What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• ; multivalency; pre-organization; Review Recognition of carbohydrate ligands For the recognition of carbohydrate ligands, nature has explored binding sites of different shapes and properties. The large family of C-type lectins (CLECs) exhibits carbohydrate-recognition domains (CRDs) which incorporate a calcium

• binding site pre-organization, are more difficult to assess and accordingly have been highlighted in this review. Mannose-binding CLECs are involved in various pathways of the human innate immune response, including the blood dendritic cell antigen 2 (BDCA-2, also known as CD303) [18], langerin (CD207

• desolvation penalty [69][70]. Pre-organization vs flexibility. Carbohydrate–lectin interactions benefit from the low conformational flexibility of pyranoses. This could be impressively demonstrated in a case study comparing a septanose with a manno-configured pyranose derivative [71]. Although in both cases

Mechanochemical synthesis of thioureas, ureas and guanidines

• Vjekoslav Štrukil

Beilstein J. Org. Chem. 2017, 13, 1828–1849, doi:10.3762/bjoc.13.178

• ureas and guanidines currently available in the market. The supramolecular level of organization of thioureas in the solid-state. The supramolecular level of organization of thioureas in the solid-state. In situ Raman spectroscopy monitoring the synthesis of thiourea 28d in the solid-state. N

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

• crystals. The disagreement between solution and crystal structure in terms of complex formation and orientation/conformation of the guest indicates that the lattice forces and organization in the crystal prevail by far over the soft host–guest contacts established in solution and determines the final

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• effect self-assembly [51]. Thus, mineral surfaces and porous formations could have been excellent media to foster the emergence of “self-contained”, dispersed chemical systems. Furthermore, mineral surfaces can serve as supports for chemical systems to undergo organization. The polymerization of nucleic

• nucleic acid oligomers [53][54][55]. The presence of the mineral support is crucial here as it permits the preservation of the amphiphile bilayer structure during drying, thereby promoting the conversion of an “unreactive” organization (free floating vesicles and free monomers) into reactive chemical

• for the physical organization of molecules into functional catalytic/information networks; iii) systems foster evolutionary processes by maintaining chemicals in close proximity, that is, at physical distances permitting their further reactivity, while allowing for reaction wastes to be disposed of

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• “synthetic moves” We hope that the method developed here allows researchers, and especially chemists, to address important features of self-organization in complex systems. We briefly showed how the tuning of molecular structures allows one to explore the robustness of CRNs. From this perspective, other

• Nature Publishing Group, and [102] copyright 2016 Wiley-VCH Verlag GmbH & Co. Acknowledgements Our work is supported by the Netherlands Organization for Scientific Research (NWO, VICI Grant 700.10.44 (W.T.S.H.)), and funding from the Dutch Ministry of Education, Culture and Science (Gravity program

Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

• Ben Shirt-Ediss,
• Sara Murillo-Sánchez and
• Kepa Ruiz-Mirazo

Beilstein J. Org. Chem. 2017, 13, 1388–1395, doi:10.3762/bjoc.13.135

• -life simplifications that do not completely erase this aspect at the beginning. The combination of diverse chemical reactions with self-organization and self-assembly processes in heterogeneous, multi-phase conditions could actually be crucial at those first stages: this is the main assumption that

• (individual) organization and (ii) reproduce reliably to spread that type of organization in the population. In practice, this entails becoming autonomous from an energetic point of view (hence the importance of setting up the first energy transduction mechanisms [40]) and achieving regularity in the actual

• oversimplified explanations. First, as we suggested along the previous lines, a combination of evolutionary and organizational principles should be sought. However, this combination should not be simply conceived on a one-dimensional axis (e.g., in terms of the relative weights of ‘self-organization’ vs

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

• fashion [58][59]. Therefore, they postulated that by using the correct divalent cation and suitable Lewis acid/Lewis base pairing, the necessary transition-state organization to favor glycosylation of a glycosyl fluoride would outcompete hydrolysis in the aqueous medium. This would lead to a simple non

Strategies in megasynthase engineering – fatty acid synthases (FAS) as model proteins

• Manuel Fischer and
• Martin Grininger

Beilstein J. Org. Chem. 2017, 13, 1204–1211, doi:10.3762/bjoc.13.119

• phosphopantetheinylated [24][32], is located at the tip of the fold opposite to the N- and C-terminal attachment sites. This structural organization likely preserves linkers from interfering in ACP:domain interactions, and, concomitantly, may support the loading of the covalent acyl moiety by steering the acyl tail into

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• information, i.e., they are a molecular reader of the glyco-code. The plethora of three-dimensional structures of lectins, both in unbound form or complexed with oligosaccharides, lead to their organization in a dedicated database, available at http://glyco3d.cermav.cnrs.fr [45]. Information contained in the

• such that antibodies with similar specificity exhibit different selective cell-profiling. Up to now, crystallographic studies of carbohydrate-antibodies mainly concentrated on systems where carbohydrates are complexed with antibody (Fab) or variable fragments (Fv). The organization of a small database

• . While this new investigation corroborated the essential features of the original model, some additional fine details were revealed (Figure 18) [88]. Multiscale organization Cellulose: Knowledge of the structure of a material is necessary to understand its properties. In the case of cellulose, it is also

Correlation of surface pressure and hue of planarizable push–pull chromophores at the air/water interface

• Frederik Neuhaus,
• Fabio Zobi,
• Gerald Brezesinski,
• Marta Dal Molin,
• Stefan Matile and
• Andreas Zumbuehl

Beilstein J. Org. Chem. 2017, 13, 1099–1105, doi:10.3762/bjoc.13.109

• . Monolayers at the air/water interface are well known models for biological membranes, avoiding trans-bilayer leaflet correlation effects [11][12][13][14]. Various techniques exist to probe the surface pressure and the lateral organization of the monolayer [14]. Using monolayers of pure flipper probes, we

• were able to study the fundamental questions of surface pressure–hue correlation avoiding interfering effects from other lipids or solvents. The putative lateral organization of the hydrophobic part of the flipper probes was probed by grazing-incidence angle X-ray diffraction experiments (GIXD) [15][16

• . However, this apparently low slope is connected with the experimental problem of measuring the surface tension of stiff films and the organization of this particular flipper mechanophore. The stiffness of the layer leads to a tilting of the Wilhelmy plate (expansion leads shortly to a surface pressure

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

• Vinila N. Viswanathan,
• Arun D. Rao,
• Upendra K. Pandey,
• Arul Varman Kesavan and
• Praveen C. Ramamurthy

Beilstein J. Org. Chem. 2017, 13, 863–873, doi:10.3762/bjoc.13.87

• energy region due to π–π* transitions. A bathochromic shift in the λmax of all thin film spectra of the polymers was observed, as compared to the solution spectra. This is due to the enhanced interchain stacking and ordered structural organization of the polymers in the thin film. The intensity of the

Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems

• Katarina Kemper,
• Max Hirte,
• Markus Reinbold,
• Monika Fuchs and
• Thomas Brück

Beilstein J. Org. Chem. 2017, 13, 845–854, doi:10.3762/bjoc.13.85

• synthases are classed according to their intron/exon pattern [47] and their diverse reaction initiation mechanisms [48]. Genomic analyses of plant terpene synthases by Trapp and co-workers [47] revealed general organization of 12–14 introns for Class I terpene cyclases, 9 introns for Class II and 6 introns

Membrane properties of hydroxycholesterols related to the brain cholesterol metabolism

• Malte Hilsch,
• Ivan Haralampiev,
• Peter Müller,
• Daniel Huster and
• Holger A. Scheidt

Beilstein J. Org. Chem. 2017, 13, 720–727, doi:10.3762/bjoc.13.71

• constituents, resulting in highly characteristic effects on the packing and lateral organization of the membrane lipids and proteins [1][10][11][12][13]. Even very small alterations in the molecular structure of cholesterol cause large differences in the interaction with phospholipids and its membrane’s

Sulfamide chemistry applied to the functionalization of self-assembled monolayers on gold surfaces

• Loïc Pantaine,
• Vincent Humblot,
• Vincent Coeffard and
• Anne Vallée

Beilstein J. Org. Chem. 2017, 13, 648–658, doi:10.3762/bjoc.13.64

• the layer organization. Even if the reaction is not completely reversible, it is worth noting that the conversion rate of the hydrolysis in these mild conditions on the surface is as good as the one obtained in solution in the same conditions, e.g. 65%. While most of the previous works used only

Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces

• Enjuro Harunari,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2017, 13, 441–450, doi:10.3762/bjoc.13.47

• -butyl group. Actinomycete metabolites possessing a contiguous 1,2-diol system. Feeding experiments of 13C-labeled precursors into 1 detected by 2D-INADEQUATE NMR experiments. (a) [1,2-13C2]acetate; (b) [U-13C6]glucose. Organization of the biosynthesis gene cluster for 1. Blue, transcriptional regulator

Versatile synthesis of the signaling peptide glorin

• Robert Barnett,
• Daniel Raszkowski,
• Thomas Winckler and
• Pierre Stallforth

Beilstein J. Org. Chem. 2017, 13, 247–250, doi:10.3762/bjoc.13.27

• actin cytoskeleton organization, as a model gene. Upon glorin (1) exposure, this gene was found to be up-regulated by about 50-fold [11]. To this end, the compounds were dissolved in DMSO/water and added in two 1 μM portions (30 min apart) to a suspension of starving P. pallidum. After 1 h, the cells

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

• chemistry have demonstrated that hydrogen bonds formed by C–H bonds are not necessarily “weak”, and in certain cases are almost as strong as more traditional A–H···A bonds [20]. The C–H hydrogen bonding between the substrate and the catalyst could be of great significance for transition state organization

Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts

• Lukas J. Patalag and
• Daniel B. Werz

Beilstein J. Org. Chem. 2016, 12, 2739–2747, doi:10.3762/bjoc.12.270

• , SFB 803 “Functionality controlled by organization in and between membranes”, project A05) and the Fonds der Chemischen Industrie (FCI) for financial support (Dozentenstipendium to D.B.W.). We thank Martin Bröring (TU Braunschweig) for the possibility of measuring quantum yields by the instrument in

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

• ), respectively, towards the calf-spleen and E. coli PNPs and disclosed their satisfactory substrate activity [68]. The authors discussed the results in terms of similar spatial organization of natural nucleosides and their N-3-isomers admitting the binding and activation of the latter at the catalytic sites of

• not shown). Thus, both enzymes demonstrated severe restrictions on the bulkiness and three-dimensional structure of the substituent at the C-5 atom of the pyrimidines. The spatial organization of the very poor substrates 5-tert-butyluracil (15) and 5-phenyluracil (16) vs good substrates 5-ethyluracil

Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• deep energy levels, as well as some of the other desirable properties of the parent material [20][21][22]. However, molecular design remains only the first step towards the development of high performance devices. Mismanagement of the organization and phase-separation processes or inappropriate device

Protonated paramagnetic redox forms of di-o-quinone bridged with p-phenylene-extended TTF: A EPR spectroscopy study

• Nikolay O. Chalkov,
• Vladimir K. Cherkasov,
• Gleb A. Abakumov,
• Andrey G. Starikov and
• Viacheslav A. Kuropatov

Beilstein J. Org. Chem. 2016, 12, 2450–2456, doi:10.3762/bjoc.12.238

• proceeding at the coordination sites. Previously we reported paramagnetic derivatives of di-o-quinone (1, Figure 1) with alkali metals [3]. Using the protonated paramagnetic derivatives of the quinone-exTTF-quinone system we succeeded in organization of a symmetric surrounding for both coordination sites of

High performance p-type molecular electron donors for OPV applications via alkylthiophene catenation chromophore extension

• Paul B. Geraghty,
• Calvin Lee,
• Jegadesan Subbiah,
• Wallace W. H. Wong,
• James L. Banal,
• Mohammed A. Jameel,
• Trevor A. Smith and
• David J. Jones

Beilstein J. Org. Chem. 2016, 12, 2298–2314, doi:10.3762/bjoc.12.223

• impacts significantly on the development of highly π–π stacked materials. Shorter chromophore length leads to good stacking in thin films with dominant absorption transitions even in as-cast films for BMR, BTR and BQR. Molecular organization is improved in all films with SVA, except for the longest

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• exhibit a herringbone arrangement (Figure 2). This organization is sustained by CH–π interactions (H18∙∙∙centroid and H14′∙∙∙C10 contacts are 3.00 and 2.89 Å, respectively; symmetry code: ’ = −0.5 + x, −0.5 + y, 0.5 − z). Instead, the analysis of the packing diagrams in 4b (Figure 3) shows that only the

Rearrangements of organic peroxides and related processes

• Ivan A. Yaremenko,
• Vera A. Vil’,
• Dmitry V. Demchuk and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2016, 12, 1647–1748, doi:10.3762/bjoc.12.162

• the World Health Organization (WHO) malaria is a widely distributed illness. About 3.2 billion people remain at risk of malaria and in 2015 214 million cases of malaria and 438 thousands deaths from it have been registered [10]. Compounds with high antimalarial [11][12][13][14][15][16][17][18][19][20

Synthesis and characterization of benzodithiophene and benzotriazole-based polymers for photovoltaic applications

• Desta Gedefaw,
• Marta Tessarolo,
• Margherita Bolognesi,
• Mario Prosa,
• Renee Kroon,
• Wenliu Zhuang,
• Patrik Henriksson,
• Kim Bini,
• Ergang Wang,
• Michele Muccini,
• Mirko Seri and
• Mats R. Andersson

Beilstein J. Org. Chem. 2016, 12, 1629–1637, doi:10.3762/bjoc.12.160

• % and 4.7% were achieved for PTzBDT-1 and PTzBDT-2 based devices, respectively, likely suggesting a different BHJ self-organization as a consequence of the different material properties induced by the alkyl substitution on the aromatic side groups. Results and Discussion Synthesis of the polymers Scheme

• PTzBDT-1 (13 nm). These findings combined with the still different film absorption spectra, suggest a different self-organization of the polymer chains, as supported by additional optical, electrical and morphological investigations of PTzBDT-1 and PTzBDT-2 based blends (vide infra). The HOMO and LUMO

• ], however the subsequent different organization in the solid state might be the main factor responsible for the observed variation of the HOMO and LUMO energy levels, which is in perfect agreement with the different optical properties. Interestingly, the deep HOMO energies of both polymers would result in