A pyridinium/anilinium [2]catenane that operates as an acid–base driven optical switch

• Sarah J. Vella and
• Stephen J. Loeb

Beilstein J. Org. Chem. 2018, 14, 1908–1916, doi:10.3762/bjoc.14.165

• bis(pyridinium)ethane site, while addition of acid forms a charged benzylanilinium site. The DB24C8 then shuttles between the two charged recognition sites with occupancy favoring the bis(pyridinium)ethane site by a ratio of 4:1. The unprotonated [2]catenane has a deep yellow/orange color when the

Water-soluble SNS cationic palladium(II) complexes and their Suzuki–Miyaura cross-coupling reactions in aqueous medium

• Alphonse Fiebor,
• Richard Tia,
• Banothile C. E. Makhubela and
• Henok H. Kinfe

Beilstein J. Org. Chem. 2018, 14, 1859–1870, doi:10.3762/bjoc.14.160

• in literature [40]. The crystal structure of 17d also shows a static disorder of a CH2 carbon of one of the sec-butyl groups (C14). The atom site occupancy factors of the two positions of the CH2 carbon atom was refined to 0.571(11) and 0.429(11). This shows that the carbon atom has equal probability

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• could be applied to study QS in vivo. Results and Discussion Design and synthesis of CSP1 analogs In this work, we aimed to define the binding pockets in ComD1 that accommodate the hydrophobic side-chain residues in CSP1 and determine their degree of occupancy as a means to optimize CSP1–ComD1

• peptide to assess the occupancy level and degree of specificity. Since no structural information is available for the ComD receptors, we chose to assess the ComD1 binding pocket by synthesizing a set of CSP1 analogs bearing highly conservative point mutation in key hydrophobic positions (4, 7, 8, 11, 12

Hyper-reticulated calixarene polymers: a new example of entirely synthetic nanosponge materials

• Alberto Spinella,
• Marco Russo,
• Antonella Di Vincenzo,
• Delia Chillura Martino and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2018, 14, 1498–1507, doi:10.3762/bjoc.14.127

• possess an extensive random network of nanochannels and nanocavities. Despite their apparently low porosity and surface area (as determined by BET techniques) [11][12][13], the possibility to load them with a guest up to an almost exhaustive occupancy of the cyclodextrin host units [12] indicates that

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

• . Indeed, the phenoxodiol molecule is found having an occupancy factor of 0.5 in the β-CD dimeric cavity assumed able to be diffused through the crystal channels with the aid of the water network and the structure is characterized as ‘ship-in-a-bottle’. On the other hand, in the case of the CHL/β-CD

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• covalent step of primer extension. For each case, the concentration of the kinetically relevant species (the monomer–primer–template complex), i.e., the occupancy of the extension site by the monomer, was now known, and measuring the initial rates led to the kcov value via fitting. For OAt esters and an

• beginning of the assay. Here, hydrolysis does catch up with the desired reaction eventually, but it is inconsequently, because the low occupancy does not produce a significant level of competitive inhibition. In other words, if there is not much of a template effect to begin with, the spent monomers will

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• based on F2 using SHELXL–2016 [60] integrated in the WinGX program package [61]. All hydrogen atoms were included in calculated positions, with SHELXL–2016 defaults. Fluorine atoms of trifloromethyl groups in 5–8 were disordered and have been refined with fixed occupancy ratio of 0.60/0.40 in 5 and 8

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

• guest molecules of L-NAcTrp are enclosed in a head-to-head fashion (host:guest ratio, 1:1). The pair of L-NAcTrp molecules inside the dimer are found in orientational disorder, i.e., the guest exhibits a major orientation, molecules C and D (occupancy 65%), and a co-existing minor orientation (molecules

• E and F, occupancy 35%) in a statistical fashion. The dimers pack along the axis a at an angle of 19° thus forming a broken channel (Intermediate packing) [10][27]. The mean distance of the centers of mass of two consecutive β-CD dimers is 5.78 Å. Co-crystallized with each dimer, 21.45 water

• -Ο63Β bond in two conformations, the major (−)-gauche C-Ο63Βa (occupancy 78%) pointing outward and the minor (+)-gauche C-Ο63Βb (22%) pointing towards the interior of the cavity, the latter interacting with guests C and D of neighboring dimers (Figure 3a). The aromatic moieties of both guest

A non-canonical peptide synthetase adenylates 3-methyl-2-oxovaleric acid for auriculamide biosynthesis

• Daniel Braga,
• Dirk Hoffmeister and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 2766–2770, doi:10.3762/bjoc.12.274

• support its occupancy by a remarkably conserved lysine residue (K517 in PheA) [19], whose side chain counters the negative charge of the substrate’s carboxy group [14][20]. Also, the relationship between the expected substrate and the nonribosomal code of AulA-A2 posed itself as a conundrum. The first

From betaines to anionic N-heterocyclic carbenes. Borane, gold, rhodium, and nickel complexes starting from an imidazoliumphenolate and its carbene tautomer

• Ming Liu,
• Jan C. Namyslo,
• Martin Nieger,
• Mika Polamo and
• Andreas Schmidt

Beilstein J. Org. Chem. 2016, 12, 2673–2681, doi:10.3762/bjoc.12.264

• absorption corrections were applied. For 8, 9, and 11 an extinction correction was applied. In 9 the halogen counter anion (occupancy Cl/Br approx. 81:19) and in 11 one n-butyl group are disordered. 8: colorless crystals, C31H16BF15N2O, Mr = 728.27, crystal size 0.35 × 0.25 × 0.15 mm, monoclinic, space group

• . peak/hole = 0.404/−0.489 e Å−3, disorder of the halogen counter anion (occupancy Cl/Br 0.813(2):0.187(2)). 11: yellow crystals, C39H45N6O3Rh, Mr = 748.72, crystal size 0.38 × 0.32 × 0.16 mm, monoclinic, space group P21/n (No. 14), a = 11.7692(5) Å, b = 18.8111(7) Å, c = 16.2459(7) Å, β = 104.615(2)°, V

Experimental and theoretical investigations on the high-electron donor character of pyrido-annelated N-heterocyclic carbenes

• Michael Nonnenmacher,
• Dominik M. Buck and
• Doris Kunz

Beilstein J. Org. Chem. 2016, 12, 1884–1896, doi:10.3762/bjoc.12.178

• highest for the pyrido-annelated carbene. Going from the free carbene to the Rh(CO)2Cl(NHC) complexes, the increase in occupancy of the complete π-system of the carbene ligand upon coordination is lowest for the pyrido-annelated carbene and highest for the saturated carbene. Keywords: carbonyl complexes

• be concluded. It is surprising that the largest increase in electron occupancy (ΔRh-NHC e− (C3)) is found for the dipyridocarbene dipiy (0.16) and the weakest for the acyclic carbene (I) (0.12). However, the increase must not necessarily stem from electron density of the metal center. It could also

• originate from the π-system of the respective carbene. Therefore, we also calculated the sum of the pπ-electron occupancy for the free carbene as well as for the complex (which should sum up to 4 e− (I and II), 6 e− (III) or 14 e− (dipiy), respectively). It now becomes clear that the overall gain in π

Artificial Diels–Alderase based on the transmembrane protein FhuA

• Hassan Osseili,
• Daniel F. Sauer,
• Klaus Beckerle,
• Marcus Arlt,
• Tomoki Himiyama,
• Tino Polen,
• Akira Onoda,
• Ulrich Schwaneberg,
• Takashi Hayashi and
• Jun Okuda

Beilstein J. Org. Chem. 2016, 12, 1314–1321, doi:10.3762/bjoc.12.124

• , MALDI–TOF–MS, ThioGlo fluorescence titration, and BCA assay. All employed methods indicate the folded structure of FhuA ΔCVFtev and a high occupancy of the only accessible cysteine residue within this β-barrel protein. The biohybrid catalysts showed high activity and high endo selectivity in the Diels

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

• tether compete for host–guest complexation in the β-CD substituent annulus to form interchain linkages in the polymer network as shown by 2D 1H NMR spectroscopy. Rheological studies show that as its length shortens the tether is less able to compete for β-CD substituent annular occupancy, and that the

Inclusion complexes of 2-methoxyestradiol with dimethylated and permethylated β-cyclodextrins: models for cyclodextrin–steroid interaction

• Mino R. Caira,
• Susan A. Bourne,
• Halima Samsodien and
• Vincent J. Smith

Beilstein J. Org. Chem. 2015, 11, 2616–2630, doi:10.3762/bjoc.11.281

• host and guest during complexation [1]. Complex units A and B of TRIMEB·2ME, related by a pseudo-translation of ≈b/2, have nearly identical structural features, namely common TRIMEB host conformations and lack of host disorder, apparent twofold disorder of the 2ME methylene group at C6 (site-occupancy

Indolizines and pyrrolo[1,2-c]pyrimidines decorated with a pyrimidine and a pyridine unit respectively

• Marcel Mirel Popa,
• Emilian Georgescu,
• Mino R. Caira,
• Florentina Georgescu,
• Constantin Draghici,
• Raluca Stan,
• Calin Deleanu and
• Florea Dumitrascu

Beilstein J. Org. Chem. 2015, 11, 1079–1088, doi:10.3762/bjoc.11.121

• parent atoms were either fully occupied by carbon atoms or by nitrogen atoms, or partially occupied by carbon and nitrogen atoms simultaneously. Figure 4a and 4b show the molecular and crystal structures of 4-(2-pyridyl)pyrimidine (6). Here, all atoms in the molecule have a site-occupancy factor (s.o.f

• .) equal to 1 except the atom labeled ‘C4/N4’, where C and N atoms have equal occupancy (s.o.f. = 0.5 for each and for H-4), which is required to satisfy the condition of centrosymmetry. The molecules are linked into large concatenated rings with graph-set descriptor [33] R22(22) by one

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• 12) had marginal impact on the binding suggesting a saturation of binding site occupancy. For the structure with 6 units of maltose on each arm, a KD of 1 μM was measured which is 700-fold more potent (40-fold per sugar) than monovalent maltose. The advent of the copper-catalyzed azide–alkyne

Self-assembly of heteroleptic dinuclear metallosupramolecular kites from multivalent ligands via social self-sorting

• Christian Benkhäuser and
• Arne Lützen

Beilstein J. Org. Chem. 2015, 11, 693–700, doi:10.3762/bjoc.11.79

• the maximum occupancy rule [24] is obeyed which open-chain oligomeric or polymeric species do not do. Results and Discussion Design and synthesis Our strategy asks for the design of rigid multivalent ligands that present their metal binding sites in a way that the formation of discrete macrocyclic or

Inclusion of trans-resveratrol in methylated cyclodextrins: synthesis and solid-state structures

• Lee Trollope,
• Dyanne L. Cruickshank,
• Terence Noonan,
• Susan A. Bourne,
• Milena Sorrenti,
• Laura Catenacci and
• Mino R. Caira

Beilstein J. Org. Chem. 2014, 10, 3136–3151, doi:10.3762/bjoc.10.331

• guest molecules from the resulting difference Fourier synthesis. Successive difference maps revealed the water molecules, which were modelled with appropriate site-occupancy factors (s.o.f.s) to reconcile the model with the thermogravimetric analytical data as far as possible. Disorder of the host and

Conjugates of methylated cyclodextrin derivatives and hydroxyethyl starch (HES): Synthesis, cytotoxicity and inclusion of anaesthetic actives

• Lisa Markenstein,
• Antje Appelt-Menzel,
• Marco Metzger and
• Gerhard Wenz

Beilstein J. Org. Chem. 2014, 10, 3087–3096, doi:10.3762/bjoc.10.325

• ; occupancy; polymer; sevoflurane; solubility; starch; Introduction Cyclodextrins (CDs), α(1→4) linked cyclic oligomers of anhydroglucose, are produced nowadays in industrial scale [1]. CDs are able to complex hydrophobic or amphiphilic guest molecules in aqueous phase [2]. β-CD, the seven membered ring

Synthesis of uniform cyclodextrin thioethers to transport hydrophobic drugs

• Lisa F. Becker,
• Dennis H. Schwarz and
• Gerhard Wenz

Beilstein J. Org. Chem. 2014, 10, 2920–2927, doi:10.3762/bjoc.10.310

• derivative [CD]0 by non-linear regression according to Equation 1, as described previously in this journal [30]. The Henry constant was determined according to a known GC method [30] to kH = 2.0 at 25 °C and kH = 3.05 at 37 °C in good agreement with literature data [53]. The occupancy x of employed CD host

• constant slightly dropped in 5 wt % albumin solution and further dropped in human serum (Table 4). At 37 °C a further decrease of K was observed, but it still remained rather high. The occupancy of 3b1 was still 87 mol % in human serum at body temperature. Therefore this compound should be well suitable

• for the delivery of sevoflurane. Potentially oral aqueous dosage forms can be developed for both anaesthesia and the treatment of pain. 3b1 is also able to complex other hydrofluoric anaesthetics, like halothane [54], where the binding constant K = 9090 L/mol (occupancy of the host 98%) was even

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• Titration curve of the receptor The titration curve of the receptor was obtained by averaging the occupancy of all titrable amine groups at each pH value over 270 ns (last 90 ns of each replicate). The total titration curve (Figure 2a) shows a clear plateau between pH 4.0 and 7.0, approximately. In these

Synthesis and evaluation of cell-permeable biotinylated PU-H71 derivatives as tumor Hsp90 probes

• Tony Taldone,
• Anna Rodina,
• Erica M. DaGama Gomes,
• Matthew Riolo,
• Hardik J. Patel,
• Raul Alonso-Sabadell,
• Danuta Zatorska,
• Maulik R. Patel,
• Sarah Kishinevsky and
• Gabriela Chiosis

Beilstein J. Org. Chem. 2013, 9, 544–556, doi:10.3762/bjoc.9.60

• bound to a substantial fraction of oncogenic Hsp90 molecules. Specifically, K562 is a human leukemia cell line dependent on Hsp90 for survival [13]. Thus, in such cells, occupancy of Hsp90’s regulatory pocket by small molecules results in inhibition of its cancer-sheltering properties, leading to cell

Inclusion of the insecticide fenitrothion in dimethylated-β-cyclodextrin: unusual guest disorder in the solid state and efficient retardation of the hydrolysis rate of the complexed guest in alkaline solution

• Dyanne L. Cruickshank,
• Natalia M. Rougier,
• Raquel V. Vico,
• Susan A. Bourne,
• Elba I. Buján,
• Mino R. Caira and
• Rita H. de Rossi

Beilstein J. Org. Chem. 2013, 9, 106–117, doi:10.3762/bjoc.9.14

• components B and C, with respective site-occupancy factors (sofs) 0.44 and 0.29, adopt the same orientation, their phosphorothioate groups being located near the primary side of host molecule B (analogous to the situation in host molecule A). However, the third guest component E, with the lowest sof (0.27

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• CHARMM [97] input files from PDB files that contain carbohydrates. Various tools to predict the occupancy state of potential glycosylation sites from protein sequence data are available as well (Table 5). If a protein–carbohydrate complex is to be modeled, generally available docking tools such as

Synthesis of 2,6-disubstituted tetrahydroazulene derivatives

• Zakir Hussain,
• Henning Hopf,
• Khurshid Ayub and
• S. Holger Eichhorn

Beilstein J. Org. Chem. 2012, 8, 693–698, doi:10.3762/bjoc.8.77

• position 6; however, additional H-atoms at C(4) and C(8), each with only 50% occupancy, were found. Acid 8 was further condensed [23] with p-cyanophenol in the presence of SOCl2 and DMAP in dichloromethane to obtain the corresponding ester. The GC analysis of the product mixture indicated the presence of