me > Cl

Indenopyrans – synthesis and photoluminescence properties

• Andreea Petronela Diac,
• Ana-Maria Ţepeş,
• Albert Soran,
• Ion Grosu,
• Anamaria Terec,
• Jean Roncali and
• Elena Bogdan

Beilstein J. Org. Chem. 2016, 12, 825–834, doi:10.3762/bjoc.12.81

• the (C19–24) ring, respectively (Figure 6a). Several weak, intermolecular C–H···O hydrogen bonds could be identified in the crystal packing (Table S1, Supporting Information File 1). Although the H···O distances are close to or greater than the van der Waals limit of 2.60 Å [39], they are still within

Syntheses of dibenzo[d,d']benzo[2,1-b:3,4-b']difuran derivatives and their application to organic field-effect transistors

• Minh Anh Truong and
• Koji Nakano

Beilstein J. Org. Chem. 2016, 12, 805–812, doi:10.3762/bjoc.12.79

• ][24][25][26][27]. The oxygen atom possesses a smaller van der Waals radius than a sulfur atom. Accordingly, furan-containing π-conjugated compounds should be expected to form a denser packing structure in the solid state, which is one of the main requirements for high semiconducting properties [28][29

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• sizes proportional to the respective van der Waals radii [11]. The variance in the atom color and coordinate of pixels in the images (the structural variance) explains the changes in the bioactivities block. Thus, the MIA-QSAR method is an appropriate approach to probe the validity of 2D-QSAR methods

• representing atoms in the molecules as colored spheres with sizes proportional to the corresponding van der Waals radii. The molecules were constructed using the GaussView program [22] and each 2D projection (each image, molecule) with 342 × 300 pixels dimension was unfolded to a row vector. Combination of the

Interactions between 4-thiothymidine and water-soluble cyclodextrins: Evidence for supramolecular structures in aqueous solutions

• Vito Rizzi,
• Sergio Matera,
• Paola Semeraro,
• Paola Fini and
• Pinalysa Cosma

Beilstein J. Org. Chem. 2016, 12, 549–563, doi:10.3762/bjoc.12.54

• wavenumbers could be observed, in this case the formation of hydrogen bonds and/or van der Waals forces between CDs and the guest molecules can be supposed [49][50]. In all examined CDs, the vibration band at 1270 cm−1 related to twisting modes of C4′C5′H2OH of S4TdR, shifted towards high wavenumbers and

My maize and blue brick road to physical organic chemistry in materials

• Anne J. McNeil

Beilstein J. Org. Chem. 2016, 12, 229–238, doi:10.3762/bjoc.12.24

• structures, such as ribbons, fibers, and sheets. This self-aggregation is driven by noncovalent interactions, including hydrogen bonding, π stacking, van der Waals interactions, and halogen bonding. Physical interactions amongst these larger structures lead to gel formation. Because noncovalent interactions

• . Surprisingly, three nongelators exhibited Hirshfeld surface areas similar to the gelators, suggesting the types of intermolecular interactions (e.g., van der Waals, H-bonding, π-stacking) were similar amongst the gelators and nongelators. Because this analysis involves counting interactions without weighting

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