NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• bound form [84]. The extent of line broadening depends on the kinetics of the exchange between the two forms. If the exchange is slow relative to the NMR time scale, which roughly comprises a millisecond time frame, two separate sets of signals for both components are observed, where the signal

• experiments. While these methods can be useful for investigating supramolecular ligands binding to proteins, there are a few drawbacks one needs to keep in mind. All these methods require medium to weak (µM to mM) binding such that the binding kinetics lies in the intermediate to fast exchange regime because

• . If a signal broadens beyond detection and thus disappears from the spectrum, be it due to aggregation or intermediate exchange kinetics, it is also impossible to trace its trajectory and determine the chemical shift perturbation. In the case of a bifunctional GCP ligand binding to survivin [46], the

Dawn of a new era in industrial photochemistry: the scale-up of micro- and mesostructured photoreactors

• Emine Kayahan,
• Mathias Jacobs,
• Leen Braeken,
• Leen C.J. Thomassen,
• Simon Kuhn,
• Tom van Gerven and
• M. Enis Leblebici

Beilstein J. Org. Chem. 2020, 16, 2484–2504, doi:10.3762/bjoc.16.202

• reactor design. The flow field (momentum transport), mass transport, and light field (radiative transport) need to be coupled to compute the reaction kinetics (Figure 1) [11]. Microstructured chips used in photochemistry have various channel geometries, such as straight line, serpentine, square serpentine

• applications. The lab-on-a-chip concept has enabled researchers to work on intrinsic kinetics. Intrinsic data acquisition is crucial while designing and operating large-scale reactors. Several microreactors, such as a spiral channel microreactor carved on a flat aluminum plate [23], a capillary tube [24], a

• microchannel cast, and cured on polydimethylsiloxane (PDMS) slab [25] or a rectangular slab micromachined on teflon [26] were used to determine the intrinsic kinetics of different photochemical reactions. Such demonstrations suggest that if they are scaled up properly, microreactors could be operated with

Synergy between supported ionic liquid-like phases and immobilized palladium N-heterocyclic carbene–phosphine complexes for the Negishi reaction under flow conditions

• Edgar Peris,
• Raúl Porcar,
• María Macia,
• Jesús Alcázar,
• Eduardo García-Verdugo and
• Santiago V. Luis

Beilstein J. Org. Chem. 2020, 16, 1924–1935, doi:10.3762/bjoc.16.159

• additional phosphine ligand produced a clear positive effect on the activity, enhancing the catalytic performance of the immobilized NHC–Pd complexes assayed as clearly shown in the kinetics profiles depicted in Figure 1. Both NHC–Pd–RuPhos catalysts showed an activity increase: ca. 10-fold for 8a and ca

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• transport phenomena and this semicircle was attributed to slow ion transfer kinetics at the ISM interfaces. Potentiometric calibrations in sodium acetate solutions were used to determine the linear ranges (R2 ≥ 0.999), slopes, and detection limits of the sensors (Table 2). Examples of the calibration curves

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pKa values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors

• (trifluoromethyl)prolines would be much weaker. The effects of their presence is a polypeptide structure should rather be associated with the increase in the molecular volume and hydrophobicity, and less with the backbone folding. Amide-bond rotation: kinetics Amide-bond rotation is known as an intrinsically slow

• , acid–base transition, and kinetics of the amide-bond rotation. Interestingly it was found that the side-chain conformational preferences translate differently into the energy of the trans/cis amide equilibrium. While in the monofluoroprolines the effect was relatively strong, in the trifluoromethylated

When metal-catalyzed C–H functionalization meets visible-light photocatalysis

• Lucas Guillemard and
• Joanna Wencel-Delord

Beilstein J. Org. Chem. 2020, 16, 1754–1804, doi:10.3762/bjoc.16.147

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• for the observed unique kinetics, yields and selectivity in these one-pot reactions. In addition, such in-depth fundamental mechanistic and kinetic studies should enable determining the key structural parameters of the catalytic platform that govern its efficiency hence supporting the design of novel

Mechanochemical green synthesis of hyper-crosslinked cyclodextrin polymers

• Alberto Rubin Pedrazzo,
• Fabrizio Caldera,
• Marco Zanetti,
• Silvia Lucia Appleton,
• Nilesh Kumar Dhakar and
• Francesco Trotta

Beilstein J. Org. Chem. 2020, 16, 1554–1563, doi:10.3762/bjoc.16.127

• example, drug-delivery systems [3][4][5]: together with their capability of hosting drugs, they are biocompatible and nontoxic. In the last few years nanosponges were employed to encapsulate and release a wide variety of drugs [6][7], associated with an improvement in bioavailability and release kinetics

• -carbonyldiimidazole as the crosslinker, for the following reasons: the reaction was usually performed at 90 °C, therefore, the heating of the system related to the ball friction is not only acceptable but also useful for the kinetics of the reaction, and the solvent for solubilizing the reactants was DMF. We herein

• consistent with what was reported in the literature: the first activation of an alcohol by carbonyl imidazole showed faster kinetics than the second one, which needed longer reaction times and/or a higher temperature (from 60 °C to 80 °C) to obtain a significant yield [31][32]. To distinguish between the

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• accessible to the reaction media and the excitation photons, preventing the photocatalyst from being wasted in the bulk material. The immobilisation will generally reduce the reaction kinetics of the homogeneous photocatalyst as it is no longer dispersed in solution, but this can be mitigated through flow

Oxime radicals: generation, properties and application in organic synthesis

• Igor B. Krylov,
• Stanislav A. Paveliev,
• Alexander S. Budnikov and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2020, 16, 1234–1276, doi:10.3762/bjoc.16.107

• corresponding to the free iminoxyl radical, which indicates the reversibility of dimerization [53]. During the oxidation of pivalic aldoxime 1e by Ag2O, the formation of nitrile oxide 6e was observed, which then slowly dimerized to the corresponding furoxan 7e. The kinetics of the decomposition of dialkyl

• established that the studied iminoxyl radicals reversibly dimerized in the solution. For sterically unhindered dialkyliminoxyl radicals, the radical–dimer equilibrium was quickly reached, shifted toward the dimer, while a first-order decay kinetics of was observed for the iminoxyl radical. For sterically

• hindered tert-butylmethyliminoxyl and diisopropyliminoxyl radicals, as well as for diaryl and alkylaryliminoxyl radicals, the radical–dimer equilibrium was reached slowly, it was shifted toward the free radical, and a second-order decay kinetics was observed. The first synthesized long-lived iminoxyl

Suzuki–Miyaura cross coupling is not an informative reaction to demonstrate the performance of new solvents

• James Sherwood

Beilstein J. Org. Chem. 2020, 16, 1001–1005, doi:10.3762/bjoc.16.89

• the key fundamental principles of boron and palladium speciation and the role of the base in the Suzuki–Miyaura reaction. For researchers developing safer solvents, the Mizoroki–Heck reaction is a more suitable cross-coupling methodology to demonstrate solvent performance [28]. The reaction kinetics

Bipyrrole boomerangs via Pd-mediated tandem cyclization–oxygenation. Controlling reaction selectivity and electronic properties

• Liliia Moshniaha,
• Marika Żyła-Karwowska,
• Joanna Cybińska,
• Piotr J. Chmielewski,
• Ludovic Favereau and
• Marcin Stępień

Beilstein J. Org. Chem. 2020, 16, 895–903, doi:10.3762/bjoc.16.81

• of cNMI3O could not be separated, presumably because of very rapid racemization. The half-life time of cNDA3O enantiomers (ca. 0.54 min) was too short to record their CD spectra, but was long enough for a kinetics study (Supporting Information File 1, Figures S8 and S9). Enantioenriched samples of

Exploring the scope of DBU-promoted amidations of 7-methoxycarbonylpterin

• Anna R. Bockman and
• Jeffrey M. Pruet

Beilstein J. Org. Chem. 2020, 16, 509–514, doi:10.3762/bjoc.16.46

• explored this reaction to assess its scope and identify structural features in the amines which significantly affect success, monitored the reaction kinetics using a pseudo-first order kinetics model, and further adapted the reaction conditions to allow for product formation in as little as 5 min, with

• reaction by employing a pseudo-first order kinetics model. Furthermore, we adapted the reaction to allow for reaction times as little as 5 minutes, with yields reaching up to 99%. Results and Discussion The general procedure for the DBU-promoted amidation involved the initial suspension of 7-CMP (1) in a

• the relative reactivity of the various amines, a pseudo-first order kinetics of the amidation reaction was probed. The reaction was followed by 1H NMR spectroscopy at room temperature, following the disappearance of 7-CMP and appearance of the amide product (Figure 3). By monitoring the reaction

Recent advances in photocatalyzed reactions using well-defined copper(I) complexes

• Mingbing Zhong,
• Xavier Pannecoucke,
• Philippe Jubault and
• Thomas Poisson

Beilstein J. Org. Chem. 2020, 16, 451–481, doi:10.3762/bjoc.16.42

• and propylene oxide as a proton scavenger under flow conditions (0.05 mL/min; residence time = 20 h). The use of flow conditions drastically enhanced the kinetics of the reaction, moving from 120 h reaction time in batch to 20 h using a continuous flow reactor. The reaction allowed the synthesis of a

Architecture and synthesis of P,N-heterocyclic phosphine ligands

• Wisdom A. Munzeiwa,
• Bernard Omondi and
• Vincent O. Nyamori

Beilstein J. Org. Chem. 2020, 16, 362–383, doi:10.3762/bjoc.16.35

• solvents may substantially influence reaction kinetics and product formation [102]. Biricik et al. [98] reported the preparation of polydentate aminophosphine 111 through a condensation–elimination–aminolysis reaction (Scheme 21). Reactions performed in diethyl ether and toluene resulted in bisphosphine

Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis

• David C. B. Siebert,
• Roman Sommer,
• Domen Pogorevc,
• Michael Hoffmann,
• Silke C. Wenzel,
• Rolf Müller and
• Alexander Titz

Beilstein J. Org. Chem. 2019, 15, 2922–2929, doi:10.3762/bjoc.15.286

• kinetics under the standard conditions in the cultivation medium. The HPLC–MS analysis revealed a rather rapid degradation of the analysed mutasynthon, as after only 2 h of incubation time the majority was degraded and after 4 h of incubation almost complete degradation of the compound was observed

Arylisoquinoline-derived organoboron dyes with a triaryl skeleton show dual fluorescence

• Vânia F. Pais,
• Tristan Neumann,
• Ignacio Vayá,
• M. Consuelo Jiménez,
• Abel Ros and
• Uwe Pischel

Beilstein J. Org. Chem. 2019, 15, 2612–2622, doi:10.3762/bjoc.15.254

• acetonitrile (containing 0.4 vol % DMF as co-solvent). Transient absorption spectrum (600 ns delay) of dye 17 in nitrogen-purged acetonitrile on excitation at 308 nm. The inset shows the corresponding kinetics at 600 nm. Fluorescence titrations of the dyes (ca. 4–11 μM) with Bu4NF in acetonitrile. a) 16 (up to

Safe and highly efficient adaptation of potentially explosive azide chemistry involved in the synthesis of Tamiflu using continuous-flow technology

• Cloudius R. Sagandira and
• Paul Watts

Beilstein J. Org. Chem. 2019, 15, 2577–2589, doi:10.3762/bjoc.15.251

• % yield, respectively. Consequently, the reaction was strictly done at 0 °C and below. Therefore, the use of NaN3 in high equivalence (4 equiv) was to probably improve reaction kinetics at low temperatures. Karpf and Trussardi [9] reported the synthesis of azide 5 from mesyl shikimate 4 and NaN3 (1.1

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• %; Table 3, right) with faster kinetics (Figure 5B) without compromising the specificity of the system. More importantly, this new set up led to slightly higher differences between isomers and pointed out the dual-labelled probe 10 as the best one, which is consistent with the melting experiments (Table 2

• and Figure 3). Among the single mutated PNAs, those with lower TM, displayed the best performance in our kinetics studies (Figure 5B). Finally, in an attempt of gaining insight into the general low photoresponsivity, we performed CD (Figure S53, Supporting Information File 1) and UV–vis (Figures S54

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• even upon excitation at 350 nm, because of the induced E/Z photoisomerization process occurring within the experiment. Finally, the kinetics of the fluorescence decay of the Z-isomer has also been determined in acetonitrile, upon excitation at 400 nm, resulting in a lifetime of 479 ps (Figure S2

• evolution, also associated to the rise of a positive band at <380 nm, whose observation is precluded due to scattering in polar solvents, reveals the occurrence of Z/E isomerization, whose kinetics is thus similar in toluene and acetonitrile. In the latter solvent, the signal intensity then decreases on a

• 50 ps timescale and recovers almost completely in about 500 ps. In methanol, although the spectral evolution is qualitatively similar to that observed in acetonitrile, the kinetics associated with the detected spectral changes differ substantially. The initial evolution, corresponding to the recovery

Reversible switching of arylazopyrazole within a metal–organic cage

• Anton I. Hanopolskyi,
• Soumen De,
• Michał J. Białek,
• Yael Diskin-Posner,
• Liat Avram,
• Moran Feller and
• Rafal Klajn

Beilstein J. Org. Chem. 2019, 15, 2398–2407, doi:10.3762/bjoc.15.232

• affected by their confinement to the surfaces of inorganic nanoparticles. Among other examples, the isomerization kinetics of azobenzene could be tuned by a factor of >5000 by the molecules with which it was co-adsorbed on gold nanoparticles [23], and donor–acceptor Stenhouse adduct (DASA) switches were

• once again featuring a single set of diffusion coefficients (Figure 7, right; D1 = 2.22 (±0.04) · 10−10 m2·s−1 and D2 = 2.04 (±0.08) · 10−10 m2·s−1). Finally, we were interested in how the presence of cage 2 affects the kinetics of the thermal back-isomerization of 1 (i.e., Z-1 → E-1 in the dark). This

• linear profile of the recovery suggests that the reaction obeys first-order kinetics, with a rate constant of 0.0975 h−1, corresponding to a thermal half-life of Z-1, τ1/2 ≈ 7.1 hours. This value of τ1/2 is surprisingly small vis-à-vis the previously reported [35] τ1/2 ≈ 10 days in acetonitrile. To

Excited state dynamics for visible-light sensitization of a photochromic benzil-subsituted phenoxyl-imidazolyl radical complex

• Yoichi Kobayashi,
• Yukie Mamiya,
• Katsuya Mutoh,
• Hikaru Sotome,
• Masafumi Koga,
• Hiroshi Miyasaka and
• Jiro Abe

Beilstein J. Org. Chem. 2019, 15, 2369–2379, doi:10.3762/bjoc.15.229

• isomer A accumulated by 8 shots are slightly fluctuated most probably because of the low signal-to-noise ratio, the decay kinetics do not change by repeated irradiation with UV-light pulses. It shows that both isomers generate the same biradical form by UV-light irradiation as shown in Scheme 1

• (355 nm). The difference may affect the ratio of isomer A and isomer B at the photostationary state (PSS) and initial relaxation kinetics at sub-picosecond time scales. Benzil was used for a reference sample. Figure 3a shows the time evolution of the transient absorption spectra of benzil in benzene

Mono- and bithiophene-substituted diarylethene photoswitches with emissive open or closed forms

• A. Lennart Schleper,
• Mariano L. Bossi,
• Vladimir N. Belov and
• Stefan W. Hell

Beilstein J. Org. Chem. 2019, 15, 2344–2354, doi:10.3762/bjoc.15.227

• open forms with rather low emission efficiency. The photoswitching kinetics was studied at several wavelengths with UV and visible light. New diarylethenes underwent ring-closure reactions by irradiation with UV light (365 nm, 405 nm), and the reversible ring-opening by irradiation with visible light

• example, Figures S26 and S38 in Supporting Information File 1). Emission properties of the CF’s were obtained from solutions at the PSS365 nm, with excitation at a wavelength at which the OF’s do not absorb (only the CF absorbs). The data on switching kinetics is given in Table 2 and discussed in the next

• nonemissive. This important property will be taken into account in the design of the future photoswitchable compounds with ratiometric fluorescence modulation. Switching kinetics Table 2 contains an overview of the most important parameters related to the switching kinetics. All compounds, except AsOTh2 and

Characterization of two new degradation products of atorvastatin calcium formed upon treatment with strong acids

• Jürgen Krauß,
• Monika Klimt,
• Markus Luber,
• Peter Mayer and
• Franz Bracher

Beilstein J. Org. Chem. 2019, 15, 2085–2091, doi:10.3762/bjoc.15.206

• stress tests on atorvastatin (and its salts), and an overview has been published by Sirén [5]. Hereby, atorvastatin was found to be sensitive to acidic, oxidative, photochemical and thermal stress. Acidic degradation of atorvastatin was reported to follow first order kinetics, but decomposition products

Genome mining in Trichoderma viride J1-030: discovery and identification of novel sesquiterpene synthase and its products

• Xiang Sun,
• You-Sheng Cai,
• Yujie Yuan,
• Guangkai Bian,
• Ziling Ye,
• Zixin Deng and
• Tiangang Liu

Beilstein J. Org. Chem. 2019, 15, 2052–2058, doi:10.3762/bjoc.15.202

• dependency of Tvi09626 and its kinetics As reported previously, most terpene synthases are active in the presence of Mg2+ ions [8][37]. To test the Mg2+ dependency of Tvi09626, an in vitro assay was performed. The GC–MS analysis showed that in the presence of Mg2+, compound 1 can be obtained, whereas without

• Mg2+ or added EDTA (2.5 mM), compound 1 cannot be detected (Figure 5). This assay demonstrated that Tvi09626 was a Mg2+-dependent sesquiterpene synthase. In a kinetics analysis, the turnover rate (kcat) of the enzyme with FPP was (15 ± 0.3) × 10−2, which is similar to those of omp6 and omp7. Its