Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• background spectrum should be subtracted. It takes about 10–20 min to collect one spectrum by multiple accumulations. During that time, the previously recorded spectra can be processed and compared to follow in real time the evolution of spectra. Any deviation from the baseline in the range where the studied

Photocatalytic formation of carbon–sulfur bonds

• Alexander Wimmer and
• Burkhard König

Beilstein J. Org. Chem. 2018, 14, 54–83, doi:10.3762/bjoc.14.4

• generate a carbon-centred radical intermediate. The cobalt-catalyst is involved in two ways: oxidation and deprotonation of the radical species yielding the desired product and oxidation of the Eosin Y radical anion to close the photocatalytic cycle. The H2 evolution was not quantitative, which was

• explained by the decomposition of the organic photocatalyst during the H2 evolution process. Increasing amounts of the photocatalyst increased the yield of product and H2. Very recently, the same group reported a regioselective photoredox-catalyzed preparation of vinyl sulfones in Markovnikov orientation

Halogen-containing thiazole orange analogues – new fluorogenic DNA stains

• Aleksey A. Vasilev,
• Meglena I. Kandinska,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• David Sucunza,
• Juan J. Vaquero,
• Obis D. Castaño,
• Stanislav Baluschev and
• Silvia E. Angelova

Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283

• interchange of the alkyl groups at the thioalkyl unit and nitrogen atom in the quaternized 2-alkylthio starting materials, which leads to unexpected reaction products [45][46]. The other major disadvantage is the evolution of methylmercaptan – a toxic pollutant with a very unpleasant odor. Results and

¹⁵N-Labelling and structure determination of adamantylated azolo-azines in solution

• Sergey L. Deev,
• Alexander S. Paramonov,
• Tatyana S. Shestakova,
• Igor A. Khalymbadzha,
• Oleg N. Chupakhin,
• Julia O. Subbotina,
• Oleg S. Eltsov,
• Pavel A. Slepukhin,
• Vladimir L. Rusinov,
• Alexander S. Arseniev and
• Zakhar O. Shenkarev

Beilstein J. Org. Chem. 2017, 13, 2535–2548, doi:10.3762/bjoc.13.250

• ). (A) Fragment of the 1D 1H amplitude-modulated spin-echo spectrum measured without (black trace) or with selective inversion of the 15N2 (blue trace) or 15N3 (red trace) nuclei. The spectrum was measured using a spin-echo delay (delay for the evolution of JHN) of 1 s. The measured JHN values are

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• significantly more light than the same mass of small particles. Thus, a fairly small amount of large aggregates might dominate the scattering making the contribution of small particles negligible. The long-time evolution of all the isomers after filtration was evaluated according to the approach of Bonini [22

• size continuously fluctuate (Supporting Information File 1, Figure S5), which could be easily monitored by scattering intensities behavior. The evolution of the 2-O-isomer in time has also been investigated, but no trend was observed in this case (Supporting Information File 1, Figure S6). The long

• -time evolution of the 6-O-filtered sample revealed that the size of particles continuously increased with time (Supporting Information File 1, Figure S6), starting from 2 nm particles appearing immediately after the filtration and reaching larger particles that grew in the sample standing overnight

Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity

• Tathagata Mukherjee,
• Soumik Biswas,
• Andreas Ehnbom,
• Subrata K. Ghosh,
• Ibrahim El-Zoghbi,
• Nattamai Bhuvanesh,
• Hassan S. Bazzi and
• John A. Gladysz

Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246

• structure of which is determined, reacts with Cl2 to give a 75:25 ArICl2/ArI mixture, but partial Cl2 evolution occurs upon work-up. The latter gives the easily isolated dichloride 1,2,4-(Rf8CH2CH2)2C6H3ICl2 (89%). The relative thermodynamic ease of dichlorination of these and other iodine(I) compounds is

• in 80–89% yields. Although these were clean by NMR, only one gave a correct microanalysis. As illustrated in Figure S1 (Supporting Information File 1), CDCl3/C6F6 solutions of 1,3-Rf6C6H4ICl2 and 1,4-Rf6C6H4ICl2 containing an internal standard were monitored by 1H NMR. Slow partial evolution of Cl2

• )2C6H3ICl2 were unsuccessful. It was concluded that 1,3,5-(Rf6)2C6H3ICl2 was much more labile with respect to Cl2 evolution than the fluorous aryliodine(III) dichlorides shown in Scheme 5, and that the 75–80% conversions reflected a thermodynamic limit. Next, analogs of 1,3,5-(Rf6)2C6H3ICl2 with less

Synthesis of naturally-derived macromolecules through simplified electrochemically mediated ATRP

• Paweł Chmielarz,
• Tomasz Pacześniak,
• Katarzyna Rydel-Ciszek,
• Izabela Zaborniak,
• Paulina Biedka and
• Andrzej Sobkowiak

Beilstein J. Org. Chem. 2017, 13, 2466–2472, doi:10.3762/bjoc.13.243

• purification (in CDCl3). Synthesis of PtBA homopolymers grafted from quercetin-based macroinitiator via seATRP under constant potential conditions; (a) Mn and Mw/Mn vs monomer conversion, and (b) GPC traces of tBA polymerization and their evolution over time. Reaction conditions: [tBA]/[QC-Br5 (per 5

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

• even after 15 minutes milling. Surprisingly, monitoring the mechanochemical formation of 5 by milling with brass balls (method 2c) enabled a clear insight into the evolution of the reaction mixture (Figure 3a). The luminescent peak remained weak throughout the experiment, leaving the Raman signals of

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• -CD, and γ-CDs were recorded in phosphate buffered saline (PBS) at pH 7.4 using an Evolution 220 UV–vis spectrometer (Thermo Scientific) in the range of 200–450 nm. Evaluation of association constants (Kas) of native CDs with PTX. UV–vis titrations: The change in absorption was measured as a function

Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

• José Enrique Barquera-Lozada and
• Gabriel Cuevas

Beilstein J. Org. Chem. 2017, 13, 1969–1976, doi:10.3762/bjoc.13.192

• energetic evolution of germacranolides’ Cope transformations. Computational methods DFT has been proved to be a good method for the study of reaction mechanisms of natural products' biogenesis and it has been used in many studies [44][45][46][47][48][49][50][51][52][53][54][55] and it is the method of

A novel application of 2-silylated 1,3-dithiolanes for the synthesis of aryl/hetaryl-substituted ethenes and dibenzofulvenes

• Grzegorz Mlostoń,
• Paulina Pipiak,
• Róża Hamera-Fałdyga and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 1900–1906, doi:10.3762/bjoc.13.185

• some dihetaryl thioketones, e.g., 1d and 1e, were reported [22]. In contrast to CH2N2, TMS-CHN2 reacted with thiobenzophenone (1a) with evolution of N2 even at −75 °C and led to a mixture of 4,4,5,5-tetraphenyl-1,3-dithiolane 6a and 2,2,3,3-tetraphenyl-1,4-dithiane 7 (Scheme 2). This result

Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides

• Jihen Ati,
• Pierre Lafite and
• Richard Daniellou

Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180

• . Rational mutagenesis, directed evolution, or even de novo design have dramatically broaden the applicability of enzymes in biocatalysis [7]. In the glycochemistry field, a vast array of carbohydrate-metabolizing enzymes [8] has been used to synthesize glycosides, even using multiple enzymes systems

Mechanochemical synthesis of thioureas, ureas and guanidines

• Vjekoslav Štrukil

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

• inorganic chemical into an organic product, at that time only available from living organisms, was in contradiction with the prevailing doctrine of vitalism, which was in the years to come abandoned enabling a rapid evolution of organic chemistry in the 19th century. During the 20th century, synthetic

A recursive microfluidic platform to explore the emergence of chemical evolution

• David Doran,
• Marc Rodriguez-Garcia,
• Rebecca Turk-MacLeod,
• Geoffrey J. T. Cooper and
• Leroy Cronin

Beilstein J. Org. Chem. 2017, 13, 1702–1709, doi:10.3762/bjoc.13.164

• an automated recursive platform based on droplet microfluidics, could be used to induce artificial chemical evolution by iterations of growth, speciation, selection, and propagation. To explore this, we set about designing an open source prototype of a fully automated evolution machine, comprising

• : artificial life; autocatalysis; automated platforms; chemical evolution; evolution before genes; evolution first; microfluidics; Introduction The transition from an inanimate inorganic world, principally consisting of minerals, gases and small organic compounds, to the living world with the first life forms

• external environment. ii) Metabolism: chemical reaction networks that extract energy from the environment in a useable form. iii) Heritance: reliable transmission of functional information from one generation to the next. iv) Evolution: a means of undergoing an evolutionary selection process, driven by

Oxidative dehydrogenation of C–C and C–N bonds: A convenient approach to access diverse (dihydro)heteroaromatic compounds

• Santanu Hati,
• Ulrike Holzgrabe and
• Subhabrata Sen

Beilstein J. Org. Chem. 2017, 13, 1670–1692, doi:10.3762/bjoc.13.162

• cyclisation and oxidative dehydrogenation in the presence of barium manganate to produce benzimidazoles, benzoxazoles and benzothiazoles 54, respectively in appropriate solvent at ambient or lower temperature (Scheme 16). Catalytic approaches As a normal evolution of any synthetic approaches, oxidative

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

• characteristics of various biomolecules, e.g., the catalytic activity of RNAs and their evolution potential [9][10][11], as well as processes that were essential for their syntheses, such as Fischer–Tropsch-like reactions [12], non-enzymatic RNA [13] or peptide polymerization [14]. Moreover, it has also allowed

• for the determination of environmental conditions conducive to the self-assembly of several cellular-like components, such as bilayer membranes [15] and simple energy systems [16], or dynamic processes, such as growth and division [17][18] and potential evolution [19]. However, the experimental set

• membrane components. Furthermore, experimental conditions are sometimes implausible from the geochemical perspective. Finally, the evolutionary continuity of the systems, which should be paramount to explain the emergence of protocellular systems and evolution towards true cells, is often neglected in

Photocatalyzed synthesis of isochromanones and isobenzofuranones under batch and flow conditions

• Manuel Anselmo,
• Lisa Moni,
• Hossny Ismail,
• Davide Comoretto,
• Renata Riva and
• Andrea Basso

Beilstein J. Org. Chem. 2017, 13, 1456–1462, doi:10.3762/bjoc.13.143

• evolution started within the first few minutes of irradiation, shorter residence times resulted in lower conversions, as shown in Table 3 for model compound 4c (with slower flow rates the diazonium salt started to decompose in the supplying syringe, as demonstrated by formation of nitrogen bubbles). All

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

• proper units of prebiotic evolution. We highlight, in particular, how the organisational features of those chemically active and reactive protocells, at different stages of the process, would strongly influence their corresponding evolutionary capacities. As a result of our analysis, we suggest three

• evolution; protocells; Introduction Living beings on Earth, even in their simplest prokaryote versions, are extremely complex systems, made of a great diversity of molecular components in continuous transformation and interaction. At the base level, each cell is sustained by means of an impressive

• provide a very natural connection to real cells, which is attractive both for research groups investigating the chemical roots of biological organisation and for others trying to determine the first steps of biological evolution. Discussion This commentary is aimed at providing a global vision of how

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science

• , medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis

• methods and their potential impacts in chemistry, engineering, and medicine. Keywords: automated chemical synthesis; deep learning; evolutionary algorithms; in silico evolution; machine learning; materials design and development; neural networks; Introduction There is still not a clear understanding of

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

• always been the competing hydrolysis reaction, which is thermodynamically favored. However, due to incredible efforts in the field this problem can be mostly circumvented by the selection of the appropriate mutant through directed evolution [12] and advancements in donor design being the key players [15

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

• duplication has been ranked as a rather late event during the course of evolution [25]. In the light of the key role of ACP in substrate shuttling, multiple ACP domains might be beneficial in increasing the substrate concentration at which type I synthesis is performed [26][27]. The conformationally more

• specificity of the system via domain–domain interactions, evolution has likely not selected for strict substrate specificity as compared to diffusion-loaded proteins, and megasynthases might be inherently substrate tolerant [53][54][55]. Preserve-and-adapt approach on the example of FAS Given the detailed

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• discuss systems of self-replicating molecules in the context of the origin of life and the synthesis of de novo life. One of the important aspects of life is the ability to reproduce and evolve continuously. In this review we consider some of the prerequisites for obtaining unbounded evolution of self

• -replicating molecules and describe some recent advances in this field. While evolution experiments involving self-replicating molecules have shown promising results, true open-ended evolution has not been realized so far. A full understanding of the requirements for open-ended evolution would provide a better

• understanding of how life could have emerged from molecular building blocks and what is needed to create a minimal form of life in the laboratory. Keywords: autocatalysis; open-ended evolution; origin of life; self-replication; synthetic life; Introduction Mankind has always pondered upon its own existence

Characterization of non-heme iron aliphatic halogenase WelO5* from Hapalosiphon welwitschii IC-52-3: Identification of a minimal protein sequence motif that confers enzymatic chlorination specificity in the biosynthesis of welwitindolelinones

• Qin Zhu and
• Xinyu Liu

Beilstein J. Org. Chem. 2017, 13, 1168–1173, doi:10.3762/bjoc.13.115

• engineering and evolution of these proteins for biocatalyst application. Keywords: alkaloid biogenesis; biosynthetic divergency; C–H activation; halogenase; non-heme iron enzyme; Introduction Carbon–halogen (C–X) bonds are prevalent structural motifs in modern agrochemicals, pharmaceuticals and bioactive

• sequence motif, initially discovered in the comparative characterization of WelO5 and AmbO5 [18]. This further confirms the functional significance of this conserved sequence motif in this new halogenase family that may guide the rational engineering and evolution of these proteins for biocatalyst

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

• biology and the investigation of macromolecular structure and function relationships. Major contributions also came from considerable advances in high resolution NMR spectrometry and electron microscopy along with the continuous evolution of synchrotron radiation and free electron laser light sources

• structure of biological macromolecules. Among the 128,000 structures deposited in the Protein Data Bank (January 2017) more than 80% have been measured and solved at synchrotron radiation facilities [18]. Macromolecular crystallography beamlines underwent a constant evolution over last decade that had a

• modifications. Transporters and proteins purely involved in recognition (lectin, antibodies, carbohydrate binding modules, glycosaminoglycan binding proteins) are the other important classes of carbohydrate-binding proteins. Figure 7 shows the evolution of the number of carbohydrate interacting proteins that

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• ]. A main problem that lies behind the difficulty of defining what is a function is its relationships with evolution (how did this particular function come into being?), and this is what I discuss. A key idea behind the view I support is that beside the four currencies constituting our world (matter

• , the processes that allow aged organisms to construct young ones are of key interest. These processes, in turn, give a direction to the very process of “life and evolution” via accumulation of information, in a ratchet-like manner. Combining “action” with “orientation” will help us to understand the

• concepts. Instead it comprises just a handful of essential albeit very deep concepts, among which the process of coding has a paramount position. Yet, amusingly, it appears that everybody may talk about biology, give their opinion on natural selection, evolution of the species, or the benefits or misdeeds