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

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