Thioester derivatives of the natural product psammaplin A as potent histone deacetylase inhibitors

• Matthias G. J. Baud,
• Thomas Leiser,
• Vanessa Petrucci,
• Mekala Gunaratnam,
• Stephen Neidle,
• Franz-Josef Meyer-Almes and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2013, 9, 81–88, doi:10.3762/bjoc.9.11

• . Keywords: epigenetics; histone deacetylase; natural product; prodrug; psammaplin A; thioester; Introduction Chromatin is a macromolecular complex consisting of DNA, histone and nonhistone proteins. The epigenetic control of chromatin organization plays a major role in the regulation of gene expression

The chemistry of bisallenes

• Henning Hopf and
• Georgios Markopoulos

Beilstein J. Org. Chem. 2012, 8, 1936–1998, doi:10.3762/bjoc.8.225

• chemistry. Today the situation has completely changed, as is, among other things, demonstrated by numerous review articles and a recent two volumes monograph on modern allene chemistry [12][13][14]. As far as the organization of the present review is concerned, we have tried to cover the literature up to

Self-assembled organic–inorganic magnetic hybrid adsorbent ferrite based on cyclodextrin nanoparticles

• Ângelo M. L. Denadai,
• Frederico B. De Sousa,
• Joel J. Passos,
• Fernando C. Guatimosim,
• Kirla D. Barbosa,
• Ana E. Burgos,
• Fernando Castro de Oliveira,
• Jeann C. da Silva,
• Bernardo R. A. Neves,
• Nelcy D. S. Mohallem and
• Rubén D. Sinisterra

Beilstein J. Org. Chem. 2012, 8, 1867–1876, doi:10.3762/bjoc.8.215

• . Ferrite morphology in the solid state was affected by βCD insertion, probably due to its size and key role as modulator during inorganic nucleation. Ferrites presented at least three different organization scales, from the micrometric to the nanometric level, and on the nanometric scale it was possible to

• verify the material organization and particle size distribution. Lower domains, and greater specific area and free volume were observed for the Fe-Ni/Zn/βCD material. On the micrometric level, both ferrites have comparable behavior, with quite similar size distribution and ZP values, although Fe-Ni/Zn

Polysiloxane ionic liquids as good solvents for β-cyclodextrin-polydimethylsiloxane polyrotaxane structures

• Narcisa Marangoci,
• Rodinel Ardeleanu,
• Laura Ursu,
• Constanta Ibanescu,
• Maricel Danu,
• Mariana Pinteala and
• Bogdan C. Simionescu

Beilstein J. Org. Chem. 2012, 8, 1610–1618, doi:10.3762/bjoc.8.184

• number of works that showed their use as solvents or as solvents for synthesis and catalysis [4][5][6]. In this context ILs, which have polar and nonpolar regions, could play an important role in the field of supramolecular organization of different supramolecular structures (such as polyrotaxanes or

Synthesis of trifunctional cyclo-β-tripeptide templates

• Frank Stein,
• Tahir Mehmood,
• Tilman Plass,
• Javid H. Zaidi and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2012, 8, 1576–1583, doi:10.3762/bjoc.8.180

• N-terminal amino group at the activated carbonyl group provided cleavage of the cyclized β-tripeptide from the resin. Purification did not require any chromatography since organization by intermolecular hydrogen bonding resulted in decreased solubility and precipitation of the β-tripeptide template

• ]-cycloaddition under mild conditions. The template approach allows for the preparation of constructs that, e.g., combine biological activity, fluorescence labelling and cell-penetrating or cell-directing units in one molecule to be used for in vivo studies. The defined spatial organization of recognition units

Restructuring polymers via nanoconfinement and subsequent release

• Alan E. Tonelli

Beilstein J. Org. Chem. 2012, 8, 1318–1332, doi:10.3762/bjoc.8.151

• consequence of the structural organization of the polymer–host-ICs. Polymer chains in host-IC crystals are confined to occupy narrow channels (diameter ~0.5–1.0 nm) formed by the small-molecule hosts around the included guest polymers during IC crystallization. This results in the separation and high

• . In this review we summarize the behaviors and uses of coalesced polymers, and attempt to draw conclusions on the relationship between their behavior and the organization/structures/conformations of the constituent polymer chains achieved upon coalescence from their ICs. Keywords: cyclodextrins

• ; inclusion compounds; nanoconfinement; organization; polymers; properties; release; urea; Introduction The behaviors and properties of polymer materials are closely related to the organizations, structures, and morphologies of their constituent chains, which can be significantly altered during their

Design of a novel tryptophan-rich membrane-active antimicrobial peptide from the membrane-proximal region of the HIV glycoprotein, gp41

• Evan F. Haney,
• Leonard T. Nguyen,
• David J. Schibli and
• Hans J. Vogel

Beilstein J. Org. Chem. 2012, 8, 1172–1184, doi:10.3762/bjoc.8.130

• not disrupt bilayer organization in neutral liposomes to the same extent as gp41w or gp41w-4R (Figure 4C). Differential scanning calorimetry The gp41w derivatives were added to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG) lipid

• added to the DPPC lipid suspensions, the resulting thermograms showed that these peptides had very drastic effects on the organization of DPPC bilayers (Figure 5). The final heating scan of gp41w-4R mixed with DPPC phospholipids shows a sharp transition at ~36 °C with a broad shoulder between 37–40 °C

• formation of peptide–lipid aggregates. The addition of gp41w-4R to DPPG yields peaks in the thermogram at 33 and 36 °C, suggesting that when gp41w-4R binds to negatively charged liposomes, it destabilizes the organization of the bilayer. Apparently, some unbound DPPG remains as well because there is still a

Control over molecular motion using the cis–trans photoisomerization of the azo group

• Estíbaliz Merino and
• María Ribagorda

Beilstein J. Org. Chem. 2012, 8, 1071–1090, doi:10.3762/bjoc.8.119

• conformational changes in polymers. There may also be variations in the organization of large assemblies of molecules in gels or liquid crystals. When polarized light is used, the photoisomerization often induces a reorganization of chromophores that can be reflected in the circular dichroism spectra. The basic

Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

• Marco Caricato,
• Nerea Jordana Leza,
• Claudia Gargiulli,
• Giuseppe Gattuso,
• Daniele Dondi and
• Dario Pasini

Beilstein J. Org. Chem. 2012, 8, 967–976, doi:10.3762/bjoc.8.109

• (resulting in preorganization [5]); (b) shape persistency is a requirement for the formation of organic nanotubes by means of supramolecular organization of macrocycles in the third dimension [6][7][8][9][10][11][12]. Amide functionalities are hydrogen-bonding tools of widespread use for the conformational

Multistep organic synthesis of modular photosystems

• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2012, 8, 897–904, doi:10.3762/bjoc.8.102

• central naphthalenediimide (NDI) [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19] to act as a template for the central stack and two peripheral NDIs to act as templates for stack exchange. They are embedded into hydrogen-bonded networks, to assure self-organization, and four geminal

An easy α-glycosylation methodology for the synthesis and stereochemistry of mycoplasma α-glycolipid antigens

• Yoshihiro Nishida,
• Yuko Shingu,
• Yuan Mengfei,
• Kazuo Fukuda,
• Hirofumi Dohi,
• Sachie Matsuda and
• Kazuhiro Matsuda

Beilstein J. Org. Chem. 2012, 8, 629–639, doi:10.3762/bjoc.8.70

• Organization (NEDO) of Japan and from the Science & Technology Project for a Safe & Secure Society from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.

Liquid-crystalline heterodimesogens and ABA-heterotrimesogens comprising a bent 3,5-diphenyl-1,2,4-oxadiazole central unit

• Govindaswamy Shanker,
• Marko Prehm and
• Carsten Tschierske

Beilstein J. Org. Chem. 2012, 8, 472–485, doi:10.3762/bjoc.8.54

• comparable to the molecular length Lmol = 4.5–4.6 nm in the most stretched conformation (determined with CPK models). This indicates a kind of monolayer organization of the molecules in the cybotactic clusters. In the SmA-like clusters the alkyl chains are segregated from the aromatic cores, and the

• . As the maxima of the scattering peaks in the wide- and small-angle regions are perpendicular to each other, the molecules are on average nontilted. Because the position of the small-angle scattering is not significantly shifted, the organization of the molecules should be identical to the model

• proposed for the SmA-type clusters forming the NcybA phase (Figure 4a). This means that at this phase transition the molecular organization does not change fundamentally, but instead the short-range SmA-like clusters simply become fused to much larger clusters. The correlation length in this phase (T = 130

The interplay of configuration and conformation in helical perylenequinones: Insights from chirality induction in liquid crystals and calculations

• Elisa Frezza,
• Silvia Pieraccini,
• Stefania Mazzini,
• Alberta Ferrarini and
• Gian Piero Spada

Beilstein J. Org. Chem. 2012, 8, 155–163, doi:10.3762/bjoc.8.16

• ) calculations, and with the prediction of the twisting ability of conformers, by the surface chirality (SC) method [29]. Results and Discussion HTP measurement The propensity of a dopant to induce a helical organization in the liquid-crystalline matrix is measured by its helical twisting power, which is defined

Computational evidence for intramolecular hydrogen bonding and nonbonding X···O interactions in 2'-haloflavonols

• Tânia A. O. Fonseca,
• Matheus P. Freitas,
• Rodrigo A. Cormanich,
• Teodorico C. Ramalho,
• Cláudio F. Tormena and
• Roberto Rittner

Beilstein J. Org. Chem. 2012, 8, 112–117, doi:10.3762/bjoc.8.12

• interactions; theoretical calculations; Introduction Intermolecular hydrogen bonding (HB) is an interaction governing self-assembly and is responsible for the architecture and organization of molecular aggregates [1], and also ligand–receptor interactions that are responsible for the bioactivity of compounds

Valence isomerization of cyclohepta-1,3,5-triene and its heteroelement analogues

• Helen Jansen,
• J. Chris Slootweg and
• Koop Lammertsma

Beilstein J. Org. Chem. 2011, 7, 1713–1721, doi:10.3762/bjoc.7.201

• interconversion barriers, and the barriers for ring inversion of the monocycles. Acknowledgements This work was supported by the Council for Chemical Sciences of the Netherlands Organization for Scientific Research (NWO/CW).

Gold-catalyzed alkylation of silyl enol ethers with ortho-alkynylbenzoic acid esters

• Haruo Aikawa,
• Tetsuro Kaneko,
• Naoki Asao and
• Yoshinori Yamamoto

Beilstein J. Org. Chem. 2011, 7, 648–652, doi:10.3762/bjoc.7.76

• Haruo Aikawa Tetsuro Kaneko Naoki Asao Yoshinori Yamamoto Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan International Advanced Research and Education Organization, Tohoku University, Sendai 980-8578, Japan WPI-Advanced Institute for Materials

Amphiphilic dendritic peptides: Synthesis and behavior as an organogelator and liquid crystal

• Baoxiang Gao,
• Hongxia Li,
• Defang Xia,
• Sufang Sun and
• Xinwu Ba

Beilstein J. Org. Chem. 2011, 7, 198–203, doi:10.3762/bjoc.7.26

• behavior, where a LC mesophase, on a second cooling, appeared at 40 °C and then disappeared at 145°C to form an isotropic melt (Figure 4). The high temperature for the isotropic melt of G3 is the result of hydrogen bond interactions of the amide groups which reinforce the columnar organization. The

Towards racemizable chiral organogelators

• Jian Bin Lin,
• Debarshi Dasgupta,
• Seda Cantekin and
• Albertus P. H. J. Schenning

Beilstein J. Org. Chem. 2010, 6, 960–965, doi:10.3762/bjoc.6.107

• and coworkers have reported a chiral gelator in which the supramolecular organization of the chiral assemblies can be switched using UV/visible light combined with heating and cooling [7]. Chiral gels that respond to other stimuli such as metal ions [8], guest molecules [9] and temperature [10] have

Oxalyl retro-peptide gelators. Synthesis, gelation properties and stereochemical effects

• Janja Makarević,
• Milan Jokić,
• Leo Frkanec,
• Vesna Čaplar,
• Nataša Šijaković Vujičić and
• Mladen Žinić

Beilstein J. Org. Chem. 2010, 6, 945–959, doi:10.3762/bjoc.6.106

• modeling and XRPD studies of diasteroisomeric diesters (S,S)-1b/(S,R)-1b and diacids (S,S)-1b/(S,R)-1a, a basic packing model in their gel aggregates is proposed. The intermolecular hydrogen bonding between extended gelator molecules utilizing both, the oxalamide and peptidic units and layered organization

• finally result in the formation of amyloid plaques [1][2][3][4]. During the last two decades there has been a growing interest in self-organization of small peptide models capable of self-assembling into highly organized supramolecular structures with potential use as novel bio- or nano-materials

• cases such organization results in formation of gels consisting of self-assembled fibrous aggregates usually containing a large volume of solvent [16]. In gels, the fibers are heavily entangled into 3-dimensional networks which immobilize the solvent and prevent fluidity in the system [17][18][19][20

Aromatic and heterocyclic perfluoroalkyl sulfides. Methods of preparation

• Vladimir N. Boiko

Beilstein J. Org. Chem. 2010, 6, 880–921, doi:10.3762/bjoc.6.88

Synthesis, characterization and photoinduced curing of polysulfones with (meth)acrylate functionalities

• Cemil Dizman,
• Sahin Ates,
• Lokman Torun and
• Yusuf Yagci

Beilstein J. Org. Chem. 2010, 6, No. 56, doi:10.3762/bjoc.6.56

• polysulfones. Acknowledgements The authors thank the State Planning Organization of Turkey (DPT) for the financial support (Project no: 2005K120920). We also want to thank Nursen Turdu for NMR studies and Zekayi Korlu for TGA studies. Special thanks go to Turgay Balci for the technical support.

Self-assembled ordered structures in thin films of HAT5 discotic liquid crystal

• Piero Morales,
• Jan Lagerwall,
• Paolo Vacca,
• Sabine Laschat and
• Giusy Scalia

Beilstein J. Org. Chem. 2010, 6, No. 51, doi:10.3762/bjoc.6.51

• compared to the bulk situation, where the same material crystallizes into a polymorphic structure at 68 °C. Keywords: AFM; discotic liquid crystals; hexapentyloxytriphenylene; self-organization; thin films; Introduction Discotic liquid crystals are an interesting type of organic semiconductors that allow

• long-range charge transport thanks to the spontaneous formation of channels as a result of molecular self-organization into columns and the orbital overlap of neighboring molecules [1][2]. In particular, columnar phases are very appealing for applications since the transport of charges occurs along the

• between indium tin oxide (ITO)-coated glass plates at micrometer distance, very little is known about the organization of HAT5 in films of submicrometer thickness and their characteristics. Such films, produced by drop-casting and spin-coating, are the focus of this study. Results and Discussion Different

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

• selective recognition of ammonium ions depends on steric and molecular complementarity and the pre-organization [17] of interacting functional groups. As far back as 1890, Fischer suggested that enzyme–substrate interactions function like a “lock and key” between an initially empty host and a guest that

• “key” in the complementary binding site or an inclusion compound. This host pre-organization leads to a major enhancement of the overall energy of guest complexation. The binding is energetically favored: Both enthalpic – a less solvent accessible area leads to a less strongly solvated guest with fewer

• hetero crown ethers) and N+–H bonds [101]. The cyclic arrangement leads to a pre-organization of the host [102], whereby selectivity is determined by the ring size. Primary ammonium ions are complexed with highest affinity by 18-crown-6 derivatives [9] (Figure 2). Table 1 summarizes exemplarily the

Synthesis of a new class of aminocyclitol analogues with the conduramine D-2 configuration

• Latif Kelebekli,
• Yunus Kara and
• Murat Celik

Beilstein J. Org. Chem. 2010, 6, No. 15, doi:10.3762/bjoc.6.15

• 16: Experimental Section The experimental section describes the synthesis, purification and characterization data of all substances given in this article. Acknowledgements The authors are indebted to the Department of Chemistry (Atatürk University), state planning organization of Turkey (DPT) for

The subtle balance of weak supramolecular interactions: The hierarchy of halogen and hydrogen bonds in haloanilinium and halopyridinium salts

• Kari Raatikainen,
• Massimo Cametti and
• Kari Rissanen

Beilstein J. Org. Chem. 2010, 6, No. 4, doi:10.3762/bjoc.6.4

• bonded 1 and the only hydrogen bonded 4. When the polarizability of the halogen atom is increased (I > Br > Cl > F), thus increasing the effect of the halogen bond, the changed balance of the intermolecular interactions will influence the spatial organization of the adjacent molecules leading to a