Back to the future: Why we need enzymology to build a synthetic metabolism of the future

• Tobias J. Erb

Beilstein J. Org. Chem. 2019, 15, 551–557, doi:10.3762/bjoc.15.49

• feasible metabolic intermediates [13][14][15][16]. In a subsequent realization phase, the corresponding enzymes to realize the theoretical network are identified and/or engineered and a first version of the synthetic network is reconstructed. The network is further optimized or evolved in following rounds

• synthetic metabolic networks From above examples it becomes evident that for building completely novel pathways and/or complex reaction cascades, resources are required that provide synthetic biologists with the information to find individual enzymes for a given synthetic metabolic network. More than 116

• synthetic network, most likely because they lack a common evolutionary history that selects for stringent substrate specificity [57]. These unwanted side reactivities are able to compete with the wanted reactions of the synthetic network and can lead to the accumulation of dead-end products, thus decreasing

Silanediol versus chlorosilanol: hydrolyses and hydrogen-bonding catalyses with fenchole-based silanes

• Falco Fox,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2019, 15, 167–186, doi:10.3762/bjoc.15.17

• available (+)-fenchone has 98% enantiomeric purity, BIFOXSi(OH)2 can be further purified. rac-BIFOXSi(OH)2 crystallizes as a dimer from toluene (Figure 14). BIFOXSi(OH)2 (9) crystallizes as a tetramer from n-hexane (Figure 15), where six OH groups build a network of hydrogen bonds. Thus the polar core is

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• interchangeable (Table 1). Model E: active site of BFDC with (R)-mandelate bound In model E, in which the active site of BFDC contains the inhibitor (R)-mandelate, the hydrogen-bonding network is very similar to that of benzoylformate in model D. However, as shown in Figure 6, the benzylic hydroxy group provides

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

Synthesis of a tubugi-1-toxin conjugate by a modulizable disulfide linker system with a neuropeptide Y analogue showing selectivity for hY1R-overexpressing tumor cells

• Rainer Kufka,
• Robert Rennert,
• Goran N. Kaluđerović,
• Lutz Weber,
• Wolfgang Richter and
• Ludger A. Wessjohann

Beilstein J. Org. Chem. 2019, 15, 96–105, doi:10.3762/bjoc.15.11

• (Figure 1) [44][45][46]. Tubulysins were originally discovered and isolated from myxobacteria [47][48], with picomolar in vitro activities [45][46][49][50][51][52][53][54], that are caused by a destabilization and degradation of the microtubuli network undermining its function in mitosis of eukaryotic

Olefin metathesis catalysts embedded in β-barrel proteins: creating artificial metalloproteins for olefin metathesis

• Daniel F. Sauer,
• Johannes Schiffels,
• Takashi Hayashi,
• Ulrich Schwaneberg and
• Jun Okuda

Beilstein J. Org. Chem. 2018, 14, 2861–2871, doi:10.3762/bjoc.14.265

• are generally regarded to be more rigid than disordered or α-helix structures [30][31]. β-Barrels are structural motifs found in numerous proteins in which (mostly) antiparallel β-strands twist and coil to form closed, quasi-cylindrical structures held together by a network of hydrogen bonds [32

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• coordinate population-wide group behaviours in the infection process like concerted secretion of virulence factors. One very important signalling network is the Pseudomonas quinolone signal (PQS) QS. With the aim to devise novel and innovative anti-infectives, inhibitors have been designed to address the

• network with compensatory mechanisms ensuring environmental adaptability and fine-tuned control of associated virulence genes (Figure 1). All four have been studied in the pursuit of quorum sensing inhibitors (QSI) to be used as blockers of P. aeruginosa pathogenicity [11][23]. Typically, a QS system of

• complex network of biosynthetic pathways and effector molecules renders selection of the perfect point for intervention difficult. Due to their rather peripheral role in AQ synthesis, PqsH and PqsL, have not been of significant interest for QSI discovery to date. However, all enzymes of the primary

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• -dimensional network consisting of a linear unit connected by hydrogen bonds between N3–H and the triazole N3’’ of a second molecule (Figure 3, Supporting Information File 1, Figures S3 and S4). Additionally, the molecules are bridged by water molecules connecting O2 of the base moiety and N2’’ of the triazole

• ellipsoids are drawn at the 50% probability level and H-atoms are shown as small spheres of arbitrary size. Hydrogen bonds are shown as dashed lines. The crystal packing of 8 shows the intramolecular hydrogen-bonding network (projection parallel to the x-axis). N- and S-conformation for cyclonucleoside 8. B

Evaluation of dispersion type metal···π arene interaction in arylbismuth compounds – an experimental and theoretical study

• Ana-Maria Preda,
• Małgorzata Krasowska,
• Lydia Wrobel,
• Philipp Kitschke,
• Phil C. Andrews,
• Jonathan G. MacLellan,
• Lutz Mertens,
• Marcus Korb,
• Tobias Rüffer,
• Heinrich Lang,
• Alexander A. Auer and
• Michael Mehring

Beilstein J. Org. Chem. 2018, 14, 2125–2145, doi:10.3762/bjoc.14.187

• (arenecentroid) distances of 2.760 Å (black dashed line, γ = 6.4°) to give a 2D network (Figure 1c). Other additional C–HPh···π (arenecentroid) intermolecular contacts with C36–H36Ph···π (arenecentroid) distances of 2.740 Å (red dashed line, γ = 11.2°) lead to the formation of a 3D network in the solid state

• (arenecentroid) intermolecular contacts with C15–H15Ph···π (arenecentroid) 3.034 Å (black dashed line, γ = 8.4°) and C28–H28Ph···π (arenecentroid) 2.890 Å (brown dashed line, γ = 13.5°) and lead to the formation of a 2D network (Figure 2b). Another polymorph of Ph3Bi (1c) was reported by Neumann and co-workers

• layers are connected via two C–HPh···π (arenecentroid) intermolecular contacts, with C3–H3Ph···π (arenecentroid) 3.037 Å (blue dashed line, γ = 7.9°) to give a 3D network in the solid state (Figure 3c). It is worth to note that Wetzel has reported another crystal structure of Ph3Bi (1d) in 1942, which

Synthesis and supramolecular self-assembly of glutamic acid-based squaramides

• Juan V. Alegre-Requena,
• Marleen Häring,
• Isaac G. Sonsona,
• Alex Abramov,
• Eugenia Marqués-López,
• Raquel P. Herrera and
• David Díaz Díaz

Beilstein J. Org. Chem. 2018, 14, 2065–2073, doi:10.3762/bjoc.14.180

• 3D network with the solvent molecules trapped in the interstices by means of surface tension and capillary forces. This provides the typical solid-like appearance and viscoelastic features to physical gels [32]. Recently, we have demonstrated the potential of isosteric substitution for tuning the

• of a self-assembled network in organic solvents is likely driven by the formation of hydrogen bonds between different gelator molecules (polar head) as well as hydrophobic interactions between the long aliphatic chains. Considering our previous results obtained with diacids 1 and 2 [33], we initially

• agreement with our previous observations made with a different squaramide, where we hypothesized that ultrasound could help to preserve only the thermodynamically more stable aggregates through a self-sorting mechanism, thus providing a more robust starting platform for rebuilding the gel network [21]. At

Functionalization of graphene: does the organic chemistry matter?

• Artur Kasprzak,
• Agnieszka Zuchowska and
• Magdalena Poplawska

Beilstein J. Org. Chem. 2018, 14, 2018–2026, doi:10.3762/bjoc.14.177

• is well-known that the hydrogen-bonding network and/or salt formation have significant influence on, for example, the shift of the absorption band coming from carboxyl moieties (IR analyses). Although scholars [40] have presented further studies on the functionalized GO and RGO materials, the

A self-assembled photoresponsive gel consisting of chiral nanofibers

• Lei Zou,
• Dan Han,
• Zhiyi Yuan,
• Dongdong Chang and
• Xiang Ma

Beilstein J. Org. Chem. 2018, 14, 1994–2001, doi:10.3762/bjoc.14.174

• and π–π stacking in DMSO. However, beautiful acicular fibers could be detected on the surface treated with a chloroform solution, and a dendritic network was observed on the sample made from benzene solution (Figure S9, Supporting Information File 1). The photoresponsiveness of compound 3 was also

• gel was investigated and found to meet the basic requirement of a gel. The inner structure of the gel was determined to be a cross-linked network made of chiral nanotwists. This work provides a novel method to build chiro-optical soft material systems. Experimental Synthesis of compound 1 1-Ethyl-3-(3

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• spectra of labeling experiments. Acknowledgements Financial support by the DFG-Cluster of Excellence “Inflammation at Interfaces” and by the DFG Collaborative Network SFB 677 is gratefully acknowledged.

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

• Rakesh Puttreddy,
• Ngong Kodiah Beyeh,
• S. Maryamdokht Taimoory,
• Daniel Meister,
• John F. Trant and
• Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

• made possible by the facilities of the Shared Hierarchical Academic Research Computing Network (SHARCNET: http://www.sharcnet.ca) and Compute/Calcul Canada.

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• NH2+]3(–OOC)3C6H3 (Figure 1, linear connection, as a six-membered chelate, to the m-trivalent core), the H-bonding network in model 10 determined simpler angular connections of the P-1 piperazin-1-ium melamine G-1 cations around the trimesic tris-carboxylate anion core in a statistically favoured

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• network. We have carefully looked into the properties of oxatub[n]arenes and found that the macrocycles have many unique properties. For example, oxatub[4]arene has a wide guest scope and can bind almost all of the common organic cations [32]. It also shows conformational responses to solvent change [33

• conformer III (C2h symmetry) [37] to be the most favored conformation for all complexes. Obviously the conformational network of ZB4 shows no response to the electronic substituents on the guests. This is quite different from TA4. In addition, there has been a linear free energy relationship between

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

• preliminary tests to assess their supramolecular absorption abilities towards a set of suitable organic guests, selected as pollutant models. The synthesis was accomplished by means of a CuAAC reaction between a tetrakis(propargyloxy)calix[4]arene and an alkyl diazide. The formation of the polymeric network

• 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

• number of azido groups present in the molecule. The actual accomplishment of the CuAAC reaction, and therefore the formation of the reticulated polymer network, was first assessed by means of FTIR spectroscopy. The FTIR spectra of the propargyloxycalixarene precursor Ca-OP, of the diazide A2 and the

Are dispersion corrections accurate outside equilibrium? A case study on benzene

• Tim Gould,
• Erin R. Johnson and
• Sherif Abdulkader Tawfik

Beilstein J. Org. Chem. 2018, 14, 1181–1191, doi:10.3762/bjoc.14.99

• Western Australia. ERJ thanks the Natural Sciences and Engineering Research Council (NSERC) of Canada for financial support and the Atlantic Computational Excellence Network (ACEnet) for computing resources.

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

• . 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

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

Nanoreactors for green catalysis

• M. Teresa De Martino,
• Loai K. E. A. Abdelmohsen,
• Floris P. J. T. Rutjes and
• Jan C. M. van Hest

Beilstein J. Org. Chem. 2018, 14, 716–733, doi:10.3762/bjoc.14.61

• based on poly(acrylamide-co-acryl acid) (poly(AAm-co-AAc)) [117]. These nanogels were transformed into their catalytic counterparts by growing silver nanoparticles (Ag NPs) inside the cross-linked polymeric network. These catalytic nanogels were also used to catalyse the reduction of 4-nitrophenol to 4

An alternative to hydrogenation processes. Electrocatalytic hydrogenation of benzophenone

• Cristina Mozo Mulero,
• Alfonso Sáez,
• Jesús Iniesta and
• Vicente Montiel

Beilstein J. Org. Chem. 2018, 14, 537–546, doi:10.3762/bjoc.14.40

• bottlenecks or blockage of network across the electrocatalytic layer, or likely some of these Pd nanoparticles could be covered up each other so those ones would be hidden. Once Pd nanoparticle-based cathodes were manufactured and characterised, electrolytic hydrogenation of benzophenone in a cathodic process

The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

• Yaochun Xu,
• Isabelle Correia,
• Tap Ha-Duong,
• Nadjib Kihal,
• Jean-Louis Soulier,
• Julia Kaffy,
• Benoît Crousse,
• Olivier Lequin and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276

• bond network. Methanol was used because of the limited solubility of these compounds in aqueous solutions. The 1H and 13C chemical shifts of these pentapeptides were assigned using 1D 1H, 2D 1H,1H-TOCSY, 2D 1H,1H-ROESY, 2D 1H,13C-HSQC, and 2D 1H,13C-HMBC spectra. The 1H and 13C chemical shift

The photodecarboxylative addition of carboxylates to phthalimides as a key-step in the synthesis of biologically active 3-arylmethylene-2,3-dihydro-1H-isoindolin-1-ones

• Ommid Anamimoghadam,
• Saira Mumtaz,
• Anke Nietsch,
• Gaetano Saya,
• Cherie A. Motti,
• Jun Wang,
• Peter C. Junk,
• Ashfaq Mahmood Qureshi and
• Michael Oelgemöller

Beilstein J. Org. Chem. 2017, 13, 2833–2841, doi:10.3762/bjoc.13.275

• photoaddition products 3a and 3b were unambiguously confirmed by X-ray crystallography (Figure 2). In the solid state, molecules of both compounds undergo hydrogen bonding between the newly formed hydroxy group and the intact carbonyl group, resulting in a one-dimensional network (see Supporting Information

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