Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• demonstrates the potential of base–base FRET in short time-scale kinetics investigations [82]. Conclusion Base–base FRET has a great potential as a detailed structure and dynamics tool in biomolecular sciences. It serves as an interesting complement to FRET pairs based on external fluorophores enabling higher

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

• ) characterization of single molecule binding would be studied at large excess (10 to 50-fold) of DNA/RNA over ligand; b) ligand aggregation within DNA/RNA would be studied at excess of ligand over DNA/RNA; c) kinetics of binding would be studied at different temperatures and instrument response times; d

• binding events shown in Figure 2 are usually detectable and can be subjected to detailed analysis). The incubation time prior to the collection of the spectrum depends on the kinetics of binding, determined previously by other methods (UV–vis or fluorimetric titration). After each addition, the buffer

A Brønsted base-promoted diastereoselective dimerization of azlactones

• Danielle L. J. Pinheiro,
• Gabriel M. F. Batista,
• Pedro P. de Castro,
• Leonã S. Flores,
• Gustavo F. S. Andrade and
• Giovanni W. Amarante

Beilstein J. Org. Chem. 2017, 13, 2663–2670, doi:10.3762/bjoc.13.264

• analogue of streptopyrrolidine was accomplished in 65% overall yield. Keywords: azlactones; dimerization; diasteoreselective synthesis; kinetics; streptopyrrolidine analogue; Findings Azlactones have been acknowledged as a common nucleophilic reagent to introduce a quaternary carbon stereocenter in the α

• into this kind of transformation, we carried out some kinetics experiments. Taking into account the dimerization kinetic studies suggested by Mazurkiewicz et al. and experiments by NMR spectroscopy, we report here kinetic studies revealing mechanistic features on the dimerization reaction catalyzed by

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

• regeneration of the CuIIBr2/TPMA complex. To investigate the kinetics of the electrochemical catalytic process, the dependence of the ratio (catalytic current)/(reduction peak current in the absence of QC-Br5) – for the peak at −0.3 V, on the square root of different QC-Br5 concentration was analyzed (Figures

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• abundant in the unfolded protein states [91]. Hydrolytic stability in peptides Finally, we tested hydrolytic stability in esterified peptides 8b, 9b and 10b by observing hydrolysis of the ester using 19F NMR in buffered deuterium oxide (pH 7). We expected pseudo-first order kinetics as for the hydrolysis

• of esters 1–5 at pH 11. Nonetheless, for the peptide esters 8b, 9b and 10b, the experimental decay (Figure 7) of the ester concentration resembled pseudo-zero order kinetics, which was also observed for another amino acid ester hydrolysis not shown here. Both fittings to the zero (Equations 6 and 7

• decoupling) spectra at 298 K by integration. The kinetics was measured in 1H and/or 19F{1H} z-cross-relaxation experiments at either 310 K (for deuterium oxide samples) or 298 K (for benzene samples). The Jαβ-coupling values were obtained by visual inspection of the α-CH resonances in the 1H NMR spectra, and

The effect of milling frequency on a mechanochemical organic reaction monitored by in situ Raman spectroscopy

• Patrick A. Julien,
• Ivani Malvestiti and
• Tomislav Friščić

Beilstein J. Org. Chem. 2017, 13, 2160–2168, doi:10.3762/bjoc.13.216

• reactivity on small variations in milling frequency. In particular, in situ measurements revealed the establishment of two different regimes of reaction kinetics at different frequencies, providing tentative insight into processes of mechanical activation in organic mechanochemical synthesis. Keywords

• mechanochemical synthesis of a MOF from ZnO and imidazole in the presence of a small amount of N,N-dimethylformamide [41]. This study revealed reaction kinetics consistent with a 2nd order reaction rate law, rationalized through a “pseudo-fluid” reaction model in which the rate-determining factor is the frequency

• particular frequency are mutually consistent when milling at 30 Hz, 27.5 Hz, 22.5 Hz and 20 Hz. At 25 Hz, however, the behavior of the reaction for each of the triplicate measurements was highly erratic and generally irreproducible. Overall, there is a clear difference in the kinetics of product formation

Solid-state studies and antioxidant properties of the γ-cyclodextrin·fisetin inclusion compound

• Joana M. Pais,
• Maria João Barroca,
• Maria Paula M. Marques,
• Filipe A. Almeida Paz and
• Susana S. Braga

Beilstein J. Org. Chem. 2017, 13, 2138–2145, doi:10.3762/bjoc.13.212

• corresponding hydrazine (pale yellow in color), a reaction which can be monitored by UV–vis spectroscopy. As the kinetics of the reaction varies from sample to sample, the stabilization time for a complete reduction of the DPPH· free radical was determined. For all samples studied, the steady-state

Influence of the milling parameters on the nucleophilic substitution reaction of activated β-cyclodextrins

• László Jicsinszky,
• Kata Tuza,
• Giancarlo Cravotto,
• Andrea Porcheddu,
• Francesco Delogu and
• Evelina Colacino

Beilstein J. Org. Chem. 2017, 13, 1893–1899, doi:10.3762/bjoc.13.184

• Supporting Information File 1, Table S1 entries 6–8 and 13 show no dramatic change in reaction rate. TU exhibits a slower kinetics than NaN3 under the same milling conditions (Supporting Information File 1, Table S1, entry 13 vs. 16), which hints at substrate-dependent reactivity (Figure 3b and Supporting

• the kinetics and the mechanisms of organic reactions is still question of investigation in the scientific community. Even though our contribution tries to delineate some trends, additional investigations and experiments need to be performed for a fully understanding of this still understudied and

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

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

• ], copyright 2006 Nature Publishing Group. (b) Minimal network motifs that describe the dynamics of minimal bistable or oscillatory systems using mass-action kinetics [49]. Belousov–Zhabotinsky (BZ) reaction. (a) Classical example of pattern formation in the BZ reaction when perturbed with a silver thread

Mechanochemical synthesis of graphene oxide-supported transition metal catalysts for the oxidation of isoeugenol to vanillin

• Ana Franco,
• Sudipta De,
• Alina M. Balu,
• Araceli Garcia and
• Rafael Luque

Beilstein J. Org. Chem. 2017, 13, 1439–1445, doi:10.3762/bjoc.13.141

• significant. Another problem related to the slow reaction rates, unsuitable for commercial production. As a result, chemical oxidation pathways were also followed. To achieve faster kinetics and better selectivity of vanillin, homogeneous catalysts based on different transition metal salts/complexes were

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

• functional capacities (see [15] for a review). In particular, fatty acid vesicles have become the standard protocell model, not just because of their prebiotic plausibility [27][28], but also because of their remarkable stability as compartments [29][30]; their rapid self-assembly kinetics and amenability to

• devoted to control division processes. Challenge 3: characterizing the evolutionary dynamics of pre-Darwinian protocells. Rather than focusing on the reaction kinetics and evolutionary dynamics of populations of naked nucleic acid molecules (the core idea underlying the ‘RNA world’ hypothesis), or even

Sugar-based micro/mesoporous hypercross-linked polymers with in situ embedded silver nanoparticles for catalytic reduction

• Qing Yin,
• Qi Chen,
• Li-Can Lu and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 1212–1221, doi:10.3762/bjoc.13.120

• , the absorption peak at 400 nm disappeared, implying full conversion of 4-NP to 4-AP. The reaction kinetics of the reduction of 4-NP is considered to be pseudo-first order [48] and can be expressed by the following equation: where rt is the consumption rate of 4-NP at time t, ct is the concentration

• calculated via the corresponding absorbance ratio of the absorption at 400 nm. There is obviously a linear relationship consistent with the pseudo-first-order kinetics between ln(ct/c0) and reaction time (t). The rate constant k of the reaction in the presences of the AgNPs/SugPOP-1 composite was 0.307 min−1

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

• formation of the TCD template. 2.3 Reaction kinetics and its implications When considering a mixture containing only building blocks A and B in the minimal replicator model (Figure 2), the formation of template molecules T can initially only take place via the bimolecular reaction pathway. The bimolecular

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

• of polysaccharides. Insights into the kinetics of catalytic events observed in the crystalline state are also presented as well as some aspects of structure determination of protein in solution. Keywords: antibodies; carbohydrate binding domains; cellulose; glycosaminoglycans; glycolipids; glycosyl

• the kinetics of catalytic events occurring in the crystalline state are also described as well as some aspects of the determination of structure of proteins in solution. Review Synchrotron radiation Synchrotrons are particle accelerators in which charged particles circulate along a closed path

Synthesis and enzymatic ketonization of the 5-(halo)-2-hydroxymuconates and 5-(halo)-2-hydroxy-2,4-pentadienoates

• Tyler M. M. Stack,
• William H. Johnson Jr. and
• Christian P. Whitman

Beilstein J. Org. Chem. 2017, 13, 1022–1031, doi:10.3762/bjoc.13.101

• . The implications of these findings are discussed. The availability of these compounds will facilitate future studies of the haloaromatic catabolic pathways. Keywords: dienol; enzyme kinetics; fluoride; halogen; Introduction Aromatic hydrocarbons and their halogenated derivatives are well known

Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

• Chinmay A. Shukla and
• Amol A. Kulkarni

Beilstein J. Org. Chem. 2017, 13, 960–987, doi:10.3762/bjoc.13.97

• kinetics parameters of a series-parallel substitution reaction [38]. Reizman et al. have studied Suzuki–Miyaura cross-coupling optimization using a DoE-based algorithm and feedback system [45]. The authors studied both continuous and discrete variables for optimization. Recently Fitzpatrick and Ley have

The effect of cyclodextrin complexation on the solubility and photostability of nerolidol as pure compound and as main constituent of cabreuva essential oil

• Joyce Azzi,
• Pierre-Edouard Danjou,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2017, 13, 835–844, doi:10.3762/bjoc.13.84

• samples followed a first-order kinetics. First, a constant concentration of Ner (0.1 mM) was added to various concentrations of HP-β-CD (0.1, 1 and 10 mM). Figure 5 represents the percentage of cis, trans-Ner and the mixture remaining in the solution after irradiation in function of time. It can be

• diagrams of CD/trans-Ner inclusion complexes. Phase solubility profile of cabreuva EO obtained by the TOC method. a) 2D ROESY spectrum of β-CD/trans-Ner inclusion complex in D2O and b) representation of the most stable inclusion complex conformer. Photodegradation kinetics of cis-Ner (a), trans-Ner (b

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

• in the liquid phase, covering the main contributions appeared in the literature from 1997 up to August 2016. Some aspects of the topic have been surveyed in the past [28][29]. Details of alkyne hydrogenation reactions in general, including mechanism [30][31], kinetics [32][33], adsorption phenomena

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

• 50 mM. Dithionite ions rapidly quench the fluorescence of the lipid analogs localized in the outer leaflet, which is reflected by a rapid initial decrease of fluorescence intensity (kinetics not shown). Subsequently, the fluorescence intensity decreased slowly caused by a slow permeation of

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

• Addy Pross and
• Robert Pascal

Beilstein J. Org. Chem. 2017, 13, 665–674, doi:10.3762/bjoc.13.66

• develops these lines of thought and argues against the validity of a thermodynamic approach in which the maximisation of the rate of energy dissipation/entropy production is considered to direct the evolutionary process. More generally, our analysis reaffirms the predominant role of kinetics in the self

• thermodynamic data. Indeed, there are many examples in which product formation is controlled by kinetics (reactions under kinetic control, corresponding to the situation in Figure 2), rather than by thermodynamic stabilities. In fact the presence of kinetic barriers is actually a requirement for the system to

Structure–efficiency relationships of cyclodextrin scavengers in the hydrolytic degradation of organophosphorus compounds

• Sophie Letort,
• Michaël Bosco,
• Benedetta Cornelio,
• Frédérique Brégier,
• Sébastien Daulon,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2017, 13, 417–427, doi:10.3762/bjoc.13.45

• pesticides and soman was evaluated. Some structural features of the scavengers could be identified as the key elements in charge to accelerate the decontamination of organophosphorus compounds: (1) the degradation kinetics of organophosphorus constituents is dependent on their affinity for the cyclodextrin

Decarboxylative and dehydrative coupling of dienoic acids and pentadienyl alcohols to form 1,3,6,8-tetraenes

• Ghina’a I. Abu Deiab,
• Mohammed H. Al-Huniti,
• I. F. Dempsey Hyatt,
• Emma E. Nagy,
• Kristen E. Gettys,
• Sommayah S. Sayed,
• Christine M. Joliat,
• Paige E. Daniel,
• Rupa M. Vummalaneni,
• Andrew T. Morehead Jr,
• Andrew L. Sargent and
• Mitchell P. Croatt

Beilstein J. Org. Chem. 2017, 13, 384–392, doi:10.3762/bjoc.13.41

• greater amounts of triphenylphosphine lowering the reaction yield when using the Pd2dba3 catalyst (Table 1, entries 12–14). It was determined that reactions performed in the presence of electron-rich ligands had both quicker kinetics and more efficient yields compared to electron-deficient ligands (Table

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

• with a line of <1 Hz in ethanol. As a proof-of-concept, the integrated flow system (microreactor-stripline NMR chip) was tested in the acylation of benzyl alcohol with acetyl chloride (Figure 7) using DIPEA as the base. The kinetics were studied by in situ monitoring and it was found that 70

• -pressure and thus adjusts the system pressure. In this way a new kinetic model could be developed for this reaction taking into consideration a wide range of temperatures and pH values. The results obtained extend the knowledge of the reaction kinetics for this industrially important system. Similarly

• , Steinhof et al. [47] studied the equilibria and kinetics of the reaction of 1,3-dimethylurea with formaldehyde, which is a model for the industrially relevant urea–formaldehyde system. The reaction was performed in a batch reactor and the analysis was carried out using a commercial NMR flow probe (Figure

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

• physical process is reported in the right-hand side panel of Figure 1. The oscillatory CP kinetics is described [16] by the Equation 3: where b is the heteronuclear dipolar coupling. Further mathematical developments allow determining the composition of the spin cluster. The oscillatory behaviour of the

• couplings [14]. In the opposite case, i.e., when weak I*−S and strong I−I* couplings are present, the CP kinetics follow the more general I−S model. As a final remark, we wish to stress that the oscillatory behaviour described above has not been reported frequently so far, and that the data reported and

• detected via 1H NMR and discussed in the previous section is likely to involve two IbuH units in the formation of dimers. Dynamics of cross polarization We applied variable contact time (VCT) 1H-13C CP-MAS NMR techniques to study the CP kinetics of both the CDNS polymers. As an example, the array of 13C CP