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

• for the sustainability of any type of cell [7][8]. Furthermore, this more encompassing approach to life is fully congruent with other insights coming from investigations on reaction–diffusion processes in biology, which have revealed, since the pioneering work of Turing [9], the enormous potential of

• coupling chemistry with the constrained spatial diffusion of the molecules involved [10][11]. Therefore, given the cellular nature of all life known on our planet, and given the importance of compartmentalized chemistries for understanding many biological phenomena, it may be productive to try origin-of

• negative and positive feedback loops (autocatalytic cycles) that can take place within the internal water pool, the presence of closed lipid bilayers strongly restricts the free diffusion of the various soluble species involved, allows the selective passage of precursors and excludes water in limited areas

Mechanochemistry-assisted synthesis of hierarchical porous carbons applied as supercapacitors

• Desirée Leistenschneider,
• Nicolas Jäckel,
• Felix Hippauf,
• Volker Presser and
• Lars Borchardt

Beilstein J. Org. Chem. 2017, 13, 1332–1341, doi:10.3762/bjoc.13.130

• influence of the pore size and the pore structure on (electro)sorption in energy storage devices [15][16][17]. Moreover, purely microporous carbons suffer from diffusion limitations resulting in low electrochemical performances at high charge/discharge rates [4][18][19]. Larger pores, like mesopores, or

• ), the porogens could be partially removed by HF (CarbHF-LA-3). We assume that the carbon matrix obtained from a solvent-free approach is possibly denser and thus the diffusion of HF to the particles is inhibited (incomplete removal). This aligns with the assumption that the energy-input and accordingly

Detection of therapeutic radiation in three-dimensions

• John A. Adamovics

Beilstein J. Org. Chem. 2017, 13, 1325–1331, doi:10.3762/bjoc.13.129

• ferrous/agarose/xylenol orange (FAX) gel shows visible-light absorption at 440 nm; after exposure to ionizing radiation, there is an increase in absorption at 585 nm. Even though diffusion has been diminished it continues to be an issue [12]. These diffusion limitations were overcome in a gel matrix by

One-pot synthesis of block-copolyrotaxanes through controlled rotaxa-polymerization

• Jessica Hilschmann,
• Gerhard Wenz and
• Gergely Kali

Beilstein J. Org. Chem. 2017, 13, 1310–1315, doi:10.3762/bjoc.13.127

• of the polyrotaxanes [41]. This peak broadening was indeed observed in the 1H NMR spectra of both polymers (Figure 1b and Supporting Information File 1) and was regarded as the first indication for a polyrotaxane structure. In addition, the agreement of the diffusion coefficients D for all proton NMR

• signals of the polymeric axis, RAMEB and the stopper in the diffusion-ordered NMR spectrum (DOSY, Figure 1b) further proved the existence of the polyrotaxane [42]. The D values of 1.0 × 10−10 and 4.1 × 10−11 m2/s were found for TRIS-AAm, and HEMA stoppered polyrotaxanes, respectively. The weight average

• –2.3 and 5.0 ppm and of polyHEMA at 0.7–2.1 and 3.3–4.0 ppm. The noticeable peak broadening again is indicative of the formation of ABA triblock-copolyrotaxane. The DOSY measurements were carried out for the block-copolymer polyrotaxanes in DMSO. The same diffusion coefficients were detected for all

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

• translocation of the cargo to the downstream modules in modular PKS, which largely accounts for the assembly-line character of these proteins (Figure 2c). As part of the multienzyme compartment, the mode of ACP action is best described as enabling limited diffusion within a conformational space that is

• 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

• , with potential impact on evolutionary behavior [40]. Another interesting dynamic emergent property of self-replicating systems was demonstrated by Philp and coworkers [41]. They showed how self-replicating molecules can create a reaction-diffusion front when seeded to a homogeneous mixture of building

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

• transport proteins GLUTs are responsible for the diffusion of glucose, galactose, fructose, urate, myoinositol, and dehydroascorbic acid. SGLTs are sodium-glucose symporters that couple the transport of glucose to sodium ions. SWEETs have been characterized the most recently. Major carbohydrate transporters

• shorter than the time scale of substrate diffusion in the crystals. For example, when UDP-GalNAc was soaked for 24 minutes, experiments resulted in structures with UDP-GalNAc in several conformations that are difficult to interpret. The “freeze-trigger” route was started using a series of cage compounds

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

• obtained. The active layer morphology in polymer solar cells is crucial and can drastically affect the performance of the devices. For optimum performance of an OPV device, the phase-separated donor and acceptor domain sizes should be twice the exciton diffusion length, which is typically of the order of 7

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• wall and minimize diffusion limits (Figure 2). Without bubbles, the yield of 4a would have been ca. 57% at the same residence time. The catalyst was used for weeks without significant deactivation. 1-Cyclohexyl-2-methyl-3-butyn-1-ol In the course of their studies on diastereoselective chain-elongation

• from a diffusion-controlled to kinetic-limited regime [163][181]. The non-accumulation of co-products adsorbed on the catalyst surface may also significantly contribute to the minimization of active site inhibition under the conditions of continuous flow [27]. Flow reactor design. Performance

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

• the membrane bilayer, which guides their ability to cross the blood–brain barrier. This process consists of three steps at the membrane level, (i) incorporation of sterols into the plasma membrane, (ii) their transbilayer diffusion and (iii) their release from the membrane. With regard to the transfer

• sterols, it is generally assumed that cholesterol traverses the bilayer very rapidly by passive diffusion, although at certain conditions, e.g., special membrane compositions, its transbilayer movement could be compounded (see [35]). For hydroxycholesterols, the transbilayer movement has not been

• diffusion of dithionite [18][19][27]. The assay was performed in a similar manner to the procedure described in [19]. Briefly, LUVs containing POPC and 0.5 mol % NBD-PC without or with cholesterol or the respective hydroxycholesterol (molar ratio 0.8:0.2) were prepared. The NBD fluorescence intensity of 33

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• anion is one of the key reactive species which is implicated in various metabolic and physiological processes [35]. Thus, it is important to provide analytical methods to detect and quantify its presence, however, due to its high reactivity, low concentration levels and quick diffusion, it has been

Contribution of microreactor technology and flow chemistry to the development of green and sustainable synthesis

• Flavio Fanelli,
• Giovanna Parisi,
• Leonardo Degennaro and
• Renzo Luisi

Beilstein J. Org. Chem. 2017, 13, 520–542, doi:10.3762/bjoc.13.51

• following characteristics: a) fast mixing: in a flow microreactor, in striking contrast to batch conditions, mixing takes place by molecular diffusion so that a concentration gradient can be avoided; b) high surface-to-volume ratio: the microstructure of microreactors allows for a very rapid heat transfer

NMR reaction monitoring in flow synthesis

• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2017, 13, 285–300, doi:10.3762/bjoc.13.31

• product is continuously eluted from the end of the flow reactor. This approach can be used from microscale to laboratory scale and even to production scale [4][5]. Some important advantages of flow chemistry are: Diffusion is clearly improved with regard to chemistry in batch (reagents and products), thus

Highly bulky and stable geometry-constrained iminopyridines: Synthesis, structure and application in Pd-catalyzed Suzuki coupling of aryl chlorides

• Yi Lai,
• Zhijian Zong,
• Yujie Tang,
• Weimin Mo,
• Nan Sun,
• Baoxiang Hu,
• Zhenlu Shen,
• Liqun Jin,
• Wen-hua Sun and
• Xinquan Hu

Beilstein J. Org. Chem. 2017, 13, 213–221, doi:10.3762/bjoc.13.24

• by slow diffusion of diethyl ether to a saturated dichloromethane solution and the molecular structure in solid state was determined by X-ray diffraction [73]. Presented in Figure 2, the molecular structure and the predicted conformation was unambiguously confirmed. The same as before, the complexes

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

• Monica Ferro,
• Franca Castiglione,
• Nadia Pastori,
• Carlo Punta,
• Lucio Melone,
• Walter Panzeri,
• Barbara Rossi,
• Francesco Trotta and
• Andrea Mele

Beilstein J. Org. Chem. 2017, 13, 182–194, doi:10.3762/bjoc.13.21

• isolated S spins and an extended network of coupled I spins. The heat capacity of the rare S spins is much lower than that of I spins. According to this model, the spins I are characterized by a rapid spin diffusion so that they behave as a single spin system at a uniform spin temperature. After the

• *–S model, the reservoir of the I (1H) nuclei surrounding a given S (13C) nucleus is divided into two subsets: I* indicates the protons closest to the observed S nucleus, I the nuclei at longer distances. This model was proposed to explain the case when the proton spin diffusion rate 1/TDiff is not

• fast enough so that the I spins do not behave as a whole spin system. The I*–S spin pairs are isolated from the spin network and exchange polarization in an oscillatory mode. The oscillations are damped by the spin-diffusion contact with the whole I spin system. A schematic representation of the

Poly(ethylene glycol)s as grinding additives in the mechanochemical preparation of highly functionalized 3,5-disubstituted hydantoins

• Andrea Mascitti,
• Massimiliano Lupacchini,
• Ruben Guerra,
• Ilya Taydakov,
• Lucia Tonucci,
• Nicola d’Alessandro,
• Frederic Lamaty,
• Jean Martinez and
• Evelina Colacino

Beilstein J. Org. Chem. 2017, 13, 19–25, doi:10.3762/bjoc.13.3

• instead of PEGs as additive (Table 1, entry 14). As a result, the effect of using different end terminal groups was not markedly significant, the yield was a function of the average molecular weight of the PEG used: HO-PEG-5000-OH (Table 1, entry 11) was probably too viscous to allow the diffusion of

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934

• Veronika Ulrich,
• Clara Brieke and
• Max J. Cryle

Beilstein J. Org. Chem. 2016, 12, 2849–2864, doi:10.3762/bjoc.12.284

• crystallisation Crystals were grown using hanging drop vapour diffusion at 4 °C. The StaF protein (140 µM) was mixed (1:1) with the reservoir solution (0.1 M phosphate/citrate buffer (pH 4.2), 1.2 M Na2PO4, 0.3 M K2HPO4; final pH 5.2) and equilibrated against the reservoir solution. After 10 days red diamonds

Synthesis of spiro[isoindole-1,5’-isoxazolidin]-3(2H)-ones as potential inhibitors of the MDM2-p53 interaction

• Salvatore V. Giofrè,
• Santa Cirmi,
• Raffaella Mancuso,
• Francesco Nicolò,
• Giuseppe Lanza,
• Laura Legnani,
• Agata Campisi,
• Maria A. Chiacchio,
• Michele Navarra,
• Bartolo Gabriele and
• Roberto Romeo

Beilstein J. Org. Chem. 2016, 12, 2793–2807, doi:10.3762/bjoc.12.278

• , as white amorphous mass in 60% yield. The 1H NMR spectrum shows the presence of (R,R)/(S,S)- and (R,S)/(S,R)-isomers respectively in 85:15 ratio. A single crystal of 7a suitable for X-ray diffraction studies was obtained by slow diffusion of diethyl ether into a hot dichloromethane solution of

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

• ., differences in membrane thickness and stiffness, different diffusion coefficients etc.) [5][6]. Tools to investigate lipid membranes are multifaceted; however, all optical methods are hampered by the missing absorption and fluorescence properties of natural occurring lipid components. Therefore, indirect

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• ]. As these criteria apply only to absorption by passive diffusion of compounds through cell membranes, the absorption of the native CDs and their hydrophilic derivatives are not allowed in their intact form and any cellular absorption, if it occurs, is by passive transport through cytoplasmic membranes

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

• effective voltages, (V0 − V < ≈0.1 V) implying a small electric field, the photocurrent of both devices linearly increases with voltage. This is due to the competition between drift and diffusion of photogenerated charges to the contacts [49]. In the device processed with DIO, beyond V0 − V = 0.2 V the JPh

Biomimetic synthesis and HPLC–ECD analysis of the isomers of dracocephins A and B

• Viktor Ilkei,
• András Spaits,
• Anita Prechl,
• Áron Szigetvári,
• Zoltán Béni,
• Miklós Dékány,
• Csaba Szántay Jr,
• Judit Müller,
• Árpád Könczöl,
• Ádám Szappanos,
• Attila Mándi,
• Sándor Antus,
• Ana Martins,
• Attila Hunyadi,
• György Tibor Balogh,
• György Kalaus (†),
• Hedvig Bölcskei,
• László Hazai and
• Tibor Kurtán

Beilstein J. Org. Chem. 2016, 12, 2523–2534, doi:10.3762/bjoc.12.247

• permeability assay)-BBB model system, which indicates passive diffusion of test compounds across the brain capillary endothelium. Although naringenin ((±)-1) showed a medium penetration characteristic in this model system, dracocephins A (2a–d) and B (3a–d) had been described as poorly and practically non

Efficient mechanochemical synthesis of regioselective persubstituted cyclodextrins

• Laszlo Jicsinszky,
• Marina Caporaso,
• Katia Martina,
• Emanuela Calcio Gaudino and
• Giancarlo Cravotto

Beilstein J. Org. Chem. 2016, 12, 2364–2371, doi:10.3762/bjoc.12.230

• simplicity and flexibility [18][19][20][21]. While the mechanochemical manipulation of covalent bonds is hardly a brand new concept, its diffusion into carbohydrate chemistry, and particularly into CD derivatization, has been rather slow [22][23]. The ability of HEBM to favour the nucleophilic substitution

• various CD complexes [26][31]. Lack of solvents the diffusion/decomplexation of NaI from the cavity is slow. The higher amounts of sodium azide can exclude the formed NaI from the CD cavity in solid state. However, on a larger multigram scale the higher amount of used NaN3 can be easily regenerated

Diels–Alder reactions in confined spaces: the influence of catalyst structure and the nature of active sites for the retro-Diels–Alder reaction

• Ángel Cantín,
• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2016, 12, 2181–2188, doi:10.3762/bjoc.12.208

• effect within the pore and diffusion limitations are discussed. Introduction of Lewis or Brønsted acid sites on the walls of the zeolite strongly increases the reaction rate. However, contrary to what occurs with mesoporous molecular sieves (MCM-41), Beta zeolite does not catalyse the retro-Diels–Alder

• limited by a slow diffusion of reactants and products, unless microporous molecular sieves with the appropriated pore dimensions are used as catalyst. Thus, microporous molecular sieves with optimized pore diameters and topologies can be of interest to catalyze DAR [17][18][19][20][21][22][23][24][25][26

• , if any, should only occur on the catalyst surface and the porous structure has not any effect on the reaction. Another hypothesis to explain these results is that diffusion of the products through the channels, if ever formed inside, is strongly restricted and the products remain adsorbed within the